TY - JOUR TI - Comparison of Pollen Transfer Dynamics by Multiple Floral Visitors: Experiments with Pollen and Fluorescent Dye AU - Adler, Lynn S. AU - Irwin, Rebecca E. T2 - Annals of Botany AB - Most plant species are visited by a diversity of floral visitors. Pollen transfer of the four most common pollinating bee species and one nectar-robbing bee of the distylous plant Gelsemium sempervirens were compared.Naturally occurring pollen loads carried by the common floral visitor species of G. sempervirens were compared. In addition, dyed pollen donor flowers and sequences of four emasculated recipient flowers in field cages were used to estimate pollen transfer, and the utility of fluorescent dye powder as an analogue for pollen transfer was determined.Xylocopa virginica, Osmia lignaria and Habropoda laboriosa carried the most G. sempervirens pollen on their bodies, followed by Bombus bimaculatus and Apis mellifera. However, B. bimaculatus, O. lignaria and H. laboriosa transferred significantly more pollen than A. mellifera. Nectar-robbing X. virginica transferred the least pollen, even when visiting legitimately. Dye particles were strongly correlated with pollen grains on a stigma, and therefore provide a good analogue for pollen in this system. The ratio of pollen : dye across stigmas was not affected by bee species or interactions between bee species and floral morphology. However, dye transfer was more sensitive than pollen transfer to differences in floral morphology.The results from this study add to a growing body of literature highlighting that floral visitors vary in pollination effectiveness, and that visitors carrying the most pollen on their bodies may not always be the most efficient at depositing pollen on stigmas. Understanding the magnitude of variability in pollinator quality is one important factor for predicting how different pollinator taxa may influence the evolution of floral traits. DA - 2005/11/18/ PY - 2005/11/18/ DO - 10.1093/aob/mcj012 VL - 97 IS - 1 SP - 141-150 LA - en OP - SN - 1095-8290 0305-7364 UR - http://dx.doi.org/10.1093/aob/mcj012 DB - Crossref ER - TY - JOUR TI - Flower Color Microevolution in Wild Radish: Evolutionary Response to Pollinator‐Mediated Selection AU - Irwin, Rebecca E. AU - Strauss, Sharon Y. T2 - The American Naturalist AB - Evolutionary ecologists are fundamentally interested in how species interactions affect evolutionary change. We tested the degree to which plant‐pollinator interactions affect the frequency of flower color morphs of Raphanus sativus. Petal color in R. sativus is determined by two independently assorting loci, producing four petal colors (yellow, white, pink, and bronze). We assessed the impact of pollinator discrimination on changes in flower color variation by comparing the frequency of colors produced in the presence (open pollination) versus absence (null pollination) of pollinator discrimination. We also assessed the impact of postpollination and developmental effects on progeny colors using equal pollinations with all four color morphs. Our results from open pollinations found an overrepresentation of yellow progeny in the next generation, when compared with both null pollinations and cumulative ratios based on Hardy‐Weinberg and linkage equilibria assumptions. When these results were combined with those from equal pollinations, the overrepresentation of yellow could be attributed to selection from pollinators. Yet, surveys in the field the following year found no flower color frequency changes in the next generation. These results illustrate that flower color microevolution can be driven by both pollinator discrimination and other nonpollinator selective forces acting during the seed‐to‐adult transition, countering selection imposed by pollinators. DA - 2005/2// PY - 2005/2// DO - 10.2307/3473147 VL - 165 IS - 2 SP - 225-237 J2 - The American Naturalist LA - en OP - SN - 0003-0147 1537-5323 UR - http://dx.doi.org/10.1086/426714 DB - Crossref ER - TY - JOUR TI - TEMPORAL AND SPATIAL VARIATION IN POLLINATION OF A MONTANE HERB: A SEVEN-YEAR STUDY AU - Price, Mary V. AU - Waser, Nickolas M. AU - Irwin, Rebecca E. AU - Campbell, Diane R. AU - Brody, Alison K. T2 - Ecology AB - Pollination by animals is critical to sexual reproduction of most angiosperms. However, little is known about variation in pollination service to single plant species. We report results of a long-term study of Ipomopsis aggregata, a semelparous montane herb whose flowers are visited by hummingbird and insect pollinators as well as “floral larcenists.” We censused flower visitors over seven summers at permanent study sites separated by several hundred meters, and counted pollen delivered to flowers on a subset of plants observed for visitation. The species composition of the community of visitors varied significantly across years and within the flowering season; sites varied significantly only in the magnitude of parallel annual changes in the visitor community. Rates of flower visitation fluctuated over an order of magnitude or more. Variation in mean stigma pollen load among plants flowering in the same site and year was explained by a causal path model in which visitation rates by pollinators and larcenists had linear positive and negative effects, respectively. A simplified model including only pollinators explained almost as much variance as did the full model. However, qualitatively different parameter estimates were produced by an analogous causal model based on population means across site–year combinations. Discrepant results from within- and between-population levels of analysis suggest that pollen receipt is influenced by environmental factors that vary among sites and years, as well as by pollinator visit rates. We present a heuristic causal model that includes such factors, and we note its implications for ecological and evolutionary studies of pollination. DA - 2005/8// PY - 2005/8// DO - 10.1890/04-1274 VL - 86 IS - 8 SP - 2106-2116 J2 - Ecology LA - en OP - SN - 0012-9658 UR - http://dx.doi.org/10.1890/04-1274 DB - Crossref ER - TY - JOUR TI - ECOLOGICAL COSTS AND BENEFITS OF DEFENSES IN NECTAR AU - Adler, Lynn S. AU - Irwin, Rebecca E. T2 - Ecology AB - The nectar of many plant species contains defensive compounds that have been hypothesized to benefit plants through a variety of mechanisms. However, the relationship between nectar defenses and plant fitness has not been established for any species. We experimentally manipulated gelsemine, the principal alkaloid of Carolina jessamine (Gelsemium sempervirens), in nectar to determine its effect on pollinator visitation, nectar robber visitation, and male and female plant reproduction. We found that nectar robbers and most pollinators probed fewer flowers and spent less time per flower on plants with high compared to low nectar alkaloids. High alkaloids decreased the donation of fluorescent dye, an analogue of pollen used to estimate male plant reproduction, to neighboring plants by one-third to one-half. However, nectar alkaloids did not affect female plant reproduction, measured as pollen receipt, fruit set, seed set, and seed mass. The weak effects of nectar alkaloids on female reproduction could represent a balance between the altered behavior of nectar robbers and pollinators, or it could be that neither of these interactions affected plant reproduction. Taken together, these results suggest that secondary compounds in nectar may have more costs than benefits for plants. DA - 2005/11// PY - 2005/11// DO - 10.1890/05-0118 VL - 86 IS - 11 SP - 2968-2978 J2 - Ecology LA - en OP - SN - 0012-9658 UR - http://dx.doi.org/10.1890/05-0118 DB - Crossref ER - TY - CONF TI - Identification of QTL for productive traits and milk somatic cell count in the Italian Simmental cattle AU - Bagnato, A. AU - Romani, C. AU - Fontana, S. AU - Dubini, S. AU - Schiavini, F. AU - Rossoni, A. AU - Maltecca, C. AU - Vicario, D. T2 - Associazione per la Scienza e le Produzioni Animali (ASPA) Congress C2 - 2005/// C3 - Proceedings of the Associazione per la Scienza e le Produzioni Animali (ASPA) Congress CY - Torino, Italy DA - 2005/// PY - 2005/6/28/ ER - TY - JOUR TI - The Amino-Terminal Region of Drosophila MSL1 Contains Basic, Glycine-Rich, and Leucine Zipper-Like Motifs That Promote X Chromosome Binding, Self-Association, and MSL2 Binding, Respectively AU - Li, Fang AU - Parry, David A. D. AU - Scott, Maxwell J. T2 - Molecular and Cellular Biology AB - In Drosophila melanogaster, X chromosome dosage compensation is achieved by doubling the transcription of most X-linked genes. The male-specific lethal (MSL) complex is required for this process and binds to hundreds of sites on the male X chromosome. The MSL1 protein is essential for X chromosome binding and serves as a central scaffold for MSL complex assembly. We find that the amino-terminal region of MSL1 binds to hundreds of sites on the X chromosome in normal males but only to approximately 30 high-affinity sites in the absence of endogenous MSL1. Binding to the high-affinity sites requires a basic motif at the amino terminus that is conserved among Drosophila species. X chromosome binding also requires a conserved leucine zipper-like motif that binds to MSL2. A glycine-rich motif between the basic and leucine-zipper-like motifs mediates MSL1 self-association in vitro and binding of the amino-terminal region of MSL1 to the MSL complex assembled on the male X chromosome. We propose that the basic region may mediate DNA binding and that the glycine-rich region may promote the association of MSL complexes to closely adjacent sites on the X chromosome. DA - 2005/10/1/ PY - 2005/10/1/ DO - 10.1128/MCB.25.20.8913-8924.2005 VL - 25 IS - 20 SP - 8913-8924 J2 - Molecular and Cellular Biology LA - en OP - SN - 1098-5549 UR - http://dx.doi.org/10.1128/MCB.25.20.8913-8924.2005 DB - Crossref ER - TY - JOUR TI - Organisation and Expression of a Cluster of Female-specific Genes in the Australian Sheep Blowfly, Lucilia cuprina AU - Scott, MJ AU - Sarkar, A AU - Belikoff, EJ T2 - Area-Wide Control of Insect Pests DA - 2005/// PY - 2005/// ER - TY - CHAP TI - Characterizing ecological risks of introductions and invasions AU - Andow, D.A. T2 - Invasive alien species: A new synthesis A2 - Mooney, H.A. A2 - Mack, R.N. A2 - McNeely, J.A. A2 - Neville, L.E. A2 - Schei, P.J. A2 - Waage, J.K. PY - 2005/// SP - 84–103 PB - Island Press ER - TY - JOUR TI - Multifunctional Agriculture in the United States AU - Boody, George AU - Vondracek, Bruce AU - Andow, David A. AU - Krinke, Mara AU - Westra, John AU - Zimmerman, Julie AU - Welle, Patrick T2 - BioScience AB - We evaluated possible changes to current farming practices in two Minnesota watersheds to provide insight into how farm policy might affect environmental, social, and economic outcomes. Watershed residents helped develop four scenarios to evaluate alternative future trends in agricultural management and to project potential economic and environmental outcomes. We found that environmental and economic benefits can be attained through changes in agricultural land management without increasing public costs. The magnitude of these benefits depends on the magnitude of changes to agricultural practices. Environmental benefits include improved water quality, healthier fish, increased carbon sequestration, and decreased greenhouse gas emissions, while economic benefits include social capital formation, greater farm profitability, and avoided costs. Policy transitions that emphasize functions of agriculture in addition to food production are crucial for creating change. We suggest that redirecting farm payments by using alternative incentives could lead to substantial environmental changes at little or no extra cost to the taxpayer. DA - 2005/// PY - 2005/// DO - 10.1641/0006-3568(2005)055[0027:maitus]2.0.co;2 VL - 55 IS - 1 SP - 27 J2 - BioScience LA - en OP - SN - 0006-3568 UR - http://dx.doi.org/10.1641/0006-3568(2005)055[0027:maitus]2.0.co;2 DB - Crossref ER - TY - JOUR TI - Genetically engineered organisms and the environment: current status and recommendations AU - Snow, A. A. AU - Andow, D. A. AU - Gepts, P. AU - Hallerman, E. M. AU - Power, A. AU - Tiedje, J. M. AU - Wolfenbarger, L. L. T2 - Ecological Applications AB - The Ecological Society of America has evaluated the ecological effects of current and potential uses of field‐released genetically engineered organisms (GEOs), as described in this Position Paper. Some GEOs could play a positive role in sustainable agriculture, forestry, aquaculture, bioremediation, and environmental management, both in developed and developing countries. However, deliberate or inadvertent releases of GEOs into the environment could have negative ecological effects under certain circumstances. Possible risks of GEOs could include: (1) creating new or more vigorous pests and pathogens; (2) exacerbating the effects of existing pests through hybridization with related transgenic organisms; (3) harm to nontarget species, such as soil organisms, non‐pest insects, birds, and other animals; (4) disruption of biotic communities, including agroecosystems; and (5) irreparable loss or changes in species diversity or genetic diversity within species. Many potential applications of genetic engineering extend beyond traditional breeding, encompassing viruses, bacteria, algae, fungi, grasses, trees, insects, fish, and shellfish. GEOs that present novel traits will need special scrutiny with regard to their environmental effects. The Ecological Society of America supports the following recommendations. (1) GEOs should be designed to reduce environmental risks. (2) More extensive studies of the environmental benefits and risks associated with GEOs are needed. (3) These effects should be evaluated relative to appropriate baseline scenarios. (4) Environmental release of GEOs should be prevented if scientific knowledge about possible risks is clearly inadequate. (5) In some cases, post‐release monitoring will be needed to identify, manage, and mitigate environmental risks. (6) Science‐based regulation should subject all transgenic organisms to a similar risk assessment framework and should incorporate a cautious approach, recognizing that many environmental effects are GEO‐ and site‐specific. (7) Ecologists, agricultural scientists, molecular biologists, and others need broader training and wider collaboration to address these recommendations. In summary, GEOs should be evaluated and used within the context of a scientifically based regulatory policy that encourages innovation without compromising sound environmental management. The Ecological Society of America is committed to providing scientific expertise for evaluating and predicting the ecological effects of field‐released transgenic organisms. DA - 2005/4// PY - 2005/4// DO - 10.1890/04-0539 VL - 15 IS - 2 SP - 377–404 SN - 1051-0761 UR - http://dx.doi.org/10.1890/04-0539 ER - TY - JOUR TI - New Concepts in Agroecology: A Service-Learning Course AU - Jordan, Nicholas R. AU - Andow, David A. AU - Mercer, Kristin L. T2 - Journal of Natural Resources and Life Sciences Education AB - We describe our pedagogical approaches and experiences with a novel course in agroecology (one semester, three credit-hours, for graduate students and upper level undergraduates). Our course responds to recent proposals that agroecology expand its disciplinary focus to include human factors as well as ecological factors, thus taking a more holistic and systemic perspective. The course structure and service-learning component are organized around the focal concept of “transformation,” that is, a systemic change that addresses a certain ecological problem in an agricultural system. Our goal is to help train agricultural professionals who can work effectively in collaborative efforts to implement such transformations. Toward this end, we have integrated methods from systems thinking, soft-systems methodology, and agroecosystems analysis, and used a service-learning component to provide students with an opportunity to apply and evaluate these methods in practice. Most students favorably evaluated the course. Ultimately, we expect that the course will help our students to develop a civic professionalism through which they apply their professional skills to complex public problems in agriculture. DA - 2005/// PY - 2005/// DO - 10.2134/jnrlse.2005.0083 VL - 34 IS - 1 SP - 83-89 J2 - Journal of Natural Resources and Life Sciences Education LA - en OP - SN - 1059-9053 UR - http://dx.doi.org/10.2134/jnrlse.2005.0083 DB - Crossref ER - TY - JOUR TI - Assessing environmental risks of transgenic plants AU - Andow, D. A. AU - Zwahlen, Claudia T2 - Ecology Letters AB - By the end of the 1980s, a broad consensus had developed that there were potential environmental risks of transgenic plants requiring assessment and that this assessment must be done on a case-by-case basis, taking into account the transgene, recipient organism, intended environment of release, and the frequency and scale of the intended introduction. Since 1990, there have been gradual but substantial changes in the environmental risk assessment process. In this review, we focus on changes in the assessment of risks associated with non-target species and biodiversity, gene flow, and the evolution of resistance. Non-target risk assessment now focuses on risks of transgenic plants to the intended local environment of release. Measurements of gene flow indicate that it occurs at higher rates than believed in the early 1990s, mathematical theory is beginning to clarify expectations of risks associated with gene flow, and management methods are being developed to reduce gene flow and possibly mitigate its effects. Insect pest resistance risks are now managed using a high-dose/refuge or a refuge-only strategy, and the present research focuses on monitoring for resistance and encouraging compliance to requirements. We synthesize previous models for tiering risk assessment and propose a general model for tiering. Future transgenic crops are likely to pose greater challenges for risk assessment, and meeting these challenges will be crucial in developing a scientifically coherent risk assessment framework. Scientific understanding of the factors affecting environmental risk is still nascent, and environmental scientists need to help improve environmental risk assessment. DA - 2005/11/22/ PY - 2005/11/22/ DO - 10.1111/j.1461-0248.2005.00846.x VL - 9 IS - 2 SP - 196-214 LA - en OP - SN - 1461-023X UR - http://dx.doi.org/10.1111/j.1461-0248.2005.00846.x DB - Crossref ER - TY - JOUR TI - Host–Parasitoid Interactions in a Transgenic Landscape: Spatial Proximity Effects of Host Density AU - White, Jennifer A. AU - Andow, D. A. T2 - Environmental Entomology AB - Widespread management practices such as transgenic insecticidal crops influence the distribution and density of targeted pest species across the agricultural landscape. Natural enemies must cope with this altered distribution, and their response potentially influences the rate of resistance evolution in the pest. The purpose of this study was to examine spatial patterns of parasitism by the specialist parasitoid Macrocentrus grandii Goidanich (Hymenoptera: Braconidae) in response to the density of its host, the European corn borer (Ostrinia nubilalis Hübner [Lepidoptera: Crambidae]). When we manipulated host distribution and observed resulting patterns of wasp density and parasitism, we found that the smallest host aggregations had the lowest parasitism, but only when not associated with larger host aggregations. A subsequent field experiment confirmed that proximity to large host aggregations increased parasitism in small host aggregations. Theory indicates that such positive density-dependent parasitism should accelerate the evolution of toxin resistance in pest species, but our study suggests that close spatial proximity between insecticidal crops and refuges may help equalize M. grandii parasitism and that simple management techniques such as in-field refuges could potentially increase the complementarity of transgenic and biological control of European corn borer in this system. Further research is needed, however, before extrapolating the results of our small-scale study to field-level patterns and concluding that M. grandii will necessarily hasten resistance evolution in the European corn borer. DA - 2005/12/1/ PY - 2005/12/1/ DO - 10.1603/0046-225x-34.6.1493 VL - 34 IS - 6 SP - 1493-1500 J2 - en LA - en OP - SN - 0046-225X 0046-225X UR - http://dx.doi.org/10.1603/0046-225x-34.6.1493 DB - Crossref ER - TY - JOUR TI - Field evidence for the exposure of ground beetles to Cry1Ab from transgenic corn AU - Zwahlen, Claudia AU - Andow, David A. T2 - Environmental Biosafety Research AB - Non-target organisms associated with the soil might be adversely affected by exposure to the CrylAb protein from Bacillus thuringiensis (Bt) in transgenic corn (Zea mays L.). To check for such exposure, we used ELISA to test for Cry1Ab in ground beetles collected live from fields with Bt corn residues and Bt corn (Bt/Bt), Bt corn residues and non-Bt crops (Bt/non-Bt), or non-Bt corn residues and non-Bt crops (non-Bt/non-Bt). In fields with Bt corn residues (Bt/Bt and Bt/non-Bt), Cry1Ab was present in all seven species of ground beetles examined (Agonum placidum, Bembidion rupicola, Clivina impressefrons, Cyclotrachelus iowensis, Harpalus pensylvanicus, Poecilus chalcites, and Poecilus lucublandus). For the two most abundant species, P. chalcites and P. lucublandus, the proportion of beetles with Cry1Ab was significantly higher in Bt/Bt fields (0.50-1.0) and Bt/non-Bt fields (0.41-0.50) than in non-Bt/non-Bt fields (0.0). This is the first field evidence that some ground beetle species are exposed to Cry1Ab. The implications of exposure on the performance of these non-target organisms are unclear. DA - 2005/4// PY - 2005/4// DO - 10.1051/ebr:2005014 VL - 4 IS - 2 SP - 113-117 J2 - Environ. Biosafety Res. OP - SN - 1635-7922 1635-7930 UR - http://dx.doi.org/10.1051/ebr:2005014 DB - Crossref ER - TY - JOUR TI - Natural Enemies and the Evolution of Resistance to Transgenic Insecticidal Crops by Pest Insects: The Role of Egg Mortality AU - Heimpel, George E. AU - Neuhauser, Claudia AU - Andow, D. A. T2 - Environmental Entomology AB - We explore the influence of egg mortality dynamics on the rate at which target pests evolve resistance to high-dose transgenic insecticidal crops. We develop a two-patch deterministic population genetic model in which pests can develop in either toxic or nontoxic (refuge) fields, and their eggs are subject to varying levels and forms of egg mortality. The three standard forms of egg mortality are studied: density independence (DI), positive density dependence (PDD), and inverse density dependence (IDD). Resistance is modeled as a single locus with a fully recessive allele that confers complete resistance with no fitness cost. Insect movement and oviposition is modeled as follows: males move panmictically before mating and females may either stay in their natal patch to oviposit or move after mating before oviposition. While our simulations show that both the magnitude and form of egg mortality can influence the rate of resistance evolution, important caveats apply. Higher levels of DI egg mortality can lead to substantial delays in resistance evolution, but this effect is dependent on the presence of intraspecific competition among larvae. The rate of resistance evolution is affected by the form of density dependence (DI versus PDD versus IDD), but these effects are dependent on at least some females ovipositing in their natal field. If this condition is met, the rate of resistance evolution is fastest when eggs are subject to PDD mortality and slowest when eggs are subject to IDD egg mortality. DI egg mortality produces intermediate rates of resistance evolution. DA - 2005/6/1/ PY - 2005/6/1/ DO - 10.1603/0046-225x-34.3.512 VL - 34 IS - 3 SP - 512-526 J2 - Environ Entomol LA - en OP - SN - 0046-225X 1938-2936 UR - http://dx.doi.org/10.1603/0046-225x-34.3.512 DB - Crossref ER - TY - JOUR TI - Response of coccinellids to their aphid prey at different spatial scales AU - Schellhorn, Nancy A. AU - Andow, David A. T2 - Population Ecology AB - In Table 2, unnecessary words appeared in two entries in column 1. “Grid plot*plant” should read “Plot*plant,” and “Rid error” should read “Error.” The correct table appears here. Source df MS F P C. maculata Plot 38 0.5599 1.46 0.0002 Plant 1 0.6565 1.71 0.1919 Plot*plant 38 0.5878 1.53 0.0241 Error 597 0.3845 H. convergens Plot 38 0.1199 0.81 0.7832 Plant 1 1.5524 10.51 0.0013 Plot*plant 38 0.2430 1.65 0.0098 Error 598 0.1477 DA - 2005/10/5/ PY - 2005/10/5/ DO - 10.1007/s10144-005-0237-9 VL - 47 IS - 3 SP - 281-281 J2 - Population Ecology LA - en OP - SN - 1438-3896 1438-390X UR - http://dx.doi.org/10.1007/s10144-005-0237-9 DB - Crossref ER - TY - JOUR TI - Response of coccinellids to their aphid prey at different spatial scales AU - Schellhorn, Nancy A. AU - Andow, David A. T2 - Population Ecology AB - Abstract Predators that have an increasing numerical response for aggregation, attack and oviposition to increasing prey density are thought to be ideal for biological control. However density‐dependent processes are infrequently detected and explanations include differences in the scales at which observations are made, behavioral differences among species, and habitat features. We examined the aggregation of four species of colonizing adult coccinellids to varying prey densities at two spatial scales in a maize system. Three of the species, Adalia bipunctata , Hippodamia tredecimpunctata , and Hippodamia convergens , responded to aphid abundance at the plant scale, and one species, Coleomegilla maculata , responded to the average aphid density at the plot (10×10 m) scale. In addition, H. convergens responded to individual plants with high aphid abundance in those plots with many plants of high aphid abundance. These results suggests that C. maculata (and possibly H. convergens ) may be better able to colonize fields before aphid populations reach high levels, whereas A. bipunctata and H. tredecimpunctata may only be able to respond to high aphid abundance at the plant scale. This study suggests that spatial scale can affect predator–prey dynamics in a species‐specific manner. However, the differences among coccinellid species in the community appear to be complementary, potentially contributing to greater aphid suppression. DA - 2005/1/20/ PY - 2005/1/20/ DO - 10.1007/s10144-004-0204-x VL - 47 IS - 1 SP - 71-76 J2 - Population Ecology LA - en OP - SN - 1438-3896 1438-390X UR - http://dx.doi.org/10.1007/s10144-004-0204-x DB - Crossref ER - TY - JOUR TI - Genomic regions governing soybean sulfur containing amino acids AU - Pantalone, V.R. AU - Panthee, D.R. AU - Sams, C.E. AU - Saxton, A.M. AU - West, D.R. T2 - AOCS Abstracts DA - 2005/// PY - 2005/// VL - 35 M3 - Abstracts ER - TY - JOUR TI - Conditional expression of the mutant Ki- rasG12C allele results in formation of benign lung adenomas: development of a novel mouse lung tumor model AU - Floyd, Heather S. AU - Farnsworth, Charles L. AU - Kock, Nancy D. AU - Mizesko, Melissa C. AU - Little, Joy L. AU - Dance, Stephanie T. AU - Everitt, Jeff AU - Tichelaar, Jay AU - Whitsett, Jeffrey A. AU - Miller, Mark Steven T2 - Carcinogenesis AB - To determine the effects of expression of mutant Ki-ras on lung tumorigenesis, we developed a bitransgenic mouse model that expresses the human Ki-ras(G12C) allele in alveolar type II and/or Clara cells in a tetracycline-inducible, lung-specific manner. Expression of Ki-ras(G12C) caused multiple, small lung tumors over a 12-month time period. Although tumor multiplicity increased upon continued Ki-ras expression, most lung lesions were hyperplasias or well-differentiated adenomas. This is in contrast to the more severe phenotypes observed in other transgenic mouse models in which different mutant Ki-ras alleles were expressed in the lung. Expression of Ki-ras(G12C) was associated with a 2-fold increase in the activation of the Ras and Ral signaling pathways and increased phosphorylation of Ras downstream effectors, including Erk, p90 ribosomal S6 kinase, ribosomal S6 protein, p38 and MAPKAPK-2. In contrast, expression of the transgene had no effect on the activation of the JNK and Akt signaling pathways. Withdrawal of doxycycline for 1 month resulted in almost a complete absence of proliferative pulmonary lesions, suggesting tumor regression in the absence of Ki-ras expression. Mutant Ki-ras(G12C) expression was sufficient for initial lung tumor transformation, required for maintenance of tumor phenotype, and induced transformation of lung epithelial cells by the activation of multiple effector pathways. These results describe a novel mouse lung tumor model demonstrating benign tumor development in the absence of tumor progression, which will provide a new tool for understanding the early stages of lung tumor pathogenesis. DA - 2005/7/28/ PY - 2005/7/28/ DO - 10.1093/carcin/bgi190 VL - 26 IS - 12 SP - 2196-2206 LA - en OP - SN - 1460-2180 0143-3334 UR - http://dx.doi.org/10.1093/carcin/bgi190 DB - Crossref ER - TY - JOUR TI - The BovMAS consortium: Identification of QTL for milk yield and milk protein percent on chromosome 14 in the Brown Swiss breed AU - Bagnato, A. AU - Schiavini, F. AU - Dolezal, M. AU - Dubini, S. AU - Rossoni, A. AU - Maltecca, C. AU - Santus, E. AU - Medugorac, I. AU - Sölkner, J. AU - Fontanesi, L. AU - Friedman, A. AU - Lipkin, E. AU - Soller, M. T2 - Italian Journal of Animal Science AB - RiassuntoIdentificazione di QTL per quantità di latte e tenore proteico sul cromosoma 14 nella razza Bruna. Numerosi progetti di mappaggio di QTL hanno permesso di identificare diverse regioni cromosomiche associate a caratteri di interesse produttivo. In questo lavoro sono state identificate 2 possibili regioni QTL sul cromosoma 14 (0-20 cM e 70-110) nelle quali sono stati trovati marcatori in associazione con latte (kg) e proteina (%). Nella regione centromerica è stato inoltre studiato il genotipo per i geni DGAT1 e TG, il primo dei quali è stato recentemente proposto come causativo di un maggior contenuto lipidico nel latte. DA - 2005/// PY - 2005/// DO - 10.4081/ijas.2005.2s.13 VL - 4 SP - 13-15 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33645795921&partnerID=MN8TOARS ER - TY - JOUR TI - Effects of the osteopontin gene variants on milk production traits in dairy cattle AU - Leonard, S. AU - Khatib, H. AU - Schutzkus, V. AU - Chang, Y.M. AU - Maltecca, C. T2 - Journal of Dairy Science AB - Osteopontin (OPN) is a highly phosphorylated glycoprotein whose gene has been cloned and sequenced in different species. Several whole genome scans have identified quantitative trait loci (QTL) affecting milk production traits on bovine chromosome 6 close to the osteopontin gene (OPN) location. The presence of OPN in milk and its elevated expression in mammary gland epithelial cells together with previous QTL studies have prompted us to investigate the effects of OPN variants on milk production traits in the Holstein dairy cattle population. A single nucleotide polymorphism in intron 4 (C/T) was detected and primers were designed to amplify genomic DNA from 1362 bulls obtained from Cooperative Dairy DNA Repository and from 214 cows from the University of Wisconsin herd. For the Repository population, the C allele was associated with an increase in milk protein percentage and milk fat percentage. Correlation between milk protein percentage and milk fat percentage was about 0.57. For the University of Wisconsin herd, the estimates of the effects of allele C were in the same direction as for the Repository population, although these estimates did not reach statistical significance. Our results are consistent with other studies that showed a significant association of the microsatellite markers in the region of OPN with milk protein percentage and other correlated traits. DA - 2005/// PY - 2005/// DO - 10.3168/jds.S0022-0302(05)73092-7 VL - 88 IS - 11 SP - 4083-4086 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-27644525204&partnerID=MN8TOARS KW - osteopontin KW - quantitative trait loci KW - production trait ER - TY - JOUR TI - Kinetics and nucleation for driven thin film flow AU - Levy, Rachel AU - Shearer, Michael T2 - Physica D: Nonlinear Phenomena AB - The lubrication theory of thin liquid films, driven by a constant surface stress opposing gravity, is described by a scalar fourth order PDE for the film height h:ht+(h2−h3)x=−γ(h3hxxx)x, in which γ is a positive constant related to surface tension. In this paper, the wave structure of solutions observed in numerical simulations with γ>0 is related to the recent hyperbolic theory of the underlying scalar conservation law, in which γ=0. This theory involves a kinetic relation, describing possible undercompressive shocks, and a nucleation condition, governing the transition from classical to non-classical solution of the Riemann problem. The kinetic relation and nucleation condition are derived from consideration of traveling wave solutions (with γ>0). The kinetic relation is identified with a codimension-one bifurcation of the corresponding vector field, for which there is a traveling wave approximating an undercompressive shock. The nucleation condition is identified as a transition in the vector field at which there is no traveling wave connecting upstream and downstream heights. The thresholds defined by these conditions are incorporated into a Riemann solver map, which is tested for initial value problems for the full PDE. It is found that the parameter γ determines a limit to the applicability of the hyperbolic theory, in which the fourth order diffusion can dominate short-time transients, resulting in long-time convergence to the classical solution when the hyperbolic theory would predict a non-classical solution. DA - 2005/9// PY - 2005/9// DO - 10.1016/j.physd.2005.07.003 VL - 209 IS - 1-4 SP - 145-163 J2 - Physica D: Nonlinear Phenomena LA - en OP - SN - 0167-2789 UR - http://dx.doi.org/10.1016/j.physd.2005.07.003 DB - Crossref KW - kinetics KW - nucleation KW - Marangoni KW - Riemann solver KW - thin films KW - hyperbolic conservation laws KW - traveling waves ER - TY - JOUR TI - 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Induces Organ- Specific Differential Gene Expression in Male Japanese Medaka (Oryzias latipes) AU - Volz, David C. AU - Bencic, David C. AU - Hinton, David E. AU - Law, J. McHugh AU - Kullman, Seth W. T2 - Toxicological Sciences AB - 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a ubiquitous environmental contaminant with well-known adverse effects in fish. In this study, we initially exploited suppression subtractive hybridization (SSH) as a screening tool to assess qualitative gene expression changes in whole brain, liver, and testis of adult male Japanese medaka (Oryzias latipes) exposed for 48 h to a single intraperitoneal-injected dose of TCDD (10 microg TCDD/kg body weight). Across these three organs, SSH identified a total of 335 unique genes. Each set of forward- and reverse-subtracted organ cDNA libraries consisted of a distinct gene list and corresponding distribution of biological processes, suggesting that transcript profiles of these libraries were highly organ-specific. Based on sequence match significance and frequencies within each set of organ libraries, genes hypothesized to be strongly responsive (42 total) within male medaka brain, liver, or testis were semi-quantitatively screened with replicate cDNA nylon membrane arrays. In addition, TCDD-treated male medaka were surveyed for gross histological analysis of brain, liver, and testis. In general, adverse histopathological changes were not observed in the brain, and glycogen depletion was observed only in the liver. However, significant histological changes occurred in the testis, and included disorganization of spermatogenesis at the testis periphery, disruption of the interstitium, Leydig cell swelling, and Sertoli cell vacuolation. Of the 42 genes screened by cDNA array analysis, cytochrome P450 1A (CYP1A) mRNA was the only transcript significantly higher in TCDD-exposed brain, whereas 12 transcripts (including CYP1A) were significantly higher in TCDD-exposed liver, and 34 transcripts were significantly lower in TCDD-exposed testis. Therefore, the degree of TCDD-induced alterations observed in each organ at a gross histological level corresponded well with the number and ontology of gene transcripts affected on the array. Based on real-time reverse transcription polymerase chain reaction (RT-PCR), relative CYP1A (but not AHR1) transcript levels were confirmed to be significantly higher in TCDD-treated brain and liver. However, CYP1A was not significantly induced in TCDD-exposed testis, suggesting that gene expression and histopathological responses observed in the testis at 48 h may be CYP1A-independent. Based on these data, unique liver-specific and testis-specific mRNA-level targets in male medaka were identified as promising biomarkers of acute TCDD-induced toxicity. DA - 2005/2/9/ PY - 2005/2/9/ DO - 10.1093/toxsci/kfi109 VL - 85 IS - 1 SP - 572-584 LA - en OP - SN - 1096-6080 1096-0929 UR - http://dx.doi.org/10.1093/toxsci/kfi109 DB - Crossref KW - Japanese medaka KW - TCDD KW - gene expression KW - brain KW - liver KW - testis ER - TY - JOUR TI - Par for the course: pesticides on golf courses AU - Phillips, T. AU - Cooper, C.B. T2 - Birdscope DA - 2005/// PY - 2005/// VL - 19 IS - 3 ER - TY - JOUR TI - Beyond the Call AU - Cooper, C.B. T2 - Birdscope DA - 2005/// PY - 2005/// VL - 19 IS - 1 ER - TY - CONF TI - Practicing Scientific Dissent AU - Howard, J. AU - Durant, D. AU - Delborne, Jason T2 - Annual Meetings of the Society for Social Studies of Science C2 - 2005/10/21/ CY - 10 DA - 2005/10/21/ PY - 2005/// ER - TY - CONF TI - Pathways of Scientific Dissent in Agricultural Biotechnology AU - Delborne, J. T2 - Annual Meetings of the Society for Social Studies of Science C2 - 2005/10/21/ CY - Pasadena, CA DA - 2005/10/21/ PY - 2005/10/21/ ER - TY - JOUR TI - Structural insights into the first incision reaction during nucleotide excision repair AU - Truglio, James J AU - Rhau, Benjamin AU - Croteau, Deborah L AU - Wang, Liqun AU - Skorvaga, Milan AU - Karakas, Erkan AU - DellaVecchia, Matthew J AU - Wang, Hong AU - Van Houten, Bennett AU - Kisker, Caroline T2 - The EMBO Journal AB - Article3 February 2005free access Structural insights into the first incision reaction during nucleotide excision repair James J Truglio James J Truglio Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA Search for more papers by this author Benjamin Rhau Benjamin Rhau Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA Search for more papers by this author Deborah L Croteau Deborah L Croteau Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA Search for more papers by this author Liqun Wang Liqun Wang Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA Search for more papers by this author Milan Skorvaga Milan Skorvaga Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA Department of Molecular Genetics, Cancer Research Institute, Slovak Academy of Sciences, Bratislava, Slovakia Search for more papers by this author Erkan Karakas Erkan Karakas Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA Search for more papers by this author Matthew J DellaVecchia Matthew J DellaVecchia Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA Search for more papers by this author Hong Wang Hong Wang Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA Search for more papers by this author Bennett Van Houten Bennett Van Houten Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA Search for more papers by this author Caroline Kisker Corresponding Author Caroline Kisker Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA Search for more papers by this author James J Truglio James J Truglio Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA Search for more papers by this author Benjamin Rhau Benjamin Rhau Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA Search for more papers by this author Deborah L Croteau Deborah L Croteau Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA Search for more papers by this author Liqun Wang Liqun Wang Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA Search for more papers by this author Milan Skorvaga Milan Skorvaga Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA Department of Molecular Genetics, Cancer Research Institute, Slovak Academy of Sciences, Bratislava, Slovakia Search for more papers by this author Erkan Karakas Erkan Karakas Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA Search for more papers by this author Matthew J DellaVecchia Matthew J DellaVecchia Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA Search for more papers by this author Hong Wang Hong Wang Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA Search for more papers by this author Bennett Van Houten Bennett Van Houten Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA Search for more papers by this author Caroline Kisker Corresponding Author Caroline Kisker Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA Search for more papers by this author Author Information James J Truglio1, Benjamin Rhau1, Deborah L Croteau2, Liqun Wang1, Milan Skorvaga2,3, Erkan Karakas1, Matthew J DellaVecchia2, Hong Wang2, Bennett Van Houten2 and Caroline Kisker 1 1Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY, USA 2Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA 3Department of Molecular Genetics, Cancer Research Institute, Slovak Academy of Sciences, Bratislava, Slovakia *Corresponding author. Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794-5115, USA. Tel.: +1 631 632 1465; Fax: +1 631 632 1555; E-mail: [email protected] The EMBO Journal (2005)24:885-894https://doi.org/10.1038/sj.emboj.7600568 PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Nucleotide excision repair is a highly conserved DNA repair mechanism present in all kingdoms of life. The incision reaction is a critical step for damage removal and is accomplished by the UvrC protein in eubacteria. No structural information is so far available for the 3′ incision reaction. Here we report the crystal structure of the N-terminal catalytic domain of UvrC at 1.5 Å resolution, which catalyzes the 3′ incision reaction and shares homology with the catalytic domain of the GIY-YIG family of intron-encoded homing endonucleases. The structure reveals a patch of highly conserved residues surrounding a catalytic magnesium-water cluster, suggesting that the metal binding site is an essential feature of UvrC and all GIY-YIG endonuclease domains. Structural and biochemical data strongly suggest that the N-terminal endonuclease domain of UvrC utilizes a novel one-metal mechanism to cleave the phosphodiester bond. Introduction Nucleotide excision repair (NER) stands apart from other DNA repair mechanisms available to the cell in its ability to recognize a broad range of structurally unrelated DNA damages (Van Houten, 1990; Friedberg et al, 1995; Lloyd and Van Houten, 1995; Sancar, 1996; Goosen and Moolenaar, 2001) including carcinogenic cyclobutane pyrimidine dimers induced by UV radiation, benzo[a]pyrene-guanine adducts caused by smoking and burning of fossil fuels, and guanine-cisplatinum adducts formed during cancer chemotherapy (Sancar, 1994). The strategy employed by NER is the same in all three kingdoms of life. NER in prokaryotes was one of the first repair mechanisms discovered (Boyce and Howard-Flanders, 1964; Setlow and Carrier, 1964) and is mediated by the UvrA, UvrB and UvrC proteins. These three proteins recognize and cleave damaged DNA in an ATP-dependent multistep reaction. UvrA is involved in damage recognition and either forms a heterotrimeric (UvrA2UvrB) (reviewed in Theis et al, 2000) or heterotetrameric (UvrA2UvrB2) (Verhoeven et al, 2002) complex with UvrB. This complex is believed to scan the DNA helix for conformational perturbations induced by DNA lesions (Theis et al, 2000). After the damage has been identified, UvrA dissociates from the protein–DNA complex, leaving UvrB bound to the DNA (Orren and Sancar, 1990) forming a stable preincision complex (Theis et al, 2000; Skorvaga et al, 2002). UvrC binds to this complex and mediates the incision three or four nucleotides 3′ to the damaged site, followed by a second incision seven nucleotides 5′ to the damaged site (Sancar and Rupp, 1983; Lin and Sancar, 1992a, 1992b; Verhoeven et al, 2000). UvrD (helicase II) and DNA polymerase I (polI) are required for turnover of the UvrABC proteins (Caron et al, 1985; Husain et al, 1985). UvrD removes both UvrC and the oligonucleotide containing the lesion, while UvrB remains bound to the gapped DNA until it is displaced by DNA polI (Orren et al, 1992). The reaction is completed by DNA ligase, which closes the nicked DNA. This multistep process of DNA recognition and repair ensures a high degree of discrimination between the damaged and nondamaged strand. Site-directed mutagenesis and sequence alignments have shown that UvrC catalyzes both the 3′ and 5′ incisions and each of these incisions is performed by a distinct catalytic site that can be inactivated independently (Lin and Sancar, 1992b; Verhoeven et al, 2000). The domain responsible for 3′ incision is located in the N-terminal half of the molecule and consists of approximately the first hundred residues. This domain shares limited homology with a small module found in members of the GIY-YIG endonuclease family (Aravind et al, 1999). Also included in the N-terminal half is a region that interacts with the C-terminal domain of UvrB (Aravind et al, 1999). The 5′ catalytic domain, which is distantly related to Escherichia coli endonuclease V, is located in the C-terminal half of the protein along with two helix-hairpin-helix motifs employed in DNA binding (Aravind et al, 1999). After recruitment to the UvrB:DNA preincision complex, UvrC first catalyzes cleavage of the DNA on the 3′ side of the lesion (Verhoeven et al, 2000). This incision requires the interaction between the C-terminal domain of UvrB and the homologous UvrB binding domain of UvrC (Moolenaar et al, 1995, 1998a), which is not required for 5′ incision (Moolenaar et al, 1995). In order to obtain a better understanding of the 3′ incision event, we have solved the crystal structure of the N-terminal endonuclease domain of UvrC from two different thermophilic organisms, Bacillus caldotenax and Thermotoga maritima, at 2.0 and 1.5 Å resolution, respectively. This domain shares structural and sequence similarity to the catalytic domain found in I-TevI, a GIY-YIG homing endonuclease (Van Roey et al, 2002). I-TevI is one of at least 60 known GIY-YIG endonuclease family members that are present in bacteriophage T4, bacteria, archaea, algal chloroplasts and mitochondria, and fungal mitochondria. Members of this family are characterized by a 70–100 residues long module containing a conserved GIY-(X9–11)-YIG motif. We have identified a patch of highly conserved residues on the surface of the N-terminal domain of UvrC to which a single divalent cation is bound. The residues that form the metal binding pocket are conserved throughout all GIY-YIG endonucleases, suggesting the site to be a common feature of all family members. We mutated seven amino acids within the conserved patch and analyzed whether full-length UvrC was still able to incise damaged DNA, in the complete UvrABC reaction. Combined with the structural data, the results indicate that the conserved patch is the active site and the bound divalent cation is the catalytic metal. Based on our data, we propose that UvrC uses a novel one-metal mechanism to catalyze cleavage of the fourth or fifth phosphodiester bond 3′ to the DNA lesion. Results Crystal structure of the N-terminal endonuclease domain of UvrC The N-terminal catalytic domain of UvrC was initially cloned from B. caldotenax (UvrCN-Bca; residues 1–98) and its structure was solved by multiwavelength anomalous diffraction (MAD) (Table I). The protein crystallized in space group C2 and contained four molecules in the asymmetric unit arranged as a tetramer with C4 symmetry. Each of the four subunits has nearly identical conformations, with an average root mean square (r.m.s.) deviation of 0.62 Å for the Cα atoms of residues 8–94. The structure was refined at 2.0 Å resolution to an R-factor of 0.203 and Rfree of 0.252 (Table I). Residues 95–98 of subunit A, 1–8 and 95–98 of subunit B, 95–98 of subunit C, as well as 1 and 96–98 of subunit D are disordered. Table 1. Crystallographic statistics Data set Native (Bca) SeMet peak (Bca) SeMet inflection (Bca) SeMet remote (Bca) Native (Tma) Mn2+ bound native (Tma) Mg2+ bound native (Tma) Resolution (Å) 2.0 2.0 2.0 2.0 1.8 1.5 1.8 Wavelength (Å) 1.0 0.9794 0.9798 0.9538 1.1 1.1 1.1 Unique reflections 29 029 56 919 56 982 56 947 16 312 27 459 16 305 〈I〉/〈σI〉 37.2 (5.58) 31.1 (2.74) 31.6 (3.36) 31.6 (3.34) 47.5 (4.88) 40.5 (4.57) 35.8 (4.02) Completeness (%) 100.0 (100.0) 98.2 (97.6) 98.2 (97.6) 98.2 (97.6) 99.9 (100.0) 98.4 99.7 Rsym 0.07 (0.43) 0.07 (0.70) 0.06 (0.53) 0.06 (0.53) 0.06 (0.60) 0.04 (0.31) 0.06 (0.52) Phasing to 3.0 Å FOM (from SOLVE) 0.78 (0.68) Map correlation 0.45 Mean phase difference (deg) 55.0 (60.7) Rcryst (Rfree) 0.203 (0.252) 0.185 (0.199) 0.167 (0.185) 0.175 (0.202) r.m.s. deviation bond lengths (Å) 0.014 0.017 0.013 0.017 r.m.s. deviation bond angles (deg) 1.5 1.4 1.5 1.5 Mean B-factor 36.1 26.0 24.8 21.8 Ramachandran Statistics 94.3/4.8/0.9/0.0 94.9/3.8/1.3/0.0 94.9/5.1/0.0/0.0 96.2/2.6/1.3/0.0 Tma and Bca refer to T. maritima and B. caldotenax UvrC, respectively. Rsym=∑hkl∑i∣Ii–〈I〉∣/∑hkl∑i〈I〉, where Ii is the ith measurement and 〈I〉 is the weighted mean of all measurements of I. 〈I〉/〈σI〉 indicates the average of the intensity divided by its average standard deviation. Numbers in parentheses refer to the respective highest resolution data shell in each data set. Rcryst=∑∣∣Fo∣−∣Fc∣∣/∑∣Fo∣, where Fo and Fc are the observed and calculated structure factor amplitudes. Rfree is same as Rcryst for 5% of the data randomly omitted from the refinement. The map correlation coefficient describes the correlation between the electron density map calculated from the final model and the map corresponding to the experimental set of phases, averaged over all grid points. The mean phase difference is the mean differences between the initial phases calculated from SOLVE and phases calculated from the final wild-type model. Ramachandran statistics indicates the fraction of residues in the most favored, additionally allowed, generously allowed and disallowed regions of the Ramachandran diagram, as defined by the program PROCHECK (Laskowski et al, 1993). The corresponding domain was also cloned from T. maritima (UvrCN-Tma; residues 1–97) and crystallized in space group P43212 containing one molecule in the asymmetric unit. Crystals were soaked with manganese or magnesium chloride. The structure of UvrCN-Tma bound to manganese was solved by molecular replacement using the UvrCN-Bca monomer as a search model (see Materials and methods). This structure was refined at 1.5 Å resolution to an R-factor of 0.167 and Rfree of 0.185 (Table I), and consists of residues 1–89. The structure of magnesium-bound UvrCN-Tma was solved using difference Fourier methods (Table I). For the remainder of the discussion, residue numbering will correspond to UvrC from T. maritima, unless specified otherwise. The B. caldotenax and T. maritima structures have similar conformations with an r.m.s. deviation of 1.55 Å for 88 Cα atoms. Both have an αββααβα(α) topology with the C-terminal α-helix (α5) not present in UvrCN-Tma. The core of the molecule is a three-stranded β-sheet, which is flanked by the first three helices on one side and helix 4 on the other (Figure 1). Helices α1, α2 and α4 run approximately parallel to the β-sheet, while helix α3 is positioned almost perpendicular to these secondary structural elements, making contact only with the bottom edge of the sheet. In UvrCN-Bca helix α3 also interacts with the C-terminus, connecting the two helical halves of the protein across the β-sheet. Figure 1.: Stereo view of the N-terminal endonuclease domain of UvrCN-Tma. The central β-sheet (β1–β3) is shown in yellow and the surrounding helices (α1–α4) in green. Conserved residues are shown in ball-and-stick representation and the Mg2+ ion as a magenta sphere. The N- and C-termini of the domain are indicated. This figure and Figures 2A, 4 and 8 were generated with the programs MOLSCRIPT (Kraulis, 1991) and RASTER3D (Merritt and Murphy, 1994). Download figure Download PowerPoint Comparison to the catalytic domain of I-TevI A search using DALI (Holm and Sander, 1995), a network service for comparing three-dimensional protein structures (http://www.ebi.ac.uk/dali), identified the catalytic domain of I-TevI (Van Roey et al, 2002) (PDB codes 1LN0 and 1MK0) as the only structure with a fold similar to the N-terminal domain of UvrC (Z-score of 7.8). I-TevI is a member of the GIY-YIG family of homing endonucleases, which in turn belong to the larger GIY-YIG superfamily that includes UvrC. The only entity in common among all superfamily members is the domain presented here. It is a small, 70–100 residues module, containing a conserved GIY-(X9–11)-YIG motif (Van Roey et al, 2002) (Gly 17, Val 18, Tyr 19–Tyr 29, Ile 30, Gly 31), four invariant residues (Gly 31, Arg 39, Glu 76, Asn 88) and two highly conserved residues (Tyr 19, Tyr 29) (Figure 1). These amino acids are all located in proximity to each other and form, in part, a highly conserved surface. The catalytic domains of UvrC and I-TevI have likely diverged long ago as reflected by their low sequence identity of only 15% (Figure 2B). UvrCN-Tma superimposes onto the catalytic domain of I-TevI with an r.m.s. deviation of 2.2 Å for 60 out of 89 possible Cα atoms. However, there are notable differences in secondary and tertiary structure (Figure 2A). UvrCN-Tma/Bca contains an additional helix, α1, as compared to I-TevI. The function of α1 in UvrC is undoubtedly structural, as the residues that form this helix are not conserved among UvrCs, and sequence alignments show that like I-TevI, certain UvrC proteins lack this N-terminal helix (Figure 3B). Secondly, the fragment in UvrCN-Tma/Bca spanning α2 and β3, which includes α3, is not structurally conserved compared to I-TevI. Regardless of this dissimilarity, the position of Ile 54 from UvrCN-Tma (Leu 56 in UvrCBca) is conserved and superimposes well with Leu 45 in I-TevI (Figure 2A and B). This residue is structurally important and stabilizes the hydrophobic core of the domain. Lastly, UvrCN-Bca contains an additional helix, α5, at its C-terminus that is replaced by a loop region in both I-TevI and UvrCN-Tma (Figure 2A and B). Figure 2.Structural comparison of the two 3′ endonuclease domains from UvrC and the analogous domain in I-TevI. (A) Following their superposition, the three proteins were separated and displayed side by side: UvrCN-Tma (left), UvrCN-Bca (middle) and I-TevI (right). Selected residues are shown in ball-and-stick representation; hydrogen bonds are indicated by dotted lines. (B) Structure-based sequence alignment of UvrC from T. maritima and B. caldotenax, and I-TevI. Secondary structure elements are indicated above and below the sequence alignment corresponding to UvrC and I-TevI, respectively. The blue lines below the secondary structure elements indicate large regions of structural dissimilarity. Uppercase letters indicate residues that align structurally, while lowercase letters indicate residues that are not structurally aligned. Selected, structurally aligned residues are highlighted in red. Residues in a similar position, but not structurally aligned are highlighted in blue. Numbers above the sequence alignment correspond to residue numbering in UvrCN-Tma and UvrCN-Bca with numbering from UvrCN-Bca in superscript. Numbers below the alignment relate to residue numbering in I-TevI. Download figure Download PowerPoint Figure 3.Sequence conservation of the 3′ endonuclease domain of UvrC. (A) Two different views of the N-terminal domain in surface representation. The right view is rotated 90° relative to the left view around the vertical axis. Only the most conserved residues with solvent-accessible side chains are labeled with the addition of Phe 73. Color-coding is according to conservation (green: strictly conserved; blue: highly conserved; black: moderately conserved). (B) Sequence alignment of the N-terminal GIY-YIG domain from four selected UvrCs. The sequences are from T. maritima (gi:8134799), B. caldotenax, E. coli (gi:38704033) and Deinococcus radiodurans (gi:6116772). Secondary structure elements are indicated above the sequence and refer to the structure of UvrCN-Tma. They are color-coded according to Figure 1. Conserved residues are color-coded as in (A). The conserved GIY-(X9–11)-YIG sequence for which the domain was named is indicated by two red lines above the sequences. Part A and Figure 6 were generated with the programs SPOCK (Christopher and Baldwin, 1998) and RASTER3D. Download figure Download PowerPoint Both UvrCN-Tma/Bca and I-TevI contain a strictly conserved glutamate, arginine and asparagine, and a pair of highly conserved tyrosine residues (Tyr 19 and Tyr 29 in UvrCTma; Tyr 6 and Tyr 17 in I-TevI) (Figure 2A). The third tyrosine, Tyr 43 in UvrCN-Tma, corresponds to His 31 in I-TevI (Figure 2A and B). Sequence alignments reveal that this residue is either a tyrosine or a histidine in all UvrCs (Figure 3B) and all other GIY-YIG family members. Both Tyr 43 of UvrCN-Tma and His 31 of I-TevI form a hydrogen bond to Tyr 19 and Tyr 6, respectively (Figure 2A). His 31 of I-TevI in turn forms a hydrogen bond to His 40, which occupies the position of Val 51 in UvrC. In place of a hydrogen bond, Val 51 forms van der Waals interactions with Tyr 43. The conserved surface Mapping the sequence conservation of UvrC proteins from different organisms onto the surface reveals a conserved patch of amino acids (Figure 3A and B). Six strictly conserved residues are located in the center on one side of the surface: Tyr 19, Tyr 29, Lys 32, Arg 39, Glu 76 and Asn 88. These strictly conserved amino acids are surrounded by a number of highly conserved residues: Tyr 43, Phe 73 and Ile 80. The conserved residues form a shallow, concave surface with dimensions of 16 Å × 15 Å and 5 Å deep, which could easily accommodate double-stranded DNA. This is in agreement with biochemical data, which have shown that the 3′ endonuclease site only recognizes double-stranded DNA as a substrate and DNA containing an unpaired region of more than eight nucleotides overlapping the 3′ incision site is not incised (Zou and Van Houten, 1999). The cleft is sufficient for nuclease activity; however, the isolated domain does not bind to DNA (data not shown) and requires either the UvrB interacting domain and/or the C-terminal helix-hairpin-helix DNA binding domain of UvrC for catalysis to occur. The divalent cation Phosphodiester bonds, although thermodynamically labile, require large activation energies for cleavage at physiological pH (Galburt and Stoddard, 2002). This is mainly due to the negative charge of the phosphoryl group at this pH, which repels potential attacking nucleophiles. Three chemical entities are required to catalyze efficiently the cleavage of the phosphodiester bond: a general base to position and activate the nucleophile (usually a water molecule) for inline attack of the 5′ phosphate, a general acid to protonate the 3′ leaving group and a Lewis acid to stabilize the pentacovalent phosphoanion transition state. A number of different strategies to satisfy these requirements have evolved. A common feature of most nucleases is the use of one, two or even three divalent cations in the active site to lower the free energy of the transition state (Galburt and Stoddard, 2002). Metal ions can decrease the pKa of coordinating water molecules, resulting in a bound hydroxide, which could take the role of either a nucleophile or a general base. Alternatively, a metal-coordinated water molecule can be acidic and has the potential to serve as the general acid necessary to protonate the 3′ OH leaving group. However, the most substantial reduction in free energy derives from the metal's ability to stabilize the negative charge of the phosphoanion transition state (Galburt and Stoddard, 2002). No divalent cation was observed in the B. caldotenax structure after soaking and cocrystallization attempts. This is presumably due to the crystallization conditions, which