TY - CHAP TI - Trust-Based Secure Workflow Path Construction AU - Altunay, M. AU - Brown, D. AU - Byrd, G. AU - Dean, R. T2 - Service-Oriented Computing – ICSOC 2007 A2 - Benatallah, B. A2 - Casati, F. A2 - Traverso, P. T3 - Lecture Notes in Computer Science AB - Security and trust relationships between services significantly govern their willingness to collaborate and participate in a workflow. Existing workflow tools do not consider such relationships as an integral part of their planning logic: rather, they approach security as a run-time issue. We present a workflow management framework that fully integrates trust and security into the workflow planning logic. It considers not only trust relationships between the workflow requestor and individual services, but also trust relationships among the services themselves. It allows each service owner to define an upper layer of collaboration policies (rules that specify the terms under which participation in a workflow is allowed) and integrates them into the planning logic. Services that are unfit for collaboration due to security violations are replaced at the planning stage. This approach increases the services owners’ control over the workflow path, their willingness for collaboration, and avoids run-time security failures. PY - 2005/// DO - 10.1007/11596141_29 SP - 382–395 PB - Springer Berlin Heidelberg SN - 9783540749738 9783540749745 SV - 3826 UR - http://dx.doi.org/10.1007/11596141_29 ER - TY - JOUR TI - Genome sequence, comparative analysis and haplotype structure of the domestic dog AU - Lindblad-Toh, Kerstin AU - Wade, Claire M AU - Mikkelsen, Tarjei S. AU - Karlsson, Elinor K. AU - Jaffe, David B. AU - Kamal, Michael AU - Clamp, Michele AU - Chang, Jean L. AU - Kulbokas, Edward J., III AU - Zody, Michael C. AU - Mauceli, Evan AU - Xie, Xiaohui AU - Breen, Matthew AU - Wayne, Robert K. AU - Ostrander, Elaine A. AU - Ponting, Chris P. AU - Galibert, Francis AU - Smith, Douglas R. AU - deJong, Pieter J. AU - Kirkness, Ewen AU - Alvarez, Pablo AU - Biagi, Tara AU - Brockman, William AU - Butler, Jonathan AU - Chin, Chee-Wye AU - Cook, April AU - Cuff, James AU - Daly, Mark J. AU - DeCaprio, David AU - Gnerre, Sante AU - Grabherr, Manfred AU - Kellis, Manolis AU - Kleber, Michael AU - Bardeleben, Carolyne AU - Goodstadt, Leo AU - Heger, Andreas AU - Hitte, Christophe AU - Kim, Lisa AU - Koepfli, Klaus-Peter AU - Parker, Heidi G. AU - Pollinger, John P. AU - Searle, Stephen M. J. AU - Sutter, Nathan B. AU - Thomas, Rachael AU - Webber, Caleb AU - Lander, Eric S. T2 - Nature AB - Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health. DA - 2005/12// PY - 2005/12// DO - 10.1038/nature04338 VL - 438 IS - 7069 SP - 803-819 J2 - Nature LA - en OP - SN - 0028-0836 1476-4687 UR - http://dx.doi.org/10.1038/nature04338 DB - Crossref ER - TY - CHAP TI - Explicit construction of the hilbert class fields of imaginary quadratic fields with class numbers 7 and 11 AU - Kaltofen, Erich AU - Yui, Noriko T2 - EUROSAM 84 PY - 2005/12/1/ DO - 10.1007/bfb0032853 SP - 310-320 OP - PB - Springer-Verlag SN - 354013350X UR - http://dx.doi.org/10.1007/bfb0032853 DB - Crossref ER - TY - JOUR TI - Detection of Medically Important Ehrlichia by Quantitative Multicolor TaqMan Real-Time Polymerase Chain Reaction of the dsb Gene AU - Doyle, C. Kuyler AU - Labruna, Marcelo B. AU - Breitschwerdt, Edward B. AU - Tang, Yi-Wei AU - Corstvet, Richard E. AU - Hegarty, Barbara C. AU - Bloch, Karen C. AU - Li, Ping AU - Walker, David H. AU - McBride, Jere W. T2 - The Journal of Molecular Diagnostics AB - Ehrlichia species are the etiological agents of emerging and life-threatening tick-borne human zoonoses, in addition to causing serious and fatal infections in companion animals and livestock. We developed the first tricolor TaqMan real-time polymerase chain reaction assay capable of simultaneously detecting and discriminating medically important ehrlichiae in a single reaction. Analytical sensitivity of 50 copies per reaction was attained with templates from Ehrlichia chaffeensis, Ehrlichia ewingii, and Ehrlichia canis by amplifying the genus-specific disulfide bond formation protein gene (dsb). Ehrlichia genus-specific dsb primers amplified DNA from all known Ehrlichia species but not from other rickettsial organisms including Anaplasma platys, Anaplasma phagocytophilum, Rickettsia conorii, or Rickettsia typhi. High species specificity was attained as each species-specific TaqMan probe (E. chaffeensis, E. ewingii, and E. canis) identified homologous templates but did not cross-hybridize with heterologous Ehrlichia templates at concentrations as high as 10(8) copies. Identification of E. chaffeensis, E. ewingii, and E. canis from natural and experimental infections, previously confirmed by polymerase chain reaction and serological or microscopic evidence, demonstrated the comparable specificity and sensitivity of the dsb real-time assay. This assay provides a powerful tool for prospective medical diagnosis for human and canine ehrlichioses and for ecologic and epidemiological studies involving arthropod and mammalian hosts. DA - 2005/10// PY - 2005/10// DO - 10.1016/s1525-1578(10)60581-8 VL - 7 IS - 4 SP - 504-510 J2 - The Journal of Molecular Diagnostics LA - en OP - SN - 1525-1578 UR - http://dx.doi.org/10.1016/s1525-1578(10)60581-8 DB - Crossref ER - TY - JOUR TI - Structural and Electron-Transfer