TY - CHAP TI - Chemical Carcinogenesis and Mutagenesis AU - Smart, R.C. T2 - Modern Toxicology A2 - Hodgson, E. PY - 2010/// ET - 4th PB - J. Wiley and Sons ER - TY - JOUR TI - Ablation of TAK1 Upregulates Reactive Oxygen Species and Selectively Kills Tumor Cells AU - Omori, Emily AU - Matsumoto, Kunihiro AU - Zhu, Songyun AU - Smart, Robert C. AU - Ninomiya-Tsuji, Jun T2 - Cancer Research AB - Abstract TAK1 kinase activates multiple transcription factors and regulates the level of reactive oxygen species (ROS). We have previously reported that ablation of TAK1 in keratinocytes causes hypersensitivity to ROS-induced cell apoptosis. It is known that some tumor cells produce ROS at higher levels compared with normal cells. We used inducible epidermal-specific TAK1 knockout mice and examined whether ablation of TAK1 in preexisting skin tumors could cause an increase in ROS and result in tumor cell death. Deletion of tak1 gene in skin tumors caused the accumulation of ROS and increased apoptosis, and skin tumors totally regressed within 5 to 10 days. Normal skin did not exhibit any significant abnormality on tak1 gene deletion. Thus, TAK1 kinase could be a new and effective molecular target for ROS-based tumor killing. Cancer Res; 70(21); 8417–25. ©2010 AACR. DA - 2010/10/19/ PY - 2010/10/19/ DO - 10.1158/0008-5472.can-10-1227 VL - 70 IS - 21 SP - 8417-8425 J2 - Cancer Res LA - en OP - SN - 0008-5472 1538-7445 UR - http://dx.doi.org/10.1158/0008-5472.can-10-1227 DB - Crossref ER - TY - RPRT TI - The Role of Symbolic, Numeric and Algebraic Computation in Cyber-Enabled Discovery and Innovation (CDI) AU - Kaltofen, Erich L. A3 - University of Rhode Island DA - 2010/// PY - 2010/// PB - University of Rhode Island ER - TY - JOUR TI - Growth and Maintenance of Mosquito Cell Lines AU - Hernandez, Raquel AU - Brown, Dennis T. T2 - Current Protocols in Microbiology AB - Abstract Mosquito cells ( Aedes albopictus) are among the most common insect cells emerging as new sources of cell cultures to use in basic research and in the pharmaceutical industry. They adapt well to growth in suspension; can be used in bioreactors for the production of expressed proteins, virus, and virus‐like particles; can be used in studies requiring lower growth temperatures than mammalian cells (28°C or below); and (because they are cholesterol auxotrophs) can be adapted to grow in dilipidated or serum‐free medium for experiments requiring these conditions. Procedures applicable to the laboratory maintenance of mosquito cell lines are described. Curr. Protoc. Microbiol . 17:A.4J.1‐A.4J.8. © 2010 by John Wiley & Sons, Inc. DA - 2010/5// PY - 2010/5// DO - 10.1002/9780471729259.MCA04JS17 VL - 17 IS - 1 SP - A.4J.1-A.4J.8 J2 - Current Protocols in Microbiology LA - en OP - SN - 1934-8525 UR - http://dx.doi.org/10.1002/9780471729259.MCA04JS17 DB - Crossref ER - TY - JOUR TI - Growth and Maintenance of Baby Hamster Kidney (BHK) Cells AU - Hernandez, Raquel AU - Brown, Dennis T. T2 - Current Protocols in Microbiology AB - Abstract The BHK21 cell line was established in 1961 from the kidneys of 5 Syrian hamsters from litter number 21. Since this time, this cell line has been a laboratory standard for the growth of countless viruses and the study of many biological processes. The specific use for the growth of Sindbis virus is described, although it may apply to many types of viruses. Curr. Protoc. Microbiol . 17:A.4H.1‐A.4H.7. © 2010 by John Wiley & Sons, Inc. DA - 2010/5// PY - 2010/5// DO - 10.1002/9780471729259.MCA04HS17 VL - 17 IS - 1 SP - A.4H.1-A.4H.7 J2 - Current Protocols in Microbiology LA - en OP - SN - 1934-8525 UR - http://dx.doi.org/10.1002/9780471729259.MCA04HS17 DB - Crossref ER - TY - JOUR TI - Growth and Maintenance of Chick Embryo Fibroblasts (CEF) AU - Hernandez, Raquel AU - Brown, Dennis T. T2 - Current Protocols in Microbiology AB - Primary cultures of chick embryo fibroblasts (CEF) are widely used for the cultivation of viruses. Protocols for the growth and maintenance of CEF cells in the laboratory are provided. DA - 2010/5// PY - 2010/5// DO - 10.1002/9780471729259.MCA04IS17 VL - 17 IS - 1 SP - A.4I.1-A.4I.8 J2 - Current Protocols in Microbiology LA - en OP - SN - 1934-8525 UR - http://dx.doi.org/10.1002/9780471729259.MCA04IS17 DB - Crossref ER - TY - RPRT TI - Power, sample size and confidence interval for quantitative trait loci mapping on multiple traits AU - E Silva, L.D.C. AU - Chang, S.-M. AU - Zeng, Z.-B. DA - 2010/// PY - 2010/// ER - TY - CONF TI - Survival of bartonella henselae in the blood of cats used for transfusion AU - Bradbury, C.A. AU - Green, M. AU - Brewer, M. AU - Breitschwerdt, E. AU - Lappin, M. T2 - 2010 American College of Veterinary Internal Medicine Forum C2 - 2010/// C3 - Journal of Veterinary Internal Medicine CY - Anaheim, CA DA - 2010/// PY - 2010/6/9/ VL - 24 SP - 759 M1 - 3 ER - TY - CONF TI - Diversity of bartonella species in 62 dogs using the bapgm pre-enrichment culture method AU - Perez, C. AU - Diniz, P.P.V.P. AU - Maggi, R.G. AU - Breitschwerdt, E.B. T2 - 2010 American College of Veterinary Internal Medicine Forum C2 - 2010/// C3 - Journal of Veterinary Internal Medicine CY - Anaheim, CA DA - 2010/// PY - 2010/6/9/ VL - 24 SP - 759 M1 - 3 ER - TY - CONF TI - Performance comparison of species-specific peptide-based assays with immunofluorescence assays for detection of canine antibodies to anaplasma and ehrlichia spp AU - Stillman, B.A. AU - Beall, M.J. AU - Shields, P. AU - Hegarty, B. AU - Breitschwerdt, E. AU - Chandrashekar, R. T2 - 2010 American College of Veterinary Internal Medicine Forum C2 - 2010/// C3 - Journal of Veterinary Internal Medicine CY - Anaheim, CA DA - 2010/// PY - 2010/6// VL - 24 SP - 765–766 M1 - 3 ER - TY - CONF TI - Immunologic testing of dog urine requires neutralization of matrix effects to allow for accurate measurement of il-6 concentrations AU - Wood, M. AU - Breitschwerdt, E. AU - Vaden, S. AU - Nordone, S. T2 - American College Of Veterinary Internal Medicine C2 - 2010/// C3 - Journal of Veterinary Internal Medicine CY - Anaheim, CA DA - 2010/// PY - 2010/6/9/ VL - 24 SP - 770 M1 - 3 ER - TY - JOUR TI - Performance of a commercially available in-clinic ELISA for the detection of antibodies against Anaplasma phagocytophilum, Ehrlichia canis, and Borrelia burgdorferi and Dirofilaria immitis antigen in dogs AU - Chandrashekar, Ramaswamy AU - Mainville, Celine A. AU - Beall, Melissa J. AU - O'Connor, Thomas AU - Eberts, Matthew D. AU - Alleman, A. Rick AU - Gaunt, Stephen D. AU - Breitschwerdt, Edward B. T2 - American Journal of Veterinary Research AB - To evaluate the sensitivity and specificity of a commercially available in-clinic ELISA for detection of heartworm infection and tick-borne diseases in dogs.846 serum, plasma, or blood samples obtained from dogs.Samples were evaluated via the in-clinic ELISA to detect antibodies against Anaplasma phagocytophilum, Ehrlichia canis, and Borrelia burgdorferi and Dirofilaria immitis (heartworm) antigen. True infection or immunologic status of samples was assessed by use of results of necropsy, an antigen assay for D immitis, and immunofluorescence assay or western blot analysis for antibodies against B burgdorferi, E canis, and A phagocytophilum.Sensitivity and specificity of the in-clinic ELISA for detection of heartworm antigen (99.2% and 100%, respectively), antibodies against B burgdorferi (98.8% and 100%, respectively), and antibodies against E canis (96.2% and 100%, respectively) were similar to results for a similar commercial ELISA. In samples obtained from dogs in the northeast and upper Midwest of the United States, sensitivity and specificity of the in-clinic ELISA for antibodies against Anaplasma spp were 99.1% and 100%, respectively, compared with results for an immunofluorescence assay. Samples from 2 dogs experimentally infected with the NY18 strain of A phagocytophilum were tested by use of the in-clinic ELISA, and antibodies against A phagocytophilum were detected by 8 days after inoculation. Antibodies against Anaplasma platys in experimentally infected dogs cross-reacted with the A phagocytophilum analyte. Coinfections were identified in several of the canine serum samples.The commercially available in-clinic ELISA could be used by veterinarians to screen dogs for heartworm infection and for exposure to tick-borne pathogens. DA - 2010/12// PY - 2010/12// DO - 10.2460/ajvr.71.12.1443 VL - 71 IS - 12 SP - 1443–1450 SN - 0002-9645 UR - http://dx.doi.org/10.2460/ajvr.71.12.1443 ER - TY - JOUR TI - Autocrine Effects of Interleukin-6 Mediate Acute-Phase Proinflammatory and Tissue-Reparative Transcriptional Responses of Canine Bladder Mucosa AU - Wood, Michael W. AU - Breitschwerdt, Edward B. AU - Gookin, Jody L. T2 - Infection and Immunity AB - During early urinary tract infection (UTI) the interplay between invading bacteria and the urothelium elicits a mucosal response aimed at clearing infection. Unfortunately, the resultant inflammation and associated local tissue injury are responsible for patient symptoms. Interleukin-6 (IL-6), a cytokine released during acute UTI, has both pro- and anti-inflammatory effects on other body systems. Within the urothelium, the IL-6 native-tissue origin, the target cell type(s), and ultimate effect of the cytokine on target cells are largely unknown. In the present study we modeled the UTI IL-6 response ex vivo using canine bladder mucosa mounted in Ussing chambers to determine the inflammatory and reparative role of IL-6. We demonstrated that uropathogenic Escherichia coli infection stimulates the synthesis of IL-6 by all urothelial cell layers, with the urothelial cells alone representing the only site of unequivocal IL-6 receptor expression. Autocrine effects of IL-6 were supported by the activation of urothelial STAT3 signaling and SOCS3 expression. Using exogenous IL-6, a microarray approach, and quantitative reverse transcriptase PCR (q-RT-PCR), 5 target genes (tumor necrosis factor alpha, interleukin-1β, matrix metallopeptidase 2, heparan sulfate d-glucosaminyl 3-O-sulfotransferase 3A1, and hyaluronan synthase 2) that have direct or indirect roles in promoting a proinflammatory state were identified. Two of these genes, heparan sulfate d-glucosaminyl 3-O-sulfotransferase 3A1 and hyaluronan synthase 2, are also potentially important mediators of wound repair via the production of glycosaminoglycan components. These findings suggest that IL-6 secretion during acute UTI may serve a dual biological role by initiating the inflammatory response while also repairing urothelial defenses. DA - 2010/11/29/ PY - 2010/11/29/ DO - 10.1128/IAI.01102-10 VL - 79 IS - 2 SP - 708-715 J2 - Infect. Immun. LA - en OP - SN - 0019-9567 1098-5522 UR - http://dx.doi.org/10.1128/IAI.01102-10 DB - Crossref ER - TY - JOUR TI - Presentation Skills for Scientists. E. Zanders & L. MacLeod. Cambridge University Press. 2010. 80 pages. ISBN 9780521741033. Price £19.99 (paperback with DVD-ROM). AU - Anholt, Robert R. H. T2 - Genetics Research AB - An abstract is not available for this content. As you have access to this content, full HTML content is provided on this page. A PDF of this content is also available in through the ‘Save PDF’ action button. DA - 2010/8// PY - 2010/8// DO - 10.1017/S0016672310000431 VL - 92 IS - 4 SP - 323-324 J2 - Genet. Res. LA - en OP - SN - 0016-6723 1469-5073 UR - http://dx.doi.org/10.1017/S0016672310000431 DB - Crossref ER - TY - CONF TI - The 2009 potato and tomato late blight epidemics: Genealogical history, multiple sources and migration events AU - Ristaino, JB T2 - AMER PHYTOPATHOLOGICAL SOC 3340 PILOT KNOB ROAD, ST PAUL, MN 55121 USA C2 - 2010/// C3 - Phytopathology DA - 2010/// VL - 100 SP - S161-S161 M1 - 6 ER - TY - CONF TI - Rapid diagnostic tools for Phytophthora on horticultural crops AU - Ristaino, Jean Beagle AU - Ivors, Kelly AU - Bonans, P AU - Gómez-Alpizar, L AU - Blanco-Meneses, M C2 - 2010/// C3 - Workshop: Implementación de herramientas de diagnóstico rápido para Phytophthora en cultivos agŕıcolas en Centro América. Universidad de Costa Rica, San José, Costa Rica Junio DA - 2010/// ER - TY - JOUR TI - Propiconazole distribution and effects on Ceratocystis fagacearum survival in roots of treated red oaks AU - Blaedow, Ryan A AU - Juzwik, Jennifer AU - Barber, Brian T2 - Phytopathology DA - 2010/// PY - 2010/// VL - 100 IS - 10 SP - 979-985 ER - TY - CONF TI - Inferring evolutionary relationships of species in the Phytophthora Ic clade using nuclear and mitochondrial genes AU - Lassiter, ES AU - Russ, C AU - Nusbaum, C AU - Zeng, Q AU - Hu, C AU - Thorne, J AU - Ristaino, JB T2 - AMER PHYTOPATHOLOGICAL SOC 3340 PILOT KNOB ROAD, ST PAUL, MN 55121 USA C2 - 2010/// C3 - Phytopathology DA - 2010/// VL - 100 SP - S68-S68 M1 - 6 ER - TY - CONF TI - Genetic structure of Phytophthora infestans population in eastern North America, 2002-2009 AU - Hu, C AU - Perez, FG AU - Donahoo, R AU - McLeod, A AU - Myers, KL AU - Ivors, KL AU - Roberts, PD AU - Fry, WE AU - Deah, KL AU - Ristaino, JB T2 - AMER PHYTOPATHOLOGICAL SOC 3340 PILOT KNOB ROAD, ST PAUL, MN 55121 USA C2 - 2010/// C3 - Phytopathology DA - 2010/// VL - 100 SP - S52-S52 M1 - 6 ER - TY - CONF TI - Computing the radius of positive semidefiniteness of a multivariate real polynomial via a dual of Seidenberg's method AU - Hutton, Sharon AU - Kaltofen, Erich L. AU - Zhi, Lihong T2 - the 2010 International Symposium AB - We give a stability criterion for real polynomial inequalities with floating point or inexact scalars by estimating from below or computing the radius of semidefiniteness. That radius is the maximum deformation of the polynomial coefficient vector measured in a weighted Euclidean vector norm within which the inequality remains true. A large radius means that the inequalities may be considered numerically valid. C2 - 2010/// C3 - Proceedings of the 2010 International Symposium on Symbolic and Algebraic Computation - ISSAC '10 DA - 2010/// DO - 10.1145/1837934.1837979 PB - ACM Press SN - 9781450301503 UR - http://dx.doi.org/10.1145/1837934.1837979 DB - Crossref ER - TY - CONF TI - Fifteen years after DSC and WLSS2 what parallel computations I do today AU - Kaltofen, Erich L. T2 - the 4th International Workshop AB - A second wave of parallel and distributed computing research is rolling in. Today's multicore/multiprocessor computers facilitate everyone's parallel execution. In the mid 1990s, manufactures of expensive main-frame parallel computers faltered and computer science focused on the Internet and the computing grid. After a ten year hiatus, the Parallel Symbolic Computation Conference (PASCO) is awakening with new vigor. C2 - 2010/// C3 - Proceedings of the 4th International Workshop on Parallel and Symbolic Computation - PASCO '10 DA - 2010/// DO - 10.1145/1837210.1837213 PB - ACM Press SN - 9781450300674 UR - http://dx.doi.org/10.1145/1837210.1837213 DB - Crossref ER - TY - JOUR TI - Glycine and a Glycine Dehydrogenase (GLDC) SNP as Citalopram/Escitalopram Response Biomarkers in Depression: Pharmacometabolomics-Informed Pharmacogenomics AU - Ji, Y AU - Hebbring, S AU - Zhu, H AU - Jenkins, G D AU - Biernacka, J AU - Snyder, K AU - Drews, M AU - Fiehn, O AU - Zeng, Z AU - Schaid, D AU - Mrazek, D A AU - Kaddurah-Daouk, R AU - Weinshilboum, R M T2 - Clinical Pharmacology & Therapeutics AB - Major depressive disorder (MDD) is a common psychiatric disease. Selective serotonin reuptake inhibitors (SSRIs) are an important class of drugs used in the treatment of MDD. However, many patients do not respond adequately to SSRI therapy. We used a pharmacometabolomics-informed pharmacogenomic research strategy to identify citalopram/escitalopram treatment outcome biomarkers. Metabolomic assay of plasma samples from 20 escitalopram remitters and 20 nonremitters showed that glycine was negatively associated with treatment outcome (P = 0.0054). This observation was pursued by genotyping tag single-nucleotide polymorphisms (SNPs) for genes encoding glycine synthesis and degradation enzymes, using 529 DNA samples from SSRI-treated MDD patients. The rs10975641 SNP in the glycine dehydrogenase (GLDC) gene was associated with treatment outcome phenotypes. Genotyping for rs10975641 was carried out in 1,245 MDD patients in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study, and its presence was significant (P = 0.02) in DNA taken from these patients. These results highlight a possible role for glycine in SSRI response and illustrate the use of pharmacometabolomics to “inform” pharmacogenomics. Clinical Pharmacology & Therapeutics (2011) 89 1, 97–104. doi: 10.1038/clpt.2010.250 DA - 2010/11/24/ PY - 2010/11/24/ DO - 10.1038/clpt.2010.250 VL - 89 IS - 1 SP - 97-104 J2 - Clin Pharmacol Ther OP - SN - 0009-9236 1532-6535 UR - http://dx.doi.org/10.1038/clpt.2010.250 DB - Crossref ER - TY - JOUR TI - Lipidomic analysis of variation in response to simvastatin in the Cholesterol and Pharmacogenetics Study AU - Kaddurah-Daouk, Rima AU - Baillie, Rebecca A. AU - Zhu, Hongjie AU - Zeng, Zhao-Bang AU - Wiest, Michelle M. AU - Nguyen, Uyen Thao AU - Watkins, Steven M. AU - Krauss, Ronald M. T2 - Metabolomics AB - Statins are commonly used for reducing cardiovascular disease risk but therapeutic benefit and reductions in levels of low-density lipoprotein cholesterol (LDL-C) vary among individuals. Other effects, including reductions in C-reactive protein (CRP), also contribute to treatment response. Metabolomics provides powerful tools to map pathways implicated in variation in response to statin treatment. This could lead to mechanistic hypotheses that provide insight into the underlying basis for individual variation in drug response. Using a targeted lipidomics platform, we defined lipid changes in blood samples from the upper and lower tails of the LDL-C response distribution in the Cholesterol and Pharmacogenetics study. Metabolic changes in responders are more comprehensive than those seen in non-responders. Baseline cholesterol ester and phospholipid metabolites correlated with LDL-C response to treatment. CRP response to therapy correlated with baseline plasmalogens, lipids involved in inflammation. There was no overlap of lipids whose changes correlated with LDL-C or CRP responses to simvastatin suggesting that distinct metabolic pathways govern statin effects on these two biomarkers. Metabolic signatures could provide insights about variability in response and mechanisms of action of statins. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-010-0207-x) contains supplementary material, which is available to authorized users. DA - 2010/4/1/ PY - 2010/4/1/ DO - 10.1007/s11306-010-0207-x VL - 6 IS - 2 SP - 191-201 J2 - Metabolomics LA - en OP - SN - 1573-3882 1573-3890 UR - http://dx.doi.org/10.1007/s11306-010-0207-x DB - Crossref KW - Cardiovascular disease KW - Lipidomics KW - Metabolomics KW - Pharmacogenomics KW - Pharmacometabolomics KW - Simvastatin ER - TY - JOUR TI - IFN-α expression and antiviral effects are subtype and cell type specific in the cardiac response to viral infection AU - Li, Lianna AU - Sherry, Barbara T2 - Virology AB - The interferon-β (IFN-β) response is critical for protection against viral myocarditis in several mouse models, and IFN-α or -β treatment is beneficial against human viral myocarditis. The IFN-β response in cardiac myocytes and cardiac fibroblasts forms an integrated network for organ protection; however, the different IFN-α subtypes have not been studied in cardiac cells. We developed a quantitative RT-PCR assay that distinguishes between 13 highly conserved IFN-α subtypes and found that reovirus T3D induces five IFN-α subtypes in primary cardiac myocyte and fibroblast cultures: IFN-α1, -α2, -α4, -α5, and -α8/6. Murine IFN-α1, -α2, -α4, or -α5 treatment induced IRF7 and ISG56 and inhibited reovirus T3D replication in both cell types. This first investigation of IFN-α subtypes in cardiac cells for any virus demonstrates that IFN-α is induced in cardiac cells, that it is both subtype and cell type specific, and that it is likely important in the antiviral cardiac response. DA - 2010/1// PY - 2010/1// DO - 10.1016/j.virol.2009.10.013 VL - 396 IS - 1 SP - 59-68 J2 - Virology LA - en OP - SN - 0042-6822 UR - http://dx.doi.org/10.1016/j.virol.2009.10.013 DB - Crossref KW - Interferon KW - Cardiac myocyte KW - Cardiac fibroblast KW - Myocarditis KW - Reovirus ER - TY - CONF TI - Ex situ seed collection represents genetic variation present in natural stands of Carolina hemlock AU - Potter, K.M. AU - Jetton, R.M. AU - Dvorak, W.S. AU - Frampton, J. AU - Rhea, J. C2 - 2010/// C3 - Proceedings of the Fifth Symposium on Hemlock Woolly Adelgid in the Eastern United States DA - 2010/// SP - 181-190 ER - TY - JOUR TI - Making scents of behavioural genetics: lessons from Drosophila AU - Anholt, Robert R. H. T2 - GENETICS RESEARCH AB - Summary The expression of behaviours is influenced by many segregating genes. Behaviours are, therefore, complex traits. They have, however, unique characteristics that set them apart from physiological and morphological quantitative traits. First, behaviours are the ultimate expression of the nervous system. This means that understanding the genetic underpinnings of behaviours requires a neurobiological context, i.e. an understanding of the genes–brain–behaviour axis. In other words, how do ensembles of genes empower specific neural circuits to drive behaviours? Second, behaviours represent the interface between an organism and its environment. Thus, environmental effects are likely to make substantial contributions to determining behavioural outputs and genotype-by-environment interactions are expected to be prominent. It is important to differentiate between genes that contribute to the manifestation of the behavioural phenotype and genes that contribute to phenotypic variation in behaviour. The former are identified by classical mutagenesis experiments, whereas the latter can be detected through quantitative genetic approaches. Genes that contribute to phenotypic variation in behaviour harbour polymorphisms that provide the substrates for evolution. This review focuses on olfactory behaviour in Drosophila with the goal to illustrate how fundamental insights derived from studies on chemosensation can be applied to a wide range of behavioural phenotypes. DA - 2010/// PY - 2010/// DO - 10.1017/s0016672310000492 VL - 92 IS - 5-6 SP - 349-359 SN - 1469-5073 ER - TY - JOUR TI - Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation AU - Uzan, Marc AU - Miller, Eric S. T2 - VIROLOGY JOURNAL AB - Over 50 years of biological research with bacteriophage T4 includes notable discoveries in post-transcriptional control, including the genetic code, mRNA, and tRNA; the very foundations of molecular biology. In this review we compile the past 10 - 15 year literature on RNA-protein interactions with T4 and some of its related phages, with particular focus on advances in mRNA decay and processing, and on translational repression. Binding of T4 proteins RegB, RegA, gp32 and gp43 to their cognate target RNAs has been characterized. For several of these, further study is needed for an atomic-level perspective, where resolved structures of RNA-protein complexes are awaiting investigation. Other features of post-transcriptional control are also summarized. These include: RNA structure at translation initiation regions that either inhibit or promote translation initiation; programmed translational bypassing, where T4 orchestrates ribosome bypass of a 50 nucleotide mRNA sequence; phage exclusion systems that involve T4-mediated activation of a latent endoribonuclease (PrrC) and cofactor-assisted activation of EF-Tu proteolysis (Gol-Lit); and potentially important findings on ADP-ribosylation (by Alt and Mod enzymes) of ribosome-associated proteins that might broadly impact protein synthesis in the infected cell. Many of these problems can continue to be addressed with T4, whereas the growing database of T4-related phage genome sequences provides new resources and potentially new phage-host systems to extend the work into a broader biological, evolutionary context. DA - 2010/12/3/ PY - 2010/12/3/ DO - 10.1186/1743-422x-7-360 VL - 7 SP - SN - 1743-422X ER - TY - JOUR TI - PCR amplification of Bartonella koehlerae from human blood and enrichment blood cultures AU - Breitschwerdt, Edward B AU - Maggi, Ricardo G AU - Robert Mozayeni, B AU - Hegarty, Barbara C AU - Bradley, Julie M AU - Mascarelli, Patricia E T2 - Parasites & Vectors AB - Cats appear to be the primary reservoir host for Bartonella koehlerae, an alpha Proteobacteria that is most likely transmitted among cat populations by fleas (Ctenocephalides felis). Bartonella koehlerae has caused endocarditis in a dog and in one human patient from Israel, but other clinically relevant reports involving this bacterium are lacking. Despite publication of numerous, worldwide epidemiological studies designed to determine the prevalence of Bartonella spp. bacteremia in cats, B. koehlerae has never been isolated using conventional blood agar plates. To date, successful isolation of B. koehlerae from cats and from the one human endocarditis patient has consistently required the use of chocolate agar plates. In this study, Bartonella koehlerae bacteremia was documented in eight immunocompetent patients by PCR amplification and DNA sequencing, either prior to or after enrichment blood culture using Bartonella alpha Proteobacteria growth medium. Presenting symptoms most often included fatigue, insomnia, joint pain, headache, memory loss, and muscle pain. Four patients were also infected with Bartonella vinsonii subsp. berkhoffii genotype II. After molecular documentation of B. koehlerae infection in these patients, a serological test was developed and serum samples were tested retrospectively. Bartonella koehlerae antibodies were not detected (titers < 1:16) in 30 healthy human control sera, whereas five of eight patient samples had B. koehlerae antibody titers of 1:64 or greater. Although biased by a study population consisting of individuals with extensive arthropod and animal exposure, the results of this study suggest that B. koehlerae bacteremia is more common in immunocompetent people than has been previously suspected. Future studies should more thoroughly define modes of transmission and risk factors for acquiring infection with B. koehlerae. In addition, studies are needed to determine if B. koehlerae is a cause or cofactor in the development of arthritis, peripheral neuropathies or tachyarrhythmias in patients. DA - 2010/// PY - 2010/// DO - 10.1186/1756-3305-3-76 VL - 3 IS - 1 SP - 76 J2 - Parasites Vectors LA - en OP - SN - 1756-3305 UR - http://dx.doi.org/10.1186/1756-3305-3-76 DB - Crossref ER - TY - JOUR TI - Mature Hair Follicles Generated from Dissociated Cells: A Universal Mechanism of Folliculoneogenesis AU - Zheng, Ying AU - Nace, Arben AU - Chen, Wei AU - Watkins, Krystal AU - Sergott, Luke AU - Homan, Ying AU - Vandeberg, John L. AU - Breen, Matthew AU - Stenn, Kurt T2 - DEVELOPMENTAL DYNAMICS AB - Abstract The hair follicle is considered to be a model system for studying organogenesis. In our initial study using mouse cells (Zheng et al., 2005) we found that new hair follicle formation always starts from an epithelial platform: the epidermal cells aggregate, the aggregates encyst, and from the periphery of the cysts, centrifugally, hair buds, pegs, and follicles form. In this report, we extend our initial study to four distantly related mammals: opossum, rat, dog and human. We find that in these four species, plus mouse, the most trichogenic cells are found in the earliest stages of hair follicle development and that the cellular mechanism of new hair follicle formation starting from dissociated cells is largely the same. These studies suggest that there is essentially one way by which dissociated mammalian skin cells form a new hair follicle in vivo and that this mechanism has been highly conserved. Developmental Dynamics 239:2619–2626, 2010. © 2010 Wiley‐Liss, Inc. DA - 2010/10// PY - 2010/10// DO - 10.1002/dvdy.22398 VL - 239 IS - 10 SP - 2619-2626 SN - 1097-0177 KW - hair follicle KW - morphogenesis KW - organogenesis ER - TY - JOUR TI - Lignin and Biomass: A Negative Correlation for Wood Formation and Lignin Content in Trees AU - Novaes, Evandro AU - Kirst, Matias AU - Chiang, Vincent AU - Winter-Sederoff, Heike AU - Sederoff, Ronald T2 - PLANT PHYSIOLOGY AB - Studies in populations of forest tree hybrids have shown a negative correlation of biomass growth (usually measured as wood volume) and lignin content ([Kirst et al., 2004][1]; [Novaes et al., 2009][2]). The control of growth and lignin appears to be highly regulated, implying that selection for DA - 2010/10// PY - 2010/10// DO - 10.1104/pp.110.161281 VL - 154 IS - 2 SP - 555-561 SN - 0032-0889 ER - TY - JOUR TI - Genetic variation of stem forking in loblolly pine AU - Xiong, J. S. AU - Isik, F. AU - McKeand, S. E. AU - Whetten, R. W. T2 - Forest Science DA - 2010/// PY - 2010/// VL - 56 IS - 5 SP - 429-436 ER - TY - JOUR TI - Efficiently Certifying Non-Integer Powers AU - Kaltofen, Erich AU - Lavin, Mark T2 - COMPUTATIONAL COMPLEXITY DA - 2010/9// PY - 2010/9// DO - 10.1007/s00037-010-0297-x VL - 19 IS - 3 SP - 355-366 SN - 1420-8954 KW - Integer roots KW - integer powers KW - linear-time algorithm KW - bit complexity KW - Chebotarev density theorem ER - TY - JOUR TI - Discovery of a minimal form of RNase P in Pyrobaculum AU - Lai, Lien B. AU - Chan, Patricia P. AU - Cozen, Aaron E. AU - Bernick, David L. AU - Brown, James W. AU - Gopalan, Venkat AU - Lowe, Todd M. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - RNase P RNA is an ancient, nearly universal feature of life. As part of the ribonucleoprotein RNase P complex, the RNA component catalyzes essential removal of 5′ leaders in pre-tRNAs. In 2004, Li and Altman computationally identified the RNase P RNA gene in all but three sequenced microbes: Nanoarchaeum equitans , Pyrobaculum aerophilum , and Aquifex aeolicus (all hyperthermophiles) [Li Y, Altman S (2004) RNA 10:1533–1540]. A recent study concluded that N. equitans does not have or require RNase P activity because it lacks 5′ tRNA leaders. The “missing” RNase P RNAs in the other two species is perplexing given evidence or predictions that tRNAs are trimmed in both, prompting speculation that they may have developed novel alternatives to 5′ pre-tRNA processing. Using comparative genomics and improved computational methods, we have now identified a radically minimized form of the RNase P RNA in five Pyrobaculum species and the related crenarchaea Caldivirga maquilingensis and Vulcanisaeta distributa , all retaining a conventional catalytic domain, but lacking a recognizable specificity domain. We confirmed 5′ tRNA processing activity by high-throughput RNA sequencing and in vitro biochemical assays. The Pyrobaculum and Caldivirga RNase P RNAs are the smallest naturally occurring form yet discovered to function as trans -acting precursor tRNA-processing ribozymes. Loss of the specificity domain in these RNAs suggests altered substrate specificity and could be a useful model for finding other potential roles of RNase P. This study illustrates an effective combination of next-generation RNA sequencing, computational genomics, and biochemistry to identify a divergent, formerly undetectable variant of an essential noncoding RNA gene. DA - 2010/12/28/ PY - 2010/12/28/ DO - 10.1073/pnas.1013969107 VL - 107 IS - 52 SP - 22493-22498 SN - 0027-8424 KW - catalytic RNA KW - gene finding KW - RNA processing ER - TY - JOUR TI - Basal Signaling Regulates Plant Growth and Development AU - Boss, Wendy F. AU - Sederoff, Heike Winter AU - Im, Yang Ju AU - Moran, Nava AU - Grunden, Amy M. AU - Perera, Imara Y. T2 - PLANT PHYSIOLOGY AB - The term signal transduction refers to the classical paradigm where an external stimulus is sensed and initiates an increase in second messengers. Each second messenger transmits and amplifies the signal by activating a subset of downstream pathways. This complex network of interwoven downstream DA - 2010/10// PY - 2010/10// DO - 10.1104/pp.110.161232 VL - 154 IS - 2 SP - 439-443 SN - 0032-0889 ER - TY - JOUR TI - Autophosphorylation of Tyr-610 in the receptor kinase BAK1 plays a role in brassinosteroid signaling and basal defense gene expression (Retracted article. See vol. 113, pg. E3987, 2016) AU - Oh, Man-Ho AU - Wang, Xiaofeng AU - Wu, Xia AU - Zhao, Youfu AU - Clouse, Steven D. AU - Huber, Steven C. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - BAK1 is a leucine-rich repeat receptor-like kinase that functions as a coreceptor with the brassinosteroid (BR) receptor BRI1 and the flagellin receptor FLS2, and as a negative regulator of programmed cell death. BAK1 has been shown to autophosphorylate on numerous serine/threonine sites in vitro as well as to transphosphorylate associated receptor kinases both in vitro and in planta. In the present study we identify Tyr-610 in the carboxyl-terminal domain of BAK1 as a major site of autophosphorylation that is brassinolide-induced in vivo and requires a kinase-active BAK1. Expression of BAK1(Y610F)-Flag in transgenic plants lacking the endogenous bak1 and its functional paralogue, bkk1, produced plants that were viable but extremely small and generally resembled BR signaling mutants, whereas an acidic substitution for Tyr-610 to mimic phosphorylation restored normal growth. Several lines of evidence support the notion that BR signaling is impaired in the BAK1(Y610F)-Flag plants, and are consistent with the recently proposed sequential transphosphorylation model for BRI1/BAK1 interaction and activation. In contrast, the FLS2-mediated inhibition of seedling growth by the flg22 elicitor occurred normally in the Y610F-directed mutant. However, expression of many defense genes was dramatically reduced in BAK1(Y610F) plants and the nonpathogenic hrpA mutant of Pseudomonas syringae was able to grow rapidly in the mutant. These results indicate that phosphorylation of Tyr-610 is required for some but not all functions of BAK1, and adds significantly to the emerging notion that tyrosine phosphorylation could play an important role in plant receptor kinase signaling. DA - 2010/10/12/ PY - 2010/10/12/ DO - 10.1073/pnas.0915064107 VL - 107 IS - 41 SP - 17827-17832 SN - 0027-8424 KW - basal immunity KW - flagellin signaling KW - receptor-like kinase KW - tyrosine phosphorylation KW - phosphospecific antibodies ER - TY - JOUR TI - Activation Energies for Oxidation of Porphyrin Monolayers Anchored to Au(111) AU - Jiao, Jieying AU - Taniguchi, Masahiko AU - Lindsey, Jonathan S. AU - Bocian, David F. T2 - LANGMUIR AB - The activation energy for the oxidation of porphyrin monolayers anchored to gold surfaces is determined via measurement of the temperature dependence of the electron-transfer rates. The activation energy (1) increases with increasing surface concentration of the porphyrin and (2) is significantly lower (8.1-17 versus 37-49 kJ mol(-1)) when smaller, more mobile counterions (Cl(-) versus PF(6)(-)) are used as the supporting electrolyte. Regardless, the lower activation energies do not result in radically different electron-transfer rates for the different types of counterions owing to compensating entropic effects. DA - 2010/10/19/ PY - 2010/10/19/ DO - 10.1021/la102802n VL - 26 IS - 20 SP - 15718-15721 SN - 0743-7463 ER - TY - JOUR TI - Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology AU - Torto-Alalibo, Trudy AU - Collmer, Candace W. AU - Gwinn-Giglio, Michelle AU - Lindeberg, Magdalen AU - Meng, Shaowu AU - Chibucos, Marcus C. AU - Tseng, Tsai-Tien AU - Lomax, Jane AU - Biehl, Bryan AU - Ireland, Amelia AU - Bird, David AU - Dean, Ralph A. AU - Glasner, Jeremy D. AU - Perna, Nicole AU - Setubal, Joao C. AU - Collmer, Alan AU - Tyler, Brett M. T2 - MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS AB - SUMMARY Microbes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. Common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. Genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. Effective comparisons among these symbioses, however, are hampered by inconsistent descriptive terms in the literature for functionally similar genes. Bioinformatic approaches that use homology-based tools are limited to identifying functionally similar genes based on similarities in their sequences. An effective solution to these limitations is provided by the Gene Ontology (GO), which provides a standardized language to describe gene products from all organisms. The GO comprises three ontologies that enable one to describe the molecular function(s) of gene products, the biological processes to which they contribute, and their cellular locations. Beginning in 2004, the Plant-Associated Microbe Gene Ontology (PAMGO) interest group collaborated with the GO consortium to extend the GO to accommodate terms for describing gene products associated with microbe-host interactions. Currently, over 900 terms that describe biological processes common to diverse plant- and animal-associated microbes are incorporated into the GO database. Here we review some unifying themes common to diverse host-microbe associations and illustrate how the new GO terms facilitate a standardized description of the gene products involved. We also highlight areas where new terms need to be developed, an ongoing process that should involve the whole community. DA - 2010/12// PY - 2010/12// DO - 10.1128/mmbr.00017-10 VL - 74 IS - 4 SP - 479-503 SN - 1098-5557 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-78650086447&partnerID=MN8TOARS ER - TY - JOUR TI - Genomes of the T4-related bacteriophages as windows on microbial genome evolution AU - Petrov, Vasiliy M. AU - Ratnayaka, Swarnamala AU - Nolan, James M. AU - Miller, Eric S. AU - Karam, Jim D. T2 - VIROLOGY JOURNAL AB - The T4-related bacteriophages are a group of bacterial viruses that share morphological similarities and genetic homologies with the well-studied Escherichia coli phage T4, but that diverge from T4 and each other by a number of genetically determined characteristics including the bacterial hosts they infect, the sizes of their linear double-stranded (ds) DNA genomes and the predicted compositions of their proteomes. The genomes of about 40 of these phages have been sequenced and annotated over the last several years and are compared here in the context of the factors that have determined their diversity and the diversity of other microbial genomes in evolution. The genomes of the T4 relatives analyzed so far range in size between ~160,000 and ~250,000 base pairs (bp) and are mosaics of one another, consisting of clusters of homology between them that are interspersed with segments that vary considerably in genetic composition between the different phage lineages. Based on the known biological and biochemical properties of phage T4 and the proteins encoded by the T4 genome, the T4 relatives reviewed here are predicted to share a genetic core, or "Core Genome" that determines the structural design of their dsDNA chromosomes, their distinctive morphology and the process of their assembly into infectious agents (phage morphogenesis). The Core Genome appears to be the most ancient genetic component of this phage group and constitutes a mere 12-15% of the total protein encoding potential of the typical T4-related phage genome. The high degree of genetic heterogeneity that exists outside of this shared core suggests that horizontal DNA transfer involving many genetic sources has played a major role in diversification of the T4-related phages and their spread to a wide spectrum of bacterial species domains in evolution. We discuss some of the factors and pathways that might have shaped the evolution of these phages and point out several parallels between their diversity and the diversity generally observed within all groups of interrelated dsDNA microbial genomes in nature. DA - 2010/10/28/ PY - 2010/10/28/ DO - 10.1186/1743-422x-7-292 VL - 7 SP - SN - 1743-422X ER - TY - JOUR TI - Excited-State Photodynamics of Perylene-Porphyrin Dyads 5 Tuning Light-Harvesting Characteristics via Perylene Substituents, Connection Motif, and Three-Dimensional Architecture AU - Kirmaier, Christine AU - Song, Hee-eun AU - Yang, Eunkyung AU - Schwartz, Jennifer K. AU - Hindin, Eve AU - Diers, James R. AU - Loewe, Robert S. AU - Tomizaki, Kin-ya AU - Chevalier, Fabien AU - Ramos, Lavoisier AU - Birge, Robert R. AU - Lindsey, Jonathan S. AU - Bocian, David F. AU - Holten, Dewey T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - Seven perylene-porphyrin dyads were examined with the goal of identifying those most suitable for components of light-harvesting systems. The ideal dyad should exhibit strong absorption by the perylene in the green, undergo rapid and efficient excited-state energy transfer from perylene to porphyrin, and avoid electron-transfer quenching of the porphyrin excited state by the perylene in the medium of interest. Four dyads have different perylenes at the p-position of the meso-aryl group on the zinc porphyrin. The most suitable perylene identified in that set was then incorporated at the m- or o-position of the zinc porphyrin, affording two other dyads. An analogue of the o-substituted architecture was prepared in which the zinc porphyrin was replaced with the free base porphyrin. The perylene in each dyad is a monoimide derivative; the perylenes differ in attachment of the linker (either via a diphenylethyne linker at the N-imide or an ethynylphenyl linker at the C9 position) and the number (0-3) of 4-tert-butylphenoxy groups (which increase solubility and slightly alter the electrochemical potentials). In the p-linked dyad, the monophenoxy perylene with an N-imide diphenylethyne linker is superior in providing rapid and essentially quantitative energy transfer from excited perylene to zinc porphyrin with minimal electron-transfer quenching in both toluene and benzonitrile. The dyads with the same perylene at the m- or o-position exhibited similar results except for one case, the o-linked dyad bearing the zinc porphyrin in benzonitrile, where significant excited-state quenching is observed; this phenomenon is facilitated by close spatial approach of the perylene and porphyrin and the associated thermodynamic/kinetic enhancement of the electron-transfer process. Such quenching does not occur with the free base porphyrin because electron transfer is thermodynamically unfavorable even in the polar medium. The p-linked dyad containing a zinc porphyrin attached to a bis(4-tert-butylphenoxy)perylene via an ethynylphenyl linker at the C9 position exhibits ultrafast and quantitative energy transfer in toluene; the same dyad in benzonitrile exhibits ultrafast (<0.5 ps) perylene-to-porphyrin energy transfer, rapid (∼5 ps) porphyrin-to-perylene electron transfer, and fast (∼25 ps) charge recombination to the ground state. Collectively, this study has identified suitable perylene-porphyrin constructs for use in light-harvesting applications. DA - 2010/11/18/ PY - 2010/11/18/ DO - 10.1021/jp910705q VL - 114 IS - 45 SP - 14249-14264 SN - 1520-5207 ER - TY - JOUR TI - Bacteriophage T4 and its relatives AU - Karam, Jim D. AU - Miller, Eric S. T2 - VIROLOGY JOURNAL AB - Bacteriophage T4 and its relatives (A series of critical reviews) Jim Karam & Eric Miller In the coming months Virology Journal will publish a number of authoritative reviews about the biochemistry, structural biology and genomics of the bacteriophage T4 and the T4-related phages. Phage T4 is one of the most extensively investigated viruses and has been the central focus of several monographs and reviews over the last 25 years. Its popularity among experimental biologists is related to the ease with which this phage and some of its relatives can be propagated in widely available nonpathogenic laboratory strains of Escherichia coli and the diversity of experimental approaches that can be used to analyze its DNA genome and the RNA and protein products it encodes. The T4 biological system is amenable to investigation by genetic, phylogenetic, biochemical, biophysical, structural, computational and other tools. Advances in T4 science have paralleled advances in Molecular Biology since the birth of this interdisciplinary field around the middle of the 20 Century [1,2]. Such seminal discoveries as the chemical nature of the gene, the existence of messenger RNA, how the genetic code is read, how genes determine protein structure, how DNA is replicated by multicomponent protein machines and many other findings that have become integral to our current understanding of basic molecular mechanism in biology have typically involved important contributions from the T4 and T4-related experimental systems. The last monograph to comprehensively review all aspects of the molecular biosciences of the T4 virus was published in 1994 [3]. Since that time, the field of Molecular Biology has undergone considerable transformation, particularly as a consequence of advancements in the methods for sequencing microbial and eukaryotic genomes and using DNA sequence data for novel experimental designs that have yielded numerous rewards in resolving biological mysteries and stimulating the growth of biotechnology. The review series to be published in Virology Journal will emphasize advances and seminal discoveries in four major areas of T4 research: Genomics, Gene Expression, DNA Replication and Phage Morphogenesis. DA - 2010/10/28/ PY - 2010/10/28/ DO - 10.1186/1743-422x-7-293 VL - 7 SP - SN - 1743-422X ER - TY - JOUR TI - Leishmaniasis in a dog native to Colorado AU - Freeman, Kate S. AU - Miller, Matthew D. AU - Breitschwerdt, Edward B. AU - Lappin, Michael R. T2 - Journal of the American Veterinary Medical Association AB - A 1-year-old 32.5-kg (71.5-lb) sexually intact male foxhound-Treeing Walker Coonhound cross was evaluated because of a 2.5-month history of dermatologic lesions, weight loss, and diarrhea.Physical examination revealed muscle wasting, lymphadenopathy, and multifocal pruritic dermatologic lesions of alopecia, thickening, erythema, and follicular casting. Hematologic and serum biochemical analyses revealed nonregenerative anemia, mono-cytosis, hypercalcemia, hyperproteinemia, and hyperglobulinemia. Proteinuria was identified on urinalysis. Hepatomegaly, splenomegaly, and diffuse abdominal lymphadenomegaly were detected on abdominal ultrasonography. A diagnosis of leishmaniasis was confirmed by ELISA detection of serum antibodies against Leishmania spp, a high serum indirect fluorescent antibody titer (1:1,024) against Leishmania infantum, amplification of Leishmania DNA on PCR assay of a whole blood sample and a lymph node aspirate, and histologic identification of suspected Leishmania amastigotes in skin specimens. In addition, the dog had a low CD4+:CD8+ lymphocyte ratio of 1:1.The dog was euthanized because of the severity of leishmaniasis and poor prognosis. This dog was from a litter of 10 puppies that included 4 stillborn puppies, 2 puppies that died as neonates, and 1 littermate that was euthanized at 1 year of age because of a high serum antibody titer against Leishmania spp. Eventually the foxhound dam was euthanized because of a high serum antibody titer against Leishmania spp. The dog had been raised with an unaffected littermate, its sire, and an unrelated Treeing Walker Coonhound female that were seronegative for Leishmania infection.Although vertical disease transmission was suspected, it is possible that L infantum is now endemic in Colorado. Leishmaniasis should be considered in dogs with scaly dermatoses. DA - 2010/12// PY - 2010/12// DO - 10.2460/javma.237.11.1288 VL - 237 IS - 11 SP - 1288-1291 J2 - Journal of the American Veterinary Medical Association LA - en OP - SN - 0003-1488 UR - http://dx.doi.org/10.2460/javma.237.11.1288 DB - Crossref ER - TY - JOUR TI - Overexpression of Transcription Factor Sp2 Inhibits Epidermal Differentiation and Increases Susceptibility to Wound- and Carcinogen-Induced Tumorigenesis AU - Kim, Tae-Hyung AU - Chiera, Shannon L. AU - Linder, Keith E. AU - Trempus, Carol S. AU - Smart, Robert C. AU - Horowitz, Jonathan M. T2 - CANCER RESEARCH AB - Abstract Sp proteins are evolutionarily conserved transcription factors required for the expression of a wide variety of genes that are critical for development and cell cycle progression. Deregulated expression of certain Sp proteins is associated with the formation of a variety of human tumors; however, direct evidence that any given Sp protein is oncogenic has been lacking. Here, we report that Sp2 protein abundance in mice increases in concert with the progression of carcinogen-induced murine squamous cell carcinomas. Transgenic mice specifically overexpressing murine Sp2 in epidermal basal keratinocytes were highly susceptible to wound- and carcinogen-induced papillomagenesis. Transgenic animals that were homozygous rather than hemizygous for the Sp2 transgene exhibited a striking arrest in the epidermal differentiation program, perishing within 2 weeks of birth. Our results directly support the likelihood that Sp2 overexpression occurring in various human cancers has significant functional effect. Cancer Res; 70(21); 8507–16. ©2010 AACR. DA - 2010/11/1/ PY - 2010/11/1/ DO - 10.1158/0008-5472.can-10-1213 VL - 70 IS - 21 SP - 8507-8516 SN - 1538-7445 ER - TY - JOUR TI - Crystallization and preliminary X-ray diffraction analysis of red clover necrotic mosaic virus AU - Martin, Stanton L. AU - Guenther, Richard H. AU - Sit, Tim L. AU - Swartz, Paul D. AU - Meilleur, Flora AU - Lommel, Steven A. AU - Rose, Robert B. T2 - ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS AB - Red clover necrotic mosaic virus (RCNMV) is a species that belongs to the Tombusviridae family of plant viruses with a T = 3 icosahedral capsid. RCNMV virions were purified and were crystallized for X-ray analysis using the hanging-drop vapor-diffusion method. Self-rotation functions and systematic absences identified the space group as I23, with two virions in the unit cell. The crystals diffracted to better than 4 Å resolution but were very radiation-sensitive, causing rapid decay of the high-resolution reflections. The data were processed to 6 Å in the analysis presented here. DA - 2010/11// PY - 2010/11// DO - 10.1107/s1744309110032483 VL - 66 SP - 1458-1462 SN - 2053-230X KW - red clover necrotic mosaic virus KW - dianthoviruses KW - viruses ER - TY - JOUR TI - Three nicotine demethylase genes mediate nornicotine biosynthesis in Nicotiana tabacum L Functional characterization of the CYP82E10 gene AU - Lewis, Ramsey S. AU - Bowen, Steven W. AU - Keogh, Matthew R. AU - Dewey, Ralph E. T2 - PHYTOCHEMISTRY AB - In most tobacco (Nicotiana tabacum L.) plants, nornicotine is a relatively minor alkaloid, comprising about 2–5% of the total pyridine alkaloid pool in the mature leaf. Changes in gene expression at an unstable locus, however, can give rise to plants that produce high levels of nornicotine, specifically during leaf senescence and curing. Minimizing the nornicotine content in tobacco is highly desirable, because this compound serves as the direct precursor in the synthesis of N′-nitrosonornicotine, a potent carcinogen in laboratory animals. Nornicotine is likely produced almost entirely via the N-demethylation of nicotine, in a process called nicotine conversion that is catalyzed by the enzyme nicotine N-demethylase (NND). Previous studies have identified CYP82E4 as the specific NND gene responsible for the unstable conversion phenomenon, and CYP82E5v2 as a putative minor NND gene. Here, by discovery and characterization of CYP82E10, a tobacco NND gene, is reported. PCR amplification studies showed that CYP82E10 originated from the N. sylvestris ancestral parent of modern tobacco. Using a chemical mutagenesis strategy, knockout mutations were induced and identified in all three tobacco NND genes. By generating a series of mutant NND genotypes, the relative contribution of each NND gene toward the nornicotine content of the plant was assessed. Plants possessing knockout mutations in all three genes displayed nornicotine phenotypes that were much lower (∼0.5% of total alkaloid content) than that found in conventional tobacco cultivars. The introduction of these mutations into commercial breeding lines promises to be a viable strategy for reducing the levels of one of the best characterized animal carcinogens found in tobacco products. DA - 2010/12// PY - 2010/12// DO - 10.1016/j.phytochem.2010.09.011 VL - 71 IS - 17-18 SP - 1988-1998 SN - 1873-3700 KW - Nicotiana tabacum KW - Solanaceae KW - Gene function KW - Alkaloids KW - Nornicotine KW - Tobacco specific nitrosamine (TSNA) KW - Cytochrome P450 KW - CYP82E10 ER - TY - JOUR TI - Specific down-regulation of PAL genes by artificial microRNAs in Populus trichocarpa AU - Shi, Rui AU - Yang, Chenmin AU - Lu, Shanfa AU - Sederoff, Ronald AU - Chiang, Vincent L. T2 - PLANTA DA - 2010/11// PY - 2010/11// DO - 10.1007/s00425-010-1253-3 VL - 232 IS - 6 SP - 1281-1288 SN - 0032-0935 KW - Artificial microRNA KW - Phenylalanine ammonia-lyase KW - Populus trichocarpa transformation KW - Down-regulation KW - PolyA tailing-based real time RT-PCR KW - Quantitation ER - TY - JOUR TI - RSK-Mediated Phosphorylation in the C/EBP beta Leucine Zipper Regulates DNA Binding, Dimerization, and Growth Arrest Activity AU - Lee, Sook AU - Shuman, Jon D. AU - Guszczynski, Tad AU - Sakchaisri, Krisada AU - Sebastian, Thomas AU - Copeland, Terry D. AU - Miller, Maria AU - Cohen, Michael S. AU - Taunton, Jack AU - Smart, Robert C. AU - Xiao, Zhen AU - Yu, Li-Rong AU - Veenstra, Timothy D. AU - Johnson, Peter F. T2 - MOLECULAR AND CELLULAR BIOLOGY AB - The bZIP transcription factor C/EBPbeta is a target of Ras signaling that has been implicated in Ras-induced transformation and oncogene-induced senescence (OIS). To gain insights into Ras-C/EBPbeta signaling, we investigated C/EBPbeta activation by oncogenic Ras. We show that C/EBPbeta DNA binding is autorepressed and becomes activated by the Ras-Raf-MEK-ERK-p90(RSK) cascade. Inducible phosphorylation by RSK on Ser273 in the leucine zipper was required for DNA binding. In addition, three other modifications (phosphorylation on Tyr109 [p-Tyr109], p-Ser111, and monomethylation of Arg114 [me-Arg114]) within an N-terminal autoinhibitory domain were important for Ras-induced C/EBPbeta activation and cytostatic activity. Apart from its role in DNA binding, Ser273 phosphorylation also creates an interhelical g<-->e' salt bridge with Lys268 that increases attractive electrostatic interactions between paired leucine zippers and promotes homodimerization. Mutating Ser273 to Ala or Lys268 to Glu decreased C/EBPbeta homodimer formation, whereas heterodimerization with C/EBPgamma was relatively unaffected. The S273A substitution also reduced the antiproliferative activity of C/EBPbeta in Ras(V12)-expressing fibroblasts and decreased binding to target cell cycle genes, while a phosphomimetic substitution (S273D) maintained growth arrest function. Our findings identify four novel C/EBPbeta-activating modifications, including RSK-mediated phosphorylation of a bifunctional residue in the leucine zipper that regulates DNA binding and homodimerization and thereby promotes cell cycle arrest. DA - 2010/6// PY - 2010/6// DO - 10.1128/mcb.00782-09 VL - 30 IS - 11 SP - 2621-2635 SN - 0270-7306 ER - TY - JOUR TI - Proteomic Analysis Reveals Virus-Specific Hsp25 Modulation in Cardiac Myocytes AU - Li, Lianna AU - Sevinsky, Joel R. AU - Rowland, Megan D. AU - Bundy, Jonathan L. AU - Stephenson, James L. AU - Sherry, Barbara T2 - JOURNAL OF PROTEOME RESEARCH AB - Viruses frequently infect the heart but clinical myocarditis is rare, suggesting that the cardiac antiviral response is uniquely effective. Indeed, the Type I interferon (IFN) response is cardiac cell-type specific and provides one integrated network of protection for the heart. Here, a proteomic approach was used to identify additional proteins that may be involved in the cardiac antiviral response. Reovirus-induced murine myocarditis reflects direct viral damage to cardiac cells and offers an excellent system for study. Primary cultures of murine cardiac myocytes were infected with myocarditic or nonmyocarditic reovirus strains, and whole cell lysates were compared by two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF/TOF) tandem mass spectrometry. Results were quantitative and reproducible and demonstrated that whole proteome changes clustered according to viral pathogenic phenotype. Moreover, the data suggest that the heat shock protein Hsp25 is modulated differentially by myocarditic and nonmyocarditic reoviruses and may play a role in the cardiac antiviral response. Members of seven virus families modulate Hsp25 or Hsp27 expression in a variety of cell types, suggesting that Hsp25 participation in the antiviral response may be widespread. However, results here provide the first evidence for a virus-induced decrease in Hsp25/27 and suggest that viruses may have evolved a mechanism to subvert this protective response, as they have for IFN. DA - 2010/5// PY - 2010/5// DO - 10.1021/pr901151k VL - 9 IS - 5 SP - 2460-2471 SN - 1535-3907 KW - cardiac myocyte KW - myocarditis KW - reovirus KW - Hsp25 KW - Hsp27 KW - proteome KW - DIGE ER - TY - JOUR TI - Prediction of whole-stem alpha-cellulose yield, lignin content, and wood density in juvenile and mature loblolly pine AU - Aspinwall, M. J. AU - Li, B. L. AU - McKeand, S. E. AU - Isik, F. AU - Gumpertz, M. L. T2 - Southern Journal of Applied Forestry DA - 2010/// PY - 2010/// VL - 34 IS - 2 SP - 84-90 ER - TY - JOUR TI - Predicting Residential Air Exchange Rates from Questionnaires and Meteorology: Model Evaluation in Central North Carolina AU - Breen, Michael S. AU - Breen, Miyuki AU - Williams, Ronald W. AU - Schultz, Bradley D. T2 - ENVIRONMENTAL SCIENCE & TECHNOLOGY AB - A critical aspect of air pollution exposure models is the estimation of the air exchange rate (AER) of individual homes, where people spend most of their time. The AER, which is the airflow into and out of a building, is a primary mechanism for entry of outdoor air pollutants and removal of indoor source emissions. The mechanistic Lawrence Berkeley Laboratory (LBL) AER model was linked to a leakage area model to predict AER from questionnaires and meteorology. The LBL model was also extended to include natural ventilation (LBLX). Using literature-reported parameter values, AER predictions from LBL and LBLX models were compared to data from 642 daily AER measurements across 31 detached homes in central North Carolina, with corresponding questionnaires and meteorological observations. Data was collected on seven consecutive days during each of four consecutive seasons. For the individual model-predicted and measured AER, the median absolute difference was 43% (0.17 h(-1)) and 40% (0.17 h(-1)) for the LBL and LBLX models, respectively. Additionally, a literature-reported empirical scale factor (SF) AER model was evaluated, which showed a median absolute difference of 50% (0.25 h(-1)). The capability of the LBL, LBLX, and SF models could help reduce the AER uncertainty in air pollution exposure models used to develop exposure metrics for health studies. DA - 2010/12/15/ PY - 2010/12/15/ DO - 10.1021/es101800k VL - 44 IS - 24 SP - 9349-9356 SN - 0013-936X ER - TY - JOUR TI - Current Progress on Statistical Methods for Mapping Quantitative Trait Loci from Inbred Line Crosses AU - Silva, Luciano Da Costa E. AU - Zeng, Zhao-Bang T2 - JOURNAL OF BIOPHARMACEUTICAL STATISTICS AB - Tremendous progress has been made in recent years on developing statistical methods for mapping quantitative trait loci (QTL) from crosses of inbred lines. Most of the recent research is focused on strategies for mapping multiple-QTL and associated model selection procedures and criterion. We review the progress of research in this area on one trait and multiple traits by maximum likelihood and Bayesian methods. DA - 2010/// PY - 2010/// DO - 10.1080/10543400903572845 VL - 20 IS - 2 SP - 454-481 SN - 1520-5711 KW - Inbred lines KW - Quantitative trait loci KW - Statistical methods ER - TY - JOUR TI - Association Mapping of Quantitative Disease Resistance in a Natural Population of Loblolly Pine (Pinus taeda L.) AU - Quesada, Tania AU - Gopal, Vikneswaran AU - Cumbie, W. Patrick AU - Eckert, Andrew J. AU - Wegrzyn, Jill L. AU - Neale, David B. AU - Goldfarb, Barry AU - Huber, Dudley A. AU - Casella, George AU - Davis, John M. T2 - GENETICS AB - Abstract Genetic resistance to disease incited by necrotrophic pathogens is not well understood in plants. Whereas resistance is often quantitative, there is limited information on the genes that underpin quantitative variation in disease resistance. We used a population genomic approach to identify genes in loblolly pine (Pinus taeda) that are associated with resistance to pitch canker, a disease incited by the necrotrophic pathogen Fusarium circinatum. A set of 498 largely unrelated, clonally propagated genotypes were inoculated with F. circinatum microconidia and lesion length, a measure of disease resistance, data were collected 4, 8, and 12 weeks after inoculation. Best linear unbiased prediction was used to adjust for imbalance in number of observations and to identify highly susceptible and highly resistant genotypes (“tails”). The tails were reinoculated to validate the results of the full population screen. Significant associations were detected in 10 single nucleotide polymorphisms (SNPs) (out of 3938 tested). As hypothesized for genes involved in quantitative resistance, the 10 SNPs had small effects and proposed roles in basal resistance, direct defense, and signal transduction. We also discovered associated genes with unknown function, which would have remained undetected in a candidate gene approach constrained by annotation for disease resistance or stress response. DA - 2010/10// PY - 2010/10// DO - 10.1534/genetics.110.117549 VL - 186 IS - 2 SP - 677-U336 SN - 1943-2631 ER - TY - JOUR TI - Arabidopsis thaliana as a model for gelatinous fiber formation AU - Wyatt, S. E. AU - Sederoff, R. AU - Flaishman, M. A. AU - Lev-Yadun, S. T2 - RUSSIAN JOURNAL OF PLANT PHYSIOLOGY DA - 2010/5// PY - 2010/5// DO - 10.1134/s1021443710030076 VL - 57 IS - 3 SP - 363-367 SN - 1021-4437 KW - Arabidpsis thaliana KW - cambium KW - gelatinous fibers KW - gravity KW - reaction wood KW - tension wood ER - TY - JOUR TI - The Structure of Sindbis Virus Produced from Vertebrate and Invertebrate Hosts as Determined by Small-Angle Neutron Scattering AU - He, Lilin AU - Piper, Amanda AU - Meilleur, Flora AU - Myles, Dean A. A. AU - Hernandez, Raquel AU - Brown, Dennis T. AU - Heller, William T. T2 - JOURNAL OF VIROLOGY AB - The complex natural cycle of vectored viruses that transition between host species, such as between insects and mammals, makes understanding the full life cycle of the virus an incredibly complex problem. Sindbis virus, an arbovirus and prototypic alphavirus having an inner protein shell and an outer glycoprotein coat separated by a lipid membrane, is one example of a vectored virus that transitions between vertebrate and insect hosts. While evidence of host-specific differences in Sindbis virus has been observed, no work has been performed to characterize the impact of the host species on the structure of the virus. Here, we report the first study of the structural differences between Sindbis viruses grown in mammalian and insect cells, which were determined by small-angle neutron scattering (SANS), a nondestructive technique that did not decrease the infectivity of the Sindbis virus particles studied. The scattering data and modeling showed that, while the radial position of the lipid bilayer did not change significantly, it was possible to conclude that it did have significantly more cholesterol when the virus was grown in mammalian cells. Additionally, the outer protein coat was found to be more extended in the mammalian Sindbis virus. The SANS data also demonstrated that the RNA and nucleocapsid protein share a closer interaction in the mammalian-cell-grown virus than in the virus from insect cells. DA - 2010/5// PY - 2010/5// DO - 10.1128/jvi.00044-10 VL - 84 IS - 10 SP - 5270-5276 SN - 1098-5514 ER - TY - JOUR TI - Successful treatment ofBartonella henselaeendocarditis in a cat AU - Perez, Cristina AU - Hummel, James B. AU - Keene, Bruce W. AU - Maggi, Ricardo G. AU - Diniz, Pedro P.V.P. AU - Breitschwerdt, Edward B. T2 - Journal of Feline Medicine and Surgery AB - This report describes the clinical presentation, diagnosis and treatment of a cat with vegetative valvular endocarditis temporally associated with natural infection with Bartonella henselae. Lethargy, abnormal gait and weakness were the main clinical signs that resulted in referral for diagnostic evaluation. Using a novel and sensitive culture approach, B henselae was isolated from the blood. Following antibiotic therapy there was total resolution of clinical signs, the heart murmur, the valvular lesion by echocardiography, and no Bartonella species was isolated or amplified from a post-treatment blood culture. In conjunction with previous case reports, infective endocarditis can be associated with natural B henselae infection in cats; however, early diagnosis and treatment may result in a better prognosis than previously reported. DA - 2010/6// PY - 2010/6// DO - 10.1016/j.jfms.2009.12.018 VL - 12 IS - 6 SP - 483-486 J2 - Journal of Feline Medicine and Surgery LA - en OP - SN - 1098-612X 1532-2750 UR - http://dx.doi.org/10.1016/j.jfms.2009.12.018 DB - Crossref ER - TY - JOUR TI - Probing the Rate of Hole Transfer in Oxidized Synthetic Chlorin Dyads via Site-Specific C-13-Labeling AU - Nieves-Bernier, Elias J. AU - Diers, James R. AU - Taniguchi, Masahiko AU - Holten, Dewey AU - Bocian, David F. AU - Lindsey, Jonathan S. T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Understanding electronic communication among interacting constituents of multicomponent molecular architectures is important for rational design in diverse fields including artificial photosynthesis and molecular electronics. One strategy for examining ground-state hole/electron transfer in an oxidized tetrapyrrolic array relies on analysis of the hyperfine interactions observed in the EPR spectrum of the π-cation radical. This strategy has been previously employed to probe the hole/electron-transfer process in oxidized multiporphyrin arrays of normal isotopic composition, wherein 1H and 14N serve as the hyperfine “clocks”, and in arrays containing site-specific 13C-labels, which serve as additional hyperfine clocks. Herein, the hyperfine-clock strategy is applied to dyads of dihydroporphyrins (chlorins). Chlorins are more closely related structurally to chlorophylls than are porphyrins. A de novo synthetic strategy has been employed to introduce a 13C label at the 19-position of the chlorin macrocycle, which is a site of large electron/hole density and is accessible synthetically beginning with 13C-nitromethane. The resulting singly 13C-labeled chlorin was coupled with an unlabeled chlorin to give a dyad wherein a diphenylethyne linker spans the 10-positions of the two zinc chlorins. EPR studies of the monocations of both the natural abundance and 13C-labeled zinc chlorin dyads and benchmark zinc chlorin monomers reveal that the time scale for hole/electron transfer is in the 4−7 ns range, which is 5−10-fold longer than that in analogous porphyrin arrays. The slower hole/electron transfer rate observed for the chlorin versus porphyrin dyads is attributed to the fact that the HOMO is a1u-like for the chlorins versus a2u-like for the porphyrins; the a1u-like orbital exhibits little (or no) electron/hole density at the site of linker attachment whereas the a2u-like orbital exhibits significant electron/hole density at this site. Collectively, the studies of the chlorin and porphyrin dyads provide insights into the structural features that influence the hole/electron-transfer process. DA - 2010/5/21/ PY - 2010/5/21/ DO - 10.1021/jo100527h VL - 75 IS - 10 SP - 3193-3202 SN - 1520-6904 ER - TY - JOUR TI - Molecular Evidence of Perinatal Transmission of Bartonella vinsonii subsp. berkhoffii and Bartonella henselae to a Child AU - Breitschwerdt, E. B. AU - Maggi, R. G. AU - Farmer, P. AU - Mascarelli, P. E. T2 - Journal of Clinical Microbiology AB - Bartonella vinsonii subsp. berkhoffii, Bartonella henselae, or DNA of both organisms was amplified and sequenced from blood, enrichment blood cultures, or autopsy tissues from four family members. Historical and microbiological results support perinatal transmission of Bartonella species in this family. It is of clinical relevance that Bartonella spp. may adversely influence human reproductive performance. DA - 2010/4/14/ PY - 2010/4/14/ DO - 10.1128/jcm.00326-10 VL - 48 IS - 6 SP - 2289-2293 J2 - Journal of Clinical Microbiology LA - en OP - SN - 0095-1137 UR - http://dx.doi.org/10.1128/JCM.00326-10 DB - Crossref ER - TY - PCOMM TI - IDH1 and IDH2 hotspot mutations are not found in canine glioma AU - Reitman, Zachary J. AU - Olby, Natasha J. AU - Mariani, Christopher L. AU - Thomas, Rachael AU - Breen, Matthew AU - Bigner, Darell D. AU - McLendon, Roger E. AU - Yan, Hai AB - Human diffuse and anaplastic astrocytomas, well-differentiated and anaplastic oligodendrogliomas and secondary glioblastomas frequently (>70%) contain somatic mutations of the R132 codon of the cytoplasmic NADP+-dependent isocitrate dehydrogenase (IDH1) or the corresponding R172 codon in its homolog, IDH2.1-5 Other gliomas, such as primary glioblastomas, contain IDH1 R132 mutations more rarely.2, 4, 6-8 Less frequent IDH1 R132 mutations have also been identified in acute myeloid leukemia,9 prostate cancer8 and colorectal cancer.10 IDH1 R132 and IDH2 R172 are conserved in all known species and are important for the enzymatic function of the encoded proteins,2, 4, 11 but the significance of these changes in cancer is not fully clear. Canines develop oligodendrogliomas and astrocytomas that resemble the human versions of these tumors. Previously, canine gliomas have been shown to contain common alterations observed in human gliomas, including EGFR expression and amplification, VEGF expression and aberrant p53 overexpression and gene mutation.12-14 Of note, IDH1 and IDH2 are highly conserved between dog and human, with 96.9 and 96.4% identity at the protein level, respectively (HomoloGene). The arginines mutated in human gliomas are also conserved between these species, with canine IDH1 R132 corresponding to human IDH1 R132 and canine IDH2 R238 corresponding to human IDH2 R172. The conservation of some genetic mechanisms of gliomagenesis in dogs, the conserved nature of the IDH genes between human and dog and the high frequency of IDH gene mutations in some human glioma subtypes led us to test whether canine gliomas contain IDH gene mutations. IDH status was determined for 25 formalin-fixed, paraffin-embedded (FFPE) samples from 25 brain tumors that developed spontaneously. Canine glioma types analyzed included 8 oligodendrogliomas, 4 anaplastic oligodendrogliomas, 3 astrocytomas, 3 anaplastic astrocytomas and 2 glioblastomas, all of which have been shown to contain IDH gene mutations in humans, as well as 1 gliomatosis cerebri. Three meningiomas and 1 anaplastic ependymoma were also analyzed. Genomic DNA was isolated using a microtome and the QIAamp DNA FFPE tissue kit (Qiagen, Valencia, CA). H&E slides were created from sections derived from paraffin sections flanking the material used for DNA extraction, and a neuropathologist confirmed the presence of tumor on all slides. Three samples contained 30–50% tumor on both slides, 5 samples contained 50–70% tumor on both slides and all other slides contained 70–100% tumor on both slides. For the 8 samples with less than 70% tumor tissue identified on either slide, DNA was also isolated from scrapings of the tumor area to analyze pure tumor tissue. PCR and sequencing primers were designed using Primer 3 (http://www-genome.wi.mit.edu/cgibin/primer/primer3_www.cgi) and synthesized by integrated DNA technologies (Coralville, IA). Primers were designed to amplify a 202 bp region surrounding the canine IDH1 R132 and a 212 bp region surrounding the canine IDH2 R238. PCR amplification and amplimer sequencing were performed using standard methods. IDH1 R132 and IDH2 R238 were unambiguously wild-type in all 25 canine tumors analyzed. These results suggest that dog gliomas rarely or never associate with mutations in these codons. We recently showed that canine gliomas contain copy number alterations analogous to those observed in human gliomas. However, the frequency of such alterations often varies between tumors from either species, and analogues for some alterations that are frequent in human gliomas, such as 1p/19q loss in oligodendrogliomas, are not frequent in the canine tumors.15 Together, these results may indicate that canine tumors develop using mechanisms that are distinct from human tumors with IDH mutations or 1p/19q loss. Alternatively, other unknown genetic alterations may produce the same effect as IDH mutation, 1p/19q loss or other changes in dogs. Pet dogs that develop spontaneous gliomas have been proposed as a model to test human glioma therapies,16 and these results emphasize the importance of considering the genetic differences between human and canine tumors for studies using this model. Dr. Roger E. McLendon performed histopathological evaluation of all slides. The authors thank Mr. Christopher G. Duncan, Mr. Patrick Killela and Dr. B. Ahmed Rasheed for assistance with DNA sequencing and sequence interpretation. Yours sincerely, Zachary J. Reitman, Natasha J. Olby, Christopher L. Mariani, Rachael Thomas, Matthew Breen, Darell D. Bigner, Roger E. Mclendon, Hai Yan. DA - 2010/7/1/ PY - 2010/7/1/ DO - 10.1002/ijc.25017 SP - 245-246 ER - TY - JOUR TI - Feline immunodeficiency virus, feline leukemia virus and Bartonella species in stray cats on St Kitts, West Indies AU - Kelly, Patrick J. AU - Moura, Lenita AU - Miller, Tanya AU - Thurk, Jaime AU - Perreault, Nicole AU - Weil, Adriana AU - Maggio, Ricardo AU - Lucas, Helene AU - Breitschwerdt, Edward T2 - Journal of Feline Medicine and Surgery AB - Stray cats trapped in various areas of Basseterre, the capital of St Kitts in the West Indies, were tested for infection with feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) using commercial kits. Of 99 (51 male and 48 female) cats trapped in 2006/7, 15% (12 males and three females) were positive for FIV while none were positive for FeLV. Of 72 (41 males and 31 females) cats trapped in 2009, 14% (nine males and one female) were positive for FIV while none were positive for FeLV. Polymerase chain reaction analysis revealed DNA of Bartonella species in whole blood collected from 60/95 (63%) cats trapped in 2006/7. Sequencing of the 16S-23S rRNA gene intergenic transcribed spacer (ITS) region of a convenience sample of nine amplicons and the 11 isolates made from 43 blood samples which were cultured using Bartonella alpha Proteobacteria (BAPGM) enrichment medium revealed B henselae (14) and B clarridgeiae (six). DA - 2010/6// PY - 2010/6// DO - 10.1016/j.jfms.2009.12.015 VL - 12 IS - 6 SP - 435-440 J2 - Journal of Feline Medicine and Surgery LA - en OP - SN - 1098-612X 1532-2750 UR - http://dx.doi.org/10.1016/j.jfms.2009.12.015 DB - Crossref ER - TY - JOUR TI - Diagnosis of Canine Vector-Borne Diseases in Young Dogs: a Longitudinal Study AU - Otranto, D. AU - Testini, G. AU - Dantas-Torres, F. AU - Latrofa, M. S. AU - Diniz, P. P. V. d. P. AU - de Caprariis, D. AU - Lia, R. P. AU - Mencke, N. AU - Stanneck, D. AU - Capelli, G. AU - Breitschwerdt, E. B. T2 - Journal of Clinical Microbiology AB - Canine vector-borne diseases (CVBDs) pose a diagnostic challenge, particularly when a dog is coinfected with more than one pathogen. The purpose of this study was to generate information about the diagnosis of CVBDs in young dogs following their first exposure to flea, tick, sand fly, louse, and mosquito vectors. From March 2008 to May 2009, 10 purpose-bred young naive beagle dogs and a cohort of 48 mixed-breed dogs living in an area to which CVBD is endemic in southern Italy were monitored using different diagnostic tests (cytology, serology, and PCR). Overall, PCR detected the highest number of dogs infected with Anaplasma platys, Babesia vogeli, and Ehrlichia canis, whereas seroconversion was a more sensitive indicator of exposure to Leishmania infantum. For A. platys infection, combining blood and buffy coat cytology in parallel enhanced the relative sensitivity (SE(rel)) (87.3%). For B. vogeli, the best diagnostic combination was buffy coat cytology and serology used in parallel (SE(rel), 67.5%), whereas serology and PCR used in parallel (SE(rel), 100%) was the best combination for L. infantum. Overall, 12 (20.7%) dogs were coinfected; however, the percentage of new coinfections decreased from baseline (50%) to the first (33.3%) and second (16.6%) follow-up time points. Numbers of coinfections with A. platys and B. vogeli were significantly higher (P < 0.05) than coinfections with other pathogen combinations. The data generated in this study provide insights on the incidence of certain pathogens infecting young dogs in southern Italy, highlight important diagnostic testing limitations, and support the use of multiple diagnostic modalities when attempting to confirm a tick-borne infection in an individual dog or in a canine population. DA - 2010/7/21/ PY - 2010/7/21/ DO - 10.1128/jcm.00379-10 VL - 48 IS - 9 SP - 3316-3324 J2 - Journal of Clinical Microbiology LA - en OP - SN - 0095-1137 UR - http://dx.doi.org/10.1128/JCM.00379-10 DB - Crossref ER - TY - JOUR TI - Towards reliable isoform quantification using RNA-SEQ data AU - Howard, Brian E. AU - Heber, Steffen T2 - BMC BIOINFORMATICS AB - In eukaryotes, alternative splicing often generates multiple splice variants from a single gene. Here we explore the use of RNA sequencing (RNA-Seq) datasets to address the isoform quantification problem. Given a set of known splice variants, the goal is to estimate the relative abundance of the individual variants.Our method employs a linear models framework to estimate the ratios of known isoforms in a sample. A key feature of our method is that it takes into account the non-uniformity of RNA-Seq read positions along the targeted transcripts.Preliminary tests indicate that the model performs well on both simulated and real data. In two publicly available RNA-Seq datasets, we identified several alternatively-spliced genes with switch-like, on/off expression properties, as well as a number of other genes that varied more subtly in isoform expression. In many cases, genes exhibiting differential expression of alternatively spliced transcripts were not differentially expressed at the gene level.Given that changes in isoform expression level frequently involve a continuum of isoform ratios, rather than all-or-nothing expression, and that they are often independent of general gene expression changes, we anticipate that our research will contribute to revealing a so far uninvestigated layer of the transcriptome. We believe that, in the future, researchers will prioritize genes for functional analysis based not only on observed changes in gene expression levels, but also on changes in alternative splicing. DA - 2010/// PY - 2010/// DO - 10.1186/1471-2105-11-s3-s6 VL - 11 SP - SN - 1471-2105 ER - TY - JOUR TI - Stable Synthetic Cationic Bacteriochlorins as Selective Antimicrobial Photosensitizers AU - Huang, Liyi AU - Huang, Ying-Ying AU - Mroz, Pawel AU - Tegos, George P. AU - Zhiyentayev, Timur AU - Sharma, Sulbha K. AU - Lu, Zongshun AU - Balasubramanian, Thiagarajan AU - Krayer, Michael AU - Ruzie, Christian AU - Yang, Eunkyung AU - Kee, Hooi Ling AU - Kirmaier, Christine AU - Diers, James R. AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. AU - Hamblin, Michael R. T2 - ANTIMICROBIAL AGENTS AND CHEMOTHERAPY AB - Photodynamic inactivation is a rapidly developing antimicrobial treatment that employs a nontoxic photoactivatable dye or photosensitizer in combination with harmless visible light to generate reactive oxygen species that are toxic to cells. Tetrapyrroles (e.g., porphyrins, chlorins, bacteriochlorins) are a class of photosensitizers that exhibit promising characteristics to serve as broad-spectrum antimicrobials. In order to bind to and efficiently penetrate into all classes of microbial cells, tetrapyrroles should have structures that contain (i) one or more cationic charge(s) or (ii) a basic group. In this report, we investigate the use of new stable synthetic bacteriochlorins that have a strong absorption band in the range 720 to 740 nm, which is in the near-infrared spectral region. Four bacteriochlorins with 2, 4, or 6 quaternized ammonium groups or 2 basic amine groups were compared for light-mediated killing against a gram-positive bacterium (Staphylococcus aureus), a gram-negative bacterium (Escherichia coli), and a dimorphic fungal yeast (Candida albicans). Selectivity was assessed by determining phototoxicity against human HeLa cancer cells under the same conditions. All four compounds were highly active (6 logs of killing at 1 microM or less) against S. aureus and showed selectivity for bacteria over human cells. Increasing the cationic charge increased activity against E. coli. Only the compound with basic groups was highly active against C. albicans. Supporting photochemical and theoretical characterization studies indicate that (i) the four bacteriochlorins have comparable photophysical features in homogeneous solution and (ii) the anticipated redox characteristics do not correlate with cell-killing ability. These results support the interpretation that the disparate biological activities observed stem from cellular binding and localization effects rather than intrinsic electronic properties. These findings further establish cationic bacteriochlorins as extremely active and selective near-infrared activated antimicrobial photosensitizers, and the results provide fundamental information on structure-activity relationships for antimicrobial photosensitizers. DA - 2010/9// PY - 2010/9// DO - 10.1128/aac.00125-10 VL - 54 IS - 9 SP - 3834-3841 SN - 1098-6596 ER - TY - JOUR TI - QTL Identification Using Combined Linkage and Linkage Disequilibrium Mapping for Milk Production Traits on BTA6 in Chinese Holstein Population AU - Hu, F. AU - Liu, J. F. AU - Zeng, Z. B. AU - Ding, X. D. AU - Yin, C. C. AU - Gong, Y. Z. AU - Zhang, Q. T2 - ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES AB - Milk production traits are important economic traits for dairy cattle. The aim of the present study was to refine the position of previously detected quantitative trait loci (QTL) on bovine chromosome 6 affecting milk production traits in Chinese Holstein dairy cattle. A daughter design with 918 daughters from 8 elite sire families and 14 markers spanning the previously identified QTL region were used in the analysis. We employed a combined linkage and linkage disequilibrium analysis (LDLA) approach with two options for calculating the IBD probabilities, one was based on haplotypes of all 14 markers (named Method 1) and the other based on haplotypes with sliding windows of 5 markers (named Method 2). For milk fat yield, the two methods revealed a highly significant QTL located within a 6.5 cM interval (Method 1) and a 4.0 cM interval (Method 2), respectively. For milk protein yield, a highly significant QTL was detected within a 3.0 cM interval (Method 1) or a 2.5 cM interval (Method 2). These results confirmed the findings of our previous study and other studies, and greatly narrowed down the QTL positions. DA - 2010/10// PY - 2010/10// DO - 10.5713/ajas.2010.10011 VL - 23 IS - 10 SP - 1261-1267 SN - 1976-5517 KW - Fine Mapping KW - QTL KW - Bos Taurus autosome 6 KW - Milk Production Traits ER - TY - JOUR TI - Phytophthora andina sp nov., a newly identified heterothallic pathogen of solanaceous hosts in the Andean highlands AU - Oliva, R. F. AU - Kroon, L. P. N. M. AU - Chacon, G. AU - Flier, W. G. AU - Ristaino, J. B. AU - Forbes, G. A. T2 - PLANT PATHOLOGY AB - A blight disease on fruits and foliage of wild and cultivated Solanum spp. was found to be associated with a new species of Phytophthora . The proposed novel species is named Phytophthora andina Adler & Flier, sp. nov. based on morphological characteristics, pathogenicity assays, mitochondrial DNA haplotyping, AFLP fingerprinting and nuclear and mitochondrial DNA sequence analyses. Isolates of P. andina ( n = 48) from the Andean highland tropics of Ecuador were collected from 1995 to 2006. Phytophothora andina is closely related to P. infestans and has semipapillate, ellipsoidal sporangia borne on sympodially branched sporangiophores. It is heterothallic and produces amphigynous antheridia. The species consists of several clonal lineages, including the EC‐2 and EC‐3 RFLP lineages, which were described previously as P. infestans . Approximately 75% of isolates react as compatibility type A2 when paired with an A1 compatibility type isolate of P. infestans . However, when A2 isolates from the Anarrhichomenum section of Solanum were paired in all combinations, viable oospores were obtained in several crosses, suggesting that there is a unique compatibility interaction in P. andina that is complementary to that described in P. infestans. Nuclear and mitochondrial sequence analysis supported the species designation of P. andina . This newly identified heterothallic pathogen shares a common ancestor with P. infestans and may have arisen from hybridization events with sister taxa in the Andes. DA - 2010/8// PY - 2010/8// DO - 10.1111/j.1365-3059.2010.02287.x VL - 59 IS - 4 SP - 