contained high salt concentrations at low pH (5.4). In addition, there were protein–protein interactions in proximity to the only strictly conserved negatively charged amino acid, Glu 76, where metal binding was predicted to occur. Fortunately, crystals of UvrCN-Tma grew in PEG 8000 at high pH (8.5), a condition more suitable for soaking experiments. Additionally, Glu 76 was completely solvent accessible with no nearby protein–protein interactions. These crystals were briefly soaked with either MnCl2 or MgCl2 and the resulting structures provided similar results: a single divalent cation coordinated by Glu 76 and five well-ordered water molecules in an octahedral arrangement (Figure 4). These structures provide the first view of the metal and its exact coordination geometry for any member of the GIY-YIG superfamily and thus structural insight into the catalytic mechanism. The bound manganese was clearly identified in anomalous density maps, while omit maps revealed the octahedral arrangement of the chelating water molecules (Figure 4). The refined density for the water molecules in both structures is unambiguous with B-factors ranging from 17.1 to 23.6 Å2 for the manganese structure and 21.1 to 28.1 Å2 for the magnesium structure. The B-factors for the manganese and magnesium ion are 18.8 and 25.6 Å2, respectively. The manganese structure superimposes onto the magnesium structure with an r.m.s. deviation of 0.1 Å, and the two metal-water clusters superimpose with an r.m.s. deviation of 0.1 Å as well. Figure 4.Stereo view of the active site of the 3′ endonuclease domain. The metal ion is shown as a magenta sphere and the five surrounding water molecules as red spheres. Hydrogen bonds are shown as dotted lines. A simulated annealing omit map omitting the magnesium-water cluster, Glu 76, Arg 39 and Tyr 29 is shown at 1σ (blue, transparent) and an anomalous map is shown at 7σ (green cage). Residues in close proximity to the metal ion are shown in ball-and-stick representation. Download figure Download PowerPoint Although Glu 76 is the only protein residue bound directly to the metal, the water molecules coordinating to the metal form additional contacts to the protein (Figure 4). One of the waters forms hydrogen bonds to both the hydroxyl group of Tyr 29 and the main-chain carbonyl of Ile 30. A second water forms a hydrogen bond to the carboxylate of Glu 76, while a third water forms a hydrogen bond to the backbone amide of Lys 32. Residues forming the binding pocket for the metal-water cluster are highly conserved, suggesting the metal binding site to be a conserved feature of all GIY-YIG family members. Mutational analysis of the conserved surface Based on our structural data, we generated mutations of the highly conserved surface residues Y29A, Y29F, K32A, R39A, F73A, F73E, E76A, I80A, I80E and N88A in full-length UvrCTma and tested these mutant proteins in an incision assay using a defined substrate and the two other NER proteins UvrABca and UvrBBca (Figure 5). In addition, we verified that all of the mutants were able to bind and crosslink to double-stranded DNA. Electrophoretic mobility shift assays were performed using wild-type and mutant UvrC proteins (in the absence of UvrA or UvrB) with a 40 bp duplex containing a centrally located (+)-trans-BPDE adduct. Crosslinking was performed using wild-type and mutant UvrC proteins (in the absence of UvrA or UvrB) with 50 bp duplex containing a site-specific arylazido-modified photoaffinity reagent (as described in DellaVecchia et al, 2004) (data not shown). Figure 5.Incision activity of T. maritima UvrC mutants. The 5′ (A) or 3′ (B) end-labeled 50-mer double-stranded DNA substrates containing a centrally located fluorescein (FldT) were incubated with 20 nM UvrABca, 100 nM UvrBBca and 12.5 nM of the indicated UvrCTma protein for 30 min at 55°C in reaction buffer. The reactions were terminated with stop buffer, and the incision products were analyzed on a 10% denaturing polyacrylamide gel. (C) Comparison of the incision activity using the 3′-labeled substrate (gray bars) and 5′-labeled substrate (black bars) and the indicated UvrC proteins. Data are reported as the mean±the standard deviation of the mean of at least four incision assays per UvrC protein. Download figure Download PowerPoint Mutation of the sole metal ligand, Glu 76, to alanine renders UvrC unable to mediate either the 3′ or 5′ incision (Figure 5). UvrC from Tma, like E. coli UvrC, cannot achieve 5′ incision without prior 3′ incision, and thus inactivation of the 3′ nuclease active site inhibits the 5′ nuclease activity. Other inactive mutants were N88A, Y29A, Y29F, R39A and I80E. Mutant I80A showed an approximately 50% reduction in activity. Mutation of Lys 32 to alanine resulted in a protein that was 25–30% less active than wild-type UvrC and mutation of Phe 73 to either alanine or glutamate resulted in an enzyme with wild-type UvrC activity (Figure 5). The Y19F and Y43F mutants did not overexpress and could not be studied. In addition to the full-length mutants, we generated mutations in the isolated N-terminal domain (Y19F, Y29F, Y43F and N88A) and determined the structures of these mutants to inspect whether structural changes within the mutants lead to the inactivation of the enzyme (see Supplementary Table I). Discussion In this study, we have crystallized and solved the s DA - 2005/2/3/ PY - 2005/2/3/ DO - 10.1038/sj.emboj.7600568 VL - 24 IS - 5 SP - 885-894 J2 - EMBO J OP - SN - 0261-4189 1460-2075 UR - http://dx.doi.org/10.1038/sj.emboj.7600568 DB - Crossref KW - crystallography KW - DNA damage KW - DNA repair KW - nucleotide excision repair KW - UvrC ER - TY - CHAP TI - Can Neural Network Constraints in GP Provide Power to Detect Genes Associated with Human Disease? AU - Bush, William S. AU - Motsinger, Alison A. AU - Dudek, Scott M. AU - Ritchie, Marylyn D. T2 - Applications of Evolutionary Computing. EvoWorkshops 2005 A2 - Rothlauf, F. T3 - Lecture Notes in Computer Science AB - A major goal of human genetics is the identification of susceptibility genes associated with common, complex diseases. Identifying gene-gene and gene-environment interactions which comprise the genetic architecture for a majority of common diseases is a difficult challenge. To this end, novel computational approaches have been applied to studies of human disease. Previously, a GP neural network (GPNN) approach was employed. Although the GPNN method has been quite successful, a clear comparison of GPNN and GP alone to detect genetic effects has not been made. In this paper, we demonstrate that using NN evolved by GP can be more powerful than GP alone. This is most likely due to the confined search space of the GPNN approach, in comparison to a free form GP. This study demonstrates the utility of using GP to evolve NN in studies of the genetics of common, complex human disease. PY - 2005/// DO - 10.1007/978-3-540-32003-6_5 SP - 44–53 PB - Springer SN - 9783540253969 9783540320036 SV - 3449 UR - http://dx.doi.org/10.1007/978-3-540-32003-6_5 ER - TY - RPRT TI - Bivalves as biomonitors in the Neuse River AU - Levine, J.F. AU - Lewis, T. AU - Taylor, S. AU - Stoskopf, M. AU - Shea, D. AU - Showers, W. AU - Eads, C. DA - 2005/// PY - 2005/// ER - TY - SOUND TI - Effects of Electrofishing On Survival and Behavior of Native Freshwater Mussels AU - Holliman, F.M. AU - Kwak, T.J. AU - Cope, WG AU - Levine, J.F. DA - 2005/2// PY - 2005/2// ER - TY - CONF TI - Spring Viremia of Carp in the United States: Current Status and Diagnostics AU - Shivappa, R. AU - Kozlowicz, S. AU - Rolland, J. AU - Levine, J.F. T2 - Asian Fisheries Society 6th Annual Meeting C2 - 2005/10// CY - Sri Lanka DA - 2005/10// PY - 2005/10// ER - TY - RPRT TI - Assessment of the Impact of Highway Runoff on the Health of Freshwater Mussels AU - Levine, J.F. AU - Cope, G. AU - Stoskopf, M. AU - Bogan, M AU - Gustafson, L AU - Showers, B. AU - Shea, D. AU - Eads, C. AU - Lazaro, P AU - Thorsen, W AU - Forestier, D AU - Anderson, EF A3 - North Carolina Department of Transportation DA - 2005/// PY - 2005/// M1 - FHWA/NC/2004-03 M3 - Final Report PB - North Carolina Department of Transportation SN - FHWA/NC/2004-03 UR - https://rosap.ntl.bts.gov/view/dot/37846 ER - TY - CONF TI - Biomarkers of Oxidative Damage Due to Environmental Exposure to PCBs in Asiatic Clams AU - Lehmann, DW AU - Heltsley, Rm AU - Shea, D AU - Levine, Jf AU - Law, Jm C2 - 2005/11// CY - Society for Environmental Toxicology and Chemistry, Baltimore, MD DA - 2005/11// PY - 2005/11// ER - TY - CONF TI - Effects of Electrofishing on Survival and Behavior of Native Freshwater Mussels AU - Holliman, F.M. AU - Kwak, T.J. AU - Cope, WG AU - Levine, J.F. T2 - American Fisheries Society Annual Meeting C2 - 2005/9// CY - Anchorage, Alaska DA - 2005/9// PY - 2005/9// ER - TY - CONF TI - Characterization of Salmonella Fecal Isolates From a Commercial Laying Hen Complex By Serotype, Antibiotic Susceptibility and Pulsed Field Gel Electrophoresis AU - Li, X. AU - Payne, Jb AU - Santos, Fbo AU - Levine, JF AU - Sheldon, Bw T2 - Poultry Science Association Annual Meeting C2 - 2005/7// CY - Auburn, Alabama DA - 2005/7// PY - 2005/7// ER - TY - CONF TI - Conservation genetics of the endangered genus Alasmidonta (Unionidae: Anodontinae) in North America AU - Huang, Y. AU - Raley, M.E. AU - Levine, J.F. AU - Bogan, A.E. T2 - Flow-Weighted Mean Concentrations (FWMCS) C2 - 2005/5// CY - Minneapolis, Minnesota, US DA - 2005/5// PY - 2005/5// ER - TY - CONF TI - Evaluation of Physiochemical Conditions on the Valve Movement Response of Asian clams: Implications for Broadband Biomonitoring of Surface Waters AU - Turner, P.M. AU - Cope, W.G. AU - Shea, D. AU - Levine, J.F. AU - Moody, R T2 - Society of Environmental Toxicology and Chemistry (SETAC) C2 - 2005/11// CY - Baltimore, MD DA - 2005/11// PY - 2005/11// ER - TY - CONF TI - Characterization of Salmonella Isolates From A Commercial Laying Hen Complex by Serotype, Antibiotic Susceptibility Test and PFGE AU - Li, X AU - Levine, Jf AU - Sheldon, Bw T2 - Poultry Science Association Annual Meeting C2 - 2005/7// CY - Auburn, Alabama DA - 2005/7// PY - 2005/7// ER - TY - CONF TI - In vitro Sensitivity and Specificity Analysis of Spring Viremia of Carp Virus Diagnostic Tests AU - Shivappa, R. AU - Kozlowicz, S. AU - Corsin, F. AU - Levine, JF T2 - 30th Annual Eastern Fish Health Workshop C2 - 2005/6// CY - Shepardstown, West Virginia DA - 2005/6// PY - 2005/6// ER - TY - JOUR TI - ‘Close-fitting sleeves’: DNA damage recognition by the UvrABC nuclease system AU - Van Houten, Bennett AU - Croteau, Deborah L. AU - DellaVecchia, Matthew J. AU - Wang, Hong AU - Kisker, Caroline T2 - Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis AB - DNA damage recognition represents a long-standing problem in the field of protein-DNA interactions. This article reviews our current knowledge of how damage recognition is achieved in bacterial nucleotide excision repair through the concerted action of the UvrA, UvrB, and UvrC proteins. DA - 2005/9// PY - 2005/9// DO - 10.1016/j.mrfmmm.2005.03.013 VL - 577 IS - 1-2 SP - 92-117 J2 - Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis LA - en OP - SN - 0027-5107 UR - http://dx.doi.org/10.1016/j.mrfmmm.2005.03.013 DB - Crossref KW - protein-DNA interaction KW - bacterial nucleotide excision repair KW - DNA damage recognition ER - TY - JOUR TI - Structural insights into the first incision reaction during nucleotide excision repair AU - Truglio, James J AU - Rhau, Benjamin AU - Croteau, Deborah L AU - Wang, Liqun AU - Skorvaga, Milan AU - Karakas, Erkan AU - DellaVecchia, Matthew J AU - Wang, Hong AU - Van Houten, Bennett AU - Kisker, Caroline T2 - The EMBO journal DA - 2005/// PY - 2005/// VL - 24 IS - 5 SP - 885-894 ER - TY - JOUR TI - Copepod grazing impact on the trophic structure of the microbial assemblage of the San Pedro Channel, California AU - Schnetzer, Astrid AU - Caron, David A. T2 - Journal of Plankton Research AB - In August 2002 and March 2003 the trophic structure of the microbial assemblage from the San Pedro Channel, California was studied following the experimental alteration of the number of copepods. Changes in the abundance/biomass of microorganisms <80 μm during 3-day incubations were monitored in (i) the absence of metazoa >80 μm, (ii) the presence of natural abundances of metazoa and (iii) the presence of an elevated number of copepods. Prokaryotes and small-sized eukaryotes (<4 μm) dominated plankton biomass during both experimental months. Diatoms numerically dominated the 10–80 μm plankton in August 2002, but ciliate and heterotrophic dinoflagellate biomass generally exceeded diatom biomass on both dates. Ingestion of protozooplankton (predominantly ciliates) contributed substantially to copepod daily carbon rations. The adult copepod assemblage removed 4.6 and 36% per day of the microzooplankton standing stocks (10–80 μm size fraction) in August and March, respectively. Elevated copepod grazing pressure on protozooplankton resulted in increased biomass of nanoplankton (<5 μm) presumably via a trophic cascade. Accordingly, the copepod–protozoan trophic link appears to be a key factor structuring the planktonic microbial assemblage in the San Pedro Channel. DA - 2005/10/1/ PY - 2005/10/1/ DO - 10.1093/plankt/fbi049 VL - 27 IS - 10 SP - 959-971 UR - http://dx.doi.org/10.1093/plankt/fbi049 ER - TY - JOUR TI - New software for quantifying incubation behavior from time-series recordings AU - Cooper, Caren B. AU - Mills, Harold T2 - Journal of Field Ornithology AB - Recordings of temperature fluctuations in the nests of birds can be used to infer incubation behavior such as the frequency and duration of off-bouts. Until recently, collecting temperature recordings from a large number of nests was limited by the size and expense of data logger equipment. In this paper, we describe software we developed to help simplify the analysis of recordings of temperature or mass fluctuations over time. The software program, called Rhythm, works in conjunction with Raven, a bioacoustical analysis program, to partially automate the measurement of incubation off-bout duration and related statistics such as percent constancy. This novel application of Raven combined with advances in data logger technology facilitates investigation in several areas of ecological and behavioral research. DA - 2005/10// PY - 2005/10// DO - 10.1648/0273-8570-76.4.352 VL - 76 IS - 4 SP - 352-356 J2 - Journal of Field Ornithology LA - en OP - SN - 0273-8570 1557-9263 UR - http://dx.doi.org/10.1648/0273-8570-76.4.352 DB - Crossref KW - automated analysis KW - data logger KW - incubation rhythm KW - Raven KW - The Birdhouse Network ER - TY - JOUR TI - Seasonal and Latitudinal Trends in Clutch Size: Thermal Constraints During Laying and Incubation AU - Cooper, Caren B. AU - Hochachka, Wesley M. AU - Butcher, Greg AU - Dhondt, André A. T2 - Ecology AB - Explaining patterns of latitudinal and seasonal trends in clutch size are two of the oldest and most fundamental endeavors in avian life history research. Underlying the majority of studies regarding any type of clutch size variation (i.e., individual, seasonal, latitudinal) of altricial birds is the premise that the primary cost of reproduction stems from feeding offspring. However, both altricial and precocial species of birds display latitudinal and seasonal variation in clutch size. Additionally, individual variation in costs of laying and incubation, recently demonstrated, indicates that understanding latitudinal and seasonal clutch size trends will require increased attention to earlier phases of reproduction. Given the strength and ubiquity of the clutch size patterns, many environmental factors, such as food supply and predation, have been proposed to account for the patterns, but temperature has been largely overlooked. Gradients in many variables may be important because the primacy of selection pressures may also vary in space and time. Furthermore, physiological systems may constrain responses to selection pressures. Thus, it is possible that intraspecific geographic and seasonal patterns in clutch size are at least partially influenced by temperature-dependent physiological processes. Therefore, we suggest that it is important to examine physiological responses of birds (e.g., embryo development, incubation energetics) directly influenced by physical properties of the environment, which exhibit predictable types of spatial and temporal variation (e.g., temperature, humidity, day length). We review two recently proposed, complementary hypotheses that are excellent candidates for this approach. By one mechanism, the thermal inertia of large clutches makes them favorable in cooler weather (the clutch-cooling hypothesis of J. M. Reid et al.). By the other, the reduction in egg viability under warm temperatures favors small clutches (the egg-viability hypothesis of S. H. Stoleson and S. R. Beissinger). Using general linear mixed models, we found that large-scale nesting patterns of Eastern Bluebirds and Red-winged Blackbirds are consistent with the egg-viability hypothesis in that females appear to initiate incubation before clutch completion when they lay large clutches at low latitudes. Although attempts have been made to overcome the logistical obstacles associated with studying large-scale phenomena through meta-analyses and multiple small-scale study sites, we demonstrate the significant potential of new technologies combined with volunteer-based studies to validate these hypotheses as we outline directions for future research. Table 1. Predictions arising from the egg-viability hypothesis (EV) and the clutch-cooling hypothesis (CC) DA - 2005/8// PY - 2005/8// DO - 10.1890/03-8028 VL - 86 IS - 8 SP - 2018–2031 SN - 0012-9658 UR - http://dx.doi.org/10.1890/03-8028 KW - clutch size variation KW - Cornell Nest Record Program KW - critical temperatures KW - egg viability KW - hatching failure KW - incubation period KW - latitude gradients KW - onset of incubation KW - seasonal constraints ER - TY - JOUR TI - Latitudinal trends in within-year reoccupation of nest boxes and their implications AU - Cooper, Caren B. AU - Hochachka, Wesley M. AU - Dhondt, André A. T2 - Journal of Avian Biology AB - Multiple brooding can substantially increase the annual reproductive output of birds, and the propensity for multiple brooding can vary geographically. Thus, studies attempting to understand the evolution of geographic variation in nesting success need to account for variation in re‐nesting potential. However, direct assessment of rates of multiple brooding requires individually recognizable breeding adults, which are not generally available. We explore the possibility of comparing relative indices of multiple broodedness across a latitudinal gradient from studies of un‐banded birds locally restricted to nest boxes. We analyzed nest box reoccupation by a multiple‐brooding species, the eastern bluebird Sialia sialis , reported by volunteers in a citizen‐participation project (1998–2002) in which nest boxes were monitored throughout much of the breeding range of the bluebirds. We found nest boxes in the southern portion of the bluebird range (30° latitude) had, on average 17–33% higher likelihood of repeated egg‐laying, brooding, and successful fledging events than boxes in the north (48° latitude). Latitudinal variation in the reoccupation of nest boxes may indicate that either (1) the number of broods per female varies with latitude, (2) female breeding dispersal/site fidelity varies with latitude, (3) the density, distribution, and/or availability of suitable nest sites varies with latitude, or (4) observer bias varies with latitude. Various lines of evidence suggest that nest re‐occupancy is a useful index of latitudinal variation in re‐nesting. During the time‐frame of second attempts, first‐time box occupancy was as likely as second occupancy and approximately 45% more likely in the south than north, suggesting that, despite considerable breeding dispersal, observed trends in box reoccupation conservatively reflect latitudinal trends in the number of nest attempts/broods per female. Furthermore, despite a compressed nesting cycle in the north (shorter incubation and re‐nesting interval), the shorter duration of the breeding season in the north restricted the potential number of broods. Studies of banded birds are necessary to confirm the behavior underlying the latitudinal trends in box reoccupation. DA - 2005/1// PY - 2005/1// DO - 10.1111/j.0908-8857.2005.03319.x VL - 36 IS - 1 SP - 31-39 LA - en OP - SN - 0908-8857 1600-048X UR - http://dx.doi.org/10.1111/j.0908-8857.2005.03319.x DB - Crossref ER - TY - CHAP TI - Design and use of a highly responsive and rigidly controllable hypoxia exposure system AU - Lehmann, D AU - Levine, J AU - Law, J T2 - Techniques in Aquatic Toxicology A2 - Ostrander, G.K. PY - 2005/1/27/ DO - 10.1201/9780203501597.ch31 VL - 2 PB - CRC Press SN - 9781566706643 9780203501597 UR - http://dx.doi.org/10.1201/9780203501597.ch31 ER - TY - JOUR TI - Measures of human population structure show heterogeneity among genomic regions AU - Weir, B. S. AU - Cardon, L.R. AU - Anderson, A.D. AU - Nelson, D.M. AU - Hill, W.G. T2 - Genome Research AB - Estimates of genetic population structure (F(ST)) were constructed from all autosomes in two large SNP data sets. The Perlegen data set contains genotypes on approximately 1 million SNPs segregating in all three samples of Americans of African, Asian, and European descent; and the Phase I HapMap data set contains genotypes on approximately 0.6 million SNPs segregating in all four samples from specific Caucasian, Chinese, Japanese, and Yoruba populations. Substantial heterogeneity of F(ST) values was found between segments within chromosomes, although there was similarity between the two data sets. There was also substantial heterogeneity among population-specific F(ST) values, with the relative sizes of these values often changing along each chromosome. Population-structure estimates are often used as indicators of natural selection, but the analyses presented here show that individual-marker estimates are too variable to be useful. There is inherent variation in these statistics because of variation in genealogy even among neutral loci, and values at pairs of loci are correlated to an extent that reflects the linkage disequilibrium between them. Furthermore, it may be that the best indications of selection will come from population-specific F(ST) values rather than the usually reported population-average values. DA - 2005/11/1/ PY - 2005/11/1/ DO - 10.1101/gr.4398405 VL - 15 IS - 11 SP - 1468–1476 SN - 1088-9051 UR - http://dx.doi.org/10.1101/gr.4398405 ER - TY - RPRT TI - The Global Climate and Economic Development A3 - Center for Science, Technology, and Public Policy. Humphrey Institute DA - 2005/// PY - 2005/// PB - Center for Science, Technology, and Public Policy. Humphrey Institute ER - TY - RPRT TI - The Nanotechnology-Biology Interface: Exploring Models for Oversight A3 - Center for Science, Technology, and Public Policy, University of Minnesota DA - 2005/9/15/ PY - 2005/9/15/ M3 - Workshop Report PB - Center for Science, Technology, and Public Policy, University of Minnesota ER - TY - RPRT TI - Global Challenges and Biotechnology AU - Kuzma, J. DA - 2005/10// PY - 2005/10// ER - TY - JOUR TI - Gravity and light: integrating transcriptional regulation in roots. AU - Salinas-Mondragon, R. AU - Brogan, A. AU - Ward, N. AU - Perera, I. AU - Boss, W. AU - Brown, C.S. AU - Sederoff, H.W. T2 - Gravitational and space biology bulletin : publication of the American Society for Gravitational and Space Biology DA - 2005/// PY - 2005/// VL - 18 IS - 2 SP - 121-122 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-24944540197&partnerID=MN8TOARS ER - TY - JOUR TI - Co-expression and hormonal regulation of genes in response to gravity and mechanical stimulation in the Arabidopsis root apex. AU - Kimbrough, J.M. AU - Brown, C.S. AU - Sederoff, H.W. T2 - Gravitational and space biology bulletin : publication of the American Society for Gravitational and Space Biology DA - 2005/// PY - 2005/// VL - 18 IS - 2 SP - 117-118 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-26944462406&partnerID=MN8TOARS ER - TY - CONF TI - USING CHICKEN GENOME SEQUENCES TO SEARCH FOR NEW MICROSATELLITE BIOMARKERS AU - Kuo, Alice AU - Fulton, Janet AU - Ashwell, Christopher C2 - 2005/// C3 - Plant and Animal Genome VX Conference Abstracts DA - 2005/// VL - 206 ER - TY - JOUR TI - changes in the efficiency of muscular contraction under pressure AU - Ozden, Ozkan AU - Black, Betty L AU - Ashwell, Christopher M AU - Tipsmark, Christian K AU - Borski, Russell J AU - others T2 - Journal of Cellular and Comparative Physiology DA - 2005/// PY - 2005/// ER - TY - CONF TI - Use of biotechnology in nutrition research AU - Ashwell, Christopher M C2 - 2005/// C3 - CAROLINA POULTRY NUTRITION CONFERENCE DA - 2005/// VL - 32 SP - 107-116 ER - TY - JOUR TI - MICROSATELLITE MARKERS FROM CHROMOSOME 27 BY USING THE CHICKEN GENOME SEQUENCE (GENBANK BV680374-BV680405) AU - Kuo, Alice AU - Fulton, Janet AU - Ashwell, Christopher T2 - Genbank DA - 2005/// PY - 2005/// ER - TY - CONF TI - GENOME-WIDE LINKAGE AND QTL MAPPING IN CHICKEN F2 POPULATIONS AU - Zhou, H AU - Deeb, Nader AU - Evock-Clover, C AU - Ashwell, CM AU - Lamont, SJ C2 - 2005/// C3 - Plant and Animal Genome VX Conference Abstracts DA - 2005/// SP - 209 ER - TY - JOUR TI - Environmental and management factors affecting the welfare of chickens on commercial farms in the United Kingdom and Denmark stocked at five densities AU - Jones, TA AU - Donnelly, CA AU - Stamp Dawkins, M T2 - Poultry Science DA - 2005/// PY - 2005/// VL - 84 IS - 8 SP - 1155-1165 ER - TY - JOUR TI - Effects of chemically amended litter on broiler performances, atmospheric ammonia concentration, and phosphorus solubility in litter AU - Do, JC AU - Choi, IH AU - Nahm, KH T2 - Poultry science DA - 2005/// PY - 2005/// VL - 84 IS - 5 SP - 679-686 ER - TY - JOUR TI - ENVIRONMENT, WELL-BEING, AND BEHAVIOR AU - Do, JC AU - Choi, IH AU - Nahm, KH T2 - Poultry Science DA - 2005/// PY - 2005/// VL - 84 SP - 679-686 ER - TY - JOUR TI - Interactions among endocrine, nutritional and genetic factors controlling metabolism in the broiler AU - Rosebrough, RW AU - McMurtry, JP AU - Richards, MP AU - Mitchell, AD AU - Ramsay, TG AU - Ashwell, CM T2 - Avian and Poultry Biology Reviews DA - 2005/// PY - 2005/// VL - 16 IS - 2 SP - 95-100 ER - TY - JOUR TI - Insulin-like growth factor-I gene polymorphism associations with growth, body composition, skeleton integrity, and metabolic traits in chickens AU - Zhou, H AU - Mitchell, AD AU - McMurtry, JP AU - Ashwell, CM AU - Lamont, Susan J T2 - Poultry Science DA - 2005/// PY - 2005/// VL - 84 IS - 2 SP - 212-219 ER - TY - JOUR TI - Expressed sequence tag analysis of Eimeria-stimulated intestinal intraepithelial lymphocytes in chickens AU - Min, Wongi AU - Lillehoj, Hyun S AU - Ashwell, Christopher M AU - Van Tassell, Curtis P AU - Dalloul, Rami A AU - Matukumalli, Lakshmi K AU - Han, Jae Y AU - Lillehoj, Erik P T2 - Molecular biotechnology DA - 2005/// PY - 2005/// VL - 30 IS - 2 SP - 143-149 ER - TY - JOUR TI - Evaluation of the broiler’s ability to adapt to an early moderate deficiency of phosphorus and calcium AU - Yan, F AU - Angel, R AU - Ashwell, Christopher AU - Mitchell, Alva AU - Christman, M T2 - Poultry science DA - 2005/// PY - 2005/// VL - 84 IS - 8 SP - 1232-1241 ER - TY - JOUR TI - ENVIRONMENT, WELL-BEING, AND BEHAVIOR AU - Woodward, CL AU - Kwon, YM AU - Kubena, LF AU - Byrd, JA AU - Moore, RW AU - Nisbet, DJ AU - Ricke, SC T2 - Poultry Science DA - 2005/// PY - 2005/// VL - 84 SP - 185-193 ER - TY - JOUR TI - Assignment of 42 Microsatellite Markers from Chromosome 28 on Chicken Genome (Genbank Bv 680436-Bv680477) AU - Kuo, Alice AU - Fulton, Janet AU - Ashwell, Christopher T2 - Genbank DA - 2005/// PY - 2005/// ER - TY - JOUR TI - Chicken quantitative trait loci for growth and body composition associated with the very low density apolipoprotein-II gene AU - Li, H AU - Deeb, Nader AU - Zhou, H AU - Ashwell, CM AU - Lamont, Susan J T2 - Poultry science DA - 2005/// PY - 2005/// VL - 84 IS - 5 SP - 697-703 ER - TY - JOUR TI - Measures of human population structure show heterogeneity among genomic regions AU - Weir, B. S. AU - Cardon, L. R. AU - Anderson, A. D. AU - Nielsen, D. M. AU - Hill, W. G. T2 - Genome Res DA - 2005/// PY - 2005/// VL - 15 IS - 11 SP - 1468-1476 ER - TY - JOUR TI - 752. Equine Infectious Anemia Virus Pseudotyped with the Vesicular Stomatitis Virus G-Protein, Preferentially Targets Neural Precursors in the Adult Mouse Brain AU - Ghashghaei, Troy AU - Patel, Manij AU - Olsen, John AU - Anton, Eva T2 - Molecular Therapy AB - The ongoing neurogenesis in the adult mammalian brain depends on mitotic activity of specialized stem cells in the subventricular zone. The majority of these stem cells have now been identified to have an astrocytic phenotype. Manipulation of these stem cells, especially through viral mediated gene transfer techniques, can be useful in a wide-range of experimental and potentially therapeutic settings. We used an Equine Infectious Anemia Virus (EIAV) to express Ehanced Green Fluorescent Protein (EGFP) in cells of the subventricular zone (SVZ). The virus, which was pseudotyped with the vesicular stomatitis virus G-protein (VSV-G), seemed to preferentially infect subset of glial fibrillary acidic protein expressing (GFAP+) astrocytic cells that line the ventricles. Furthermore, some of these cells may have given rise to migrating neuroblasts in the rostral migratory stream, which eventually develop into interneurons in the olfactory bulb. The preferential targeting of GFAP+ astrocytes in the SVZ by the EIAV lentivirus is potentially useful for the molecular manipulation of these stem cells. DA - 2005/5// PY - 2005/5// DO - 10.1016/j.ymthe.2005.07.293 VL - 11 IS - Supplement 1 SP - S292 SN - 1525-0016 UR - http://dx.doi.org/10.1016/j.ymthe.2005.07.293 ER - TY - JOUR TI - 803. The Effects of Intratumoral Injection of a Replicating Morbillivirus in a Canine Model of Naturally Occurring Lymphoma AU - Henson, Michael S. AU - Suter, Steven E. AU - von Messling, Veronika A. AU - Cattaneo, Roberto AU - Fielding, Adele K. T2 - Molecular Therapy AB - Many viruses have a greater capacity to replicate within and lyse transformed cells than in normal cells. Those replicating oncolytic viruses with low pathogenicity in humans are receiving increasing attention as potential therapies for cancer. We previously established that the non-pathogenic, vaccine strain of measles virus (MV) could cause regression of established lymphoma xenografts in mice. However, murine models have considerable limitations in predicting response in humans; this is particularly true in the case of studies with MV in particular, since MV does not infect murine cells. DA - 2005/5// PY - 2005/5// DO - 10.1016/j.ymthe.2005.07.340 VL - 11 IS - Supplement 1 SP - S312 SN - 1525-0016 UR - http://dx.doi.org/10.1016/j.ymthe.2005.07.340 ER - TY - JOUR TI - Catalytic Reduction of Amides to Amines with Hydrosilanes Using a Triruthenium Carbonyl Cluster as the Catalyst​ AU - Motoyama, Y. AU - Itonaga, C. AU - Ishida, T. AU - Takasaki, M. AU - Nagazhima, H. T2 - Organic Syntheses DA - 2005/// PY - 2005/// DO - 10.15227/orgsyn.082.0188 VL - 82 SP - 188 SN - 0078-6209 2333-3553 UR - http://dx.doi.org/10.15227/orgsyn.082.0188 ER - TY - JOUR TI - Lipase-Catalyzed Resolution of 4-Trimethylsilyl-3-Butyn-2-ol and Conversion of the (R)-Enantiomer to (R)-3-Butyn-2-yl Mesylate and (P)-1-Tributylstannyl-1,2-Butadiene AU - Marshall, James A. AU - Chobanian, Harry T2 - Organic Syntheses AB - Abstract (R)‐4‐Trimethylsilyl‐3‐butyn‐2‐yl acetate (S)‐4‐Trimethylsilyl‐3‐butyn‐2‐yl succinate 4‐Trimethylsilyl‐3‐butyn‐2‐ol (R)‐4‐Trimethylsilyl‐3‐butyn‐2‐yl mesylate Vinyl acetate Diisobutylaluminum hydride Butyllithium Cuprous bromide‐dimethylsulfide complex ( P )‐1‐Tributylstannyl‐1, 2‐butadiene DA - 2005/4/15/ PY - 2005/4/15/ DO - 10.1002/0471264229.os082.07 VL - 4 SP - 43-55 UR - http://dx.doi.org/10.1002/0471264229.os082.07 ER - TY - JOUR TI - Structure-guided saturation mutagenesis of N-acetylneuraminic acid lyase for the synthesis of sialic acid mimetics AU - Williams, G.J. AU - Woodhall, T. AU - Nelson, A. AU - Berry, A. T2 - Protein Engineering, Design and Selection AB - Analogues of N-acetylneuraminic acid (sialic acid, NANA, Neu5Ac), including 6-dipropylcarboxamides, have been found to be selective and potent inhibitors of influenza sialidases. Sialic acid analogues are, however, difficult to synthesize by traditional chemical methods and the enzyme N-acetylneuraminic acid lyase (NAL) has previously been used for the synthesis of a number of analogues. The activity of this enzyme towards 6-dipropylcarboxamides is, however, low. Here, we used structure-guided saturation mutagenesis to produce variants of NAL with improved activity and specificity towards 6-dipropylcarboxamides. Three residues were targeted for mutagenesis, Asp191, Glu192 and Ser208. Only substitution at position 192 produced significant improvements in activity towards the dipropylamide. One variant, E192N, showed a 49-fold improvement in catalytic efficiency towards the target analogue and a 690-fold shift in specificity from sialic acid towards the analogue. These engineering efforts provide a scaffold for the further tailoring of NAL for the synthesis of sialic acid mimetics. DA - 2005/5/1/ PY - 2005/5/1/ DO - 10.1093/protein/gzi027 VL - 18 IS - 5 SP - 239-246 LA - en OP - SN - 1741-0134 1741-0126 UR - http://dx.doi.org/10.1093/protein/gzi027 DB - Crossref KW - N-acetylneuraminic acid lyase KW - sialic acid mimetics KW - structure-guided saturation mutagenesis KW - synthesis ER - TY - CHAP TI - Biochemistry and Molecular Biology of Pheromone Production AU - Blomquist, G.J. AU - Jurenka, R. AU - Schal, C. AU - Tittiger, C. T2 - Comprehensive Molecular Insect Science PY - 2005/// DO - 10.1016/b0-44-451924-6/00046-6 VL - 3 SP - 705–751 PB - Elsevier SN - 9780444519245 UR - http://dx.doi.org/10.1016/b0-44-451924-6/00046-6 ER - TY - JOUR TI - Computational analysis of EGFR inhibition by Argos AU - Reeves, Gregory T. AU - Kalifa, Rachel AU - Klein, Daryl E. AU - Lemmon, Mark A. AU - Shvartsman, Stanislav Y. T2 - Developmental Biology AB - Argos, a secreted inhibitor of the Drosophila epidermal growth factor receptor, and the only known secreted receptor tyrosine kinase inhibitor, acts by sequestering the EGFR ligand Spitz. We use computational modeling to show that this biochemically-determined mechanism of Argos action can explain available genetic data for EGFR/Spitz/Argos interactions in vivo. We find that efficient Spitz sequestration by Argos is key for explaining the existing data and for providing a robust feedback loop that modulates the Spitz gradient in embryonic ventral ectoderm patterning. Computational analysis of the EGFR/Spitz/Argos module in the ventral ectoderm shows that Argos need not be long-ranged to account for genetic data, and can actually have very short range. In our models, Argos with long or short length scale functions to limit the range and action of secreted Spitz. Thus, the spatial range of Argos does not have to be tightly regulated or may act at different ranges in distinct developmental contexts. DA - 2005/8// PY - 2005/8// DO - 10.1016/j.ydbio.2005.05.013 VL - 284 IS - 2 SP - 523-535 J2 - Developmental Biology LA - en OP - SN - 0012-1606 UR - http://dx.doi.org/10.1016/j.ydbio.2005.05.013 DB - Crossref KW - EGFR inhibition KW - Argos KW - Spitz ER - TY - CONF TI - One pretty amazing T.rex : A presentation for "100 years of tyrannosaurus rex AU - Schweitzer, M.H. AU - Wittmeyer, J.L. T2 - 100 years of Tyrannosaurus rex symposium A2 - Carpenter, K. A2 - Larson, P. C2 - 2005/// CY - Black Hills Museum of Natural History DA - 2005/// PY - 2005/6/10/ ER - TY - JOUR TI - A cardiac myosin binding protein C mutation in the Maine Coon cat with familial hypertrophic cardiomyopathy AU - Meurs, K.M. AU - Sanchez, X. AU - David, R.M. AU - Bowles, N.E. AU - Towbin, J.A. AU - Reiser, P.J. AU - Kittleson, J.A. AU - Munro, M.J. AU - Dryburgh, K. AU - MacDonald, K.A. AU - Kittleson, M.D. T2 - Human Molecular Genetics AB - Hypertrophic cardiomyopathy (HCM) is one of the most common causes of sudden cardiac death in young adults and is a familial disease in at least 60% of cases. Causative mutations have been identified in several sarcomeric genes, including the myosin binding protein C (MYBPC3) gene. Although numerous causative mutations have been identified, the pathogenetic process is still poorly understood. A large animal model of familial HCM in the cat has been identified and may be used for additional study. As the first spontaneous large animal model of this familial disease, feline familial HCM provides a valuable model for investigators to evaluate pathophysiologic processes and therapeutic (pharmacologic or genetic) manipulations. The MYBPC3 gene was chosen as a candidate gene in this model after identifying a reduction in the protein in myocardium from affected cats in comparison to control cats (P<0.001). DNA sequencing was performed and sequence alterations were evaluated for evidence that they changed the amino acid produced, that the amino acid was conserved and that the protein structure was altered. We identified a single base pair change (G to C) in the feline MYBPC3 gene in affected cats that computationally alters the protein conformation of this gene and results in sarcomeric disorganization. We have identified a causative mutation in the feline MYBPC3 gene that results in the development of familial HCM. This is the first report of a spontaneous mutation causing HCM in a non-human species. It should provide a valuable model for evaluating pathophysiologic processes and therapeutic manipulations. DA - 2005/12/1/ PY - 2005/12/1/ DO - 10.1093/hmg/ddi386 VL - 14 IS - 23 SP - 3587–3593 ER - TY - CHAP TI - Molecular genetics of dilated cardiomyaopthy in the dog AU - Stabej, P. AU - Meurs, K.M. AU - van Oost, B.A. T2 - Canine Genetics PY - 2005/// SP - 365–382 PB - Cold Spring Harbor ER - TY - CHAP TI - Canine Myocardial Disease AU - Meurs, K.M. T2 - Textbook of Veterinary Internal Medicine PY - 2005/// ET - 6th SP - 1077-1081 PB - WB Saunders ER - TY - JOUR TI - Escorrentía superficial en bosques montanos naturales y plantados de Antioquia, Colombia AU - Ruiz, O.A. AU - Acosta, J.J. AU - León, J.D. T2 - Revista Facultad Nacional de Agronomía DA - 2005/// PY - 2005/// VL - 58 IS - 1 SP - 2635–2649 UR - http://www.bdigital.unal.edu.co/24359/1/21509-73485-1-PB.pdf ER - TY - JOUR TI - Phytochrome-Specific Type 5 Phosphatase Controls Light Signal Flux by Enhancing Phytochrome Stability and Affinity for a Signal Transducer AU - Ryu, Jong Sang AU - Kim, Jeong-Il AU - Kunkel, Tim AU - Kim, Byung Chul AU - Cho, Dae Shik AU - Hong, Sung Hyun AU - Kim, Seong-Hee AU - Fernández, Aurora Piñas AU - Kim, Yumi AU - Alonso, Jose M. AU - Ecker, Joseph R. AU - Nagy, Ferenc AU - Lim, Pyung Ok AU - Song, Pill-Soon AU - Schäfer, Eberhard AU - Nam, Hong Gil T2 - Cell AB - Environmental light information such as quality, intensity, and duration in red (approximately 660 nm) and far-red (approximately 730 nm) wavelengths is perceived by phytochrome photoreceptors in plants, critically influencing almost all developmental strategies from germination to flowering. Phytochromes interconvert between red light-absorbing Pr and biologically functional far-red light-absorbing Pfr forms. To ensure optimal photoresponses in plants, the flux of light signal from Pfr-phytochromes should be tightly controlled. Phytochromes are phosphorylated at specific serine residues. We found that a type 5 protein phosphatase (PAPP5) specifically dephosphorylates biologically active Pfr-phytochromes and enhances phytochrome-mediated photoresponses. Depending on the specific serine residues dephosphorylated by PAPP5, phytochrome stability and affinity for a downstream signal transducer, NDPK2, were enhanced. Thus, phytochrome photoreceptors have developed an elaborate biochemical tuning mechanism for modulating the flux of light signal, employing variable phosphorylation states controlled by phosphorylation and PAPP5-mediated dephosphorylation as a mean to control phytochrome stability and affinity for downstream transducers. DA - 2005/2// PY - 2005/2// DO - 10.1016/j.cell.2004.12.019 VL - 120 IS - 3 SP - 395-406 J2 - Cell LA - en OP - SN - 0092-8674 UR - http://dx.doi.org/10.1016/j.cell.2004.12.019 DB - Crossref ER - TY - JOUR TI - Characteristics of the Structure of Minor Variants of External Transcribed Spacers of Ribosomal DNA of the Cockroach Blattella germanica AU - Mukha, D. V. AU - Mysina, V. A. AU - Schal, C. T2 - Doklady Biological Sciences DA - 2005/9// PY - 2005/9// DO - 10.1007/s10630-005-0132-8 VL - 404 IS - 1-6 SP - 348-351 J2 - Dokl Biol Sci LA - en OP - SN - 0012-4966 1608-3105 UR - http://dx.doi.org/10.1007/s10630-005-0132-8 DB - Crossref ER - TY - JOUR TI - Discovery of retrotransposons of the cockroach Blattella germanica AU - Chumachenko, A. G. AU - Schal, C. AU - Mukha, D. V. T2 - Doklady Biochemistry and Biophysics DA - 2005/3// PY - 2005/3// DO - 10.1007/s10628-005-0044-4 VL - 401 IS - 1-6 SP - 104-107 J2 - Dokl Biochem Biophys LA - en OP - SN - 1607-6729 1608-3091 UR - http://dx.doi.org/10.1007/s10628-005-0044-4 DB - Crossref ER - TY - JOUR TI - Association of genetic polymorphisms with risk of renal injury after coronary bypass graft surgery AU - Stafford-Smith, Mark AU - Podgoreanu, Mihai AU - Swaminathan, Madhav AU - Phillips-Bute, Barbara AU - Mathew, Joseph P. AU - Hauser, Elizabeth H. AU - Winn, Michelle P. AU - Milano, Carmelo AU - Nielsen, Dahlia M. AU - Smith, Mike AU - Morris, Richard AU - Newman, Mark F. AU - Schwinn, Debra A. T2 - American Journal of Kidney Diseases AB - Background: Post-cardiac surgery renal dysfunction is a common, serious, multifactorial disorder, with interpatient variability predicted poorly by preoperative clinical, procedural, and biological markers. Therefore, we tested the hypothesis that selected gene variants are associated with acute renal injury, reflected by a serum creatinine level increase after cardiac surgery. Methods: One thousand six hundred seventy-one patients undergoing aortocoronary surgery were studied. Clinical covariates were recorded. DNA was isolated from preoperative blood; mass spectrometry was used for genotype analysis. A model was developed relating clinical and genetic factors to postoperative acute renal injury. Results: A race effect was found; therefore, Caucasians and African Americans were analyzed separately. Overall, clinical factors alone account poorly for postoperative renal injury, although more so in African Americans than Caucasians. When 12 candidate polymorphisms were assessed, 2 alleles (interleukin 6 −572C and angiotensinogen 842C) showed a strong association with renal injury in Caucasians (P < 0.0001; >50% decrease in renal filtration when they present together). Using less stringent criteria for significance (0.01 > P > 0.001), 4 additional polymorphisms are identified (apolipoproteinE 448C [ϵ4], angiotensin receptor1 1166C, and endothelial nitric oxide synthase [eNOS] 894T in Caucasians; eNOS 894T and angiotensin-converting enzyme deletion and insertion in African Americans). Adding genetic to clinical factors resulted in the best model, with overall ability to explain renal injury increasing approximately 4-fold in Caucasians and doubling in African Americans (P < 0.0005). Conclusion: In this study, we identify genetic polymorphisms that collectively provide 2- to 4-fold improvement over preoperative clinical factors alone in explaining post-cardiac surgery renal dysfunction. From a mechanistic perspective, most identified genetic variants are associated with increased renal inflammatory and/or vasoconstrictor responses. Background: Post-cardiac surgery renal dysfunction is a common, serious, multifactorial disorder, with interpatient variability predicted poorly by preoperative clinical, procedural, and biological markers. Therefore, we tested the hypothesis that selected gene variants are associated with acute renal injury, reflected by a serum creatinine level increase after cardiac surgery. Methods: One thousand six hundred seventy-one patients undergoing aortocoronary surgery were studied. Clinical covariates were recorded. DNA was isolated from preoperative blood; mass spectrometry was used for genotype analysis. A model was developed relating clinical and genetic factors to postoperative acute renal injury. Results: A race effect was found; therefore, Caucasians and African Americans were analyzed separately. Overall, clinical factors alone account poorly for postoperative renal injury, although more so in African Americans than Caucasians. When 12 candidate polymorphisms were assessed, 2 alleles (interleukin 6 −572C and angiotensinogen 842C) showed a strong association with renal injury in Caucasians (P < 0.0001; >50% decrease in renal filtration when they present together). Using less stringent criteria for significance (0.01 > P > 0.001), 4 additional polymorphisms are identified (apolipoproteinE 448C [ϵ4], angiotensin receptor1 1166C, and endothelial nitric oxide synthase [eNOS] 894T in Caucasians; eNOS 894T and angiotensin-converting enzyme deletion and insertion in African Americans). Adding genetic to clinical factors resulted in the best model, with overall ability to explain renal injury increasing approximately 4-fold in Caucasians and doubling in African Americans (P < 0.0005). Conclusion: In this study, we identify genetic polymorphisms that collectively provide 2- to 4-fold improvement over preoperative clinical factors alone in explaining post-cardiac surgery renal dysfunction. From a mechanistic perspective, most identified genetic variants are associated with increased renal inflammatory and/or vasoconstrictor responses. DA - 2005/3// PY - 2005/3// DO - 10.1053/j.ajkd.2004.11.021 VL - 45 IS - 3 SP - 519-530 J2 - American Journal of Kidney Diseases LA - en OP - SN - 0272-6386 UR - http://dx.doi.org/10.1053/j.ajkd.2004.11.021 DB - Crossref KW - acute renal failure (ARF) KW - polymorphism KW - genetic KW - postoperative KW - intensive care KW - cardiopulmonary bypass (CPB) KW - heart surgery KW - cardiac surgery KW - human KW - angiotensin-converting enzyme (ACE) KW - associate study KW - candidate genes ER - TY - JOUR TI - Genetic Polymorphisms and the Risk of Stroke After Cardiac Surgery AU - Grocott, Hilary P. AU - White, William D. AU - Morris, Richard W. AU - Podgoreanu, Mihai V. AU - Mathew, Joseph P. AU - Nielsen, Dahlia M. AU - Schwinn, Debra A. AU - Newman, Mark F. T2 - Stroke AB - Stroke represents a significant cause of morbidity and mortality after cardiac surgery. Although the risk of stroke varies according to both patient and procedural factors, the impact of genetic variants on stroke risk is not well understood. Therefore, we tested the hypothesis that specific genetic polymorphisms are associated with an increased risk of stroke after cardiac surgery.Patients undergoing cardiac surgery utilizing cardiopulmonary bypass surgery were studied. DNA was isolated from preoperative blood and analyzed for 26 different single-nucleotide polymorphisms. Multivariable logistic regression modeling was used to determine the association of clinical and genetic characteristics with stroke. Permutation analysis was used to adjust for multiple comparisons inherent in genetic association studies.A total of 1635 patients experiencing 28 strokes (1.7%) were included in the final genetic model. The combination of the 2 minor alleles of C-reactive protein (CRP; 3'UTR 1846C/T) and interleukin-6 (IL-6; -174G/C) polymorphisms, occurring in 583 (35.7%) patients, was significantly associated with stroke (odds ratio, 3.3; 95% CI, 1.4 to 8.1; P=0.0023). In a multivariable logistic model adjusting for age, the CRP and IL-6 single-nucleotide polymorphism combination remained significantly associated with stroke (P=0.0020).We demonstrate that common genetic variants of CRP (3'UTR 1846C/T) and IL-6 (-174G/C) are significantly associated with the risk of stroke after cardiac surgery, suggesting a pivotal role of inflammation in post-cardiac surgery stroke. DA - 2005/9// PY - 2005/9// DO - 10.1161/01.str.0000177482.23478.dc VL - 36 IS - 9 SP - 1854-1858 J2 - Stroke LA - en OP - SN - 0039-2499 1524-4628 UR - http://dx.doi.org/10.1161/01.str.0000177482.23478.dc DB - Crossref KW - cardiac surgical procedures KW - C-reactive protein KW - interleukin-6 KW - polymorphism KW - stroke ER - TY - JOUR TI - Thrips and tospoviruses come of age: Mapping determinants of insect transmission AU - Ullman, D. E. AU - Whitfield, A. E. AU - German, T. L. T2 - Proceedings of the National Academy of Sciences AB - With advancements in stem cell technology, in vitro models using iPSC (induced pluripotent stem cells)-derived cardiomyocytes (iPSC-CM) and engineered heart tissues (EHT) can serve as powerful tools for disease modeling and drug screening. ...Fluorescent reporters of cardiac electrophysiology provide valuable information on heart cell and tissue function. However, motion artifacts caused by cardiac muscle contraction interfere with accurate measurement of fluorescence signals. Although drugs ... DA - 2005/3/28/ PY - 2005/3/28/ DO - 10.1073/PNAS.0501341102 VL - 102 IS - 14 SP - 4931-4932 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/PNAS.0501341102 DB - Crossref ER - TY - JOUR TI - Tomato spotted wilt virus glycoprotein GC is cleaved at acidic pH AU - Whitfield, Anna E. AU - Ullman, Diane E. AU - German, Thomas L. T2 - Virus Research AB - Tomato spotted wilt virus (TSWV) is a plant-infecting member of the family Bunyaviridae. TSWV encodes two envelope glycoproteins, G(N) and G(C), which are required for virus infection of the arthropod vector. Other members of the Bunyaviridae enter host cells by pH-dependent endocytosis. During this process, the glycoproteins are exposed to conditions of acidic pH within endocytic vesicles causing the G(C) protein to change conformation. This conformational change renders G(C) more sensitive to protease cleavage. We subjected TSWV virions to varying pH conditions and determined that TSWV G(C), but not G(N), was cleaved under acidic pH conditions, and that this phenomenon did not occur at neutral or alkaline pH. This data provides evidence that G(C) changes conformation at low pH which results in altered protease sensitivity. Furthermore, sequence analysis of G(C) predicts the presence of internal hydrophobic domains, regions that are characteristic of fusion proteins. Like studies with other members of the Bunyaviridae, this study is the first step towards characterizing the nature of cell entry by TSWV. DA - 2005/6// PY - 2005/6// DO - 10.1016/j.virusres.2005.01.007 VL - 110 IS - 1-2 SP - 183-186 J2 - Virus Research LA - en OP - SN - 0168-1702 UR - http://dx.doi.org/10.1016/j.virusres.2005.01.007 DB - Crossref KW - envelope glycoprotein KW - Frankliniella occidentalis KW - Tospovirus ER - TY - JOUR TI - Tertiary amide chemistry at the Ge(100)-2×1 surface AU - Keung, Albert J. AU - Filler, Michael A. AU - Porter, David W. AU - Bent, Stacey F. T2 - Surface Science AB - We have investigated the adsorption of several tertiary amides, including N,N-dimethylformamide, N,N-dimethylformamide-d7, 1-methyl-2-pyrrolidinone, and N-methylcaprolactam, on Ge(1 0 0)-2 × 1 using multiple internal reflection Fourier transform infrared spectroscopy and density functional theory. At 310 K, all four tertiary amides were observed to selectively form a dative bond to the germanium surface through the oxygen atom. While previous work has shown that oxygen dative bonds are unstable near room temperature, tertiary amides exhibit delocalization of electron density from nitrogen to oxygen, which appears to increase the stability of the oxygen dative-bonded state. Partial desorption of these surface adducts on the timescale of minutes indicates weakly bound surface adducts with coverage dependent binding energies. DA - 2005/12// PY - 2005/12// DO - 10.1016/j.susc.2005.09.035 VL - 599 IS - 1-3 SP - 41-54 J2 - Surface Science LA - en OP - SN - 0039-6028 UR - http://dx.doi.org/10.1016/j.susc.2005.09.035 DB - Crossref KW - density functional calculations KW - vibrational spectroscopies KW - germanium KW - organic molecules KW - organo-functionalization of surfaces KW - desorption KW - amide KW - Ge(100) ER - TY - JOUR TI - A previously uncharacterized role for estrogen receptor  : Defeminization of male brain and behavior AU - Kudwa, A. E. AU - Bodo, C. AU - Gustafsson, J.