Characteristics of O-, S-, and Se-Tethered Porphyrin Monolayers on Si(100) [J. Am. Chem. Soc.2004,126, 15603−15612]. AU - Yasseri, Amir A. AU - Syomin, Dennis AU - Loewe, Robert S. AU - Lindsey, Jonathan S. AU - Zaera, Francisco AU - Bocian, David F. T2 - Journal of the American Chemical Society AB - ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionStructural and Electron-Transfer Characteristics of O-, S-, and Se-Tethered Porphyrin Monolayers on Si(100) [J. Am. Chem. Soc. 2004, 126, 15603−15612].Amir A. Yasseri, Dennis Syomin, Robert S. Loewe, Jonathan S. Lindsey, Francisco Zaera, and David F. BocianCite this: J. Am. Chem. Soc. 2005, 127, 25, 9308Publication Date (Web):June 2, 2005Publication History Published online2 June 2005Published inissue 1 June 2005https://doi.org/10.1021/ja053081dCopyright © 2005 American Chemical SocietyRequest reuse permissions This publication is free to access through this site. Learn MoreArticle Views438Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (10 KB) Get e-Alertsclose Get e-Alerts DA - 2005/6// PY - 2005/6// DO - 10.1021/ja053081d VL - 127 IS - 25 SP - 9308-9308 J2 - J. Am. Chem. Soc. LA - en OP - SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/ja053081d DB - Crossref ER - TY - JOUR TI - Conversion of nicotine to nornicotine in Nicotiana tabacum is mediated by CYP82E4, a cytochrome P450 monooxygenase AU - Siminszky, B. AU - Gavilano, L. AU - Bowen, S. W. AU - Dewey, R. E. T2 - Proceedings of the National Academy of Sciences AB - Nornicotine is a secondary tobacco alkaloid that is produced by the N-demethylation of nicotine. Nornicotine production and accumulation in tobacco are undesirable because nornicotine serves as the precursor in the synthesis of the well characterized carcinogen N ′-nitrosonornicotine during the curing and processing of tobacco. Although nornicotine is typically a minor alkaloid in tobacco plants, in many tobacco populations a high percentage of individuals can be found that convert a substantial proportion of the nicotine to nornicotine during leaf senescence and curing. We used a microarray-based strategy to identify genes that are differentially regulated between closely related tobacco lines that accumulate either nicotine (nonconverters) or nornicotine (converters) as the predominant alkaloid in the cured leaf. These experiments led to the identification of a small number of closely related cytochrome P450 genes, designated the CYP82E2 family, whose collective transcript levels were consistently higher in converter versus nonconverter tobacco lines. RNA interference-induced silencing of the CYP82E2 gene family suppressed the synthesis of nornicotine in strong converter plants to levels similar to that observed in nonconverter individuals. Although each of the six identified members of the P450 family share >90% nucleotide sequence identity, sense expression of three selected isoforms revealed that only one ( CYP82E4v1 ) was involved in the conversion of nicotine to nornicotine. Yeast expression analysis revealed that CYP82E4v1 functions as a nicotine demethylase. Identification of the gene(s) responsible for nicotine demethylation provides a potentially powerful tool toward efforts to minimize nornicotine levels, and thereby N ′-nitrosonornicotine formation, in tobacco products. DA - 2005/9/28/ PY - 2005/9/28/ DO - 10.1073/pnas.0506581102 VL - 102 IS - 41 SP - 14919-14924 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.0506581102 DB - Crossref KW - N '-nitrosonornicotine KW - N-demethylation KW - tobacco KW - alkaloid KW - tobacco-specific nitrosamines ER - TY - CONF TI - Generic matrix multiplication and memory management in linBox AU - Kaltofen, Erich AU - Morozov, Dmitriy AU - Yuhasz, George T2 - the 2005 international symposium AB - We describe the design and implementation of two components in the LinBox library. The first is an implementation of black box matrix multiplication as a lazy matrix-times-matrix product. The implementation uses template meta-programming to set the intermediate vector type used during application of the matrix product. We also describe an interface mechanism that allows incorporation of external components with native memory management such as garbage collection into LinBox. An implementation of the interface based on SACLIB's field arithmetic procedures is presented. C2 - 2005/// C3 - Proceedings of the 2005 international symposium on Symbolic and algebraic computation - ISSAC '05 DA - 2005/// DO - 10.1145/1073884.1073915 PB - ACM Press SN - 1595930957 UR - http://dx.doi.org/10.1145/1073884.1073915 DB - Crossref ER - TY - CONF TI - On the complexity of factoring bivariate supersparse (Lacunary) polynomials AU - Kaltofen, Erich AU - Koiran, Pascal T2 - the 2005 international symposium AB - We present algorithms that compute the linear and quadratic factors of supersparse (lacunary) bivariate polynomials over the rational numbers in polynomial-time in the input size. In supersparse polynomials, the term degrees can have hundreds of digits as binary numbers. Our algorithms are Monte Carlo randomized for quadratic factors and deterministic for linear factors. Our approach relies on the results by H. W. Lenstra, Jr., on computing factors of univariate supersparse polynomials over the rational numbers. Furthermore, we show that the problem of determining the irreducibility of a supersparse bivariate