613-625 SN - 1365-3059 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-77955022185&partnerID=MN8TOARS KW - pepino KW - Phytophthora infestans KW - potato KW - Solanum spp. KW - tomato KW - tree tomato ER - TY - JOUR TI - Genetic Structure of Phytophthora infestans Populations in China Indicates Multiple Migration Events AU - Guo, Liyun AU - Zhu, Xiao-Qiong AU - Hu, Chia-Hui AU - Ristaino, Jean Beagle T2 - PHYTOPATHOLOGY AB - One hundred isolates of Phytophthora infestans collected from 10 provinces in China between 1998 and 2004 were analyzed for mating type, metalaxyl resistance, mitochondrial DNA (mtDNA) haplotype, allozyme genotype, and restriction fragment length polymorphism (RFLP) with the RG-57 probe. In addition, herbarium samples collected in China, Russia, Australia, and other Asian countries were also typed for mtDNA haplotype. The Ia haplotype was found during the first outbreaks of the disease in China (1938 and 1940), Japan (1901, 1930, and 1931), India (1913), Peninsular Malaysia (1950), Nepal (1954), The Philippines (1910), Australia (1917), Russia (1917), and Latvia (1935). In contrast, the Ib haplotype was found after 1950 in China on both potato and tomato (1952, 1954, 1956, and 1982) and in India (1968 and 1974). Another migration of a genotype found in Siberia called SIB-1 (Glucose-6-phosphate isomerase [Gpi] 100/100, Peptidase [Pep] 100/100, IIa mtDNA haplotype) was identified using RFLP fingerprints among 72% of the isolates and was widely distributed in the north and south of China and has also been reported in Japan. A new genotype named CN-11 (Gpi 100/111, Pep 100/100, IIb mtDNA haplotype), found only in the south of China, and two additional genotypes (Gpi 100/100, Pep 100/100, Ia mtDNA haplotype) named CN-9 and CN-10 were identified. There were more diverse genotypes among isolates from Yunnan province than elsewhere. The SIB-1 (IIa) genotype is identical to those from Siberia, suggesting later migration of this genotype from either Russia or Japan into China. The widespread predominance of SIB-1 suggests that this genotype has enhanced fitness compared with other genotypes found. Movement of the pathogen into China via infected seed from several sources most likely accounts for the distribution of pathogen genotypes observed. MtDNA haplotype evidence and RFLP data suggest multiple migrations of the pathogen into China after the initial introduction of the Ia haplotype in the 1930s. DA - 2010/10// PY - 2010/10// DO - 10.1094/phyto-05-09-0126 VL - 100 IS - 10 SP - 997-1006 SN - 1943-7684 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-77958041881&partnerID=MN8TOARS KW - genetic diversity KW - late blight KW - mtDNA haplotypes ER - TY - JOUR TI - Experimental infection and co-infection of dogs with Anaplasma platys and Ehrlichia canis: hematologic, serologic and molecular findings AU - Gaunt, SD AU - Beall, MJ AU - Stillman, BA AU - Lorentzen, L AU - Diniz, PPVP AU - Chandrashekar, R AU - Breitschwerdt, EB T2 - Parasites & Vectors AB - Rhipicephalus sanguineus is a ubiquitous tick responsible for transmitting Ehrlichia canis and most likely Anaplasma platys to dogs, as either single or co-infections. The objective of this study was to assess the effects of either simultaneous or sequential experimental infections with E. canis and A. platys on hematological and serological parameters, duration of infection, and efficacy of doxycycline therapy in dogs infected with one or both organisms. Six dogs per group were either uninfected, A. platys infected, E. canis infected, A. platys and E. canis co-infected, A. platys infected and E. canis challenged or E. canis infected and A. platys challenged at day 112 post-infection (PI). Doxycycline treatment was initiated at 211 days PI, followed by dexamethasone immunosuppression beginning 410 days PI.Initially, transient decreases in hematocrit occurred in all groups infected with E. canis, but the mean hematocrit was significantly lower in the A. platys and E. canis co-infected group. All dogs except the controls developed marked thrombocytopenia after initial infection followed by gradually increased platelet counts by 112 days PI in groups with the single infections, while platelet counts remained significantly lower in the A. platys and E. canis co-infected group. Both sequential and simultaneous infections of A. platys and E. canis produced an enhanced humoral immune response to A. platys when compared to infection with A. platys alone. Likewise, co-infection with E. canis and A. platys resulted in a more persistent A. platys infection compared to dogs infected with A. platys only, but nearly all A. platys infected dogs became A. platys PCR negative prior to doxycycline treatment. E. canis infected dogs, whether single or co-infected, remained thrombocytopenic and E. canis PCR positive in blood for 420 days. When treated with doxycycline, all E. canis infected dogs became E. canis PCR negative and the thrombocytopenia resolved. Despite immunosuppression, neither A. platys nor E. canis DNA was PCR amplified from doxycycline-treated dogs.The results of this study demonstrate that simultaneous or sequential infection with A. platys and E. canis can alter various pathophysiological parameters in experimentally infected dogs, and because natural exposure to multiple tick-borne pathogens occurs frequently in dogs, awareness of co-infection is important in clinical practice. DA - 2010/// PY - 2010/// DO - 10.1186/1756-3305-3-33 VL - 3 IS - 1 SP - 33 J2 - Parasites Vectors LA - en OP - SN - 1756-3305 UR - http://dx.doi.org/10.1186/1756-3305-3-33 DB - Crossref ER - TY - JOUR TI - Benchmarking multi-rate codon models AU - Delport, W. AU - Scheffler, K. AU - Gravenor, M. B. AU - Muse, S. V. AU - Pond, S. K. T2 - PLoS One DA - 2010/// PY - 2010/// VL - 5 IS - 7 ER - TY - JOUR TI - Bartonella vinsonii subsp. berkhoffii and Bartonella henselae bacteremia in a father and daughter with neurological disease AU - Breitschwerdt, Edward B AU - Maggi, Ricardo G AU - Lantos, Paul M AU - Woods, Christopher W AU - Hegarty, Barbara C AU - Bradley, Julie M T2 - Parasites & Vectors AB - Bartonella vinsonii subsp. berkhoffii is an important, emerging, intravascular bacterial pathogen that has been recently isolated from immunocompetent patients with endocarditis, arthritis, neurological disease and vasoproliferative neoplasia. Vector transmission is suspected among dogs and wild canines, which are the primary reservoir hosts. This investigation was initiated to determine if pets and family members were infected with one or more Bartonella species. PCR and enrichment blood culture in Bartonella alpha Proteobacteria growth medium (BAPGM) was used to determine infection status. Antibody titers to B. vinsonii subsp. berkhoffii genotypes I-III and B. henselae were determined using a previously described indirect fluorescent antibody test. Two patients were tested sequentially for over a year to assess the response to antibiotic treatment. Intravascular infection with B. vinsonii subsp. berkhoffii genotype II and Bartonella henselae (Houston 1 strain) were confirmed in a veterinarian and his daughter by enrichment blood culture, followed by PCR and DNA sequencing. Symptoms included progressive weight loss, muscle weakness, lack of coordination (the father) and headaches, muscle pain and insomnia (the daughter). B. vinsonii subsp. berkhoffii genotype II was also sequenced from a cerebrospinal fluid BAPGM enrichment culture and from a periodontal swab sample. After repeated courses of antibiotics, post-treatment blood cultures were negative, there was a decremental decrease in antibody titers to non-detectable levels and symptoms resolved in both patients. B. vinsonii subsp. berkhoffii and B. henselae are zoonotic pathogens that can be isolated from the blood of immunocompetent family members with arthralgias, fatigue and neurological symptoms. Therapeutic elimination of Bartonella spp. infections can be challenging, and follow-up testing is recommended. An increasing number of arthropod vectors, including biting flies, fleas, keds, lice, sandflies and ticks have been confirmed or are suspected as the primary mode of transmission of Bartonella species among animal populations and may also pose a risk to human beings. DA - 2010/// PY - 2010/// DO - 10.1186/1756-3305-3-29 VL - 3 IS - 1 SP - 29 J2 - Parasites Vectors LA - en OP - SN - 1756-3305 UR - http://dx.doi.org/10.1186/1756-3305-3-29 DB - Crossref ER - TY - JOUR TI - Bacillary angiomatosis in an immunosuppressed dog AU - Yager, Julie A. AU - Best, Susan J. AU - Maggi, Ricardo G. AU - Varanat, Mrudula AU - Znajda, Nadine AU - Breitschwerdt, Edward B. T2 - Veterinary Dermatology AB - A dog being treated with immunosuppressive doses of prednisone and azathioprine for pancytopenia of unknown origin, developed, over a 2-week period, multiple erythematous nodular lesions in the skin including footpads. Skin samples revealed lesions identical to those of human bacillary angiomatosis (BA). The nodules were composed of multifocal proliferations of capillaries, each lined by protuberant endothelial cells. The capillary clusters were separated by an oedematous connective tissue, lightly infiltrated with degenerate inflammatory cells, including neutrophils and macrophages. Tissue sections stained with Warthin-Starry silver stain revealed large numbers of positively stained bacilli in the stromal tissue, most heavily concentrated around the proliferating capillaries. Lesions of vascular degeneration and inflammation were evident. Bartonella vinsonii subsp. berkhoffii genotype 1 was independently amplified and sequenced from the blood and the skin tissue. The pathognomonic nature of the histological lesions, demonstration of compatible silver-stained bacilli in the tissue, and identification of B. vinsonii subsp. berkhoffii in the blood and tissue indicates that this is most likely the aetiologic agent responsible for the lesions. Antibiotic therapy was successful in resolving the nodules. It would appear that B. vinsonii subsp berkhoffii, like Bartonella henselae and Bartonella quintana, has the rare ability to induce angioproliferative lesions, most likely in association with immunosuppression. The demonstration of lesions identical to those of human BA in this dog is further evidence that the full range of clinical manifestations of human Bartonella infection occurs also in canines. DA - 2010/3// PY - 2010/3// DO - 10.1111/j.1365-3164.2010.00879.x VL - 21 IS - 4 SP - 420–428 LA - en OP - SN - 0959-4493 1365-3164 UR - http://dx.doi.org/10.1111/j.1365-3164.2010.00879.x DB - Crossref ER - TY - JOUR TI - Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State AU - Lee, Tae-Jin AU - Pascuzzi, Pete E. AU - Settlage, Sharon B. AU - Shultz, Randall W. AU - Tanurdzic, Milos AU - Rabinowicz, Pablo D. AU - Menges, Margit AU - Zheng, Ping AU - Main, Dorrie AU - Murray, James A. H. AU - Sosinski, Bryon AU - Allen, George C. AU - Martienssen, Robert A. AU - Hanley-Bowdoin, Linda AU - Vaughn, Matthew W. AU - Thompson, William F. T2 - PLoS Genetics AB - DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about replication programs in plants. We used flow cytometry and tiling microarrays to profile DNA replication of Arabidopsis thaliana chromosome 4 (chr4) during early, mid, and late S phase. Replication profiles for early and mid S phase were similar and encompassed the majority of the euchromatin. Late S phase exhibited a distinctly different profile that includes the remaining euchromatin and essentially all of the heterochromatin. Termination zones were consistent between experiments, allowing us to define 163 putative replicons on chr4 that clustered into larger domains of predominately early or late replication. Early-replicating sequences, especially the initiation zones of early replicons, displayed a pattern of epigenetic modifications specifying an open chromatin conformation. Late replicons, and the termination zones of early replicons, showed an opposite pattern. Histone H3 acetylated on lysine 56 (H3K56ac) was enriched in early replicons, as well as the initiation zones of both early and late replicons. H3K56ac was also associated with expressed genes, but this effect was local whereas replication time correlated with H3K56ac over broad regions. The similarity of the replication profiles for early and mid S phase cells indicates that replication origin activation in euchromatin is stochastic. Replicon organization in Arabidopsis is strongly influenced by epigenetic modifications to histones and DNA. The domain organization of Arabidopsis is more similar to that in Drosophila than that in mammals, which may reflect genome size and complexity. The distinct patterns of association of H3K56ac with gene expression and early replication provide evidence that H3K56ac may be associated with initiation zones and replication origins. C2 - PMC2883604 DA - 2010/6/10/ PY - 2010/6/10/ DO - 10.1371/journal.pgen.1000982 VL - 6 IS - 6 SP - e1000982 J2 - PLoS Genet LA - en OP - SN - 1553-7404 UR - http://dx.doi.org/10.1371/journal.pgen.1000982 DB - Crossref ER - TY - JOUR TI - Trans-10, cis-12-conjugated linoleic acid alters hepatic gene expression in a polygenic obese line of mice displaying hepatic lipidosis AU - Ashwell, Melissa S. AU - Ceddia, Ryan P. AU - House, Ralph L. AU - Cassady, Joseph P. AU - Eisen, Eugene J. AU - Eling, Thomas E. AU - Collins, Jennifer B. AU - Grissom, Sherry F. AU - Odle, Jack T2 - JOURNAL OF NUTRITIONAL BIOCHEMISTRY AB - The trans-10, cis-12 isomer of conjugated linoleic acid (CLA) causes a rapid reduction of body and adipose mass in mice. In addition to changes in adipose tissue, numerous studies have reported alterations in hepatic lipid metabolism. Livers of CLA-fed mice gain mass, partly due to lipid accumulation; however, the precise molecular mechanisms are unknown. To elucidate these mechanisms, we examined fatty acid composition and gene expression profiles of livers from a polygenic obese line of mice fed 1% trans-10, cis-12-CLA for 14 days. Analysis of gene expression data led to the identification of 1393 genes differentially expressed in the liver of CLA-fed male mice at a nominal P value of .01, and 775 were considered significant using a false discovery rate (FDR) threshold of .05. While surprisingly few genes in lipid metabolism were impacted, pathway analysis found that protein kinase A (PKA) and cyclic adenosine monophosphate (cAMP) pathways signaling pathways were affected by CLA treatment and 98 of the 775 genes were found to be regulated by hepatocyte nuclear factor 4alpha, a transcription factor important in controlling liver metabolic status. DA - 2010/9// PY - 2010/9// DO - 10.1016/j.jnutbio.2009.06.013 VL - 21 IS - 9 SP - 848-855 SN - 1873-4847 KW - Gene expression KW - Mice KW - Liver, Conjugated linoleic acid KW - Obesity, Hepatic steatosis, Fatty liver ER - TY - JOUR TI - Synthesis of oligo(p-phenylene)-linked dyads containing free base, zinc(II) or thallium(III) porphyrins for studies in artificial photosynthesis AU - Taniguchi, Masahiko AU - Lindsey, Jonathan S. T2 - TETRAHEDRON AB - A series of (p-phenylene)n-linked meso-mesityl-substituted porphyrin dyads (n=2–4) was prepared via Suzuki coupling of zinc(II) and free base porphyrin building blocks. The resulting zinc(II)/free base porphyrin dyads were demetalated. The series of free base porphyrin dimers (n=1–4), four other porphyrin dimers (with p-phenylene, diphenylethyne or diphenylbutadiyne linkers; and aryl or tridec-7-yl meso substituents), and several benchmark monomers were converted to the thallium(III)chloride complexes under mild conditions. The collection of eight Tl(III)Cl/Tl(III)Cl dimers is designed for studies of ground-state hole-transfer processes and comparison with the excited-state energy- and hole-transfer processes of the corresponding Zn(II)/free base dyads. Altogether, 18 new porphyrin arrays and benchmark monomers have been prepared. DA - 2010/7/24/ PY - 2010/7/24/ DO - 10.1016/j.tet.2010.05.059 VL - 66 IS - 30 SP - 5549-5565 SN - 0040-4020 KW - Artificial photosynthesis KW - Porphyrin KW - Building block KW - Array KW - Electron transfer KW - Energy transfer KW - Hole transfer KW - Thallium KW - Zinc KW - Free base KW - Suzuki KW - Sonogashira ER - TY - JOUR TI - Suspected Needle Stick Transmission of Bartonella vinsonii subspecies berkhoffii to a Veterinarian AU - Oliveira, A.M. AU - Maggi, R.G. AU - Woods, C.W. AU - Breitschwerdt, E.B. T2 - Journal of Veterinary Internal Medicine AB - A 7-year-old male Newfoundland dog was referred to the North Carolina State University Veterinary Teaching Hospital (NCSU-VTH) for evaluation of multiple, diffuse cutaneous masses. Fine-needle aspiration yielded a population of round cells consistent with a histiocytic, lymphocytic, or highly undifferentiated epithelial neoplasm. Because of the poor prognosis associated with cutaneous disseminated cancers, the owner declined additional diagnostic evaluation and after discharge from the NCSU-VTH elected euthanasia. The dog was very fractious during aspiration of the cutaneous mass, and the veterinarian experienced a needle stick to the right index finger with the 22 G needle used for aspiration. Because ehrlichiosis was diagnosed serologically in the dog 5 months earlier, the Intracellular Pathogens Research Laboratory (IPRL) was consulted relative to the zoonotic risk of needle stick transmission of an Ehrlichia spp. Ehrlichia canis seroreactive dogs residing in the southeastern United States often are concurrently seroreactive to Bartonella vinsonii subsp. berkhoffii antigens and can be coinfected with both organisms,1 therefore the potential transmission of both of these alpha Proteobacteria was investigated. Bartonella and Ehrlichia spp. antibodies were determined by previously described immunofluorescence antibody assays (IFA), with titers ≥1 : 64 considered seroreactive.2 Using the Bartonella alpha Proteobacteria growth medium (BAPGM) diagnostic platform,3,4 polymerase chain reaction (PCR) was performed after direct extraction from blood and serum, after enrichment culture for at least 14 days (typically at 7 and at 14 days) and from subculture colonies, if visualized. Methods used for DNA extraction, conventional PCR targeting of the Bartonella 16S–23S intergenic spacer region, cloning, and sequencing have been described previously.5–8 Sequences were aligned and compared with GenBank sequences with AlignX software.a,5–8 Historically, the veterinarian had always been healthy. During the 1-year period before, and at the time of the needle stick (day 0), the veterinarian reported no headaches, fatigue, or other medical problems. On postinoculation day (PID) 5, when the 1st blood sample was obtained, there was no serological or molecular evidence to support Ehrlichia or Bartonella spp. exposure or infection. Specifically, B. vinsonii subsp. berkhoffii genotypes I, II, and III, Bartonella henselae, and E. canis antibodies were not detected, Ehrlichia spp. DNA was not amplified from the extracted blood sample and Bartonella spp. DNA was not amplified from any of the samples generated as a component of the BAPGM diagnostic platform (Table 1). By PID 34, the veterinarian reported frequent headaches (near daily for the previous week), fatigue, and intermittent paresthesias in the left arm in focal, nondermatomal areas. B. vinsonii subsp. berkhoffii genotype I was amplified and sequenced after direct extraction of DNA from both PID 34 acid-citrate-dextrose and ethylenediaminetetraacetic acid-anticoagulated blood tubes, but PCR from both BAPGM enrichment cultures and subcultures was negative and the patient had not seroconverted to any Bartonella sp. antigen. Repeated blood culture on PID 81 resulted in amplification and sequencing of B. vinsonii subsp. berkhoffii genotype I from the BAPGM enrichment culture and there was an indication that the patient was generating an antibody response to B. vinsonii subsp. berkhoffii genotypes I and III. Subsequent serological testing confirmed seroconversion to B. vinsonii subsp. berkhoffii genotypes I and III (≥4-fold rise in antibody titer). For serum samples obtained on PIDs 97 and 123, antibody titers remained unchanged, but all BAPGM platform PCR results were negative. Because of continued headaches and fatigue, the patient was evaluated by an infectious disease physician. Serum biochemical profile results were within reference ranges and neither B. henselae or Bartonella quintana IgM or IgG antibodies were detected. On PID 138, treatment with doxycycline (100 mg PO q12h) and rifampin (300 mg PO q12h) for 6 weeks was instituted by the attending physician. During the first 2 weeks after starting antibiotics, the patient reported a substantial increase in the severity and frequency of fatigue and headaches, which were accompanied by occasional episodes of dizziness and a single episode of epistaxis. After completion of the antibiotic treatment, all clinical signs resolved and the patient has remained healthy during a 1-year follow-up period. BAPGM platform PCR results obtained on PIDs 144, 180, 206, and 234 were negative, and antibodies to B. vinsonii subsp. berkhoffii genotypes I decreased to the screening dilution of 1 : 16 and genotype III antibodies were no longer detectable (ie, there was no organism fluorescence at the standard screening dilution of 1 : 16) in the patient's serum samples. The patient did not seroconvert to E. canis antigens and Ehrlichia sp. DNA was not amplified from any blood sample. A single tumor aspiration cytology slide represented the only diagnostic sample obtained from the dog at the time of examination. Therefore, cells were retrospectively scraped with a scalpel blade from the Wright-Giemsa stained microscope slide into a sterile vial, DNA was extracted and B. vinsonii subsp. berkhoffii genotype III was amplified and sequenced. Despite multiple cloning attempts, B. vinsonii subsp. berkhoffii genotype I (the genotype detected in the patient's blood on 2 independent occasions) was not sequenced from the extracted cytological specimen. We cannot rule out the possibility that amplification of B. vinsonii subsp. berkhoffii genotype III DNA from the cytology slide represents DNA carryover during slide processing in the laboratory rather than the presence of this bacteria in the dog at the time of cytological sampling.9 B. vinsonii subsp. berkhoffii initially was isolated from a dog with endocarditis in 1993, after which 4 B. vinsonii subsp. berkhoffii 16S–23S intergenic spacer region genotypes were described in dogs, coyotes, foxes, and humans.10 All 4 genotypes have been reported in dogs in association with endocarditis and a spectrum of other clinical manifestations.11 Dogs are the primary reservoir hosts for B. vinsonii subsp. berkhoffii, which is an important emerging zoonotic pathogen.5–7,12,13 The veterinarian in this study experienced a needle stick while obtaining a fine-needle aspiration sample, after which clinical signs, including headaches, fatigue, and intermittent paresthesias, developed. As the veterinarian had not experienced any of these clinical signs previously and because the clinical signs resolved after antibiotic treatment, it seems possible that infection with B. vinsonii subsp. berkhoffii caused or contributed to the illness. The patient seroconverted to B. vinsonii subsp. berkhoffii genotypes I and III and antibody titers to these 2 genotypes persisted between PIDs 97 through 180. As reported previously for B. vinsonii subsp. berkhoffii infection in dogs, this patient became nonseroreactive after being treated with antibiotics.14 As this individual did not produce detectable antibodies to B. vinsonii subsp. berkhoffii genotype II or to B. henselae antigens, there appeared to be a substantial degree of specificity in the serological response after the needle stick; however, serological cross reactivity between genotypes I and III cannot be ruled out. Previous studies from our laboratory indicate that approximately half of human patients infected with a Bartonella sp. do not have detectable IFA antibodies, whereas other patients are broadly reactive against a panel of Bartonella spp. antigens.5,6 As B. vinsonii subsp. berkhoffii genotype IV has not been successfully isolated, serology could not be performed against this genotype.11 In this veterinarian, active infection with B. vinsonii subsp. berkhoffii genotype I was confirmed by amplification and sequencing of DNA directly from 2 blood samples obtained on PID 34 and subsequently from a BAPGM enrichment blood culture on PID 81, which would reflect growth of the bacteria in the liquid culture medium. B. vinsonii subsp. berkhoffii genotype I most often infects dogs and coyotes,1 but has been reported in 2 human patients from the United States.3 Based upon the cumulative testing experience with animal or human patient samples in the IPRL, genotype II has been most frequently amplified and sequenced from blood samples derived from cats, dogs, and people 5–8,12,13 whereas genotypes I or III are only rarely found. Genotype III was first described in a human patient with endocarditis from France 15 and was subsequently isolated from a military working dog that originated from Germany and was subsequently diagnosed with endocarditis while stationed in Texas.16 Genotype III also has been sequenced from gray foxes from California,17 from dogs in Greece and Italy,18 from dogs in China,19 and from feral swine and foxes in the southeastern United States (A. Beard, R. Maggi, and E. Breitschwerdt, unpublished data). Presumably because of technical limitations, we were only able to confirm infection with genotype III in the small quantity of DNA that was obtained from the dog's cytology specimen. Alternatively, genotype III DNA may have been because of carryover in the laboratory.9 Based upon the patient's pattern of seroconversion, it is possible that 2 genotypes were transmitted to the veterinarian by needle inoculation. Alternatively, we cannot rule out the possibility of a switch from genotype III in the dog to genotype I in the patient, perhaps induced by immune pressure on the bacteria. However, the 16S–23S intergenic spacer region does not code for proteins, and in previous studies from our laboratory sequential passage of B. vinsonii subsp. berkhoffii genotype I in BAPGM did not result in a change in genotype.10 In addition, differences in the amino acid sequence-based alignments of the phage-associated protein 31 of B. vinsonii subsp. berkhoffii genotypes I and III 10 also suggest that a switch of genotype is unlikely. Simultaneous infection with more than 1 Bartonella sp. or genotype has been reported in dogs, rodents, and human beings.5,6,11,20 However, molecular documentation of a single Bartonella sp. in diagnostic samples from dogs and human patients remains technically challenging, and documentation of coinfection with more than 1 Bartonella spp. in patient samples is more difficult.18,20 It is becoming increasingly evident that dogs can serve as a source for human infection with B. vinsonii subsp. berkhoffii. Recently, dog bite transmission of B. vinsonii to a child in France was inferred based upon serological testing.21 Also, B. vinsonii subsp. berkhoffii genotypes I and II have been sequenced from dog saliva.22 Although our patient had cat and dog contact, this veterinarian reported no history of animal scratches or bites in the 24 months before or during the follow-up period after the accidental needle stick. Obviously, other modes of transmission (eg, arthropod exposure) are possible, but this individual rarely participated in outdoor activities. A serosurvey from the southeastern United States identified exposure to fleas, ticks, cattle, and a rural environment as risk factors associated with B. vinsonii subsp. berkhoffii seroreactivity in dogs.1 The dog in this report lived in a rural environment, was regularly infested with ticks and fleas, and had historically been treated for infection with an Ehrlichia sp. In dogs experimentally infected with E. canis, there was no serological cross-reactivity with B. vinsonii subsp. berkhoffii antigens.1 As B. vinsonii subsp. berkhoffii antibodies were found in 36–42% of E. canis seroreactors,1 we investigated the potential transmission of both organisms to this veterinarian. Five days after the needle stick, the veterinarian remained asymptomatic and there was no serologic, microbiologic, or molecular evidence of Bartonella spp. infection. Subsequently, headaches, numbness, and parethesias in the extremities developed. These clinical signs have been described previously in a small number of immunocompetent persons