-A. AU - Rissman, E. F. T2 - Proceedings of the National Academy of Sciences AB - Sex differences in brain and behavior are ubiquitous in sexually reproducing species. One cause of sexual dimorphisms is developmental differences in circulating concentrations of gonadal steroids. Neonatal testes produce androgens; thus, males are exposed to both testosterone and estradiol, whereas females are not exposed to high concentrations of either hormone until puberty. Classically, the development of neural sex differences is initiated by estradiol, which activates two processes in male neonates; masculinization, the development of male-type behaviors, and defeminization, the loss of the ability to display female-type behaviors. Here, we test the hypothesis that defeminization is regulated by estrogen receptor beta (ERbeta). Adult male ERbeta knockout and WT mice were gonadectomized, treated with female priming hormones, and tested for receptive behavior. Indicative of incomplete defeminization, male ERbeta knockout mice showed significantly higher levels of female receptivity as compared with WT littermates. Testes-intact males did not differ in any aspects of their male sexual behavior, regardless of genotype. In olfactory preference tests, males of both genotypes showed equivalent preferences for female-soiled bedding. Based on these results, we hypothesize that ERbeta is involved in defeminization of brain and behavior. This aspect of ERbeta function may lead to developments in our understanding of neural-based sexually dimorphic human behaviors. DA - 2005/3/10/ PY - 2005/3/10/ DO - 10.1073/pnas.0500752102 VL - 102 IS - 12 SP - 4608-4612 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.0500752102 DB - Crossref KW - developmental neurobiology KW - neuroendocrinology KW - sexual differentiation ER - TY - JOUR TI - Effects of galanin-like peptide (GALP) on locomotion, reproduction, and body weight in female and male mice AU - Kauffman, Alexander S. AU - Buenzle, Jennifer AU - Fraley, Gregory S. AU - Rissman, Emilie F. T2 - Hormones and Behavior AB - Galanin-like peptide (GALP) has been implicated in the neuroendocrine regulation of both feeding and reproduction. In male rodents and primates, intracerebroventricular (icv) infusions of GALP stimulate luteinizing hormone (LH) release, induce Fos expression in brain areas implicated in feeding and reproduction, and affect food intake and body weight in rodents. In gonad-intact and castrated male rats, icv administration of GALP also stimulates male sexual behavior. While the effects of GALP on male physiology and behavior are well documented, no studies have addressed such a role of GALP in females. We tested the effects of icv GALP infusions on LH release, locomotor activity, motor control, and body weight regulation in adult ovariectomized female mice hormonally primed with estradiol benzoate and progesterone. In addition, sexually-experienced male and female mice were treated with GALP and tested for sexual behavior. In females, GALP reduced open-field locomotor activity, the ability to maintain grip on an accelerating rotarod, and 24-h body weight in a dose-dependent manner. GALP also increased LH secretion in female mice, an effect that was blocked by pre-treatment with Antide, a gonadotropin-releasing hormone (GnRH) type-1 receptor antagonist. GALP infusions slightly decreased the occurrence of lordosis behavior in female mice and significantly increased the latencies with which females displayed receptivity. Unlike previous reports in male rats, GALP inhibited male sexual behavior in mice. Our data indicate that in female mice, GALP stimulates LH release via GnRH, and decreases body weight, motor control, and locomotor activity via GnRH-independent pathways. Furthermore, our sexual behavior and locomotor findings suggest species-specific differences in the mechanism and/or location of GALP action in the brains of rats and mice. DA - 2005/8// PY - 2005/8// DO - 10.1016/j.yhbeh.2005.01.010 VL - 48 IS - 2 SP - 141-151 J2 - Hormones and Behavior LA - en OP - SN - 0018-506X UR - http://dx.doi.org/10.1016/j.yhbeh.2005.01.010 DB - Crossref KW - sexual behavior KW - energy balance KW - motor control KW - coordination KW - exploration KW - luteinizing hormone KW - gonadotropin-releasing hormone ER - TY - JOUR TI - Lack of functional estrogen receptor β influences anxiety behavior and serotonin content in female mice AU - Imwalle, D. Bradley AU - Gustafsson, Jan-Åke AU - Rissman, Emilie F. T2 - Physiology & Behavior AB - Estrogen has been linked to the modulation of anxiety in females. Here we report results of anxiety tests conducted in female estrogen receptor β (ERβ) knockout (ERβKO) and wild-type (WT) mice. Ovariectomized (OVX) mice treated with chronic estradiol (E2) replacement did not behave differently on the elevated plus-maze when compared with OVX mice that did not experience hormone replacement. However, a genotype difference was noted; WT females were more likely to explore the distal portion of the open arm of the maze than ERβKO littermates. In addition, ERβKO female mice had significantly lower serotonin (5-HT) content than WT littermates in several brain regions including: the bed nucleus of the stria terminalis, preoptic area, and hippocampus. A similar trend was noted in the dorsal raphe nucleus. Dopamine content was reduced within the caudate putamen in ERβKO mice as compared to brains from WT animals. Thus, in the absence of functional ERβ, regardless of the presence or absence of circulating E2 in plasma, female mice exhibited enhanced anxiety and decreased concentrations of 5-HT or dopamine in several brain regions. We hypothesize that ERβ is required during development to modulate the effects of estrogen on anxiety and catecholamine concentrations in female mouse brains. DA - 2005/1// PY - 2005/1// DO - 10.1016/j.physbeh.2004.11.002 VL - 84 IS - 1 SP - 157-163 J2 - Physiology & Behavior LA - en OP - SN - 0031-9384 UR - http://dx.doi.org/10.1016/j.physbeh.2004.11.002 DB - Crossref KW - SSRI KW - menopause KW - estrogen receptor KW - depression KW - anxiety KW - serotonin ER - TY - JOUR TI - Dopamine D5 receptor modulates male and female sexual behavior in mice AU - Kudwa, A. E. AU - Dominguez-Salazar, E. AU - Cabrera, D. M. AU - Sibley, D. R. AU - Rissman, E. F. T2 - Psychopharmacology DA - 2005/2/5/ PY - 2005/2/5/ DO - 10.1007/s00213-005-2150-5 VL - 180 IS - 2 SP - 206-214 J2 - Psychopharmacology LA - en OP - SN - 0033-3158 1432-2072 UR - http://dx.doi.org/10.1007/s00213-005-2150-5 DB - Crossref KW - sexual behavior KW - dopamine KW - conditioned place preference KW - drugs KW - motivation KW - knockout mice KW - reward KW - attention deficit hyperactivity disorder ER - TY - JOUR TI - Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures AU - Varnek, A. AU - Fourches, D. AU - Hoonakker, F. AU - Solov’ev, V. P. T2 - Journal of Computer-Aided Molecular Design DA - 2005/9// PY - 2005/9// DO - 10.1007/s10822-005-9008-0 VL - 19 IS - 9-10 SP - 693-703 J2 - J Comput Aided Mol Des LA - en OP - SN - 0920-654X 1573-4951 UR - http://dx.doi.org/10.1007/s10822-005-9008-0 DB - Crossref KW - chemical reactions KW - clustering KW - condensed graphs of reactions KW - exchange of information KW - hydrogen bonds KW - QSPR KW - similarity KW - solubility KW - substructural fragments ER - TY - JOUR TI - Genetic Modifiers of Lung Disease in Cystic Fibrosis AU - Drumm, Mitchell L. AU - Konstan, Michael W. AU - Schluchter, Mark D. AU - Handler, Allison AU - Pace, Rhonda AU - Zou, Fei AU - Zariwala, Maimoona AU - Fargo, David AU - Xu, Airong AU - Dunn, John M. AU - Darrah, Rebecca J. AU - Dorfman, Ruslan AU - Sandford, Andrew J. AU - Corey, Mary AU - Zielenski, Julian AU - Durie, Peter AU - Goddard, Katrina AU - Yankaskas, James R. AU - Wright, Fred A. AU - Knowles, Michael R. T2 - New England Journal of Medicine AB - Polymorphisms in genes other than the cystic fibrosis transmembrane conductance regulator (CFTR) gene may modify the severity of pulmonary disease in patients with cystic fibrosis.We performed two studies with different patient samples. We first tested 808 patients who were homozygous for the DeltaF508 mutation and were classified as having either severe or mild lung disease, as defined by the lowest or highest quartile of forced expiratory volume in one second (FEV1), respectively, for age. We genotyped 16 polymorphisms in 10 genes reported by others as modifiers of disease severity in cystic fibrosis and tested for an association in patients with severe disease (263 patients) or mild disease (545). In the replication (second) study, we tested 498 patients, with various CFTR genotypes and a range of FEV1 values, for an association of the TGFbeta1 codon 10 CC genotype with low FEV1.In the initial study, significant allelic and genotypic associations with phenotype were seen only for TGFbeta1 (the gene encoding transforming growth factor beta1), particularly the -509 and codon 10 polymorphisms (with P values obtained with the use of Fisher's exact test and logistic regression ranging from 0.006 to 0.0002). The odds ratio was about 2.2 for the highest-risk TGFbeta1 genotype (codon 10 CC) in association with the phenotype for severe lung disease. The replication study confirmed the association of the TGFbeta1 codon 10 CC genotype with more severe lung disease in comparisons with the use of dichotomized FEV1 for severity status (P=0.0002) and FEV1 values directly (P=0.02).Genetic variation in the 5' end of TGFbeta1 or a nearby upstream region modifies disease severity in cystic fibrosis. DA - 2005/10/6/ PY - 2005/10/6/ DO - 10.1056/NEJMoa051469 VL - 353 IS - 14 SP - 1443-1453 J2 - N Engl J Med LA - en OP - SN - 0028-4793 1533-4406 UR - http://dx.doi.org/10.1056/NEJMoa051469 DB - Crossref ER - TY - JOUR TI - Group A Streptococcus Transcriptome Dynamics during Growth in Human Blood Reveals Bacterial Adaptive and Survival Strategies AU - Graham, Morag R. AU - Virtaneva, Kimmo AU - Porcella, Stephen F. AU - Barry, William T. AU - Gowen, Brian B. AU - Johnson, Claire R. AU - Wright, Fred A. AU - Musser, James M. T2 - The American Journal of Pathology AB - The molecular basis for bacterial responses to host signals during natural infections is poorly understood. The gram-positive bacterial pathogen group A Streptococcus (GAS) causes human mucosal, skin, and life-threatening systemic infections. During the transition from a throat or skin infection to an invasive infection, GAS must adapt to changing environments and host factors. To better understand how GAS adapts, we used transcript profiling and functional analysis to investigate the transcriptome of a wild-type serotype M1 GAS strain in human blood. Global changes in GAS gene expression occur rapidly in response to human blood exposure. Increased transcription was observed for many genes that likely enhance bacterial survival, including those encoding superantigens and host-evasion proteins regulated by a multiple gene activator called Mga. GAS also coordinately expressed genes involved in proteolysis, transport, and catabolism of oligopeptides to obtain amino acids in this protein-rich host environment. Comparison of the transcriptome of the wild-type strain to that of an isogenic deletion mutant (DeltacovR) mutated in the two-component regulatory system designated CovR-CovS reinforced the hypothesis that CovR-CovS has an important role linking key biosynthetic, catabolic, and virulence functions during transcriptome restructuring. Taken together, the data provide crucial insights into strategies used by pathogenic bacteria for thwarting host defenses and surviving in human blood. DA - 2005/2// PY - 2005/2// DO - 10.1016/S0002-9440(10)62268-7 VL - 166 IS - 2 SP - 455-465 J2 - The American Journal of Pathology LA - en OP - SN - 0002-9440 UR - http://dx.doi.org/10.1016/S0002-9440(10)62268-7 DB - Crossref ER - TY - JOUR TI - Mutations in Serac1 or Synj2 cause proximal t haplotype-mediated male mouse sterility but not transmission ratio distortion AU - Schimenti, J. C. AU - Reynolds, J. L. AU - Planchart, A. T2 - Proceedings of the National Academy of Sciences AB - Transmission ratio distortion (TRD) and sterility are male-specific quantitative trait phenomena associated with the mouse t haplotype. TRD occurs in t haplotype-heterozygous males and is caused by the deleterious action of distorter products on sperm bearing a wild-type responder locus. It has been proposed that t-mediated male sterility is a severe manifestation of TRD caused by homozygosity for distorter loci; thus, the distorter and sterility loci would be identical. In this, study a transgenic approach was used to identify the proximal sterility locus, tcs1 (S1), and test its role in TRD. Mice transgenic for a wild-type bacterial artificial chromosome (BAC) derived from the S1-critical region were bred onto t haplotype backgrounds. Mating results conclusively showed that the BAC is sufficient to restore fertility in otherwise sterile males. Multiple mutations were identified in the t alleles of Synj2 and Serac1, two genes in the BAC; thus, they are candidates for S1. In addition, whereas the BAC transgene rescued sterility, it had no effect on TRD. These results uncouple the proximal t haplotype sterility locus, S1, from TRD, demonstrating that S1 and the proximal distorter locus, D1, are not the same gene. DA - 2005/2/18/ PY - 2005/2/18/ DO - 10.1073/pnas.0407970102 VL - 102 IS - 9 SP - 3342-3347 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.0407970102 DB - Crossref ER - TY - JOUR TI - Synthesis of Homoallylic Amines by Hydrozirconation−Imine Addition of Allenes AU - Wipf, Peter AU - Pierce, Joshua G. T2 - Organic Letters AB - Hydrozirconation of allenes followed by in situ transmetalation to dialkylzinc leads to the formation of an allylic zinc species that, upon addition of aldimines to the reaction mixture, provides homoallylic amines in 64−85% yield. DA - 2005/8// PY - 2005/8// DO - 10.1021/ol051266j VL - 7 IS - 16 SP - 3537-3540 J2 - Org. Lett. LA - en OP - SN - 1523-7060 1523-7052 UR - http://dx.doi.org/10.1021/ol051266j DB - Crossref ER - TY - JOUR TI - Silver(I)-Catalyzed Addition of Zirconocenes to Glycal Epoxides. A New Synthesis of α-C-Glycosides AU - Wipf, Peter AU - Pierce, Joshua G. AU - Zhuang, Nian T2 - Organic Letters AB - Hydrozirconation of terminal alkynes, followed by AgClO4-catalyzed in situ addition of the resultant alkenylzirconocenes to 1,2-anhydrosugars (glycal epoxides) leads to α-C-glycosides in moderate to high yields. DA - 2005/2// PY - 2005/2// DO - 10.1021/ol0475414 VL - 7 IS - 3 SP - 483-485 J2 - Org. Lett. LA - en OP - SN - 1523-7060 1523-7052 UR - http://dx.doi.org/10.1021/ol0475414 DB - Crossref ER - TY - JOUR TI - Resolving mechanisms of toxicity while pursuing ecotoxicological relevance? AU - Hinton, David E. AU - Kullman, Seth W. AU - Hardman, Ron C. AU - Volz, David C. AU - Chen, Pei-Jen AU - Carney, Michael AU - Bencic, David C. T2 - Marine Pollution Bulletin AB - In this age of modern biology, aquatic toxicological research has pursued mechanisms of action of toxicants. This has provided potential tools for ecotoxicologic investigations. However, problems of biocomplexity and issues at higher levels of biological organization remain a challenge. In the 1980s and 1990s and continuing to a lesser extent today, organisms residing in highly contaminated field sites or exposed in the laboratory to calibrated concentrations of individual compounds were carefully analyzed for their responses to priority pollutants. Correlation of biochemical and structural analyses in cultured cells and tissues, as well as the in vivo exposures led to the production and application of biomarkers of exposure and effect and to our awareness of genotoxicity and its chronic manifestations, such as neoplasms, in wild fishes. To gain acceptance of these findings in the greater environmental toxicology community, “validation of the model” versus other, better-established often rodent models, was necessary and became a major focus. Resultant biomarkers were applied to heavily contaminated and reference field sites as part of effects assessment and with investigations following large-scale disasters such as oil spills or industrial accidents. Over the past 15 years, in the laboratory, small aquarium fish models such as medaka (Oryzias latipes), zebrafish (Danio rerio), platyfish (Xiphophorus species), fathead minnow (Pimephales promelas), and sheepshead minnow (Cyprinodon variegatus) were increasingly used establishing mechanisms of toxicants. Today, the same organisms provide reliable information at higher levels of biological organization relevant to ecotoxicology. We review studies resolving mechanisms of toxicity and discuss ways to address biocomplexity, mixtures of contaminants, and the need to relate individual level responses to populations and communities. DA - 2005/1// PY - 2005/1// DO - 10.1016/j.marpolbul.2005.07.020 VL - 51 IS - 8-12 SP - 635-648 J2 - Marine Pollution Bulletin LA - en OP - SN - 0025-326X UR - http://dx.doi.org/10.1016/j.marpolbul.2005.07.020 DB - Crossref ER - TY - JOUR TI - Functional characterization of medaka CYP3A38 and CYP3A40: Kinetics and catalysis by expression in a recombinant baculovirus system AU - Kashiwada, Shosaku AU - Hinton, David E. AU - Kullman, Seth W. T2 - Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology AB - Phylogenic analysis of the teleost genomic lineages has demonstrated the precedent for multiple genome duplications. Among many of the genes duplicated, cytochrome P450 genes have undergone independent diversification, which can be traced to a single ancestral gene. In teleosts, cytochrome P450s, from all major families, have been identified. Among these, the CYP3A family has been cloned in several teleost species and demonstrated to contain multiple paralogs differing in gene expression patterns and tissue distribution. Herein we characterized the catalytic and kinetic activities of two medaka CYP3A paralogs (CYP3A38 and CYP3A40) with benzyloxyresorufin (BFC), a fluorescent 3A-selective substrate, and testosterone, a known metabolic substrate for CYP3A enzymes. Recombinant CYP3A was produced using the baculovirus expression vector system in Spodoptera frugiperda (Sf9) and Trichoplusia ni (Tn5) insect cells and accounted for up to 24% of total cellular protein. Following addition of a heme-albumin conjugate to log phase cells, spectral P450 content reached a maximum of 560 and 2350 pmol/mg microsomal protein for CYP3A38 and CYP3A40, respectively. Incubations containing recombinant CYP3A, human NADPH-cytochrome P-450 oxidoreductase reductase, human cytochrome b5, and a NADPH generation system catalyzed the dealkylation of BFC and hydroxylation of testosterone with a high degree of stereoselectivity. However, efficiencies and specificities were significantly different between the two isoforms. Km and Vmax activities based on BFC-catalysis were 0.116 and 0.363 muM, and 7.95 and 7.77 nmol/min/nmol P450 for CYP3A38 and CYP3A40, respectively. CYP3A38 preferentially catalyzed testosterone hydroxylation at the 6beta-, 2beta- and 16beta-positions with minor hydroxylation at other positions within the steroid nucleus. Testosterone catalysis with CYP3A40 was limited predominantly to the 6beta- and 2beta-positions. Putative identification of CYP3A substrate recognition sites (SRS) 1-6 indicates that 12 of the 49 amino acid differences between CYP3A38 and CYP3A40 OFRs occur in SRS regions previously known to be associated with steroid hydroxylation. We suggest that differences in kinetics and catalytic activities are a result of amino acid substitutions in SRS regions 1, 3 and 5 within the CYP3A38 and CYP3A40 protein sequence. DA - 2005/8// PY - 2005/8// DO - 10.1016/j.cca.2005.07.006 VL - 141 IS - 4 SP - 338-348 J2 - Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology LA - en OP - SN - 1532-0456 UR - http://dx.doi.org/10.1016/j.cca.2005.07.006 DB - Crossref KW - medaka KW - CYP3A KW - baculovirus KW - cytochrome P450 KW - kinetics KW - testosterone KW - BFC KW - metabolism ER - TY - JOUR TI - High-Affinity CD25-Binding IL-2 Mutants Potently Stimulate Persistent T Cell Growth† AU - Rao, Balaji M. AU - Driver, Ian AU - Lauffenburger, Douglas A. AU - Wittrup, K. Dane T2 - Biochemistry AB - We have used directed evolution to construct IL-2 mutants that bind the IL-2 alpha receptor subunit (IL-2Ralpha, CD25) with affinities comparable to that of the IL-15-IL-15 alpha receptor subunit (IL-15Ralpha) interaction. T cells proliferate for up to 6 days following a 30 minute incubation with these IL-2 mutants, which may lead to potential applications for cancer and viral immunotherapy. Several alternative mechanisms have been proposed to explain the contrasting effects of IL-2 and IL-15 on T cell proliferation and death. These IL-2 mutants exhibit T cell growth response-receptor occupancy curves indistinguishable from that for IL-15, suggesting that much of the difference between wild-type IL-2 and IL-15 effects arises simply from their 1000-fold differing affinities for their private alpha receptor subunits. DA - 2005/8// PY - 2005/8// DO - 10.1021/bi050436x VL - 44 IS - 31 SP - 10696-10701 J2 - Biochemistry LA - en OP - SN - 0006-2960 1520-4995 UR - http://dx.doi.org/10.1021/bi050436x DB - Crossref ER - TY - JOUR TI - Dietary metformin effects on in vitro and in vivo metabolism in the chicken AU - Rosebrough, Robert W. AU - Ashwell, Christopher M. T2 - Nutrition Research AB - Chickens were fed diets containing 0, 0.25, 0.5, and 1 and 0, 2.5, 5, and 10 g metformin (MET)/kg diet in 2 separate experiments to determine whether MET (1,1 dimethylbiguanidine hydrochloride) regulated plasma glucose and, possibly, feed intake in broiler chickens. Feed intakes in the first experiment were equal, but, in the second experiment, MET at 5 and 10 g/kg reduced feed intake. The first series of diets had no effect on plasma glucose and lactate. The second series of dietary treatments did not affect plasma glucose but did increase plasma lactate, uric acid, and triglycerides linearly. In the second experiment, there were significant decreases in lipogenesis that accompanied increasing doses of MET. The increase in plasma lactic acid suggests that MET stimulates pyruvate kinase in the chicken, as it does in mammals. The lack of effect on plasma glucose also suggests that regulation occurs downstream of pyruvate in the chicken. These findings may explain MET's ability to reduce hepatic triglyceride synthesis and suppress appetite. DA - 2005/5// PY - 2005/5// DO - 10.1016/j.nutres.2005.03.001 VL - 25 IS - 5 SP - 491-497 J2 - Nutrition Research LA - en OP - SN - 0271-5317 UR - http://dx.doi.org/10.1016/j.nutres.2005.03.001 DB - Crossref KW - biguanides KW - blood glucose KW - appetite KW - metabolism KW - chicken ER - TY - JOUR TI - Conversion of nicotine to nornicotine in Nicotiana tabacum is mediated by CYP82E4, a cytochrome P450 monooxygenase AU - Siminszky, B. AU - Gavilano, L. AU - Bowen, S. W. AU - Dewey, R. E. T2 - Proceedings of the National Academy of Sciences AB - Nornicotine is a secondary tobacco alkaloid that is produced by the N-demethylation of nicotine. Nornicotine production and accumulation in tobacco are undesirable because nornicotine serves as the precursor in the synthesis of the well characterized carcinogen N ′-nitrosonornicotine during the curing and processing of tobacco. Although nornicotine is typically a minor alkaloid in tobacco plants, in many tobacco populations a high percentage of individuals can be found that convert a substantial proportion of the nicotine to nornicotine during leaf senescence and curing. We used a microarray-based strategy to identify genes that are differentially regulated between closely related tobacco lines that accumulate either nicotine (nonconverters) or nornicotine (converters) as the predominant alkaloid in the cured leaf. These experiments led to the identification of a small number of closely related cytochrome P450 genes, designated the CYP82E2 family, whose collective transcript levels were consistently higher in converter versus nonconverter tobacco lines. RNA interference-induced silencing of the CYP82E2 gene family suppressed the synthesis of nornicotine in strong converter plants to levels similar to that observed in nonconverter individuals. Although each of the six identified members of the P450 family share >90% nucleotide sequence identity, sense expression of three selected isoforms revealed that only one ( CYP82E4v1 ) was involved in the conversion of nicotine to nornicotine. Yeast expression analysis revealed that CYP82E4v1 functions as a nicotine demethylase. Identification of the gene(s) responsible for nicotine demethylation provides a potentially powerful tool toward efforts to minimize nornicotine levels, and thereby N ′-nitrosonornicotine formation, in tobacco products. DA - 2005/9/28/ PY - 2005/9/28/ DO - 10.1073/pnas.0506581102 VL - 102 IS - 41 SP - 14919-14924 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.0506581102 DB - Crossref KW - N '-nitrosonornicotine KW - N-demethylation KW - tobacco KW - alkaloid KW - tobacco-specific nitrosamines ER - TY - JOUR TI - Mammalian nest predators respond to greenway width, landscape context and habitat structure AU - Sinclair, K AU - Hess, G AU - Moorman, C AU - Mason, J T2 - Landscape and Urban Planning AB - Birds of conservation concern breed in suburban greenways, yet abundant populations of mammals that depredate bird nests might reduce nest success. We evaluated how three factors influenced the abundance of mammalian nest predators in thirty-four 300-m long forested greenway segments in Raleigh and Cary, North Carolina, USA: (1) the width of the forested corridor containing the greenway, (2) the land-use adjacent to the forested corridor, and (3) the habitat structure within the greenway. Forest corridor width and adjacent land-use were measured using aerial photographs. Attributes of adjacent land use included categorical measures of development intensity (low-density residential, high-density residential, office/institutional), and the proportions of forest canopy, grass, buildings, and pavement. Several measures of habitat structure within the greenway were collected in the field, including trail width and surface type, and percentage of mature forest. We measured the relative abundance of mammalian nest predators with scent-station transects, operated for five nights during the 2002 breeding bird season. Total abundance of mammalian nest predators increased significantly as forest corridor width decreased. We found no relationship between categorical measures of land-use and total abundance of mammalian nest predators. Specific attributes of the landscape adjacent to the greenway, however, did have an effect. Greenways adjacent to landscapes with fewer buildings had a higher abundance of mammalian nest predators. The abundance of individual species varied with the amount of canopy, lawn, and pavement in the adjacent landscape. Some measures of habitat structure of greenways also were correlated with the abundance of mammalian nest predators. Greenway segments with wider trails had a higher abundance of mammalian nest predators, as did segments with a higher percentage of mature forest. No habitat structure variables were significant for all species. To reduce the overall risk of avian nest predation by mammals, forested greenways should be designed with wider forest corridors and narrower, unpaved trails. Some greenway characteristics that favor high-nest predator populations also favor birds of conservation concern. Similarly, some characteristics correlated with lower predator occurrence are also correlated with lower abundance of birds of conservation concern. Thus, management of greenways and the surrounding landscape must balance reduction of predator communities with the promotion of desired bird communities and other conservation goals. DA - 2005/3/28/ PY - 2005/3/28/ DO - 10.1016/S0169-2046(04)00082-9 VL - 71 IS - 2-4 SP - 277-293 J2 - Landscape and Urban Planning LA - en OP - SN - 0169-2046 UR - http://dx.doi.org/10.1016/S0169-2046(04)00082-9 DB - Crossref KW - corridor KW - greenway KW - landscape context KW - mammal KW - nest predator ER - TY - JOUR TI - Escorrentía superficial en bosques montanos naturales y plantados de Antioquia, Colombia AU - Ruiz Suescún, Oscar Andrés T2 - Revista Facultad Nacional de Agronomía, Medellín. DA - 2005/4/26/ PY - 2005/4/26/ VL - S.l.], v. 58, n. 1 SP - 2635–2649, UR - https://revistas.unal.edu.co/index.php/refame/article/view/21509/22498 ER - TY - JOUR TI - Male genital size reflects a tradeoff between attracting mates and avoiding predators in two live-bearing fish species AU - Langerhans, R. B. AU - Layman, C. A. AU - DeWitt, T. J. T2 - Proceedings of the National Academy of Sciences AB - Male genitalia may experience more rapid, divergent evolution than any other animal character, but why? Research during the past several decades has culminated in the view that genital diversification primarily results from postmating sexual selection (e.g., sperm competition or cryptic female choice). However, the potential roles of premating sexual selection (e.g., mate choice) and natural selection have received little attention. We examined the possible importance of these mechanisms by investigating divergence in male genitalia among populations differing in predator regime for two species of live-bearing fish (Gambusia affinis in Texas and Gambusia hubbsi in The Bahamas). When controlled for body size, males exhibited a larger gonopodium (sperm-transfer organ) in predator-free environments than in predatory environments, a trend that persisted across space (multiple populations), time (multiple years), and species. By conducting laboratory experiments with G. affinis, we found that premating sexual selection seems to favor larger male genitalia (females exhibited mating preference for males having larger gonopodia), but natural selection in the presence of predatory fishes seems to favor reduced genital size (larger gonopodium size was associated with reduced burst-swimming performance, an important antipredator behavior). Although postmating sexual selection is widely presumed to be the most important mechanism driving genital diversification, these findings suggest that alternative mechanisms, particularly for organisms that cannot retract their genitalia, may also prove important. DA - 2005/5/13/ PY - 2005/5/13/ DO - 10.1073/pnas.0500935102 VL - 102 IS - 21 SP - 7618-7623 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.0500935102 DB - Crossref KW - fitness tradeoff KW - genital evolution KW - mate choice KW - natural selection KW - sexual selection ER - TY - JOUR TI - Proanthocyanidin biosynthesis – still more questions than answers? AU - Xie, De-Yu AU - Dixon, Richard A. T2 - Phytochemistry AB - Proanthocyanidins, also known as condensed tannins, are oligomers or polymers of flavan-3-ol units. In spite of important breakthroughs in our understanding of the biosynthesis of the major building blocks of proanthocyanidins, (+)-catechin and (-)-epicatechin, important questions still remain to be answered as to the exact nature of the molecular species that undergo polymerization, and the mechanisms of assembly. We review the structures of proanthocyanidins reported over the past 12 years in the context of biosynthesis, and summarize the outstanding questions concerning synthesis of proanthocyanidins from the chemical, biochemical and molecular genetic perspectives. DA - 2005/9// PY - 2005/9// DO - 10.1016/j.phytochem.2005.01.008 VL - 66 IS - 18 SP - 2127-2144 J2 - Phytochemistry LA - en OP - SN - 0031-9422 UR - http://dx.doi.org/10.1016/j.phytochem.2005.01.008 DB - Crossref KW - proanthocyanidins KW - tannins KW - flavan-3-ols KW - catechin KW - epicatechin KW - anthocyanidin reductase ER - TY - JOUR TI - Mean latitudinal range sizes of bird assemblages in six Neotropical forest chronosequences AU - Dunn, R.R. AU - Romdal, T.S. T2 - Global Ecology and Biogeography AB - Abstract Aim The geographical range size frequency distributions of animal and plant assemblages are among the most important factors affecting large‐scale patterns of diversity. Nonetheless, the relationship between habitat type and the range size distributions of species forming assemblages remains poorly understood. We examined how the mean latitudinal range sizes of species in Neotropical bird species assemblages shift during forest clearance and subsequent regeneration. We tested the hypothesis that bird species assemblages in early successional habitats tend to have larger latitudinal ranges than those in more mature forests. Location We considered breeding bird chronosequence data from six Neotropical forests. Results Breeding bird assemblages were found to have the species with the largest average latitudinal range sizes in cleared areas, intermediate in young secondary forests and smallest in old secondary and mature forests. Similar differences were also found when we compared congeners differing in their successional preferences. Sizes of regional ranges (within the Neotropics) did not, however, differ consistently among successional stages. The larger latitudinal (but not regional) ranges of early successional species was as a result in part of the tendency of early successional species to have ranges that extend beyond the Neotropical forest biome. Conclusions Our analysis of chronosequences suggests that as early successional habitats mature, a consistent shift from large‐ranged species towards more small ranged species occurs. Even relatively old secondary forests have bird species with larger average ranges than mature forests. As a consequence, conservation of secondary forests alone will miss many of the species most at risk of extinction and most unlikely to be conserved in other locations or biomes. DA - 2005/// PY - 2005/// DO - 10.1111/j.1466-822X.2005.00155.x VL - 14 IS - 4 SP - 359-366 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-22144482417&partnerID=MN8TOARS KW - beta diversity KW - birds KW - disturbance KW - range size frequency distribution KW - secondary forest KW - tropical forest ER - TY - JOUR TI - Modern insect extinctions, the neglected majority AU - Dunn, R.R. T2 - Conservation Biology AB - Abstract: Most extinctions estimated to have occurred in the historical past, or predicted to occur in the future, are of insects. Despite this, the study of insect extinctions has been neglected. Only 70 modern insect extinctions have been documented, although thousands are estimated to have occurred. By focusing on some of the 70 documented extinctions as case studies, I considered ways in which insect extinctions may differ from those of other taxa. These case studies suggested that two types of extinction might be common for insects but rare for other taxa: extinction of narrow habitat specialists and coextinctions of affiliates with the extinctions of their hosts. Importantly, both of these forms of extinction are often ignored by conservation programs focused on vertebrates and plants. Anecdotal evidence and recent simulations suggest that many insect extinctions may have already occurred because of loss of narrow habitat specialists from restricted habitats and the loss of hosts. If we are serious about insect conservation, we need to spend more time and money documenting such extinctions. To neglect such extinctions is to ignore the majority of species that are or were in need of conservation. DA - 2005/// PY - 2005/// DO - 10.1111/j.1523-1739.2005.00078.x VL - 19 IS - 4 SP - 1030-1036 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-27944449967&partnerID=MN8TOARS KW - coextinction KW - extinction rates KW - parasites ER - TY - JOUR TI - Jaws of life. Thousands of plant species place their fates in the mandibles of ants AU - Dunn, R.R. T2 - Natural History DA - 2005/// PY - 2005/// VL - 114 IS - 7 SP - 30-35 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-24644458957&partnerID=MN8TOARS ER - TY - JOUR TI - Fine-mapping milk production quantitative trait loci on BTA6: Analysis of the bovine osteopontin gene AU - Schnabel, R. D. AU - Kim, J.-J. AU - Ashwell, M. S. AU - Sonstegard, T. S. AU - Van Tassell, C. P. AU - Connor, E. E. AU - Taylor, J. F. T2 - Proceedings of the National Academy of Sciences AB - Bovine chromosome six (BTA6) harbors up to six quantitative trait loci (QTL) influencing the milk production of dairy cattle. In stark contrast to human, there is long-range linkage disequilibrium in dairy cattle, which has previously made it difficult to identify the mutations underlying these QTL. Using 38 microsatellite markers in a pedigree of 3,147 Holstein bulls, we fine mapped regions of BTA6 that had previously been shown to harbor QTL. Next, we sequenced a 12.3-kb region harboring Osteopontin, a positional candidate for the statistically most significant of the identified QTL. Nine mutations were identified, and only genotypes for the OPN3907 indel were concordant with the QTL genotypes of eight bulls that were established by segregation analysis. Four of these mutations were genotyped, and a joint linkage/linkage disequilibrium mapping analysis was used to demonstrate the existence of only two functionally distinct clusters of haplotypes within the QTL region, which were uniquely defined by OPN3907 alleles. We estimate a probability of 0.40 that no other mutation within this region is concordant with the QTL genotypes of these eight bulls. Finally, we demonstrate that the motif harboring OPN3907 , which is upstream of the promoter and within a region known to harbor tissue-specific osteopontin regulatory elements, is moderately conserved among mammals. The motif was not retrieved from database queries and may be a novel regulatory element. DA - 2005/5/2/ PY - 2005/5/2/ DO - 10.1073/pnas.0502398102 VL - 102 IS - 19 SP - 6896-6901 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.0502398102 DB - Crossref KW - linkage disequilibrium ER - TY - JOUR TI - A century of avifaunal turnover in a small tropical rainforest fragment AU - Sodhi, Navjot S. AU - Lee, Tien Ming AU - Koh, Lian Pin AU - Dunn, Robert R. T2 - Animal Conservation AB - Despite the alarming rate of tropical deforestation, the long-term conservation value of forest fragments remains poorly understood. We report on the avifaunal turnover in an isolated 4 ha tropical forest fragment in Singapore (i.e. Singapore Botanic Gardens rainforest fragment (SBGRF)) between 1898 and 1998. Over 100 years, the SBGRF lost 18 (49%) species and gained 20 species. More forest-dependent species (3) were lost from the SBGRF than survived (1) or colonised it (no species). Conversely, significantly more introduced species (4) colonised the fragment than were previously recorded (1 species). Significantly more nectarivores survived (8 species) or colonised (9 species) than were lost (two species). In essence, while the avian species richness in the SBGRF remained relatively constant after a century, its species composition underwent significant changes. The avian species composition in the SBGRF in 1998 appeared to be more similar to that of the contemporary smaller and younger Singaporean secondary forest patches than to either the larger and older forest reserves or to the SBGRF 100 years ago. Our study suggests that small isolated tropical forest fragments may have limited long-term conservation value for native forest bird species. DA - 2005/5// PY - 2005/5// DO - 10.1017/S1367943005001927 VL - 8 IS - 2 SP - 217-222 J2 - Animal Conservation LA - en OP - SN - 1367-9430 1469-1795 UR - http://dx.doi.org/10.1017/S1367943005001927 DB - Crossref ER - TY - CHAP TI - Biology and Detection of Fungal Pathogens of Humans and Plants AU - Payne, Gary A. AU - Cubeta, Marc A. T2 - Microbial Forensics AB - This chapter reviews fungi, their taxonomy, growth, reproduction, pathogenicity, epidemiology, detection, and identification. Fungi have greatly shaped the history of humankind. However, not all fungi are beneficial; some fungi are harmful pathogens and can cause diseases. They represent an important group of pathogens that significantly impact human and plant health and are responsible for the majority of plant diseases and important agents of infectious diseases of immuno compromised humans. Kingdom Fungi include four phyla: Ascomycota (sac fungi), Basidiomycota (club and mushroom fungi; rusts; and smuts), Chytridiomycota (chytrids), and Zygomycota (bread molds), and are often referred to as the “true fungi” or Eumycota. Disease is the result of an interaction between a pathogen and a susceptible host within a favorable environment. Repeated dispersal and cycles of infection on the same plant are common attributes of many plant pathogens. In contrast, fungal diseases of humans are usually not communicable. Polymerase Chain Reaction (PCR) and Deoxyribonucleic Acid (DNA) sequence based methods allow a closer examination of the ecology and epidemiology of human and plant pathogens. Although databases are useful in identifying a wide range of fungi, in certain instances, these available databases may not be sufficient to place a DNA sequence within a previously sampled genus or species. A powerful tool for the identification of fungi is the detection of DNA sequence that varies from multiple regions of the fungal genome coupled with appropriate statistical analysis of the data. As newer techniques —such as; PCR, micro fluidic methods, mitochondrial, and nuclear DNA sequence data are available, rapid identification of genetically distinct individuals will be possible, facilitating fungal forensics. PY - 2005/// DO - 10.1016/b978-012088483-4/50009-3 SP - 109-130 OP - PB - Elsevier SN - 9780120884834 UR - http://dx.doi.org/10.1016/b978-012088483-4/50009-3 DB - Crossref ER - TY - JOUR TI - Nematode gene sequences: Update for December 2005 AU - McCarter, J.P. AU - Bird, D.McK. AU - Mitreva, M. T2 - Journal of Nematology DA - 2005/// PY - 2005/// VL - 37 IS - 4 SP - 417-421 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33744980477&partnerID=MN8TOARS ER - TY - JOUR TI - A white paper on nematode comparative genomics AU - Bird, D.McK. AU - Blaxter, M.L. AU - McCarter, J.P. AU - Mitreva, M. AU - Sternberg, P.W. AU - Thomas, W.K. T2 - Journal of Nematology DA - 2005/// PY - 2005/// VL - 37 IS - 4 SP - 408-416 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33744994353&partnerID=MN8TOARS ER - TY - JOUR TI - Genetic Linkage Maps of the Red Flour Beetle, Tribolium castaneum, Based on Bacterial Artificial Chromosomes and Expressed Sequence Tags AU - Lorenzen, Marcé D. AU - Doyungan, Zaldy AU - Savard, Joel AU - Snow, Kathy AU - Crumly, Lindsey R. AU - Shippy, Teresa D. AU - Stuart, Jeffrey J. AU - Brown, Susan J. AU - Beeman, Richard W. T2 - Genetics AB - Abstract A genetic linkage map was constructed in a backcross family of the red flour beetle, Tribolium castaneum, based largely on sequences from bacterial artificial chromosome (BAC) ends and untranslated regions from random cDNA's. In most cases, dimorphisms were detected using heteroduplex or single-strand conformational polymorphism analysis after specific PCR amplification. The map incorporates a total of 424 markers, including 190 BACs and 165 cDNA's, as well as 69 genes, transposon insertion sites, sequence-tagged sites, microsatellites, and amplified fragment-length polymorphisms. Mapped loci are distributed along 571 cM, spanning all 10 linkage groups at an average marker separation of 1.3 cM. This genetic map provides a framework for positional cloning and a scaffold for integration of the emerging physical map and genome sequence assembly. The map and corresponding sequences can be accessed through BeetleBase (http://www.bioinformatics.ksu.edu/BeetleBase/). DA - 2005/4/16/ PY - 2005/4/16/ DO - 10.1534/genetics.104.032227 VL - 170 IS - 2 SP - 741-747 J2 - Genetics LA - en OP - SN - 0016-6731 1943-2631 UR - http://dx.doi.org/10.1534/genetics.104.032227 DB - Crossref ER - TY - JOUR TI - The Tribolium chitin synthase genes TcCHS1 and TcCHS2 are specialized for synthesis of epidermal cuticle and midgut peritrophic matrix AU - Arakane, Y. AU - Muthukrishnan, S. AU - Kramer, K. J. AU - Specht, C. A. AU - Tomoyasu, Y. AU - Lorenzen, M. D. AU - Kanost, M. AU - Beeman, R. W. T2 - Insect Molecular Biology AB - Functional analysis of the two chitin synthase genes, TcCHS1 and TcCHS2, in the red flour beetle, Tribolium castaneum, revealed unique and complementary roles for each gene. TcCHS1-specific RNA interference (RNAi) disrupted all three types of moult (larval-larval, larval-pupal and pupal-adult) and greatly reduced whole-body chitin content. Exon-specific RNAi showed that splice variant 8a of TcCHS1 was required for both the larval-pupal and pupal-adult moults, whereas splice variant 8b was required only for the latter. TcCHS2-specific RNAi had no effect on metamorphosis or on total body chitin content. However, RNAi-mediated down-regulation of TcCHS2, but not TcCHS1, led to cessation of feeding, a dramatic shrinkage in larval size and reduced chitin content in the midgut. DA - 2005/10// PY - 2005/10// DO - 10.1111/j.1365-2583.2005.00576.x VL - 14 IS - 5 SP - 453-463 J2 - Insect Mol Biol LA - en OP - SN - 0962-1075 1365-2583 UR - http://dx.doi.org/10.1111/j.1365-2583.2005.00576.x DB - Crossref KW - Tribolium castaneum KW - chitin synthase KW - RNAi KW - peritrophic matrix KW - cuticle ER - TY - JOUR TI - Dynamic relationships between soil properties and foliar disease as affected by annual additions of organic amendment to a sandy-soil vegetable production system AU - Rotenberg, Dorith AU - Cooperband, Leslie AU - Stone, Alexandra T2 - Soil Biology and Biochemistry AB - Additions of organic amendments to agricultural soils can lead to improved soil quality and reduced severity of crop diseases. However, the relationship between disease severity and soil properties as affected by repeated additions of these amendments is poorly understood. The primary objectives of this study were to (i) resolve multivariate relationships between soil properties and foliar disease severity and (ii) identify soil properties that contribute to disease severity in an intensive irrigated vegetable production system receiving annual additions of fresh and composted paper mill residuals (PMR). Foliar diseases caused by Pseudomonas syringae pv. syringae on snap bean (bacterial brown spot) and P. s. pv. lachrymans on cucumber (angular leaf spot) are the focus of this report. The experiment consisted of a 3-year crop rotation of potato (1998 and 2001), snap bean (1999 and 2002), and cucumber (2000). Treatments included a non-amended fertilizer control and two rates of fresh PMR, PMR composted alone (PMRC), and PMR composted with bark (PMRB). Soil measures included total soil carbon (TC) and nitrogen (TN), particulate organic matter carbon (POMC) and nitrogen (POMN), volumetric soil moisture (VM) and in situ NO3-N. Multiple regression (MR) and principal component analyses (PCA) were conducted to identify key soil properties that influenced the amount of disease. On average, the amount of TC in plots amended with PMR composts increased 77–178% from 1999 to 2002 compared to the non-amended soils. In 1999, a year in which compost additions reduced the amount of bacterial brown spot of bean, TC explained 42% of the total variation in disease severity in the best MR model. Midseason TN alone was inversely related to angular leaf spot incidence in 2000, while POMN explained 51% of the variation in the best MR model for that year. In 2002, a year in which PMRC-amended soils exacerbated brown spot symptoms, midseason quantities of TN explained 80% of the variation in disease severity. Unique to 2002, NO3-N alone positively correlated with disease severity. Overall, the influence of soil carbon on disease severity was displaced by the increasing importance of TN and NO3-N, indicating a transition from a C-dependent to an N-dependent system. DA - 2005/7// PY - 2005/7// DO - 10.1016/j.soilbio.2004.12.006 VL - 37 IS - 7 SP - 1343-1357 J2 - Soil Biology and Biochemistry LA - en OP - SN - 0038-0717 UR - http://dx.doi.org/10.1016/j.soilbio.2004.12.006 DB - Crossref KW - paper mill residuals KW - compost KW - disease control KW - soil organic matter KW - aerial bacteria KW - plant available nitrogen ER - TY - JOUR TI - PAPER MILL RESIDUALS AND COMPOST EFFECTS ON PARTICULATE ORGANIC MATTER AND RELATED SOIL FUNCTIONS IN A SANDY SOIL AU - Newman, C. M. AU - Rotenberg, D. AU - Cooperband, L. R. T2 - Soil Science AB - Amending sandy soils with paper mill residuals (PMR) and/or PMR composts should build soil organic matter pools, thereby increasing carbon and nutrient availability for biologically mediated soil functions. We investigated the effects of PMR and PMR composts on total and particulate organic matter (POM) and their relationships with plant available water (PAW) and mineral nitrogen. From 1998 to 2001, we applied PMR, PMR composted alone (PMR-C), and PMR composted with bark (PMR-B) annually at two agronomic rates to sandy soils in a 3-year vegetable rotation of potato, snap bean, and cucumber. After 4 years, all PMR amendments increased total soil C and N (TC, TN), POM-C, and POM-N 2- to 4-fold, relative to a nonamended control. After 3 years of annual amendment additions, the soil achieved an elevated steady state of POM-C, indicating a net balance between C-input and C-decay. Either TC or POM-C explained greater than 50% of the variation in PAW in years 2 through 4, indicating the functional similarities between the two carbon pools. The first sign of a significant but weak relationship between mineral N and POM-N (R2 = 15%) or TN (R2 = 34%) occurred during the final year of study. Annual additions of PMR and PMR composts produced sustained increases in labile soil C and N pools; however, increases in these OM pools did not translate into short-term nutrient availability in these sandy soils. DA - 2005/10// PY - 2005/10// DO - 10.1097/01.ss.0000190506.33675.e6 VL - 170 IS - 10 SP - 788-801 J2 - Soil Science LA - en OP - SN - 0038-075X UR - http://dx.doi.org/10.1097/01.ss.0000190506.33675.e6 DB - Crossref KW - paper mill residuals KW - compost KW - sandy soil KW - particulate organic matter KW - plant available water ER - TY - JOUR TI - Electrophysiological Properties of Neurons in the Basal Ganglia of the Domestic Chick: Conservation and Divergence in the Evolution of the Avian Basal Ganglia AU - Farries, Michael A. AU - Meitzen, John AU - Perkel, David J. T2 - Journal of Neurophysiology AB - Although the basal ganglia of birds and mammals share an enormous number of anatomical, histochemical, and electrophysiological characteristics, studies in songbirds have revealed some important differences. Specifically, a specialized region of songbird striatum (the input structure of the basal ganglia) has an anatomical projection and a physiologically defined cell type that are characteristic of the globus pallidus. At present, it is not clear if these differences result from adaptations specific to songbirds and perhaps a few other avian taxa or are common to all birds. We shed some light on this issue by characterizing the morphology and electrophysiological properties of basal ganglia neurons in an avian species that is only distantly related to songbirds: the domestic chick. We recorded neurons in chick basal ganglia in a brain slice preparation, using the whole cell technique. We found that chick striatum, like songbird striatum, contains a pallidum-like cell type never reported in mammalian striatum, supporting the hypothesis that this feature is common to all birds. We also discovered that spiny neurons, the most common cell type in the striatum of all amniotes, possess a diverse set of physiological properties in chicks that distinguish them from both mammals and songbirds. This study revealed an unexpectedly complex pattern of conservation and divergence in the properties of neurons recorded in avian striatum. DA - 2005/7// PY - 2005/7// DO - 10.1152/jn.00539.2004 VL - 94 IS - 1 SP - 454-467 J2 - Journal of Neurophysiology LA - en OP - SN - 0022-3077 1522-1598 UR - http://dx.doi.org/10.1152/jn.00539.2004 DB - Crossref ER - TY - JOUR TI - Seasonal-like plasticity of spontaneous firing rate in a songbird pre-motor nucleus AU - Park, Kevin H. J. AU - Meitzen, John AU - Moore, Ignacio T. AU - Brenowitz, Eliot A. AU - Perkel, David J. T2 - Journal of Neurobiology AB - Abstract Many animals exhibit seasonal changes in behavior and its underlying neural substrates. In seasonally breeding songbirds, the brain nuclei that control song learning and production undergo substantial structural changes at the onset of each breeding season, in association with changes in song behavior. These changes are largely mediated by photoperiod‐dependent changes in circulating concentrations of gonadal steroid hormones. Little is known, however, about whether changes in the electrophysiological activity of neurons accompany the dramatic morphological changes in the song nuclei. Here we induced seasonal‐like changes in the song systems of adult white‐crowned sparrows and used extracellular recording in acute brain slices from those individuals to study physiological properties of neurons in the robust nucleus of the arcopallium (RA), a pre‐motor nucleus necessary for song production. We report that: RA neurons from birds in breeding condition show a more than twofold increase in spontaneous firing rate compared to those from nonbreeding condition; this change appears to require both androgenic and estrogenic actions; and this change is intrinsic to the RA neurons. Thus, neurons in the song circuit exhibit both morphological and physiological adult seasonal plasticity. © 2005 Wiley Periodicals, Inc. J Neurobiol, 2005 DA - 2005/// PY - 2005/// DO - 10.1002/neu.20145 VL - 64 IS - 2 SP - 181-191 J2 - J. Neurobiol. LA - en OP - SN - 0022-3034 1097-4695 UR - http://dx.doi.org/10.1002/neu.20145 DB - Crossref KW - androgen KW - estrogen KW - testosterone KW - electrophysiology KW - birdsong ER - TY - JOUR TI - Differing Roles of Inhibition in Hierarchical Processing of Species-Specific Calls in Auditory Brainstem Nuclei AU - Xie, Ruili AU - Meitzen, John AU - Pollak, George D. T2 - Journal of Neurophysiology AB - Here we report on response properties and the roles of inhibition in three brain stem nuclei of Mexican-free tailed bats: the inferior colliculus (IC), the dorsal nucleus of the lateral lemniscus (DNLL) and the intermediate nucleus of the lateral lemniscus (INLL). In each nucleus, we documented the response properties evoked by both tonal and species-specific signals and evaluated the same features when inhibition was blocked. There are three main findings. First, DNLL cells have little or no surround inhibition and are unselective for communication calls, in that they responded to ∼97% of the calls that were presented. Second, most INLL neurons are characterized by wide tuning curves and are unselective for species-specific calls. The third finding is that the IC population is strikingly different from the neuronal populations in the INLL and DNLL. Where DNLL and INLL neurons are unselective and respond to most or all of the calls in the suite we presented, most IC cells are selective for calls and, on average, responded to ∼50% of the calls we presented. Additionally, the selectivity for calls in the majority of IC cells, as well as their tuning and other response properties, are strongly shaped by inhibitory innervation. Thus we show that inhibition plays only limited roles in the DNLL and INLL but dominates in the IC, where the various patterns of inhibition sculpt a wide variety of emergent response properties from the backdrop of more expansive and far less specific excitatory innervation. DA - 2005/12// PY - 2005/12// DO - 10.1152/jn.00688.2005 VL - 94 IS - 6 SP - 4019-4037 J2 - Journal of Neurophysiology LA - en OP - SN - 0022-3077 1522-1598 UR - http://dx.doi.org/10.1152/jn.00688.2005 DB - Crossref ER - TY - CHAP TI - THE MOUSE IN BIOMEDICAL RESEARCH AU - Roberts, R. B. AU - Threadgill, D. W. T2 - The Mouse in Animal Genetics and Breeding Research PY - 2005/6// DO - 10.1142/9781860947162_0015 SP - 319-340 OP - PB - PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO. SN - 9781860945656 9781860947162 UR - http://dx.doi.org/10.1142/9781860947162_0015 DB - Crossref ER - TY - JOUR TI - Masking in Waved‐2 Mice: EGF Receptor Control of Locomotion Questioned AU - Mrosovsky, N. AU - Redlin, U. AU - Roberts, R. B. AU - Threadgill, D. W. T2 - Chronobiology International AB - It has been suggested that epidermal growth factors (EGF) are responsible for the inhibition of locomotion by light (i.e., masking) in nocturnal rodents (Kramer et al., ). The poor masking response of waved‐2 (Egfrwa2) mutant mice, with reduced EGF receptor activity, was adduced in support of this idea. In the present work, we studied the responses to light over a large range in illumination levels, in a variety of tests, with pulses of light and with ultradian light‐dark cycles in Egfrwa2 mutant mice. No evidence suggested that normal functioning of epidermal growth factor receptors was required, or even involved, in masking. DA - 2005/1// PY - 2005/1// DO - 10.1080/07420520500395086 VL - 22 IS - 6 SP - 963–974 SN - 0742-0528 1525-6073 UR - http://dx.doi.org/10.1080/07420520500395086 KW - circadian rhythm KW - epidermal growth factor KW - locomotion KW - masking KW - subparaventricular zone KW - waved-2 KW - mutants ER - TY - JOUR TI - Genomic features of lactic acid bacteria effecting bioprocessing and health AU - Klaenhammer, Todd R. AU - Barrangou, Rodolphe AU - Buck, B. Logan AU - Azcarate-Peril, M. Andrea AU - Altermann, Eric T2 - FEMS Microbiology Reviews AB - The lactic acid bacteria are a functionally related group of organisms known primarily for their bioprocessing roles in food and beverages. More recently, selected members of the lactic acid bacteria have been implicated in a number of probiotic roles that impact general health and well-being. Genomic analyses of multiple members of the lactic acid bacteria, at the genus, species, and strain level, have now elucidated many genetic features that direct their fermentative and probiotic roles. This information is providing an important platform for understanding core mechanisms that control and regulate bacterial growth, survival, signaling, and fermentative processes and, in some cases, potentially underlying probiotic activities within complex microbial and host ecosystems. DA - 2005/8// PY - 2005/8// DO - 10.1016/j.fmrre.2005.04.007 VL - 29 IS - 3 SP - 393-409 ER - TY - JOUR TI - Population structure of the tobacco blue mold pathogen Peronospora tabacina in the USA, the Caribbean and Central America AU - Blanco-Meneses, M AU - Ristaino, J T2 - Phytopathology DA - 2005/// PY - 2005/// VL - 95 IS - 6 ER - TY - CONF TI - Molecular evolution in the mitochondrial genome of the Irish Potato famine pathogen, Phytophthora infestans AU - Ristaino, J AU - Avila-Adame, C AU - Buell, R T2 - AMER PHYTOPATHOLOGICAL SOC 3340 PILOT KNOB ROAD, ST PAUL, MN 55121 USA C2 - 2005/// C3 - PHYTOPATHOLOGY DA - 2005/// VL - 95 SP - S89-S89 M1 - 6 ER - TY - JOUR TI - A 3-year field measurement of methane and nitrous oxide emissions from rice paddies in China: Effects of water regime, crop residue, and fertilizer application AU - Zou, Jianwen AU - Huang, Yao AU - Jiang, Jingyan AU - Zheng, Xunhua AU - Sass, Ronald L T2 - Global biogeochemical cycles DA - 2005/// PY - 2005/// VL - 19 IS - 2 ER - TY - JOUR TI - Gene genealogies inferred from nuclear and mitochondrial DNA sequences suggest a South American origin of Phytophthora infestans. Genealoǵıas de los genes deducidas de las secuencias de ADN nuclear y mitocondrial sugiere un origen suramericano de Phytophthora infestans. AU - Ristaino, J AU - Gomez-Alpizar, L AU - Thorne, J AU - Carbone, I T2 - Phytopathology. DA - 2005/// PY - 2005/// VL - 95 IS - 6 ER - TY - JOUR TI - Functional and species diversity of soil microbial communities in soils from organic, sustainable, and conventional farms in North Carolina AU - Bo, L AU - Ristaino, J AU - Glenn, D AU - Tu, C AU - Hu, S AU - Buckley, K AU - Gumpertz, M T2 - Phytopathology DA - 2005/// PY - 2005/// VL - 95 IS - 6 ER - TY - JOUR TI - Sequencing the Phytophthora infestans genome: preliminary studies AU - Zody, MC AU - O’Neill, K AU - Handsaker, B AU - Karlsson, E AU - Govers, F AU - Vondervoort, P AU - Weide, R AU - Whisson, S AU - Birch, P AU - LiJun, Ma AU - others DA - 2005/// PY - 2005/// ER - TY - JOUR TI - Ethylene signalling and response pathway: A unique signalling cascade with a multitude of inputs and outputs AU - Stepanova, A.N. AU - Alonso, J.M. T2 - Physiologia Plantarum AB - Plants as immobile organisms need to constantly monitor the changes in the environment to modify and adjust developmental and metabolic pathways accordingly. The responses to these environmental cues require an integrative mechanism where external and internal signals are detected and processed to trigger an appropriate ‘reaction’ in the plant. Hormones play a key role in mediating some of these integrative processes and in generating the response reactions. The identification and characterization of the basic hormone signalling components and their interactions represent the first step towards comprehensive understanding of plant responses to intrinsic and extrinsic cues. A relatively well‐characterized ethylene signalling and response pathway, together with numerous evidences of its interactions with other signalling/response pathways, provide an excellent example to illustrate our current knowledge and perspective on how signal integration occurs in plants. DA - 2005/// PY - 2005/// DO - 10.1111/j.1399-3054.2005.00447.x VL - 123 IS - 2 SP - 195-206 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-14644388900&partnerID=MN8TOARS ER - TY - JOUR TI - Ethylene signaling pathway. AU - Stepanova, A.N. AU - Alonso, J.M. T2 - Science's STKE : signal transduction knowledge environment DA - 2005/// PY - 2005/// VL - 2005 IS - 276 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33644877967&partnerID=MN8TOARS ER - TY - JOUR TI - Arabidopsis ethylene signaling pathway. AU - Stepanova, A.N. AU - Alonso, J.M. T2 - Science's STKE : signal transduction knowledge environment DA - 2005/// PY - 2005/// VL - 2005 IS - 276 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33644876995&partnerID=MN8TOARS ER - TY - JOUR TI - Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer AU - Ryu, Jong Sang AU - Kim, Jeong-Il AU - Kunkel, Tim AU - Kim, Byung Chul AU - Cho, Dae Shik AU - Hong, Sung Hyun AU - Kim, Seong-Hee AU - Fernández, Aurora Piñas AU - Kim, Yumi AU - Alonso, Jose M. T2 - Cell DA - 2005/// PY - 2005/// VL - 120 IS - 3 SP - 395-406 ER - TY - JOUR TI - NPH4/ARF7 and ARF19 promote leaf expansion and auxin‐induced lateral root formation AU - Wilmoth, Jill C. AU - Wang, Shucai AU - Tiwari, Shiv B. AU - Joshi, Atul D. AU - Hagen, Gretchen AU - Guilfoyle, Thomas J. AU - Alonso, Jose M. AU - Ecker, Joseph R. AU - Reed, Jason W. T2 - The Plant Journal DA - 2005/// PY - 2005/// VL - 43 IS - 1 SP - 118-130 ER - TY - JOUR TI - Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis AU - Mason, Michael G. AU - Mathews, Dennis E. AU - Argyros, D. Aaron AU - Maxwell, Bridey B. AU - Kieber, Joseph J. AU - Alonso, Jose M. AU - Ecker, Joseph R. AU - Schaller, G. Eric T2 - The Plant Cell Online DA - 2005/// PY - 2005/// VL - 17 IS - 11 SP - 3007-3018 ER - TY - JOUR TI - Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana AU - Overvoorde, Paul J. AU - Okushima, Yoko AU - Alonso, José M. AU - Chan, April AU - Chang, Charlie AU - Ecker, Joseph R. AU - Hughes, Beth AU - Liu, Amy AU - Onodera, Courtney AU - Quach, Hong T2 - The Plant Cell Online DA - 2005/// PY - 2005/// VL - 17 IS - 12 SP - 3282-3300 ER - TY - JOUR TI - Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19 AU - Okushima, Yoko AU - Overvoorde, Paul J. AU - Arima, Kazunari AU - Alonso, Jose M. AU - Chan, April AU - Chang, Charlie AU - Ecker, Joseph R. AU - Hughes, Beth AU - Lui, Amy AU - Nguyen, Diana T2 - The Plant Cell Online DA - 2005/// PY - 2005/// VL - 17 IS - 2 SP - 444-463 ER - TY - JOUR TI - Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development AU - Prigge, Michael J. AU - Otsuga, Denichiro AU - Alonso, Jose M. AU - Ecker, Joseph R. AU - Drews, Gary N. AU - Clark, Steven E. T2 - The Plant Cell Online DA - 2005/// PY - 2005/// VL - 17 IS - 1 SP - 61-76 ER - TY - JOUR TI - Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation AU - Nagpal, Punita AU - Ellis, Christine M. AU - Weber, Hans AU - Ploense, Sara E. AU - Barkawi, Lana S. AU - Guilfoyle, Thomas J. AU - Hagen, Gretchen AU - Alonso, José M. AU - Cohen, Jerry D. AU - Farmer, Edward E. T2 - Development DA - 2005/// PY - 2005/// VL - 132 IS - 18 SP - 4107-4118 ER - TY - JOUR TI - Arabidopsis ethylene signaling pathway AU - Stepanova, Anna N. AU - Alonso, Jose M. T2 - Science Signaling DA - 2005/// PY - 2005/// VL - 2005 IS - 276 SP - cm4 ER - TY - JOUR TI - " Flagellin is not a major defense elicitor in Ralstonia solanacearum cells (vol 17, pg 696, 2005) AU - Pfund, C. AU - Tans-Kersten, J. AU - Dunning, F. M. AU - Alonso, J. M. AU - Ecker, J. R. AU - Allen, C. AU - Bent, A. F. T2 - MOLECULAR PLANT-MICROBE INTERACTIONS DA - 2005/// PY - 2005/// VL - 18 IS - 9 SP - 1024 ER - TY - JOUR TI - Plant invasion alters nitrogen cycling by modifying the soil nitrifying community AU - Hawkes, Christine V. AU - Wren, Ian F. AU - Herman, Donald J. AU - Firestone, Mary K. T2 - Ecol Letters AB - Abstract Plant invasions have dramatic aboveground effects on plant community composition, but their belowground effects remain largely uncharacterized. Soil microorganisms directly interact with plants and mediate many nutrient transformations in soil. We hypothesized that belowground changes to the soil microbial community provide a mechanistic link between exotic plant invasion and changes to ecosystem nutrient cycling. To examine this possible link, monocultures and mixtures of exotic and native species were maintained for 4 years in a California grassland. Gross rates of nitrogen (N) mineralization and nitrification were quantified with 15 N pool dilution and soil microbial communities were characterized with DNA‐based methods. Exotic grasses doubled gross nitrification rates, in part by increasing the abundance and changing the composition of ammonia‐oxidizing bacteria in soil. These changes may translate into altered ecosystem N budgets after invasion. Altered soil microbial communities and their resulting effects on ecosystem processes may be an invisible legacy of exotic plant invasions. DA - 2005/9// PY - 2005/9// DO - 10.1111/j.1461-0248.2005.00802.x VL - 8 IS - 9 SP - 976-985 KW - ammonia-oxidizing bacteria KW - annual grass invasion KW - Avena barbata KW - Bromus hordeaceus KW - gross mineralization KW - gross nitrification KW - Lupinus bicolor KW - Nassella pulchra ER - TY - JOUR TI - Assessment of plasma brain natriuretic peptide concentration in Boxers with arrhythmogenic right ventricular cardiomyopathy AU - Baumwart, Ryan D. AU - Meurs, Kathryn M. T2 - American Journal of Veterinary Research AB - Abstract Objective —To determine whether Boxers with a clinical diagnosis of arrhythmogenic right ventricular cardiomyopathy (ARVC) have increased plasma concentrations of brain natriuretic peptide (BNP), compared with concentrations in clinically normal dogs. Animals —13 Boxers with ARVC, 9 clinically normal Boxers, 10 clinically normal non-Boxer dogs, and 5 hound dogs with systolic dysfunction. Procedure —All Boxers were evaluated via 24-hour ambulatory electrocardiography and echocardiography; the number of ventricular premature contractions (VPCs) per 24 hours was assessed. Hound dogs with cardiac pacing-induced systolic dysfunction (positive control dogs) and clinically normal non-Boxer dogs (negative control dogs) were evaluated echocardiographically. Three milliliters of blood was collected from each dog for measurement of plasma BNP concentration by use of a radioimmunoassay. Results —Mean ± SD plasma BNP concentration for the ARVC-affected Boxers, clinically normal Boxers, negative control dogs, and positive control dogs was 11.0 ± 4.6 pg/mL, 7.9 ± 3.2 pg/mL, 11.5 ± 4.9 pg/mL, and 100.8 ± 56.8 pg/mL, respectively. Compared with findings in the positive control group, plasma BNP concentration in each of the other 3 groups was significantly different. There was no significant difference in BNP concentration between the 2 groups of Boxers. A significant correlation between plasma BNP concentration and number of VPCs per 24 hours in the ARVC-affected Boxers was