polynomial over a large finite field of any characteristic is co-NP-hard via randomized reductions. C2 - 2005/// C3 - Proceedings of the 2005 international symposium on Symbolic and algebraic computation - ISSAC '05 DA - 2005/// DO - 10.1145/1073884.1073914 PB - ACM Press SN - 1595930957 UR - http://dx.doi.org/10.1145/1073884.1073914 DB - Crossref ER - TY - JOUR TI - Nematode gene sequences: Update for December 2005 AU - McCarter, J.P. AU - Bird, D.McK. AU - Mitreva, M. T2 - Journal of Nematology DA - 2005/// PY - 2005/// VL - 37 IS - 4 SP - 417-421 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33744980477&partnerID=MN8TOARS ER - TY - JOUR TI - A white paper on nematode comparative genomics AU - Bird, D.McK. AU - Blaxter, M.L. AU - McCarter, J.P. AU - Mitreva, M. AU - Sternberg, P.W. AU - Thomas, W.K. T2 - Journal of Nematology DA - 2005/// PY - 2005/// VL - 37 IS - 4 SP - 408-416 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-33744994353&partnerID=MN8TOARS ER - TY - JOUR TI - Population structure of the tobacco blue mold pathogen Peronospora tabacina in the USA, the Caribbean and Central America AU - Blanco-Meneses, M AU - Ristaino, J T2 - Phytopathology DA - 2005/// PY - 2005/// VL - 95 IS - 6 ER - TY - CONF TI - Molecular evolution in the mitochondrial genome of the Irish Potato famine pathogen, Phytophthora infestans AU - Ristaino, J AU - Avila-Adame, C AU - Buell, R T2 - AMER PHYTOPATHOLOGICAL SOC 3340 PILOT KNOB ROAD, ST PAUL, MN 55121 USA C2 - 2005/// C3 - PHYTOPATHOLOGY DA - 2005/// VL - 95 SP - S89-S89 M1 - 6 ER - TY - JOUR TI - A 3-year field measurement of methane and nitrous oxide emissions from rice paddies in China: Effects of water regime, crop residue, and fertilizer application AU - Zou, Jianwen AU - Huang, Yao AU - Jiang, Jingyan AU - Zheng, Xunhua AU - Sass, Ronald L T2 - Global biogeochemical cycles DA - 2005/// PY - 2005/// VL - 19 IS - 2 ER - TY - JOUR TI - Gene genealogies inferred from nuclear and mitochondrial DNA sequences suggest a South American origin of Phytophthora infestans. Genealoǵıas de los genes deducidas de las secuencias de ADN nuclear y mitocondrial sugiere un origen suramericano de Phytophthora infestans. AU - Ristaino, J AU - Gomez-Alpizar, L AU - Thorne, J AU - Carbone, I T2 - Phytopathology. DA - 2005/// PY - 2005/// VL - 95 IS - 6 ER - TY - JOUR TI - Functional and species diversity of soil microbial communities in soils from organic, sustainable, and conventional farms in North Carolina AU - Bo, L AU - Ristaino, J AU - Glenn, D AU - Tu, C AU - Hu, S AU - Buckley, K AU - Gumpertz, M T2 - Phytopathology DA - 2005/// PY - 2005/// VL - 95 IS - 6 ER - TY - JOUR TI - Sequencing the Phytophthora infestans genome: preliminary studies AU - Zody, MC AU - O’Neill, K AU - Handsaker, B AU - Karlsson, E AU - Govers, F AU - Vondervoort, P AU - Weide, R AU - Whisson, S AU - Birch, P AU - LiJun, Ma AU - others DA - 2005/// PY - 2005/// ER - TY - CONF TI - Seedling resistance to Phytophthora cinammomi in the Genus Abies AU - Frampton, J. AU - Benson, D. M. AU - Li, J. AU - Brahan, A. M. AU - Hudson, E. E. AU - Potter, K. M. C2 - 2005/// C3 - Proceedings of the 28th Southern Forest Tree Improvement Conference DA - 2005/// SP - 146-147 ER - TY - CONF TI - Impacts of balsam woolly adelgid on the Southern Appalachian spruce-fir ecosystem and the North Carolina Christmas Tree Industry AU - Potter, K. AU - Frampton, J. AU - Sidebottom, J. C2 - 2005/// C3 - Third Symposium on Hemlock Woolly Adelgid in the Eastern United States, February 1-3, 2005, Renaissance Asheville Hotel, Asheville, North Carolina DA - 2005/// SP - 25-41 PB - USFS Forest Health Technology Enterprise Team ER - TY - CONF TI - Fraser fir population size and pollen dispersal: a landscape genetics model AU - Potter, K. M. AU - Frampton, J. AU - Potter, K. AU - Hess, G. R. C2 - 2005/// C3 - 20th Annual Symposium for the US Regional Chapter of the International Association for Landscape Ecology DA - 2005/// ER - TY - JOUR TI - Chestnut mast (newsletter of the Carolinas Chapter of The American Chestnut Foundation) AU - Frampton, J. AU - Frampton, J. T2 - Chestnut Mast DA - 2005/// PY - 2005/// VL - 6 IS - 1 ER - TY - CONF TI - An ex situ gene conservation plan for Fraser fir AU - Potter, K. M. AU - Frampton, J. C2 - 2005/// C3 - Proceedings of the 28th Southern Forest Tree Improvement Conference DA - 2005/// SP - 148-159 ER - TY - JOUR TI - My trip to Germany AU - Frampton, J. T2 - Limbs & Needles DA - 2005/// PY - 2005/// VL - 32 IS - 2 SP - 7-9 ER - TY - JOUR TI - Exotic fir research in North Carolina AU - Frampton, J. T2 - Nova Scotia Christmas Tree Journal DA - 2005/// PY - 2005/// VL - 19 IS - 3 SP - 5-10 ER - TY - JOUR TI - Building a better variety of Virginia pine AU - Frampton, J. T2 - American Christmas Tree Journal DA - 2005/// PY - 2005/// VL - 49 IS - 5 SP - 14-16 ER - TY - CONF TI - Variation of a-cellulose content and related metabolites during wood formation in loblolly pine AU - Morris, C. R. AU - Goldfarb, B. AU - Isik, F. AU - Li, C. S. AU - Chang, H.