infected with B. vinsonii subsp. berkhoffii or B. henselae.5–7 After initiation of antibiotic treatment, this patient had 1 episode of epistaxis, a rarely reported clinical sign in cat scratch disease patients and a clinical sign associated with bartonellosis in dogs.23 If the mode of transmission was because of the needle stick, this patient required approximately 12 weeks before seroconversion was detected. Although seroconversion may have been delayed because of a low-dose inoculum, there are minimal data that define the pattern of seroconversion after transmission of any Bartonella spp. to a human. In this patient, we were fortunate to have access to 9 serum samples, spanning PID 5 through PID 234, which were all retested blindly by the same research technician at the same time, and with the same conjugate and antigen preparations. This was done to generate the most consistent serological comparisons possible. Because all known Bartonella spp. are vector-transmitted blood-borne pathogens, inadvertent transmission by needle stick or by blood transfusion seems plausible. B. henselae was successfully isolated from units of human blood after experimental inoculation and after storage at 4°C for 35 days.24 On an ultrastructural basis, the same research group implicated infection with a Bartonella spp. in an aplastic anemia patient, who died after receiving multiple red blood cell transfusions.25 At the NCSU-VTH, canine and feline blood donors are routinely screened using the BAPGM platform for evidence of Bartonella sp. infection. As evolving evidence indicates that there are numerous Bartonella spp. that have coevolved as highly adapted intravascular and intraerythrocytic organisms in pets and numerous wildlife species, animal health professionals should exercise special caution when obtaining, handling, or processing diagnostic specimens derived from animals. In conclusion, the clinical history as well as serological and molecular microbiological findings suggest the possibility of needle stick transmission of B. vinsonii subsp. berkhoffii genotypes I and III to this veterinarian. After administration of antibiotics, all clinical signs resolved, B. vinsonii subsp. berkhoffii antibodies decreased to nondiagnostic levels and repeated enrichment blood cultures were PCR negative. a Vector NTI Suite 6.0, InforMax Inc, Bethesda, MD We thank Julie Bradley for serological testing, Barbara Hegarty for preparation of Ehrlichia and Bartonella spp. antigens, and Tonya Lee for editorial assistance. This research was supported in part by a grant from the American College of Veterinary Internal Medicine Foundation and by the State of North Carolina. The data in this report were not presented previously. Disclosure : In conjunction with Dr Sushama Sontakke and North Carolina State University, Dr Breitschwerdt holds US Patent No. 7,115,385; Media and Methods for Cultivation of Microorganisms, which was issued October 3, 2006. He is the chief scientific officer for Galaxy Diagnostics, a newly formed company that provides diagnostic testing for the detection of Bartonella species infection in animals and in human patient samples. Dr Ricardo Maggi is the Scientific Technical Advisor and Laboratory Director for Galaxy Dx. DA - 2010/8/2/ PY - 2010/8/2/ DO - 10.1111/j.1939-1676.2010.0563.x VL - 24 IS - 5 SP - 1229-1232 LA - en OP - SN - 0891-6640 UR - http://dx.doi.org/10.1111/j.1939-1676.2010.0563.x DB - Crossref ER - TY - JOUR TI - Proteomic and Bioinformatic Analysis of the Root-Knot Nematode Meloidogyne hapla: The Basis for Plant Parasitism AU - Mbeunkui, Flaubert AU - Scholl, Elizabeth H. AU - Opperman, Charles H. AU - Goshe, Michael B. AU - Bird, David McK. T2 - Journal of Proteome Research AB - On the basis of the complete genome sequence of the root-knot nematode Melodogyne hapla, we have deduced and annotated the entire proteome of this plant-parasite to create a database of 14,420 proteins. We have made this database, termed HapPep3, available from the Superfamily repository of model organism proteomes (http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY). To experimentally confirm the HapPep3 assignments using proteomics, we applied a data-independent LC/MS(E) analysis to M. hapla protein extracts fractionated by SDS-PAGE. A total of 516 nonredundant proteins were identified with an average of 9 unique peptides detected per protein. Some proteins, including examples with complex gene organization, were defined by more than 20 unique peptide matches, thus, providing experimental confirmation of computational predictions of intron/exon structures. On the basis of comparisons of the broad physicochemical properties of the experimental and computational proteomes, we conclude that the identified proteins reflect a true and unbiased sampling of HapPep3. Conversely, HapPep3 appears to broadly cover the protein space able to be experimentally sampled. To estimate the false discovery rate, we queried human, plant, and bacterial databases for matches to the LC/MS(E)-derived peptides, revealing fewer than 1% of matches, most of which were to highly conserved proteins. To provide a functional comparison of the acquired and deduced proteomes, each was subjected to higher order annotation, including comparisons of Gene Ontology, protein domains, signaling, and localization predictions, further indicating concordance, although those proteins that did deviate seem to be highly significant. Approximately 20% of the experimentally sampled proteome was predicted to be secreted, and thus potentially play a role at the host-parasite interface. We examined reference pathways to determine the extent of proteome similarity of M. hapla to that of the free-living nematode, Caenorhabditis elegans, revealing significant similarities and differences. Collectively, the analyzed protein set provides an initial foundation to experimentally dissect the basis of plant parasitism by M. hapla. DA - 2010/10// PY - 2010/10// DO - 10.1021/pr1006069 VL - 9 IS - 10 SP - 5370–5381 SN - 1535-3893 1535-3907 UR - http://dx.doi.org/10.1021/pr1006069 KW - LC/MSE KW - plant-parasite KW - nematode KW - data-independent acquisition KW - computational proteome ER - TY - JOUR TI - Prevention of endemic canine vector-borne diseases using imidacloprid 10% and permethrin 50% in young dogs: A longitudinal field study AU - Otranto, D. AU - de Caprariis, D. AU - Lia, R.P. AU - Tarallo, V. AU - Lorusso, V. AU - Testini, G. AU - Dantas-Torres, F. AU - Latrofa, S. AU - Diniz, P.P.V.P. AU - Mencke, N. AU - Maggi, R.G. AU - Breitschwerdt, E. AU - Capelli, G. AU - Stanneck, D. T2 - Veterinary Parasitology AB - Canine vector-borne diseases (CVBDs) are highly prevalent and increasing in distribution worldwide. A longitudinal study was conducted in southern Italy to determine the incidence of and protection against CVBD-causing pathogens in dogs treated with a combination of imidacloprid 10% and permethrin 50% (ImPer). One hundred eleven autochthonous young dogs were divided into group A (n = 63) and group B (n = 48), both groups containing dogs positive and negative for one or more CVBD-causing pathogens. Additionally, 10 naïve male beagles were introduced in each group in May 2008. Group A was treated with ImPer on day 0 and every 21 ± 2 days whereas group B was left untreated. Blood and skin samples were collected at baseline (March–April 2008) and at the first, second and third follow-up times (July and October 2008 and April 2009). Bone marrow was sampled at baseline and at the third follow-up. Serological, cytological and molecular tests were performed to detect Anaplasma platys, Babesia spp., Bartonella spp., Dirofilaria immitis, Ehrlichia canis, Hepatozoon canis and Leishmania infantum. Ectoparasites (fleas, ticks, and sand flies) were monitored throughout the study. The baseline prevalence of CVBDs was 39.6% with 44 dogs positive for at least one pathogen. A. platys (27.5%) and Babesia spp. (15.6%) were the most prevalent species and co-infections with up to two pathogens were detected in 16 (14.7%) individuals. At the end of the evaluation period, there was a 90.7% reduction in overall CVBD incidence density rate (IDR) in group A, as following: 100% reduction in L. infantum; 94.6% in E. canis; 94.4% in Babesia spp.; and 81.8% in A. platys. Initially positive treated dogs showed significantly lower pathogen prevalence at the third follow-up than untreated ones. At the end of the evaluation period, 8 of the 10 untreated beagles were infected with at least one pathogen whereas one of the treated beagles was A. platys positive at a single time point (second follow-up). Overall efficacy against ticks was 97.9%. In October 2009, samples were collected from the remaining 83 dogs (44 from group A and 39 from group B) to investigate the annual incidence of CVBDs in the same, at this time untreated, dog population. A high year incidence for tick-borne diseases (78.1%) and for L. infantum (13.6%) was detected in dogs from group A, seven months after the treatment had been withdrawn. The results demonstrate that ImPer preventive treatment against arthropods protects autochthonous and naïve beagle dogs against CVBD-causing pathogens. DA - 2010/9// PY - 2010/9// DO - 10.1016/j.vetpar.2010.05.017 VL - 172 IS - 3-4 SP - 323-332 J2 - Veterinary Parasitology LA - en OP - SN - 0304-4017 UR - http://dx.doi.org/10.1016/j.vetpar.2010.05.017 DB - Crossref KW - Canine vector-borne diseases KW - Anaplasma platys KW - Babesia KW - Ehrlichia canis KW - Hepatozoon canis KW - Leishmania infantum KW - Prevention KW - Imidacloprid KW - Permethrin ER - TY - JOUR TI - Prevalence of Selected Vector-borne Organisms and Identification of Bartonella Species DNA in North American River Otters (Lontra canadensis) AU - Chinnadurai, Sathya K. AU - Birkenheuer, Adam J. AU - Blanton, Hunter L. AU - Maggi, Ricardo G. AU - Belfiore, Natalia AU - Marr, Henry S. AU - Breitschwerdt, Edward B. AU - Stoskopf, Michael K. T2 - JOURNAL OF WILDLIFE DISEASES AB - Trapper-killed North American river otters (Lontra canadensis) in North Carolina, USA, were screened for multiple vector-borne bacteria known to be pathogenic to mammals. Blood was collected from 30 carcasses in 2006, from 35 in 2007, and from one live otter in 2008. Samples were screened using conventional polymerase chain reaction (PCR) tests for DNA from Bartonella spp., Ehrlichia spp., and spotted fever group Rickettsia spp. All samples were negative for Rickettsia spp. Twelve of 30 samples from 2006 produced amplicons using the assay designed to detect Ehrlichia spp., but sequencing revealed that the amplified DNA fragment was from a novel Wolbachia sp., thought to be an endosymbiote of a Dirofilaria sp. Between 2006 and 2007, DNA from a novel Bartonella sp. was detected in 19 of 65 animals (29%). Blood from one live otter captured in 2008 was found positive for this Bartonella sp. by both PCR and culture. The pathogenicity of this Bartonella species in river otters or other mammals is unknown. DA - 2010/7// PY - 2010/7// DO - 10.7589/0090-3558-46.3.947 VL - 46 IS - 3 SP - 947-950 SN - 1943-3700 KW - Bartonella KW - disease KW - Ehrlichia KW - Lontra canadensis KW - Ricketisia KW - river otter ER - TY - JOUR TI - Immunization with the Haemophilus ducreyi Hemoglobin Receptor HgbA with Adjuvant Monophosphoryl Lipid A Protects Swine from a Homologous but Not a Heterologous Challenge AU - Fusco, William G. AU - Afonina, Galyna AU - Nepluev, Igor AU - Cholon, Deborah M. AU - Choudhary, Neelima AU - Routh, Patricia A. AU - Almond, Glenn W. AU - Orndorff, Paul E. AU - Staats, Herman AU - Hobbs, Marcia M. AU - Leduc, Isabelle AU - Elkins, Christopher T2 - INFECTION AND IMMUNITY AB - Haemophilus ducreyi, the etiological agent of chancroid, has a strict requirement for heme, which it acquires from its only natural host, humans. Previously, we showed that a vaccine preparation containing the native hemoglobin receptor HgbA purified from H. ducreyi class I strain 35000HP (nHgbAI) and administered with Freund's adjuvant provided complete protection against a homologous challenge. In the current study, we investigated whether nHgbAI dispensed with monophosphoryl lipid A (MPL), an adjuvant approved for use in humans, offered protection against a challenge with H. ducreyi strain 35000HP expressing either class I or class II HgbA (35000HPhgbAI and 35000HPhgbAII, respectively). Pigs immunized with the nHgbAI/MPL vaccine were protected against a challenge from homologous H. ducreyi strain 35000HPhgbAI but not heterologous strain 35000HPhgbAII, as evidenced by the isolation of only strain 35000HPhgbAII from nHgbAI-immunized pigs. Furthermore, histological analysis of the lesions showed striking differences between mock-immunized and nHgbAI-immunized animals challenged with strains 35000HPhgbAI but not those challenged with strain 35000HPhgbAII. Mock-immunized pigs were not protected from a challenge by either strain. The enzyme-linked immunosorbent assay (ELISA) activity of the nHgbAI/MPL antiserum was lower than the activity of antiserum from animals immunized with the nHgbAI/Freund's vaccine; however, anti-nHgbAI from both studies bound whole cells of 35000HPhgbAI better than 35000HPhgbAII and partially blocked hemoglobin binding to nHgbAI. In conclusion, despite eliciting lower antibody ELISA activity than the nHgbAI/Freund's, the nHgbAI/MPL vaccine provided protection against a challenge with homologous but not heterologous H. ducreyi, suggesting that a bivalent HgbA vaccine may be needed. DA - 2010/9// PY - 2010/9// DO - 10.1128/iai.00217-10 VL - 78 IS - 9 SP - 3763-3772 SN - 1098-5522 ER - TY - JOUR TI - Human Coinfection with Bartonella henselae and Two Hemotropic Mycoplasma Variants Resembling Mycoplasma ovis AU - Sykes, J. E. AU - Lindsay, L. L. AU - Maggi, R. G. AU - Breitschwerdt, E. B. T2 - Journal of Clinical Microbiology AB - Two variants of an organism resembling the ovine hemoplasma, Mycoplasma ovis, were detected by PCR in blood samples from a veterinarian in Texas. Coinfection with similar variants has been described in sheep. This represents the first report of human infection with this organism. The veterinarian was coinfected with Bartonella henselae. DA - 2010/8/11/ PY - 2010/8/11/ DO - 10.1128/jcm.01029-10 VL - 48 IS - 10 SP - 3782-3785 J2 - Journal of Clinical Microbiology LA - en OP - SN - 0095-1137 UR - http://dx.doi.org/10.1128/JCM.01029-10 DB - Crossref ER - TY - JOUR TI - Grafting Fraser fir (Abies fraseri): Effect of grafting date, shade, and irrigation AU - Hibbert-Frey, H. AU - Frampton, J. AU - Blazich, F. A. AU - Hinesley, L. E. T2 - HortScience DA - 2010/// PY - 2010/// VL - 45 IS - 4 SP - 617-620 ER - TY - JOUR TI - Genomics of forest and ecosystem health in the Fagaceae: meeting report AU - Kremer, Antoine AU - Sederoff, Ronald AU - Wheeler, Nicholas T2 - TREE GENETICS & GENOMES AB - A summary of 35 keynote, invited and volunteer papers delivered at a recent international conference is provided along with web links to PDFs of those presentations. Major conference themes targeted Genomic Tool Development for the Fagaceae and Application of Genomic Resources. The meeting provided a venue for reviewing the rapidly expanding knowledge base on Fagaceae genomics and for developing collaborations between scientists from Europe and North America. DA - 2010/10// PY - 2010/10// DO - 10.1007/s11295-010-0277-y VL - 6 IS - 5 SP - 815-820 SN - 1614-2942 KW - Fagaceae KW - Genomics ER - TY - JOUR TI - Factors Associated with the Acquisition and Severity of Gestational Listeriosis AU - Suyemoto, M. Mitsu AU - Spears, Patricia A. AU - Hamrick, Terri S. AU - Barnes, Jill A. AU - Havell, Edward A. AU - Orndorff, Paul E. T2 - PLOS ONE AB - Gravid mammals are more prone to listeriosis than their nongravid counterparts. However, many features of the disease in gravid animals are not well defined. We determined, in mice, that increased susceptibility to lethal infection following oral inoculation begins surprisingly early in pregnancy and extends through embryonic development. Pregnancy did not demonstrably increase the spread of listeriae from the intestine to the liver and spleen in the initial 96 h period post inoculation. Consequently, it appeared that gravid animals were competent to contain an enteric infection, but in those instances where escape did occur, a lethal outcome was more likely. Interestingly, colonic colonization level and prevalence, measured 96 h post inoculation, was significantly higher in gravid individuals. In terms of human risk factors for listeriosis, our results suggest that the window of listeriosis susceptibility afforded by pregnancy may be open longer than previously appreciated. Our results also suggest that while gravid animals are competent to contain an enteric infection, enteric carriage rate may be more of a factor in defining disease incidence than previously considered. DA - 2010/9/27/ PY - 2010/9/27/ DO - 10.1371/journal.pone.0013000 VL - 5 IS - 9 SP - SN - 1932-6203 ER - TY - JOUR TI - Evaluation of peptide- and recombinant protein-based assays for detection of anti-Ehrlichia ewingii antibodies in experimentally and naturally infected dogs AU - O'Connor, Thomas P. AU - Saucier, Jill M. AU - Daniluk, Daryn AU - Stillman, Brett A. AU - Krah, Regis AU - Rikihisa, Yasuko AU - Xiong, Qingming AU - Yabsley, Michael J. AU - Adams, Dustin S. AU - Diniz, Pedro Paulo V P AU - Breitschwerdt, Edward B. AU - Gaunt, Stephen D. AU - Chandrashekar, Ramaswamy T2 - American Journal of Veterinary Research AB - Abstract Objective —To evaluate microtiter-plate format ELISAs constructed by use of different diagnostic targets derived from the Ehrlichia ewingii p28 outer membrane protein for detection of E ewingii antibodies in experimentally and naturally infected dogs. Sample Population —Serum samples from 87 kenneled dogs, 9 dogs experimentally infected with anti- E ewingii , and 180 potentially naturally exposed dogs from Missouri. Procedures —The capacities of the synthetic peptide and truncated recombinant protein to function as detection reagents in ELISAs were compared by use of PCR assay, western blot analysis, and a full-length recombinant protein ELISA. Diagnostic targets included an E ewingii synthetic peptide (EESP) and 2 recombinant proteins: a full-length E ewingii outer membrane protein (EEp28) and a truncated E ewingii outer membrane protein (EETp28) Results —A subset of Ehrlichia canis -positive samples cross-reacted in the EEp28 ELISA; none were reactive in the EESP and EETp28 ELISAs. The EESP- and EETp28-based ELISAs detected E ewingii seroconversion at approximately the same time after infection as the EEp28 ELISAs. In afield population, each of the ELISAs identified the same 35 samples as reactive and 27 samples as nonreactive. Anaplasma and E can is peptides used in a commercially available ELISA platform did not detect anti- E ewingii antibodies in experimentally infected dogs. Conclusions and Clinical Relevance —The EESP and EETp28 ELISAs were suitable for specifically detecting anti- E ewingii antibodies in experimentally and naturally infected dogs. [ Am J Vet Res 2010;71:1195-1200) DA - 2010/10// PY - 2010/10// DO - 10.2460/ajvr.71.10.1195 VL - 71 IS - 10 SP - 1195–1200 SN - 0002-9645 UR - http://dx.doi.org/10.2460/ajvr.71.10.1195 ER - TY - JOUR TI - Correcting the bias of empirical frequency parameter estimators in codon models AU - Pond, S. K. AU - Delport, W. AU - Muse, S. V. AU - Scheffler, K. T2 - PLoS One DA - 2010/// PY - 2010/// VL - 5 IS - 7 ER - TY - JOUR TI - Clonal evaluation for fusiform rust disease resistance: effects of pathogen virulence and disease escape AU - Kayihan, Goegce C. AU - Nelson, C. Dana AU - Huber, Dudley A. AU - Amerson, Henry V. AU - White, Timothy L. AU - Davis, John M. T2 - CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE AB - We evaluated the precision of phenotypic classification for fusiform rust resistance of Pinus taeda L. in a clonally propagated population segregating for the pathotype-specific resistance gene Fr1. In all marker-defined Fr1/fr1 clones screened with low complexity or ambient inoculum, marker–trait cosegregation was complete with no exceptions. Uncommon exceptions (4 of 30) in which marker-defined Fr1/fr1 clones screened with high complexity inoculum were diseased were probably due to a low frequency of spores virulent to Fr1 resistance. Marker–trait cosegregation for fr1/fr1 clones was less reliable, as all ramets of a few clones (5 of 29, 3 of 25, and 4 of 16) remained disease-free with low complexity, high complexity, or ambient inoculum, respectively. We termed disease-free fr1/fr1 ramets “escapes”, since the genetics of the host–pathogen interaction predicted them to be diseased. For nonmarker-defined materials, we considered escapes to be disease-free ramets within clones that had at least one diseased ramet. Narrow-sense heritability estimates for escape rate were 29% and 23% for the low and high complexity inocula, respectively, suggesting that genetic variation in the host is an important component of this resistance mechanism. DA - 2010/6// PY - 2010/6// DO - 10.1139/x10-045 VL - 40 IS - 6 SP - 1042-1050 SN - 0045-5067 ER - TY - JOUR TI - Adaptation in a Mouse Colony Monoassociated with Escherichia coli K-12 for More than 1,000 Days AU - Lee, Sean M. AU - Wyse, Aaron AU - Lesher, Aaron AU - Everett, Mary Lou AU - Lou, Linda AU - Holzknecht, Zoie E. AU - Whitesides, John F. AU - Spears, Patricia A. AU - Bowles, Dawn E. AU - Lin, Shu S. AU - Tonkonogy, Susan L. AU - Orndorff, Paul E. AU - Bollinger, R. Randal AU - Parker, William T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - Although mice associated with a single bacterial species have been used to provide a simple model for analysis of host-bacteria relationships, bacteria have been shown to display adaptability when grown in a variety of novel environments. In this study, changes associated with the host-bacterium relationship in mice monoassociated with Escherichia coli K-12 over a period of 1,031 days were evaluated. After 80 days, phenotypic diversification of E. coli was observed, with the colonizing bacteria having a broader distribution of growth rates in the laboratory than the parent E. coli. After 1,031 days, which included three generations of mice and an estimated 20,000 generations of E. coli, the initially homogeneous bacteria colonizing the mice had evolved to have widely different growth rates on agar, a potential decrease in tendency for spontaneous lysis in vivo, and an increased tendency for spontaneous lysis in vitro. Importantly, mice at the end of the experiment were colonized at an average density of bacteria that was more than 3-fold greater than mice colonized on day 80. Evaluation of selected isolates on day 1,031 revealed unique restriction endonuclease patterns and differences between isolates in expression of more than 10% of the proteins identified by two-dimensional electrophoresis, suggesting complex changes underlying the evolution of diversity during the experiment. These results suggest that monoassociated mice might be used as a tool for characterizing niches occupied by the intestinal flora and potentially as a method of targeting the evolution of bacteria for applications in biotechnology. DA - 2010/7// PY - 2010/7// DO - 10.1128/aem.00358-10 VL - 76 IS - 14 SP - 4655-4663 SN - 0099-2240 ER - TY - JOUR TI - The potential for caspases in drug discovery AU - MacKenzie, S. H. AU - Schipper, J. L. AU - Clark, A. C. T2 - Current Opinion in Drug Discovery & Development DA - 2010/// PY - 2010/// VL - 13 IS - 5 SP - 568-576 ER - TY - JOUR TI - Structural studies of sparsely substituted synthetic chlorins and phorbines establish benchmarks for changes in the ligand core and framework of chlorophyll macrocycles AU - Taniguchi, Masahiko AU - Mass, Olga AU - Boyle, Paul D. AU - Tang, Qun AU - Diers, James R. AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - JOURNAL OF MOLECULAR STRUCTURE AB - Understanding the changes in molecular structure of tetrapyrrole macrocycles upon derivatization of the organic framework is essential for diverse studies ranging from metal complexation to formation of supramolecular assemblies. New, sparsely substituted free base chlorin, 17-oxochlorin, phorbine and 131-oxophorbine macrocycles provide benchmarks for naturally occurring hydroporphyrins and have been examined here by X-ray crystallography, resonance Raman spectroscopy, and density functional theoretical (DFT) calculations. The macrocycles contain no substituents other than a geminal-dimethyl group attached to the reduced, pyrroline ring. The X-ray studies indicate that the benchmark compounds exhibit only slight distortion from planarity, which increases along the series porphine < chlorin < oxochlorin < phorbine < oxophorbine. The elongated CβCβ bond distance due to sp3 versus sp2 hybridization in the pyrroline ring (ring D) of the (oxo)chlorins and (oxo)phorbines (1.52–1.54 Å) versus that of porphine (1.35 Å) is accompanied by altered bond angles in ring D. Introduction of ring E (exocyclic ring) in a chlorin to give the phorbine or oxophorbine causes alteration of the bond angles at many sites in the framework of the macrocycle; for example, the bond angles of N3C14C15 in the (oxo)phorbine are widened by ∼11° compared to those of porphine or the analogous sparsely substituted chlorin. As a result, the shape of the macrocycle core changes along the series of porphine (nearly square), (oxo)chlorin (kite-shaped), and (oxo)phorbine (right-angled trapezoid), and the core size increases in the order porphine < phorbine ∼ oxophorbine < oxochlorin ∼ chlorin. Comparison of the bond distances and angles in ring E of the phorbine versus oxophorbine indicates that the shortening of the C13C131 bond owing to the presence of the oxo-group is quite small, only 0.024 Å; thus, the unsymmetrical structure of ring E does not appear to be due to conjugation with the C131O group but may be a characteristic feature of the (oxo)phorbine framework. The X-ray data further indicate that the lengths of the oxochlorin C17O and oxophorbine C131O groups are essentially identical, a result also predicted by DFT calculations. Regardless, the observed frequencies for the stretching vibrations of the C17O (1721 cm−1) and C131O (1701 cm−1) groups are different and suggest that conjugation of the latter group with the π-system of the macrocycle is greater than that of the former group. Collectively, the studies provide new insights into the individual factors that give rise to the overall structural characteristics of various macrocycles. DA - 2010/8/27/ PY - 2010/8/27/ DO - 10.1016/j.molstruc.2010.05.035 VL - 979 IS - 1-3 SP - 27-45 SN - 1872-8014 KW - Chlorophyll KW - Chlorin KW - Phorbine KW - Isocyclic ring KW - Chiral volume KW - Aromaticity ER - TY - JOUR TI - Stable synthetic bacteriochlorins overcome the resistance of melanoma to photodynamic therapy AU - Mroz, Pawel AU - Huang, Ying-Ying AU - Szokalska, Angelika AU - Zhiyentayev, Timur AU - Janjua, Sahar AU - Nifli, Artemissia-Phoebe AU - Sherwood, Margaret E. AU - Ruzie, Christian AU - Borbas, K. Eszter AU - Fan, Dazhong AU - Krayer, Michael AU - Balasubramanian, Thiagarajan AU - Yang, Eunkyung AU - Kee, Hooi Ling AU - Kirmaier, Christine AU - Diers, James R. AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. AU - Hamblin, Michael R. T2 - FASEB JOURNAL AB - Cutaneous malignant melanoma remains a therapeutic challenge, and patients with advanced disease have limited survival. Photodynamic therapy (PDT) has been successfully used to treat many malignancies, and it may show promise as an antimelanoma modality. However, high melanin levels in melanomas can adversely affect PDT effectiveness. Herein the extent of melanin contribution to melanoma resistance to PDT was investigated in a set of melanoma cell lines that markedly differ in the levels of pigmentation; 3 new bacteriochlorins successfully overcame the resistance. Cell killing studies determined that bacteriochlorins are superior at (LD(50) approximately 0.1 microM) when compared with controls such as the FDA-approved Photofrin (LD(50) approximately 10 microM) and clinically tested LuTex (LD(50) approximately 1 microM). The melanin content affects PDT effectiveness, but the degree of reduction is significantly lower for bacteriochlorins than for Photofrin. Microscopy reveals that the least effective bacteriochlorin localizes predominantly in lysosomes, while the most effective one preferentially accumulates in mitochondria. Interestingly all bacteriochlorins accumulate in melanosomes, and subsequent illumination leads to melanosomal damage shown by electron