not identified. Conclusions and Clinical Relevance —A significant difference in BNP concentration between Boxers with ARVC and clinically normal Boxers was not identified. Results suggest that BNP concentration may not be an indicator of ARVC in Boxers. ( Am J Vet Res 2005;66:2086–2089) DA - 2005/12// PY - 2005/12// DO - 10.2460/ajvr.2005.66.2086 VL - 66 IS - 12 SP - 2086-2089 J2 - American Journal of Veterinary Research LA - en OP - SN - 0002-9645 UR - http://dx.doi.org/10.2460/ajvr.2005.66.2086 DB - Crossref ER - TY - JOUR TI - Tei Index of Myocardial Performance Applied to the Right Ventricle in Normal Dogs AU - Baumwart, Ryan D. AU - Meurs, Kathryn M. AU - Bonagura, John D. T2 - Journal of Veterinary Internal Medicine AB - Right ventricular (RV) dysfunction is a cause of exercise intolerance, hypotension, syncope, and heart failure in dogs with cardiac and respiratory disorders. The study objective was to determine Doppler-derived reference values that reflect global RV function in healthy dogs. We measured systolic time intervals and an RV index of myocardial performance (IMP) in 45 healthy dogs between 8 months and 8 years of age. Pulsed-wave Doppler recordings of mitral, tricuspid, aortic, and pulmonic were acquired. Pre-ejection period (PEP), ejection time (ET), PEP/ET, and IMP were determined for both ventricles by separate cardiac cycles. Compared to the mean left ventricular (LV) IMP (0.410; 95% confidence intervals [CI] 0.378–0.442), mean RV IMP (0.250; 95% CI 0.222–0.278) was significantly smaller, and mean ET for the RV (187 millisecond [ms]; 95% CI 182–192) was significantly longer than the LV (173 ms; 95% CI 168–179). A clinically relevant correlation was not found among RV IMP and body weight, heart rate, RV ET, RV PEP, or RV PEP/ET. Calculation of LV IMP with 2 separate sample volumes yielded smaller values than from a single sample volume, with a difference in means of 0.040. We conclude that the RV IMP is relatively independent of body weight and heart rate within the ranges studied and is consistently lower than values derived from the LV in healthy dogs. This study provides additional reference values for RV function in dogs and may be useful for identification of RV dysfunction in dogs. DA - 2005/11// PY - 2005/11// DO - 10.1111/j.1939-1676.2005.tb02772.x VL - 19 IS - 6 SP - 828-832 LA - en OP - SN - 0891-6640 1939-1676 UR - http://dx.doi.org/10.1111/j.1939-1676.2005.tb02772.x DB - Crossref ER - TY - JOUR TI - Survival times in dogs with severe subvalvular aortic stenosis treated with balloon valvuloplasty or atenolol AU - Meurs, Kathryn M. AU - Lehmkuhl, Linda B. AU - Bonagura, John D. T2 - Journal of the American Veterinary Medical Association AB - To determine survival times in dogs with severe subvalvular aortic stenosis (SAS) treated by means of balloon valvuloplasty or with atenolol, a beta-adrenoceptor blocking drug.Prospective study.38 dogs < 24 months old with severe SAS (peak systolic pressure gradient > or = 80 mm Hg).10 dogs underwent balloon valvuloplasty and were reexamined 6 weeks later to determine the feasibility of the procedure. The remaining 28 dogs were randomly assigned to undergo balloon valvuloplasty (n = 15) or to be treated with atenolol long term (13) and were reexamined annually for 9 years or until the time of death.For the first 10 dogs, mean pressure gradient 6 weeks after balloon valvuloplasty (mean +/- SD, 119 +/- 32.6 mm Hg) was significantly decreased, compared with mean baseline pressure gradient (167 +/- 40.1 mm Hg). Median survival time for dogs that underwent balloon valvuloplasty (55 months) was not significantly different from median survival time for dogs treated with atenolol (56 months).Results suggest that balloon valvuloplasty can result in a significant decrease in the peak systolic pressure gradient in dogs with severe SAS, at least for the short term. No clear benefit in survival times was seen for dogs that underwent balloon valvuloplasty versus dogs that were treated with atenolol. DA - 2005/8// PY - 2005/8// DO - 10.2460/javma.2005.227.420 VL - 227 IS - 3 SP - 420-424 J2 - Journal of the American Veterinary Medical Association LA - en OP - SN - 0003-1488 UR - http://dx.doi.org/10.2460/javma.2005.227.420 DB - Crossref ER - TY - JOUR TI - Clinical, echocardiographic, and electrocardiographic abnormalities in Boxers with cardiomyopathy and left ventricular systolic dysfunction: 48 cases (1985-2003) AU - Baumwart, Ryan D. AU - Meurs, Kathryn M. AU - Atkins, Clarke E. AU - Bonagura, John D. AU - DeFrancesco, Teresa C. AU - Keene, Bruce W. AU - Koplitz, Shianne AU - Fuentes, Virginia Luis AU - Miller, Matthew W. AU - Rausch, William AU - Spier, Alan W. T2 - Journal of the American Veterinary Medical Association AB - To identify clinical, echocardiographic, and electrocardiographic abnormalities in Boxers with cardiomyopathy and echocardiographic evidence of left ventricular systolic dysfunction.Retrospective study.48 mature Boxers.Medical records were reviewed for information on age; sex; physical examination findings; and results of electrocardiography, 24-hour ambulatory electrocardiography, thoracic radiography, and echocardiography.Mean age of the dogs was 6 years (range, 1 to 11 years). Twenty (42%) dogs had a systolic murmur, and 9 (19%) had ascites. Congestive heart failure was diagnosed in 24 (50%) dogs. Seventeen (35%) dogs had a history of syncope. Mean fractional shortening was 14.4% (range, 1% to 23%). Mean left ventricular systolic and diastolic diameters were 4.5 cm (range, 3 to 6.3 cm) and 5.3 cm (range, 3.9 to 7.4 cm), respectively. Twenty-eight (58%) dogs had a sinus rhythm with ventricular premature complexes (VPCs), and 20 had supraventricular arrhythmias (15 with atrial fibrillation and 5 with sinus rhythm and atrial premature complexes). Sixteen of the dogs with supraventricular arrhythmias also had occasional VPCs. Morphology of the VPCs seen on lead II ECGs was consistent with left bundle branch block in 25 dogs, right bundle branch block in 8, and both in 11.Results suggest that Boxers with cardiomyopathy and left ventricular dysfunction frequently have arrhythmias of supraventricular or ventricular origin. Whether ventricular dysfunction was preceded by electrical disturbances could not be determined from these data, and the natural history of myocardial disease in Boxers requires further study. DA - 2005/4// PY - 2005/4// DO - 10.2460/javma.2005.226.1102 VL - 226 IS - 7 SP - 1102-1104 J2 - Journal of the American Veterinary Medical Association LA - en OP - SN - 0003-1488 UR - http://dx.doi.org/10.2460/javma.2005.226.1102 DB - Crossref ER - TY - JOUR TI - RacGap50C Negatively Regulates Wingless Pathway Activity During Drosophila Embryonic Development AU - Jones, Whitney M. AU - Bejsovec, Amy T2 - Genetics AB - Abstract The Wingless (Wg)/Wnt signal transduction pathway directs a variety of cell fate decisions in developing animal embryos. Despite the identification of many Wg pathway components to date, it is still not clear how these elements work together to generate cellular identities. In the ventral epidermis of Drosophila embryos, Wg specifies cells to secrete a characteristic pattern of denticles and naked cuticle that decorate the larval cuticle at the end of embryonic development. We have used the Drosophila ventral epidermis as our assay system in a series of genetic screens to identify new components involved in Wg signaling. Two mutant lines that modify wg-mediated epidermal patterning represent the first loss-of-function mutations in the RacGap50C gene. These mutations on their own cause increased stabilization of Armadillo and cuticle pattern disruptions that include replacement of ventral denticles with naked cuticle, which suggests that the mutant embryos suffer from ectopic Wg pathway activation. In addition, RacGap50C mutations interact genetically with naked cuticle and Axin, known negative regulators of the Wg pathway. These phenotypes suggest that the RacGap50C gene product participates in the negative regulation of Wg pathway activity. DA - 2005/2/3/ PY - 2005/2/3/ DO - 10.1534/genetics.104.039735 VL - 169 IS - 4 SP - 2075-2086 J2 - Genetics LA - en OP - SN - 0016-6731 1943-2631 UR - http://dx.doi.org/10.1534/genetics.104.039735 DB - Crossref ER - TY - JOUR TI - Cellular damage induced by cadmium and mercury in Medicago sativa AU - Ortega-Villasante, C. AU - Rellan-Alvarez, R. AU - Del Campo, F. F. AU - Carpena-Ruiz, R. O. AU - Hernandez, L. E. T2 - Journal of Experimental Botany AB - Alfalfa (Medicago sativa) plantlets were exposed to Cd or Hg to study the kinetics of diverse stress indexes. In the so-called beaker-size hydroponic system, plantlets were grown in 30 μM of Cd or Hg for 7 d. Oxidative stress took place and increased over time, a linear response being observed with Cd but not with Hg. To improve the sensitivity of the stress assays used, a micro-assay system, in which seedlings were exposed for 24 h, was developed. Phytotoxicity of metals, quantified as growth inhibition, was observed well before there was any change in the non-protein thiol tissue concentration. When measured with conventional techniques, oxidative stress indexes did not show significant variation. To trace early and small plant responses to Cd and Hg, a microscopic analysis with novel fluorescent dyes, which had not yet been exploited to any significant extent for use in plants, was conducted. These fluorescent probes, which allowed minute cellular responses to 0, 3, 10, and 30 μM of both metals to be visualized in the roots of the alfalfa seedlings, were: (i) 2′,7′-dichlorofluorescin diacetate that labels peroxides; (ii) monochlorobimane that stains reduced glutathione/homoglutathione (GSH/hGSH); and (iii) propidium iodide that marks nuclei of dead cells. Oxidative stress and cell death increased after exposure for 6–24 h to Cd and Hg, but labelling of GSH/hGSH decreased acutely. This diminution might be the result of direct interaction of GSH/hGSH with both Cd and Hg, as inferred from an in vitro conjugation assay. Therefore, both Cd and Hg not only compromised severely the cellular redox homeostasis, but also caused cell necrosis. In plants treated with 1 mM L-buthionine sulphoximine, a potent inhibitor of GSH/hGSH synthesis, only the oxidative stress symptoms appeared, indicating that the depletion of the GSH/hGSH pool was not sufficient to promote cell death, and that other phytotoxic mechanisms might be involved. DA - 2005/// PY - 2005/// DO - 10.1093/jxb/eri223 VL - 56 IS - 418 SP - 2239-2251 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-24944536376&partnerID=MN8TOARS KW - alfalfa KW - Cd KW - cell damage KW - fluorescence KW - GSH/hGSH KW - H(2)DCFDA KW - Hg KW - MCB KW - microscopy KW - oxidative stress ER - TY - JOUR TI - BIOLOGY OF CHROMATIN DYNAMICS AU - Hsieh, Tzung-Fu AU - Fischer, Robert L. T2 - Annual Review of Plant Biology AB - During the development of a multicellular organism, cell differentiation involves activation and repression of transcription programs that must be stably maintained during subsequent cell divisions. Chromatin remodeling plays a crucial role in regulating chromatin states that conserve transcription programs and provide a mechanism for chromatin states to be maintained as cells proliferate, a process referred to as epigenetic inheritance. A large number of factors and protein complexes are now known to be involved in regulating the dynamic states of chromatin structure. Their biological functions and molecular mechanisms are beginning to be revealed. DA - 2005/6// PY - 2005/6// DO - 10.1146/annurev.arplant.56.032604.144118 VL - 56 IS - 1 SP - 327-351 J2 - Annu. Rev. Plant Biol. LA - en OP - SN - 1543-5008 1545-2123 UR - http://dx.doi.org/10.1146/annurev.arplant.56.032604.144118 DB - Crossref KW - chromatin remodeling KW - epigenetic inheritance KW - histone modification KW - DNA methylation KW - RNA interference ER - TY - JOUR TI - The rarity of gene shuffling in conserved genes. AU - Conant, G.C. AU - Wagner, A. T2 - Genome biology DA - 2005/// PY - 2005/// VL - 6 IS - 6 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33646556197&partnerID=MN8TOARS ER - TY - JOUR TI - GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments AU - Kirov, SA AU - Peng, X AU - Baker, E AU - Schmoyer, D AU - Zhang, B AU - Snoddy, J T2 - BMC Bioinformatics AB - The analysis of biological data is greatly enhanced by existing or emerging databases. Most existing databases, with few exceptions are not designed to easily support large scale computational analysis, but rather offer exclusively a web interface to the resource. We have recognized the growing need for a database which can be used successfully as a backend to computational analysis tools and pipelines. Such database should be sufficiently versatile to allow easy system integration. GeneKeyDB is a gene-centered relational database developed to enhance data mining in biological data sets. The system provides an underlying data layer for computational analysis tools and visualization tools. GeneKeyDB relies primarily on existing database identifiers derived from community databases (NCBI, GO, Ensembl, et al.) as well as the known relationships among those identifiers. It is a lightweight, portable, and extensible platform for integration with computational tools and analysis environments. GeneKeyDB can enable analysis tools and users to manipulate the intersections, unions, and differences among different data sets. C2 - 1274265 DA - 2005/// PY - 2005/// DO - 10.1186/1471-2105-6-72 VL - 6 IS - 1 SP - 72 SN - 1471-2105 UR - http://dx.doi.org/10.1186/1471-2105-6-72 ER - TY - CONF TI - Preliminary Results for GAMI: A Genetic Algorithms Approach to Motif Inference AU - Congdon, C.B. AU - Fizer, C.W. AU - Smith, N.W. AU - Gaskins, H.R. AU - Aman, J. AU - Nava, G.M. AU - Mattingly, C. T2 - 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology AB - We have developed GAMI, an approach to motif inference that uses a genetic algorithms search and is designed specifically to work with divergent species and possibly long nucleotide sequences. The system design reduces the size of the search space as compared to typical window-location approaches for motif inference. This paper describes the motivation and system design for GAMI, discusses how we have designed the search space and compares this to the search space of other approaches, and presents initial results with data from the literature and from novel tasks. GAMI is able to find a host of putative conserved patterns; possible approaches for validating the utility of the conserved regions are discussed. C2 - 2005/// C3 - 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology DA - 2005/// DO - 10.1109/cibcb.2005.1594904 PB - IEEE SN - 0780393872 UR - http://dx.doi.org/10.1109/cibcb.2005.1594904 DB - Crossref ER - TY - JOUR TI - In vitro Canine Distemper Virus Infection of Canine Lymphoid Cells: A Prelude to Oncolytic Therapy for Lymphoma AU - Suter, S. E. T2 - Clinical Cancer Research AB - Abstract Purpose: Measles virus (MV) causes the regression of human lymphoma xenografts. The purpose of this study was to determine if canine lymphoid cells could be infected in vitro with MV or canine distemper virus (CDV, the canine Morbillivirus equivalent of MV) and determine if in vitro viral infection leads to apoptotic cell death. Experimental Design: Reverse transcriptase-PCR was used to examine the expression of both signal lymphocyte activation molecule (CD150) and membrane cofactor molecule (CD46) mRNA. An attenuated CDV expressing enhanced green fluorescent protein was used to infect canine cells in vitro. Both flow cytometry and reverse transcriptase-PCR was used to document CDV infection. Cell death was examined using a propidium iodide staining assay and Annexin V binding. Results: Canine lymphoid cell lines and neoplastic B and T lymphocytes collected from dogs with spontaneous lymphoma expressed the Morbillivirus receptor CD150 mRNA. In contrast, only neoplastic lymphocytes expressed detectable levels of CD46 mRNA. Although MV did not infect canine cells, CDV efficiently infected between 40% and 70% of all three canine lymphoid lines tested. More importantly, CDV infected 50% to 90% of neoplastic lymphocytes isolated from dogs with both B and T cell lymphoma. Apoptosis of CDV-infected cell lines was documented. Conclusions: Attenuated CDV may be a useful treatment for canine lymphoma. As such, dogs with lymphoma may represent a biologically relevant large animal model to investigate the feasibility, safety, and efficacy of Morbillivirus therapy in a clinical setting with findings that may have direct applicability in the treatment of human non-Hodgkin's lymphoma. DA - 2005/2/15/ PY - 2005/2/15/ DO - 10.1158/1078-0432.ccr-04-1944 VL - 11 IS - 4 SP - 1579-1587 J2 - Clinical Cancer Research LA - en OP - SN - 1078-0432 1557-3265 UR - http://dx.doi.org/10.1158/1078-0432.ccr-04-1944 DB - Crossref ER - TY - JOUR TI - Quantitative Trait Loci for Seed Protein and Oil Concentration, and Seed Size in Soybean AU - Panthee, D. R. AU - Pantalone, V. R. AU - West, D. R. AU - Saxton, A. M. AU - Sams, C. E. T2 - Crop Science AB - Soybean [ Glycine max (L.) Merr.] is an important crop because of its high oil and protein concentration. However, there is an inverse relationship between seed protein and oil concentration, making it difficult to improve both traits simultaneously. Molecular breeding may be helpful to facilitate a balanced accumulation of desirable alleles. The objective of this study was to identify quantitative trait loci (QTL) governing soybean protein, oil and seed size. To achieve this objective, 101 F 6 –derived recombinant inbred lines (RIL) from a population developed from a cross of N87‐984‐16 × TN93‐99 were used. Heritability estimates on an entry mean basis for protein and oil concentrations, and seed size were 0.66, 0.54, and 0.71, respectively. A total of 585 simple sequence repeat (SSR) molecular genetic markers were screened and 94 were polymorphic in the RIL. Single factor ANOVA was used to identify candidate QTL, which were then confirmed by composite interval mapping. One novel molecular marker (Satt570) on molecular linkage group (MLG) G associated with a protein QTL was detected. Novel molecular markers (Satt274, Satt420, and Satt479) located on MLG D1b, O, and O respectively and a previously reported marker (Satt317) located on MLG H were associated with oil QTL in this study. Molecular markers Satt002 (MLG D2) and Satt184 (MLG D1a) associated with seed size QTL were verified whereas Satt147 (MLG D1a) was novel. The individual QTL explained 20.2, 9.4‐15, and 10 to 16.5% of the phenotypic variation for protein and oil concentrations, and seed size, respectively. Thus, we identified major loci for improving soybean seed quality. DA - 2005/// PY - 2005/// DO - 10.2135/cropsci2004.0720 VL - 45 IS - 5 SP - 2015 LA - en OP - SN - 1435-0653 UR - http://dx.doi.org/10.2135/cropsci2004.0720 DB - Crossref ER - TY - JOUR TI - Quantitative trait loci controlling sulfur containing amino acids, methionine and cysteine, in soybean seeds AU - Panthee, D. R. AU - Pantalone, V. R. AU - Sams, C. E. AU - Saxton, A. M. AU - West, D. R. AU - Orf, J. H. AU - Killam, A. S. T2 - Theoretical and Applied Genetics DA - 2005/12/10/ PY - 2005/12/10/ DO - 10.1007/s00122-005-0161-6 VL - 112 IS - 3 SP - 546-553 J2 - Theor Appl Genet LA - en OP - SN - 0040-5752 1432-2242 UR - http://dx.doi.org/10.1007/s00122-005-0161-6 DB - Crossref ER - TY - JOUR TI - The effect of bioactive glass ceramics on the expression of bone-related genes and proteins in vitro. AU - Knabe, C AU - Stiller, M AU - Berger, G AU - Reif, D AU - Gildenhaar, R AU - Howlett, CR AU - Zreiqat, H T2 - Clinical oral implants research AB - Abstract: Using biodegradable bone substitutes in alveolar ridge augmentation avoids second‐site surgery for autograft harvesting. Considerable efforts have been undertaken to develop rapidly resorbable bone substitute materials with a higher degree of biodegradability than tricalcium phosphate (TCP). This study examines the effect of novel biodegradable glass ceramics on the expression of bone‐related genes and proteins by human bone‐derived cells (HBDC) and compares this behavior with that of TCP. Test materials used were α‐TCP, a surface‐treated glass ceramic GB9N with crystalline phase Ca 2 KNa(PO 4 ) 2 and a small amount of amorphous silica phosphate; AP40 – a glass ceramic based on crystalline phases of apatite and wollastonite; and a glass ceramic Mg5 composed of 20.6% CaO, 58.5% P 2 O 5 , 14.4% Na 2 O, 4.1% MgO and 2.4% CaF 2 (wt%). HBDC were grown on the substrata for 3, 5, 7, 14 and 21 days, counted and probed for various bone‐related mRNAs and proteins (type I collagen (Col I), osteocalcin (OC), osteopontin (OP), osteonectin (ON), alkaline phosphatase (ALP) and bone sialoprotein (BSP)). The substrata supported continuous cellular growth for 21 days. By day 21, GB9N had the highest number of HBDC. GB9N induced significantly enhanced expression of Col I, ALP, OP, OC and ON mRNA at 3 days; of OP, OC and ON mRNA and protein at 7 and 14 days; and of ALP, OP and OC mRNA and Col I, ALP, BSP, ON and OP protein at 21 days. Since all novel glass ceramics supported cellular proliferation together with expression of bone‐related genes and proteins at least as much as TCP, these ceramics can be regarded as potential bone substitutes. GB9N had the most effect on osteoblastic differentiation, thus suggesting that this material may possess a higher potency to enhance osteogenesis than TCP. DA - 2005/2// PY - 2005/2// DO - 10.1111/j.1600-0501.2004.01066.x VL - 16 IS - 1 SP - 119–127 UR - http://europepmc.org/abstract/med/15642039 KW - bone-substitutes KW - cell-biomaterial interactions KW - glass ceramics KW - human bone-derived cells KW - in situ hybridization ER - TY - JOUR TI - Exploratory visual analysis of pharmacogenomic results. AU - Reif, DM AU - Dudek, SM AU - Shaffer, CM AU - Wang, J AU - Moore, JH T2 - Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing DA - 2005/// PY - 2005/// UR - http://europepmc.org/abstract/med/15759635 ER - TY - CONF TI - Exploratory visual analysis of pharmacogenomic results AU - Reif, D.M. AU - Dudek, S.M. AU - Shaffer, C.M. AU - Wang, J. AU - Moore, J.H. C2 - 2005/// C3 - Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005 DA - 2005/// SP - 296-307 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-15944408038&partnerID=MN8TOARS ER - TY - CONF TI - A statistical comparison of grammatical evolution strategies in the domain of human genetics AU - White, B.C. AU - Gilbert, J.C. AU - Reif, D.M. AU - Moore, J.H. C2 - 2005/// C3 - 2005 IEEE Congress on Evolutionary Computation, IEEE CEC 2005. Proceedings DA - 2005/// VL - 1 SP - 676-682 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-27144535907&partnerID=MN8TOARS ER - TY - JOUR TI - Combinatorial Pharmacogenetics AU - Wilke, Russell A. AU - Reif, David M. AU - Moore, Jason H. T2 - Nat Rev Drug Discov DA - 2005/11// PY - 2005/11// DO - 10.1038/nrd1874 VL - 4 IS - 11 SP - 911–918 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-27844492326&partnerID=MN8TOARS ER - TY - JOUR TI - The tortoise and the hare II: Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis AU - Shaw, J. AU - Lickey, E.B. AU - Beck, J.T. AU - Farmer, S.B. AU - Liu, W. AU - Miller, J. AU - Siripun, K.C. AU - Winder, C.T. AU - Schilling, E.E. AU - Small, R.L. T2 - American Journal of Botany AB - Chloroplast DNA sequences are a primary source of data for plant molecular systematic studies. A few key papers have provided the molecular systematics community with universal primer pairs for noncoding regions that have dominated the field, namely trnL-trnF and trnK/matK. These two regions have provided adequate information to resolve species relationships in some taxa, but often provide little resolution at low taxonomic levels. To obtain better phylogenetic resolution, sequence data from these regions are often coupled with other sequence data. Choosing an appropriate cpDNA region for phylogenetic investigation is difficult because of the scarcity of information about the tempo of evolutionary rates among different noncoding cpDNA regions. The focus of this investigation was to determine whether there is any predictable rate heterogeneity among 21 noncoding cpDNA regions identified as phylogenetically useful at low levels. To test for rate heterogeneity among the different cpDNA regions, we used three species from each of 10 groups representing eight major phylogenetic lineages of phanerogams. The results of this study clearly show that a survey using as few as three representative taxa can be predictive of the amount of phylogenetic information offered by a cpDNA region and that rate heterogeneity exists among noncoding cpDNA regions. DA - 2005/// PY - 2005/// DO - 10.3732/ajb.92.1.142 VL - 92 IS - 1 SP - 142-166 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-19944430021&partnerID=MN8TOARS ER - TY - JOUR TI - Multiple-scale landscape predictors of benthic macroinvertebrate community structure in North Carolina AU - POTTER, K AU - CUBBAGE, F AU - SCHABERG, R T2 - Landscape and Urban Planning DA - 2005/3// PY - 2005/3// DO - 10.1016/s0169-2046(04)00028-3 VL - 71 IS - 2-4 SP - 77-90 KW - nonpoint source pollution KW - aquatic ecosystems KW - Geographic Information Systems KW - landscape ecology KW - land cover KW - water quality KW - watershed management ER - TY - JOUR TI - Identification of AFLP markers linked to reduced aflatoxin accumulation in A. cardenasii-derived germplasm lines of peanut AU - Milla, S.R. AU - Isleib, T.G. AU - Tallury, S.P. T2 - Proceedings of the American Peanut Research and Education Society DA - 2005/// PY - 2005/// VL - 37 IS - 90 ER - TY - CONF TI - Identificación de marcadores moleculares asociados con resistencia al virus del bronceado del tomate (TSWV) en un mapa genético (genetic linkage map) de especies silvestres de maní (Arachis hypogaea L.) AU - Milla, S.R. AU - Isleib, T.G. AU - Stalker, H.T. AU - Tallury, S.P. C2 - 2005/// C3 - Libro de Resúmenes del IV Encuentro Científico Internacional de Invierno DA - 2005/// SP - 10 ER - TY - SOUND TI - Mejoramiento genético de maní en NCSU: uniendo métodos convencionales y técnicas moleculares AU - Milla, S.R. AU - Isleib, T.G. AU - Tallury, S.P. DA - 2005/8/5/ PY - 2005/8/5/ M3 - invited presentation ER - TY - SOUND TI - Uso de marcadores moleculares en el mejoramiento genético de maní (Arachis hypogaea L.) AU - Milla, S.R. AU - Isleib, T.G. AU - Tallury, S.P. DA - 2005/8/2/ PY - 2005/8/2/ M3 - invited presentation ER - TY - SOUND TI - Tobacco genomic improvement at N.C. State University AU - Lewis, R.S. AU - Milla, S.R. AU - Levin, J.S. AU - Wilkinson, W.C. DA - 2005/6/21/ PY - 2005/6/21/ M3 - invited presentation ER - TY - SOUND TI - Uso de marcadores moleculares en mejoramiento genético de maní AU - Milla, S.R. AU - Isleib, T.G. AU - Tallury, S.P. DA - 2005/7/30/ PY - 2005/7/30/ M3 - invited presentation ER - TY - CONF TI - Comparison of agronomic traits and disease reactions between high-oleic backcross-derived lines and their normal-oleic recurrent parents AU - Isleib, T.G. AU - Milla, S.R. AU - Copeland, S.C. AU - Graeber, J.B. C2 - 2005/// C3 - Proceedings of the American Peanut Research and Education Society DA - 2005/// VL - 37 SP - 24 ER - TY - CONF TI - Using molecular markers to investigate parentage of azaleodendron hybrids AU - Contreras, R.N. AU - Ranney, T.G. AU - Tallury, S.P. AU - Milla, S.R. C2 - 2005/// C3 - Proceedings of the Southern Nursery Association Research Conference, 50th Annual Report DA - 2005/// VL - 50 SP - 632–635 ER - TY - CONF TI - Shiloh Splash’ river birch AU - Ranney, T.G. AU - Eaker, T.A. AU - Mowrey, J.A. AU - Lynch, N.P. C2 - 2005/// C3 - Proceedings of the Southern Nursery Association Research Conference, 50th Annual Report DA - 2005/// SP - 653–655 ER - TY - CONF TI - Intergeneric hybrids between Gordonia lasianthus and Franklinia alatamaha AU - Ranney, T.G. AU - Eaker, T.A. AU - Mowrey, J.A. AU - Lynch, N.P. C2 - 2005/// C3 - Proceedings of the Southern Nursery Association Research Conference, 50th Annual Report DA - 2005/// SP - 651–652 ER - TY - CONF TI - Heritability of ornamental foliage characteristics in diploid, triploid, and tetraploid Hypericum androsaemum L AU - Olsen, R.T. AU - Ranney, T.G. AU - Werner, D.J. C2 - 2005/// C3 - Proceedings of the Southern Nursery Association Research Conference, 50th Annual Report DA - 2005/// SP - 648–650 ER - TY - JOUR TI - Two-faced cyclins with eyes on the targets AU - Archambault, V. AU - Buchler, N.E. AU - Wilmes, G.M. AU - Jacobson, M.D. AU - Cross, F.R. T2 - Cell Cycle AB - We recently reported that the 'hydrophobic patch' (HP) of the Saccharomyces cerevisiae S-phase cyclin Clb5 facilitates its interaction with Orc6 (via its Cy or RXL motif), providing a mechanism that helps prevent rereplication from individual origins. This is the first finding of a biological function for an interaction between a cyclin and a cyclin-binding motif (Cy or RXL motif) in a target protein in Saccharomyces cerevisiae. It is also the first such example involving a B-type cyclin in any organism. Yet, some of our observations as well as work from other groups suggest that HP-RXL interactions are functionally important for cyclin-Cdk signaling to other targets. The evolutionary conservation of the HP motif suggests that it allows cyclins to carry out important and specialized functions. DA - 2005/// PY - 2005/// DO - 10.4161/CC.4.1.1402 VL - 4 IS - 1 SP - 125-130 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-14844287697&partnerID=MN8TOARS KW - Clb5 KW - hydrophobic patch KW - B-type cyclin KW - RXL KW - DNA replication ER - TY - JOUR TI - Transcriptional regulation by the numbers: Models AU - Bintu, L. AU - Buchler, N.E. AU - Garcia, H.G. AU - Gerland, U. AU - Hwa, T. AU - Kondev, J. AU - Phillips, R. T2 - Current Opinion in Genetics and Development AB - The expression of genes is regularly characterized with respect to how much, how fast, when and where. Such quantitative data demands quantitative models. Thermodynamic models are based on the assumption that the level of gene expression is proportional to the equilibrium probability that RNA polymerase (RNAP) is bound to the promoter of interest. Statistical mechanics provides a framework for computing these probabilities. Within this framework, interactions of activators, repressors, helper molecules and RNAP are described by a single function, the "regulation factor". This analysis culminates in an expression for the probability of RNA polymerase binding at the promoter of interest as a function of the number of regulatory proteins in the cell. DA - 2005/// PY - 2005/// DO - 10.1016/j.gde.2005.02.007 VL - 15 IS - 2 SP - 116-124 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-15744394192&partnerID=MN8TOARS ER - TY - JOUR TI - Transcriptional regulation by the numbers: Applications AU - Bintu, L. AU - Buchler, N.E. AU - Garcia, H.G. AU - Gerland, U. AU - Hwa, T. AU - Kondev, J. AU - Kuhlman, T. AU - Phillips, R. T2 - Current Opinion in Genetics and Development AB - With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to their respective context. Thermodynamic models provide a useful framework for the quantitative analysis of bacterial transcription regulation. This framework can facilitate the quantification of vastly different forms of gene expression from several well-characterized bacterial promoters that are regulated by one or two species of transcription factors; it is useful because it requires only a few parameters. As such, it provides a compact description useful for higher-level studies (e.g. of genetic networks) without the need to invoke the biochemical details of every component. Moreover, it can be used to generate hypotheses on the likely mechanisms of transcriptional control. DA - 2005/// PY - 2005/// DO - 10.1016/j.gde.2005.02.006 VL - 15 IS - 2 SP - 125-135 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-15744387380&partnerID=MN8TOARS ER - TY - JOUR TI - Nonlinear protein degradation and the function of genetic circuits AU - Buchler, N.E. AU - Gerland, U. AU - Hwa, T. T2 - Proceedings of the National Academy of Sciences of the United States of America AB - The functions of most genetic circuits require a sufficient degree of cooperativity in the circuit components. Although mechanisms of cooperativity have been studied most extensively in the context of transcriptional initiation control, cooperativity from other processes involved in the operation of the circuits can also play important roles. In this work, we examine a simple kinetic source of cooperativity stemming from the nonlinear degradation of multimeric proteins. Ample experimental evidence suggests that protein subunits can degrade less rapidly when associated in multimeric complexes, an effect we refer to as "cooperative stability." For dimeric transcription factors, this effect leads to a concentration-dependence in the degradation rate because monomers, which are predominant at low concentrations, will be more rapidly degraded. Thus, cooperative stability can effectively widen the accessible range of protein levels in vivo. Through theoretical analysis of two exemplary genetic circuits in bacteria, we show that such an increased range is important for the robust operation of genetic circuits as well as their evolvability. Our calculations demonstrate that a few-fold difference between the degradation rate of monomers and dimers can already enhance the function of these circuits substantially. We discuss molecular mechanisms of cooperative stability and their occurrence in natural or engineered systems. Our results suggest that cooperative stability needs to be considered explicitly and characterized quantitatively in any systematic experimental or theoretical study of gene circuits. DA - 2005/// PY - 2005/// DO - 10.1073/pnas.0409553102 VL - 102 IS - 27 SP - 9559-9564 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-22144443131&partnerID=MN8TOARS KW - amplification KW - dimerization KW - bistability KW - oscillation ER - TY - ENCYC TI - Cornales AU - Xiang, Q.-Y. T2 - Encyclopedia of Life Sciences DA - 2005/5// PY - 2005/5// DO - 10.1002/9780470015902 PB - John Wiley & Sons, Ltd. ER - TY - CHAP TI - Cornaceae, Mastixiaceae, Toricelliaceae, Helwingiacaee, Aucubaceae AU - Xiang, Q.-Y. AU - Boufford, D.E. T2 - Flora of China A2 - Wu, Z.Y. A2 - Raven, P.H. PY - 2005/// VL - 14 SP - 206-234 PB - Science Press, Beijing, and Missouri botanical Garden Press, St. Louis ER - TY - JOUR TI - The power of chemical genomics to study the link between endomembrane system components and the gravitropic response AU - Surpin, M. AU - Rojas-Pierce, M. AU - Carter, C. AU - Hicks, G.R. AU - Vasquez, J. AU - Raikhel, N.V. T2 - Proceedings of the National Academy of Sciences of the United States of America AB - Chemical genomics is a powerful approach to dissect processes that may be intractable using conventional genetics because of gene lethality or redundancy. Recently, a link has been established between endomembrane trafficking and gravitropism. To understand this link, we screened a library of 10,000 diverse chemicals for compounds that affected the gravitropism of Arabidopsis seedlings positively or negatively. Sixty-nine of 219 compounds from the primary screen were retested, and 34 of these were confirmed to inhibit or enhance gravitropism. Four of the 34 compounds were found to cause aberrant endomembrane morphologies. The chemicals affected gravitropism and vacuole morphology in concert in a tissue-specific manner, underscoring the link between endomembranes and gravitropism. One of the chemicals (5403629) was structurally similar to the synthetic auxin 2,4-dichlorophenoxy acetate, whereas the other three chemicals were unique in their structures. An in vivo functional assay using the reporter beta-glucuronidase under the auxin-inducible DR5 promoter confirmed that the unique compounds were not auxins. Interestingly, one of the unique chemicals (5850247) appeared to decrease the responsiveness to auxin in roots, whereas another (5271050) was similar to pyocyanin, a bacterial metabolite that has been suggested to target the endomembranes of yeast. These reagents will be valuable for dissecting endomembrane trafficking and gravitropism and for cognate target identification. DA - 2005/// PY - 2005/// DO - 10.1073/pnas.0500222102 VL - 102 IS - 13 SP - 4902-4907 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-16344363588&partnerID=MN8TOARS KW - chemicals KW - GFP KW - gravitropism KW - trafficking KW - vacuoles ER - TY - CONF TI - Nitrogen removal from anaerobically pretreated swine wastewater in an intermittent aeration process C2 - 2005/// C3 - 2005 ASAE Annual International Meeting DA - 2005/// UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-70349157669&partnerID=MN8TOARS ER - TY - JOUR TI - High levels of nitrifying bacteria in intermittently aerated reactors treating high ammonia wastewater. AU - Mota, C. AU - Ridenoure, J. AU - Cheng, J. AU - Los Reyes, F. L. T2 - FEMS Microbiol Ecol DA - 2005/// PY - 2005/// DO - S0168-6496(05)00121-2 [pii] 10.1016/j.femsec.2005.05.001 VL - 54 IS - 3 SP - 391-400 KW - ammonia oxidizing bacteria KW - nitrite oxidizing bacteria KW - nitrification KW - oligonucleotide probes KW - intermittent aeration KW - swine wastewater ER - TY - JOUR TI - Effects of aeration cycles on nitrifying bacterial populations and nitrogen removal in intermittently aerated reactors. AU - Mota, C. AU - Head, M. A. AU - Ridenoure, J. A. AU - Cheng, J. J. AU - Los Reyes, F. L. T2 - Appl Environ Microbiol DA - 2005/// PY - 2005/// DO - 71/12/8565 [pii] 10.1128/AEM.71.12.8565-8572.2005 VL - 71 IS - 12 SP - 8565-72 ER - TY - JOUR TI - Effects of aeration cycles on nitrifying bacterial populations and nitrogen removal in intermittently aerated reactors T2 - Applied and Environmental Microbiology AB - ABSTRACT The effects of the lengths of aeration and nonaeration periods on nitrogen removal and the nitrifying bacterial community structure were assessed in intermittently aerated (IA) reactors treating digested swine wastewater. Five IA reactors were operated in parallel with different aeration-to-nonaeration time ratios (ANA). Populations of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were monitored using 16S rRNA slot blot hybridizations. AOB species diversity was assessed using amoA gene denaturant gradient gel electrophoresis. Nitrosomonas and Nitrosococcus mobilis were the dominant AOB and Nitrospira spp. were the dominant NOB in all reactors, although Nitrosospira and Nitrobacter were also detected at lower levels. Reactors operated with the shortest aeration time (30 min) showed the highest Nitrosospira rRNA levels, and reactors operated with the longest anoxic periods (3 and 4 h) showed the lowest levels of Nitrobacter , compared to the other reactors. Nitrosomonas sp. strain Nm107 was detected in all reactors, regardless of the reactor's performance. Close relatives of Nitrosomonas europaea , Nitrosomonas sp. strain ENI-11, and Nitrosospira multiformis were occasionally detected in all reactors. Biomass fractions of AOB and effluent ammonia concentrations were not significantly different among the reactors. NOB were more sensitive than AOB to long nonaeration periods, as nitrite accumulation and lower total NOB rRNA levels were observed for an ANA of 1 h:4 h. The reactor with the longest nonaeration time of 4 h performed partial nitrification, followed by denitrification via nitrite, whereas the other reactors removed nitrogen through traditional nitrification and denitrification via nitrate. Superior ammonia removal efficiencies were not associated with levels of specific AOB species or with higher AOB species diversity. DA - 2005/// PY - 2005/// DO - 10.1128/AEM.71.12.8565-8572.2005 VL - 71 IS - 12 SP - 8565-8572 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-29144451509&partnerID=MN8TOARS ER - TY - JOUR TI - Changes in the rRNA levels of specific microbial groups in activated sludge during sample handling and storage. AU - Keith, J. E. AU - Boyer, J. G. AU - Reyes, F. L. T2 - Lett Appl Microbiol DA - 2005/// PY - 2005/// DO - LAM1745 [pii] 10.1111/j.1472-765X.2005.01745.x VL - 41 IS - 2 SP - 208-15 KW - 16S rRNA KW - membrane hybridization KW - oligonucleotide probe hybridization KW - postsampling conditions ER - TY - JOUR TI - WHAT DO FILAMENTS LIKE TO EAT? USING DGGE AND FISH TO TEST THE EFFECT OF CARBON SOURCE AND SEED SLUDGE ON FILAMENTOUS GROWTH IN ACTIVATED SLUDGE AU - Gulez, Gamze AU - Reyes, Francis L. T2 - proc water environ fed AB - WHAT DO FILAMENTS LIKE TO EAT? USING DGGE AND FISH TO TEST THE EFFECT OF CARBON SOURCE AND SEED SLUDGE ON FILAMENTOUS GROWTH IN ACTIVATED SLUDGEThe effects of eight carbon sources and three inoculum sources on the growth of filamentous bacteria were tested in lab scale sequencing batch reactors. Microscopic (Gram and Neisser staining) and molecular methods (Denaturing Gradient Gel Electrophoresis [DGGE], Fluorescent in Situ Hybridization [FISH]) were used to track the microbial population changes in the reactors. Sludge volume index (SVI)...Author(s)Gamze GulezFrancis L. de los ReyesSourceProceedings of the Water Environment FederationSubjectSession 71: Leading Edge Research: Activated Sludge: Molecular MethodsDocument typeConference PaperPublisherWater Environment FederationPrint publication date Jan, 2005ISSN1938-6478SICI1938-6478(20050101)2005:9L.5890;1-DOI10.2175/193864705783815005Volume / Issue2005 / 9Content sourceWEFTECFirst / last page(s)5890 - 5900Copyright2005Word count213 DA - 2005/1/1/ PY - 2005/1/1/ DO - 10.2175/193864705783815005 VL - 2005 IS - 9 SP - 5890-5900 ER - TY - JOUR TI - Molecular Methods in Biological Systems AU - Angenent, Largus T. AU - Reyes, Francis L. AU - Oerther, Daniel B. AU - Mcmahon, Katherine D. T2 - water environ res AB - Water Environment ResearchVolume 77, Issue 6 p. 718-779 Monitoring and MeasurementFree Access Molecular Methods in Biological Systems Largus T. Angenent, Largus T. AngenentSearch for more papers by this authorFrancis L. de los Reyes III, Francis L. de los Reyes IIISearch for more papers by this authorDaniel B. Oerther, Daniel B. OertherSearch for more papers by this authorKatherine D. McMahon, Katherine D. McMahonSearch for more papers by this author Largus T. Angenent, Largus T. AngenentSearch for more papers by this authorFrancis L. de los Reyes III, Francis L. de los Reyes IIISearch for more papers by this authorDaniel B. Oerther, Daniel B. OertherSearch for more papers by this authorKatherine D. McMahon, Katherine D. McMahonSearch for more papers by this author First published: 01 October 2005 https://doi.org/10.2175/106143005X54344AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat Volume77, Issue62005 Literature ReviewSeptember-October 2005Pages 718-779 RelatedInformation DA - 2005/10/1/ PY - 2005/10/1/ DO - 10.2175/106143005x54344 VL - 77 IS - 6 SP - 718-779 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84904252096&partnerID=MN8TOARS ER - TY - JOUR TI - The title-page: Its early development, 1460-1510 [Review] AU - Orcutt, D. T2 - Library Resources & Technical Services DA - 2005/1// PY - 2005/1// VL - 49 IS - 1 SP - 67 ER - TY - JOUR TI - Historical dictionary of Jainism [Review] AU - Orcutt, D. T2 - Choice DA - 2005/1// PY - 2005/1// VL - 42 IS - 5 SP - 828 ER - TY - JOUR TI - Dialogue on the Internet: Language, civic identity, and computer-mediated communication [Review] AU - Orcutt, D. T2 - Choice DA - 2005/1// PY - 2005/1// VL - 42 IS - 9 SP - 1580 ER - TY - SOUND TI - Genetics of early blight resistance in tomato AU - Sharma, A. AU - Ashrafi, H. AU - Foolad, M.R. DA - 2005/1/15/ PY - 2005/1/15/ M3 - poster N1 - Abstract published in the Proceedings for the meeting, p. 191 RN - Abstract published in the Proceedings for the meeting, p. 191 ER - TY - SOUND TI - Genetic mapping of candidate resistance genes in tomato using an F2 and a RIL population of a Lycopersicon esculentum × L. pimpinellifolium cross AU - Ashrafi, H. AU - Sharma, A. AU - Niño-Liu, D. AU - Foolad, M.R. DA - 2005/3/16/ PY - 2005/3/16/ ER - TY - SOUND TI - Comparative mapping of early blight resistance QTLs and candidate resistance genes in F2, F3, F4 and a RIL population of Tomato AU - Ashrafi, H. AU - Sharma, A. AU - Niño-Liu, D. AU - Zhang, L. AU - Foolad, M.R. DA - 2005/// PY - 2005/// M3 - poster ER - TY - JOUR TI - Genetics and Breeding of Early Blight Resistance in Tomato AU - Foolad, M.R. AU - Sharma, A. AU - Ashrafi, H. AU - Lin, G. T2 - HortScience DA - 2005/// PY - 2005/// VL - 40 SP - 1114–1114 ER - TY - JOUR TI - (13) Comparative Mapping of Early Blight Resistance QTLs and Candidate Resistance Genes in F2, F3, F4 and a RIL Population of Tomato AU - Ashrafi, H. AU - Sharma, A. AU - Niño-Liu, D. AU - Zhang, L. AU - Foolad, M. T2 - HortScience DA - 2005/// PY - 2005/// VL - 40 IS - 4 SP - 1040 ER - TY - CHAP TI - Agricultural Biotechnology Science Compromised AU - Worthy, K. A. AU - Strohman, R. C. AU - Billings, P. R. AU - Delborne, J. A. AU - Duarte-Trattner, E. AU - Gove, N. AU - Latham, D. R. AU - Manahan, Carol M. T2 - Controversies in Science and Technology: From Maize to Menopause A2 - Daniel Lee Kleinman, Abby J. Kinchy A2 - Handelsman, Jo PY - 2005/// SP - 135-49 PB - Madison, Wis. : University of Wisconsin Press SN - 0299203905 ER - TY - JOUR TI - Integrating cell-level kinetic modeling into the design of engineered protein therapeutics AU - Rao, BM AU - Lauffenburger, DA AU - Wittrup, KD T2 - NATURE BIOTECHNOLOGY DA - 2005/2// PY - 2005/2// DO - 10.1038/nbt1064 VL - 23 IS - 2 SP - 191-194 SN - 1546-1696 ER - TY - JOUR TI - Engineering protein therapeutics within a systems-level computational context AU - Rao, B.M. AU - Lauffenburger, D. A. AU - Wittrup, K. D. T2 - Nature Biotechnology DA - 2005/// PY - 2005/// VL - 23 IS - 2 SP - 191-194 ER - TY - JOUR TI - Culture development for human embryonic stem cell propagation: molecular aspects and challenges AU - Rao, BM AU - Zandstra, PW T2 - CURRENT OPINION IN BIOTECHNOLOGY AB - Basic fibroblast growth factor and members of the transforming growth factor-β superfamily are important regulators of human embryonic stem cell (hESC) self-renewal. Extensive cross-talk between the intracellular signaling pathways activated by these factors contributes to maintenance of the undifferentiated hESC state. Understanding the molecular regulation of hESC self-renewal will facilitate the design of improved systems for hESC propagation and provide a foundation for strategies to direct the differentiation of hESCs to clinically relevant cell types. DA - 2005/10// PY - 2005/10// DO - 10.1016/j.copbio.2005.08.001 VL - 16 IS - 5 SP - 568-576 SN - 1879-0429 ER - TY - CONF TI - Seedling resistance to Phytophthora cinammomi in the Genus Abies AU - Frampton, J. AU - Benson, D. M. AU - Li, J. AU - Brahan, A. M. AU - Hudson, E. E. AU - Potter, K. M. C2 - 2005/// C3 - Proceedings of the 28th Southern Forest Tree Improvement Conference DA - 2005/// SP - 146-147 ER - TY - CONF TI - Impacts of balsam woolly adelgid on the Southern Appalachian spruce-fir ecosystem and the North Carolina Christmas Tree Industry AU - Potter, K. AU - Frampton, J. AU - Sidebottom, J. C2 - 2005/// C3 - Third Symposium on Hemlock Woolly Adelgid in the Eastern United States, February 1-3, 2005, Renaissance Asheville Hotel, Asheville, North Carolina DA - 2005/// SP - 25-41 PB - USFS Forest Health Technology Enterprise Team ER - TY - CONF TI - Fraser fir population size and pollen dispersal: a landscape genetics model AU - Potter, K. M. AU - Frampton, J. AU - Potter, K. AU - Hess, G. R. C2 - 2005/// C3 - 20th Annual Symposium for the US Regional Chapter of the International Association for Landscape Ecology DA - 2005/// ER - TY - CONF TI - An ex situ gene conservation plan for Fraser fir AU - Potter, K. M. AU - Frampton, J. C2 - 2005/// C3 - Proceedings of the 28th Southern Forest Tree Improvement Conference DA - 2005/// SP - 148-159 ER - TY - CONF TI - Variation of a-cellulose content and related metabolites during wood formation in loblolly pine AU - Morris, C. R. AU - Goldfarb, B. AU - Isik, F. AU - Li, C. S. AU - Chang, H.-M. AU - Sederoff, R. AU - Kadla, J. F. C2 - 2005/// C3 - 13th ISWFPC Proceedings DA - 2005/// VL - 13 ER - TY - JOUR TI - Genotypic selectivity of test environments on different ecological zones AU - Isik, K. AU - Isik, F. AU - Kurt, Y. AU - Semiz, G. T2 - 10th European Ecological Congress DA - 2005/// PY - 2005/// VL - 10 ER - TY - CONF TI - Genetic variation in MFA, MOE and wood density among clones of Pinus taeda L. AU - Isik, F. AU - Li, B. AU - Goldfarb, B. C2 - 2005/// C3 - 28th Southern Forest Tree Improvement Conference DA - 2005/// VL - 28 ER - TY - JOUR TI - Genetic improvement of Virginia pine (Pinus virginiana Mill.) for Christmas tree production AU - Frampton, J. AU - Isik, F. T2 - Forest Genetics DA - 2005/// PY - 2005/// VL - 11 SP - 137-147 ER - TY - CONF TI - Total inside-bark volume estimation for loblolly pine (Pinus taeda L.) in genetic trials AU - Sherrill, J. R. AU - Mullin, T. J. AU - Bullock, B. P. AU - McKeand, S. E. AU - Purnell, R. C. AU - Gumpertz, M. L. C2 - 2005/// C3 - Proceedings of the 28th Southern Forest Tree Improvement Conference DA - 2005/// SP - 123-125 ER - TY - JOUR TI - Forest genetics and tree breeding in the age of genomics--IUFRO Conference AU - Li, B. AU - McKeand, S. E. T2 - Forest Genetics DA - 2005/// PY - 2005/// VL - 12 IS - 2 SP - 141-143 ER - TY - CONF TI - Comparing parameter estimation techniques for diameter distributions of loblolly pine AU - Smith, B. C. AU - Bullock, B. P. AU - McKeand, S. E. C2 - 2005/// C3 - Proceedings of the 28th Southern Forest Tree Improvement Conference DA - 2005/// SP - 104-106 ER - TY - CONF TI - Genetic variation in young Fraser fir progeny tests AU - Emerson, J. L. AU - Frampton, L. J. AU - McKeand, S. E. C2 - 2005/// C3 - Proceedings of the 28th Southern Forest Tree Improvement Conference DA - 2005/// SP - 115-117 ER - TY - JOUR TI - Comparison of individual and pooled sampling methods for detecting bacterial pathogens of fish AU - Mumford, S AU - Patterson, C AU - Evered, J AU - Brunson, R AU - Levine, J AU - Winton, J T2 - JOURNAL OF VETERINARY DIAGNOSTIC INVESTIGATION AB - Examination of finfish populations for viral and bacterial pathogens is an important component of fish disease control programs worldwide. Two methods are commonly used for collecting tissue samples for bacteriological culture, the currently accepted standards for detection of bacterial fish pathogens. The method specified in the Office International des Epizooties Manual of Diagnostic Tests for Aquatic Animals permits combining renal and splenic tissues from as many as 5 fish into pooled samples. The American Fisheries Society (AFS) Blue Book/US Fish and Wildlife Service (USFWS) Inspection Manual specifies the use of a bacteriological loop for collecting samples from the kidney of individual fish. An alternative would be to more fully utilize the pooled samples taken for virology. If implemented, this approach would provide substantial savings in labor and materials. To compare the relative performance of the AFS/USFWS method and this alternative approach, cultures of Yersinia ruckeri were used to establish low-level infections in groups of rainbow trout (Oncorhynchus mykiss) that were sampled by both methods. Yersinia ruckeri was cultured from 22 of 37 groups by at least 1 method. The loop method yielded 18 positive groups, with 1 group positive in the loop samples but negative in the pooled samples. The pooled samples produced 21 positive groups, with 4 groups positive in the pooled samples but negative in the loop samples. There was statistically significant agreement (Spearman coefficient 0.80, P < 0.001) in the relative ability of the 2 sampling methods to permit detection of low-level bacterial infections of rainbow trout. DA - 2005/7// PY - 2005/7// DO - 10.1177/104063870501700401 VL - 17 IS - 4 SP - 305-310 SN - 1943-4936 KW - bacteria KW - disease KW - fish KW - pooling KW - sampling KW - trout KW - Yersinia ER - TY - JOUR TI - The Southeastern U.S. fusarium head blight epidemic of 2003 AU - Cowger, Christina AU - Sutton, A. L. T2 - Plant Health Progress AB - Fusarium head blight (FHB) caused unprecedented losses to southeastern U.S. wheat producers and millers in 2003. The epidemic was documented afterward through interviews with 120 researchers, extension agents, millers, and growers. Sixty-two counties in five states were assigned an FHB impact score of 1 to 4, and 2003 yield and weather data were obtained for those counties. The relationships of yield and pre- and post-flowering weather variables to impact score were evaluated using regression and correlation analyses. Yield as a percentage of the 10-year average was negatively correlated with FHB impact (r = -0.588, P < 0.0001). FHB impact was positively correlated with hours of post-flowering rainfall (r = 0.465, 0.590, and 0.619 for 10, 20, and 30 days post-flowering, respectively; P = 0.0001), but not correlated with hours of pre-flowering rainfall (P = 0.99). While this was not a controlled study, the results suggest that pre-flowering weather may have played a less significant role than post-flowering weather, and was unlikely to have been a good predictor of FHB severity in the southeast in 2003. Using 10-year average production data, premilling economic losses were estimated for 40 counties in Maryland, Virginia, and North Carolina at over $13.6 million. Wheat production in those counties comprised just 71.7%, 45.8%, and 48.0% of the statewide totals, respectively; thus, actual 2003 FHB-related losses to growers in those states were probably much higher. Additionally, mills in the region suffered losses of several million dollars in 2003 due to increased shipping, testing, and handling costs brought on by FHB. Accepted for publication 26 September 2005. Published 26 October 2005. DA - 2005/// PY - 2005/// DO - 10.1094/php-2005-1026-01-rs SP - 1 ER - TY - JOUR TI - Bartonella henselae and Rickettsia seroreactivity in a sick cat population from North Carolina AU - Breitschwerdt, E. B. AU - Levine, J. F. AU - Radulovic, S. AU - Hanby, S. B. AU - Kordick, D. L. AU - Perle, K. M. D. la T2 - International Journal of Applied Research in Veterinary Medicine DA - 2005/// PY - 2005/// VL - 3 IS - 4 SP - 287 ER - TY - JOUR TI - The impact of transgenic cottons expressing one or two proteins from Bacillus thuringiensis on survival and damage potential of first and second instars of Ostrinia nubilalis (Lepidoptera: Crambidae) AU - Jackson, R. E. AU - Mahaffey, J. S. AU - Bradley, J. R., Jr. AU - Van Duyn, J. W. AU - Sorenson, C. E. T2 - Journal of Cotton Science (Online) DA - 2005/// PY - 2005/// VL - 9 IS - 4 SP - 199 ER - TY - JOUR TI - Genomic Perspectives on Probiotic Lactic Acid Bacteria AU - Klaenhammer, Todd R. AU - Peril, Andrea Azcarate AU - Barrangou, Rodolphe AU - Duong, Tri AU - Altermann, Eric T2 - Bioscience and Microflora AB - The lactic acid bacteria are Gram-positive fermentative microorganisms known primarily for their roles as starter cultures and probiotics. The food industry represents one of the largest manufacturing industries in the world and recent trends are rapidly expanding the use of probiotic cultures within functional foods. Understanding and control of lactic acid bacteria is now being revolutionized by genomic sciences and the appearance of the complete genome sequences for Bifidobacterium longum, Lactobacillus johnsonii, Lactobacillus plantarum, and draft sequences for Lactobacillus gasseri and Lactobacillus casei. This explosion of DNA sequence information, accompanied by the development of bioinformatic tools for nucleic acid and protein analysis, now allows rapid characterization of the lactic acid bacteria for their genomic content and expression profiles across the entire genome. Comparative genomics has already revealed important similarities and differences in strains, species, and genera and will likely identify key genetic features responsible for the beneficial properties ascribed to probiotic lactic acid bacteria. Practical genomics for the lactic acid bacteria promises to establish the genetic landscape, correlate genotypes with desirable phenotypes, establish genetic criteria for strain selection, improve culture stability by stress preconditioning, provide opportunities for metabolic engineering, and uncover a mechanistic basis for the beneficial activities of probiotics when delivered in various foods. This presentation will examine the genomic content of probiotic Lactobacillus cultures, compared to those lactic acid bacterial genomes that have appeared recently. In addition, expression profiling by whole genome microarrays will be used to illustrate how environmental conditions encountered during biomanufacturing, fermentation, and the gastrointestinal tract can impact gene expression and culture functionality. DA - 2005/// PY - 2005/// DO - 10.12938/bifidus.24.31 VL - 24 IS - 2 SP - 31-33 ER - TY - JOUR TI - Genetic variation among Rhizoctonia solani isolates from warm-season turfgrasses AU - Li, J. F. AU - Martin, S. B. AU - Jeffers, S. N. AU - Dean, R. A. AU - Camberato, J. J. T2 - International Turfgrass Society Research Journal DA - 2005/// PY - 2005/// VL - 10 SP - 230 ER - TY - JOUR TI - Historical dictionary of Jainism [Review] AU - Orcutt, Darby T2 - Choice AB - 1 Editor's Foreword 2 Preface 3 Jain Scriptures 4 Reader's Notes 5 Map of Major Jain Sites in India 6 Chronology 7 Introduction 8 The Dictionary 9 Appendix *The Fourteen Gunasthanas*The Eleven Pratimas*The Jain Festival Calendar*Tirthankaras Cognizances*Tirthankaras' Birth and Nirvana Sites*Tirthankaras' Yaksas and Yaksis 10 Bibliography 11 About the Author DA - 2005/// PY - 2005/// DO - 10.5860/choice.42-2549 VL - 42 IS - 5 SP - 828 ER - TY - JOUR TI - Dialogue on the Internet: Language, civic identity, and computer-mediated communication [Review] AU - Orcutt, Darby T2 - Choice AB - Introduction: The World in the Post and the Page The Development of Dialogism: An Exploration of Major Influence E-Mail Discussion Messages: A Means for Constructing Civic Identity Websites as Means for Propagating Civic, Political, and Ideological Concepts Conclusion References Cited Index DA - 2005/// PY - 2005/// DO - 10.5860/choice.42-5071 VL - 42 IS - 9 SP - 1580 ER - TY - JOUR TI - Long-term night chilling of cotton (Gossypium hirsutum) does not result in reduced CO2 assimilation AU - Singh, B AU - Haley, L AU - Nightengale, J AU - Kang, WH AU - Haigler, CH AU - Holaday, AS T2 - FUNCTIONAL PLANT BIOLOGY AB - The aim of this study was to characterise the response of CO2 assimilation (A) of cotton (Gossypium hirsutum L.) to short- and long-term exposures to night chilling. We hypothesised that short-term exposures to night chilling would induce reductions in gs and, therefore, A during the following days, while growth of cotton plants for several weeks in cool night conditions would cause elevated leaf carbohydrate content, leading to the down-regulation of the capacity for A. Transferring warm-grown seedlings of wild type cotton, transgenic cotton with elevated sucrose-phosphate synthase activity (SPS+) that might produce and export more sucrose from the leaf, and a segregating null to cool nights (9°C minimum) for 1 or 2 d caused a small reduction in A (12%) and gs (21-50%) measured at 28°C. Internal CO2 did not change, suggesting some biochemical restriction of A along with a gs restriction. After 30 d, new leaves that developed in cool nights exhibited acclimation of A and partial acclimation of gs. Despite the elevated leaf carbohydrate content when plants were grown to maturity with night chilling, no reduction in A, gs, carboxylation capacity, electron transport capacity, or triose-phosphate utilisation capacity occurred. Instead, growth in cool nights tended to retard the diminishing of photosynthetic parameters and gs for aging stem and subtending leaves. However, elevated SPS activity did not affect any photosynthetic parameters. Therefore, when cotton that is well fertilised with nitrogen is grown with continuous night chilling, photosynthesis should not be negatively affected. However, an occasional exposure to cool nights could result in a small reduction in A and gs for leaves that have developed in warm night conditions. DA - 2005/// PY - 2005/// DO - 10.1071/FP05018 VL - 32 IS - 7 SP - 655-666 SN - 1445-4416 KW - carbohydrates KW - cotton KW - night chilling KW - photosynthesis KW - sucrose-phosphate synthase ER - TY - BOOK TI - Nanotechnology for the forest products industry: Vision and technology roadmap AU - Atalla, R. AU - Beecher, J. AU - Caron, B. AU - Catchmark, J. AU - Deng, Y. AU - Glasser, W. AU - Gray, D. AU - Haigler, Candace H. AU - Jones, P. AU - Joyce, M. AU - Kohlman, J. AU - Koukoulas, A. AU - Lancaster, P. AU - Perine, L. AU - Rodriguez, A. AU - Ragauskas, A. AU - Wegner, T. AU - Zhu, J. AB - A roadmap for Nanotechnology in the Forest Products Industries has been developed under the umbrella of the Agenda 2020 program overseen by the CTO committee. It is expected that the use of new analytical techniques and methodologies will allow us to understand the complex nature of wood based materials and allow the dramatically enhanced use of the major strategic asset the US has in renewable, recyclable resources based on its well managed Forests. DA - 2005/// PY - 2005/// DO - 10.2172/1218797 PB - Madison, WI: USDA Forest Products Laboratory SN - 1595100873 ER - TY - JOUR TI - Verification of QTL linked markers for propagation traits in Eucalyptus AU - Marques, C. M. AU - Carocha, V. J. AU - Sa, A. R. Pereira AU - Oliveira, M. R. AU - Pires, A. M. AU - Sederoff, R. AU - Borralho, N. M. G. T2 - TREE GENETICS & GENOMES DA - 2005/11// PY - 2005/11// DO - 10.1007/s11295-005-0013-1 VL - 1 IS - 3 SP - 103-108 SN - 1614-2950 KW - Eucalyptus KW - AFLP KW - QTL verification KW - vegetative propagation KW - marker-aided selection ER - TY - JOUR TI - NSAIDs AU - Blikslager, A AU - Jones, S T2 - JOURNAL OF EQUINE VETERINARY SCIENCE AB - Objective pain assessment is important to guide and tailor therapy in clinical practice. This study describes the clinical applicability and validity of two pain scales, the Composite Pain Scale (CPS) and the Equine Utrecht University Scale for Facial Assessment of Pain (EQUUS-FAP) in horses with orthopaedic trauma or after orthopaedic surgery. A cohort follow-up study was performed using 77 adult horses (n = 43 with orthopaedic trauma or injury; n = 34 controls). Composite and facial expression-based pain scores were assessed by direct observations of pairs of two independent observers. All horses were assessed at arrival, and on the first and second day after arrival or after surgery.Both CPS and EQUUS-FAP scores demonstrated high inter-observer reliability (Crohnbach’s alpha = 0.97 for CPS; Crohnbach’s alpha = 0.93 for EQUUS-FAP; P < 0.001), with low bias (0.07 and −0.08 respectively) and limits of agreement of −1.9 to 1.9 for CPS and −1.9 to 1.9 for EQUUS-FAP. Both CPS and EQUUS-FAP scores showed significant differences between control horses and orthopaedic cases (P < 0.001). Trauma cases had significantly higher pain scores compared to postoperative cases for both CPS (P < 0.05) and for EQUUS-FAP (P < 0.01) and both pain scores significantly decreased after nonsteroidal anti-inflammatory drug (NSAID) administration. In accordance with the findings in other types of equine pain, the CPS and FAP proved useful and valid for objective and repeatable assessment of pain in horses with orthopaedic trauma or after orthopaedic surgery. This can further aid treatment of horses in clinical practice and might improve equine welfare. DA - 2005/3// PY - 2005/3// DO - 10.1016/j.jevs.2005.02.004 VL - 25 IS - 3 SP - 98-102 SN - 0737-0806 ER - TY - JOUR TI - Molecular characterization of Listeria monocytogenes of the serotype 4b complex (4b, 4d, 4e) from two turkey processing plants AU - Eifert, J. D. AU - Curtis, P. A. AU - Bazaco, M. C. AU - Meinersmann, R. J. AU - Berrang, M. E. AU - Kernodle, S. AU - Stam, C. AU - Jaykus, L. -A. AU - Kathariou, S. T2 - FOODBORNE PATHOGENS AND DISEASE AB - Most foodborne outbreaks of listeriosis have been found to involve a small number of closely related strains of Listeria monocytogenes serotype 4b. The ecology of these organisms and their reservoirs in nature or in the processing plant environment, however, remain poorly understood. Surveys of environmental samples from two turkey processing plants in the United States indicated presence of L. monocytogenes of the serotype 4b complex (serotype 4b and the closely related serotypes 4d and 4e). In addition, environmental and raw product samples from one plant repeatedly yielded isolates with genetic markers typical of two major serotype 4b epidemic clonal groups, ECI and ECII. The pulsed field gel electrophoresis (PFGE) profiles of these isolates, however, were clearly distinct from those of confirmed epidemic-associated strains. Furthermore, we observed minor but consistent differences in PFGE profiles of isolates that harbored ECI- or ECII-specific genetic markers, and that were obtained at different sampling times from the same plant. The findings suggest processing plant persistence (or repeated introductions) and genomic diversification of L. monocytogenes serotype 4b isolates that harbor ECI- or ECII-specific genetic markers. Such diversification would need to be taken into consideration in further efforts to elucidate the evolution and epidemiology of these organisms. DA - 2005/// PY - 2005/// DO - 10.1089/fpd.2005.2.192 VL - 2 IS - 3 SP - 192-200 SN - 1556-7125 ER - TY - PAT TI - Compositions for fracturing subterranean formations AU - Kelly, R. M. AU - Khan, S. A. AU - Leduc, P. AU - Tayal, A. AU - Prud'homme, R. K. C2 - 2005/// DA - 2005/// PY - 2005/// ER - TY - JOUR TI - Taxonomy of the Gonolobus complex (Apocynaceae - Asclepiadoideae) in the southeastern US: ISSR evidence and parsimony analysis AU - Krings, A. AU - Xiang, Qiu-Yun T2 - Harvard Papers in Botany AB - In a recent morphometric analysis of the Gonolobus complex (subgenus Gonolobus) in the southeastern United States, we found former specific concepts untenable as stated, as the diagnostic characters could not consistently assign individuals to one of two groups. However, our analysis showed a strong geographical component to the distribution of individuals delimited by uniformly and multicolored corollas, which we used as a basis for suggesting that two entities do appear to exist in the Southeast that may deserve recognition at some taxonomic rank. In the present study, we performed analysis of Inter-Simple Sequence Repeats (ISSR) to assess whether the two entities are genetically differentiated and, if so, to what level. We also conducted a cladistic analysis of morphological characters of the subgenus to determine whether the entities emerge as closest relatives. Our ISSR results showed substantial genetic differentiation at 18 loci between the two entities, although no fixed differences between them were detected. At 7 loci, the frequencies of band presence are significantly higher in the multicolored corolla group (MCCG) than in the uniformly colored corolla group (UCCG). At 11 loci they are significantly higher in the UCCG. Nineteen bands are unique to the MCCG, although at various frequencies (3.5–39.0%), whereas only a single band is unique to the UCCG, suggesting that the latter possesses a subset of the MCCG gene pool and is likely a derivative of it. Analysis of 61 parsimony-informative characters using Neighbor-Joining (NJ) and Unweighted Pair-Group Method using Arithmetic means (UPGMA) did not resolve the two groups, consistent with the view of a single species. In a parsimony analysis of morphological characters of 14 species of the subgenus, the two groups consistently appear as closest relatives. This evidence indicates that the complex represents a single evolutionary lineage with two incompletely differentiated morphological subgroups. On the basis of these results, we propose to treat the MCCG and UCCG as two varieties of Gonolobus suberosus. Gonolobus granulatus Scheele is neotypified in association with the required new combination for the UCCG variety. A key to the infraspecific taxa is provided. DA - 2005/// PY - 2005/// DO - 10.3100/1043-4534(2005)10[147:totgca]2.0.co;2 VL - 10 SP - 147–159 ER - TY - JOUR TI - A trichloroacetic acid-acetone method greatly reduces infrared autofluorescence of protein extracts from plant tissue AU - Shultz, RW AU - Settlage, SB AU - Hanley-Bowdoin, L AU - Thompson, WF T2 - PLANT MOLECULAR BIOLOGY REPORTER DA - 2005/12// PY - 2005/12// DO - 10.1007/BF02788888 VL - 23 IS - 4 SP - 405-409 SN - 0735-9640 KW - Arabidopsis KW - autofluorescence KW - immunoblot KW - infrared KW - Odyssey KW - plant ER - TY - JOUR TI - Strain persistence and fluctuation of multiple-antibiotic resistant Campylobacter coli colonizing turkeys over successive production cycles AU - Lee, Bong Choon AU - Reimers, Nancy AU - Barnes, H. John AU - D'Lima, Carol AU - Carver, Donna AU - Kathariou, Sophia T2 - FOODBORNE PATHOGENS AND DISEASE AB - The dynamics of colonization of turkeys by thermophilic campylobacters that are resistant to multiple antibiotics is poorly understood. In this study, we monitored cecal colonization of turkeys by Campylobacter over three successive production cycles at the same farm. Campylobacter isolated from the ceca was predominantly C. coli in all three flocks. Isolates with two distinct fla types that represented a single clonal group based on pulsed-field gel electrophoresis and that were resistant to multiple antibiotics (tetracycline, streptomycin, ampicillin, erythromycin, kanamycin, nalidixic acid, and ciprofloxacin) predominated throughout the three production cycles. The relative prevalence of each fla type, however, varied significantly from one flock to the next. The repeated isolation of these multiresistant C. coli from successive flocks likely reflected persistence of the organisms in currently unknown reservoirs in the production environment or, alternatively, repeated introduction events followed by establishment of these bacteria in each successive flock. DA - 2005/// PY - 2005/// DO - 10.1089/fpd.2005.2.103 VL - 2 IS - 1 SP - 103-110 SN - 1556-7125 ER - TY - JOUR TI - Genotypes and Antibiotic Resistance ofSalmonellaNewport Isolates from U.S. Market Oysters AU - Brands, Danielle A. AU - Billington, Stephen J. AU - Levine, Jay F. AU - Joens, Lynn A. T2 - Foodborne Pathogens and Disease AB - The consumption of raw oysters contributes to food-borne diseases such as salmonellosis. Prevalence studies in our laboratory have shown that Salmonella spp. were present in 7.4% of U.S. market oysters, with the majority (78/101) of isolates being of the Salmonella enterica Newport serovar. E-tests were performed to assess the susceptibility of the S. Newport oyster isolates to antibiotics used for treatment of Salmonella infections. The oyster isolates were susceptible to Gentamicin, Trimethoprim/Sulphamethoxazole, and Ciprofloxacin, while for the most part they were resistant to Ampicillin and Tetracycline. Consistent with the uniform antibiotic susceptibility profile of these isolates, only three pulsed-field gel electrophoresis (PFGE) profiles were identified among the isolates. Of these three profiles, one was present in 63 of the 78 isolates, indicating not only the presence of S. Newport in oysters, but the predominance of a single PFGE type. DA - 2005/3// PY - 2005/3// DO - 10.1089/fpd.2005.2.111 VL - 2 IS - 1 SP - 111-114 J2 - Foodborne Pathogens and Disease LA - en OP - SN - 1535-3141 1556-7125 UR - http://dx.doi.org/10.1089/fpd.2005.2.111 DB - Crossref ER - TY - JOUR TI - Velocity of spread of wheat stripe rust epidemics AU - Cowger, Christina AU - Wallace, L. R. D. AU - Mundt, C. C. T2 - Phytopathology DA - 2005/// PY - 2005/// DO - 10.1094/PHYTO.95-0972 VL - 95 IS - 9 SP - 972–982 ER - TY - JOUR TI - The onset of bioconvection in a suspension of negatively geotactic microorganisms with high-frequency vertical vibration AU - Kuznetsov, A T2 - INTERNATIONAL COMMUNICATIONS IN HEAT AND MASS TRANSFER AB - The effect of vertical vibration on the stability of a dilute suspension of negatively geotactic microorganisms in a fluid layer of finite depth is investigated. For the case of high-frequency vibration, solutions of governing equations are decomposed into two components: one which varies slowly with time and a second which varies rapidly with time. An averaging method is utilized to derive the equations describing the mean flow. Linear stability analysis is used to investigate stability of the obtained averaged equations. DA - 2005/10// PY - 2005/10// DO - 10.1016/j.icheatmasstransfer.2005.05.004 VL - 32 IS - 9 SP - 1119-1127 SN - 1879-0178 KW - vertical vibration KW - negatively geotactic microorganisms KW - stability KW - averaging method ER - TY - JOUR TI - Substrate uptake tests and quantitative FISH show differences in kinetic growth of bulking and non-bulking activated sludge AU - Lou, I AU - Reyes, FL T2 - BIOTECHNOLOGY AND BIOENGINEERING AB - Abstract The competition between filaments and floc formers in activated sludge has been historically described using kinetic selection. However, recent studies have suggested that bacterial storage may also be an important factor in microbial selection, since the dynamic nature of substrate flows into wastewater treatment plants elicit transient responses from microorganisms. Respirometry‐based kinetic selection should thus be reevaluated by considering cell storage, and a more reliable method should be developed to include bacterial storage in the analysis of growth of filaments and floc formers in activated sludge. In this study, we applied substrate uptake tests combined with metabolic modeling to determine the growth rates, yields and maintenance coefficients of bulking and non‐bulking activated sludge developed in lab scale reactors under feast and famine conditions. The results of quantitative fluorescence in situ hybridization (FISH) showed that the filaments Eikelboom Type 1851, Type 021N, and Thiothrix nivea were dominant in bulking sludge, comprising 42.0 % of mixed liquor volatile suspended solids (MLVSS), with 61.6% of the total filament length extending from flocs into bulk solution. Only low levels of Type 1851 filament length (4.9% of MLVSS) occurred in non‐bulking sludge, 83.0% of which grew inside the flocs. The kinetic parameters determined from the substrate uptake tests were consistent with those from respirometry and showed that filamentous bulking sludge had lower growth rates and maintenance coefficients than non‐bulking sludge. These results provide support for growth kinetic differences in explaining the competitive strategy of filamentous bacteria. © 2005 Wiley Periodicals, Inc. DA - 2005/12/20/ PY - 2005/12/20/ DO - 10.1002/bit.20662 VL - 92 IS - 6 SP - 729-739 SN - 1097-0290 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-28844437811&partnerID=MN8TOARS KW - growth rate KW - yield KW - maintenance coefficient KW - substrate uptake KW - metabolic modeling KW - quantitative FISH ER - TY - JOUR TI - Renal biopsy: A retrospective study of methods and complications in 283 dogs and 65 cats AU - Vaden, SL AU - Levine, JE AU - Lees, GE AU - Groman, RP AU - Grauer, GE AU - Forrester, SD T2 - JOURNAL OF VETERINARY INTERNAL MEDICINE AB - Renal biopsy often is required to establish a definitive diagnosis in dogs and cats with renal disease. In this retrospective study, we determined the complications of renal biopsy as well as factors that may be associated with development of complications and procurement of adequate renal biopsy specimens in 283 dogs and 65 cats. Data extracted from medical records at 4 institutions were evaluated using logistic regression. Proteinuria was the most common indication for renal biopsy in dogs. Complications were reported in 13.4 and 18.5% of dogs and cats, respectively. The most common complication was severe hemorrhage; hydronephrosis and death were uncommon. Dogs that developed complications after renal biopsy were more likely to have been 4 to <7 years of age and >9 years, to weigh ≤5 kg, and to have serum creatinine concentrations >5 mg/dL. The majority of biopsies from both dogs (87.6%) and cats (86.2%) were considered to be of satisfactory quality. Biopsies from dogs were more likely to be of high quality if they were obtained when the patient was under general anesthesia and more likely to contain only renal cortex if they were obtained by surgery. We concluded that renal biopsy is a relatively safe procedure, with a low frequency of severe complications. Hospital practices and patient variables have the potential to impact both the quality of the specimen obtained and the rate of complications. DA - 2005/// PY - 2005/// DO - 10.1892/0891-6640(2005)19[794:RBARSO]2.0.CO;2 VL - 19 IS - 6 SP - 794-801 SN - 1939-1676 KW - kidney biopsy KW - renal biopsy quality ER - TY - JOUR TI - Quantitative trait loci affecting the difference in pigmentation between Drosophila yakuba and D. santomea AU - Carbone, MA AU - Llopart, A AU - DeAngelis, M AU - Coyne, JA AU - Mackay, TFC T2 - GENETICS AB - Using quantitative trait locus (QTL) mapping, we studied the genetic basis of the difference in pigmentation between two sister species of Drosophila: Drosophila yakuba, which, like other members of the D. melanogaster subgroup, shows heavy black pigmentation on the abdomen of males and females, and D. santomea, an endemic to the African island of São Tomé, which has virtually no pigmentation. Here we mapped four QTL with large effects on this interspecific difference in pigmentation: two on the X chromosome and one each on the second and third chromosomes. The same four QTL were detected in male hybrids in the backcrosses to both D. santomea and D. yakuba and in the female D. yakuba backcross hybrids. All four QTL exhibited strong epistatic interactions in male backcross hybrids, but only one pair of QTL interacted in females from the backcross to D. yabuka. All QTL from each species affected pigmentation in the same direction, consistent with adaptive evolution driven by directional natural selection. The regions delimited by the QTL included many positional candidate loci in the pigmentation pathway, including genes affecting catecholamine biosynthesis, melanization of the cuticle, and many additional pleiotropic effects. DA - 2005/9// PY - 2005/9// DO - 10.1534/genetics.105.044412 VL - 171 IS - 1 SP - 211-225 SN - 1943-2631 ER - TY - JOUR TI - Porous medium model for investigating transient heat and moisture transport in firefighter protective clothing under high-intensity thermal exposure AU - Chitrphiromsri, P. AU - Kuznetsov, A. V. T2 - Journal of Porous Media AB - The aim of this study is to understand the performance of firefighter protective clothing in preventing thermal injury of skin that may result from exposure to high-intensity thermal radiation. A mathematical model is developed to study transient heat and moisture transport through multilayer fabric assemblies. The model accounts for changes in thermophysical and transport properties of the fabric due to the presence of moisture. Numerical simulations are performed to study heat and moisture transport in wet fabrics that are subjected to intensive flash fire exposure. The numerical solutions are further analyzed to provide a detailed physical understanding of the transport processes. Moisture in the fabric tends to vaporize starting from the outside surface of the fabric to the inside surface of the fabric during heating, and then part of it recondenses in the interior of the fabric during the cooldown. It is observed that the temperature distribution in the fabric layers and the total heat flux to the skin are significantly influenced by the amount and distribution of the moisture in the protective clothing. DA - 2005/// PY - 2005/// DO - 10.1615/jpormedia.v8.i5.80 VL - 8 IS - 5 SP - 511-528 ER - TY - JOUR TI - Oleate desaturase enzymes of soybean: evidence of regulation through differential stability and phosphorylation AU - Tang, GQ AU - Novitzky, WP AU - Griffin, HC AU - Huber, SC AU - Dewey, RE T2 - PLANT JOURNAL AB - The endoplasmic reticulum-associated oleate desaturase FAD2 (1-acyl-2-oleoyl-sn-glycero-3-phosphocholine Delta12-desaturase) is the key enzyme responsible for the production of linoleic acid in non-photosynthetic tissues of plants. Little is known, however, concerning the post-transcriptional mechanisms that regulate the activity of this important enzyme. The soybean genome possesses two seed-specific isoforms of FAD2, designated FAD2-1A and FAD2-1B, which differ at only 24 amino acid residues. Expression studies in yeast revealed that the FAD2-1A isoform is more unstable than FAD2-1B, particularly when cultures were maintained at elevated growth temperatures. Analysis of chimeric FAD2-1 constructs led to the identification of two domains that appear to be important in mediating the temperature-dependent instability of the FAD2-1A isoform. The enhanced degradation of FAD2-1A at high growth temperatures was partially abrogated by treating the cultures with the 26S proteasome-specific inhibitor MG132, and by expressing the FAD2-1A cDNA in yeast strains devoid of certain ubiquitin-conjugating activities, suggesting a role for ubiquitination and the 26S proteasome in protein turnover. In addition, phosphorylation state-specific antipeptide antibodies demonstrated that the Serine-185 of FAD2-1 sequences is phosphorylated during soybean seed development. Expression studies of phosphopeptide mimic mutations in yeast suggest that phosphorylation may downregulate enzyme activity. Collectively, the results show that post-translational regulatory mechanisms are likely to play an important role in modulating FAD2-1 enzyme activities. DA - 2005/11// PY - 2005/11// DO - 10.1111/j.1365-313X.2005.02535.x VL - 44 IS - 3 SP - 433-446 SN - 1365-313X KW - oleate desaturase KW - FAD2 KW - protein phosphorylation KW - 26S proteasome KW - polyunsaturated fatty acids KW - soybean (Glycine max) ER - TY - JOUR TI - Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea AU - Kulkarni, R. D. AU - Thon, M. R. AU - Pan, H. Q. AU - Dean, R. A. T2 - Genome Biology DA - 2005/// PY - 2005/// VL - 6 IS - 3 ER - TY - JOUR TI - Male and female antennal responses in Heliothis virescens and H subflexa to conspecific and heterospecific sex pheromone compounds AU - Groot, A AU - Gemeno, C AU - Brownie, C AU - Gould, F AU - Schal, C T2 - ENVIRONMENTAL ENTOMOLOGY AB - Journal Article Male and Female Antennal Responses in Heliothis virescens and H. subflexa to Conspecific and Heterospecific Sex Pheromone Compounds Get access Astrid Groot, Astrid Groot 1 1Corresponding author: Department of Entomology, Box 7614, North Carolina State University, Raleigh, NC 27695-7613 (e-mail: astrid_groot@ncsu.edu). Search for other works by this author on: Oxford Academic PubMed Google Scholar César Gemeno, César Gemeno 2Present address: University of Lleida, Department Producció Vegetal i Ciència Forestal, Rovira Roure, 177, 25198 Lleida, Spain. Search for other works by this author on: Oxford Academic PubMed Google Scholar Cavell Brownie, Cavell Brownie 3Department of Statistics, North Carolina State University, Raleigh, NC 27695-7613. Search for other works by this author on: Oxford Academic PubMed Google Scholar Fred Gould, Fred Gould Search for other works by this author on: Oxford Academic PubMed Google Scholar Coby Schal Coby Schal Search for other works by this author on: Oxford Academic PubMed Google Scholar Environmental Entomology, Volume 34, Issue 2, 1 April 2005, Pages 256–263, https://doi.org/10.1603/0046-225X-34.2.256 Published: 01 April 2005 Article history Received: 06 May 2004 Accepted: 03 December 2004 Published: 01 April 2005 DA - 2005/4// PY - 2005/4// DO - 10.1603/0046-225X-34.2.256 VL - 34 IS - 2 SP - 256-263 SN - 1938-2936 KW - Heliothis virescens KW - Heliothis subflexa KW - electroantennogram KW - species specificity KW - female autodetection ER - TY - JOUR TI - Investigation of laminar flow in a helical pipe filled with a fluid saturated porous medium AU - Cheng, L AU - Kuznetsov, AV T2 - EUROPEAN JOURNAL OF MECHANICS B-FLUIDS AB - Laminar flow in a helical pipe filled with a fluid saturated porous medium is investigated numerically. The analysis is based on a full momentum equation for the flow in porous media that accounts for the Brinkman and Forchheimer extensions of the Darcy law as well as for the flow inertia. Accounting for the flow inertia is shown to be important for predicting secondary flow in a helical pipe. The effects of the Darcy number, the Forchheimer coefficient as well as the curvature and torsion of the helical pipe on the axial flow velocity and secondary flow are investigated numerically. DA - 2005/// PY - 2005/// DO - 10.1016/j.euromechflu.2004.08.002 VL - 24 IS - 3 SP - 338-352 SN - 1873-7390 KW - helical pipe KW - porous medium KW - laminar flow KW - orthogonal helical coordinates ER - TY - JOUR TI - Herbivorous insect response to group selection cutting in a southeastern bottomland hardwood forest AU - Ulyshen, MD AU - Hanula, JL AU - Horn, S AU - Kilgo, JC AU - Moorman, CE T2 - ENVIRONMENTAL ENTOMOLOGY AB - Malaise and pitfall traps were used to sample herbivorous insects in canopy gaps created by group-selection cutting in a bottomland hardwood forest in South Carolina. The traps were placed at the centers, edges, and in the forest adjacent to gaps of different sizes (0.13, 0.26, and 0.50 ha) and ages (1 and 7 yr old) during four sampling periods in 2001. Overall, the abundance and species richness of insect herbivores were greater at the centers of young gaps than at the edge of young gaps or in the forest surrounding young gaps. There were no differences in abundance or species richness among old gap locations (i.e., centers, edges, and forest), and we collected significantly more insects in young gaps than old gaps. The insect communities in old gaps were more similar to the forests surrounding them than young gap communities were to their respective forest locations, but the insect communities in the two forests locations (surrounding young and old gaps) had the highest percent similarity of all. Although both abundance and richness increased in the centers of young gaps with increasing gap size, these differences were not significant. We attribute the increased numbers of herbivorous insects to the greater abundance of herbaceous plants available in young gaps. DA - 2005/4// PY - 2005/4// DO - 10.1603/0046-225X-34.2.395 VL - 34 IS - 2 SP - 395-402 SN - 1938-2936 KW - selection cutting KW - uneven-aged silviculture KW - forest openings KW - forest management ER - TY - JOUR TI - Heat transfer in a laminar flow in a helical pipe filled with a fluid saturated porous medium AU - Cheng, LP AU - Kuznetsov, AV T2 - INTERNATIONAL JOURNAL OF THERMAL SCIENCES AB - This paper presents the first attempt to investigate numerically heat transfer in a helical pipe filled with a fluid saturated porous medium; the analysis is based on the full momentum equation for porous media that accounts for the Brinkman and Forchheimer extensions of the Darcy law as well as for the flow inertia. Numerical computations are performed in an orthogonal helical coordinate system. The effects of the Darcy number, the Forchheimer coefficient as well as the Dean and Germano numbers on the axial flow velocity, secondary flow, temperature distribution, and the Nusselt number are investigated. DA - 2005/8// PY - 2005/8// DO - 10.1016/j.ijthermalsci.2004.12.009 VL - 44 IS - 8 SP - 787-798 SN - 1778-4166 KW - heat transfer KW - helical pipe KW - porous medium KW - laminar flow KW - orthogonal helical coordinates ER - TY - JOUR TI - Geographical variation in pheromone response of the European corn borer, Ostrinia nubilalis (Lepidoptera : Crambidae), in North Carolina: A 20-Y perspective AU - Sorenson, CE AU - Kennedy, GG AU - Schal, C AU - Walgenbach, JF T2 - ENVIRONMENTAL ENTOMOLOGY AB - Abstract Pheromone traps were used to assess the distribution of two pheromone races of European corn borer, Ostrinia nubilalis (Hubner), in North Carolina, ≈10 and 20 yr after previous, similar assessments. In the previous studies, moths responding to a 97Z: 3E isomeric blend (Z blend) of 11-tetradecenyl acetate predominated in the far western parts of the state, whereas moths responding to a 3Z: 97E blend (E blend) prevailed in the east, with a substantial zone of overlap occurring in the eastern Piedmont. There was evidence that the E responsive population had expanded westward between 1978 and 1988. In this study, the distribution of the two races seemed to remain essentially unchanged from that observed in the late 1980s, and no evidence of a continued westward expansion of E responsive moths was detected. DA - 2005/10// PY - 2005/10// DO - 10.1603/0046-225X(2005)034[1057:GVIPRO]2.0.CO;2 VL - 34 IS - 5 SP - 1057-1062 SN - 0046-225X KW - pheromone race distribution KW - landscape effects KW - pheromone trapping KW - cone trap ER - TY - JOUR TI - Genomic affinities in Arachis section Arachis (Fabaceae): molecular and cytogenetic evidence AU - Tallury, SP AU - Hilu, KW AU - Milla, , SR AU - Friend, SA AU - Alsaghir, M AU - Stalker, HT AU - Quandt, D T2 - THEORETICAL AND APPLIED GENETICS DA - 2005/11// PY - 2005/11// DO - 10.1007/s00122-005-0017-0 VL - 111 IS - 7 SP - 1229-1237 SN - 1432-2242 ER - TY - JOUR TI - Genome sequence, comparative analysis and haplotype structure of the domestic dog AU - Lindblad-Toh, Kerstin AU - Wade, Claire M AU - Mikkelsen, Tarjei S. AU - Karlsson, Elinor K. AU - Jaffe, David B. AU - Kamal, Michael AU - Clamp, Michele AU - Chang, Jean L. AU - Kulbokas, Edward J., III AU - Zody, Michael C. AU - Mauceli, Evan AU - Xie, Xiaohui AU - Breen, Matthew AU - Wayne, Robert K. AU - Ostrander, Elaine A. AU - Ponting, Chris P. AU - Galibert, Francis AU - Smith, Douglas R. AU - deJong, Pieter J. AU - Kirkness, Ewen AU - Alvarez, Pablo AU - Biagi, Tara AU - Brockman, William AU - Butler, Jonathan AU - Chin, Chee-Wye AU - Cook, April AU - Cuff, James AU - Daly, Mark J. AU - DeCaprio, David AU - Gnerre, Sante AU - Grabherr, Manfred AU - Kellis, Manolis AU - Kleber, Michael AU - Bardeleben, Carolyne AU - Goodstadt, Leo AU - Heger, Andreas AU - Hitte, Christophe AU - Kim, Lisa AU - Koepfli, Klaus-Peter AU - Parker, Heidi G. AU - Pollinger, John P. AU - Searle, Stephen M. J. AU - Sutter, Nathan B. AU - Thomas, Rachael AU - Webber, Caleb AU - Lander, Eric S. T2 - Nature AB - Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health. DA - 2005/12// PY - 2005/12// DO - 10.1038/nature04338 VL - 438 IS - 7069 SP - 803-819 J2 - Nature LA - en OP - SN - 0028-0836 1476-4687 UR - http://dx.doi.org/10.1038/nature04338 DB - Crossref ER - TY - JOUR TI - Genetic Improvement of Virginia Pine (Pinus virginiana Mill.) for Christmas Tree Production. AU - Isik, F. T2 - Forest Genetics DA - 2005/// PY - 2005/// VL - 11 SP - 137-147 ER - TY - JOUR TI - Gender-specific reproductive tissue in ratites and Tyrannosaurus rex AU - Schweitzer, MH AU - Wittmeyer, JL AU - Horner, , JR T2 - SCIENCE AB - Unambiguous indicators of gender in dinosaurs are usually lost during fossilization, along with other aspects of soft tissue anatomy. We report the presence of endosteally derived bone tissues lining the interior marrow cavities of portions of Tyrannosaurus rex (Museum of the Rockies specimen number 1125) hindlimb elements, and we hypothesize that these tissues are homologous to specialized avian tissues known as medullary bone. Because medullary bone is unique to female birds, its discovery in extinct dinosaurs solidifies the link between dinosaurs and birds, suggests similar reproductive strategies, and provides an objective means of gender differentiation in dinosaurs. DA - 2005/6/3/ PY - 2005/6/3/ DO - 10.1126/science.1112158 VL - 308 IS - 5727 SP - 1456-1460 SN - 0036-8075 ER - TY - JOUR TI - Effect of fouling on stability of bioconvection of gyrotactic microorganisms in a porous medium AU - Kuznetsov, AV AU - Avramenko, AA T2 - JOURNAL OF POROUS MEDIA AB - The main objective of this article is to investigate the effect of fouling on the stability of a uniform suspension of gyrotactic motile microorganisms in a fluid-saturated porous medium. Fouling occurs because of the deposition of microorganisms on a porous matrix. This deposition decreases porosity and permeability of the porous medium. Stability analysis carried out in this article reveals that there is a critical porosity of the porous medium. If the porous medium utilized for this process has a smaller porosity than critical, the uniform suspension of gyrotactic microorganisms is stable and bioconvection does not develop. If the porous medium has larger porosity than critical, the uniform suspension is unstable and bioconvection develops. In this article, a combination of analytical and numerical methods is utilized to solve this problem. First, a linear stability analysis is carried out analytically. Then, at the final stage of the research, numerical methods are utilized to compute the critical Darcy number. DA - 2005/// PY - 2005/// DO - 10.1615/JPorMedia.v8.i1.40 VL - 8 IS - 1 SP - 45-53 SN - 1934-0508 ER - TY - JOUR TI - Denaturation and aggregation of three alpha-lactalbumin preparations at neutral pH AU - McGuffey, MK AU - Epting, KL AU - Kelly, RM AU - Foegeding, EA T2 - JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY AB - The denaturation and aggregation of reagent-grade (Σα-La), ion-exchange chromatography purified (IEXα-La), and a commercial-grade (Cα-La) α-lactalbumin were studied with differential scanning calorimetry (DSC), polyacrylamide gel electrophoresis, and turbidity measurement. All three preparations had similar thermal denaturation temperatures with an average of 63.7 °C. Heating pure preparations of α-lactalbumin produced three non-native monomer species and three distinct dimer species. This phenomenon was not observed in Cα-La. Turbidity development at 95 °C (τ95°C) indicated that pure preparations rapidly aggregate at pH 7.0, and evidence suggests that hydrophobic interactions drove this phenomenon. The Cα-La required 4 times the phosphate or excess Ca2+ concentrations to develop a similar τ95°C to the pure preparations and displayed a complex pH-dependent τ95°C behavior. Turbidity development dramatically decreased when the heating temperature was below 95 °C. A mechanism is provided, and the interrelationship between specific electrostatic interactions and hydrophobic attraction, in relation to the formation of disulfide-bonded products, is discussed. Keywords: α-Lactalbumin; whey proteins; denaturation and aggregation DA - 2005/4/20/ PY - 2005/4/20/ DO - 10.1021/jf048863p VL - 53 IS - 8 SP - 3182-3190 SN - 1520-5118 KW - alpha-lactalbumin KW - whey proteins KW - denaturation and aggregation ER - TY - JOUR TI - An AFLP-based survey of genetic diversity among accessions of sea oats (Uniola paniculata, Poaceae) from the southeastern Atlantic and Gulf coast states of the United States AU - Subudhi, PK AU - Parami, NP AU - Harrison, SA AU - Materne, MD AU - Murphy, JP AU - Nash, D T2 - THEORETICAL AND APPLIED GENETICS DA - 2005/11// PY - 2005/11// DO - 10.1007/s00122-005-0096-y VL - 111 IS - 8 SP - 1632-1641 SN - 0040-5752 KW - amplified fragment length polymorphism KW - dune stabilizing grass KW - gene flow KW - genetic variation KW - population structure KW - sea oats KW - Uniola paniculata ER - TY - JOUR TI - Transposable element insertion location bias and the dynamics of gene drive in mosquito populations AU - Rasgon, JL AU - Gould, F T2 - INSECT MOLECULAR BIOLOGY AB - Some vector-borne disease control strategies using transgenic mosquitoes require transgene spread to high frequency in populations. Transposable elements (TEs) are DNA sequences that replicate and transpose within the genomes of other organisms and may therefore be represented in the next generation in higher frequencies than predicted by Mendelian segregation. This over-representation has allowed some TEs to spread through natural populations. Transgenes incorporated within a TE sequence are expected to be driven into populations as long as there is a positive balance between fitness costs and over-representation. Models have been used to examine parameters that affect this balance but did not take into account biased insertion of TEs to linked sites in the genome. A simulation model was created to examine the impact of insertion bias on TE spread in mosquito populations. TEs that induce no fitness costs are predicted to increase in frequency over a wide range of parameter values but spread is slower for lower levels of transposition and non-local movement. If TEs are costly, high proportions of local movement can slow or halt spread. To function as a robust transgene drive mechanism a TE should replicate and transpose > 10%/insert/generation, induce < 1% fitness cost/insert, and move preferentially to unlinked sites in the genome. DA - 2005/10// PY - 2005/10// DO - 10.1111/j.1365-2583.2005.00580.x VL - 14 IS - 5 SP - 493-500 SN - 0962-1075 KW - transposon KW - gene drive KW - mathematical model KW - mosquito KW - vector-borne disease ER - TY - JOUR TI - SNAP: workbench management tool for evolutionary population genetic analysis AU - Price, EW AU - Carbone, I T2 - BIOINFORMATICS AB - Abstract Summary: The reconstruction of population processes from DNA sequence variation requires the coordinated implementation of several coalescent-based methods, each bound by specific assumptions and limitations. In practice, the application of these coalescent-based methods for parameter estimation is difficult because they make strict assumptions that must be verified a priori and their parameter-rich nature makes the estimation of all model parameters very complex and computationally intensive. A further complication is their distribution as console applications that require the user to navigate through console menus or specify complex command-line arguments. To facilitate the implementation of these coalescent-based tools we developed SNAP Workbench, a Java program that manages and coordinates a series of programs. The workbench enhances population parameter estimation by ensuring that the assumptions and program limitations of each method are met and by providing a step-by-step methodology for examining population processes that integrates both summary-statistic methods and coalescent-based population genetic models. Availability: SNAP Workbench is freely available at http://snap.cifr.ncsu.edu. The workbench and tools can be downloaded for Mac, Windows and Unix operating systems. Each package includes installation instructions, program documentation and a sample dataset. Contact: ignazio_carbone@ncsu.edu Supplementary information: A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu DA - 2005/2/1/ PY - 2005/2/1/ DO - 10.1093/bioinformatics/bti003 VL - 21 IS - 3 SP - 402-404 SN - 1460-2059 ER - TY - JOUR TI - Resolving tylenchid evolutionary relationships through multiple gene analysis derived from EST data AU - Scholl, EH AU - Bird, DM T2 - MOLECULAR PHYLOGENETICS AND EVOLUTION AB - Sequence-based phylogenetic analyses typically are based on a small number of character sets and report gene trees which may not reflect the true species tree. We employed an EST mining strategy to suppress such incongruencies, and recovered the most robust phylogeny for five species of plant-parasitic nematode (Meloidogyne arenaria, M. chitwoodi, M. hapla, M. incognita, and M. javanica), three closely related tylenchid taxa (Heterodera glycines, Globodera pallida, and G. rostochiensis) and a distant taxon, Caenorhabditis elegans. Our multiple-gene approach is based on sampling more than 80,000 publicly available tylenchid EST sequences to identify phylum-wide orthologues. Bayesian inference, minimum evolution, maximum likelihood and protein distance methods were employed for phylogenetic reconstruction and hypothesis tests were constructed to elucidate differential selective pressures across the phylogeny for each gene. Our results place M. incognita and M. javanica as sister taxa, with M. arenaria as the next closely related nematode. Significant differences in selective pressure were revealed for some genes under some hypotheses, though all but one gene are exclusively under purifying selection, indicating conservation across the orthologous groups. This EST-based multi-gene analysis is a first step towards accomplishing genome-wide coverage for tylenchid evolutionary analyses. DA - 2005/9// PY - 2005/9// DO - 10.1016/j.ympev.2005.03.016 VL - 36 IS - 3 SP - 536-545 SN - 1095-9513 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-21744452353&partnerID=MN8TOARS KW - Bayesian KW - Caenorhabditis elegans KW - COG KW - cyst nematode KW - orthologues KW - root-knot nematode ER - TY - JOUR TI - RAPD and SCAR markers linked to an introgressed gene conditioning resistance to Peronospora tabacina D.B. Adam in tobacco AU - Milla, S.R. AU - Levin, J.S. AU - Lewis, R.S. AU - Rufty, R.C. T2 - Crop Science AB - Blue mold, caused by the fungal pathogen Peronospora tabacina D.B. Adam, is one of the most important foliar diseases of tobacco ( Nicotiana tabacum L.). Identification of molecular markers linked to genetic factors controlling resistance would facilitate development of resistant cultivars. Bulked segregant analysis was used to screen 1216 random amplified polymorphic DNA (RAPD) primers for their ability to reveal polymorphism between DNA bulks from susceptible doubled haploid (DH) lines and resistant DH lines possessing resistance derived from cultivar Ovens 62. Fifteen RAPD markers were tentatively identified as being linked to a major gene conditioning resistance to blue mold. These 15 markers (12 in coupling phase linkage with resistance and three in repulsion phase) were found to lie within a single linkage group of 36.6 cM and were subsequently tested on 122 DH lines derived from crosses between resistant and susceptible parents. F tests revealed statistically significant associations between resistance and each of the 15 RAPD markers. Interval mapping was used to more accurately place the quantitative trait locus (QTL) controlling resistance on the linkage map. The RAPD markers were screened on a set of 45 resistant and susceptible cultivars or breeding lines and four Nicotiana species. At variance with previous reports, marker genotypes indicated that resistance in Ovens 62 and most other blue mold resistant lines likely originated from N. debneyi Domin. Two RAPD markers flanking the most likely QTL position were converted to sequence characterized amplified region (SCAR) markers. These markers should aid in development of blue mold‐resistant tobacco cultivars worldwide. DA - 2005/// PY - 2005/// DO - 10.2135/cropsci2004.0754 VL - 45 IS - 6 SP - 2346–2354 SN - 1435-0653 ER - TY - JOUR TI - Putative transposases conserved in Exiguobacterium isolates from ancient Siberian permafrost and from contemporary surface habitats AU - Vishnivetskaya, TA AU - Kathariou, S T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT Gram-positive bacteria of the genus Exiguobacterium have been repeatedly isolated from Siberian permafrost ranging in age from 20,000 to 2 to 3 million years and have been sporadically recovered from markedly diverse habitats, including microbial mats in Lake Fryxell (Antarctic), surface water, and food-processing environments. However, there is currently no information on genomic diversity of this microorganism or on the physiological strategies that have allowed its survival under prolonged freezing in the permafrost. Analysis of the genome sequence of the most ancient available Exiguobacterium isolate ( Exiguobacterium sp. strain 255-15, from 2 to 3 million-year-old Siberian permafrost) revealed numerous putative transposase sequences, primarily of the IS 200 /IS 605 , IS 30 , and IS 3 families, with four transposase families identified. Several of the transposase genes appeared to be part of insertion sequences. Southern blots with different transposase probes yielded high-resolution genomic fingerprints which differentiated the different permafrost isolates from each other and from the Exiguobacterium spp. type strains which have been derived from diverse surface habitats. Each of the Exiguobacterium sp. strain 255-15 transposases that were used as probes had highly conserved homologs in the genome of other Exiguobacterium strains, both from permafrost and from modern sites. These findings suggest that, prior to their entrapment in permafrost, Exiguobacterium isolates had acquired transposases and that conserved transposases are present in Exiguobacterium spp., which now can be isolated from various modern surface habitats. DA - 2005/11// PY - 2005/11// DO - 10.1128/AEM.71.11.6954-6962.2005 VL - 71 IS - 11 SP - 6954-6962 SN - 1098-5336 ER - TY - JOUR TI - Phylogeny, biogeography, and molecular dating of cornelian cherries (Cornus, Cornaceae) – tracking Tertiary plant migration AU - Xiang, Q.-Y AU - Sr, Manchester AU - Thomas, D. AU - Zhang, WH. AU - Fan, CZ T2 - Evolution AB - Data from four DNA regions (rbcL, matK, 26S rDNA, and ITS) as well as extant and fossil morphology were used to reconstruct the phylogeny and biogeographic history of an intercontinentally disjunct plant group, the cornelian cherries of Cornus (dogwoods). The study tests previous hypotheses on the relative roles of two Tertiary land bridges, the North Atlantic land bridge (NALB) and the Bering land bridge (BLB), in plant migration across continents. Three approaches, the Bayesian, nonparametric rate smoothing (NPRS), and penalized likelihood (PL) methods, were employed to estimate the times of geographic isolations of species. Dispersal and vicariance analysis (DIVA) was performed to infer the sequence and directionality of biogeographic pathways. Results of phylogenetic analyses suggest that among the six living species, C. sessilis from western North America represents the oldest lineage, followed by C. volkensii from Africa. The four Eurasian species form a clade consisting of two sister pairs, C. mas– C. officinalis and C. chinensis–C. eydeana. Results of DIVA and data from fossils and molecular dating indicate that the cornelian cherry subgroup arose in Europe as early as the Paleocene. Fossils confirm that the group was present in North America by the late Paleocene, consistent with the DIVA predictions that, by the end of the Eocene, it had diversified into several species and expanded its distribution to North America via the NALB and to Africa via the last direct connection between Eurasia and Africa prior to the Miocene, or via long-distance dispersal. The cornelian cherries in eastern Asia appear to be derived from two independent dispersal events from Europe. These events are inferred to have occurred during the Oligocene and Miocene. This study supports the hypothesis that the NALB served as an important land bridge connecting the North American and European floras, as well as connecting American and African floras via Europe during the early Tertiary. DA - 2005/// PY - 2005/// DO - 10.1554/03-763.1 VL - 59 IS - 8 SP - 139–155 ER - TY - JOUR TI - Phylogenetic analysis of Themira (Sepsidae : Diptera): sensitivity analysis, alignment, and indel treatment in a multigene study AU - Laamanen, TR AU - Meier, R AU - Miller, MA AU - Hille, A AU - Wiegmann, BM T2 - CLADISTICS AB - Abstract In this study we use sensitivity analysis sensu Wheeler (1995 ) for a matrix entirely composed of DNA sequences. We propose that not only congruence but also phylogenetic structure, as measured by character resampling, should be used to choose among competing weighting regimes. An extensive analysis of a five‐gene data set for Themira (Sepsidae: Diptera) reveals that even with different ways of partitioning the data, measures of topological congruence, character incongruence, and phylogenetic structure favor similar weighting regimes involving the down‐weighting of transitions. We furthermore use sensitivity analysis for obtaining empirical evidence that allows us to select weights for third positions, deciding between treating indels as fifth character states or missing values, and choosing between manual and computational alignments. For our data, sensitivity analysis favors manual alignment over a Clustal‐generated numerical alignment, the treatment of indels as fifth character states over considering them missing values, and equal weights for all positions in protein‐encoding genes over the down‐weighting of third positions. Among the topological congruence measures compared, symmetric tree distance performed best. Partitioned Bremer Support analysis reveals that COI contributes the largest amount of support for our phylogenetic tree for Themira . © The Willi Hennig Society 2005. DA - 2005/6// PY - 2005/6// DO - 10.1111/j.1096-0031.2005.00066.x VL - 21 IS - 3 SP - 258-271 SN - 1096-0031 ER - TY - JOUR TI - Organ-specific roles for transcription factor NF-kappa B in reovirus-induced apoptosis and disease AU - Sherry, B. T2 - Journal of Clinical Investigation DA - 2005/// PY - 2005/// VL - 115 IS - 9 SP - 2341-2350 ER - TY - JOUR TI - Mutations of phosphatase and tensin homolog deleted from chromosome 10 in canine hemangiosarcoma AU - Dickerson, EB AU - Thomas, R AU - Fosmire, SP AU - Lamerato-Kozicki, AR AU - Bianco, , SR AU - Wojcieszyn, JW AU - Breen, M AU - Helfand, SC AU - Modiano, JF T2 - VETERINARY PATHOLOGY AB - We examined the presence of phosphatase and tensin homolog deleted from chromosome 10 (PTEN) abnormalities that could contribute to the origin or progression of naturally occurring canine endothelial tumors (hemangiosarcoma). Our results document somatic point mutations or deletions encompassing the PTEN C-terminal domain in canine hemangiosarcoma that might provide cells a survival advantage within their microenvironment. This represents the first characterization of a naturally occurring, highly metastatic tumor with biologically significant mutations of PTEN in the C-terminal domain. DA - 2005/9// PY - 2005/9// DO - 10.1354/vp.42-5-618 VL - 42 IS - 5 SP - 618-632 SN - 1544-2217 KW - canine KW - endothelial cells KW - hemangiosarcoma KW - mutations KW - PTEN KW - tumor progression ER - TY - JOUR TI - Molecular and genetic characterization of N. glutinosa L. chromosome segments in tobacco mosaic virus (TMV)-resistant tobacco accessions AU - Lewis, R.S. AU - Milla, S.R. AU - Levin, J.S. T2 - Crop Science AB - Tobacco mosaic virus (TMV)‐resistant flue‐cured tobacco ( Nicotiana tabacum L.) cultivars have been developed using the N gene derived from N. glutinosa L. Their adoption has been low, however, because of unfavorable linkage drag effects. Strategies to overcome this problem might include pursuit of alternative introgression events and/or use of molecular markers for selection against deleterious alien chromatin. Previous workers demonstrated the presence of a TMV‐resistance mechanism on more than one chromosome of the tobacco genome. The objectives of this research were to determine the relative genomic positions of TMV resistance loci in a set of 12 TMV‐resistant tobacco accessions and to use amplified fragment length polymorphism (AFLP) markers for characterization of this material with respect to linked alien chromatin. Five accessions were found to carry a TMV resistance gene on chromosome H. Seven accessions were found to carry a resistance factor on an alternative chromosome. Polymerase chain reaction results indicated that the N gene from N. glutinosa is responsible for resistance in all 12 accessions. A set of 168 AFLP markers specific to the N. glutinosa donor chromosome was identified and used to reveal variability among the 12 accessions for the relative amounts of N. glutinosa chromatin linked to the N gene. The relative propensity for crossing over within the alien segment when in different genomic positions was evaluated in BC 1 F 1 families derived from three different accessions. Lines possessing the N gene on chromosome H may be of greater practical value because of relatively smaller introgressed alien segments and increased potential for obtaining crossover events within the segments. DA - 2005/// PY - 2005/// DO - 10.2135/cropsci2005.0121 VL - 45 IS - 6 SP - 2355–2362 SN - 1435-0653 ER - TY - JOUR TI - Genes determining rind pattern inheritance in watermelon: A review AU - Gusmini, G. AU - Wehner, T. C. T2 - HortScience DA - 2005/// PY - 2005/// VL - 40 IS - 6 SP - 1928-1930 ER - TY - JOUR TI - Cuticular hydrocarbon synthesis and its maternal provisioning to embryos in the viviparous cockroach Diploptera punctata AU - Youngsteadt, E AU - Fan, YL AU - Stay, B AU - Schal, C T2 - JOURNAL OF INSECT PHYSIOLOGY AB - Embryos of the viviparous cockroach Diploptera punctata accumulate large amounts of hydrocarbon (HC) of either maternal or embryonic origin. HC synthesis and its accumulation in maternal and embryonic tissues were measured over the course of gestation. Female abdominal integument was the only tissue that synthesized appreciable amounts of HC in vitro, and did so at an increasing rate from the time of mating to mid-pregnancy, when rates of synthesis declined. The embryos synthesized HC at rates <1% those of the female, showing that the majority of HC detected in and on embryos was of maternal origin. The brood sac that houses the developing embryos did not synthesize HC in vitro, indicating that HC must be transported from the female abdominal integument to the embryos. The mass of female epicuticular HC was constant at ∼183 μg, while her internal HC increased fourfold from mating to mid-pregnancy, then declined until parturition. The decline in internal HC reflected both declining HC synthesis in the female and greater export to the embryos, as embryonic internal HC increased 250-fold prior to parturition. An external HC coating over the oothecal covering and chorion of the embryos increased to mid-pregnancy, then declined. Unlike oviparous cockroaches, D. punctata females fed throughout the reproductive cycle, reflecting the nutritional demands of continuously provisioning the developing embryos. DA - 2005/7// PY - 2005/7// DO - 10.1016/j.jinsphys.2005.03.008 VL - 51 IS - 7 SP - 803-809 SN - 1879-1611 KW - Diploptera punctata KW - hydrocarbons KW - viviparity KW - maternal investment KW - feeding ER - TY - JOUR TI - Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors AU - Thomas, R AU - Scott, A AU - Langford, CF AU - Fosmire, SP AU - Jubala, CM AU - Lorentzen, TD AU - Hitte, C AU - Karlsson, EK AU - Kirkness, E AU - Ostrander, EA AU - Galibert, F AU - Lindblad-Toh, K AU - Modiano, JF AU - Breen, M T2 - GENOME RESEARCH AB - Recognition of the domestic dog as a model for the comparative study of human genetic traits has led to major advances in canine genomics. The pathophysiological similarities shared between many human and dog diseases extend to a range of cancers. Human tumors frequently display recurrent chromosome aberrations, many of which are hallmarks of particular tumor subtypes. Using a range of molecular cytogenetic techniques we have generated evidence indicating that this is also true of canine tumors. Detailed knowledge of these genomic abnormalities has the potential to aid diagnosis, prognosis, and the selection of appropriate therapy in both species. We recently improved the efficiency and resolution of canine cancer cytogenetics studies by developing a small-scale genomic microarray comprising a panel of canine BAC clones representing subgenomic regions of particular interest. We have now extended these studies to generate a comprehensive canine comparative genomic hybridization (CGH) array that comprises 1158 canine BAC clones ordered throughout the genome with an average interval of 2 Mb. Most of the clones (84.3%) have been assigned to a precise cytogenetic location by fluorescence in situ hybridization (FISH), and 98.5% are also directly anchored within the current canine genome assembly, permitting direct translation from cytogenetic aberration to DNA sequence. We are now using this resource routinely for high-throughput array CGH and single-locus probe analysis of a range of canine cancers. Here we provide examples of the varied applications of this resource to tumor cytogenetics, in combination with other molecular cytogenetic techniques. DA - 2005/12// PY - 2005/12// DO - 10.1101/gr.3825705 VL - 15 IS - 12 SP - 1831-1837 SN - 1549-5469 ER - TY - JOUR TI - Characterization of the dinuclear metal center of Pyrococcus furiosus prolidase by analysis of targeted mutants AU - Du, XL AU - Tove, S AU - Kast-Hutcheson, K AU - Grunden, AM T2 - FEBS LETTERS AB - Prolidases are dipeptidases specific for cleavage of Xaa‐Pro dipeptides. Pyrococcus furiosus prolidase is a homodimer having one Co‐bound dinuclear metal cluster per monomer with one tightly bound Co(II) site and the other loosely bound ( K d 0.24 mM). To identify which Co site is tight‐binding and which is loose‐binding, site‐directed mutagenesis was used to modify amino acid residues that participate in binding the Co1 (E‐313 and H‐284), the Co2 site (D‐209) or the bidentate ligand (E‐327). Metal‐content, enzyme activity and CD‐spectra analyses of D209A‐, H284L‐, and E327L‐prolidase mutants show that Co1 is the tight‐binding and Co2 the loose‐binding metal center. DA - 2005/11/7/ PY - 2005/11/7/ DO - 10.1016/j.febslet.2005.09.086 VL - 579 IS - 27 SP - 6140-6146 SN - 1873-3468 KW - prolidase KW - aminopeptidase KW - dinuclear metal center KW - cobalt enzyme KW - Pyrococcus furiosus ER - TY - CHAP TI - Trust-based secure workflow path construction AU - Altunay, M. AU - Brown, D. AU - Byrd, Gregory AU - Dean, Ralph T2 - Service-oriented computing, ICSOC 2005: Third International Conference, Amsterdam, The Netherlands, December 12-15, 2005; proceedings (Lecture notes in computer science; 3826) A2 - Benatallah, F. Casati B. A2 - Traverso, P. AB - Security and trust relationships between services significantly govern their willingness to collaborate and participate in a workflow. Existing workflow tools do not consider such relationships as an integral part of their planning logic: rather, they approach security as a run-time issue. We present a workflow management framework that fully integrates trust and security into the workflow planning logic. It considers not only trust relationships between the workflow requestor and individual services, but also trust relationships among the services themselves. It allows each service owner to define an upper layer of collaboration policies (rules that specify the terms under which participation in a workflow is allowed) and integrates them into the planning logic. Services that are unfit for collaboration due to security violations are replaced at the planning stage. This approach increases the services owners’ control over the workflow path, their willingness for collaboration, and avoids run-time security failures. CN - [Electronic Resource] PY - 2005/// DO - 10.1007/11596141_29 VL - 3826 SP - 382–395 PB - Berlin: Springer SN - 3540308172 ER - TY - JOUR TI - The dog as a sentinel for human infection: Prevalence of Borrelia burgdorferi C6 antibodies in dogs from southeastern and mid-Atlantic states AU - Duncan, AW AU - Correa, MT AU - Levine, JF AU - Breitschwerdt, EB T2 - VECTOR-BORNE AND ZOONOTIC DISEASES AB - Lyme disease is the most frequently reported human vector-associated disease in the United States. Infection occurs after the bite of an Ixodid tick that is infected with Borrelia burgdorferi. Dogs have often been reported to serve as effective sentinel animals to assess the risk of human B. burgdorferi infection. Based on published data of human Lyme disease case numbers and our clinical impressions, we hypothesized that canine exposure to B. burgdorferi would be lower in North Carolina when compared to the exposure in Virginia, Maryland, and Pennsylvania. To address this hypothesis, we evaluated B. burgdorferi exposure status utilizing a specific and sensitive C6 peptide-based enzyme-linked immunosorbent assay. Our convenience sample included 1,666 canine serum samples submitted to the Vector-Borne Disease Diagnostic Laboratory from North Carolina (n = 987), Virginia (n = 472), Maryland (n = 167), and Pennsylvania (n = 40). Comparisons among states were made using the Chisquare test or the Fisher's exact test; p-values were adjusted for multiple comparisons using the Bonferroni correction. A Chi-square test for trend was used to determine if there was an increase in the frequency of seroreactors associated with the geographical origin of the samples. The proportion of seroreactive dogs in North Carolina was markedly lower (p < 0.008) than that observed in dogs from Virginia, Maryland, and Pennsylvania. These results support the hypothesis that B. burgdorferi transmission seems to occur infrequently in North Carolina dogs as compared to dogs residing in other southeastern and mid-Atlantic states. Furthermore, they support the utility of dogs as a sentinel to characterize the risk of B. burgdorferi transmission to humans in a defined geographical location. DA - 2005/// PY - 2005/// DO - 10.1089/vbz.2005.5.101 VL - 5 IS - 2 SP - 101-109 SN - 1557-7759 KW - Borrelia burgdorferi C6 KW - dogs KW - lyme disease ER - TY - JOUR TI - Structural analysis of divalent metals binding to the Bacillus subtilis response regulator Spo0F: the possibility for In vitro metalloregulation in the initiation of sporulation AU - Kojetin, DJ AU - Thompson, RJ AU - Benson, LM AU - Naylor, S AU - Waterman, J AU - Davies, KG AU - Opperman, CH AU - Stephenson, K AU - Hoch, JA AU - Cavanagh, J T2 - BIOMETALS DA - 2005/10// PY - 2005/10// DO - 10.1007/s10534-005-4303-8 VL - 18 IS - 5 SP - 449-466 SN - 1572-8773 KW - metal binding KW - NMR spectroscopy KW - response regulator KW - sporulation KW - two-component signal transduction ER - TY - JOUR TI - Production of a thermostable archaeal superoxide reductase in plant cells AU - Im, YJ AU - Ji, MK AU - Lee, AM AU - Boss, WF AU - Grunden, AM T2 - FEBS LETTERS AB - Pyrococcus furiosus superoxide reductase (SOR) is a thermostable archaeal enzyme that reduces superoxide without producing oxygen. When produced as a fusion protein with the green fluorescent protein in plant cells, P. furiosus SOR is located in the cytosol and nucleus. The recombinant SOR enzyme retains its function and heat stability when assayed in vitro. Importantly, expressing SOR in plant cells enhances their survival at high temperature indicating that it functions in vivo. The archaeal SOR provides a novel mechanism to reduce superoxide and demonstrates the potential for using archaeal genes to alter eukaryotic metabolism. DA - 2005/10/24/ PY - 2005/10/24/ DO - 10.1016/j.febslet.2005.09.015 VL - 579 IS - 25 SP - 5521-5526 SN - 1873-3468 KW - archaeal KW - heat-stress KW - hyperthermophile KW - plant KW - reactive oxygen species KW - superoxide dismutase KW - superoxide reductase ER - TY - JOUR TI - Prediction of loblolly pine wood properties using transmittance near-infrared spectroscopy AU - Sykes, R AU - Li, BL AU - Hodge, G AU - Goldfarb, B AU - Kadla, J AU - Chang, HM T2 - CANADIAN JOURNAL OF FOREST RESEARCH AB - Near-infrared (NIR) spectroscopy is a rapid nondestructive technique that has been used to characterize chemical and physical properties of a wide range of materials. In this study, transmittance NIR spectra from thin wood wafers cut from increment cores were used to develop calibration models for the estimation of α-cellulose content, average fiber length, fiber coarseness, and lignin content in the laboratory. Eleven-year-old trees from two sites were sampled using 12-mm increment cores. Earlywood and latewood of ring 3 and ring 8 from these samples were analyzed in the laboratory using microanalytical methods for α-cellulose content, average fiber length, fiber coarseness, and lignin content. NIR calibrations and laboratory measurements based on one site were generally reliable, with coefficients of determination (R 2 ) ranging from 0.54 to 0.88 for average fiber length and α-cellulose content, respectively. Predicting ring 8 properties using ring 3 calibration equations showed potential for predicting α-cellulose content and fiber coarseness, with R 2 values of approximately 0.60, indicating the potential for early selection. Predicting the wood properties using the calibration equations from one site to predict another showed moderate success for α-cellulose content (R 2 = 0.64) and fiber coarseness (R 2 = 0.63), but predictions for fiber length were relatively poor (R 2 = 0.43). Prediction of lignin content using transmittance NIR spectroscopy was not as reliable in this study, partially because of low variation in lignin content in these wood samples and large errors in measuring lignin content in the laboratory. DA - 2005/10// PY - 2005/10// DO - 10.1139/X05-161 VL - 35 IS - 10 SP - 2423-2431 SN - 1208-6037 ER - TY - JOUR TI - Inheritance and chromosomal assignment of powdery mildew resistance genes in two winter wheat germplasm lines AU - Srnic, G AU - Murphy, JP AU - Lyerly, JH AU - Leath, S AU - Marshall, DS T2 - CROP SCIENCE AB - Powdery mildew of wheat ( Triticum aestivum L.), caused by Blumeria graminis DC f. sp. tritici Em. Marchal, occurs annually in eastern North America resulting in reduced grain yield and end‐use quality in susceptible cultivars. The objectives of this study were to determine the inheritance, chromosomal location, and linkage with molecular markers of powdery mildew resistance genes in the two recently released germplasm lines NC96BGTA4 and NC99BGTAG11. Between 99 and 194 F 2:3 progenies plus parents in two populations, ‘Saluda’ × NC96BGTA4 and Saluda × NC99BGTAG11, were evaluated in greenhouse and field nurseries for reaction to powdery mildew infection. Results indicated that the germplasm lines each contained a different, partially dominant, major resistance gene. The two segregating populations were subjected to amplified fragment length polymorphism (AFLP) and simple sequence repeat, or microsatellite (SSR) analyses. Both resistance genes were located on the long arm of chromosome 7A. The most likely locus order indicated that the resistance gene in NC96BGTA4 was flanked by the SSR loci Xbarc292 and Xwmc525 The resistance gene in NC99BGTAG11 was most likely flanked by the AFLP markers XE38M54‐196 and XE36M55‐126 , and the SSR loci Xgwm332 and Xwmc525 Both genes mapped to a chromosome arm that contains the powdery mildew resistance loci Pm1 and Pm9 The resistance genes in the two germplasms are different from the Pm1a allele. Our mapping results suggested that the resistance genes were not alleles at the Pm1 or Pm9 loci, but further allelism tests are necessary to determine the relationships both between the two genes themselves and between the two genes and named Pm loci on chromosome 7AL. DA - 2005/// PY - 2005/// DO - 10.2135/cropsci2004.0530 VL - 45 IS - 4 SP - 1578-1586 SN - 1435-0653 ER - TY - JOUR TI - High levels of nitrifying bacteria in intermittently aerated reactors treating high ammonia wastewater AU - Mota, C AU - Ridenoure, J AU - Cheng, JY AU - Reyes, FL T2 - FEMS MICROBIOLOGY ECOLOGY AB - Changes in the fractions of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria in two laboratory-scale reactors were investigated using 16S rRNA probe hybridizations. The reactors were operated in intermittent aeration mode and different aeration cycles to treat anaerobically digested swine wastewater with ammonia concentrations up to 175 mg NH3-N/L. High ammonia removals (>98.8%) were achieved even with increased nitrogen loads and lower aeration: non-aeration time ratios of 1 h:3 h. Nitrosomonas/Nitrosococcus mobilis were the dominant ammonia-oxidizing bacteria in the reactors. Nitrospira-like organisms were the dominant nitrite-oxidizing bacteria during most of the investigation, but were occasionally outcompeted by Nitrobacter. High levels of nitrifiers were measured in the biomass of both reactors, and ammonia-oxidizing bacteria and nitrite-oxidizing bacterial levels adjusted to changing aeration: non-aeration time ratios. Theoretical ammonia-oxidizer fractions, determined by a mathematical model, were comparable to the measured values, although the measured biomass fractions were different at each stage while the theoretical values remained approximately constant. Stable ammonia removals and no nitrite accumulation were observed even when rRNA levels of ammonia oxidizers and nitrite-oxidizers reached a minimum of 7.2% and 8.6% of total rRNA, respectively. Stable nitrogen removal performance at an aeration: non-aeration ratio of 1 h:3 h suggests the possibility of significant savings in operational costs. DA - 2005/11/1/ PY - 2005/11/1/ DO - 10.1016/j.femsec.2005.05.001 VL - 54 IS - 3 SP - 391-400 SN - 1574-6941 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-26244460968&partnerID=MN8TOARS KW - ammonia oxidizing bacteria KW - nitrite oxidizing bacteria KW - nitrification KW - oligonucleotide probes KW - intermittent aeration KW - swine wastewater ER - TY - JOUR TI - Detection of quantitative trait loci influencing conformation traits and calving ease in Holstein-Friesian cattle AU - Ashwell, MS AU - Heyen, DW AU - Weller, JI AU - Ron, M AU - Sonstegard, TS AU - Van Tassell, CP AU - Lewin, HA T2 - JOURNAL OF DAIRY SCIENCE AB - An extension of our previous genome scan of a North American Holstein-Friesian population was conducted to identify quantitative trait loci (QTL) affecting conformation traits. Resource families consisted of 1404 sons of 10 elite sires. Genome coverage was estimated to be 2713.5 cM (90%) for 406 markers using a granddaughter design. Regression interval mapping was used to detect QTL affecting 22 conformation traits, including body, udder, feet and legs, and dairy conformation as well as calving ease. Analysis of the families jointly identified 41 chromosome-wise significant QTL influencing conformation traits and 3 significant QTL influencing calving ease on 20 chromosomes. The false discovery rate method was used to account for multiple testing and 3/4 of the suggestive and 5/6 of significant QTL should be real effects. Fourteen of the 44 QTL were significant at the genome-wise level. Comparison of these results with other published reports identifies common QTL affecting conformation traits. Regions on 10 chromosomes appear to affect multiple traits, including conformation, milk production, and somatic cell score, within these particular US Holstein families. Additional work is needed to determine the precise locations of the QTL and select positional candidate genes influencing these traits. DA - 2005/11// PY - 2005/11// DO - 10.3168/jds.S0022-0302(05)73095-2 VL - 88 IS - 11 SP - 4111-4119 SN - 0022-0302 KW - genome scan KW - dairy KW - conformation KW - quantitative trait loci ER - TY - JOUR TI - Campylobacter coli in swine production: Antimicrobial resistance mechanisms and molecular epidemiology AU - Thakur, S AU - Gebreyes, WA T2 - JOURNAL OF CLINICAL MICROBIOLOGY AB - The aim of this study was to determine antimicrobial resistance, to evaluate and compare the use of two genotyping methods for molecular epidemiology purposes, and to determine the genotypic diversity of Campylobacter coli of porcine origin. A total of 100 C. coli isolates from swine were tested for susceptibility to six antimicrobials using the agar dilution method and genotyped using two high-resolution fingerprinting approaches: multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Evaluation of the methods was based on their resistance patterns, discriminatory indexes (DI), high test throughputs, costs, and turnaround times. Resistance to erythromycin and tetracycline was the most common. Both genotypic methods were found to have high discriminatory power, although MLST had a higher DI (0.936) than PFGE (DI = 0.889). It also had a higher throughput than PFGE. Isolates were clustered into 27 groups by MLST compared to 11 by PFGE. MLST was able to further discriminate the isolates grouped under the same cluster by PFGE. Out of the 65 MLST sequence types (STs) identified among the total isolates, 50 were reported for the first time. Most STs were found to be specific to the farm (n = 38) and to slaughter (n = 22). Resistance against tetracycline and erythromycin was encoded by the tet(O) gene and a A2075G point mutation in the 23S rRNA gene, respectively. A high ciprofloxacin MIC (>64 microg/liter) was conferred by a point mutation in the gyrA gene. The weak clonal structure of the C. coli population among swine was further highlighted by the index of association value of 0.293. The findings of this study indicate that multidrug-resistant diverse C. coli strains exhibiting resistance to ciprofloxacin and erythromycin are concerning, since these are the drugs of choice for treating invasive campylobacteriosis cases in humans. DA - 2005/11// PY - 2005/11// DO - 10.1128/JCM.43.11.5705-5714.2005 VL - 43 IS - 11 SP - 5705-5714 SN - 1098-660X ER - TY - JOUR TI - Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system AU - Diener, S. E. AU - Houfek, T. D. AU - Kalat, S. E. AU - Windham, D. E. AU - Burke, M. AU - Opperman, C. AU - Dean, R. A. T2 - BMC Bioinformatics DA - 2005/// PY - 2005/// VL - 6 ER - TY - JOUR TI - A link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis AU - Stepanova, AN AU - Hoyt, JM AU - Hamilton, AA AU - Alonso, JM T2 - PLANT CELL AB - The plant hormone ethylene participates in the regulation of a variety of developmental processes and serves as a key mediator of plant responses to biotic and abiotic stress factors. The diversity of ethylene functions is achieved, at least in part, by combinatorial interactions with other hormonal signals. Here, we show that ethylene-triggered inhibition of root growth, one of the classical effects of ethylene in Arabidopsis thaliana seedlings, is mediated by the action of the WEAK ETHYLENE INSENSITIVE2/ANTHRANILATE SYNTHASE alpha1 (WEI2/ASA1) and WEI7/ANTHRANILATE SYNTHASE beta1 (ASB1) genes that encode alpha- and beta-subunits of a rate-limiting enzyme of Trp biosynthesis, anthranilate synthase. Upregulation of WEI2/ASA1 and WEI7/ASB1 by ethylene results in the accumulation of auxin in the tip of primary root, whereas loss-of-function mutations in these genes prevent the ethylene-mediated auxin increase. Furthermore, wei2 and wei7 suppress the high-auxin phenotypes of superroot1 (sur1) and sur2, two auxin-overproducing mutants, suggesting that the roles of WEI2 and WEI7 in the regulation of auxin biosynthesis are not restricted to the ethylene response. Together, these findings reveal that ASA1 and ASB1 are key elements in the regulation of auxin production and an unexpected node of interaction between ethylene responses and auxin biosynthesis in Arabidopsis. This study provides a mechanistic explanation for the root-specific ethylene insensitivity of wei2 and wei7, illustrating how interactions between hormones can be used to achieve response specificity. DA - 2005/8// PY - 2005/8// DO - 10.1105/tpc.105.033365 VL - 17 IS - 8 SP - 2230-2242 SN - 1532-298X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-27744445823&partnerID=MN8TOARS ER - TY - JOUR TI - Variable intake, compensatory growth, and increased growth efficiency in fish: Models and mechanisms AU - Skalski, GT AU - Picha, ME AU - Gilliam, JF AU - Borski, RJ T2 - ECOLOGY AB - Resources fluctuate in space and time, and animals routinely experience temporally varying opportunities for resource intake, and variation in intake itself. We investigate consequences of such variation in intake on growth and growth efficiency (growth per unit intake) in juvenile hybrid striped bass. We observed, after statistically accounting for the effects of total consumption and initial body size, that individuals receiving a low ration followed by a higher ration (the fluctuating ration) grew faster than individuals receiving a temporally constant ration (the normal ration). To interpret this increase in growth efficiency, we consider a set of alternative models representing different physiological hypotheses of the growth process. Using a simple growth model, an analytical result shows that the fluctuating ration as typically applied in experiments (a low ration followed by a high ration), independent of any change in physiology, increases growth efficiency relative to individuals on the normal ration. Growth efficiency increases because cumulative maintenance costs are lower for individuals that stay small initially and then grow rapidly in comparison to individuals that grow steadily. Further, a statistical analysis of alternative models inferred that fish receiving a variable ration show higher assimilation and/or conversion efficiencies of food and lower mass-specific maintenance costs. Our analysis suggests that the lower cumulative maintenance costs incurred over a time interval with low consumption followed by high consumption act in association with higher assimilation-conversion efficiencies, and lower overall mass-specific maintenance costs to increase growth efficiency in hybrid striped bass. DA - 2005/6// PY - 2005/6// DO - 10.1890/04-0896 VL - 86 IS - 6 SP - 1452-1462 SN - 1939-9170 KW - bioenergetics KW - compensatory growth KW - energy budget model KW - experiment KW - hybrid striped bass ER - TY - JOUR TI - Summary of IEG-40 meeting: Silviculture and genetic impacts on productivity of southern pine forests AU - McKeand, S. E. AU - Allen, H. L. T2 - Southern Journal of Applied Forestry DA - 2005/// PY - 2005/// VL - 29 IS - 2 SP - 61 ER - TY - JOUR TI - Strategies and case studies for incorporating ecophysiology into southern pine tree improvement programs AU - Martin, T. A. AU - Dougherty, P. M. AU - McKeand, S. E. T2 - Southern Journal of Applied Forestry DA - 2005/// PY - 2005/// VL - 29 IS - 2 SP - 70-79 ER - TY - JOUR TI - Seasonal activity and species composition of dung beetles (Coleoptera : Scarabaeidae and Geotrupidae) inhabiting cattle pastures in North Carolina AU - Bertone, M AU - Green, J AU - Washburn, S AU - Poore, M AU - Sorenson, C AU - Watson, DW T2 - ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA AB - Species composition and seasonal distribution of dung beetles were studied on dairy and beef cattle pastures in North Carolina. Study sites included a dairy located in the piedmont region (North Carolina Department of Agriculture Piedmont Research Station, Salisbury, NC) and a combined dairy/beef facility in the coastal plain (North Carolina Department of Agriculture Center for Environmental Farming Systems, Goldsboro, NC). Dung beetles were trapped in cattle pastures from March 2002 through September 2003 by using dung-baited pitfall traps. Trapping yielded 4,111 beetles representing 14 species from the piedmont dairy, including Aphodius prodromus Brahm, a new record for North Carolina. Totals of 57,026 beetles representing 28 species and 28,857 beetles representing 26 species were trapped from the dairy unit and beef unit in the coastal plain site, respectively. Onthophagus gazella (F.), a second new record for North Carolina, was collected from the coastal plain. Beetles common to all collection sites include Aphodius erraticus (L.), Aphodius fimetarius (L.), Aphodius granarius (L.), Aphodius pseudolividus Balthasar, Onthophagus taurus Schreber, Onthophagus hecate hecate Panzer, and Onthophagus pennsylvanicus Harold. The introduced beetle O. taurus dominated the dung beetle population, accounting for >50% of the total beetles caught at either site. Beetle activity was greatest from March until November, with activity declining during the winter. Nine exotic species in the genera Onthophagus and Aphodius represented nearly 95% of the beetles trapped. DA - 2005/5// PY - 2005/5// DO - 10.1603/0013-8746(2005)098[0309:SAASCO]2.0.CO;2 VL - 98 IS - 3 SP - 309-321 SN - 1938-2901 KW - Onthophagus KW - Aphodius KW - cattle KW - piedmont KW - coastal-plain ER - TY - JOUR TI - Risk assessment with current deployment strategies for fusiform rust-resistant loblolly and slash pines AU - Bridgwater, F. AU - Kubisiak, T. AU - Byram, T. AU - McKeand, S. T2 - Southern Journal of Applied Forestry DA - 2005/// PY - 2005/// VL - 29 IS - 2 SP - 80-87 ER - TY - JOUR TI - Planting nonlocal seed sources of loblolly pine: Managing benefits and risks AU - Lambeth, C. AU - McKeand, S. AU - Rousseau, R. AU - Schmidtling, R. T2 - Southern Journal of Applied Forestry DA - 2005/// PY - 2005/// VL - 29 IS - 2 SP - 96-104 ER - TY - JOUR TI - PACLIMS: A component LIM system for high-throughput functional genomic analysis AU - Donofrio, N. AU - Rajagopalon, R. AU - Brown, D. AU - Diener, S. AU - Windham, D. AU - Nolin, S. AU - Floyd, A. AU - Mitchell, T. AU - Galadima, N. AU - Tucker, S. AU - Orbach, M. J. AU - Patel, G. AU - Farman, M. AU - Pampanwar, V. AU - Soderlund, C. AU - Lee, Y. H. AU - Dean, R. A. T2 - BMC Bioinformatics DA - 2005/// PY - 2005/// VL - 6 ER - TY - JOUR TI - Nuclear rDNA variability in laboratory strains of the German cockroach Blattella germanica L. (Blattellidae) AU - Lazebnaya, , IV AU - Semenova, SK AU - Lazebnyi, OE AU - Schal, C AU - Mukha, DV T2 - RUSSIAN JOURNAL OF GENETICS DA - 2005/5// PY - 2005/5// DO - 10.1007/s11177-005-0112-y VL - 41 IS - 5 SP - 468-472 SN - 1022-7954 ER - TY - JOUR TI - Molecular preservation in Late Cretaceous sauropod dinosaur eggshells AU - Schweitzer, MH AU - Chiappe, L AU - Garrido, AC AU - Lowenstein, JM AU - Pincus, SH T2 - PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES AB - Exceptionally preserved sauropod eggshells discovered in Upper Cretaceous (Campanian) deposits in Patagonia, Argentina, contain skeletal remains and soft tissues of embryonic Titanosaurid dinosaurs. To preserve these labile embryonic remains, the rate of mineral precipitation must have superseded post-mortem degradative processes, resulting in virtually instantaneous mineralization of soft tissues. If so, mineralization may also have been rapid enough to retain fragments of original biomolecules in these specimens. To investigate preservation of biomolecular compounds in these well-preserved sauropod dinosaur eggshells, we applied multiple analytical techniques. Results demonstrate organic compounds and antigenic structures similar to those found in extant eggshells. DA - 2005/4/22/ PY - 2005/4/22/ DO - 10.1098/rspb.2004.2876 VL - 272 IS - 1565 SP - 775-784 SN - 0962-8452 KW - palaeoimmunology KW - dinosaur KW - immunohistochemistry KW - eggshell KW - embryo KW - histology ER - TY - JOUR TI - Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction AU - Jantasuriyarat, C AU - Gowda, M AU - Haller, K AU - Hatfield, J AU - Lu, GD AU - Stahlberg, E AU - Zhou, B AU - Li, HM AU - Kim, HR AU - Yu, YS AU - Dean, RA AU - Wing, RA AU - Soderlund, C AU - Wang, GL T2 - PLANT PHYSIOLOGY AB - To better understand the molecular basis of the defense response against the rice blast fungus (Magnaporthe grisea), a large-scale expressed sequence tag (EST) sequencing approach was used to identify genes involved in the early infection stages in rice (Oryza sativa). Six cDNA libraries were constructed using infected leaf tissues harvested from 6 conditions: resistant, partially resistant, and susceptible reactions at both 6 and 24 h after inoculation. Two additional libraries were constructed using uninoculated leaves and leaves from the lesion mimic mutant spl11. A total of 68,920 ESTs were generated from 8 libraries. Clustering and assembly analyses resulted in 13,570 unique sequences from 10,934 contigs and 2,636 singletons. Gene function classification showed that 42% of the ESTs were predicted to have putative gene function. Comparison of the pathogen-challenged libraries with the uninoculated control library revealed an increase in the percentage of genes in the functional categories of defense and signal transduction mechanisms and cell cycle control, cell division, and chromosome partitioning. In addition, hierarchical clustering analysis grouped the eight libraries based on their disease reactions. A total of 7,748 new and unique ESTs were identified from our collection compared with the KOME full-length cDNA collection. Interestingly, we found that rice ESTs are more closely related to sorghum (Sorghum bicolor) ESTs than to barley (Hordeum vulgare), wheat (Triticum aestivum), and maize (Zea mays) ESTs. The large cataloged collection of rice ESTs in this study provides a solid foundation for further characterization of the rice defense response and is a useful public genomic resource for rice functional genomics studies. DA - 2005/5// PY - 2005/5// DO - 10.1104/pp.104.055624 VL - 138 IS - 1 SP - 105-115 SN - 1532-2548 ER - TY - JOUR TI - Integrating decay, storage, kinetic selection, and filamentous backbone factors in a bacterial competition model AU - Lou, IC AU - Reyes, FL T2 - WATER ENVIRONMENT RESEARCH AB - Filamentous bulking in activated sludge systems occurs when filamentous organisms outgrow floc‐forming bacteria and interfere with sludge settling. The competition between filaments and floc formers has been described previously using the kinetic selection and filamentous backbone theories. We hypothesized that differences in decay rates and storage abilities also affect this competition. We tested this hypothesis by integrating these four factors into a substrate‐utilization model to predict and explain coexistence in a completely mixed reactor. In addition, filamentous and nonfilamentous sludges were developed in laboratory‐scale reactors and analyzed to determine decay rates. The modeling results showed coexistence of the two organism types, and sensitivity analysis showed that the kinetic parameters, storage rate constants, and backbone coefficient had the greatest effect on the simulation results. Monte Carlo simulation showed the effect of storage, and the ranges of dilution rates wherein one group outcompeted the other were delineated. DA - 2005/// PY - 2005/// DO - 10.2175/106143005X41870 VL - 77 IS - 3 SP - 287-296 SN - 1554-7531 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-18644385905&partnerID=MN8TOARS KW - bulking KW - kinetic selection KW - filamentous backbone KW - decay rate KW - storage KW - modeling ER - TY - JOUR TI - Geminivirus C3 protein: Replication enhancement and protein interactions AU - Settlage, SB AU - See, RG AU - Hanley-Bowdoin, L T2 - JOURNAL OF VIROLOGY AB - ABSTRACT Most dicot-infecting geminiviruses encode a replication enhancer protein (C3, AL3, or REn) that is required for optimal replication of their small, single-stranded DNA genomes. C3 interacts with C1, the essential viral replication protein that initiates rolling circle replication. C3 also homo-oligomerizes and interacts with at least two host-encoded proteins, proliferating cell nuclear antigen (PCNA) and the retinoblastoma-related protein (pRBR). It has been proposed that protein interactions contribute to C3 function. Using the C3 protein of Tomato yellow leaf curl virus , we examined the impact of mutations to amino acids that are conserved across the C3 protein family on replication enhancement and protein interactions. Surprisingly, many of the mutations did not affect replication enhancement activity of C3 in tobacco protoplasts. Other mutations either enhanced or were detrimental to C3 replication activity. Analysis of mutated proteins in yeast two-hybrid assays indicated that mutations that inactivate C3 replication enhancement activity also reduce or inactivate C3 oligomerization and interaction with C1 and PCNA. In contrast, mutated C3 proteins impaired for pRBR binding are fully functional in replication assays. Hydrophobic residues in the middle of the C3 protein were implicated in C3 interaction with itself, C1, and PCNA, while polar resides at both the N and C termini of the protein are important for C3-pRBR interaction. These experiments established the importance of C3-C3, C3-C1, and C3-PCNA interactions in geminivirus replication. While C3-pRBR interaction is not required for viral replication in cycling cells, it may play a role during infection of differentiated cells in intact plants. DA - 2005/8// PY - 2005/8// DO - 10.1128/jvi.79.15.9885-9895.2005 VL - 79 IS - 15 SP - 9885-9895 SN - 1098-5514 ER - TY - JOUR TI - Expression, production and excretion of Bla g 1, a major human allergen, in relation to food intake in the German cockroach, Blattella germanica AU - Gore, JC AU - Schal, C T2 - MEDICAL AND VETERINARY ENTOMOLOGY AB - Abstract. The German cockroach, Blattella germanica (Linnaeus) (Dictyoptera: Blattellidae), produces several potent human allergens, one of which, Blattella germanica allergen 1 (Bla g 1), is produced in the midgut and excreted in faeces. We tested with descriptive and experimental approaches the hypothesis that Bla g 1 production is related to food intake in adult males and females of the German cockroach. Bla g 1 mRNA expression in the female midgut (assayed by real time quantitative polymerase chain reaction), her Bla g 1 content (assayed by enzyme‐linked immunosorbent assay), and the female's faeces production and its Bla g 1 content tracked a cyclic pattern in relation to the gonadotrophic cycle. All four measures rose as food intake increased, declined before oviposition in relation to diminishing food intake, and remained low while the female carried an egg case for 20 days. After her first clutch of embryos hatched, the female resumed feeding, and faeces and Bla g 1 production increased concomitantly. Both Bla g 1 mRNA expression and Bla g 1 protein levels remained low in experimentally starved females. However, when starved females were allowed to feed, Bla g 1 production elevated and the gonadotrophic cycle resumed. Bla g 1 mRNA expression also increased six‐fold in response to feeding compared to starved females. By contrast, there were no apparent cycles in the pattern of Bla g 1 production in males, reflecting their low and non‐cyclic food intake. Our results therefore demonstrate that Bla g 1 production in B. germanica is modulated in relation to food intake. DA - 2005/6// PY - 2005/6// DO - 10.1111/j.0269-283X.2005.00550.x VL - 19 IS - 2 SP - 127-134 SN - 1365-2915 KW - Bla g 1 KW - cockroach allergen KW - food intake KW - German cockroach ER - TY - JOUR TI - Conversion of nicotine to nornicotine in Nicotiana tabacum is mediated by CYP82E4, a cytochrome P450 monooxygenase AU - Siminszky, B. AU - Gavilano, L. AU - Bowen, S. W. AU - Dewey, R. E. T2 - Proceedings of the National Academy of Sciences of the United States of America DA - 2005/// PY - 2005/// DO - 10.1073/pnas.050658102 VL - 102 IS - 41 SP - 14919-14924 ER - TY - JOUR TI - Changes in the rRNA levels of specific microbial groups in activated sludge during sample handling and storage AU - Keith, JE AU - Boyer, JG AU - Reyes, FL T2 - LETTERS IN APPLIED MICROBIOLOGY AB - Aims: To quantitatively analyse the changes in group-specific rRNA levels in activated sludge as a function of sample handling and storage procedure. Methods and Results: Quantitative membrane hybridizations with 32P-labelled oligonucleotide probes were used to analyse the effects of different sample handling and storage conditions on the relative rRNA levels of the alpha, beta, and gamma-Proteobacteria, the Cytophaga-Flavobacteria group, and the mycolic acid-containing actinomycetes in activated sludge. Group-specific rRNA levels, expressed as percentages of total 16S rRNA detected with a universal probe, in samples maintained at room temperature significantly changed after 48 h. Group-specific rRNA levels in samples treated with chloramphenicol showed significant change after 72 h. Conclusions: Sample storage at room temperature is a viable option if freezing or analysis can be performed within 24 h, while treatment with chlorampenicol can extend that time to at least 48 h. Significance and Impact of the Study: Handling, shipping, and storage of environmental samples under several conditions may result in inaccurate determination of the microbial populations in microbial ecology studies. DA - 2005/// PY - 2005/// DO - 10.1111/j.1472-765x.2005.01745.x VL - 41 IS - 2 SP - 208-215 SN - 1472-765X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-22644440453&partnerID=MN8TOARS KW - 16S rRNA KW - membrane hybridization KW - oligonucleotide probe hybridization KW - postsampling conditions ER - TY - JOUR TI - Biotechnological improvement of cotton fibre maturity AU - Haigler, CH AU - Zhang, DH AU - Wilkerson, CG T2 - PHYSIOLOGIA PLANTARUM AB - This mini‐review focuses on the prospects and tools for controlling cotton fibre secondary wall thickness. Cotton fibre secondary walls are composed of almost 100% cellulose, and are responsible for fibre maturity and a large component of fibre yield. Improved fibre yield and maturity would result from the ability to control secondary wall cellulose deposition quantitatively, including making the process less sensitive to environmental stress. Both genetic engineering and marker‐assisted breeding are possible avenues for effecting such improvements, but first key genes that participate in the regulation and control of secondary wall cellulose biogenesis must be identified. Recent advances towards understanding and manipulating cotton fibre secondary wall deposition that are discussed here include: (i) experimental approaches to identify metabolic participants in cellulose biogenesis; (ii) isolation and characterization of promoters to drive foreign gene expression preferentially during secondary wall deposition; and (iii) a novel set of cDNA sequences representing genes that are differentially expressed during cotton fibre secondary wall deposition compared with primary wall deposition. DA - 2005/7// PY - 2005/7// DO - 10.1111/j.1399-3054.2005.00480.x VL - 124 IS - 3 SP - 285-294 SN - 1399-3054 ER - TY - JOUR TI - An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima AU - Conners, SB AU - Montero, CI AU - Comfort, DA AU - Shockley, KR AU - Johnson, MR AU - Chhabra, , SR AU - Kelly, RM T2 - JOURNAL OF BACTERIOLOGY AB - ABSTRACT Comprehensive analysis of genome-wide expression patterns during growth of the hyperthermophilic bacterium Thermotoga maritima on 14 monosaccharide and polysaccharide substrates was undertaken with the goal of proposing carbohydrate specificities for transport systems and putative transcriptional regulators. Saccharide-induced regulons were predicted through the complementary use of comparative genomics, mixed-model analysis of genome-wide microarray expression data, and examination of upstream sequence patterns. The results indicate that T. maritima relies extensively on ABC transporters for carbohydrate uptake, many of which are likely controlled by local regulators responsive to either the transport substrate or a key metabolic degradation product. Roles in uptake of specific carbohydrates were suggested for members of the expanded Opp/Dpp family of ABC transporters. In this family, phylogenetic relationships among transport systems revealed patterns of possible duplication and divergence as a strategy for the evolution of new uptake capabilities. The presence of GC-rich hairpin sequences between substrate-binding proteins and other components of Opp/Dpp family transporters offers a possible explanation for differential regulation of transporter subunit genes. Numerous improvements to T. maritima genome annotations were proposed, including the identification of ABC transport systems originally annotated as oligopeptide transporters as candidate transporters for rhamnose, xylose, β-xylan, andβ -glucans and identification of genes likely to encode proteins missing from current annotations of the pentose phosphate pathway. Beyond the information obtained for T. maritima , the present study illustrates how expression-based strategies can be used for improving genome annotation in other microorganisms, especially those for which genetic systems are unavailable. DA - 2005/11// PY - 2005/11// DO - 10.1128/JB.187.21.7267-7282.2005 VL - 187 IS - 21 SP - 7267-7282 SN - 1098-5530 ER - TY - JOUR TI - 'NC-Sunshine' and 'NC-Stratford' slicing cucumber hybrids AU - Wehner, TC T2 - HORTSCIENCE AB - Four slicing (fresh-market) cucumber inbreds (NC-58, NC-59, NC-62, and NC-63) and two hybrids (‘NC-Stratford’ and ‘NCSunshine’), were developed at North Carolina State University. As with most cucumber cultivars released from N.C. State, ‘NC-Stratford’ and ‘NC-Sunshine’ were named for places around the state. ‘NC-Stratford’ is the F 1 of NC-58 × NC-59, and ‘NC-Sunshine’ is the F 1 of NC-62 × NC-63. The four inbreds have been self-pollinated past the S 12 generation, and were developed from the North Carolina Elite Determinate Slicer (NCEDS) population. The NCEDS population was developed by 1) crossing elite hybrids and inbreds with ‘Spacemaster’ dwarf-determinate inbred in 1983; 2) intercrossing the dwarf-determinate F 2 with dwarf-determinate hybrids and inbreds; and 3) intercrossing the F 1 to form a population for use in recurrent selection. Selection methods were developed that optimized gain for yield and other traits (Wehner, 1989). Selection in the NCEDS population was for fruit shape, and total, marketable and early yield in the spring season, as well as for resistance to foliar fungal diseases in the summer season. The main diseases in the summer were anthracnose [Colletotrichum orbiculare (Berk. and Curt.) Arx] and gummy stem blight [Didymella bryoniae (Auersw.) Rehm]. In addition to yield, earliness, quality and disease resistance, the cucumber families were selected for production of suffi cient seeds to plant the test and intercross plots, rapid seed germination and emergence, rapid vine growth and fl owering, and proper fruit type. DA - 2005/8// PY - 2005/8// DO - 10.21273/hortsci.40.5.1577 VL - 40 IS - 5 SP - 1577-1579 SN - 0018-5345 KW - Cucumis sativus KW - germplasm KW - processing cucumber KW - vegetable breeding ER - TY - JOUR TI - 'NC-Davie' and 'NC-Duplin' pickling cucumber hybrids AU - Wehner, TC T2 - HORTSCIENCE AB - Four pickling (processing) cucumber inbreds (NC-54, NC-55, NC-56, and NC-57) and two pickling cucumber hybrids (‘NCDavie’ and ‘NC-Duplin’), were developed at North Carolina State University. As with most cucumber cultivars released from N.C. State, ‘NC-Davie’ and ‘NC-Duplin’ were named for places around the state. ‘NC-Davie’ is the F 1 of NC-54 × NC-55, and ‘NC-Duplin’ is the F 1 of NC-56 × NC-57. The four inbreds have been self-pollinated past the S 12 generation, and were developed from the North Carolina Elite Determinate Pickling (NCEDP) cucumber population. The NCEDP population was developed by 1) crossing elite hybrids and inbreds with NCSU M 21 dwarf-determinate inbred in 1983; 2) intercrossing the determinate F 2 with determinate hybrids and inbreds; and 3) intercrossing the F 1 to form a population for use in recurrent selection. Selection methods were developed that optimized gain for yield and other traits (Wehner, 1989). Selection in the NCEDP population was for fruit shape, and total, marketable and early yield in the spring season, as well as for resistance to foliar fungal diseases in the summer season. The main diseases in the summer were anthracnose [Colletotrichum orbiculare (Berk. and Curt.) Arx] and gummy stem blight [Didymella bryoniae (Auersw.) Rehm]. In addition to yield, earliness, quality and disease resistance, the cucumber families were selected for production of suffi cient seeds to plant the test and intercross plots, rapid seed germination and emergence, rapid vine growth and fl owering, and proper fruit type. DA - 2005/8// PY - 2005/8// DO - 10.21273/hortsci.40.5.1574 VL - 40 IS - 5 SP - 1574-1576 SN - 0018-5345 KW - Cucumis sativus KW - germplasm KW - processing cucumber KW - vegetable breeding ER - TY - JOUR TI - Whole-genome scan to detect QTL for milk production, conformation, fertility and functional traits in two US Holstein families AU - Schnabel, RD AU - Sonstegard, TS AU - Taylor, JF AU - Ashwell, MS T2 - ANIMAL GENETICS AB - Summary A genome scan was conducted in two US Holstein half‐sib families to identify quantitative trait loci (QTL) affecting milk production and conformation traits using the granddaughter design. The sires of the two studied families were related as sire and son and had 96 and 212 sons respectively. A total of 221 microsatellite loci were scored in both families. Statistical analysis was performed using two different analytical methods; half‐sib least squares regression and Bayesian Monte Carlo Markov Chain. Traits analysed included five traditional milk production traits, somatic cell count, daughter pregnancy rate, male fertility and 20 conformation traits. A total of 47 tests achieved at least genome‐wise significance. However, results from the two methods of analysis were only concordant for QTL location and level of significance in eight instances. DA - 2005/10// PY - 2005/10// DO - 10.1111/j.1365-2052.2005.01337.x VL - 36 IS - 5 SP - 408-416 SN - 1365-2052 KW - conformation KW - fertility KW - milk production KW - quantitative trait loci ER - TY - JOUR TI - The rb7 matrix attachment region increases the likelihood and magnitude of transgene expression in tobacco cells: A flow cytometric study AU - Halweg, C AU - Thompson, WF AU - Spiker, S T2 - PLANT CELL AB - Many studies in both plant and animal systems have shown that matrix attachment regions (MARs) can increase expression of transgenes in whole organisms or cells in culture. Because histochemical assays often indicate variegated transgene expression, a question arises: Do MARs increase transgene expression by increasing the percentage of cells expressing the transgene (likelihood), by increasing the level of expression in expressing cells (magnitude), or both? To address this question, we used flow cytometry to measure green fluorescent protein (GFP) expression in individual tobacco (Nicotiana tabacum) cells from lines transformed by Agrobacteriumtumefaciens. We conclude that MAR-mediated overall increases in transgene expression involve both likelihood and magnitude. On average, cell lines transformed with the Rb7 MAR-containing vector expressed GFP at levels 2.0- to 3.7-fold higher than controls. MAR lines had fewer nonexpressing cells than control lines (10% versus 45%), and the magnitude of GFP expression in expressing cells was greater in MAR lines by 1.9- to 2.9-fold. We also show that flow cytometry measurements on cells from isogenic lines are consistent with those from populations of independently transformed cell lines. By obviating the need to establish isogenic lines, this use of flow cytometry could greatly simplify the evaluation of MARs or other sequence elements that affect transgene expression. DA - 2005/2// PY - 2005/2// DO - 10.1105/tpc.104.028100 VL - 17 IS - 2 SP - 418-429 SN - 1532-298X ER - TY - JOUR TI - The onset of bioconvection in a suspension of gyrotactic microorganisms in a fluid layer of finite depth heated from below AU - Kuznetsov, AV T2 - INTERNATIONAL COMMUNICATIONS IN HEAT AND MASS TRANSFER AB - The aim of this paper is to investigate the effect of heating from below on the stability of a suspension of motile gyrotactic microorganisms in a fluid layer of finite depth. This problem is relevant to a number of geophysical applications, such as investigation of the dynamics of some species of thermophiles (heat-loving microorganisms) living in hot springs. It is established that heating from below makes the system more unstable and helps the development of bioconvection. By performing a linear stability analysis, a correlation for the critical bioconvection Rayleigh number is obtained. DA - 2005/4// PY - 2005/4// DO - 10.1016/j.icheatmasstransfer.2004.10.021 VL - 32 IS - 5 SP - 574-582 SN - 1879-0178 KW - thermo-bioconvection KW - motile microorganisms KW - gyrotaxis KW - stability KW - heating from below ER - TY - JOUR TI - The distributions of the duplicate oestrogen receptors ER-beta a and ER-beta b in the forebrain of the Atlantic croaker (Micropogonias undulatus): evidence for subfunctionalization after gene duplication AU - Hawkins, MB AU - Godwin, J AU - Crews, D AU - Thomas, P T2 - PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES AB - Teleost fishes have three distinct oestrogen receptor (ER) subtypes: ER-alpha, ER-beta a (or ER-gamma) and ER-beta b. ER-beta a and ER-beta b arose from a duplication of an ancestral ER-beta gene early in the teleost lineage. Here, we describe the distribution of the three ER mRNAs in the hypothalamus and cerebellum of the Atlantic croaker to address two issues: the specific functions of multiple ERs in the neuroendocrine system and the evolution and fate of duplicated genes. ER-alpha was detected in nuclei of the preoptic area (POA) and hypothalamus previously shown to possess ER-alphas in teleosts. AcER-beta b, but not ER-beta a, labelling was detected in the magnocellular neurons of the POA, nucleus posterior tuberis, the nucleus recessus posterior and cerebellum. By contrast, acER-beta a, but not ER-beta b, was detected in the dorsal anterior parvocellular POA and suprachiasmatic nucleus. Both ER-betas were found in posterior parvocellular and ventral anterior POA nuclei, the ventral hypothalamus, and periventricular dorsal hypothalamus. The differences we observed in ER subtype mRNA distribution within well-characterized brain nuclei suggest that ER-beta a and ER-beta b have distinct functions in the neuroendocrine control of reproduction and behaviour, and provide evidence that the teleost ER-beta paralogues have partitioned functions of the ancestral ER-beta gene they shared with tetrapods. DA - 2005/3/22/ PY - 2005/3/22/ DO - 10.1098/rspb.2004.3008 VL - 272 IS - 1563 SP - 633-641 SN - 1471-2954 KW - oestrogen receptor KW - gene duplication KW - teleostfishes KW - neuroendocrine regulation KW - hypothalamus KW - brain ER - TY - JOUR TI - The distribution of genetic parameter estimates and confidence intervals from small disconnected diallels AU - Isik, F AU - Boos, DD AU - Li, BL T2 - THEORETICAL AND APPLIED GENETICS DA - 2005/5// PY - 2005/5// DO - 10.1007/s00122-005-1957-0 VL - 110 IS - 7 SP - 1236-1243 SN - 1432-2242 ER - TY - JOUR TI - Settling of bidispersed small solid particles in a dilute suspension containing gyrotactic micro-organisms AU - Geng, P AU - Kuznetsov, AV T2 - INTERNATIONAL JOURNAL OF ENGINEERING SCIENCE AB - The motivation of this research is to investigate the feasibility of utilizing bioconvection for enhancing mixing in a suspension of small solid particles. This may be important in micro-fluidic applications relevant to biotechnology and medicine, such as analyses of DNA or drugs, screening of patients, and combinatorial synthesis. Traditionally, the mixing of fluids in micro-volumes has been limited to diffusion. Due to the microscopic size of the organisms involved in bioconvection, bioconvective flows are a prospective and novel alternative for micro-fluidic mixing. This paper considers a bidispersed suspension of small solid particles that have different densities and settling velocities in a fluid that contains motile gyrotactic micro-organisms. The particles are assumed to be sufficiently small so that their Brownian diffusion is not negligible. It is found that the number density distribution of solid particles of one type impacts that of particles of the other type as well as that of micro-organisms. DA - 2005/7// PY - 2005/7// DO - 10.1016/j.ijengsci.2005.03.002 VL - 43 IS - 11-12 SP - 992-1010 SN - 1879-2197 KW - bioconvection KW - small particles KW - sedimentation KW - motile micro-organisms ER - TY - JOUR TI - Predicted genetic gains and testing efficiency from two loblolly pine clonal trials AU - Isik, F AU - Goldfarb, B AU - LeBude, A AU - Li, BL AU - McKeand, S T2 - CANADIAN JOURNAL OF FOREST RESEARCH AB - Clonal field trials were established at two sites using rooted cuttings from 450 clones of eight full-sib families of loblolly pine (Pinus taeda L.). Height, survival, fusiform rust infection (caused by Cronartium quercuum (Berk) Miyabe ex Shirai f.sp. fusiforme), bole straightness, and diameter were measured after four growing seasons. There were significant differences among full-sib families and among clones within families for all traits studied. Moderately high within-family repeatabilities of clone means (0.50 to 0.75) for growth traits and a very high within-family repeatability of clone means (0.94) for fusiform rust infection were estimated. When the best eight clones were selected regardless of family structure, the volume yield was 52% greater than that of the unimproved seedlings at two sites. Selection of the best two clones from each of four families produced only slightly lower estimated genetic gains than the above scenario. The probability of fusiform rust infection ranged from 0.08 to 0.93 among clones at the South Carolina site. Predicted genetic gain for rust resistance was relatively insensitive to selection intensity, as there were numerous clones with high apparent resistance. The number of ramets per clone necessary to reliably characterize performance on one site was estimated to be between four and six. These results contribute to estimates of the gains available from clonal forestry and will help guide clonal testing and selection programs. Implementation of clonal forestry and cost issues are discussed. DA - 2005/7// PY - 2005/7// DO - 10.1139/X05-064 VL - 35 IS - 7 SP - 1754-1766 SN - 1208-6037 ER - TY - JOUR TI - PowerMarker: an integrated analysis environment for genetic marker analysis AU - Liu, KJ AU - Muse, SV T2 - BIOINFORMATICS AB - PowerMarker delivers a data-driven, integrated analysis environment (IAE) for genetic data. The IAE integrates data management, analysis and visualization in a user-friendly graphical user interface. It accelerates the analysis lifecycle and enables users to maintain data integrity throughout the process. An ever-growing list of more than 50 different statistical analyses for genetic markers has been implemented in PowerMarker.www.powermarker.net DA - 2005/5/1/ PY - 2005/5/1/ DO - 10.1093/bioinformatics/bti282 VL - 21 IS - 9 SP - 2128-2129 SN - 1460-2059 ER - TY - JOUR TI - Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins AU - Houston, N. L. AU - Fan, C. Z. AU - Xiang, Qiu-Yun AU - Schulze, J. M. AU - Jung, R. AU - Boston, R. S. T2 - Plant Physiology AB - Abstract Protein disulfide isomerases (PDIs) are molecular chaperones that contain thioredoxin (TRX) domains and aid in the formation of proper disulfide bonds during protein folding. To identify plant PDI-like (PDIL) proteins, a genome-wide search of Arabidopsis (Arabidopsis thaliana) was carried out to produce a comprehensive list of 104 genes encoding proteins with TRX domains. Phylogenetic analysis was conducted for these sequences using Bayesian and maximum-likelihood methods. The resulting phylogenetic tree showed that evolutionary relationships of TRX domains alone were correlated with conserved enzymatic activities. From this tree, we identified a set of 22 PDIL proteins that constitute a well-supported clade containing orthologs of known PDIs. Using the Arabidopsis PDIL sequences in iterative BLAST searches of public and proprietary sequence databases, we further identified orthologous sets of 19 PDIL sequences in rice (Oryza sativa) and 22 PDIL sequences in maize (Zea mays), and resolved the PDIL phylogeny into 10 groups. Five groups (I–V) had two TRX domains and showed structural similarities to the PDIL proteins in other higher eukaryotes. The remaining five groups had a single TRX domain. Two of these (quiescin-sulfhydryl oxidase-like and adenosine 5′-phosphosulfate reductase-like) had putative nonisomerase enzymatic activities encoded by an additional domain. Two others (VI and VIII) resembled small single-domain PDIs from Giardia lamblia, a basal eukaryote, and from yeast. Mining of maize expressed sequence tag and RNA-profiling databases indicated that members of all of the single-domain PDIL groups were expressed throughout the plant. The group VI maize PDIL ZmPDIL5-1 accumulated during endoplasmic reticulum stress but was not found within the intracellular membrane fractions and may represent a new member of the molecular chaperone complement in the cell. DA - 2005/// PY - 2005/// DO - 10.1104/pp.104.056507 VL - 137 IS - 2 SP - 762–778 ER - TY - JOUR TI - New sources of resistance to gummy stem blight in watermelon AU - Gusmini, G AU - Song, RH AU - Wehner, TC T2 - CROP SCIENCE AB - Gummy stem blight, caused by Didymella bryoniae (Auersw.) Rehm, is a major disease of watermelon [ Citrullus lanatus (Thunb.) Matsum. & Nakai]. Plant breeders need sources of resistance that can be incorporated into adapted breeding lines to help control the disease. We tested all the available accessions from the USDA‐ARS watermelon germplasm collection, including C. lanatus var citroides (L.H. Bailey) Mansf., for resistance to gummy stem blight. The experiment was a randomized complete block with 1332 cultigens, two sites (field and greenhouse), two or four replications, and two to six plants per plot. The resistant check was PI 189225 and the susceptible check was ‘Charleston Gray’. PI 279461, PI 482379, PI 254744, PI 526233, PI 482276, PI 271771, PI 164248, PI 244019, PI 296332, and PI 490383 were selected as the most resistant cultigens to be used in future breeding efforts. The most susceptible cultigens were PI 183398, PI 169286, PI 223764, PI 226445, PI 525084, PI 534597, and PI 278041. DA - 2005/// PY - 2005/// DO - 10.2135/cropsci2005.0582 VL - 45 IS - 2 SP - 582-588 SN - 1435-0653 ER - TY - JOUR TI - Modeling quantitative trait loci and interpretation of models AU - Zeng, ZB AU - Wang, T AU - Zou, W T2 - GENETICS AB - A quantitative genetic model relates the genotypic value of an individual to the alleles at the loci that contribute to the variation in a population in terms of additive, dominance, and epistatic effects. This partition of genetic effects is related to the partition of genetic variance. A number of models have been proposed to describe this relationship: some are based on the orthogonal partition of genetic variance in an equilibrium population. We compare a few representative models and discuss their utility and potential problems for analyzing quantitative trait loci (QTL) in a segregating population. An orthogonal model implies that estimates of the genetic effects are consistent in a full or reduced model in an equilibrium population and are directly related to the partition of the genetic variance in the population. Linkage disequilibrium does not affect the estimation of genetic effects in a full model, but would in a reduced model. Certainly linkage disequilibrium would complicate the detection of QTL and epistasis. Using different models does not influence the detection of QTL and epistasis. However, it does influence the estimation and interpretation of genetic effects. DA - 2005/3// PY - 2005/3// DO - 10.1534/genetics.104.035857 VL - 169 IS - 3 SP - 1711-1725 SN - 0016-6731 ER - TY - JOUR TI - Model systems in agriculture: Lessons from worms AU - Bird, D.M. T2 - Annals of Applied Biology AB - Genomic tools are expanding the utility of organisms originally developed as models for biomedical research as a means to address complex agricultural problems. Conversely, agricultural pests are serving as models to help unravel questions of basic biology. Examples from C. elegans and root-knot nematode of this two-way exchange are discussed. DA - 2005/// PY - 2005/// DO - 10.1111/j.1744-7348.2005.040066.x VL - 146 IS - 2 SP - 147-154 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-16444385698&partnerID=MN8TOARS ER - TY - JOUR TI - Linear instability analysis of a suspension of oxytactic bacteria in superimposed fluid and porous layers AU - Avramenko, AA AU - Kuznetsov, AV T2 - TRANSPORT IN POROUS MEDIA DA - 2005/11// PY - 2005/11// DO - 10.1007/s11242-004-7462-0 VL - 61 IS - 2 SP - 157-175 SN - 1573-1634 KW - superimposed porous and fluid layers KW - bioconvection KW - oxytactic bacteria KW - motile microorganisms ER - TY - JOUR TI - Involvement of phospholipase C and intracellular calcium signaling in the gonadotropin-releasing hormone regulation of prolactin release from lactotrophs of tilapia (Oreochromis mossambicus) AU - Tipsmark, CK AU - Weber, GM AU - Strom, CN AU - Grau, EG AU - Hirano, T AU - Borski, RJ T2 - GENERAL AND COMPARATIVE ENDOCRINOLOGY AB - Gonadotropin-releasing hormone (GnRH) is a potent stimulator of prolactin (PRL) secretion in various vertebrates including the tilapia, Oreochromis mossambicus. The mechanism by which GnRH regulates lactotroph cell function is poorly understood. Using the advantageous characteristics of the teleost pituitary gland from which a nearly pure population of PRL cells can be isolated, we examined whether GnRH might stimulate PRL release through an increase in phospholipase C (PLC), inositol triphosphate (IP3), and intracellular calcium (Ca(i)2+) signaling. Using Ca(i)2+ imaging and the calcium-sensitive dye fura-2, we found that chicken GnRH-II (cGnRH-II) induced a rapid dose-dependent increase in Ca(i)2+ in dispersed tilapia lactotrophs. The Ca(i)2+ signal was abolished by U-73122, an inhibitor of PLC-dependent phosphoinositide hydrolysis. Correspondingly, cGnRH-II-induced tPRL188 secretion was inhibited by U-73122, suggesting that activation of PLC mediates cGnRH-II's stimulatory effect on PRL secretion. Pretreatment with 8-(N,N-diethylamino)octyl-3,4,5-trimethoxybenzoate hydrochloride (TMB-8), an inhibitor of Ca2+ release from intracellular stores, impeded the effect of cGnRH-II on Ca(i)2+. To further address the possible involvement of intracellular Ca2+ stores, IP3 concentrations in the tilapia rostral pars distalis (RPD containing 95-99% PRL cells) was determined by a radioreceptor assay. We found that GnRH-II induces a rapid (<5min) and sustained increase in IP3 concentration in the RPD. Secretion of tPRL(188) in response to cGnRH-II was suppressed by Ca2+ antagonists (TMB-8 and nifedipine). These data, along with our previous findings that show PRL release increases with a rise in Ca(i)2+, suggest that GnRH may elicit its PRL releasing effect by increasing Ca(i)2+. Furthermore, the rise in Ca(i)2+ may be derived from PLC/IP3-induced mobilization of Ca2+ from intracellular stores along with influx through L-type voltage-gated Ca2+ channels. DA - 2005/5/15/ PY - 2005/5/15/ DO - 10.1016/j.ygcen.2004.11.009 VL - 142 IS - 1-2 SP - 227-233 SN - 1095-6840 KW - GnRH KW - calcium signaling KW - prolactin KW - tilapia KW - lactotrophs ER - TY - JOUR TI - Investigation of stability of a laminar flow in a parallel-plate channel filled with a fluid saturated porous medium AU - Avramenko, AA AU - Kuznetsov, AV AU - Basok, BI AU - Blinov, DG T2 - PHYSICS OF FLUIDS AB - Instability of a laminar flow in a parallel-plate channel filled with a fluid saturated porous medium is investigated on the basis of a modified Orr-Sommerfeld equation. This equation takes into account three drag terms: the Darcy term that describes friction between the fluid and the porous matrix, the Forchheimer quadratic drag term that describes a form drag due to the solid obstacles, and the Brinkman term, which is a viscous term similar to the Laplacian term in the Navier-Stokes equations. Numerical analysis is carried out using the collocation method. The dependence of the critical Reynolds number on porosity and permeability of the porous medium is analyzed numerically. DA - 2005/9// PY - 2005/9// DO - 10.1063/1.2041607 VL - 17 IS - 9 SP - SN - 1089-7666 ER - TY - JOUR TI - In vitro reconstitution of an NADPH-dependent superoxide reduction pathway from Pyrococcus furiosus AU - Grunden, AA AU - Jenney, FE AU - Ma, KS AU - Ji, MY AU - Weinberg, MV AU - Adams, MWW T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT A scheme for the detoxification of superoxide in Pyrococcus furiosus has been previously proposed in which superoxide reductase (SOR) reduces (rather than dismutates) superoxide to hydrogen peroxide by using electrons from reduced rubredoxin (Rd). Rd is reduced with electrons from NAD(P)H by the enzyme NAD(P)H:rubredoxin oxidoreductase (NROR). The goal of the present work was to reconstitute this pathway in vitro using recombinant enzymes. While recombinant forms of SOR and Rd are available, the gene encoding P. furiosus NROR (PF1197) was found to be exceedingly toxic to Escherichia coli , and an active recombinant form (rNROR) was obtained via a fusion protein expression system, which produced an inactive form of NROR until cleavage. This allowed the complete pathway from NAD(P)H to the reduction of SOR via NROR and Rd to be reconstituted in vitro using recombinant proteins. rNROR is a 39.9-kDa protein whose sequence contains both flavin adenine dinucleotide (FAD)- and NAD(P)H-binding motifs, and it shares significant similarity with known and putative Rd-dependent oxidoreductases from several anaerobic bacteria, both mesophilic and hyperthermophilic. FAD was shown to be essential for activity in reconstitution assays and could not be replaced by flavin mononucleotide (FMN). The bound FAD has a midpoint potential of −173 mV at 23°C (−193 mV at 80°C). Like native NROR, the recombinant enzyme catalyzed the NADPH-dependent reduction of rubredoxin both at high (80°C) and low (23°C) temperatures, consistent with its proposed role in the superoxide reduction pathway. This is the first demonstration of in vitro superoxide reduction to hydrogen peroxide using NAD(P)H as the electron donor in an SOR-mediated pathway. DA - 2005/3// PY - 2005/3// DO - 10.1128/AEM.71.3.1522-1530.2005 VL - 71 IS - 3 SP - 1522-1530 SN - 1098-5336 ER - TY - JOUR TI - Identification of the Sex Pheromone of the German Cockroach, Blattella germanica AU - Nojima, S. AU - Schal, C. AU - Webster, F.X. AU - Santangelo, R.G. AU - Roelofs, W.L. T2 - Science AB - The sex pheromone of the German cockroach, Blattella germanica , has been characterized as gentisyl quinone isovalerate. This cockroach is a major cause of