-M. AU - Sederoff, R. AU - Kadla, J. F. C2 - 2005/// C3 - 13th ISWFPC Proceedings DA - 2005/// VL - 13 ER - TY - CONF TI - Genetic variation in MFA, MOE and wood density among clones of Pinus taeda L. AU - Isik, F. AU - Li, B. AU - Goldfarb, B. C2 - 2005/// C3 - 28th Southern Forest Tree Improvement Conference DA - 2005/// VL - 28 ER - TY - JOUR TI - Genetic improvement of Virginia pine (Pinus virginiana Mill.) for Christmas tree production AU - Frampton, J. AU - Isik, F. T2 - Forest Genetics DA - 2005/// PY - 2005/// VL - 11 SP - 137-147 ER - TY - CONF TI - Total inside-bark volume estimation for loblolly pine (Pinus taeda L.) in genetic trials AU - Sherrill, J. R. AU - Mullin, T. J. AU - Bullock, B. P. AU - McKeand, S. E. AU - Purnell, R. C. AU - Gumpertz, M. L. C2 - 2005/// C3 - Proceedings of the 28th Southern Forest Tree Improvement Conference DA - 2005/// SP - 123-125 ER - TY - JOUR TI - Forest genetics and tree breeding in the age of genomics--IUFRO Conference AU - Li, B. AU - McKeand, S. E. T2 - Forest Genetics DA - 2005/// PY - 2005/// VL - 12 IS - 2 SP - 141-143 ER - TY - CONF TI - Comparing parameter estimation techniques for diameter distributions of loblolly pine AU - Smith, B. C. AU - Bullock, B. P. AU - McKeand, S. E. C2 - 2005/// C3 - Proceedings of the 28th Southern Forest Tree Improvement Conference DA - 2005/// SP - 104-106 ER - TY - CONF TI - Genetic variation in young Fraser fir progeny tests AU - Emerson, J. L. AU - Frampton, L. J. AU - McKeand, S. E. C2 - 2005/// C3 - Proceedings of the 28th Southern Forest Tree Improvement Conference DA - 2005/// SP - 115-117 ER - TY - JOUR TI - Bartonella henselae and Rickettsia seroreactivity in a sick cat population from North Carolina AU - Breitschwerdt, E. B. AU - Levine, J. F. AU - Radulovic, S. AU - Hanby, S. B. AU - Kordick, D. L. AU - Perle, K. M. D. la T2 - International Journal of Applied Research in Veterinary Medicine DA - 2005/// PY - 2005/// VL - 3 IS - 4 SP - 287 ER - TY - PAT TI - Open circuit potential amperometry and voltammetry AU - Kuhr, W. AU - Bocian, D. AU - Lindsey, J. S. AU - Roth, K. A. C2 - 2005/// DA - 2005/// PY - 2005/// ER - TY - PAT TI - Attachment of organic molecules to group III, IV or V substrates AU - Bocian, D. F. AU - Lindsey, J. S. AU - Liu, Z. AU - Yasseri, A. A. AU - Loewe, R. S. C2 - 2005/// DA - 2005/// PY - 2005/// ER - TY - PAT TI - Modifying nicotine and nitrosamine levels in tobacco AU - Conkling, M. A. C2 - 2005/// DA - 2005/// PY - 2005/// ER - TY - JOUR TI - Identification and functional analysis of in vivo phosphorylation sites of the Arabidopsis BRASSINOSTEROID-INSENSITIVE1 receptor kinase AU - Wang, XF AU - Goshe, MB AU - Soderblom, EJ AU - Phinney, BS AU - Kuchar, JA AU - Li, J AU - Asami, T AU - Yoshida, S AU - Huber, SC AU - Clouse, SD T2 - PLANT CELL AB - Brassinosteroids (BRs) regulate multiple aspects of plant growth and development and require an active BRASSINOSTEROID-INSENSITIVE1 (BRI1) and BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) for hormone perception and signal transduction. Many animal receptor kinases exhibit ligand-dependent oligomerization followed by autophosphorylation and activation of the intracellular kinase domain. To determine if early events in BR signaling share this mechanism, we used coimmunoprecipitation of epitope-tagged proteins to show that in vivo association of BRI1 and BAK1 was affected by endogenous and exogenous BR levels and that phosphorylation of both BRI1 and BAK1 on Thr residues was BR dependent. Immunoprecipitation of epitope-tagged BRI1 from Arabidopsis thaliana followed by liquid chromatography-tandem mass spectrometry (LC/MS/MS) identified S-838, S-858, T-872, and T-880 in the juxtamembrane region, T-982 in the kinase domain, and S-1168 in C-terminal region as in vivo phosphorylation sites of BRI1. MS analysis also strongly suggested that an additional two residues in the juxtamembrane region and three sites in the activation loop of kinase subdomain VII/VIII were phosphorylated in vivo. We also identified four specific BAK1 autophosphorylation sites in vitro using LC/MS/MS. Site-directed mutagenesis of identified and predicted BRI1 phosphorylation sites revealed that the highly conserved activation loop residue T-1049 and either S-1044 or T-1045 were essential for kinase function in vitro and normal BRI1 signaling in planta. Mutations in the juxtamembrane or C-terminal regions had only small observable effects on autophosphorylation and in planta signaling but dramatically affected phosphorylation of a peptide substrate in vitro. These findings are consistent with many aspects of the animal receptor kinase model in which ligand-dependent autophosphorylation of the activation loop generates a functional kinase, whereas phosphorylation of noncatalytic intracellular domains is required for recognition and/or phosphorylation of downstream substrates. DA - 2005/6// PY - 2005/6// DO - 10.1105/tpc.105.031393 VL - 17 IS - 6 SP - 1685-1703 SN - 1532-298X ER - TY - JOUR TI - Verification of QTL linked markers for propagation traits in Eucalyptus AU - Marques, C. M. AU - Carocha, V. J. AU - Sa, A. R. Pereira AU - Oliveira, M. R. AU - Pires, A. M. AU - Sederoff, R. AU - Borralho, N. M. G. T2 - TREE GENETICS & GENOMES DA - 2005/11// PY - 2005/11// DO - 10.1007/s11295-005-0013-1 VL - 1 IS - 3 SP - 103-108 SN - 1614-2950 KW - Eucalyptus KW - AFLP KW - QTL verification KW - vegetative propagation KW - marker-aided selection ER - TY - JOUR TI - Synthesis of dipyrrin-containing architectures AU - Muthukumaran, Kannan AU - Zaidi, Syeda Huma H. AU - Yu, Lianhe AU - Thamyongkit, Patchanita AU - Calder, Matthew E. AU - Sharada, Duddu S. AU - Lindsey, Jonathan S. T2 - JOURNAL OF PORPHYRINS AND PHTHALOCYANINES AB - Dipyrrins are valuable precursors to dyes [dipyrrinatoboron difluoride, bis(dipyrrinato)-zinc(II) complexes] and serve as ligands in a variety of self-assembled materials. Six new dipyrrin-containing architectures have been synthesized. The architectures include bis(dipyrrinato) complexes containing copper(II) or palladium(II), a dipyrrin bearing a protected phosphonic acid unit, a porphyrin bearing two dipyrrins in a trans configuration, a linear diphenylethyne-linked dipyrromethane-dipyrrin building block, and a triad composed of two zinc porphyrins joined via an intervening bis(dipyrrinato)copper(II) complex. Two porphodimethenatozinc complexes were prepared and found to have Φ f ≤ 0.002 (in toluene at room temperature), which is substantially less than the analogous bis(dipyrrinato)zinc complexes. Taken together, the syntheses described herein should broaden access to dipyrrins for use as complexation motifs in supramolecular chemistry and as pigments in light-harvesting applications. DA - 2005/// PY - 2005/// DO - 10.1142/S108842460500085X VL - 9 IS - 10-11 SP - 745-759 SN - 1099-1409 KW - self-assembly KW - dipyrrin KW - dipyrromethene KW - porphodimethene KW - dihydroporphyrin KW - metal complex KW - porphyrin ER - TY - PAT TI - Variable-persistence molecular memory devices and methods of operation thereof AU - Rotenberg, E. AU - Lindsey, J. S. C2 - 2005/// DA - 2005/// PY - 2005/// ER - TY - PAT TI - Synthesis of perylene-porphyrin building blocks and polymers thereof for the production of light-harvesting arrays AU - Loewe, R. S. AU - Tomizaki, K.-Y. AU - Lindsey, J. S. C2 - 2005/// DA - 2005/// PY - 2005/// ER - TY - PAT TI - Refined routes to chlorin building blocks AU - Lindsey, J. S. AU - Taniguchi, M. AU - Ra, D. AU - M, G. AU - Balasubramanian, T. C2 - 2005/// DA - 2005/// PY - 2005/// ER - TY - PAT TI - Promoter fragment that is recognized by the product of the tobacco Nic gene AU - Conkling, M. A. AU - Li, Y. C2 - 2005/// DA - 2005/// PY - 2005/// ER - TY - PAT TI - Facile synthesis of 1,9-diacyldipyrromethanes AU - Lindsey, J. S. AU - Tamaru, S.-I. AU - Yu, L. C2 - 2005/// DA - 2005/// PY - 2005/// ER - TY - JOUR TI - Extension of multifactor dimensionality reduction for identifying multilocus effects in the GAW14 simulated data AU - Mei, H. AU - Ma, D. Q. AU - Ashley-Koch, A. AU - Martin, E. R. T2 - BMC Genetics DA - 2005/// PY - 2005/// VL - 6 ER - TY - JOUR TI - A trichloroacetic acid-acetone method greatly reduces infrared autofluorescence of protein extracts from plant tissue AU - Shultz, RW AU - Settlage, SB AU - Hanley-Bowdoin, L AU - Thompson, WF T2 - PLANT MOLECULAR BIOLOGY REPORTER DA - 2005/12// PY - 2005/12// DO - 10.1007/BF02788888 VL - 23 IS - 4 SP - 405-409 SN - 0735-9640 KW - Arabidopsis KW - autofluorescence KW - immunoblot KW - infrared KW - Odyssey KW - plant ER - TY - JOUR TI - Viral genetic determinants for thrips transmission of Tomato spotted wilt virus AU - Sin, SH AU - McNulty, BC AU - Kennedy, GG AU - Moyer, JW T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Tomato spotted wilt virus (TSWV) is transmitted exclusively by thrips in nature. A reassortment-based viral genetic system was used to map transmissibility by thrips to the medium (M) RNA of TSWV. To locate determinants of thrips transmission in the M RNA, 30 single-lesion isolates (SLIs) were generated from a single TSWV isolate that was inefficiently transmitted by thrips. Three of the 30 SLIs were transmitted by thrips, and 27 were not. Sequence analysis of the M RNA, thrips transmissibility assays, G C protein analysis, and transmission electron microscopic studies revealed that a specific nonsynonymous mutation (C1375A) in the G N /G C ORF of the M RNA resulted in the loss of thrips transmissibility without inhibition of virion assembly. This was in contrast to other nontransmissible SLIs, which had frameshift and/or nonsense mutations in the G N /G C ORF but were defective in virion assembly. The G C glycoprotein was detectable in the C1375A mutants but not in the frameshift or nonsense mutants. We report a specific viral determinant associated with virus transmission by thrips. In addition, the loss of transmissibility was associated with the accumulation of defective haplotypes in the population, which are not transmissible by thrips, rather than with the presence of a dominant haplotype that is inefficiently transmitted by thrips. These results also indicate that the glycoproteins may not be required for TSWV infection of plant hosts but are required for transmissibility by thrips. DA - 2005/4/5/ PY - 2005/4/5/ DO - 10.1073/pnas.0407354102 VL - 102 IS - 14 SP - 5168-5173 SN - 0027-8424 ER - TY - JOUR TI - Sarcopenia is related to physical functioning and leg strength in middle-aged women AU - Sowers, MR AU - Crutchfield, M AU - Richards, K AU - Wilkin, MK AU - Furniss, A AU - Jannausch, M AU - Zhang, DW AU - Gross, M T2 - JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES AB - In the aging process, loss of muscle is relatively continuous, but the initiation, timing, and amount of muscle loss that relate to functional compromise are poorly described. Also poorly understood is whether strength and functioning in aging are related to the amount of lean mass and its change as well as to the amount of fat mass and its change.The purpose of the study was to ascertain whether 3-year lean and fat mass change