microscopy. Fluorescent probes show that the most effective bacteriochlorin produces significantly higher levels of hydroxyl radicals, and this is consistent with the redox properties suggested by molecular-orbital calculations. The best in vitro performing bacteriochlorin was tested in vivo in a mouse melanoma model using spectrally resolved fluorescence imaging and provided significant survival advantage with 20% of cures (P<0.01). DA - 2010/9// PY - 2010/9// DO - 10.1096/fj.09-152587 VL - 24 IS - 9 SP - 3160-3170 SN - 0892-6638 KW - multidrug resistance KW - melanosomes KW - electron microscopy ER - TY - JOUR TI - Severe Hepatitis Associated with Acute Ehrlichia canis Infection in a Dog AU - Mylonakis, M. E. AU - Kritsepi-Konstantinou, M. AU - Dumler, J. S. AU - Diniz, P. P. V. P. AU - Day, M. J. AU - Siarkou, V. I. AU - Breitschwerdt, Edward AU - Psychas, V. AU - Petanides, T. AU - Koutinas, A. F. AU - al. T2 - Journal of Veterinary Internal Medicine AB - An 8-year-old, intact male German Shepherd dog was referred because of anorexia, intermittent vomiting, and diarrhea of 5 days' duration. The dog was housed outdoors and was incompletely vaccinated (booster interval in excess of 5 years for parvovirus, distember, adenovirus, and Leptospira spp.). Physical examination (including monocular indirect ophthalmoscopy) identified lethargy, weakness, moderate pain on anterior abdominal palpation, dehydration, halitosis, and fever (40.4°C). CBCa was unremarkable, whereas the important serum biochemical findings included hypoalbuminemia (2.1 g/dL; reference range, 2.5–3.5 g/dL), normoglobulinemia (3.9 g/dL; reference range, 3–4.5 g/dL), hyperbilirubinemia (2.1 mg/dL; reference range, 0.3–0.8 mg/dL), and increased alkaline phosphatase (ALP) (1,300 U/L; reference range, 50–210 U/L) and alanine aminotransferase (ALT) (160 U/L; reference range, 10–34 U/L) activities. Analysis of an orange-colored urine sample obtained by cystocentesis disclosed an average of 2 granular casts/low power field and a urine protein-to-creatinine ratio of 2.9 (reference interval, <0.5); urine culture failed to grow bacteria. On admission, a Giemsa-stained buffy coat smear was negative for Ehrlichia sp., Babesia sp., Hepatozoon canis, and Mycoplasma sp. organisms (1,000 microscopy fields). Serum was tested for Leishmania infantum and Babesia canis antibodies by indirect immunofluorescence assays (IFA), whereas Ehrlichia canis antibodies were tested by an in-office ELISAb test. All 3 tests were negative. The dog was positive for Dirofilaria immitis antigensc but negative on a modified Knott's test for microfilaria. Thoracic radiography was unremarkable, but moderate hepatomegaly and splenomegaly were evident on abdominal radiographs and confirmed by abdominal ultrasonography (enlarged and diffusely hypoechoic liver). Leptospirosis was suspected, based on epidemiologic (endemic disease in Greece), historical, and clinical data and the fact that all the infectious disease tests described above were negative. Dirofilariasis (stage 1) was not considered a contributory factor for the clinical presentation of this dog. Pending microscopic agglutination test (MAT) serology results for Leptospira spp., the dog was hospitalized and treated with crystalloidsd (60 mL/kg IV daily), ampicilline (20 mg/kg IV q8h), enrofloxacinf (10 mg/kg SC q24h), ursodeoxycholic acidg (15 mg/kg PO q24h), ranitidineh (2 mg/kg IV q12h), and sucralfatei (1 g/30 kg PO q12h). Because no clinical or biochemical improvement was noticed after 5 days of hospitalization, a diagnostic laparotomy was performed to obtain wedge liver biopsies. Apart from mild hepatomegaly and firm consistency of hepatic parenchyma, no other abnormalities were noticed. Imprint smears were made of hepatic tissue and Giemsa-stained for cytological examination. Formalin-fixed and frozen liver tissue was retained for future polymerase chain reaction (PCR) and histopathology. Impression cytology of the liver identified several round-to-oval and occasionally polyhedral hepatocytes with an eccentrically placed round nucleus (occasional cells were binucleated) and slightly basophilic cytoplasm that were distributed individually or in clusters among a slightly hemorrhagic background. Dark green intracytoplasmic granules consistent with bile and solid green to black bile casts were observed between contiguous hepatocytes. There were numerous mature lymphocytes, with fewer plasma cells, macrophages, and nondegenerate neutrophils dispersed among the hepatocytes (Fig 1). Several dark-blue cytoplasmic inclusions consistent with Ehrlichia sp. morulae were observed in lymphocytes and macrophages (Fig 1). There was also mild extramedullary hematopoiesis, identified by occasional metarubricytes, metamyelocytes, and megakaryocytes. Bone marrow (BM) cytology performed the day after liver cytology was normocellular, with normal appearing hemopoietic lineages, mild plasmacytosis, and no evidence of Ehrlichia inclusions or other infectious agents. Photomicrograph of liver impression cytology. Numerous small lymphocytes (arrows) are seen adjacent to single or clustered hepatocytes (Giemsa stain). The inset in the upper right corner contains lymphocytes and neutrophils adjacent to 2 hepatocytes. A cytoplasmic Ehrlichia sp. morula is seen in a lymphocyte (arrowhead). In the lower right corner inset, an Ehrlichia sp. morula is seen in a lymphocyte adjacent to a hepatocyte. Bar = 10 μm. Histopathology of liver tissue stained with hematoxylin and eosin disclosed moderate portal fibrosis with bile duct proliferation, dilatation of thin-walled vessels and subtle portal to portal bridging fibrosis. There also was a mild mixed inflammatory infiltrate associated with the portal areas that included lymphocytes, plasma cells, macrophages, neutrophils, and eosinophils (Fig 2). Mild portal hemorrhage accompanied by occasional hemosiderophages was present. There was mild diffuse microvesicular vacuolation of the hepatocyte cytoplasm and generalized vascular congestion. Overall, the histopathological findings were indicative of portal hepatitis. Immunohistochemistry was performed on the formalin-fixed liver tissue as previously described1 except that E. canis monospecific polyclonal antibody to E. canis gp36 (36 kDa glycoprotein) antigen was used (The Johns Hopkins University School of Medicine, Baltimore, MD). As positive controls, lung tissue from a known E. canis-infected dog and splenic tissue from a human patient infected with Ehrlichia chaffeensis were used (Fig 3). Several cells in the hepatic tissue, presumably monocytes and lymphocytes, were infected with Ehrlichia spp. (Fig 3). (A) Photomicrograph of liver histopathology showing portal fibrosis, bile duct proliferation, hemorrhage, and inflammation. There is mild microvesicular vacuolation of the cytoplasm of adjacent hepatocytes (hematoxylin and eosin stain). Bar = 200 μm. (B) Higher magnification of affected portal area showing mixed neutrophilic and mononuclear inflammation. Bar = 100 μm. Immunohistological demonstration of Ehrlichia canis from the liver of a dog with acute portal hepatitis and monocytic ehrlichiosis. E. canis morula (arrowhead) within the cytoplasm of a mononuclear cell. Upper right inset: E. canis morula within the cytoplasm of a mononuclear cell from lung tissue of a known E. canis-infected dog (E. canis positive control). Lower right inset: E. chaffeensis in the cytoplasm of a mononuclear cell from the spleen of a human patient (E. chaffeensis positive control). E. canis immunohistochemistry with hematoxylin counterstain. Bar = 10 μm. At day 7 postadmission (PA), a CBC obtained before the institution of doxycycline treatment indicated moderate thrombocytopenia (130,000/μL; reference range 200,000–500,000/μL) and buffy coat smears were negative for Ehrlichia morulae (2,000 microscopy fields). However, E. canis 16S rDNA was amplified by PCR assays from a whole blood sample (Laboratory of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, AUTh) obtained on day 7 PA. In addition, E. canis DNA subsequently was amplified and sequenced from BM aspirate material and frozen-preserved liver tissue (obtained on days 7 and 6 PA, respectively) (Intracellular Pathogens Research Laboratory, College of Veterinary Medicine, NCSU).2,3 The sequences determined by direct sequencing of the approximately 1.4 kb PCR amplicons (nearly entire length of ehrlichial 16S rDNA)3 or those obtained from clones of the 431 bp PCR amplicons from BM (E. canis-specific 16S rDNA segment) into pGem-T Easy vectorj were 99.7% identical with each other (1 base pair different in 364 bp, with primers excluded from analysis), as well as to E. canis Greek strains previously characterized (GenBank accession numbers EF011110 and EF011111).3 DNA sequence of E. canis from the liver was 100% similar to the Greek strains mentioned before. DNA from Bartonella sp. was not amplified from the liver and BM after applying a 1-step conventional PCR.4 Also, MAT for Leptospira spp. was negative. Treatment with doxycyclinek (5 mg/kg PO q12h for 4 weeks) was instituted 24 hours after visualization of morulae in impression smears (day 7 PA). Fever abated within 12 hours and clinical resolution of all clinical signs occurred within 48 hours after initiating doxycycline therapy. Serial serum biochemical analyses showed hypoalbuminemia (2.0 g/dL; reference range 2.5–3.5 g/dL), hyperbilirubinemia (1.1 mg/dL; reference range 0.3–0.8 mg/dL), increased ALP (761 U/L; reference range 50–210 U/L) and ALT (238 U/L; reference range 10–34 U/L) activities at days 8 and 20 (ALP, 322 U/L; ALT, 83 U/L) PA; all biochemical abnormalities had resolved by day 40 PA. CBC results at days 20 and 40 PA were within reference ranges. Serological results with in-office ELISA and IFA tests were negative for E. canis antibodies at 2 and 4 weeks PA, respectively. The dog was seroreactive for E. canis, however, at 6 weeks PA (IFA titer, 1 : 800; laboratory cut-off value, 1 : 100). Retrospectively, IFA for Rickettsia rickettsii, performed in paired serum samples from days 7 and 40 PA, was positive (titers 1 : 256 and 1 : 512, respectively; laboratory cut-off value, ≥ 1 : 64), but DNA from spotted fever group rickettsiae was not amplified from the liver and BM after applying a PCR assay as described previously.5 The split-dose (a single injection of 2.5 mg/kg IM, followed 1 month later, by 2 injections of the same dose, 24 hours apart) melarsominel protocol for D. immitis also was instituted after completion of doxycycline therapy. After the last clinicopathological evaluation (day 40 PA), regular phone communications indicated that the animal has remained clinically healthy during the 4-year follow-up period. An E. canis-associated severe hepatitis was suspected in this dog, based on clinical findings, liver cytology, histopathology, immunohistochemistry, PCR amplification of E. canis DNA from blood, BM, and liver by 2 different laboratories, and the temporal relationship of the clinical response to initiation of doxycycline treatment. Historically, mild-to-moderate increases in liver enzyme activities and liver histopathology frequently have been recognized in canine monocytic ehrlichiosis (CME),6–8 but E. canis-associated hepatopathy is extremely rare as a predominant clinical manifestation, especially in the acute phase of the disease. Although clinical staging in natural CME is not straightforward, the acute onset of illness in this dog in association with the seroconversion (6 weeks PA) and a normocellular BM seem to support the acute nature of E. canis infection.9 Severe hepatic disease has been reported uncommonly in pancytopenic dogs with advanced E. canis-induced BM aplasia, which could be attributed to anemic hypoxia, intrahepatic hemorrhage and occasionally, to secondary bacterial sepsis. Nevertheless, even in these chronic cases, liver is not the sole or target organ.10,11 In this dog, the histological diagnosis was portal hepatitis, based on a mixed inflammatory infiltration, portal fibrosis and cholestasis; the latter was documented by hepatic cytology (visualization of bile casts in canaliculi) along with hyperbilirubinemia and increased ALP activity.12 However, no histopathologic evidence of cholestasis was noticed, probably because of the embedding procedure.13 The moderate fibrosis seen in this dog has not been previously reported in experimentally or naturally infected dogs6 and therefore is difficult to explain in the context of the acute CME; therefore, the possibility that the E. canis-associated hepatopathy in this dog occurred in addition to a preexisting liver insult cannot be ruled out. In 2 previous experimental studies of CME, portal infiltration with lymphocytes, plasma cells, macrophages, and focal accumulations of reticuloendothelial cells compressing adjacent hepatocytes,14 or centrilobular fatty degeneration and mild-to-moderate perivascular with periportal mononuclear cell infiltration have been described.15 Also, in a retrospective pathological study of naturally infected dogs, many of which were assumed to be chronically infected, centrilobular degeneration or necrosis and portal plasmacytosis were found.6 Despite the fact that none of these dogs had overt liver disease, mixed cell or lymphoplasmacytic portal inflammation was a common histopathological finding. Interestingly, severe E. chaffeensis-associated hepatitis in acutely infected people has been associated with similar hepatic pathology (ie, mixed cell portal infiltration, cholestasis, and focal hepatic necrosis), which, similarly to this dog, may occur before seroconversion.1,16,17 The fact that hepatitis was disproportionally severe in human patients with few or no E. chaffeensis morulae in leukocytes, hepatocytes, or biliary structures has raised suspicions that pathogenesis of E. chaffeensis hepatitis is related to an overzealous host immune response to the organism, rather than the direct cytopathic effect of the organism itself. A similar pathogenesis also could apply to CME.1 Upon admission, the dog did not show many of the typical clinical and clinicopathological features of CME, such as thrombocytopenic bleeding tendency, peripheral lymphadenomegaly, and positive antibody titer to E. canis. On the other hand, documentation of an acute febrile illness accompanied by hepatic and renal clinicopathologic abnormalities raised the suspicion of leptospirosis.18 However, the ensuing treatment with ampicillin and enrofloxacin failed to improve the clinical condition of the dog. Notably, in a previous study, the lack of efficacy of enrofloxacin in dogs experimentally infected with E. canis also was documented.19 Thrombocytopenia, which is common in CME, appeared only transiently in this dog (at day 7 PA), emphasizing the fact that ehrlichiosis cannot be excluded because of a normal platelet count.6 Hypoalbuminemia, a consistent finding in CME,7,11 was attributed to protein-losing nephropathy, liver disease, vascular injury, or some combination of these. Serum albumin concentrations were normalized by day 20 PA, along with the improvement of liver disease but the proteinuria was not further evaluated. Although seroconversion is used to document acute ehrlichiosis in dogs and humans, it may lag behind clinical expression of the disease9; the same could have applied in this dog because seroconversion did not occur until 6 weeks PA. The first evidence supporting E. canis infection in this dog was obtained after a careful review of liver cytology, in which several morulae were found. In contrast, buffy coat smears (which were shown in 1 study20 to be of high diagnostic sensitivity in acute CME) were repeatedly negative in this dog between days 1 and 7 PA. It is hypothesized that this dog may have been infected with a hepatotropic strain of E. canis. In this respect, use of a quantitative real-time PCR assay could provide a more efficient demonstration of ehrlichial density in the liver, as compared with blood, BM, or other tissues, because the conventional PCR assays used in both laboratories provide only qualitative evidence (DNA detected or not detected) of the presence of E. canis in the various tissues.21 To our knowledge, this is the first case report describing immunohistological demonstration of E. canis morulae similar to what has been described in human monocytic ehrlichiosis and may be useful in establishing a diagnosis of CME.1,22 The numerous morulae found on hepatic cytology and immunohistochemistry of this dog, together with the detection of E. canis DNA in the liver and the observation of morulae in hepatic imprints of acutely infected dogs,14 suggest that the liver should be considered as a potential target organ for application of PCR testing for epidemiological studies and posttreatment monitoring.23,24 The possibility of coinfection with canine leishmaniosis, bartonellosis, and spotted fever group rickettsiosis was ruled out with the aid of serology and BM cytology (leishmaniosis), BM and liver PCR (Bartonella spp.), and BM and liver PCR (spotted fever group rickettsiosis), because these diseases have been associated with liver disease either symptomatic or asymptomatic.25–27 Based on our experience, in canine leishmaniosis the associated liver disease is asymptomatic in most cases,26 with only a few dogs showing chronic hepatitis, liver failure or both which usually responds to antileishmanial and supportive treatment. The different sequential IFA titers for R. rickettsii were interpreted as being identical, as the criterion for seroconversion (ie, a 4-fold rise in antibody titer) was not achieved.27 Interestingly, in a previous study in Greece, 10/19 dogs with CME had serological evidence of exposure to R. conorii (the agent of Mediterranean spotted fever), but PCR failed to amplify the rickettsial DNA from any of the dogs,11 suggesting that Greek dogs with CME frequently are exposed to, but rarely persistently infected by, a rickettsial agent. The authors also cannot rule out that this dog might have been chronically infected by E. canis,28 and that the dramatic response to treatment was the result of eradication of another doxycycline-responsive agent. However, the seroconversion documented in this dog strongly suggests recent infection. Dirofilariosis was considered an incidental finding in this dog, because there was no historical, clinical, or radiographic evidence of clinical disease and most importantly, the marked clinical and biochemical improvement preceded the institution of adulticide treatment with melarsomine. In conclusion, although a cause-and-effect relationship cannot be definitely established, this report provides strong evidence that acute CME may induce symptomatic hepatitis as the predominant clinical manifestation. It is therefore suggested that CME should be included in the differential diagnosis when dogs are admitted with fever and laboratory evidence of hepatic disease, especially in the endemic areas for the disease. aVetABC, Scil Animal Care Company, Viernheim, Germany bImmunoComb, Biogal-Galed, Kibbutz Galed, Israel cSnap Canine Heartworm PF; IDEXX Laboratories Inc, Westbrook, ME dLactated Ringers, Vioser, Trikala, Greece eAmpicillin, Pentrexyl, Bristol-Myers-Squibb, New York, NY fBaytril, Bayer, Leverkusen, Germany gUrsofalk, Galenica, Athens, Greece hZantac, Glaxo-S.K., Athens, Greece iPeptonorm, Uni-Pharma, Athens, Greece jPromega, Madison, WI kRonaxan, Merial, Lyon, France lImmiticide, Merial The authors thank Dr Jere McBride, Department of Pathology, University of Texas Medical Branch, Galveston, for generously providing the polyclonal antibodies to E. canis glycoproteins. DA - 2010/4/2/ PY - 2010/4/2/ DO - 10.1111/j.1939-1676.2010.0501.x VL - 24 IS - 3 SP - 633-638 LA - en OP - SN - 0891-6640 1939-1676 UR - http://dx.doi.org/10.1111/j.1939-1676.2010.0501.x DB - Crossref ER - TY - JOUR TI - Probing the Rate of Hole Transfer in Oxidized Porphyrin Dyads Using Thallium Hyperfine Clocks AU - Diers, James R. AU - Taniguchi, Masahiko AU - Holten, Dewey AU - Lindsey, Jonathan S. AU - Bocian, David F. T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - Understanding hole/electron-transfer processes among interacting constituents of multicomponent molecular architectures is central to the fields of artificial photosynthesis and molecular electronics. One strategy for examining ground-state hole/electron transfer in oxidized tetrapyrrolic arrays entails analysis of the hyperfine interactions observed in the electron paramagnetic resonance (EPR) spectrum of the pi-cation radical. Herein, it is demonstrated that (203)Tl/(205)Tl hyperfine "clocks" are greatly superior to those provided by (1)H, (14)N, or (13)C owing to the fact that the (203)Tl/(205)Tl hyperfine couplings are much larger (15-25 G) than those of the (1)H, (14)N, or (13)C nuclei (1-6 G). The large (203)Tl/(205)Tl hyperfine interactions permit accurate simulations of the EPR spectra and the extraction of specific rates of hole/electron transfer. The (203)Tl/(205)Tl hyperfine clock strategy is applied to a series of seven porphyrin dyads. All of the dyads are joined at a meso position of the porphyrin macrocycle via linkers of a range of lengths and composition (diphenylethyne, diphenylbutadiyne, and (p-phenylene)(n), where n = 1-4); substituents such as mesityl at the nonlinking meso positions are employed to provide organic solubility. The hole/electron-transfer time constants are in the hundreds of picoseconds to sub-10 ns regime, depending on the specific porphyrin and/or linker. Density functional theory calculations on the constituents of the dyads are consistent with the view that the relative energies of the porphyrin versus linker highest occupied molecular orbitals strongly influence the hole/electron-transfer rates. Variable-temperature EPR studies further demonstrate that the hole/electron-transfer process is at best weakly activated (12-15 kJ mol(-1)) at room temperature and somewhat below. At lower temperatures, the process is essentially activationless. The weak activation is attributed to restricted torsional motions of the phenyl rings of the linker. Collectively, the studies provide the physical basis for the rational design of multicomponent architectures for efficient hole/electron transfer. DA - 2010/9/1/ PY - 2010/9/1/ DO - 10.1021/ja105082d VL - 132 IS - 34 SP - 12121-12132 SN - 0002-7863 ER - TY - JOUR TI - Interferon Regulatory Factor 3 Attenuates Reovirus Myocarditis and Contributes to Viral Clearance AU - Holm, Geoffrey H. AU - Pruijssers, Andrea J. AU - Li, Lianna AU - Danthi, Pranav AU - Sherry, Barbara AU - Dermody, Terence S. T2 - JOURNAL OF VIROLOGY AB - ABSTRACT Apoptosis is a pathological hallmark of encephalitis and myocarditis caused by reovirus in newborn mice. In cell culture models, the antiviral transcription factor interferon regulatory factor 3 (IRF-3) enhances reovirus-induced apoptosis following activation via retinoic acid inducible gene I and interferon promoter-stimulating factor 1. To determine the role of IRF-3 in reovirus disease, we infected newborn IRF-3 +/+ and IRF-3 −/− mice perorally with mildly virulent strain type 1 Lang (T1L) and fully virulent strain type 3 SA+ (T3SA+) and monitored infected animals for survival. Both wild-type and IRF-3 −/− mice succumbed with equivalent frequencies to infection with T3SA+. However, the absence of IRF-3 was associated with significantly decreased survival rates following infection with T1L. The two virus strains achieved similar peak titers in IRF-3 +/+ and IRF-3 −/− mice in the intestine, brain, heart, liver, and spleen. However, by day 12 postinoculation, titers in all organs examined were 10- to 100-fold higher in IRF-3 −/− mice than those in wild-type mice. Increased titers were associated with marked pathological changes in all organs examined, especially in the heart, where absence of IRF-3 resulted in severe myocarditis. Cellular and humoral immune responses were equivalent in wild-type and IRF-3 −/− animals, suggesting that IRF-3 functions independently of the adaptive immune response to enhance reovirus clearance. Thus, IRF-3 serves to facilitate virus clearance and prevent tissue injury in response to reovirus infection. DA - 2010/7// PY - 2010/7// DO - 10.1128/jvi.01742-09 VL - 84 IS - 14 SP - 6900-6908 SN - 0022-538X ER - TY - JOUR TI - Insect response to alphavirus infection-Establishment of alphavirus persistence in insect cells involves inhibition of viral polyprotein cleavage AU - Mudiganti, Usharani AU - Hernandez, Raquel AU - Brown, Dennis T. T2 - VIRUS RESEARCH AB - Alphavirus persistence in the insect vector is an essential element in the vector–host transmission cycle of the virus and provides a model to study the biochemical and molecular basis for virus–vector coexistence. The prototype alphavirus Sindbis (SV) establishes persistent infections in invertebrate cell cultures which are characterized by low levels of virus production. We hypothesized that antiviral factors may be involved in decreasing the virus levels as virus persistence is established in invertebrate cells. Transcription profiles in Drosophila S2 cells at 5 days post-infection with SV identified families of gene products that code for factors that can explain previous observations seen in insect cells infected with alphaviruses. Genomic array analysis identified up-regulation of gene products involved in intracellular membrane vesicle formation, cell growth rate changes and immune-related functions in S2 cells infected with SV. Transcripts coding for factors involved in different aspects of the Notch signaling pathway had increased in expression. Increased expression of ankyrin, plap, syx13, unc-13, csp, rab1 and rab8 may aid in formation of virus containing vesicles and in intracellular transport of viral structural proteins. Possible functions of these gene products and relevant hypotheses are discussed. We confirmed the up-regulation of a wide-spectrum protease inhibitor, Thiol-ester containing Protein (TEP) II. We report inhibition of the viral polyprotein cleavage at 5 days post-infection (dpi) and after superinfection of SV-infected cells at 5 dpi. We propose that inefficient cleavage of the polyprotein may, at least in part, lead to reduced levels of virus seen as persistence is established. DA - 2010/6// PY - 2010/6// DO - 10.1016/j.virusres.2010.02.016 VL - 150 IS - 1-2 SP - 73-84 SN - 1872-7492 KW - Arbovirus KW - Sindbis KW - Insect cells KW - Microarray KW - Persistent infection ER - TY - JOUR TI - In vivo depletion of CD4(+)CD25(hi) regulatory T cells is associated with improved antiviral responses in cats chronically infected with feline immunodeficiency virus AU - Mikkelsen, S. Rochelle AU - Reckling, Stacie K. AU - Egan, Erin A. AU - Dean, Gregg A. T2 - VIROLOGY AB - Regulatory T (Treg) cells are activated and suppress immune responses during infection, and are characterized as CD4+CD25hiFOXP3+. Ex vivo studies demonstrate that Treg cells potentially suppress anti-HIV-1 T cell responses. Lentivirus-induced CD4+CD25hi Treg cells were first described in feline immunodeficiency virus (FIV)-infected cats. In the present study we demonstrate that anti-feline CD25 monoclonal antibody (mAb) therapy depletes Treg cells in FIV-infected cats for 4 weeks and does not exacerbate viral replication or proinflammatory cytokine production. Significant FIV-specific immune responses are revealed in Treg cell-depleted cats. These anti-FIV effector cells exist prior to Treg cell depletion and are not expanded while Treg cells are depleted. Importantly, cats receiving the Treg cell-depleting mAb are able to produce a robust humoral response to new antigen. We propose that short-term in vivo Treg cell depletion during chronic HIV-1 infection could provide a window of opportunity for therapeutic vaccination in individuals with controlled viral replication. DA - 2010/8/1/ PY - 2010/8/1/ DO - 10.1016/j.virol.2010.04.016 VL - 403 IS - 2 SP - 163-172 SN - 0042-6822 KW - Feline immunodeficiency virus KW - HIV-1 KW - Lentivirus KW - Regulatory T cell KW - Immunosuppression KW - Monoclonal antibody ER - TY - JOUR TI - In Vitro Photodynamic Therapy and Quantitative Structure-Activity Relationship Studies with Stable Synthetic Near-Infrared-Absorbing Bacteriochlorin Photosensitizers AU - Huang, Ying-Ying AU - Mroz, Pawel AU - Zhiyentayev, Timur AU - Sharma, Sulbha K. AU - Balasubramanian, Thiagarajan AU - Ruzie, Christian AU - Krayer, Michael AU - Fan, Dazhong AU - Borbas, K. Eszter AU - Yang, Eunkyung AU - Kee, Hooi Ling AU - Kirmaier, Christine AU - Diers, James R. AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. AU - Hamblin, Michael R. T2 - JOURNAL OF