allergic disease and serves as a mechanical vector of pathogens, making it one of the most important residential and food-associated pests worldwide. The sex pheromone–producing gland in adult females was identified in 1993, but thermal instability of the pheromone made characterization difficult. Now, using a new preparative gas chromatography approach coupled with electroantennographic detection, we have isolated and characterized the pheromone, which we term blattellaquinone, and confirmed the identification by chemical synthesis. The synthetic pheromone was active in behavioral assays and highly effective in field trapping tests, which suggest that it may provide a new tool in cockroach population detection, monitoring, and control. DA - 2005/2/18/ PY - 2005/2/18/ DO - 10.1126/science.1107163 VL - 307 IS - 5712 SP - 1104-1106 SN - 0036-8075 1095-9203 UR - http://dx.doi.org/10.1126/science.1107163 ER - TY - JOUR TI - Genorne-wide transcriptional variation within and between steady states for continuous growth of the hyperthermophile Thermotoga maritima AU - Shockley, KR AU - Scott, KL AU - Pysz, MA AU - Conners, SB AU - Johnson, MR AU - Montero, CI AU - Wolfinger, RD AU - Kelly, RM T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - Maltose-limited, continuous growth of the hyperthermophile Thermotoga maritima at different temperatures and dilution rates (80 degrees C/0.25 h(-1), 80 degrees C/0.17 h(-1), and 85 degrees C/0.25 h(-1)) showed that transcriptome-wide variation in gene expression within mechanical steady states was minimal compared to that between steady states, supporting the efficacy of chemostat-based approaches for functional genomics studies. DA - 2005/9// PY - 2005/9// DO - 10.1128/AEM.71.9.5572-5576.2005 VL - 71 IS - 9 SP - 5572-5576 SN - 1098-5336 ER - TY - JOUR TI - Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid AU - Kirst, M AU - Basten, CJ AU - Myburg, AA AU - Zeng, ZB AU - Sederoff, RR T2 - GENETICS AB - Species diversity may have evolved by differential regulation of a similar set of genes. To analyze and compare the genetic architecture of transcript regulation in different genetic backgrounds of Eucalyptus, microarrays were used to examine variation in mRNA abundance in the differentiating xylem of a E. grandis pseudobackcross population [E. grandis x F(1) hybrid (E. grandis x E. globulus)]. Least-squares mean estimates of transcript levels were generated for 2608 genes in 91 interspecific backcross progeny. The quantitative measurements of variation in transcript abundance for specific genes were mapped as expression QTL (eQTL) in two single-tree genetic linkage maps (F(1) hybrid paternal and E. grandis maternal). EQTL were identified for 1067 genes in the two maps, of which 811 were located in the F(1) hybrid paternal map, and 451 in the E. grandis maternal map. EQTL for 195 genes mapped to both parental maps, the majority of which localized to nonhomologous linkage groups, suggesting trans-regulation by different loci in the two genetic backgrounds. For 821 genes, a single eQTL that explained up to 70% of the transcript-level variation was identified. Hotspots with colocalized eQTL were identified in both maps and typically contained genes associated with specific metabolic and regulatory pathways, suggesting coordinated genetic regulation. DA - 2005/4// PY - 2005/4// DO - 10.1534/genetics.104.039198 VL - 169 IS - 4 SP - 2295-2303 SN - 1943-2631 ER - TY - JOUR TI - Ethylene signalling and response pathway: A unique signalling cascade with a multitude of inputs and outputs AU - STEPANOVA, ANNA AU - Alonso, Jose T2 - Physiologia Plantarum DA - 2005/// PY - 2005/// DO - 10.1111/j/1399-3054.2004.00447 VL - 123 IS - 2 SP - 195–206 ER - TY - JOUR TI - Differences in wood density and growth of fertilized and nonfertilized loblolly pine associated with a mutant gene, cad-n1 AU - Yu, Q AU - McKeand, SE AU - Nelson, CD AU - Li, B AU - Sherrill, , JR AU - Mullin, TJ T2 - CANADIAN JOURNAL OF FOREST RESEARCH AB - A rare mutant allele (cad-n1) of the cad gene in loblolly pine (Pinus taeda L.) causes a deficiency in the production of cinnamyl alcohol dehydrogenase (CAD). Effects associated with this allele were examined by comparing wood density and growth traits of cad-n1 heterozygous trees with those of wild-type trees in a 10-year-old open-pollinated family trial growing under two levels of fertilization in Scotland County, North Carolina. In all, 200 trees were sampled, with 100 trees for each fertilizer treatment. Wood density measurements were collected from wood cores at breast height using X-ray densitometry. We found that the substitution of a cad-n1 for a wild-type allele (Cad) was associated with a significant effect on wood density. The cad-n1 heterozygotes had a significantly higher wood density (+2.6%) compared with wild-type trees. The higher density was apparently due to the higher percentage of latewood in the heterozygotes. The fertilization effect was highly significant for both growth and wood density traits. This study indicates that the cad-n1 allele could be a valuable gene to the pulp and paper industry for the purpose of enhancing pulp yields by increasing wood density. DA - 2005/7// PY - 2005/7// DO - 10.1139/X05-103 VL - 35 IS - 7 SP - 1723-1730 SN - 1208-6037 ER - TY - JOUR TI - Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays AU - Wadenback, J. AU - Clapham, D. H. AU - Craig, D. AU - Sederoff, R. AU - Peter, G. F. AU - Von Arnold, S. AU - Egertsdotter, U. T2 - BMC Genomics DA - 2005/// PY - 2005/// VL - 6 IS - 61 ER - TY - JOUR TI - Campylobacter coli: prevalence and antimicrobial resistance in antimicrobial-free (ABF) swine production systems AU - Gebreyes, WA AU - Thakur, S AU - Morrow, WEM T2 - JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY AB - Objectives: To determine the prevalence and antimicrobial resistance of Campylobacter species in swine reared in the intensive and extensive antimicrobial-free (ABF) production systems at farm and slaughter. In the ABF system, antimicrobials are neither used for growth promotion nor therapeutic purposes. DA - 2005/10// PY - 2005/10// DO - 10.1093/jac/dki305 VL - 56 IS - 4 SP - 765-768 SN - 1460-2091 KW - pig KW - Campylobacter species KW - antibiotic resistance KW - antimicrobial-free production ER - TY - JOUR TI - Reference ranges for hemolymph chemistries from Elliptio complanata of North Carolina AU - Gustafson, LL AU - Stoskopf, MK AU - Showers, W AU - Cope, G AU - Eads, C AU - Linnehan, R AU - Kwak, TJ AU - Andersen, B AU - Levine, JF T2 - DISEASES OF AQUATIC ORGANISMS AB - Hemolymph chemistries may be useful nonlethal measures of bivalve health. The prognostic value of hemolymph, however, depends on a comparison of chemistry results to reference ranges from healthy individuals. Currently, knowledge of expected hemolymph values in healthy and unhealthy freshwater mussels is extremely limited. The purpose of this study was to develop a set of reference ranges for clinical evaluation of hemolymph from a freshwater mussel species common to southeastern USA. We collected hemolymph from 380 Elliptio complanata from 19 apparently healthy populations from northwest of Raleigh, North Carolina, during May through July 2001. We present reference ranges for hemolymph parameters ammonia, glucose, calcium, magnesium, phosphorus, aspartate aminotransferase (AST), bicarbonate, protein and cell count, and for tissue glycogen. We compare the subpopulations of mussels from regions with an agricultural riparian buffer to those surrounded predominantly by forested lands. We further present correlations noted between hemolymph chemistries and physical or physiologic parameters. The only statistically significant differences between populations contiguous to agricultural and forested lands were in hemolymph calcium and glucose concentrations. Other statistically significant correlations identified were between gravidity and hemolymph protein concentration and tissue glycogen content, as well as between gravidity and parasite burden, and between shell length and hemolymph glucose, AST, calcium and bicarbonate concentrations. The results of this study will aid the interpretation of health measures from populations of E. complanata of similar geographic and seasonal origin. DA - 2005/6/30/ PY - 2005/6/30/ DO - 10.3354/dao065167 VL - 65 IS - 2 SP - 167-176 SN - 1616-1580 KW - Elliptio complanata KW - hemolymph KW - hematology KW - reference ranges ER - TY - JOUR TI - Protective role of neutrophils in mice experimentally infected with Rhodococcus equi AU - Martens, RJ AU - Cohen, ND AU - Jones, SL AU - Moore, TA AU - Edwards, JF T2 - INFECTION AND IMMUNITY AB - ABSTRACT Neutrophils are important in controlling early infections with the intracellular bacterium Rhodococcus equi . Antineutrophil monoclonal antibody (RB6-8C5)-induced neutrophil deficiency during the first week after experimental infection of mice with R. equi resulted in more severe disease and significantly increased tissue concentrations of R. equi. DA - 2005/10// PY - 2005/10// DO - 10.1128/IAI.73.10.7040-7042.2005 VL - 73 IS - 10 SP - 7040-7042 SN - 0019-9567 UR - http://europepmc.org/abstract/med/16177388 ER - TY - JOUR TI - Multidrug-resistant Salmonella enterica serovar Muenchen from pigs and humans and potential interserovar transfer of antimicrobial resistance AU - Gebreyes, WA AU - Thakur, S T2 - ANTIMICROBIAL AGENTS AND CHEMOTHERAPY AB - ABSTRACT Salmonella serovars are important reservoirs of antimicrobial resistance. Recently, we reported on multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium strains among pigs with resistance to ampicillin, kanamycin, streptomycin, sulfamethoxazole, and tetracycline (resistance [R] type AKSSuT) and resistance to amoxicillin-clavulanic acid, ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (R type AxACSSuT). In the present study, 67 isolates (39 from humans and 28 from pigs) of clinically important Salmonella serovar Muenchen were characterized. Among the porcine isolates, 75% showed resistance to seven antimicrobials: ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, tetracycline, amoxicillin-clavulanic acid, and kanamycin (R type ACSSuTAxK). One isolate from humans showed resistance to 10 of the 12 antimicrobials: ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, tetracycline, amoxicillin-clavulanic acid, kanamycin, gentamicin, cephalothin, and ceftriaxone (R type ACSSuTAxKGCfCro). Pulsed-field gel electrophoresis revealed no clonality between the porcine and the human strains. The porcine and the human MDR strains carried class 1 integrons of 2.0 and 1.0 kb, respectively. Genes specific to the porcine strain included aadA2 , aphA1-Iab , and tetA (B). DNA sequencing revealed that the porcine isolates carried bla OXA-30 on a class 1 integron. Genes specific to the human strain included bla TEM , strA , strB , cmlA , tetA (A), and aadA2 . No bla CMY-2 gene was detected. Serovar Muenchen strains of porcine and human origin were able to transfer resistance genes to laboratory strain Escherichia coli MG1655 by conjugation. Plasmid restriction with four restriction enzymes, EcoRI, BamHI, HindIII, and PstI, showed that the conjugative plasmids from porcine Salmonella serovar Muenchen and Typhimurium R-type MDR strains isolated from the same farms at the same time were similar on the basis of the sizes and the numbers of bands and Southern hybridization. The plasmid profiles among the Salmonella serovar Muenchen isolates from the two host species were different. This is the first report to show a high frequency of MDR Salmonella serovar Muenchen strains from pigs and a human strain that is similar to the MDR isolates with the AmpC enzyme previously reported among Salmonella serovars Newport and Typhimurium strains. The MDR strains from the two host species independently represent public health concerns, as Salmonella serovar Muenchen is among the top 10 causes of salmonellosis in humans. DA - 2005/2// PY - 2005/2// DO - 10.1128/AAC.49.2.503-511.2005 VL - 49 IS - 2 SP - 503-511 SN - 1098-6596 ER - TY - JOUR TI - Isolation and selection of lactic acid bacteria as biocontrol agents for nonacidified, refrigerated pickles AU - Reina, LD AU - Breidt, F AU - Fleming, HP AU - Kathariou, S T2 - JOURNAL OF FOOD SCIENCE AB - ABSTRACT: A nonacidified, deli-type pickle product was used as a model system to study the potential use of biocontrol as a means to prevent the growth of pathogens in minimally processed fruits and vegetables (MPFV). Fresh pickling cucumbers were blanched and brined with sterile spices and garlic oil. The product was stored at 5 °C for 3 wk and then transferred to various abuse temperatures (16 °C, 25 °C, 30 °C). Lactic acid bacteria (LAB) were isolated and characterized as potential biocontrol agents, and the isolates were tested for bacteriocin-like activity. A total of 118 LAB isolates were obtained. Among the LAB identified were species of Lactococcus, Leuconostoc, Lactobacillus, Weissella, and Enterococcus. Three isolates showed transient bacteriocin activity against—Listeria monocytogenes, and 7 isolates (Lactococcus) had bacteriocin-like activity against other LAB. Although it did not produce a bacteriocin, a Lactobacillus curvatus isolate (LR55) was found to have desirable characteristics for use as a biocontrol (competitive exclusion) culture to enhance the safety of nonacidified deli-type pickles. DA - 2005/// PY - 2005/// DO - 10.1111/j.1365-2621.2005.tb09050.x VL - 70 IS - 1 SP - M7-M11 SN - 1750-3841 KW - lactic acid bacteria KW - minimally processed vegetables KW - bacteriocin KW - biocontrol ER - TY - JOUR TI - Investigation of the onset of thermo-bioconvection in a suspension of oxytactic microorganisms in a shallow fluid layer heated from below AU - Kuznetsov, AV T2 - THEORETICAL AND COMPUTATIONAL FLUID DYNAMICS DA - 2005/10// PY - 2005/10// DO - 10.1007/s00162-005-0167-3 VL - 19 IS - 4 SP - 287-299 SN - 1432-2250 KW - thermo-bioconvection KW - oxytactic microorganisms KW - stability KW - bioconvection Rayleigh number ER - TY - JOUR TI - Genetic basis of resistance to Cry1Ac and Cry2Aa in Heliothis virescens (Lepidoptera : Noctuidae) AU - Gahan, LJ AU - Ma, YT AU - Coble, MLM AU - Gould, F AU - Moar, WJ AU - Heckel, DG T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - The development of pest resistance to transgenic crop plants producing insecticidal toxins from Bacillus thuringiensis Berliner (Bt) poses a major threat to their sustainable use in agriculture. "Pyramiding" two toxins with different modes of actions in the same plant is now being used to delay the evolution of resistance in the insects, but this strategy could fail if a single gene in a pest confers resistance to both toxins. The CP73 strain of the cotton pest Heliothis virescens (F.) is resistant to both Cry1Ac and Cry2Aa toxins from Bt. We explored the genetic basis of resistance in this strain with a backcross, split-family design. The gene with the largest effect on Cry1Ac resistance in CP73 (BtR-5) maps to linkage group 10 of H. virescens and thus differs from the previously described linkage group 9 BtR-4 resistance found in the YHD2 strain, involving mutation of the gene encoding a 12-domain cadherin-like binding target of the Cry1A toxins. Neither BtR-4 nor BtR-5 seems to confer significant resistance to Cry2Aa. A majority of the linkage groups studied in one backcross family made a small positive contribution to resistance for both toxins. Thus, the Cry2Aa resistance in CP73 is not caused by either of the two major Cry1Ac resistance-conferring genes but instead probably has a quantitative genetic basis. DA - 2005/8// PY - 2005/8// DO - 10.1603/0022-0493-98.4.1357 VL - 98 IS - 4 SP - 1357-1368 SN - 1938-291X KW - tobacco budworm KW - linkage KW - Bacillus thuringiensis KW - resistance ER - TY - JOUR TI - Experimental support for an immunological approach to the search for life on other planets AU - Schweitzer, MH AU - Wittmeyer, J AU - Avci, R AU - Pincus, S T2 - ASTROBIOLOGY AB - We propose a three-phase approach to test for evidence of life in extraterrestrial samples. The approach capitalizes on the flexibility, sensitivity, and specificity of antibody–antigen interactions. Data are presented to support the first phase, in which various extraction protocols are compared for efficiency, and in which a preliminary suite of antibodies are tested against various antigens. The antigens and antibodies were chosen on the basis of criteria designed to optimize the detection of extraterrestrial biomarkers unique to living or once-living organisms. Astrobiology 5, 30–47. DA - 2005/2// PY - 2005/2// DO - 10.1089/ast.2005.5.30 VL - 5 IS - 1 SP - 30-47 SN - 1557-8070 KW - Antibody reactivity KW - extraction methods KW - exobiology KW - astrobiology ER - TY - JOUR TI - Evaluation of components of Fusarium head blight resistance in soft red winter wheat germ plasm using a detached leaf assay AU - Browne, RA AU - Murphy, JP AU - Cooke, BM AU - Devaney, D AU - Walsh, EJ AU - Griffey, CA AU - Hancock, JA AU - Harrison, SA AU - Hart, P AU - Kolb, FL AU - McKendry, AL AU - Milus, EA AU - Sneller, C AU - Van Sanford, DA T2 - PLANT DISEASE AB - A large environmental influence on phenotypic estimates of disease resistance and the complex polygenic nature of Fusarium head blight (FHB) resistance in wheat (Triticum aestivum) are impediments to developing resistant cultivars. The objective of this research was to investigate the utility of a detached leaf assay, inoculated using inoculum from isolates of Microdochium nivale var. majus, to identify components of FHB resistance among 30 entries of U.S. soft red winter wheat in the 2002 Uniform Southern FHB Nursery (USFHBN). Whole plant FHB resistance of the USFHBN entries was evaluated in replicated, mist-irrigated field trials at 10 locations in eight states during the 2001-2002 season. Incubation period (days from inoculation to the first appearance of a dull gray-green water-soaked lesion) was the only detached leaf variable significantly correlated across all FHB resistance parameters accounting for 45% of the variation in FHB incidence, 27% of FHB severity, 30% of Fusarium damaged kernels, and 26% of the variation in grain deoxynivalenol (DON) concentration. The results for incubation period contrasted with previous studies of moderately resistant European cultivars, in that longer incubation period was correlated with greater FHB susceptibility, but agreed with previous findings for the Chinese cultivar Sumai 3 and CIMMYT germ plasm containing diverse sources of FHB resistance. The results support the view that the detached leaf assay method has potential for use to distinguish between specific sources of FHB resistance when combined with data on FHB reaction and pedigree information. For example, entry 28, a di-haploid line from the cross between the moderately resistant U.S. cultivar Roane and the resistant Chinese line W14, exhibited detached leaf parameters that suggested a combination of both sources of FHB resistance. The USFHBN represents the combination of adapted and exotic germ plasm, but four moderately resistant U.S. commercial cultivars (Roane, McCormick, NC-Neuse, and Pat) had long incubation and latent periods and short lesion lengths in the detached leaf assay as observed in moderately FHB resistant European cultivars. The dichotomy in the relationship between incubation period and FHB resistance indicates that this may need to be considered to effectively combine exotic and existing/adapted sources of FHB resistance. DA - 2005/4// PY - 2005/4// DO - 10.1094/PD-89-0404 VL - 89 IS - 4 SP - 404-411 SN - 0191-2917 ER - TY - JOUR TI - Evaluation of a nonlethal technique for hemolymph collection in Elliptio complanata, a freshwater bivalve (Mollusca: Unionidae) AU - Gustafson, LL AU - Stoskopf, MK AU - Bogan, AE AU - Showers, W AU - Kwak, TJ AU - Hanlon, S AU - Levine, JF T2 - Diseases of Aquatic Organisms AB - Hemolymph, the circulatory fluid of bivalves, transports nutrients, respiratory gases, enzymes, metabolic wastes, and toxicants throughout the body. Hemolymph can provide information pertinent to health assessment of animals or populations, but is not commonly used in freshwater bivalves partly because of the lack of tested, practical techniques for its nonlethal collection. The objective of this study was to evaluate the effect of hemolymph collection on the growth and survival of Elliptio complanata, a freshwater bivalve (Unionidae). We describe a simple technique for the collection of hemolymph from the anterior adductor muscle sinus of E. complanata. To evaluate the effect of hemolymph sampling on mussel survival and growth, 30 mussels sampled using the technique and 30 unsampled controls were followed for 3 mo post collection. Nine animals were sampled 3 times over 7 mo to monitor effects of repeated sampling. No negative impacts on survival or growth were observed in either the singly or repeatedly sampled animals. We also compared the composition of hemolymph collected from the adductor muscle sinus with that collected from the ventricle of the heart. Calcium levels and cell count of hemolymph obtained from the adductor sinus and ventricle were significantly different. There was no significant difference between collection sites for magnesium, phosphorus, ammonia, protein, sodium, potassium, or chloride. We conclude that collection of hemolymph from the adductor sinus is safe for sampled E. complanata and should be explored as a relatively non-invasive, and potentially useful, approach to the evaluation of freshwater mussel health. DA - 2005/// PY - 2005/// DO - 10.3354/dao065159 VL - 65 IS - 2 SP - 159–165 SN - 0177-5103 1616-1580 UR - http://dx.doi.org/10.3354/dao065159 KW - unionidae KW - freshwater mussels KW - hemolymph KW - nonlethal sampling ER - TY - JOUR TI - Effect of PBAN on pheromone production by mated Heliothis virescens and Heliothis subflexa females AU - Groot, AT AU - Fan, YL AU - Brownie, C AU - Jurenka, RA AU - Gould, F AU - Schal, C T2 - JOURNAL OF CHEMICAL ECOLOGY DA - 2005/1// PY - 2005/1// DO - 10.1007/s10886-005-0970-8 VL - 31 IS - 1 SP - 14-28 SN - 1573-1561 KW - Heliothis virescens KW - Heliothis subflexa KW - sex pheromone KW - PBAN KW - temporal variation ER - TY - JOUR TI - Diminished expression of C/EBP alpha in skin carcinomas is linked to oncogenic Ras and reexpression of C/EBP alpha in carcinoma cells inhibits proliferation AU - Shim, M. AU - Powers, K. L. AU - Ewing, S. J. AU - Zhu, S. AU - Smart, R. C. T2 - Cancer Research DA - 2005/// PY - 2005/// VL - 65 IS - 3 SP - 861–867 ER - TY - JOUR TI - Comparison of mating disruption with pesticides for management of oriental fruit moth (Lepidoptera : Tortricidae) in North Carolina apple orchards AU - Kovanci, OB AU - Schal, C AU - Walgenbach, JF AU - Kennedy, GG T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - The efficacy of mating disruption by using Isomate-M 100 pheromone dispensers and two formulations of microencapsulated sprayable pheromone for management of oriental fruit moth, Grapholita molesta (Busck), was compared with conventional insecticides in large plot studies in Henderson County, North Carolina, in 2000 and 2001. In addition, experiments were conducted in small and large plots to test the response of oriental fruit moth males to different application rates of sprayable pheromone. Pheromone trap catches were significantly reduced in mating disruption blocks compared with conventional and abandoned orchards. Pheromone traps placed in the upper canopy captured significantly more moths than traps placed in the lower canopy across all treatments, and lures loaded with 100 μg of pheromone caught more moths than traps with 300 μg, but the difference between doses was statistically significant at only one location in 2001. Isomate-M 100 provided excellent trap shutdown and was significantly more effective than sprayable pheromone formulations. Fruit damage by oriental fruit moth larvae was very low (≤1%) in mating disruption blocks and was generally lower than in conventional and nonmanaged blocks. Based on male moth response to pheromone traps in small plots, there was little difference among doses of sprayable pheromone, ranging from 12.4 to 49.1 g (AI)/ha, but efficacy declined at 2.4 g (AI)/ha. With the exception of one orchard, there was no significant difference between 12.4 and 37.1 g (AI)/ha under low and high oriental fruit moth population pressure in large plot studies. Mating disruption proved to be an alternative to organophosphate insecticides for managing oriental fruit moth populations in North Carolina apple orchards. DA - 2005/8// PY - 2005/8// DO - 10.1603/0022-0493-98.4.1248 VL - 98 IS - 4 SP - 1248-1258 SN - 1938-291X KW - mating disruption KW - pheromones KW - apple ER - TY - JOUR TI - Comparison of conventional and integrated pest management programs in public schools AU - Williams, GM AU - Linker, HM AU - Waldvogel, MG AU - Leidy, RB AU - Schal, C T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - This study compared an integrated pest management (IPM) program with conventional, calendar-based pest control in nine North Carolina elementary schools. Both programs primarily targeted the German cockroach, Blattella germanica (L.). The IPM program relied heavily on monitoring and baiting, whereas the conventional approach used baseboard and crack-and-crevice sprays of insecticides. Within the constraints of an existing pest management contract, we quantified service duration, materials used, cost, levels of cockroach infestation, and the pesticide residues generated by the two service types. IPM services were significantly more time-consuming than conventional services, resulting in a significantly higher cost associated with labor. Nevertheless, the two types of treatments incurred similar total costs, and the efficacy of both treatments was also similar. Most importantly, pest monitoring, a central element of the IPM program, revealed few cockroaches and indicated that most of the conventional treatments were unnecessary. Environmental residues of the organophosphate pesticides acephate, chlorpyrifos, and propetamphos were significantly higher in swab samples taken in the conventionally treated schools. This study demonstrates that an IPM program is an appropriate and preferable alternative to conventional methods of pest control in the school environment. DA - 2005/8// PY - 2005/8// DO - 10.1603/0022-0493-98.4.1275 VL - 98 IS - 4 SP - 1275-1283 SN - 0022-0493 KW - school IPM KW - IPM KW - German cockroach KW - Blattella germanica ER - TY - JOUR TI - Changes over time in the allelochemical content of ten cultivars of rye (Secale cereale L.) AU - Reberg-Horton, SC AU - Burton, JD AU - Danehower, DA AU - Ma, GY AU - Monks, DW AU - Murphy, JP AU - Ranells, NN AU - Williamson, JD AU - Creamer, NG T2 - JOURNAL OF CHEMICAL ECOLOGY DA - 2005/1// PY - 2005/1// DO - 10.1007/s10886-005-0983-3 VL - 31 IS - 1 SP - 179-193 SN - 1573-1561 KW - allelopathy KW - cover crop KW - residue KW - redroot pigweed (Amaranthus retroflexus L.) KW - goosegrass (Eleusine indica L. Gaertn.) KW - 2,4-dihydroxy-1,4-(2H)benzoxazine-3-one KW - DIBOA KW - maturity KW - phenology KW - rye (Secale cereale L.) ER - TY - JOUR TI - Aromatase cytochrome P450: Cloning, intron variation, and ontogeny of gene expression in southern flounder (Paralichthys lethostigma) AU - Luckenbach, JA AU - Early, LW AU - Rowe, AH AU - Borski, RJ AU - Daniels, HV AU - Godwin, J T2 - JOURNAL OF EXPERIMENTAL ZOOLOGY PART A-ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY AB - Aromatase cytochrome P450 (P450arom) is the enzyme complex responsible for conversion of androgens to estrogens in vertebrates. Consequently, in some fishes its activity appears critical to ovarian differentiation. Southern flounder (Paralichthys lethostigma) is a commercially important flatfish in which females grow larger than males and sex determination is temperature sensitive. Through cloning of the P450arom gene in ovary and quantitative reverse transcription-polymerase chain reaction, we developed a biomarker for early female differentiation in southern flounder. The deduced amino acid sequence for southern flounder P450arom is similar to other teleosts. Comparison of P450arom intron sequences from fish of different populations revealed substantial inter-individual variation. Adult ovary and spleen exhibited high levels of P450arom mRNA, while P450arom mRNA was only weakly detected in testes. Brain, liver, intestine, kidney, gill, muscle, and heart showed little or no P450arom mRNA expression. Gonads of wild and hatchery-produced juvenile flounder of sizes spanning the period of sex differentiation initially exhibited low levels of P450arom mRNA followed by increases in some individuals and bifurcation into two clearly segregated groups (i.e., putative males and females) beginning at approximately 65 mm in total length. Gonadal histology confirmed predictions of sex based on P450arom expression in juvenile flounder, demonstrating that the patterns of P450arom expression observed relate to sex-specific differentiation. This research represents a unique approach to assessing sex differentiation in a natural population, and a powerful technique for better understanding mechanisms of flounder sex determination and rapidly defining conditions for controlling sex for aquaculture. DA - 2005/8/1/ PY - 2005/8/1/ DO - 10.1002/jez.a.198 VL - 303A IS - 8 SP - 643-656 SN - 2471-5646 ER - TY - JOUR TI - Prevalence and antimicrobial resistance of Campylobacter in antimicrobial-free and conventional pig production systems AU - Thakur, S AU - Gebreyes, WA T2 - JOURNAL OF FOOD PROTECTION AB - The objectives of this study were to determine and compare the prevalence and antimicrobial resistance of Campylobacter species in swine reared in conventional and antimicrobial-free (ABF) production systems. Campylobacter coli was the predominant species, with 1,459 isolates (99%) in the study. We found significantly higher prevalence of C. coli on the ABF farms (77.3%) than on the conventional farms (27.6%) among pigs at the nursery stage (P < 0.001). At slaughter, we found significantly higher prevalence at the postevisceration than at the preevisceration stage (P < 0.001) in both production systems. The 1,459 C. coli isolates were tested with the agar dilution method for their susceptibility to six antimicrobials: chloramphenicol, ciprofloxacin, erythromycin, gentamicin, nalidixic acid, and tetracycline. Resistance was most prevalent against tetracycline (66.2% of isolates) followed by erythromycin (53.6% of isolates). Frequency of resistance to these two antimicrobials was significantly higher among conventional herds (83.4% for tetracycline and 77% for erythromycin) than among ABF herds (56.2% for tetracycline and 34.5% for erythromycin). Resistance to ciprofloxacin at the MIC (> 4 mg/liter) was also found on farms in both systems. Multidrug-resistant C. coli strains were detected in both the conventional (7%) and ABF (4%) herds. This is the first report of ciprofloxacin-resistant strains of C. coli in ABF pigs in the United States. These findings highlight the high prevalence of antimicrobial-resistant C. coli in both conventional and ABF pig production systems and have significant implications for the persistence of antimicrobial-resistant Campylobacter in the pig production environment regardless of levels of antimicrobial use. DA - 2005/11// PY - 2005/11// DO - 10.4315/0362-028X-68.11.2402 VL - 68 IS - 11 SP - 2402-2410 SN - 1944-9097 ER - TY - JOUR TI - Matrix attachment regions and regulated transcription increase and stabilize transgene expression AU - Abranches, R AU - Shultz, RW AU - Thompson, WF AU - Allen, GC T2 - PLANT BIOTECHNOLOGY JOURNAL AB - Transgene silencing has been shown to be associated with strong promoters, but it is not known whether the propensity for silencing is caused by the level of transcription, or some other property of the promoter. If transcriptional activity fosters silencing, then transgenes with inducible promoters may be less susceptible to silencing. To test this idea, a doxycycline-inducible luciferase transgene was transformed into an NT1 tobacco suspension culture cell line that constitutively expressed the tetracycline repressor. The inducible luciferase gene was flanked by tobacco Rb7 matrix attachment regions (MAR) or spacer control sequences in order to test the effects of MARs in conjunction with regulated transcription. Transformed lines were grown under continuous doxycycline (CI), or delayed doxycycline induction (DI) conditions. Delayed induction resulted in higher luciferase expression initially, but continued growth in the presence of doxycycline resulted in a reduction of expression to levels similar to those found in continuously induced lines. In both DI and CI treatments, the Rb7 MAR significantly reduced the percentage of silenced lines and increased transgene expression levels. These data demonstrate that active transcription increases silencing, especially in the absence of the Rb7 MAR. Importantly, the Rb7 MAR lines showed higher expression levels under both CI and DI conditions and avoided silencing that may occur in the absence of active transcription such as what would be expected as a result of condensed chromatin spreading. DA - 2005/9// PY - 2005/9// DO - 10.1111/j.1467-7652.2005.00144.x VL - 3 IS - 5 SP - 535-543 SN - 1467-7644 KW - PTGS KW - TGS KW - RNAi KW - MARs KW - transgene expression KW - induction ER - TY - JOUR TI - Genomic features of lactic acid bacteria effecting bioprocessing and health AU - Klaenhammer, TR AU - Barrangou, R AU - Buck, BL AU - Azcarate-Peril, MA AU - Altermann, E T2 - FEMS MICROBIOLOGY REVIEWS AB - The lactic acid bacteria are a functionally related group of organisms known primarily for their bioprocessing roles in food and beverages. More recently, selected members of the lactic acid bacteria have been implicated in a number of probiotic roles that impact general health and well-being. Genomic analyses of multiple members of the lactic acid bacteria, at the genus, species, and strain level, have now elucidated many genetic features that direct their fermentative and probiotic roles. This information is providing an important platform for understanding core mechanisms that control and regulate bacterial growth, survival, signaling, and fermentative processes and, in some cases, potentially underlying probiotic activities within complex microbial and host ecosystems. DA - 2005/8// PY - 2005/8// DO - 10.1016/j.femsre.2005.04.007 VL - 29 IS - 3 SP - 393-409 SN - 1574-6976 KW - lactic acid bacteria KW - genomics KW - bioprocessing KW - probiotics KW - comparative genomics KW - functional genomics ER - TY - JOUR TI - Effects of application rate and interval on the efficacy of sprayable pheromone for mating disruption of the oriental fruit moth Grapholita molesta AU - Kovanci, OB AU - Walgenbach, JF AU - Kennedy, GG AU - Schal, C T2 - PHYTOPARASITICA DA - 2005/8// PY - 2005/8// DO - 10.1007/BF02981299 VL - 33 IS - 4 SP - 334-342 SN - 1876-7184 KW - Grapholita molesta (Busck) KW - oriental fruit moth KW - mating disruption KW - sprayable pheromone KW - integrated pest management KW - apples ER - TY - JOUR TI - Computational analysis of the feasibility of a micro-pulsejet AU - Wan, Q AU - Roberts, WL AU - Kuznetsov, AV T2 - INTERNATIONAL COMMUNICATIONS IN HEAT AND MASS TRANSFER AB - This paper investigates the feasibility of a 2-cm micro-pulsejet by numerically simulating the inviscid gas dynamic phenomena within the exhaust tube and comparing them with those for a pulsejet on the order of 50 cm in length. After initial combustion, the pressure wave propagates towards the exit and reflects back as a rarefaction wave, which generates a minimum pressure in the combustion chamber. This low pressure must be sufficient to open the reed valves to allow fresh reactants to enter. It is shown that for both large and micro-pulsejets, the minimum pressure is low enough. The characteristic operating frequency is found to be approximately inversely proportional to the pulsejet length. Estimation of the boundary layer thickness in the pulsejet shows that viscosity plays a very significant role in the micro-pulsejet and cannot be neglected. DA - 2005/1// PY - 2005/1// DO - 10.1016/j.icheatmasstransfer.2004.05.020 VL - 32 IS - 1-2 SP - 19-26 SN - 1879-0178 KW - pulsejet KW - micro-size engine KW - pulse combustion KW - numerical modeling ER - TY - JOUR TI - Characterization and comparative analysis of Arabidopsis phosphatidylinositol phosphate 5-kinase 10 reveals differences in Arabidopsis and human phosphatidylinositol phosphate kinases AU - Perera, IY AU - Davis, AJ AU - Galanopilou, D AU - Im, YJ AU - Boss, WF T2 - FEBS LETTERS AB - Arabidopsis phosphatidylinositol phosphate (PtdInsP) kinase 10 ( At PIPK10; At4g01190) is shown to be a functional enzyme of the subfamily A, type I At PtdInsP kinases. It is biochemically distinct from At PIPK1 (At1g21980), the only other previously characterized At PtdInsP kinase which is of the B subfamily. At PIPK10 has the same K m , but a 10‐fold lower V max than At PIPK1 and it is insensitive to phosphatidic acid. At PIPK10 transcript is most abundant in inflorescence stalks and flowers, whereas At PIPK1 transcript is present in all tissues. Comparative analysis of recombinant At PIPK10 and At PIPK1 with recombinant Hs PIPKIα reveals that the Arabidopsis enzymes have roughly 200‐ and 20‐fold lower V max / K m , respectively. These data reveal one explanation for the longstanding mystery of the relatively low phosphatidylinositol‐(4,5)‐bisphosphate:phosphatidylinositol‐4‐phosphate ratio in terrestrial plants. DA - 2005/6/20/ PY - 2005/6/20/ DO - 10.1016/j.febslet.2005.05.018 VL - 579 IS - 16 SP - 3427-3432 SN - 1873-3468 KW - phosphatidylinositol phosphate kinase KW - lipid kinase KW - Arabidopsis ER - TY - JOUR TI - Basal and reovirus-induced beta interferon (IFN-beta) and IFN-beta-stimulated gene expression are cell type specific in the cardiac protective response AU - Stewart, MJ AU - Smoak, K AU - Blum, MA AU - Sherry, B T2 - JOURNAL OF VIROLOGY AB - ABSTRACT Viral myocarditis is an important human disease, with a wide variety of viruses implicated. Cardiac myocytes are not replenished yet are critical for host survival and thus may have a unique response to infection. Previously, we determined that the extent of reovirus induction of beta interferon (IFN-β) and IFN-β-mediated protection in primary cardiac myocyte cultures was inversely correlated with the extent of reovirus-induced cardiac damage in a mouse model. Surprisingly, and in contrast, the IFN-β response did not determine reovirus replication in skeletal muscle cells. Here we compared the IFN-β response in cardiac myocytes to that in primary cardiac fibroblast cultures, a readily replenished cardiac cell type. We compared basal and reovirus-induced expression of IFN-β, IRF-7 (an interferon-stimulated gene [ISG] that further induces IFN-β), and another ISG (561) in the two cell types by using real-time reverse transcription-PCR. Basal IFN-β, IRF-7, and 561 expression was higher in cardiac myocytes than in cardiac fibroblasts. Reovirus T3D induced greater expression of IFN-β in cardiac myocytes than in cardiac fibroblasts but equivalent expression of IRF-7 and 561 in the two cell types (though fold induction for IRF-7 and 561 was higher in fibroblasts than in myocytes because of the differences in basal expression). Interestingly, while reovirus replicated to equivalent titers in cardiac myocytes and cardiac fibroblasts, removal of IFN-β resulted in 10-fold-greater reovirus replication in the fibroblasts than in the myocytes. Together the data suggest that the IFN-β response controls reovirus replication equivalently in the two cell types. In the absence of reovirus-induced IFN-β, however, reovirus replicates to higher titers in cardiac fibroblasts than in cardiac myocytes, suggesting that the higher basal IFN-β and ISG expression in myocytes may play an important protective role. DA - 2005/3// PY - 2005/3// DO - 10.1128/JVI.79.5.2979-2987.2005 VL - 79 IS - 5 SP - 2979-2987 SN - 1098-5514 ER - TY - JOUR TI - Assisting Hox proteins in controlling body form: are there new lessons from flies (and mammals)? AU - Mahaffey, JW T2 - CURRENT OPINION IN GENETICS & DEVELOPMENT AB - Hox proteins regulate specific sets of target genes to give rise to morphological distinctions along the anterior–posterior body axis of metazoans. Though they have high developmental specificity, Hox proteins have low DNA binding specificity, so how they select the appropriate target genes has remained enigmatic. There is general agreement that cofactors provide additional specificity, but a comprehensive model of Hox control of gene expression has not emerged. There is now evidence that a global network of zinc finger transcription factors contributes to patterning of the Drosophila embryo. These zinc finger proteins appear to establish fields in which certain Hox proteins can function. Though the nature of these fields is uncertain at this time, it is possible that these zinc finger proteins are Hox cofactors, providing additional specificity during Hox target-gene selection. Furthermore, these zinc finger proteins are conserved, as are aspects of their anterior–posterior expression, suggesting that their roles might be conserved, as well. Perhaps this layer in the genetic control of body patterning will help bridge some of the chasms that remain in our understanding of the genetic control of pattern formation. DA - 2005/8// PY - 2005/8// DO - 10.1016/j.gde.2005.06.009 VL - 15 IS - 4 SP - 422-429 SN - 0959-437X ER - TY - JOUR TI - Analysis of diltiazem in Lipoderm (R) transdermal gel using reversed-phase high-performance liquid chromatography applied to homogenization and stability studies AU - Buur, JL AU - Baynes, RE AU - Yeatts, JL AU - Davidson, G AU - DeFrancesco, TC T2 - JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS AB - A simple and novel method for the extraction and quantification of diltiazem hydrochloride was developed and applied to homogenization and stability studies. The method used solid phase extraction coupled with reversed-phase high-performance liquid chromatography (HPLC) with ultraviolet (UV) detection. Validation showed inter-day recoveries ranging from 84.00 to 96.52% with relative standard deviations ranging from 12.01 to 15.94%. Intra-day recoveries ranged from 67.95 to 106.1% with relative standard deviations less than 5%. The method showed excellent linearity from 50 to 250 mg/ml in undiluted gel (R2 = 0.996). The homogenization study showed good homogenization using both 50 and 100 depression techniques. Diltiazem was stable at a concentration of 246 mg/ml for 30 days and at a concentration of 99.6 mg/ml for 60 days no matter the storage conditions explored in this study. DA - 2005/6/1/ PY - 2005/6/1/ DO - 10.1016/j.jpba.2004.11.053 VL - 38 IS - 1 SP - 60-65 SN - 0731-7085 KW - diltiazem KW - reverse-phase liquid chromatography KW - transdermal gel KW - drug stability KW - compounded drug analysis ER - TY - JOUR TI - Anabaena sp strain PCC 7120 gene devH is required for synthesis of the heterocyst glycolipid layer AU - Ramirez, ME AU - Hebbar, PB AU - Zhou, RB AU - Wolk, CP AU - Curtis, SE T2 - JOURNAL OF BACTERIOLOGY AB - In response to deprivation for fixed nitrogen, the filamentous cyanobacterium Anabaena sp. strain PCC 7120 provides a microoxic intracellular environment for nitrogen fixation through the differentiation of semiregularly spaced vegetative cells into specialized cells called heterocysts. The devH gene is induced during heterocyst development and encodes a product with characteristics of a trans-acting regulatory protein. A devH mutant forms morphologically distinguishable heterocysts but is Fox(-), incapable of nitrogen fixation in the presence of oxygen. We demonstrate that rearrangements of nitrogen fixation genes take place normally in the devH mutant and that it is Fix(+), i.e., has nitrogenase activity under anoxic conditions. The Fox(-) phenotype was shown by ultrastructural studies to be associated with the absence of the glycolipid layer of the heterocyst envelope. The expression of glycolipid biosynthetic genes in the mutant is greatly reduced, and heterocyst glycolipids are undetectable. DA - 2005/4// PY - 2005/4// DO - 10.1128/JB.187.7.2326-2331.2005 VL - 187 IS - 7 SP - 2326-2331 SN - 1098-5530 ER - TY - JOUR TI - Tomato spotted wilt virus on potato in eastern North Carolina AU - Abad, JA AU - Moyer, JW AU - Kennedy, GG AU - Holmes, GA AU - Cubeta, MA T2 - AMERICAN JOURNAL OF POTATO RESEARCH DA - 2005/// PY - 2005/// DO - 10.1007/BF02853592 VL - 82 IS - 3 SP - 255-261 SN - 1874-9380 KW - plant virus detection KW - Tospoviruses KW - INSV KW - Solanum ER - TY - JOUR TI - The genome sequence of the rice blast fungus Magnaporthe grisea AU - Dean, RA AU - Talbot, NJ AU - Ebbole, DJ AU - Farman, ML AU - Mitchell, TK AU - Orbach, MJ AU - Thon, M AU - Kulkarni, R AU - Xu, , JR AU - Pan, HQ AU - Read, ND AU - Lee, YH AU - Carbone, I AU - Brown, D AU - Oh, YY AU - Donofrio, N AU - Jeong, JS AU - Soanes, DM AU - Djonovic, S AU - Kolomiets, E AU - Rehmeyer, C AU - Li, WX AU - Harding, M AU - Kim, S AU - Lebrun, MH AU - Bohnert, H AU - Coughlan, S AU - Butler, J AU - Calvo, S AU - Ma, LJ AU - Nicol, R AU - Purcell, S AU - Nusbaum, C AU - Galagan, JE AU - Birren, BW T2 - NATURE AB - Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation. DA - 2005/4/21/ PY - 2005/4/21/ DO - 10.1038/nature03449 VL - 434 IS - 7036 SP - 980-986 SN - 1476-4687 ER - TY - JOUR TI - The interaction of bioconvection caused by gyrotactic micro-organisms and settling of small solid particles AU - Kuznetsov, A. V. AU - Geng, P. T2 - International Journal of Numerical Methods for Heat & Fluid Flow DA - 2005/// PY - 2005/// DO - 10.1108/0961550510590597 VL - 15 IS - 4 SP - 328-347 ER - TY - JOUR TI - Taxonomic relationships among Arachis sect. Arachis species as revealed by AFLP markers AU - Milla, S.R. AU - Isleib, T.G. AU - Stalker, H.T. T2 - Genome AB - Cultivated peanut, Arachis hypogaea L., is a tetraploid (2n = 4x = 40) species thought to be of allopolyploid origin. Its closest relatives are the diploid (2n = 2x = 20) annual and perennial species included with it in Arachis sect. Arachis. Species in section Arachis represent an important source of novel alleles for improvement of cultivated peanut. A better understanding of the level of speciation and taxonomic relationships between taxa within section Arachis is a prerequisite to the effective use of this secondary gene pool in peanut breeding programs. The AFLP technique was used to determine intra- and interspecific relationships among and within 108 accessions of 26 species of this section. A total of 1328 fragments were generated with 8 primer combinations. From those, 239 bands ranging in size from 65 to 760 bp were scored as binary data. Genetic distances among accessions ranged from 0 to 0.50. Average distances among diploid species (0.30) were much higher than that detected between tetraploid species (0.05). Cluster analysis using different methods and principal component analysis were performed. The resulting grouping of accessions and species supports previous taxonomic classifications and genome designations. Based on genetic distances and cluster analysis, A-genome accessions KG 30029 (Arachis helodes) and KSSc 36009 (Arachis simpsonii) and B-genome accession KGBSPSc 30076 (A. ipaensis) were the most closely related to both Arachis hypogaea and Arachis monticola. This finding suggests their involvement in the evolution of the tetraploid peanut species. DA - 2005/// PY - 2005/// DO - 10.1139/g04-089 VL - 48 IS - 1 SP - 1–11 SN - 1480-3321 KW - peanut KW - numerical taxonomy KW - genome donors KW - classification ER - TY - JOUR TI - Soft-tissue vessels and cellular preservation in Tyrannosaurus rex AU - Schweitzer, MH AU - Wittmeyer, JL AU - Horner, , JR AU - Toporski, JK T2 - SCIENCE AB - Soft tissues are preserved within hindlimb elements of Tyrannosaurus rex (Museum of the Rockies specimen 1125). Removal of the mineral phase reveals transparent, flexible, hollow blood vessels containing small round microstructures that can be expressed from the vessels into solution. Some regions of the demineralized bone matrix are highly fibrous, and the matrix possesses elasticity and resilience. Three populations of microstructures have cell-like morphology. Thus, some dinosaurian soft tissues may retain some of their original flexibility, elasticity, and resilience. DA - 2005/3/25/ PY - 2005/3/25/ DO - 10.1126/science.1108397 VL - 307 IS - 5717 SP - 1952-1955 SN - 1095-9203 ER - TY - JOUR TI - RACE: Remote Analysis Computation for gene Expression data AU - Psarros, M AU - Heber, S AU - Sick, M AU - Thoppae, G AU - Harshman, K AU - Sick, B T2 - NUCLEIC ACIDS RESEARCH AB - The Remote Analysis Computation for gene Expression data ( RACE ) suite is a collection of bioinformatics web tools designed for the analysis of DNA microarray data. RACE performs probe-level data preprocessing, extensive quality checks, data visualization and data normalization for Affymetrix GeneChips. In addition, it offers differential expression analysis on normalized expression levels from any array platform. RACE estimates the false discovery rates of lists of potentially regulated genes and provides a Gene Ontology-term analysis tool for GeneChip data to support the biological interpretation and annotation of results. The analysis is fully automated but can be customized by flexible parameter settings. To offer a convenient starting point for subsequent analyses, and to provide maximum transparency, the R scripts used to generate the results can be downloaded along with the output files. RACE is freely available for use at http://race.unil.ch . DA - 2005/7/1/ PY - 2005/7/1/ DO - 10.1093/nar/gki490 VL - 33 SP - W638-W643 SN - 1362-4962 ER - TY - JOUR TI - Preservation of bone collagen from the late cretaceous period studied by immunological techniques and atomic force microscopy AU - Avci, R AU - Schweitzer, MH AU - Boyd, RD AU - Wittmeyer, JL AU - Arce, FT AU - Calvo, JO T2 - LANGMUIR AB - Late Cretaceous avian bone tissues from Argentina demonstrate exceptional preservation. Skeletal elements are preserved in partial articulation and suspended in three dimensions in a medium-grained sandstone matrix, indicating unusual perimortem taphonomic conditions. Preservation extends to the microstructural and molecular levels. Bone tissues respond to collagenase digestion and histochemical stains. In situ immunohistochemistry localizes binding sites for avian collagen antibodies in fossil tissues. Immunohistochemical studies do not, however, guarantee the preservation of molecular integrity. A protein may retain sufficient antigenicity for antibody binding even though degradation may render it incapable of original function. Therefore, we have applied atomic force microscopy to address the integrity and functionality of retained organic structures. Collagen pull-off measurements not only support immunochemical evidence for collagen preservation for antibody recognition but also imply preservation of the whole molecular integrity. No appreciable differences in collagen pull-off properties were measured between fossil and extant bone samples under physiological conditions. DA - 2005/4/12/ PY - 2005/4/12/ DO - 10.1021/la047682e VL - 21 IS - 8 SP - 3584-3590 SN - 0743-7463 ER - TY - JOUR TI - Matrix attachment regions increase the efficiency and stability of RNA-mediated resistance to Tomato Spotted Wilt Virus in transgenic tobacco AU - Levin, JS AU - Thompson, WF AU - Csinos, AS AU - Stephenson, MG AU - Weissinger, AK T2 - TRANSGENIC RESEARCH DA - 2005/4// PY - 2005/4// DO - 10.1007/s11248-004-5413-8 VL - 14 IS - 2 SP - 193-206 SN - 1573-9368 KW - gene silencing KW - matrix attachment regions KW - RNA-mediated virus resistance KW - Tomato Spotted Wilt Virus ER - TY - JOUR TI - Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data AU - Seo, TK AU - Kishino, H AU - Thorne, JL T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Because of the increase of genomic data, multiple genes are often available for the inference of phylogenetic relationships. The simple approach for combining multiple genes from the same taxon is to concatenate the sequences and then ignore the fact that different positions in the concatenated sequence came from different genes. Here, we discuss two criteria for inferring the optimal tree topology from data sets with multiple genes. These criteria are designed for multigene data sets where gene-specific evolutionary features are too important to ignore. One criterion is conventional and is obtained by taking the sum of log-likelihoods over all genes. The other criterion is obtained by dividing the log-likelihood for a gene by its sequence length and then taking the arithmetic mean over genes of these ratios. A similar strategy could be adopted with parsimony scores. The optimal tree is then declared to be the one for which the sum or the arithmetic mean is maximized. These criteria are justified within a two-stage hierarchical framework. The first level of the hierarchy represents gene-specific evolutionary features, and the second represents site-specific features for given genes. For testing significance of the optimal topology, we suggest a two-stage bootstrap procedure that involves resampling genes and then resampling alignment columns within resampled genes. An advantage of this procedure over concatenation is that it can effectively account for gene-specific evolutionary features. We discuss the applicability of the two-stage bootstrap idea to the Kishino–Hasegawa test and the Shimodaira–Hasegawa test. DA - 2005/3/22/ PY - 2005/3/22/ DO - 10.1073/pnas.0408313102 VL - 102 IS - 12 SP - 4436-4441 SN - 0027-8424 ER - TY - JOUR TI - Free amino acid profiles suggest a possible role for asparagine in the control of storage-product accumulation in developing seeds of low- and high-protein soybean lines AU - Hernandez-Sebastia, C AU - Marsolais, F AU - Saravitz, C AU - Israel, D AU - Dewey, RE AU - Huber, SC T2 - JOURNAL OF EXPERIMENTAL BOTANY AB - Several approaches were taken to examine the role of N-assimilate supply in the control of soybean (Glycine max) seed composition. In the first study, developing seeds were grown in vitro with D-[U-14C]sucrose (Suc) and different concentrations of Gln. Light stimulated carbon flux into oil and protein, and was required to sustain Suc uptake and anabolic processes under conditions of elevated nitrogen supply. High Gln supply resulted in higher transcript levels of β-conglycinin and oleosin. In the second study, analyses of soluble amino acid pools in two genetically related lines, NC103 and NC106 (low- and high-seed protein, respectively) showed that, in the light, NC106 accumulated higher levels of Asn and several other amino acids in developing cotyledons compared with NC103, whereas at the seed coat and apoplast levels both lines were similar. In the dark, NC103 accumulated Gln, Arg, and its precursors, suggesting a reduced availability of organic acids required for amino acid interconversions, while NC106 maintained higher levels of the pyruvate-derived amino acids Val, Leu, and Ile. Comparing NC103 and NC106, differences in seed composition were reflected in steady-state transcript levels of storage proteins and the lipogenic enzyme multi-subunit acetyl CoA carboxylase. In the third study, a positive correlation (P ≤0.05) between free Asn in developing cotyledons and seed protein content at maturity was confirmed in a comparison of five unrelated field-grown cultivars. The findings support the hypothesis that high seed-protein content in soybean is determined by the capacity of the embryo to take up nitrogen sources and to synthesize storage proteins. Asn levels are probably tightly regulated in the embryo of high-protein lines, and may act as a metabolic signal of seed nitrogen status. DA - 2005/7// PY - 2005/7// DO - 10.1093/jxb/eri191 VL - 56 IS - 417 SP - 1951-1963 SN - 1460-2431 KW - amino acid profile KW - carbon partitioning KW - seed nitrogen supply KW - seed protein content KW - soybean ER - TY - JOUR TI - Forced convective cooling via acoustic streaming in a narrow channel established by a vibrating piezoelectric bimorph AU - Wan, Q AU - Wu, T AU - Chastain, J AU - Roberts, WL AU - Kuznetsov, AV AU - Ro, PI T2 - FLOW TURBULENCE AND COMBUSTION AB - Forced convection in a narrow channel is investigated both numerically and experimentally. The flow field is established through the mechanism of acoustic streaming. This is accomplished by high frequency vibration of one of the channel walls, which is composed of a piezoelectric bimorph. In the numerical computations, the Navier-Stokes equations are decomposed into the acoustic equations and the streaming equations by the perturbation method. The acoustic field is first numerically obtained, which provides the driving force for the streaming field. The streaming field and the associated temperature field are then obtained numerically. Heat losses from a heat source are measured to determine the efficiency of this as a cooling method. The air-flow patterns in the channel between the heat source and the bimorph actuator are visualized using the particle tracking velocimetry. The visualization clearly shows that vortical streaming (acoustic streaming) can be induced by bimorph vibration, which enhances heat transfer between the heat source and the surrounding air. The temperature decreases obtained computationally and experimentally are in good agreement. DA - 2005/3// PY - 2005/3// DO - 10.1007/s10494-005-4132-4 VL - 74 IS - 2 SP - 195-206 SN - 1573-1987 KW - acoustic streaming KW - forced convection KW - cooling enhancement KW - vibrating surface ER - TY - JOUR TI - Forced convection in a composite parallel plate channel: modeling the effect of interface roughness and turbulence utilizing a kappa-epsilon model AU - Zhu, J AU - Kuznetsov, AV T2 - INTERNATIONAL COMMUNICATIONS IN HEAT AND MASS TRANSFER AB - In this paper, a composite parallel plate channel whose central part is occupied by a clear fluid and whose peripheral part is occupied by a fluid-saturated porous medium is considered. The modeling is based on the assumption that the flow in the clear fluid region is turbulent while in the porous region the flow remains laminar. The turbulent and laminar flow solutions are matched at the porous/fluid interface, which is assumed rough. Two different models are utilized for calculating turbulent viscosity in the clear fluid region, the algebraic Cebeci–Smith model and a k–ε model. Numerical results obtained utilizing both models are compared and analyzed in detail. DA - 2005/1// PY - 2005/1// DO - 10.1016/j.icheatmasstransfer.2004.05.019 VL - 32 IS - 1-2 SP - 10-18 SN - 1879-0178 KW - turbulence KW - porous media KW - kappa-epsilon model KW - rough interface ER - TY - JOUR TI - Distinct B-cell and T-cell lymphoproliferative disease prevalence among dog breeds indicates heritable risk AU - Modiano, JF AU - Breen, M AU - Burnett, RC AU - Parker, HG AU - Inusah, S AU - Thomas, R AU - Avery, PR AU - Lindblad-Toh, K AU - Ostrander, EA AU - Cutter, GC AU - Avery, AC T2 - CANCER RESEARCH AB - Abstract Immunophenotypes in lymphoproliferative diseases (LPD) are prognostically significant, yet causative factors for these conditions, and specifically those associated with heritable risk, remain elusive. The full spectrum of LPD seen in humans occurs in dogs, but the incidence and lifetime risk of naturally occurring LPD differs among dog breeds. Taking advantage of the limited genetic heterogeneity that exists within dog breeds, we tested the hypothesis that the prevalence of LPD immunophenotypes would differ among different breeds. The sample population included 1,263 dogs representing 87 breeds. Immunophenotype was determined by the presence of clonal rearrangements of immunoglobulin heavy chain or T-cell receptor γ chain. The probability of observing the number of B-cell or T-cell tumors in a particular breed or breed group was compared with three reference populations. Significance was computed using χ2 test, and logistic regression was used to confirm binomial predictions. The data show that, among 87 breeds tested, 15 showed significant differences from the prevalence of LPD immunophenotypes seen across the dog population as a whole. More significantly, elevated risk for T-cell LPD seems to have arisen ancestrally and is retained in related breed groups, whereas increased risk for B-cell disease may stem from different risk factors, or combinations of risk factors, arising