predicted functional status in 712 African American and Caucasian women, aged 34-58 years. Fat and lean mass were assessed with bioelectrical impedance. Lower leg strength (torque) was measured with a portable isometric chair, and two indices of physical functioning, walking velocity and double support (both feet touching the surface while walking), were measured with an instrumented gait mat.Almost 9% of middle-aged women had at least a 6% loss (>2.5 kg) of lean mass over the 3-year observation period. Women who lost at least 2.5 kg of lean mass had slower walking velocity and less leg strength, although women who simultaneously gained more than 2.5 kg of fat mass (at least 7.5%) did not have less leg strength. Age was significantly associated with less velocity, less leg strength, and more time in double support.Even in middle-aged women, there is loss of lean mass among almost 1 woman in 10, and this loss of lean mass (sarcopenia) is associated with greater compromise in physical functioning. DA - 2005/4// PY - 2005/4// DO - 10.1093/gerona/60.4.486 VL - 60 IS - 4 SP - 486-490 SN - 1758-535X ER - TY - JOUR TI - Quantitative trait loci affecting the difference in pigmentation between Drosophila yakuba and D. santomea AU - Carbone, MA AU - Llopart, A AU - DeAngelis, M AU - Coyne, JA AU - Mackay, TFC T2 - GENETICS AB - Using quantitative trait locus (QTL) mapping, we studied the genetic basis of the difference in pigmentation between two sister species of Drosophila: Drosophila yakuba, which, like other members of the D. melanogaster subgroup, shows heavy black pigmentation on the abdomen of males and females, and D. santomea, an endemic to the African island of São Tomé, which has virtually no pigmentation. Here we mapped four QTL with large effects on this interspecific difference in pigmentation: two on the X chromosome and one each on the second and third chromosomes. The same four QTL were detected in male hybrids in the backcrosses to both D. santomea and D. yakuba and in the female D. yakuba backcross hybrids. All four QTL exhibited strong epistatic interactions in male backcross hybrids, but only one pair of QTL interacted in females from the backcross to D. yabuka. All QTL from each species affected pigmentation in the same direction, consistent with adaptive evolution driven by directional natural selection. The regions delimited by the QTL included many positional candidate loci in the pigmentation pathway, including genes affecting catecholamine biosynthesis, melanization of the cuticle, and many additional pleiotropic effects. DA - 2005/9// PY - 2005/9// DO - 10.1534/genetics.105.044412 VL - 171 IS - 1 SP - 211-225 SN - 1943-2631 ER - TY - JOUR TI - Pinocchio, a novel protein expressed in the antenna, contributes to olfactory behavior in Drosophila melanogaster AU - Rollmann, SM AU - Mackay, TFC AU - Anholt, RRH T2 - JOURNAL OF NEUROBIOLOGY AB - Most organisms depend on chemoreception for survival and reproduction. In Drosophila melanogaster multigene families of chemosensory receptors and putative odorant binding proteins have been identified. Here, we introduce an additional distinct protein, encoded by the CG4710 gene, that contributes to olfactory behavior. Previously, we identified through P[lArB]-element mutagenesis a smell impaired (smi) mutant, smi21F, with odorant-specific defects in avoidance responses. Here, we show that the smi21F mutant also exhibits reduced attractant responses to some, but not all, of a select group of odorants. Furthermore, electroantennogram amplitudes are increased in smi21F flies. Characterization of flanking sequences of the P[lArB] insertion site, complementation mapping, phenotypic reversion through P-element excision, and expression analysis implicate a predicted gene, CG4710, as the candidate smi gene. CG4710 produces two transcripts that encode proteins that contain conserved cysteines and which are reduced in the smi21F mutant. Furthermore, in situ hybridization reveals CG4710 expression in the third antennal segment. We have named this gene of previously unknown function and its product “Pinocchio (Pino)”. © 2005 Wiley Periodicals, Inc. J Neurobiol., 2005 DA - 2005/5// PY - 2005/5// DO - 10.1002/neu.20123 VL - 63 IS - 2 SP - 146-158 SN - 0022-3034 KW - olfaction KW - P-element mutagenesis KW - behavioral genetics KW - chemoreception ER - TY - JOUR TI - Oleate desaturase enzymes of soybean: evidence of regulation through differential stability and phosphorylation AU - Tang, GQ AU - Novitzky, WP AU - Griffin, HC AU - Huber, SC AU - Dewey, RE T2 - PLANT JOURNAL AB - The endoplasmic reticulum-associated oleate desaturase FAD2 (1-acyl-2-oleoyl-sn-glycero-3-phosphocholine Delta12-desaturase) is the key enzyme responsible for the production of linoleic acid in non-photosynthetic tissues of plants. Little is known, however, concerning the post-transcriptional mechanisms that regulate the activity of this important enzyme. The soybean genome possesses two seed-specific isoforms of FAD2, designated FAD2-1A and FAD2-1B, which differ at only 24 amino acid residues. Expression studies in yeast revealed that the FAD2-1A isoform is more unstable than FAD2-1B, particularly when cultures were maintained at elevated growth temperatures. Analysis of chimeric FAD2-1 constructs led to the identification of two domains that appear to be important in mediating the temperature-dependent