MEDICINAL CHEMISTRY AB - Photodynamic therapy (PDT) is a rapidly developing approach to treating cancer that combines harmless visible and near-infrared light with a nontoxic photoactivatable dye, which upon encounter with molecular oxygen generates the reactive oxygen species that are toxic to cancer cells. Bacteriochlorins are tetrapyrrole compounds with two reduced pyrrole rings in the macrocycle. These molecules are characterized by strong absorption features from 700 to >800 nm, which enable deep penetration into tissue. This report describes testing of 12 new stable synthetic bacteriochlorins for PDT activity. The 12 compounds possess a variety of peripheral substituents and are very potent in killing cancer cells in vitro after illumination. Quantitative structure-activity relationships were derived, and subcellular localization was determined. The most active compounds have both low dark toxicity and high phototoxicity. This combination together with near-infrared absorption gives these bacteriochlorins great potential as photosensitizers for treatment of cancer. DA - 2010/5/27/ PY - 2010/5/27/ DO - 10.1021/jm901908s VL - 53 IS - 10 SP - 4018-4027 SN - 1520-4804 ER - TY - JOUR TI - Evolutionary history of two endemic Appalachian conifers revealed using microsatellite markers AU - Potter, Kevin M. AU - Frampton, John AU - Josserand, Sedley A. AU - Nelson, C. Dana T2 - CONSERVATION GENETICS AB - Fraser fir (Abies fraseri [Pursh] Poir.) and intermediate fir (Abies balsamea [L.] Mill. var. phanerolepis Fern.) exist in small populations in the Appalachian highlands of the southeastern United States. We used ten nuclear microsatellite markers to quantify genetic variation within Fraser fir and intermediate fir, and to examine their evolutionary relationships with the widespread balsam fir (Abies balsamea [L.] Mill.). We found little genetic differentiation among these taxa, suggesting that Fraser fir might best be classified as a variety of balsam fir. The results further appear to reject the hypothesis that intermediate fir was of hybrid origin between two comparatively distantly related species. Low levels of genetic diversity suggest that intermediate fir and Fraser fir have undergone at least some genetic degradation since post-Pleistocene isolation. The results may prove important for in situ and ex situ gene conservation efforts for Fraser fir and intermediate fir, which are imperiled by an exotic insect and by global climate change. DA - 2010/6// PY - 2010/6// DO - 10.1007/s10592-009-9980-3 VL - 11 IS - 4 SP - 1499-1513 SN - 1566-0621 KW - Biogeography KW - Pleistocene KW - Migration KW - Population genetics KW - Microsatellite markers KW - Abies ER - TY - JOUR TI - Codontest: modeling amino acid substitution preferences in coding sequences AU - Delport, W. AU - Scheffler, K. AU - Botha, G. AU - Gravenor, M. B. AU - Muse, S. V. AU - Pond, S. L. K. T2 - PLoS Computational Biology DA - 2010/// PY - 2010/// VL - 6 IS - 8 ER - TY - JOUR TI - Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes AU - Shi, Rui AU - Sun, Ying-Hsuan AU - Li, Quanzi AU - Heber, Steffen AU - Sederoff, Ronald AU - Chiang, Vincent L. T2 - PLANT AND CELL PHYSIOLOGY AB - As a step toward a comprehensive description of lignin biosynthesis in Populus trichocarpa, we identified from the genome sequence 95 phenylpropanoid gene models in 10 protein families encoding enzymes for monolignol biosynthesis. Transcript abundance was determined for all 95 genes in xylem, leaf, shoot and phloem using quantitative real-time PCR (qRT-PCR). We identified 23 genes that most probably encode monolignol biosynthesis enzymes during wood formation. Transcripts for 18 of the 23 are abundant and specific to differentiating xylem. We found evidence suggesting functional redundancy at the transcript level for phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate:CoA ligase (4CL), p-hydroxycinnamoyl-CoA:quinate shikimate p-hydroxycinnamoyltransferase (HCT), caffeoyl-CoA O-methyltransferase (CCoAOMT) and coniferyl aldehyde 5-hydroxylase (CAld5H). We carried out an enumeration-based motif identification and discriminant analysis on the promoters of all 95 genes. Five core motifs correctly discriminate the 18 xylem-specific genes from the 77 non-xylem genes. These motifs are similar to promoter elements known to regulate phenylpropanoid gene expression. This work suggests that genes in monolignol biosynthesis are regulated by multiple motifs, often related in sequence. DA - 2010/1// PY - 2010/1// DO - 10.1093/pcp/pcp175 VL - 51 IS - 1 SP - 144-163 SN - 1471-9053 KW - Lignin systems biology KW - Monolignol biosynthesis KW - Populus trichocarpa KW - Promoter motifs KW - Transcript abundance KW - Xylem-specific expression ER - TY - JOUR TI - The use of pooled vs serial urine samples to measure urine protein:creatinine ratios AU - LeVine, Dana N. AU - Zhang, Daowen AU - Harris, Tonya AU - Vaden, Shelly L. T2 - VETERINARY CLINICAL PATHOLOGY AB - Background: Evaluation of serial urine protein:creatinine (UPC) ratios is important in prognosticating chronic kidney disease and monitoring response to therapeutic interventions. Owing to random biologic variation in dogs with stable glomerular proteinuria, multiple determinations of UPC ratios often are recommended to reliably assess urine protein loss. This can be cost‐prohibitive. Objective: The purpose of this study was to evaluate agreement between the mean of 3 UPC ratios obtained on 3 separate urine samples per dog and a single UPC ratio obtained when aliquots of the separate samples were pooled and analyzed as 1 sample. Methods: Three separate urine samples were collected from each of 25 dogs, both client‐owned and members of a research colony. Protein and creatinine concentrations were measured in the supernatant of each sample using a biochemical analyzer, and the mean of the 3 UPC ratios was calculated. A 1.0 mL aliquot of each of the 3 samples from each dog was pooled to create a fourth sample for that dog, and the UPC ratio of the pooled sample was similarly determined. Agreement and correlation between the mean and pooled UPC ratios were assessed using Bland–Altman difference plots and regression analysis, respectively. Results: The UPC ratio in the pooled samples was highly correlated ( r =.9998, P <.0001) with the mean UPC ratio of the 3 separate samples. Strong agreement between results was demonstrated; a UPC ratio from a pooled sample was at most ±20% different than the mean UPC ratio obtained from 3 separate samples. Conclusions: Measuring the UPC ratio in a pooled sample containing equal volumes of several different urine specimens from the same dog provides a reliable and cost‐effective alternative to assessing multiple UPC ratios on several specimens from the same dog. DA - 2010/3// PY - 2010/3// DO - 10.1111/j.1939-165x.2009.00167.x VL - 39 IS - 1 SP - 53-56 SN - 0275-6382 KW - Dog KW - proteinuria KW - protein:creatinine ratio KW - UPC ER - TY - JOUR TI - Identification and Characterization of Two Bordetella avium Gene Products Required for Hemagglutination AU - Temple, Louise M. AU - Miyamoto, David M. AU - Mehta, Manju AU - Capitini, Christian M. AU - Von Stetina, Stephen AU - Barnes, H. John AU - Christensen, Vern L. AU - Horton, John R. AU - Spears, Patricia A. AU - Orndorff, Paul E. T2 - INFECTION AND IMMUNITY AB - ABSTRACT Bordetella avium causes bordetellosis in birds, a disease similar to whooping cough caused by Bordetella pertussis in children. B. avium agglutinates guinea pig erythrocytes via an unknown mechanism. Loss of hemagglutination ability results in attenuation. We report the use of transposon mutagenesis to identify two genes required for hemagglutination. The genes ( hagA and hagB ) were adjacent and divergently oriented and had no orthologs in the genomes of other Bordetella species. Construction of in-frame, unmarked mutations in each gene allowed examination of the role of each in conferring erythrocyte agglutination, explanted tracheal cell adherence, and turkey poult tracheal colonization. In all of the in vitro and in vivo assays, the requirement for the trans -acting products of hagA and hagB (HagA and HagB) was readily shown. Western blotting, using antibodies to purified HagA and HagB, revealed proteins of the predicted sizes of HagA and HagB in an outer membrane-enriched fraction. Antiserum to HagB, but not HagA, blocked B. avium erythrocyte agglutination and explanted turkey tracheal ring binding. Bioinformatic analysis indicated the similarity of HagA and HagB to several two-component secretory apparatuses in which one product facilitates the exposition of the other. HagB has the potential to serve as a useful immunogen to protect turkeys against colonization and subsequent disease. DA - 2010/6// PY - 2010/6// DO - 10.1128/iai.00140-10 VL - 78 IS - 6 SP - 2370-2376 SN - 1098-5522 ER - TY - JOUR TI - Evaluation of Brain Tissue or Cerebrospinal Fluid with Broadly Reactive Polymerase Chain Reaction for Ehrlichia, Anaplasma, Spotted Fever Group Rickettsia, Bartonella, and Borrelia Species in Canine Neurological Diseases (109 Cases) AU - Barber, R.M. AU - Li, Q. AU - Diniz, P.P.V.P. AU - Porter, B.F. AU - Breitschwerdt, E.B. AU - Claiborne, M.K. AU - Birkenheuer, A.J. AU - Levine, J.M. AU - Levine, G.J. AU - Chandler, K. AU - Kenny, P. AU - Nghiem, P. AU - Wei, S. AU - Greene, C.E. AU - Kent, M. AU - Platt, S.R. AU - Greer, K. AU - Schatzberg, S.J. T2 - Journal of Veterinary Internal Medicine AB - Background: Vector-transmitted microorganisms in the genera Ehrlichia, Anaplasma, Rickettsia, Bartonella, and Borrelia are commonly suspected in dogs with meningoencephalomyelitis (MEM), but the prevalence of these pathogens in brain tissue and cerebrospinal fluid (CSF) of dogs with MEM is unknown. Hypothesis/Objectives: To determine if DNA from these genera is present in brain tissue and CSF of dogs with MEM, including those with meningoencephalitis of unknown etiology (MUE) and histopathologically confirmed cases of granulomatous (GME) and necrotizing meningoencephalomyelitis (NME). Animals: Hundred and nine dogs examined for neurological signs at 3 university referral hospitals. Methods: Brain tissue and CSF were collected prospectively from dogs with neurological disease and evaluated by broadly reactive polymerase chain reaction (PCR) for Ehrlichia, Anaplasma, Spotted Fever Group Rickettsia, Bartonella, and Borrelia species. Medical records were evaluated retrospectively to identify MEM and control cases. Results: Seventy-five cases of MUE, GME, or NME, including brain tissue from 31 and CSF from 44 cases, were evaluated. Brain tissue from 4 cases and inflammatory CSF from 30 cases with infectious, neoplastic, compressive, vascular, or malformative disease were evaluated as controls. Pathogen nucleic acids were detected in 1 of 109 cases evaluated. Specifically, Bartonella vinsonii subsp. berkhoffii DNA was amplified from 1/6 dogs with histopathologically confirmed GME. Conclusion and Clinical Importance: The results of this investigation suggest that microorganisms in the genera Ehrlichia, Anaplasma, Rickettsia, and Borrelia are unlikely to be directly associated with canine MEM in the geographic regions evaluated. The role of Bartonella in the pathogenesis of GME warrants further investigation. DA - 2010/3// PY - 2010/3// DO - 10.1111/j.1939-1676.2009.0466.x VL - 24 IS - 2 SP - 372–378 SN - 0891-6640 1939-1676 UR - http://dx.doi.org/10.1111/j.1939-1676.2009.0466.x KW - Central nervous system (CNS) KW - Inflammation KW - Meningoencephalomyelitis KW - Vector-borne microorganisms ER - TY - JOUR TI - Detection of alternative splice variants at the proteome level in Aspergillus flavus AU - Chang, K. Y. AU - Georgianna, D. R. AU - Heber, S. AU - Payne, G. A. AU - Muddiman, D. C. T2 - Journal of Proteome Research DA - 2010/// PY - 2010/// VL - 9 IS - 3 SP - 1209-1217 ER - TY - JOUR TI - Beyond aflatoxin: four distinct expression patterns and functional roles associated with Aspergillus flavus secondary metabolism gene clusters AU - Georgianna, D. Ryan AU - Fedorova, Natalie D. AU - Burroughs, James L. AU - Dolezal, Andrea L. AU - Bok, Jin Woo AU - Horowitz-Brown, Sigal AU - Woloshuk, Charles P. AU - Yu, Jiujiang AU - Keller, Nancy P. AU - Payne, Gary A. T2 - MOLECULAR PLANT PATHOLOGY AB - Species of Aspergillus produce a diverse array of secondary metabolites, and recent genomic analysis has predicted that these species have the capacity to synthesize many more compounds. It has been possible to infer the presence of 55 gene clusters associated with secondary metabolism in Aspergillus flavus; however, only three metabolic pathways-aflatoxin, cyclopiazonic acid (CPA) and aflatrem-have been assigned to these clusters. To gain an insight into the regulation of and to infer the ecological significance of the 55 secondary metabolite gene clusters predicted in A. flavus, we examined their expression over 28 diverse conditions. Variables included culture medium and temperature, fungal development, colonization of developing maize seeds and misexpression of laeA, a global regulator of secondary metabolism. Hierarchical clustering analysis of expression profiles allowed us to categorize the gene clusters into four distinct clades. Gene clusters for the production of aflatoxins, CPA and seven other unknown compound(s) were identified as belonging to one clade. To further explore the relationships found by gene expression analysis, aflatoxin and CPA production were quantified under five different cell culture environments known to be conducive or nonconducive for aflatoxin biosynthesis and during the colonization of developing maize seeds. Results from these studies showed that secondary metabolism gene clusters have distinctive gene expression profiles. Aflatoxin and CPA were found to have unique regulation, but are sufficiently similar that they would be expected to co-occur in substrates colonized with A. flavus. DA - 2010/3// PY - 2010/3// DO - 10.1111/J.1364-3703.2009.00594.X VL - 11 IS - 2 SP - 213-226 SN - 1364-3703 ER - TY - JOUR TI - The small nucleolar ribonucleoprotein (snoRNP) database AU - Ellis, J. Christopher AU - Brown, Daniel D. AU - Brown, James W. T2 - RNA AB - Small nucleolar ribonucleoproteins (snoRNPs) are widely studied and characterized as guide RNAs for sequence-specific 2′-O-ribose methylation and psuedouridylation of ribosomal RNAs. In addition, snoRNAs have also been shown to interact with some tRNAs and direct alternative splicing in mRNA biogenesis. Recent advances in bioinformatics have resulted in new algorithms able to rapidly identify noncoding RNAs generally and snoRNAs specifically in genomic and metagenomic sequences, resulting in a rapid increase in the number and diversity of identified snoRNA sequences. The snoRNP database is a web-based collection of snoRNA and snoRNA-associated protein sequences from a wide range of species. The database currently contains 8994 snoRNA sequences from Bacteria, Archaea, and Eukaryotes and 589 snoRNA-associated protein sequences. The snoRNP database can be found at: http://evolveathome.com/snoRNA/snoRNA.php . DA - 2010/4// PY - 2010/4// DO - 10.1261/rna.1871310 VL - 16 IS - 4 SP - 664-666 SN - 1469-9001 KW - sRNA KW - sRNP KW - small nucleolar RNA KW - small nucleolar RNP ER - TY - JOUR TI - The increasing recognition of rickettsial pathogens in dogs and people AU - Nicholson, William L. AU - Allen, Kelly E. AU - McQuiston, Jennifer H. AU - Breitschwerdt, Edward B. AU - Little, Susan E. T2 - Trends in Parasitology AB - Dogs and people are exposed to and susceptible to infection by many of the same tick-borne bacterial pathogens in the order Rickettsiales, including Anaplasma phagocytophilum, Ehrlichia canis, E. chaffeensis, E. ewingii, Rickettsia rickettsii, R. conorii, and other spotted fever group rickettsiae. Recent findings include descriptions of novel Ehrlichia and Rickettsia species, recognition of the occurrence and clinical significance of co-infection, and increasing awareness of Rhipicephalus sanguineus-associated diseases. Newer molecular assays are available, although renewed efforts to encourage their use are needed. This review highlights the ecology and epidemiology of these diseases, and proposes avenues for future investigation. Dogs and people are exposed to and susceptible to infection by many of the same tick-borne bacterial pathogens in the order Rickettsiales, including Anaplasma phagocytophilum, Ehrlichia canis, E. chaffeensis, E. ewingii, Rickettsia rickettsii, R. conorii, and other spotted fever group rickettsiae. Recent findings include descriptions of novel Ehrlichia and Rickettsia species, recognition of the occurrence and clinical significance of co-infection, and increasing awareness of Rhipicephalus sanguineus-associated diseases. Newer molecular assays are available, although renewed efforts to encourage their use are needed. This review highlights the ecology and epidemiology of these diseases, and proposes avenues for future investigation. DA - 2010/4// PY - 2010/4// DO - 10.1016/j.pt.2010.01.007 VL - 26 IS - 4 SP - 205-212 J2 - Trends in Parasitology LA - en OP - SN - 1471-4922 UR - http://dx.doi.org/10.1016/j.pt.2010.01.007 DB - Crossref ER - TY - JOUR TI - Prevalence of Bartonella henselae and Borrelia burgdorferi Sensu Lato DNA in Ixodes ricinus Ticks in Europe AU - Dietrich, F. AU - Schmidgen, T. AU - Maggi, R. G. AU - Richter, D. AU - Matuschka, F.-R. AU - Vonthein, R. AU - Breitschwerdt, E. B. AU - Kempf, V. A. J. T2 - Applied and Environmental Microbiology AB - Bartonella spp. can cause persistent bloodstream infections in humans and animals. To determine whether Bartonella henselae is present in questing Ixodes ricinus ticks, we analyzed the prevalence of B. henselae DNA among tick stages compared to the prevalence of DNA from Borrelia burgdorferi sensu lato, the pathogen most frequently transmitted by ticks. B. henselae DNA was present with a prevalence of up to approximately 40% in tick populations sampled in four European sites (Eberdingen, Germany; Klasdorf, Germany; Lembach, France; and Madeira, Portugal). The odds of detecting B. henselae DNA in nymphal ticks was approximately 14-fold higher than in adult ticks. No tick was found to be coinfected with B. henselae and B. burgdorferi sensu lato. Taken together, our data indicate that ticks might serve as a vector for the transmission of B. henselae to humans. DA - 2010/1/8/ PY - 2010/1/8/ DO - 10.1128/aem.02788-09 VL - 76 IS - 5 SP - 1395-1398 J2 - Applied and Environmental Microbiology LA - en OP - SN - 0099-2240 UR - http://dx.doi.org/10.1128/AEM.02788-09 DB - Crossref ER - TY - JOUR TI - Genomic Regions Associated with Dermal Hyperpigmentation, Polydactyly and Other Morphological Traits in the Silkie Chicken AU - Dorshorst, Ben AU - Okimoto, Ron AU - Ashwell, Chris T2 - JOURNAL OF HEREDITY AB - The Silkie chicken has been a model of melanoctye precursor and neural crest cell migration and proliferation in the developing embryo due to its extensive hyperpigmentation of dermal and connective tissues. Although previous studies have focused on the distribution and structure of the Silkie's pigment or the general mechanisms by which this phenotype presents itself, the causal genetic variants have not been identified. Classical breeding experiments have determined this trait to be controlled by 2 interacting genes, the sex-linked inhibitor of dermal melanin (Id) and autosomal fibromelanosis (Fm) genes. Genome-wide single nucleotide polymorphism (SNP)-trait association analysis was used to detect genomic regions showing significant association with these pigmentation genes in 2 chicken mapping populations designed to segregate independently for Id and Fm. The SNP showing the highest association with Id was located at 72.3 Mb on chromosome Z and 10.3–13.1 Mb on chromosome 20 showed the highest association with Fm. Prior to this study, the linkage group to which Fm belonged was unknown. Although the primary focus of this study was to identify loci contributing to dermal pigmentation in the Silkie chicken, loci associated with various other morphological traits segregating in these populations were also detected. A single SNP in a highly conserved cis-regulatory region of Sonic Hedgehog was significantly associated with polydactyly (Po). Genomic regions in association with silkie feathering or hookless (h), feathered legs (Pti), vulture hock (V), rose comb (R), and duplex comb (D) were also identified. DA - 2010/// PY - 2010/// DO - 10.1093/jhered/esp120 VL - 101 IS - 3 SP - 339-350 SN - 0022-1503 KW - fibromelanosis KW - hyperpigmentation KW - inhibitor of dermal melanin KW - polydactyly KW - Silkie ER - TY - JOUR TI - Flea-associated zoonotic diseases of cats in the USA: bartonellosis, flea-borne rickettsioses, and plague AU - McElroy, Kristina M. AU - Blagburn, Byron L. AU - Breitschwerdt, Edward B. AU - Mead, Paul S. AU - McQuiston, Jennifer H. T2 - Trends in Parasitology AB - Cat-scratch disease, flea-borne typhus, and plague are three flea-associated zoonoses of cats of concern in the USA. Although flea concentrations may be heaviest in coastal and temperate climates, fleas and flea-borne disease agents can occur almost anywhere in the USA. Understanding flea-borne pathogens, and the associated risks for owners and veterinarians, is important to reduce the likelihood of zoonotic infection. DA - 2010/4// PY - 2010/4// DO - 10.1016/j.pt.2010.01.001 VL - 26 IS - 4 SP - 197-204 J2 - Trends in Parasitology LA - en OP - SN - 1471-4922 UR - http://dx.doi.org/10.1016/j.pt.2010.01.001 DB - Crossref ER - TY - JOUR TI - C/EBP alpha and C/EBP beta Are Required for Sebocyte Differentiation and Stratified Squamous Differentiation in Adult Mouse Skin AU - House, John S. AU - Zhu, Songyun AU - Ranjan, Rakesh AU - Linder, Keith AU - Smart, Robert C. T2 - PLOS ONE AB - C/EBPalpha and C/EBPbeta are bZIP transcription factors that are highly expressed in the interfollicular epidermis and sebaceous glands of skin and yet germ line deletion of either family member alone has only mild or no effect on keratinocyte biology and their role in sebocyte biology has never been examined. To address possible functional redundancies and reveal functional roles of C/EBPalpha and C/EBPbeta in postnatal skin, mouse models were developed in which either family member could be acutely ablated alone or together in the epidermis and sebaceous glands of adult mice. Acute removal of either C/EBPalpha or C/EBPbeta alone in adult mouse skin revealed modest to no discernable changes in epidermis or sebaceous glands. In contrast, co-ablation of C/EBPalpha and C/EBPbeta in postnatal epidermis resulted in disruption of stratified squamous differentiation characterized by hyperproliferation of basal and suprabasal keratinocytes and a defective basal to spinous keratinocyte transition involving an expanded basal compartment and a diminished and delayed spinous compartment. Acute co-ablation of C/EBPalpha and C/EBPbeta in sebaceous glands resulted in severe morphological defects, and sebocyte differentiation was blocked as determined by lack of sebum production and reduced expression of stearoyl-CoA desaturase (SCD3) and melanocortin 5 receptor (MC5R), two markers of terminal sebocyte differentiation. Specialized sebocytes of Meibomian glands and preputial glands were also affected. Our results indicate that in adult mouse skin, C/EBPalpha and C/EBPbeta are critically involved in regulating sebocyte differentiation and epidermal homeostasis involving the basal to spinous keratinocyte transition and basal cell cycle withdrawal. DA - 2010/3/23/ PY - 2010/3/23/ DO - 10.1371/journal.pone.0009837 VL - 5 IS - 3 SP - SN - 1932-6203 ER - TY - JOUR TI - A genomic analysis of transcytosis in the pea aphid, Acyrthosiphon pisum, a mechanism involved in virus transmission AU - Tamborindeguy, C. AU - Monsion, B. AU - Brault, V. AU - Hunnicutt, L. AU - Ju, H. J. AU - Nakabachi, A. AU - Van Fleet, E. T2 - Insect Molecular Biology DA - 2010/// PY - 2010/// VL - 19 SP - 259-272 ER - TY - JOUR TI - The Soluble Proteome of the Drosophila Antenna AU - Anholt, Robert R. H. AU - Williams, Taufika Islam T2 - CHEMICAL SENSES AB - The olfactory system of Drosophila melanogaster is one of the best characterized chemosensory systems. Identification of proteins contained in the third antennal segment, the main olfactory organ, has previously relied primarily on immunohistochemistry, and although such studies and in situ hybridization studies are informative, they focus generally on one or few gene products at a time, and quantification is difficult. In addition, purification of native proteins from the antenna is challenging because it is small and encased in a hard cuticle. Here, we describe a simple method for the large-scale detection of soluble proteins from the Drosophila antenna by chromatographic separation of tryptic peptides followed by tandem mass spectrometry with femtomole detection sensitivities. Examination of the identities of these proteins indicates that they originate both from the extracellular perilymph and from the cytoplasm of disrupted cells. We identified enzymes involved with intermediary metabolism, proteins associated with regulation of gene expression, nucleic acid metabolism and protein metabolism, proteins associated with microtubular transport, 8 odorant-binding proteins, protective enzymes associated with antibacterial defense and defense against oxidative damage, cuticular proteins, and proteins of unknown function, which represented about one-third of all soluble proteins. The procedure described here opens the way for precise quantification of any target protein in the Drosophila antenna and should be readily applicable to antennae from other insects. DA - 2010/1// PY - 2010/1// DO - 10.1093/chemse/bjp073 VL - 35 IS - 1 SP - 21-30 SN - 0379-864X KW - chemosensation KW - mass spectrometry KW - odorant-binding proteins KW - olfaction KW - proteomics ER - TY - JOUR TI - Synthetic Routes to meso-Patterned Porphyrins AU - Lindsey, Jonathan S. T2 - ACCOUNTS OF CHEMICAL RESEARCH AB - Synthetic meso-substituted porphyrins offer significant attractions compared with naturally occurring β-substituted porphyrins. The attractions include the rectilinear arrangement of the four meso substituents and potential synthetic amenability from pyrrole and simple acyl reactants, thereby avoiding the cumbersome syntheses of β-substituted pyrroles. In practice, however, the classical methods for the synthesis of meso-substituted porphyrins were characterized by high-temperature reactions, limited scope of substituents, and statistical mixtures accompanied by laborious chromatography if porphyrins bearing two different types of substituents were sought. Such methods left unrealized the tremendous utility of meso-substituted porphyrins across the enormously broad field of porphyrin science, which touches pure chemistry; energy, life and materials sciences; and medicine. This Account surveys a set of strategies, developed over a generation, that provide rational access to porphyrins bearing up to four distinct meso substituents. A “2 + 2” route employs a dipyrromethane-1,9-dicarbinol and a dipyrromethane (bearing ABC- and D-substituents, respectively) in a two-step, one-flask process of acid-catalyzed condensation followed by oxidation at room temperature to form the free base “ABCD-porphyrin.” A “bilane” route relies on the acid-catalyzed reaction of a 1-acyldipyrromethane (CD substituents) and a 9-bromodipyrromethane-1-carbinol (AB substituents) to form the corresponding 19-acyl-1-bromobilane. Reaction of the latter compound in the presence of MgBr2, 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU), and toluene at reflux exposed to air affords the corresponding magnesium(II) porphyrin. The two routes are complementary, both in scope and in implementation. A suite of methods also affords trans-A2B2-porphyrins by reaction of a dipyrromethane and an aldehyde, self-condensation of a dipyrromethane-1-carbinol, or self-condensation of a 1-acyldipyrromethane. These new routes are also useful for preparing sparsely substituted porphyrins, which bear fewer than four meso substituents (e.g., trans-AB-porphyrins, A-porphyrins). Because of their compact size and the ability to incorporate hydrophilic or amphipathic groups, such molecules are ideal for biological applications. The success of these new synthetic strategies has relied on a number of advances including (1) the development of simple yet efficient routes to dipyrromethanes, acyldipyrromethanes, and dipyrromethane-carbinols, (2) the identification of acid catalysts and reaction conditions for condensations