during the process of breed derivation and selection. The data show that domestic dogs provide a unique and valuable resource to define factors that mediate risk as well as genes involved in the initiation of B-cell and T-cell LPD. DA - 2005/7/1/ PY - 2005/7/1/ DO - 10.1158/0008-5472.CAN-04-4613 VL - 65 IS - 13 SP - 5654-5661 SN - 1538-7445 ER - TY - JOUR TI - Asymmetrical protein kinase A activity establishes neutrophil cytoskeletal polarity and enables chemotaxis AU - Jones, SL AU - Sharief, Y T2 - JOURNAL OF LEUKOCYTE BIOLOGY AB - Neutrophil chemotaxis requires precise spatial organization of the actin cytoskeleton and integrin activation to polarize the cell and enable migration. Protein kinase A (PKA) activity regulates integrin activation and actin cytoskeletal organization, suggesting that PKA is a key element in the mechanism regulating neutrophil chemotaxis. Our hypothesis is that asymmetrical PKA activity is critical for establishing neutrophil adhesive and cytoskeletal polarity required for migration during chemotaxis. To test this hypothesis, we first determined that global treatment with the PKA inhibitor KT5720 decreased formylated Met-Leu-Phe (fMLF)-induced migration. The ability of PKA inhibitors to reduce migration correlated with increased overall beta2 integrin cell-surface expression, affinity activation, and cellular adhesion. We next determined whether asymmetrical PKA activity was sufficient to induce migration. Exposure to gradient of the PKA inhibitors KT5720 or H-89 or a stearated, cell-permeant peptide (St-Ht31), which inhibits PKA binding to anchorage proteins, stimulated neutrophil migration in a chemotaxis chamber. Global treatment with KT5720 abolished the ability of fMLF to polarize the neutrophil actin cytoskeleton. In contrast to global treatment with KT5720, a point source of KT5720 was sufficient to polarize the actin cytoskeleton. The ability of KT5720 and St-Ht31 to stimulate migration was abolished by pretreatment with the phosphatidylinositol-3 kinase (PI-3K) inhibitors wortmannin and LY294002. These data suggest that asymmetrical PKA activity is necessary and sufficient for actin cytoskeletal polarization and migration during neutrophil chemotaxis. In addition, our data suggest PI-3K is an effector of PKA during chemotaxis. DA - 2005/7// PY - 2005/7// DO - 10.1189/jlb.0804459 VL - 78 IS - 1 SP - 248-258 SN - 1938-3673 UR - http://europepmc.org/abstract/med/15817703 KW - integrin KW - adhesion KW - migration KW - actin cytoskeleton KW - phosphatidylinositol-3 kinase ER - TY - JOUR TI - A silicified bird from Quaternary hot spring deposits AU - Channing, A AU - Schweitzer, MH AU - Horner, , JR AU - McEneaney, T T2 - PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES AB - The first avian fossil recovered from high-temperature hot spring deposits is a three-dimensional external body mould of an American coot (Fulica americana) from Holocene sinters of Yellowstone National Park, Wyoming, USA. Silica encrustation of the carcass, feathers and colonizing microbial communities occurred within days of death and before substantial soft tissue degradation, allowing preservation of gross body morphology, which is usually lost under other fossilization regimes. We hypothesize that the increased rate and extent of opal-A deposition, facilitated by either passive or active microbial mediation following carcass colonization, is required for exceptional preservation of relatively large, fleshy carcasses or soft-bodied organisms by mineral precipitate mould formation. We suggest physico-chemical parameters conducive to similar preservation in other vertebrate specimens, plus distinctive sinter macrofabric markers of hot spring subenvironments where these parameters are met. DA - 2005/5/7/ PY - 2005/5/7/ DO - 10.1098/rspb.2004.2989 VL - 272 IS - 1566 SP - 905-911 SN - 1471-2954 KW - hot spring deposits KW - silicification KW - fossilization KW - geomicrobiology KW - avian fossil ER - TY - JOUR TI - Virulence genes in Heterodera glycines: Allele frequencies and ror gene groups among field isolates and inbred lines AU - Dong, K AU - Barker, KR AU - Opperman, CH T2 - PHYTOPATHOLOGY AB - ABSTRACT Genetic variation in field populations of Heterodera glycines is a key issue for both resistance gene deployment and basic understanding of virulence-gene flow in populations. In this study, we examined phenotypically defined genes for virulence under selection from host resistance. We separated the most common H. glycines genotypes in the United States into two virulence groups, based on their reproductive abilities on the resistant soybean plant introduction (PI) 88788. These groups correspond to previously identified virulence genes in the nematode, as follows: the dominant gene in H. glycines to PI88788, and the recessive genes to PI90763 and Pickett/Peking. Virulence allele frequencies and virulence genotype frequencies of selected field isolates were investigated by testing the host range of single-female-derived lines, which were developed through single-female inoculation on the standard susceptible soybean 'Lee 68'. By comparing virulence genotype frequencies between the original field isolates and their single-female-derived lines, we were able to determine allele frequencies in the field populations. The results suggest that tremendous variation in H. glycines virulence genes exists among field populations. Potential mechanisms of selection which could cause virulence genotype frequency increases are discussed as related to population genetics equilibrium theory. DA - 2005/2// PY - 2005/2// DO - 10.1094/PHYTO-95-0186 VL - 95 IS - 2 SP - 186-191 SN - 1943-7684 KW - cyst nematode KW - gene frequency ER - TY - JOUR TI - Tissue localization and regulation by juvenile hormone of human allergen Bla g 4 from the German cockroach, Blattella germanica (L.) AU - Fan, Y AU - Gore, JC AU - Redding, KO AU - Vailes, LD AU - Chapman, MD AU - Schal, C T2 - INSECT MOLECULAR BIOLOGY AB - Abstract The German cockroach, Blattella germanica (L.), produces several potent protein aeroallergens, including Bla g 4, a ∼20 kDa lipocalin. RT‐PCR, Northern analyses and in situ hybridization showed that Bla g 4 is expressed only in the adult male reproductive system. Western blotting and ELISA with rBla g 4 antiserum detected immunoreactivity in the utricles and the conglobate gland, but not in other tissues of the male reproductive system. The Bla g 4 protein content of males increased from adult emergence to day 14, but during copulation Bla g 4 was depleted in the male and transferred to the female within the spermatophore. Topical application of juvenile hormone III stimulated Bla g 4 production by both conglobate gland and utricles. DA - 2005/1// PY - 2005/1// DO - 10.1111/j.1365-2583.2004.00530.x VL - 14 IS - 1 SP - 45-53 SN - 1365-2583 KW - German cockroach KW - allergen KW - Bla g 4 KW - lipocalin KW - juvenile hormone ER - TY - JOUR TI - An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance AU - Liu, GS AU - Holub, EB AU - Alonso, JM AU - Ecker, , JR AU - Fobert, PR T2 - PLANT JOURNAL AB - The Arabidopsis genome contains six NPR1-related genes. Given the pivotal role played by NPR1 in controlling salicylic acid (SA)-mediated gene expression and disease resistance, functional characterization of other family members appears to be justified. Reverse genetics was used to analyze the role of one NPR1-like gene, which we called NPR4. The NPR4 protein shares 36% identity with NPR1 and interacts with the same spectrum of TGA transcription factors in yeast two-hybrid assays. Plants with T-DNA insertions in NPR4 are more susceptible to the virulent bacterial pathogen Pseudomonas syringe pv. tomato DC3000. This phenotype is complemented by expression of the wild type NPR4 coding region. As determined by the parasite reproduction, the npr4-1 mutant is more susceptible to the fungal pathogen Erysiphe cichoracearum, but does not differ markedly from wild type in its interaction with virulent and avirulent strains of the oomycete Peronospora parasitica. In leaves of wild-type plants, NPR4 mRNA levels increase following pathogen challenge or SA treatment, and decrease rapidly following methyl jasmonic acid (MeJA) treatment. Transcripts of the pathogenesis-related (PR) genes PR-1, PR-2, and PR-5 are only marginally reduced in the npr4-1 mutant following pathogen challenge or SA treatment. This reduction of PR gene expression is more pronounced when leaves are challenged with the bacterial pathogen following SA treatment. Expression of the jasmonic acid-dependent pathway marker gene PDF1.2 is compromised in npr4-1 leaves following application of MeJA or a combination of SA and MeJA. These results indicate that NPR4 is required for basal defense against pathogens, and that it may be implicated in the cross-talk between the SA- and JA-dependent signaling pathways. DA - 2005/1// PY - 2005/1// DO - 10.1111/j.1365-313x.2004.02296.x VL - 41 IS - 2 SP - 304-318 SN - 1365-313X KW - reverse genetics KW - PR genes KW - cross-talk KW - signaling KW - salicylic acid KW - gene family ER - TY - JOUR TI - A borehole temperature during drilling in a fractured rock formation AU - Fomin, S AU - Hashida, T AU - Chugunov, V AU - Kuznestov, AV T2 - INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER AB - Drilling in brittle crystalline rocks is often accompanied by a fluid loss through the finite number of the major fractures intercepting the borehole. These fractures affect the flow regime and temperature distributions in the borehole and rock formation. In this study, the problem of borehole temperature variation during drilling of the fractured rock is analyzed analytically by applying the approximate generalized integral-balance method. The model accounts for different flow regimes in the borehole, for different drilling velocities, for different locations of the major fractures intersecting the borehole, and for the thermal history of the borehole exploitation, which may include a finite number of circulation and shut-in periods. Normally the temperature fields in the well and surrounding rocks are calculated numerically by the finite difference and finite element methods or analytically, utilizing the Laplace-transform method. The formulae obtained by the Laplace-transform method are usually complex and require tedious numerical evaluations. Moreover, in the previous research the heat interactions of circulating fluid with the rock formation were treated assuming constant bore-face temperatures. In the present study the temperature field in the formation disturbed by the heat flow from the borehole is modeled by the heat conduction equation. The thermal interaction of the circulating fluid with the formation is approximated by utilizing the Newton law of cooling at the bore-face. The discrete sinks of fluid on the bore-face model the fluid loss in the borehole through the fractures. The heat conduction problem in the rock is solved analytically by the heat balance integral method. It can be proved theoretically that the approximate solution found by this method is accurate enough to model thermal interactions between the borehole fluid and the surrounding rocks. Due to its simplicity and accuracy, the derived solution is convenient for the geophysical practitioners and can be readily used, for instance, for predicting the equilibrium formation temperatures. DA - 2005/1// PY - 2005/1// DO - 10.1016/j.ijheatmasstransfer.2004.07.042 VL - 48 IS - 2 SP - 385-394 SN - 1879-2189 KW - fluid loss KW - borehole KW - temperature KW - heat flux KW - bore-face KW - fluid circulation KW - integral-balance method ER - TY - JOUR TI - Transfer of resistance to potato virus Y (PVY) from Nicotiana africana to Nicotiana tabacum: possible influence of tissue culture on the rate of introgression AU - Lewis, RS T2 - THEORETICAL AND APPLIED GENETICS DA - 2005/2// PY - 2005/2// DO - 10.1007/s00122-004-1893-4 VL - 110 IS - 4 SP - 678-687 SN - 0040-5752 ER - TY - JOUR TI - Thermally developing forced convection in a channel occupied by a porous medium saturated by a non-Newtonian fluid AU - Nield, DA AU - Kuznetsov, A T2 - INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER AB - The classical Graetz methodology is applied to investigate the thermal development of forced convection in a parallel plate channel filled by a saturated porous medium, with walls held at constant temperature, for the case of a non-Newtonian fluid of power-law type. A Brinkman-Forchheimer model is used for the momentum equation. The analysis for the case of small modified Darcy number leads to expressions for the local Nusselt number and average Nusselt number as functions of the dimensionless longitudinal coordinate, the power-law index, a modified Darcy number, and a modified Reynolds-Forchheimer number (with the last three parameters being involved via a boundary-layer thickness). DA - 2005/3// PY - 2005/3// DO - 10.1016/j.ijheatmasstransfer.2004.09.040 VL - 48 IS - 6 SP - 1214-1218 SN - 1879-2189 ER - TY - JOUR TI - Resistance to fire blight among flowering pears and quince AU - Bell, A. C. AU - Ranney, T. G. AU - Eaker, T. A. AU - Sutton, T. B. T2 - HortScience DA - 2005/// PY - 2005/// VL - 40 IS - 2 SP - 413-415 ER - TY - JOUR TI - Junctional epidermolysis bullosa in two domestic shorthair kittens AU - Alhaidari, Z AU - Olivry, T AU - Spadafora, A AU - Thomas, RC AU - Perrin, C AU - Meneguzzi, G AU - Ortonne, JP T2 - VETERINARY DERMATOLOGY AB - Abstract This article describes two cases of junctional epidermolysis bullosa in nonrelated kittens. Both cats exhibited pinnal erosions, oral ulcerations and severe onychomadesis. Histopathology, electron microscopy and/or indirect immunoperoxidase revealed subepidermal clefting, with the lamina densa remaining attached to the floor of the vesicles. Indirect immunofluorescence revealed reduced staining for laminin‐5 γ2 subunit in case 1 and β3 subunit in case 2. DA - 2005/2// PY - 2005/2// DO - 10.1111/j.1365-3164.2005.00420.x VL - 16 IS - 1 SP - 69-73 SN - 1365-3164 ER - TY - JOUR TI - HyPhy: hypothesis testing using phylogenies AU - Pond, SLK AU - Frost, SDW AU - Muse, SV T2 - BIOINFORMATICS AB - The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution.http://www.hyphy.orgmuse@stat.ncsu.eduHyPhydocumentation and tutorials are available at http://www.hyphy.org. DA - 2005/3/1/ PY - 2005/3/1/ DO - 10.1093/bioinformatics/bti079 VL - 21 IS - 5 SP - 676-679 SN - 1460-2059 ER - TY - JOUR TI - Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM AU - Altermann, E AU - Russell, WM AU - Azcarate-Peril, MA AU - Barrangou, R AU - Buck, BL AU - McAuliffe, O AU - Souther, N AU - Dobson, A AU - Duong, T AU - Callanan, M AU - Lick, S AU - Hamrick, A AU - Cano, R AU - Klaenhammer, TR T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids. The average GC content is 34.71% with 1,864 predicted ORFs, of which 72.5% were functionally classified. Nine phage-related integrases were predicted, but no complete prophages were found. However, three unique regions designated as potential autonomous units (PAUs) were identified. These units resemble a unique structure and bear characteristics of both plasmids and phages. Analysis of the three PAUs revealed the presence of two R/M systems and a prophage maintenance system killer protein. A spacers interspersed direct repeat locus containing 32 nearly perfect 29-bp repeats was discovered and may provide a unique molecular signature for this organism. In silico analyses predicted 17 transposase genes and a chromosomal locus for lactacin B, a class II bacteriocin. Several mucus- and fibronectin-binding proteins, implicated in adhesion to human intestinal cells, were also identified. Gene clusters for transport of a diverse group of carbohydrates, including fructooligosaccharides and raffinose, were present and often accompanied by transcriptional regulators of the lacI family. For protein degradation and peptide utilization, the organism encoded 20 putative peptidases, homologs for PrtP and PrtM, and two complete oligopeptide transport systems. Nine two-component regulatory systems were predicted, some associated with determinants implicated in bacteriocin production and acid tolerance. Collectively, these features within the genome sequence of L. acidophilus are likely to contribute to the organisms' gastric survival and promote interactions with the intestinal mucosa and microbiota. DA - 2005/3/15/ PY - 2005/3/15/ DO - 10.1073/pnas.0409188102 VL - 102 IS - 11 SP - 3906-3912 SN - 0027-8424 KW - adhesion KW - stress response KW - proteolytic system KW - sugar metabolism KW - in silico analysis ER - TY - JOUR TI - Root-knot nematodes and bacterial Nod factors elicit common signal transduction events in Lotus japonicus AU - Weerasinghe, RR AU - Bird, DM AU - Allen, NS T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - The symbiosis responsible for nitrogen fixation in legume root nodules is initiated by rhizobial signaling molecules [Nod factors (NF)]. Using transgenically tagged microtubules and actin, we dynamically profiled the spatiotemporal changes in the cytoskeleton of living Lotus japonicus root hairs, which precede root-hair deformation and reflect one of the earliest host responses to NF. Remarkably, plant-parasitic root-knot nematodes (RKN) invoke a cytoskeletal response identical to that seen in response to NF and induce root-hair waviness and branching in legume root hairs via a signal able to function at a distance. Azide-killed nematodes do not produce this signal. A similar response to RKN was seen in tomato. Aspects of the host responses to RKN were altered or abolished by mutations in the NF receptor genes nfr1 , nfr5 , and symRK , suggesting that RKN produce a molecule with functional equivalence to NF, which we name NemF. Because the ability of RKN to establish feeding sites and reproduce was markedly reduced in the mutant lines, we propose that RKN have adapted at least part of the symbiont-response pathway to enhance their parasitic ability. DA - 2005/2/22/ PY - 2005/2/22/ DO - 10.1073/pnas.0407926102 VL - 102 IS - 8 SP - 3147-3152 SN - 0027-8424 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-14544295731&partnerID=MN8TOARS KW - cytoskeleton KW - NemF KW - rhizobia KW - actin KW - microtubule ER - TY - JOUR TI - QTL mapping and the genetic basis of adaptation: recent developments AU - Zeng, ZB T2 - GENETICA DA - 2005/2// PY - 2005/2// DO - 10.1007/s10709-004-2705-0 VL - 123 IS - 1-2 SP - 25-37 SN - 1573-6857 KW - genetic architecture KW - genetic basis of adaptation KW - genetic correlation KW - genotype by environment interaction KW - microarrays KW - QTL mapping KW - quantitative trait loci ER - TY - JOUR TI - Prevalence of Salmonella spp. in oysters in the United States AU - Brands, DA AU - Inman, AE AU - Gerba, CP AU - Mare, CJ AU - Billington, SJ AU - Saif, LA AU - Levine, JF AU - Joens, LA T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - Food-borne diseases such as salmonellosis can be attributed, in part, to the consumption of raw oysters. To determine the prevalence of Salmonella spp. in oysters, oysters harvested from 36 U.S. bays (12 each from the West, East, and Gulf coasts in the summer of 2002, and 12 bays, four per coast, in the winter of 2002-2003) were tested. Salmonella was isolated from oysters from each coast of the United States, and 7.4% of all oysters tested contained Salmonella. Isolation tended to be bay specific, with some bays having a high prevalence of Salmonella, while other bays had none. Differences in the percentage of oysters from which Salmonella was isolated were observed between the summer and winter months, with winter numbers much lower probably due to a variety of weather-related events. The vast majority (78/101) of Salmonella isolates from oysters were Salmonella enterica serovar Newport, a major human pathogen, confirming the human health hazard of raw oyster consumption. Contrary to previous findings, no relationship was found between the isolation of fecal coliforms and Salmonella from oysters, indicating a necessity for specific monitoring for Salmonella and other pathogens rather than the current reliance on fecal coliform testing. DA - 2005/2// PY - 2005/2// DO - 10.1128/AEM.71.2.893-897.2005 VL - 71 IS - 2 SP - 893-897 SN - 1098-5336 ER - TY - JOUR TI - Multiple-scale landscape predictors of benthic macroinvertebrate community structure in North Carolina AU - Potter, K AU - Cubbage, F AU - Schaberg, R T2 - Landscape and Urban Planning AB - Both riparian zone characteristics and watershed-wide landscape attributes affect the water quality of streams and rivers. Understanding the relative importance of these factors is significant for determining management and monitoring actions that adequately protect water quality and the ecological integrity of aquatic communities. In this study, we analyzed Geographic Information System-derived data to: (1) determine whether North Carolina benthic macroinvertebrate community structure is more closely correlated with landscape characteristics at the scale of riparian zones or entire watersheds; (2) understand which landscape attributes are correlated with aquatic invertebrate communities that reflect degraded stream conditions; (3) investigate whether the importance of streamside forest varies with watershed size. Watershed characteristics explained a greater amount of variability in macrobenthic community structure (69.5–75.4%) than riparian attributes (57.4–65.2%). While topographic complexity was the most important variable at all scales, different land cover characteristics were of secondary importance at both scales: developed land cover for watersheds, and forest cover at the riparian scale. The amount of riparian zone and watershed-wide forest cover accounted for more variability in small watersheds than in large watersheds. DA - 2005/3/28/ PY - 2005/3/28/ DO - 10.1016/j.landurbplan.2004.02.001 VL - 71 IS - 2-4 SP - 77-90 J2 - Landscape and Urban Planning LA - en OP - SN - 0169-2046 UR - http://dx.doi.org/10.1016/S0169-2046(04)00028-3 DB - Crossref KW - nonpoint source pollution KW - aquatic ecosystems KW - Geographic Information Systems KW - landscape ecology KW - land cover KW - water quality KW - watershed management ER - TY - JOUR TI - Mammalian nest predators respond to greenway width, landscape context and habitat structure AU - Sinclair, KE AU - Hess, GR AU - Moorman, CE AU - Mason, JH T2 - LANDSCAPE AND URBAN PLANNING AB - Birds of conservation concern breed in suburban greenways, yet abundant populations of mammals that depredate bird nests might reduce nest success. We evaluated how three factors influenced the abundance of mammalian nest predators in thirty-four 300-m long forested greenway segments in Raleigh and Cary, North Carolina, USA: (1) the width of the forested corridor containing the greenway, (2) the land-use adjacent to the forested corridor, and (3) the habitat structure within the greenway. Forest corridor width and adjacent land-use were measured using aerial photographs. Attributes of adjacent land use included categorical measures of development intensity (low-density residential, high-density residential, office/institutional), and the proportions of forest canopy, grass, buildings, and pavement. Several measures of habitat structure within the greenway were collected in the field, including trail width and surface type, and percentage of mature forest. We measured the relative abundance of mammalian nest predators with scent-station transects, operated for five nights during the 2002 breeding bird season. Total abundance of mammalian nest predators increased significantly as forest corridor width decreased. We found no relationship between categorical measures of land-use and total abundance of mammalian nest predators. Specific attributes of the landscape adjacent to the greenway, however, did have an effect. Greenways adjacent to landscapes with fewer buildings had a higher abundance of mammalian nest predators. The abundance of individual species varied with the amount of canopy, lawn, and pavement in the adjacent landscape. Some measures of habitat structure of greenways also were correlated with the abundance of mammalian nest predators. Greenway segments with wider trails had a higher abundance of mammalian nest predators, as did segments with a higher percentage of mature forest. No habitat structure variables were significant for all species. To reduce the overall risk of avian nest predation by mammals, forested greenways should be designed with wider forest corridors and narrower, unpaved trails. Some greenway characteristics that favor high-nest predator populations also favor birds of conservation concern. Similarly, some characteristics correlated with lower predator occurrence are also correlated with lower abundance of birds of conservation concern. Thus, management of greenways and the surrounding landscape must balance reduction of predator communities with the promotion of desired bird communities and other conservation goals. DA - 2005/3/28/ PY - 2005/3/28/ DO - 10.1016/j.landurbplan.2004.04.001 VL - 71 IS - 2-4 SP - 277-293 SN - 0169-2046 KW - corridor KW - greenway KW - landscape context KW - mammal KW - nest predator ER - TY - JOUR TI - Influence of divalent cations on the structural thermostability and thermal inactivation kinetics of class II xylose isomerases AU - Epting, KL AU - Vieille, C AU - Zeikus, JG AU - Kelly, RM AU - Kelly, RM AU - Zeikus, JG AU - Vieille, C T2 - FEBS JOURNAL AB - The effects of divalent metal cations on structural thermostability and the inactivation kinetics of homologous class II d-xylose isomerases (XI; EC 5.3.1.5) from mesophilic (Escherichia coli and Bacillus licheniformis), thermophilic (Thermoanaerobacterium thermosulfurigenes), and hyperthermophilic (Thermotoga neapolitana) bacteria were examined. Unlike the three less thermophilic XIs that were substantially structurally stabilized in the presence of Co2+ or Mn2+ (and Mg2+ to a lesser extent), the melting temperature [(Tm) approximately 100 degrees C] of T. neapolitana XI (TNXI) varied little in the presence or absence of a single type of metal. In the presence of any two of these metals, TNXI exhibited a second melting transition between 110 degrees C and 114 degrees C. TNXI kinetic inactivation, which was non-first order, could be modeled as a two-step sequential process. TNXI inactivation in the presence of 5 mm metal at 99-100 degrees C was slowest in the presence of Mn2+[half-life (t(1/2)) of 84 min], compared to Co2+ (t(1/2) of 14 min) and Mg2+ (t(1/2) of 2 min). While adding Co2+ to Mg2+ increased TNXI's t(1/2) at 99-100 degrees C from 2 to 7.5 min, TNXI showed no significant activity at temperatures above the first melting transition. The results reported here suggest that, unlike the other class II XIs examined, single metals are required for TNXI activity, but are not essential for its structural thermostability. The structural form corresponding to the second melting transition of TNXI in the presence of two metals is not known, but likely results from cooperative interactions between dissimilar metals in the two metal binding sites. DA - 2005/3// PY - 2005/3// DO - 10.1111/j.1742-4658.2005.04577.x VL - 272 IS - 6 SP - 1454-1464 SN - 1742-4658 KW - inactivation kinetics KW - metal cofactors KW - thermostability KW - xylose isomerases ER - TY - JOUR TI - A two-velocity two-temperature model for a bi-dispersed porous medium: Forced convection in a channel AU - Nield, DA AU - Kuznetsov, AV T2 - TRANSPORT IN POROUS MEDIA DA - 2005/6// PY - 2005/6// DO - 10.1007/s11242-004-1685-y VL - 59 IS - 3 SP - 325-339 SN - 0169-3913 KW - bi-dispersed medium KW - two-velocity KW - two-temperature KW - forced convection KW - channel ER - TY - JOUR TI - Predation of Colorado potato beetle eggs by a polyphagous ladybeetle in the presence of alternate prey: potential impact on resistance evolution AU - Mallampalli, N AU - Gould, F AU - Barbosa, P T2 - ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA AB - Abstract The influence of prey choice on the predation of a target prey item by a polyphagous insect predator was investigated in field plot studies. The target prey consisted of eggs of the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say (Coleoptera: Chrysomelidae), and the predator was the 12‐spotted ladybeetle, Coleomegilla maculata Lengi (Coleoptera: Coccinellidae). Eggs of the European corn borer (ECB), Ostrinia nubilalis Hübner (Lepidoptera: Pyralidae), and nymphs and adults of the green peach aphid, Myzus persicae Sulzer (Homoptera: Aphididae), comprised the alternative prey choices. The objectives of these studies were to: (1) examine predation in a multiprey scenario likely to occur in an agroecosystem, and (2) use the data to simulate the impact of predator‐induced mortality on the evolution of resistance to Bt‐transgenic plants in the target herbivore. Simulations of the rate of resistance evolution were carried out using a deterministic genetic model. Experiments were performed using potato field plots planted in a manner reflecting a 25% or 50% non‐transgenic refuge. CPB eggs were infested so as to mimic the densities of resistant and susceptible populations that might occur in commercial Bt‐transgenic plantings. Densities of predators and alternate prey species were chosen to represent those that might typically occur in potato crops in the eastern USA. Simulation results indicated that when ECB eggs were present, predation on CPB eggs either became inversely spatially density‐dependent, or increased significantly in a density‐dependent manner. When aphids were present, predation became positively density‐dependent. Model simulations predicted that ECB egg presence is beneficial, in that resistance was delayed by up to 40 pest generations (as compared to the scenario with CPB as the only prey), while aphid presence accelerated resistance evolution by 18 generations. Results suggest that resistance management strategies should take into account the composition of prey species available to generalist predators typically present, so as to best delay pest adaptation to Bt‐toxins. DA - 2005/1// PY - 2005/1// DO - 10.1111/j.0013-8703.2005.00232.x VL - 114 IS - 1 SP - 47-54 SN - 0013-8703 KW - Leptinotarsa decemlineata KW - Coleoptera KW - Chrysomelidae KW - Coccinellidae KW - Coleomegilla maculata KW - transgenic potato KW - predator-prey interactions KW - susceptible population KW - refuge ER - TY - JOUR TI - Population density-dependent regulation of exopolysaccharide formation in the hyperthermophilic bacterium Thermotoga maritima AU - Johnson, MR AU - Montero, CI AU - Conners, SB AU - Shockley, KR AU - Bridger, SL AU - Kelly, RM T2 - MOLECULAR MICROBIOLOGY AB - Co-cultivation of the hyperthermophiles Thermotoga maritima and Methanococcus jannaschii resulted in fivefold higher T. maritima cell densities when compared with monoculture as well as concomitant formation of exopolysaccharide and flocculation of heterotroph-methanogen cellular aggregates. Transcriptional analysis of T. maritima cells from these aggregates using a whole genome cDNA microarray revealed the induction of a putative exopolysaccharide synthesis pathway, regulated by intracellular levels of cyclic diguanosine 3',5'-(cyclic)phosphate (cyclic di-GMP) and mediated by the action of several GGDEF proteins, including a putative diguanylate cyclase (TM1163) and a putative phosphodiesterase (TM1184). Transcriptional analysis also showed that TM0504, which encodes a polypeptide containing a motif common to known peptide-signalling molecules in mesophilic bacteria, was strongly upregulated in the co-culture. Indeed, when a synthetically produced peptide based on TM0504 was dosed into the culture at ecologically relevant levels, the production of exopolysaccharide was induced at significantly lower cell densities than was observed in cultures lacking added peptide. In addition to identifying a pathway for polysaccharide formation in T. maritima, these results point to the existence of peptide-based quorum sensing in hyperthermophilic bacteria and indicate that cellular communication should be considered as a component of the microbial ecology within hydrothermal habitats. DA - 2005/2// PY - 2005/2// DO - 10.1111/j.1365-2958.2004.04419.x VL - 55 IS - 3 SP - 664-674 SN - 1365-2958 ER - TY - JOUR TI - Modeling heat and moisture transport in firefighter protective clothing during flash fire exposure AU - Chitrphiromsri, P AU - Kuznetsov, A T2 - HEAT AND MASS TRANSFER DA - 2005/1// PY - 2005/1// DO - 10.1007/s00231-004-0504-x VL - 41 IS - 3 SP - 206-215 SN - 1432-1181 ER - TY - JOUR TI - Thermal development of forced convection in a channel or duct partly occupied by a porous medium AU - Nield, DA AU - Kuznetsov, AV T2 - JOURNAL OF POROUS MEDIA DA - 2005/// PY - 2005/// DO - 10.1615/JPorMedia.v8.i6.70 VL - 8 IS - 6 SP - 627-638 SN - 1091-028X ER - TY - CONF TI - The 2004-05 uniform Southern fusarium head blight screening nursery AU - Murphy, J. P. AU - Navarro, R. A. AU - Lyerly, J. H. C2 - 2005/// C3 - Proceedings of the 2005 National Fusarium Head Blight Forum, 2005 Dec. 11-13, Milwaukee, WI DA - 2005/// SP - 73 PB - East Lansing: Michigan State University ER - TY - CONF TI - Intermittent aeration for nitrogen removal from high-ammonia wastewater through nitrification and denitrification in a single reactor AU - Head, M. A. AU - Mota, C. R. AU - Ridenoure, J. A., III AU - Reyes F. L., AU - Cheng, J. J. C2 - 2005/// C3 - 2005 Animal Waste Management Symposium (Research Triangle, NC) DA - 2005/// ER - TY - JOUR TI - Using intermittent aeration to remove nitrogen from swine wastewater AU - Head, M. A. AU - Ridenoure, J. A. AU - Mota, C. R., III AU - Reyes F. L., AU - Cheng, J. J. T2 - Industrial Wastewater DA - 2005/// PY - 2005/// VL - 4 IS - 4 SP - 9-12 ER - TY - CONF TI - Nitrogen removing activity of granules in intermittent aeration reactors treating high-ammonia wastewater AU - Head, M. A. AU - Williams, J. C. AU - Mota, C. R., III AU - Reyes F. L., AU - Cheng, J. J. C2 - 2005/// C3 - 4th International Water Association Specialized Conference on Microorganisms in Activated Sludge and Biofilm Systems (Gold Coast, Australia) DA - 2005/// ER - TY - CONF TI - Nitrogen Removal from Anaerobically Pretreated Swine Wastewater in an Intermittent Aeration Process AU - Head, M. A. AU - Mota, C. R. AU - Ridenoure, J. A. AU - L., Reyes F. AU - Cheng, J. J. AB - Intermittent aeration (IA) process was investigated for nitrogen removal from anaerobically pretreatedswine wastewater (APTSW) that contained a high concentration of ammonium (average 265 mgNH4-N/l) and a low sCOD (soluble chemical oxygen demand)/N ratio (average 1.4). Nitrogen removal from theAPTSW was achieved through nitrification and denitrification in a single, semi-continuously fed reactor that wasoperated with alternation of aeration and non-aeration at room temperature (23oC). To optimize the IAprocess, different Aeration:Non-Aeration (ANA) ratios and cycle lengths were used in the reactors as follows:Reactor A, l hour : 1 hour; Reactor B, 1 hour : 3 hours; Reactor C, 0.5 hour : 1.5 hours; Reactor D, 0.5 hour : 2hour; Reactor E, 1 hour : 4 hours; Reactor F, 1 hour : 5 hours; and Reactor G, 1 hour : 6 hours. The hydraulicretention time (HRT) and mean cell residence time (MCRT) for the reactors were 3 and 20 days, respectively.Over 79 % ammonium was removed in all of the reactors. The reactor with the highest ANA ratio (Reactor A)achieved the highest NH3-N removal (99%), while the reactor with the longest non-aeration period (Reactor F)achieved the highest total nitrogen removal (83%). It was found that nitrogen removal was achieved throughnitrate denitrification in Reactors A, B, C, and D, but it was via nitrite reduction in Reactors E and F. The highnitrogen removal efficiency indicated that the required organic carbon must have been obtained from thesolubilization of solids contained in the influent or from microbial decay byproducts. The substantially higherdenitrification rates observed in Reactors E and F were likely due to the decreased sCOD requirements fornitrogen removal via nitrite versus those required via nitrate. C2 - 2005/// C3 - 2005 Tampa, FL July 17-20, 2005 DA - 2005/// DO - 10.13031/2013.19488 PB - American Society of Agricultural and Biological Engineers (ASABE) UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-70349157669&partnerID=MN8TOARS ER - TY - JOUR TI - Warm-blooded AU - Schweitzer, M. H. T2 - Natural History Magazine DA - 2005/// PY - 2005/// VL - 114 IS - 4 SP - 50-51 ER - TY - JOUR TI - Thermo-bioconvection in a suspension of oxytactic bacteria AU - Kuznetsov, AV T2 - INTERNATIONAL COMMUNICATIONS IN HEAT AND MASS TRANSFER AB - This paper studies thermo-bioconvection, a macroscopic convective motion induced in a fluid layer by the combined effect of density stratification caused by the upswimming of oxytactic microorganisms and heating from below. Both agencies affecting the density are destabilizing; therefore, monotonic instability is expected. Oscillatory instability may be possible in the case of cooling from below. DA - 2005/8// PY - 2005/8// DO - 10.1016/j.icheatmasstransfer.2004.11.005 VL - 32 IS - 8 SP - 991-999 SN - 1879-0178 KW - thermo-bioconvection KW - motile microorganisms KW - oxytaxis KW - stability KW - heating from below ER - TY - JOUR TI - Phylogenetic analysis of Pasteuria penetrans by use of multiple genetic loci AU - Charles, L AU - Carbone, I AU - Davies, KG AU - Bird, D AU - Burke, M AU - Kerry, BR AU - Opperman, CH T2 - JOURNAL OF BACTERIOLOGY AB - ABSTRACT Pasteuria penetrans is a gram-positive, endospore-forming eubacterium that apparently is a member of the Bacillus-Clostridium clade. It is an obligate parasite of root knot nematodes ( Meloidogyne spp.) and preferentially grows on the developing ovaries, inhibiting reproduction. Root knot nematodes are devastating root pests of economically important crop plants and are difficult to control. Consequently, P. penetrans has long been recognized as a potential biocontrol agent for root knot nematodes, but the fastidious life cycle and the obligate nature of parasitism have inhibited progress on mass culture and deployment. We are currently sequencing the genome of the Pasteuria bacterium and have performed amino acid level analyses of 33 bacterial species (including P. penetrans ) using concatenation of 40 housekeeping genes, with and without insertions/deletions (indels) removed, and using each gene individually. By application of maximum-likelihood, maximum-parsimony, and Bayesian methods to the resulting data sets, P. penetrans was found to cluster tightly, with a high level of confidence, in the Bacillus class of the gram-positive, low-G+C-content eubacteria. Strikingly, our analyses identified P. penetrans as ancestral to Bacillus spp. Additionally, all analyses revealed that P. penetrans is surprisingly more closely related to the saprophytic extremophile Bacillus haladurans and Bacillus subtilis than to the pathogenic species Bacillus anthracis and Bacillus cereus . Collectively, these findings strongly imply that P. penetrans is an ancient member of the Bacillus group. We suggest that P. penetrans may have evolved from an ancient symbiotic bacterial associate of nematodes, possibly as the root knot nematode evolved to be a highly specialized parasite of plants. DA - 2005/8// PY - 2005/8// DO - 10.1128/JB.187.16.5700-5708.2005 VL - 187 IS - 16 SP - 5700-5708 SN - 1098-5530 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-23644445501&partnerID=MN8TOARS ER - TY - JOUR TI - In vitro selection of phage RB69 RegA RNA binding sites yields UAA repeats AU - Dean, TR AU - Allen, SV AU - Miller, ES T2 - VIROLOGY AB - The SELEX method of in vitro selection was used to isolate RNAs that bind the RB69 RegA translational repressor protein immobilized on Ni-NTA agarose. After five rounds of SELEX, the pool of selected RNA displayed striking sequence uniformity: UAAUAAUAAUAAUA was clearly enriched in the 14 nucleotides that underwent selection. Individual, cloned molecules displayed a repeating (UAA) sequence, with only two RNAs having a 3' AUG. Removing the 3' AUG slightly reduced binding in gel shift assays, moving the AUG 5' proximal of the (UAA) slightly improved binding, but (UAA)4 alone still bound the purified protein. Dissociation constants showed that RNA shortened to (UAA)3 and (UAA)2 also retained binding, whereas cytosine clearly prevented binding by RB69 RegA. Scanning of RB69 gene starts and ends with an RB69 RegA SELEX information weight matrix yielded 21 sequences as potential RegA sites. One site, on the mRNA for the pentameric (4:1) phage gp44/62 DNA polymerase clamp loader complex, has the RB69 gene 44 stop codon and 3'-adjacent gene 62 initiation codon in a sequence (GAAAUAAUAUG) that is similar to in vitro selected RNA and was shown to bind RB69 RegA. Sequences between the Shine-Dalgarno and initiation codon, which frequently contain a UAA stop codon of a 5'-adjacent gene, appear to be preferred RB69 RegA binding sites. DA - 2005/5/25/ PY - 2005/5/25/ DO - 10.1016/j.virol.2005.03.002 VL - 336 IS - 1 SP - 26-36 SN - 0042-6822 KW - RNA SELEX KW - translation repressor KW - T4-type phage ER - TY - JOUR TI - Comparative genomics of nematodes AU - Mitreva, M AU - Blaxter, ML AU - Bird, DM AU - McCarter, JP T2 - TRENDS IN GENETICS AB - Recent transcriptome and genome projects have dramatically expanded the biological data available across the phylum Nematoda. Here we summarize analyses of these sequences, which have revealed multiple unexpected results. Despite a uniform body plan, nematodes are more diverse at the molecular level than was previously recognized, with many species- and group-specific novel genes. In the genus Caenorhabditis, changes in chromosome arrangement, particularly local inversions, are also rapid, with breakpoints occurring at 50-fold the rate in vertebrates. Tylenchid plant parasitic nematode genomes contain several genes closely related to genes in bacteria, implicating horizontal gene transfer events in the origins of plant parasitism. Functional genomics techniques are also moving from Caenorhabditis elegans to application throughout the phylum. Soon, eight more draft nematode genome sequences will be available. This unique resource will underpin both molecular understanding of these most abundant metazoan organisms and aid in the examination of the dynamics of genome evolution in animals. DA - 2005/10// PY - 2005/10// DO - 10.1016/j.tig.2005.08.003 VL - 21 IS - 10 SP - 573-581 SN - 1362-4555 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-24644458584&partnerID=MN8TOARS ER - TY - JOUR TI - Site-to-site variation of synonymous substitution rates AU - Pond, SK AU - Muse, SV T2 - MOLECULAR BIOLOGY AND EVOLUTION AB - We develop a new model for studying the molecular evolution of protein-coding DNA sequences. In contrast to existing models, we incorporate the potential for site-to-site heterogeneity of both synonymous and nonsynonymous substitution rates. We demonstrate that within-gene heterogeneity of synonymous substitution rates appears to be common. Using the new family of models, we investigate the utility of a variety of new statistical inference procedures, and we pay particular attention to issues surrounding the detection of sites undergoing positive selection. We discuss how failure to model synonymous rate variation in the model can lead to misidentification of sites as positively selected. DA - 2005/12// PY - 2005/12// DO - 10.1093/molbev/msi232 VL - 22 IS - 12 SP - 2375-2385 SN - 1537-1719 KW - synonymous substitution rate KW - positive selection KW - molecular evolution KW - codon model KW - model selection ER - TY - JOUR TI - Positively selected sites in the Arabidopsis receptor-like kinase gene family AU - Strain, E AU - Muse, SV T2 - JOURNAL OF MOLECULAR EVOLUTION DA - 2005/9// PY - 2005/9// DO - 10.1007/s00239-004-0308-0 VL - 61 IS - 3 SP - 325-332 SN - 1432-1432 KW - receptor-like kinase KW - positive selection KW - gene family KW - leucine-rich repeat ER - TY - JOUR TI - Pest control by genetic manipulation of sex ratio AU - Schliekelman, P. AU - Ellner, S. AU - Gould, Fred T2 - Journal of Economic Entomology AB - We model the release of insects carrying an allele at multiple loci that shifts sex ratios in favor of males. We model two approaches to sex ratio alteration. In the first (denoted SD), meiotic segregation (or sperm fertility) is distorted in favor of gametes carrying the male-determining genetic element (e.g., Y-chromosome). It is assumed that any male carrying at least one copy of the SD allele produces only genotypically male offspring. In the second approach (denoted PM), the inserted allele alters sex ratio by causing genetically female individuals to become phenotypically male. It is assumed that any insect carrying at least one copy of the PM allele is phenotypically male. Both approaches reduce future population growth by reducing the number of phenotypic females. The models allow variation in the number of loci used in the release, the size of the release, and the negative fitness effect caused by insertion of each sex ratio altering allele. We show that such releases may be at least 2 orders of magnitude more effective than sterile male releases (SIT) in terms of numbers of surviving insects. For example, a single SD release with two released insects for every wild insect and a 5% fitness cost per inserted allele could reduce the target population to 1/1000th of the no-release population size, whereas a similar-sized SIT release would only reduce the population to one-fifth of its original size. We also compare these two sex ratio alteration approaches to a female-killing (FK) system and the sterile male technique when there are repeated releases over a number of generations. In these comparisons, the SD approach is the most efficient with equivalent pest suppression achieved by release of ≈1 SD, 1.5–20 PM, 2–70 FK, and 16–3,000 SIT insects, depending on conditions. We also calculate the optimal number of SD and PM allele insertions to be used under various conditions, assuming that there is an additional genetic load incurred for each allelic insertion. DA - 2005/// PY - 2005/// DO - 10.1093/jee/98.1.18 VL - 98 IS - 1 SP - 18–34 ER - TY - JOUR TI - Mixture model equations for marker-assisted genetic evaluation AU - Liu, Y AU - Zeng, ZB T2 - JOURNAL OF ANIMAL BREEDING AND GENETICS AB - Summary Marker‐assisted genetic evaluation needs to infer genotypes at quantitative trait loci (QTL) based on the information of linked markers. As the inference usually provides the probability distribution of QTL genotypes rather than a specific genotype, marker‐assisted genetic evaluation is characterized by the mixture model because of the uncertainty of QTL genotypes. It is, therefore, necessary to develop a statistical procedure useful for mixture model analyses. In this study, a set of mixture model equations was derived based on the normal mixture model and the EM algorithm for evaluating linear models with uncertain independent variables. The derived equations can be seen as an extension of Henderson's mixed model equations to mixture models and provide a general framework to deal with the issues of uncertain incidence matrices in linear models. The mixture model equations were applied to marker‐assisted genetic evaluation with different parameterizations of QTL effects. A sire‐QTL‐effect model and a founder‐QTL‐effect model were used to illustrate the application of the mixture model equations. The potential advantages of the mixture model equations for marker‐assisted genetic evaluation were discussed. The mixed‐effect mixture model equations are flexible in modelling QTL effects and show desirable properties in estimating QTL effects, compared with Henderson's mixed model equations. DA - 2005/8// PY - 2005/8// DO - 10.1111/j.1439-0388.2005.00525.x VL - 122 IS - 4 SP - 229-239 SN - 1439-0388 ER - TY - JOUR TI - Mathematical modelling of two-phase non-Newtonian flow in a helical pipe AU - Cheng, L AU - Kuznetsov, AV AU - Sandeep, KP T2 - INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS AB - Governing equations for a two-phase 3D helical pipe flow of a non-Newtonian fluid with large particles are derived in an orthogonal helical coordinate system. The Lagrangian approach is utilized to model solid particle trajectories. The interaction between solid particles and the fluid that carries them is accounted for by a source term in the momentum equation for the fluid. The force-coupling method (FCM), developed by M.R. Maxey and his group, is adopted; in this method the momentum source term is no longer a Dirac delta function but is spread on a numerical mesh by using a finite-sized envelop with a spherical Gaussian distribution. The influence of inter-particle and particle–wall collisions is also taken into account. Copyright © 2005 John Wiley & Sons, Ltd. DA - 2005/6/30/ PY - 2005/6/30/ DO - 10.1002/fld.950 VL - 48 IS - 6 SP - 649-670 SN - 1097-0363 KW - non-Newtonian fluid KW - two-phase flow KW - helical pipe KW - orthogonal helical coordinates KW - force-coupling method ER - TY - JOUR TI - Investigation of hysteresis in acoustically driven channel flow at ultrasonic frequency AU - Wan, Q AU - Kuznetsov, AV T2 - NUMERICAL HEAT TRANSFER PART A-APPLICATIONS DA - 2005/1/15/ PY - 2005/1/15/ DO - 10.1080/1047780590885873 VL - 47 IS - 2 SP - 137-146 SN - 1521-0634 ER - TY - JOUR TI - Immunity and resistance to astrovirus infection AU - Koci, MD T2 - VIRAL IMMUNOLOGY AB - Astroviruses are one of the leading causes of acute viral enteritis in infants, and are recognized as a clinically important pathogen in the elderly and the immunocompromised. In spite of this, we still know very little about the immune response to astrovirus infection. Clinical observations and human volunteer studies have indicated a role for the humoral response and suggest neutralizing antibodies are important in limiting infection. Studies of human intestinal biopsies have suggested that cellular immunity; specifically CD4+ T-cells may also be involved in the anti-astrovirus response. Additionally, various animal models have indicated potential roles for the innate immune system in controlling infections. How these various effector arms of the immune system collaborate to result in immunity and resistance to astrovirus infection is still unknown. This review summarizes our current understanding of the immune response to this pathogen and highlights the key concepts that still need to be addressed. Until we understand the role of the immune system in astrovirus infection or other enteric viruses, we will continue to be limited in our ability to treat and control gastrointestinal diseases. DA - 2005/// PY - 2005/// DO - 10.1089/vim.2005.18.11 VL - 18 IS - 1 SP - 11-16 SN - 0882-8245 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-17844369466&partnerID=MN8TOARS ER - TY - JOUR TI - Evolutionary-based grouping of haplotypes in association analysis AU - Tzeng, JY T2 - GENETIC EPIDEMIOLOGY AB - Haplotypes incorporate more information about the underlying polymorphisms than do genotypes for individual SNPs, and are considered as a more informative format of data in association analysis. To model haplotypes requires high degrees of freedom, which could decrease power and limit a model's capacity to incorporate other complex effects, such as gene-gene interactions. Even within haplotype blocks, high degrees of freedom are still a concern unless one chooses to discard rare haplotypes. To increase the efficiency and power of haplotype analysis, we adapt the evolutionary concepts of cladistic analyses and propose a grouping algorithm to cluster rare haplotypes to the corresponding ancestral haplotypes. The algorithm determines the cluster bases by preserving common haplotypes using a criterion built on the Shannon information content. Each haplotype is then assigned to its appropriate clusters probabilistically according to the cladistic relationship. Through this algorithm, we perform association analysis based on groups of haplotypes. Simulation results indicate power increases for performing tests on the haplotype clusters when compared to tests using original haplotypes or the truncated haplotype distribution. DA - 2005/4// PY - 2005/4// DO - 10.1002/gepi.20063 VL - 28 IS - 3 SP - 220-231 SN - 0741-0395 KW - evolutionary-based clustering KW - dimension reduction of haplotypes KW - haplotype tests for association ER - TY - JOUR TI - Endocrine changes in maturing primary queens of Zootermopsis angusticollis AU - Brent, CS AU - Schal, C AU - Vargo, EL T2 - JOURNAL OF INSECT PHYSIOLOGY AB - Termite queens are highly specialized for reproduction, but little is known about the endocrine mechanisms regulating this ability. We studied changes in the endocrinology and ovarian maturation in primary reproductive females of the dampwood termite Zootermopsis angusticollis following their release from inhibitory stimuli produced by mature queens. Winged alates were removed from their natal nest, manually dewinged, then paired in an isolated nest with a reproductive male. Development was tracked by monitoring ovarian development, in vitro rates of juvenile hormone (JH) production by corpora allata, and hemolymph titers of JH and ecdysteroids. The production rate and titer of JH were positively correlated with each other but negatively correlated with ecdysteroid titer. Four days after disinhibition, JH release and titer decreased while ecdysteroid titer increased. The new levels persisted until day 30, after which JH increased and ecdysteroids decreased. Fully mature queens had the highest rates of JH production, the lowest ecdysteroid titers, and the greatest number of functional ovarioles. The results support the hypothesis that JH plays a dual role in termite queens depending on their stage of development; an elevated JH titer in immature alates may maintain reproductive inhibition, but an elevated JH titer in mature queens may stimulate ovarian activity. The decline in JH production and the elevation in ecdysteroid titer correspond to a period of physiological reorganization and activation. The specific function of ecdysteroids is unknown but they may help to modulate the activity of the corpora allata. DA - 2005/11// PY - 2005/11// DO - 10.1016/j.jinsphys.2005.06.009 VL - 51 IS - 11 SP - 1200-1209 SN - 0022-1910 KW - reproduction KW - isoptera KW - queen KW - juvenile hormone KW - ecdysteroids ER - TY - JOUR TI - Common intervals of trees AU - Heber, S AU - Savage, CD T2 - INFORMATION PROCESSING LETTERS AB - In this survey, we review practical algorithms for graph-theoretic problems that are expressible in monadic second-order logic. Monadic second-order (MSO) logic allows quantifications over unary relations (sets) and can be used to express a host of useful graph properties such as connectivity, c-colorability (for a fixed c), Hamiltonicity and minor inclusion. A celebrated theorem in this area by Courcelle states that any graph problem expressible in MSO can be solved in linear time on graphs that admit a tree-decomposition of constant width. Courcelle’s Theorem has been used thus far as a theoretic tool to establish that linear-time algorithms exist for graph problems by demonstrating that the problem in question is expressible by an MSO formula. A straightforward implementation of the algorithm in the proof of Courcelle’s Theorem is useless as it runs into space-explosion problems even for small values of treewidth. Of late, there have been several attempts to circumvent these problems and we review some of these in this survey. This survey also introduces the reader to the notions of tree-decompositions and the basics of monadic second order logic. DA - 2005/1/31/ PY - 2005/1/31/ DO - 10.1016/j.ipl.2004.09.016 VL - 93 IS - 2 SP - 69-74 SN - 1872-6119 KW - combinatorial problems KW - algorithms KW - labeled trees ER - TY - JOUR TI - Aflatoxin conducive and non-conducive growth conditions reveal new gene associations with aflatoxin production AU - Price, MS AU - Shannon, BCB AU - Sabrina, TB AU - Robert, AKB AU - Payne, GA T2 - FUNGAL GENETICS AND BIOLOGY AB - Research on aflatoxin (AF) production has traditionally focused on defining the AF biosynthetic pathway with the goal of identifying potential targets for intervention. To understand the effect of nitrogen source, carbon source, temperature, and pH on the regulation of AF biosynthesis, a targeted cDNA microarray consisting of genes associated with AF production over time was employed. Expression profiles for genes involved in AF biosynthesis grouped into five clades. A putative regulon was identified consisting of 20 genes that were induced in the conducive nitrogen and pH treatments and the non-conducive carbon and temperature treatments, as well as four other putative regulons corresponding to each of the four variables studied. Seventeen genes exhibited consistent induction/repression profiles across all the experiments. One of these genes was consistently downregulated with AF production. Overexpression of this gene resulted in repression of AF biosynthesis. The cellular function of this gene is currently unresolved. DA - 2005/6// PY - 2005/6// DO - 10.1016/j.fgb.2005.03.009 VL - 42 IS - 6 SP - 506-518 SN - 1096-0937 KW - aflatoxin KW - gene expression KW - regulation KW - Aspergillus flavus KW - Aspergillus parasiticus ER - TY - JOUR TI - The title-page: Its early development, 1460-1510. AU - Orcutt, D T2 - LIBRARY RESOURCES & TECHNICAL SERVICES DA - 2005/1// PY - 2005/1// DO - 10.5860/lrts.49n1.67.2 VL - 49 IS - 1 SP - 67-67 SN - 0024-2527 ER - TY - JOUR TI - Identifying soft red winter wheat cultivars tolerant to Barley yellow dwarf virus AU - Weisz, R AU - Tarleton, B AU - Murphy, JP AU - Kolb, FL T2 - PLANT DISEASE AB - Barley yellow dwarf virus (BYDV) is a serious disease of soft red winter wheat. Although there has been interest in tolerant cultivars, identification and development has been slow due to a lack of precision in rating plants for response to BYDV. Visual ratings of symptoms are commonly used to evaluate cultivars, but these ratings have proven to be inconsistent. The objectives of this research were to assess BYDV visual symptom ratings of wheat cultivars under field conditions, to measure disease-related yield reductions in these cultivars, to determine if a relationship exists between BYDV visual symptoms and yield reductions, and to determine BYDV cultivar tolerance. A split-plot design with insecticide treatment (main plot) and 11 cultivars (subplots) was employed over 4 years. The overall relationship between symptom ratings and BYDV yield reductions was weak (R 2 = 0.40) and not consistent across years or cultivars. A consistency of performance analysis showed cultivars clustered into five distinct tolerance classes. Under conditions of high BYDV infestation, visual symptom ratings could be cautiously used to identify highly tolerant cultivars. The most reliable method for rating cultivar tolerance was a direct measure of disease-induced yield reduction across multiple environments. DA - 2005/2// PY - 2005/2// DO - 10.1094/PD-89-0170 VL - 89 IS - 2 SP - 170-176 SN - 1943-7692 KW - relative yield KW - visual disease symptom rating ER - TY - JOUR TI - Foundations of yield improvement in watermelon (vol 45, pg 141, 2003) AU - Gusmini, G AU - Wehner, TC T2 - CROP SCIENCE AB - Crop ScienceVolume 45, Issue 2 p. 810-810 Erratum Foundations of Yield Improvement in Watermelon Gabriele Gusmini, Gabriele Gusmini Department of Horticultural Science, North Carolina State University, Campus Box 7609, Raleigh, NC, 27695-7609Search for more papers by this authorTodd C. Wehner, Corresponding Author Todd C. Wehner [email protected] Department of Horticultural Science, North Carolina State University, Campus Box 7609, Raleigh, NC, 27695-7609Corresponding author ([email protected])Search for more papers by this author Gabriele Gusmini, Gabriele Gusmini Department of Horticultural Science, North Carolina State University, Campus Box 7609, Raleigh, NC, 27695-7609Search for more papers by this authorTodd C. Wehner, Corresponding Author Todd C. Wehner [email protected] Department of Horticultural Science, North Carolina State University, Campus Box 7609, Raleigh, NC, 27695-7609Corresponding author ([email protected])Search for more papers by this author First published: 01 March 2005 https://doi.org/10.2135/cropsci2005.0810Citations: 12Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article.Citing Literature Volume45, Issue2March–April 2005Pages 810-810 RelatedInformation DA - 2005/// PY - 2005/// DO - 10.2135/cropsci2005.0810 VL - 45 IS - 2 SP - 810-810 SN - 1435-0653 ER -