instability of the FAD2-1A isoform. The enhanced degradation of FAD2-1A at high growth temperatures was partially abrogated by treating the cultures with the 26S proteasome-specific inhibitor MG132, and by expressing the FAD2-1A cDNA in yeast strains devoid of certain ubiquitin-conjugating activities, suggesting a role for ubiquitination and the 26S proteasome in protein turnover. In addition, phosphorylation state-specific antipeptide antibodies demonstrated that the Serine-185 of FAD2-1 sequences is phosphorylated during soybean seed development. Expression studies of phosphopeptide mimic mutations in yeast suggest that phosphorylation may downregulate enzyme activity. Collectively, the results show that post-translational regulatory mechanisms are likely to play an important role in modulating FAD2-1 enzyme activities. DA - 2005/11// PY - 2005/11// DO - 10.1111/j.1365-313X.2005.02535.x VL - 44 IS - 3 SP - 433-446 SN - 1365-313X KW - oleate desaturase KW - FAD2 KW - protein phosphorylation KW - 26S proteasome KW - polyunsaturated fatty acids KW - soybean (Glycine max) ER - TY - JOUR TI - Isolation of necrotoxigenic Escherichia coli from a dog with hemorrhagic pneumonia AU - Breitschwerdt, Edward B. AU - DebRoy, Chitrita AU - Mexas, Angela M. AU - Brown, Talmage T. AU - Remick, Amera K. T2 - Journal of the American Veterinary Medical Association AB - A 7-month-old sexually intact male Cocker Spaniel was admitted to the North Carolina State University Veterinary Teaching Hospital for evaluation of lethargy, panting, and excessive salivation that had become progressively severe during a 5-hour period. Despite intensive medical care, the dog died within the first 24 hours of hospitalization, and death was attributed to acute, severe, necrotizing pneumonia. Lung tissue collected at necropsy by use of swabs was cultured and yielded an isolate of Escherichia coli; because of the rapid progression of illness in an otherwise healthy dog, the isolate underwent virulence typing and was determined to be a necrotoxigenic E. coli. Necrotoxigenic E. coli produce a toxin called cytotoxic necrotizing factor and are known to be involved in extraintestinal infections, including urinary tract infection, in humans and animals. Virulence typing of E. coli isolates from dogs with peracute pneumonia is recommended to further characterize the epidemiologic characteristics and public health importance of necrotoxigenic E. coli. DA - 2005/6// PY - 2005/6// DO - 10.2460/javma.2005.226.2016 VL - 226 IS - 12 SP - 2016-2019 J2 - Journal of the American Veterinary Medical Association LA - en OP - SN - 0003-1488 UR - http://dx.doi.org/10.2460/javma.2005.226.2016 DB - Crossref ER - TY - JOUR TI - Enzyme function of the globin dehaloperoxidase from Amphitrite ornata is activated by substrate binding AU - Belyea, J AU - Gilvey, LB AU - Davis, MF AU - Godek, M AU - Sit, TL AU - Lommel, SA AU - Franzen, S T2 - BIOCHEMISTRY AB - Amphitrite ornata dehaloperoxidase (DHP) is a heme enzyme with a globin structure, which is capable of oxidizing para-halogenated phenols to the corresponding quinones. Cloning, high-level expression, and purification of recombinant DHP are described. Recombinant DHP was assayed by stopped-flow experiments for its ability to oxidatively debrominate 2,4,6-tribromophenol (TBP). The enzymatic activity of the ferric form of recombinant DHP is intermediate between that of a typical peroxidase (horseradish peroxidase) and a typical globin (horse heart myoglobin). The present study shows that, unlike other known peroxidases, DHP activity requires the addition of substrate, TBP, prior to the cosubstrate, peroxide. The presence of a substrate-binding site in DHP is consistent with a two-electron oxidation mechanism and an obligatory order for activation of the enzyme by addition of the substrate prior to the cosubstrate. DA - 2005/12/6/ PY - 2005/12/6/ DO - 10.1021/bi051731k VL - 44 IS - 48 SP - 15637-15644 SN - 0006-2960 ER - TY - JOUR TI - Comparison of morphological and chemical properties between juvenile wood and compression wood of loblolly pine AU - Yeh, TF AU - Goldfarb, B AU - Chang, HM AU - Peszlen, I AU - Braun, JL AU - Kadla, JF T2 - HOLZFORSCHUNG AB - Abstract In conifers, juvenile wood (JW) is always associated with compression wood (CW). Due to their similar properties, there is a common belief that JW is the same as CW. To resolve whether JW is identical to CW, 24 rooted cuttings of one loblolly pine clone were planted in growth chambers under normal, artificial bending, and windy environments. The results show that the morphology of JW is significantly different from CW. Furthermore, chemical analyses revealed that JW and CW are significantly different in chemical composition. Our results indicate that JW is different from CW, and the wood formed under a controlled windy environment is a mild type of compression wood. DA - 2005/// PY - 2005/// DO - 10.1515/hf.2005.107 VL - 59 IS - 6 SP - 669-674 SN - 1437-434X KW - C9 formula KW - compression wood KW - fiber quality analysis (FQA) KW - juvenile wood KW - light microscopy KW - loblolly pine (Pinus taeda) KW - nitrobenzene oxidation KW - ozonation KW - sugar analysis ER - TY - JOUR TI - Adsorption characteristics of tripodal thiol-functionalized porphyrins on gold AU - Wei, LY AU - Tiznado, H AU - Liu, GM AU - Padmaja, K AU - Lindsey, JS AU - Zaera, F AU - Bocian, DF