of pyrromethane species without accompanying acidolysis (which underlies scrambling and formation of a mixture of porphyrin products), (3) the development of analytical methods to rapidly screen for scrambling and to characterize the distribution of oligopyrromethanes and macrocycles, (4) selection and refinement of synthetic methods to increase yields and to limit or avoid use of chromatography, thereby achieving scalability to multigram levels, and (5) exploitation of discoveries concerning the fundamental chemistry of pyrrolic species. With these developments, the prior era of porphyrin synthesis has been supplanted with rational routes that proceed under very mild conditions and afford a single porphyrin bearing up to four distinct meso substituents. The meso substituents encompass a very wide range of molecular complexity. The resulting porphyrins can serve as building blocks in the construction of model systems, as components of molecular materials, and as surrogates for naturally occurring tetrapyrrole macrocycles. DA - 2010/2// PY - 2010/2// DO - 10.1021/ar900212t VL - 43 IS - 2 SP - 300-311 SN - 0001-4842 ER - TY - JOUR TI - Potential for Tick-borne Bartonelloses AU - Angelakis, Emmanouil AU - Billeter, Sarah A. AU - Breitschwerdt, Edward B. AU - Chomel, Bruno B. AU - Raoult, Didier T2 - Emerging Infectious Diseases AB - Abstract As worldwide vectors of human infectious diseases, ticks are considered to be second only to mosquitoes. Each tick species has preferred environmental conditions and biotopes that determine its geographic distribution, the pathogens it vectors, and the areas that pose risk for tick-borne diseases. Researchers have identified an increasing number of bacterial pathogens that are transmitted by ticks, including Anaplasma, Borrelia, Ehrlichia, and Rickettsia spp. Recent reports involving humans and canines suggest that ticks should be considered as potential vectors of Bartonella spp. To strengthen this suggestion, numerous molecular surveys to detect Bartonella DNA in ticks have been conducted. However, there is little evidence that Bartonella spp. can replicate within ticks and no definitive evidence of transmission by a tick to a vertebrate host. DA - 2010/3// PY - 2010/3// DO - 10.3201/eid1603.081685 VL - 16 IS - 3 SP - 385-391 J2 - Emerg. Infect. Dis. OP - SN - 1080-6040 1080-6059 UR - http://dx.doi.org/10.3201/eid1603.081685 DB - Crossref ER - TY - JOUR TI - Placebo Effect in Canine Epilepsy Trials AU - Munana, K. R. AU - Zhang, D. AU - Patterson, E. E. T2 - JOURNAL OF VETERINARY INTERNAL MEDICINE AB - Background: The placebo effect is a well‐recognized phenomenon in human medicine; in contrast, little information exists on the effect of placebo administration in veterinary patients. Hypothesis: Nonpharmacologic therapeutic effects play a role in response rates identified in canine epilepsy trials. Animals: Thirty‐four dogs with epilepsy. Methods: Meta‐analysis of the 3 known prospective, placebo‐controlled canine epilepsy trials. The number of seizures per week was compiled for each dog throughout their participation in the trial. Log‐linear models were developed to evaluate seizure frequency during treatment and placebo relative to baseline. Results: Twenty‐two of 28 (79%) dogs in the study that received placebo demonstrated a decrease in seizure frequency compared with baseline, and 8 (29%) could be considered responders, with a 50% or greater reduction in seizures. For the 3 trials evaluated, the average reduction in seizures during placebo administration relative to baseline was 26% ( P = .0018), 29% ( P = .17), and 46% ( P = .01). Conclusions and Clinical Importance: A positive response to placebo administration, manifesting as a decrease in seizure frequency, can be observed in epileptic dogs. This is of importance when evaluating open label studies in dogs that aim to assess efficacy of antiepileptic drugs, as the reported results might be overstated. Findings from this study highlight the need for more placebo‐controlled trials in veterinary medicine. DA - 2010/// PY - 2010/// DO - 10.1111/j.1939-1676.2009.0407.x VL - 24 IS - 1 SP - 166-170 SN - 0891-6640 KW - Clinical trials KW - Dog KW - Epilepsy KW - Statistical modeling ER - TY - PCOMM TI - Molecular mechanisms of Bartonella henselae resistance to azithromycin, pradofloxacin and enrofloxacin AU - Biswas, Silpak AU - Maggi, Ricardo G. AU - Papich, Mark G. AU - Breitschwerdt, Edward B. DA - 2010/3// PY - 2010/3// DO - 10.1093/jac/dkp459 SP - 581-582 KW - in vitro resistant mutants KW - disc diffusion assay KW - bartonellosis KW - DNA gyrase A KW - 23S rRNA ER - TY - JOUR TI - Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana AU - Gou, Xiaoping AU - He, Kai AU - Yang, Hui AU - Yuan, Tong AU - Lin, Honghui AU - Clouse, Steven D. AU - Li, Jia T2 - BMC GENOMICS AB - Transmembrane receptor kinases play critical roles in both animal and plant signaling pathways regulating growth, development, differentiation, cell death, and pathogenic defense responses. In Arabidopsis thaliana, there are at least 223 Leucine-rich repeat receptor-like kinases (LRR-RLKs), representing one of the largest protein families. Although functional roles for a handful of LRR-RLKs have been revealed, the functions of the majority of members in this protein family have not been elucidated.As a resource for the in-depth analysis of this important protein family, the complementary DNA sequences (cDNAs) of 194 LRR-RLKs were cloned into the Gateway donor vector pDONR/Zeo and analyzed by DNA sequencing. Among them, 157 clones showed sequences identical to the predictions in the Arabidopsis sequence resource, TAIR8. The other 37 cDNAs showed gene structures distinct from the predictions of TAIR8, which was mainly caused by alternative splicing of pre-mRNA. Most of the genes have been further cloned into Gateway destination vectors with GFP or FLAG epitope tags and have been transformed into Arabidopsis for in planta functional analysis. All clones from this study have been submitted to the Arabidopsis Biological Resource Center (ABRC) at Ohio State University for full accessibility by the Arabidopsis research community.Most of the Arabidopsis LRR-RLK genes have been isolated and the sequence analysis showed a number of alternatively spliced variants. The generated resources, including cDNA entry clones, expression constructs and transgenic plants, will facilitate further functional analysis of the members of this important gene family. DA - 2010/1/11/ PY - 2010/1/11/ DO - 10.1186/1471-2164-11-19 VL - 11 SP - SN - 1471-2164 ER - TY - JOUR TI - Expanded Scope of Synthetic Bacteriochlorins via Improved Acid Catalysis Conditions and Diverse Dihydrodipyrrin-Acetals AU - Krayer, Michael AU - Ptaszek, Marcin AU - Kim, Han-Je AU - Meneely, Kelly R. AU - Fan, Dazhong AU - Secor, Kristen AU - Lindsey, Jonathan S. T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Bacteriochlorins are attractive candidates for a wide variety of photochemical studies owing to their strong absorption in the near-infrared spectral region. The prior acid-catalysis conditions [BF(3) x O(Et)(2) in CH(3)CN at room temperature] for self-condensation of a dihydrodipyrrin-acetal (bearing a geminal dimethyl group in the pyrroline ring) typically afforded a mixture of three macrocycles: the expected 5-methoxybacteriochlorin (MeOBC-type), a 5-unsubstituted bacteriochlorin (HBC-type), and a free base B,D-tetradehydrocorrin (TDC-type). Here, a broad survey of >20 acids identified four promising acid catalysis conditions of which TMSOTf/2,6-di-tert-butylpyridine in CH(2)Cl(2) at room temperature was most attractive owing to formation of the 5-methoxybacteriochlorin as the sole macrocycle regardless of the pyrrolic substituents in the dihydrodipyrrin-acetal (electron-withdrawing, electron-donating, or no substituent). Eleven new dihydrodipyrrin-acetals were prepared following standard routes. Application of the new acid catalysis conditions has afforded diverse bacteriochlorins (e.g., bearing alkyl/ester, aryl/ester, diester, and no substituents) in a few days from commercially available starting materials. Consideration of the synthetic steps and yields for formation of the dihydrodipyrrin-acetal and bacteriochlorin underpins evaluation of synthetic plans for early installation of bacteriochlorin substituents via the dihydrodipyrrin-acetal versus late installation via derivatization of beta-bromobacteriochlorins. Treatment of the 5-methoxybacteriochlorins with NBS gave regioselective 15-bromination when no pyrrolic substituents were present or when each pyrrole contained two substituents; on the other hand, the presence of a beta-ethoxycarbonyl group caused loss of regioselectivity. The 15 new bacteriochlorins prepared herein exhibit a long-wavelength absorption band in the range 707-759 nm, providing tunable access to the near-infrared region. Taken together, this study expands the scope of available bacteriochlorins for fundamental studies and diverse applications. DA - 2010/2/19/ PY - 2010/2/19/ DO - 10.1021/jo9025572 VL - 75 IS - 4 SP - 1016-1039 SN - 0022-3263 ER - TY - JOUR TI - De Novo Synthesis of Long-Wavelength Absorbing Chlorin-13,15-dicarboximides AU - Ptaszek, Marcin AU - Lahaye, Dorothee AU - Krayer, Michael AU - Muthiah, Chinnasamy AU - Lindsey, Jonathan S. T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Chlorins bearing a six-membered imide ring spanning positions 13-15, commonly referred to as purpurinimides, exhibit long-wavelength absorption yet have heretofore only been available via semisynthesis from naturally occurring chlorophylls. A concise route to synthetic chlorins, which bear a geminal dimethyl group in the pyrroline ring, has been extended to provide access to chlorin-13,15-dicarboximides. The new route entails (i) synthesis of a 13-bromochlorin, (ii) palladium-catalyzed carbamoylation at the 13-position, (iii) regioselective 15-bromination under acidic conditions, and (iv) one-flask palladium-mediated carbonylation and ring closure to form the imide. In some cases the ring closure reaction afforded the isomeric (and readily separable) chlorin-isoimide in addition to the chlorin-imide. The resulting chlorin-imides and chlorin-isoimides exhibit long-wavelength absorption (679-715 nm) and emission (683-720 nm) in the far-red and near-infrared spectral region. The absorption of the chlorin-(iso)imides fills the spectral window between that of analogous synthetic chlorins and 13(1)-oxophorbines (603-687 nm) and bacteriochlorins (707-792 nm). The synthetic versatility of the de novo route complements the existing semisynthetic route from chlorophylls and should enable fundamental spectroscopic studies and photochemical applications. DA - 2010/3/5/ PY - 2010/3/5/ DO - 10.1021/jo902649d VL - 75 IS - 5 SP - 1659-1673 SN - 1520-6904 ER - TY - JOUR TI - Acute mucosal pathogenesis of feline immunodeficiency virus is independent of viral dose in vaginally infected cats AU - Howard, Kristina E. AU - Reckling, Stacie K. AU - Egan, Erin A. AU - Dean, Gregg A. T2 - RETROVIROLOGY AB - The mucosal pathogenesis of HIV has been shown to be an important feature of infection and disease progression. HIV-1 infection causes depletion of intestinal lamina propria CD4+ T cells (LPL), therefore, intestinal CD4+ T cell preservation may be a useful correlate of protection in evaluating vaccine candidates. Vaccine studies employing the cat/FIV and macaque/SIV models frequently use high doses of parenterally administered challenge virus to ensure high plasma viremia in control animals. However, it is unclear if loss of mucosal T cells would occur regardless of initial viral inoculum dose. The objective of this study was to determine the acute effect of viral dose on mucosal leukocytes and associated innate and adaptive immune responses. Cats were vaginally inoculated with a high, middle or low dose of cell-associated and cell-free FIV. PBMC, serum and plasma were assessed every two weeks with tissues assessed eight weeks following infection. We found that irrespective of mucosally administered viral dose, FIV infection was induced in all cats. However, viremia was present in only half of the cats, and viral dose was unrelated to the development of viremia. Importantly, regardless of viral dose, all cats experienced significant losses of intestinal CD4+ LPL and CD8+ intraepithelial lymphocytes (IEL). Innate immune responses by CD56+CD3- NK cells correlated with aviremia and apparent occult infection but did not protect mucosal T cells. CD4+ and CD8+ T cells in viremic cats were more likely to produce cytokines in response to Gag stimulation, whereas aviremic cats T cells tended to produce cytokines in response to Env stimulation. However, while cell-mediated immune responses in aviremic cats may have helped reduce viral replication, they could not be correlated to the levels of viremia. Robust production of anti-FIV antibodies was positively correlated with the magnitude of viremia. Our results indicate that mucosal immune pathogenesis could be used as a rapid indicator of vaccine success or failure when combined with a physiologically relevant low dose mucosal challenge. We also show that innate immune responses may play an important role in controlling viral replication following acute mucosal infection, which has not been previously identified. DA - 2010/1/19/ PY - 2010/1/19/ DO - 10.1186/1742-4690-7-2 VL - 7 SP - SN - 1742-4690 ER - TY - JOUR TI - A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans AU - Mauchline, T. H. AU - Mohan, S. AU - Davies, K. G. AU - Schaff, J. E. AU - Opperman, C. H. AU - Kerry, B. R. AU - Hirsch, P. R. T2 - LETTERS IN APPLIED MICROBIOLOGY AB - Journal Article A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans Get access T.H. Mauchline, T.H. Mauchline Nematode Interactions Unit, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, UK Tim H. Mauchline, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, UK. E‐mail: tim.mauchline@bbsrc.ac.uk Search for other works by this author on: Oxford Academic Google Scholar S. Mohan, S. Mohan Nematode Interactions Unit, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, UK Division of Nematology, Indian Agricultural Research Institute, New Delhi, India Search for other works by this author on: Oxford Academic Google Scholar K.G. Davies, K.G. Davies Nematode Interactions Unit, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, UK Search for other works by this author on: Oxford Academic Google Scholar J.E. Schaff, J.E. Schaff Center for the Biology of Nematode Parasitism, North Carolina State University, Raleigh, NC, USA Search for other works by this author on: Oxford Academic Google Scholar C.H. Opperman, C.H. Opperman Center for the Biology of Nematode Parasitism, North Carolina State University, Raleigh, NC, USA Search for other works by this author on: Oxford Academic Google Scholar B.R. Kerry, B.R. Kerry Nematode Interactions Unit, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, UK Search for other works by this author on: Oxford Academic Google Scholar P.R. Hirsch P.R. Hirsch Nematode Interactions Unit, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, UK Search for other works by this author on: Oxford Academic Google Scholar Letters in Applied Microbiology, Volume 50, Issue 5, 1 May 2010, Pages 515–521, https://doi.org/10.1111/j.1472-765X.2010.02830.x Published: 01 May 2010 Article history Received: 25 October 2009 Revision received: 19 February 2010 Accepted: 19 February 2010 Published: 01 May 2010 DA - 2010/5// PY - 2010/5// DO - 10.1111/j.1472-765x.2010.02830.x VL - 50 IS - 5 SP - 515-521 SN - 0266-8254 KW - 16S rRNA gene KW - bead-beating KW - endospores KW - gyrB KW - microLYSIS (R)-PLUS KW - multiple strand amplification KW - Pasteuria penetrans KW - phi29 ER - TY - JOUR TI - Unravelling and managing fusiform rust disease: a model approach for coevolved forest tree pathosystems AU - Nelson, C. D. AU - Kubisiak, T. L. AU - Amerson, H. V. T2 - FOREST PATHOLOGY AB - Summary Fusiform rust disease remains the most destructive disease in pine plantations in the southern United States. Our ongoing research is designed to identify, map, and clone the interacting genes of the host and pathogen. Several resistance (R) genes have been identified and genetically mapped using informative pine families and single‐spore isolate inoculations. In addition, we are mapping the first of many expected corresponding avirulence (Avr) genes in the fungal pathogen. The Avr genes condition avirulence/virulence and avirulence is required for an incompatible reaction (i.e., no‐gall development) to take place within an inoculated tree that carries resistance at the corresponding R gene. We provide an overview of our methodology for identifying and mapping R and Avr genes, an update of our current progress, and a brief discussion of two approaches for predicting R gene genotypes of uncharacterized parental trees and for estimating the efficacy of specific pine genotypes at various planting locations. This paper emphasizes the critical importance of controlled genetic materials of both the host and pathogen for elucidating the genetic nature of resistance and virulence in coevolved forest pathosystems. DA - 2010/2// PY - 2010/2// DO - 10.1111/j.1439-0329.2009.00608.x VL - 40 IS - 1 SP - 64-72 SN - 1439-0329 ER - TY - PAT TI - Tobacco products with increased nicotine AU - Conkling, M. A. AU - Song, W. AU - Mendu, N. C2 - 2010/// DA - 2010/// PY - 2010/// ER - TY - JOUR TI - The E2FD/DEL2 factor is a component of a regulatory network controlling cell proliferation and development in Arabidopsis AU - Sozzani, Rosangela AU - Maggio, Caterina AU - Giordo, Roberta AU - Umana, Elisabetta AU - Ascencio-Ibanez, Jose Trinidad AU - Hanley-Bowdoin, Linda AU - Bergounioux, Catherine AU - Cella, Rino AU - Albani, Diego T2 - PLANT MOLECULAR BIOLOGY DA - 2010/3// PY - 2010/3// DO - 10.1007/s11103-009-9577-8 VL - 72 IS - 4-5 SP - 381-395 SN - 1573-5028 KW - Arabidopsis KW - Auxin KW - E2F transcription factors KW - Plant cell cycle KW - Plant development ER - TY - PAT TI - Refined routes to chlorin building blocks AU - Lindsey, J. S. AU - Taniguchi, M. AU - Ra, D. AU - Mo, G. AU - Balasubramanian, T. C2 - 2010/// DA - 2010/// PY - 2010/// ER - TY - JOUR TI - Increasing inositol (1,4,5)-trisphosphate metabolism affects drought tolerance, carbohydrate metabolism and phosphate-sensitive biomass increases in tomato AU - Khodakovskaya, M. AU - Sword, C. AU - Wu, Q. AU - Perera, I. Y. AU - Boss, W. F. AU - Brown, C. S. AU - Sederoff, H. W. T2 - Plant Biotechnology Journal AB - Summary Inositol‐(1,4,5)‐trisphosphate (InsP 3 ) is a second messenger in plants that increases in response to many stimuli. The metabolic consequences of this signalling pathway are not known. We reduced the basal level of InsP 3 in tomato ( Solanum lycopersicum cv. Micro‐Tom) by expressing the human type I inositol polyphosphate 5‐phosphatase (InsP 5‐ptase) gene. Transgenic lines producing InsP 5‐ptase protein had between 15% and 30% of the basal InsP 3 level of control plants. This increased hydrolysis of InsP 3 caused dramatic increases in drought tolerance, vegetative biomass and lycopene and hexose concentrations in the fruits. Transcript profiling of root, leaf and fruit tissues identified a small group of genes, including a cell‐wall invertase inhibitor gene, that were differentially regulated in all tissues of the InsP 5‐ptase expressing plants. Significant differences were found in the amounts of carbohydrates and organic phosphate in these plants. Plants with increased hydrolysis of InsP 3 in the cytosol also showed increased net CO 2 ‐fixation and sucrose export into sink tissue and storage of hexoses in the source leaves. The increase in biomass was dependent on the supply of inorganic phosphate in the nutrient medium. Uptake and storage of phosphate was increased in the transgene expressing lines. This suggests that in tomato, increased flux through the inositol phosphate pathway uncoupled phosphate sensing from phosphate metabolism. Altering the second messenger, InsP 3 , revealed multiple coordinated changes in development and metabolism in tomato that have potential for crop improvement. DA - 2010/// PY - 2010/// DO - 10.1111/j.1467-7652.2009.00472.x VL - 8 IS - 2 SP - 170-183 ER - TY - JOUR TI - High Prevalence of Tick-Borne Pathogens in Dogs from an Indian Reservation in Northeastern Arizona AU - Diniz, Pedro Paulo V.P. AU - Beall, Melissa J. AU - Omark, Karina AU - Chandrashekar, Ramaswamy AU - Daniluk, Daryn A. AU - Cyr, Katie E. AU - Koterski, James F. AU - Robbins, Richard G. AU - Lalo, Pamela G. AU - Hegarty, Barbara C. AU - Breitschwerdt, Edward B. T2 - Vector-Borne and Zoonotic Diseases AB - We evaluated the serological and molecular prevalence of selected organisms in 145 dogs during late spring (May/June) of 2005 and in 88 dogs during winter (February) of 2007 from the Hopi Indian reservation. Additionally, in 2005, 442 ticks attached to dogs were collected and identified as Rhipicephalus sanguineus. Infection with or exposure to at least one organism was detected in 69% and 66% of the dogs in May/June 2005 and February 2007, respectively. Exposure to spotted fever group (SFG) rickettsiae was detected in 66.4% (2005) and 53.4% (2007) of dogs, but rickettsial DNA was not detected using polymerase chain reaction. Active Ehrlichia canis infection (by polymerase chain reaction) was identified in 36.6% (2005) and 36.3% (2007) of the dogs. E. canis infection was associated with SFG rickettsiae seroreactivity (p < 0.001). Anaplasma platys DNA was detected in 8.3% (2005) and 4.5% (2007) of the dogs. Babesia canis and Bartonella vinsonii berkhoffii seroprevalences were 6.7% and 1% in 2005, whereas in 2007 prevalences were 0% and 1.1%, respectively. No Bartonella spp., Ehrlichia chaffeensis, or Ehrlichia ewingii DNA was detected. Dogs on this Hopi Indian reservation were most frequently infected with E. canis or A. platys; however, more than half of the dogs were exposed to a SFG-Rickettsia species. DA - 2010/3// PY - 2010/3// DO - 10.1089/vbz.2008.0184 VL - 10 IS - 2 SP - 117-123 J2 - Vector-Borne and Zoonotic Diseases LA - en OP - SN - 1530-3667 1557-7759 UR - http://dx.doi.org/10.1089/vbz.2008.0184 DB - Crossref KW - Anaplasma KW - Babesia KW - Bartonella KW - Ehrlichia KW - Rickettsia KW - Sentinel ER - TY - JOUR TI - Comparative Activity of Pradofloxacin, Enrofloxacin, and Azithromycin against Bartonella henselae Isolates Collected from Cats and a Human AU - Biswas, Silpak AU - Maggi, Ricardo G. AU - Papich, Mark G. AU - Keil, Daniel AU - Breitschwerdt, Edward B. T2 - JOURNAL OF CLINICAL MICROBIOLOGY AB - Using Bartonella henselae isolates from cats and a human, the activity of pradofloxacin was compared with those of enrofloxacin and azithromycin. By Etest and disc diffusion assay, pradofloxacin showed greater antimicrobial activity than did other antibiotics. We conclude that pradofloxacin may prove useful for the treatment of B. henselae infections. DA - 2010/2// PY - 2010/2// DO - 10.1128/jcm.01287-09 VL - 48 IS - 2 SP - 617-618 SN - 1098-660X ER - TY - JOUR TI - Bartonellosis: an emerging infectious disease of zoonotic importance to animals and human beings AU - Breitschwerdt, Edward B. AU - Maggi, Ricardo G. AU - Chomel, Bruno B. AU - Lappin, Michael R. T2 - Journal of Veterinary Emergency and Critical Care AB - Objective – To provide a review of clinically relevant observations related to Bartonella species as emerging pathogens in veterinary and human medicine. Data Sources – Literature as cited in PubMed and as generated by each of the authors who have contributed to various aspects of the clinical understanding of bartonellosis. Human Data Synthesis – Important historical and recent publications illustrating the evolving role of animal reservoirs as a source of human infection. Veterinary Data Synthesis – Comprehensive review of the veterinary literature. Conclusions – In addition to inducing life-threatening illnesses, such as endocarditis, myocarditis, and meningoencephalitis and contributing to chronic debilitating disease, such as arthritis, osteomyelitis, and granulomatous inflammation in cats, dogs, and potentially other animal species; pets and wildlife species can serve as persistently infected reservoir hosts for the transmission of Bartonella spp. infection to veterinary professionals and others with direct animal contact. DA - 2010/2// PY - 2010/2// DO - 10.1111/j.1476-4431.2009.00496.x VL - 20 IS - 1 SP - 8-30 LA - en OP - SN - 1479-3261 1476-4431 UR - http://dx.doi.org/10.1111/j.1476-4431.2009.00496.x DB - Crossref KW - bacteria KW - cat KW - diagnosis KW - disease KW - dog ER - TY - JOUR TI - Variable Selection for Semiparametric Mixed Models in Longitudinal Studies AU - Ni, Xiao AU - Zhang, Daowen AU - Zhang, Hao Helen T2 - BIOMETRICS AB - We propose a double-penalized likelihood approach for simultaneous model selection and estimation in semiparametric mixed models for longitudinal data. Two types of penalties are jointly imposed on the ordinary log-likelihood: the roughness penalty on the nonparametric baseline function and a nonconcave shrinkage penalty on linear coefficients to achieve model sparsity. Compared to existing estimation equation based approaches, our procedure provides valid inference for data with missing at random, and will be more efficient if the specified model is correct. Another advantage of the new procedure is its easy computation for both regression components and variance parameters. We show that the double-penalized problem can be conveniently reformulated into a linear mixed model framework, so that existing software can be directly used to implement our method. For the purpose of model inference, we derive both frequentist and Bayesian variance estimation for estimated parametric and nonparametric components. Simulation is used to evaluate and compare the performance of our method to the existing ones. We then apply the new method to a real data set from a lactation study. DA - 2010/3// PY - 2010/3// DO - 10.1111/j.1541-0420.2009.01240.x VL - 66 IS - 1 SP - 79-88 SN - 1541-0420 KW - Correlated data KW - Gaussian stochastic process KW - Linear mixed models KW - Smoothly clipped absolute deviation KW - Smoothing splines ER - TY - JOUR TI - An Assessment of the Genetic Diversity in a Field Population of Phytophthora nicotianae with a Changing Race Structure AU - Sullivan, M. J. AU - Parks, E. J. AU - Cubeta, M. A. AU - Gallup, C. A. AU - Melton, T. A. AU - Moyer, J. W. AU - Shew, H. D. T2 - PLANT DISEASE AB - One hundred fifty-three isolates of Phytophthora nicotianae that were collected over a 4-year period from a single field were subjected to amplified fragment length polymorphism (AFLP) analysis to investigate the effect of different types of resistance in tobacco (Nicotiana tabacum) on genetic diversity in the pathogen population. No race 1 isolates were detected in the field prior to initiating the study, but the race was present in multiple plots by the end of the 4-year period. There were 102 race 0 isolates and 51 race 1 isolates characterized. Seventy-six of the 153 isolates had a unique AFLP profile, whereas the remaining 77 isolates were represented by 27 AFLP profiles shared by at least two isolates. Isolates of both races were found in both the unique and shared AFLP profile groups. Twenty-three of the AFLP profiles were detected in multiple years, indicating a clonal component to the pathogen population. Race 1 isolates that were detected over multiple years were always obtained from the same plot. No race 1 profile was found in more than one plot, confirming the hypothesis that the multiple occurrences of the race throughout the field were the result of independent events and not pathogen spread. Three identical race 0 AFLP profiles occurred in noncontiguous plots, and in each case, the plots contained the same partially resistant variety. Cluster analysis provided a high level of bootstrap support for 41 isolates in 19 clusters that grouped primarily by race and rotation treatment. Estimates of genetic diversity ranged from 0.365 to 0.831 and varied depending on tobacco cultivar planted and race. When averaged over all treatments, diversity in race 1 isolates was lower than in race 0 isolates at the end of each season. Deployment of single-gene resistance initially decreased genetic diversity of the population, but the diversity increased each year, indicating the pathogen was adapting to the host genotypes deployed in the field. DA - 2010/4// PY - 2010/4// DO - 10.1094/pdis-94-4-0455 VL - 94 IS - 4 SP - 455-460 SN - 1943-7692 ER -