T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - X-ray photoelectron and Fourier transform infrared spectroscopy studies are reported for self-assembled monolayers (SAMs) of two tripodal thiol-functionalized metalloporphyrins (Zn and Cu) and three benchmark tripods on gold substrates. The tripodal unit common to all five molecules is 1-(phenyl)-1,1,1-tris(4-mercaptomethylphenyl)methane (Tpd). Both porphyrins contain S-acetyl-protected thiols and are linked to the 4-position of the phenyl ring of Tpd via a phenylethyne group. The benchmark molecules include (1) two tripods containing a bromine atom at the 4-position of the apical phenyl ring, one a free thiol and the other its S-acetyl-protected analogue, and (2) a S-acetyl-protected tripod containing a phenylethyne unit at the 4-position of the apical phenyl group. Together, the spectroscopic studies reveal that none of the five tripodal molecules bond to the gold surface via all three sulfur atoms. Instead, the average number of bound thiols ranges from 1.5 to 2, with the porphyrinic molecules generally falling at the middle to upper end of the range and the smallest benchmark tripods falling at the lower end. Similar surface binding is found for the S-acetyl-protected and free benchmark tripods, indicating that the presence of the protecting group does not influence binding. Furthermore, the surface binding characteristics of the SAMs are not sensitive to deposition conditions such as solvent type, deposition time, or temperature of the solution. DA - 2005/12/22/ PY - 2005/12/22/ DO - 10.1021/jp0537005 VL - 109 IS - 50 SP - 23963-23971 SN - 1520-6106 ER - TY - JOUR TI - The evolutionary dynamics of plant duplicate genes AU - Moore, RC AU - Purugganan, MD T2 - CURRENT OPINION IN PLANT BIOLOGY AB - Given the prevalence of duplicate genes and genomes in plant species, the study of their evolutionary dynamics has been a focus of study in plant evolutionary genetics over the past two decades. The past few years have been a particularly exciting time because recent theoretical and experimental investigations have led to a rethinking of the classic paradigm of duplicate gene evolution. By combining recent advances in genomic analysis with a new conceptual framework, researchers are determining the contributions of single-gene and whole-genome duplications to the diversification of plant species. This research provides insights into the roles that gene and genome duplications play in plant evolution. DA - 2005/4// PY - 2005/4// DO - 10.1016/j.pbi.2004.12.001 VL - 8 IS - 2 SP - 122-128 SN - 1879-0356 ER - TY - JOUR TI - Structural and electron-transfer characteristics of carbon-tethered porphyrin monolayers on Si(100) AU - Wei, LY AU - Syomin, D AU - Loewe, RS AU - Lindsey, JS AU - Zaera, F AU - Bocian, DF T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - Structural and electron-transfer characteristics are reported for two classes of zinc porphyrin monolayers attached to Si(100) surfaces via Si-C bonds. One class, designated ZnP(CH(2))(n)- (n = 2-4), contains an alkyl linker appended to the meso-position of the porphyrin, with the nonlinking substituents being p-tolyl groups. The other, designated ZnPPh(CH(2))(n)- (n = 0-3), contains a phenyl or phenylalkyl linker appended to the meso-position of the porphyrin, with the nonlinking substituents being mesityl groups. Both classes of zinc porphyrin monolayers on Si(100) were examined using Fourier transform infrared spectroscopy and various electrochemical methods. The studies reveal the following: (1) The structural and electron-transfer characteristics of the ZnP(CH(2))(n)- and ZnPPh(CH(2))(n)- monolayers are generally similar to those of monolayers formed from porphyrins with analogous linkers, but anchored with an O, a S, or a Se atom. (2) The ZnP(CH(2))(n)-, ZnPPh-, and ZnPPhCH(2)- monolayers exhibit lower saturation coverages and have their porphyrin ring more tilted with respect to the surface normal than the ZnPPh(CH(2))(2)- and ZnPPh(CH(2))(3)- monolayers. (3) The electron-transfer rates for both the ZnP(CH(2))(n)- and ZnPPh(CH(2))(n)- classes of monolayers monotonically decrease as the length of the linker increases. (4) For all the ZnP(CH(2))(n)- and ZnPPh(CH(2))(n)- monolayers, both electron-transfer rates and charge-dissipation rates decrease monotonically as the surface coverage increases. Collectively, the studies reported herein provide a detailed picture of how the linker type influences the structural and electron-transfer characteristics of these general classes of monolayers. DA - 2005/4/7/ PY - 2005/4/7/ DO - 10.1021/jp044558v VL - 109 IS - 13 SP - 6323-6330 SN - 1520-6106 ER - TY - JOUR TI - Resolving tylenchid evolutionary relationships through multiple gene analysis derived from EST data AU - Scholl, EH AU - Bird, DM T2 - MOLECULAR PHYLOGENETICS AND EVOLUTION AB - Sequence-based phylogenetic analyses typically are based on a small number of character sets and report gene trees which may not reflect the true species tree. We employed an EST mining strategy to suppress such incongruencies, and recovered the most robust phylogeny for five species of plant-parasitic nematode (Meloidogyne arenaria, M. chitwoodi, M. hapla, M. incognita, and M. javanica), three closely related tylenchid taxa (Heterodera glycines, Globodera pallida, and G. rostochiensis) and a distant taxon, Caenorhabditis elegans. Our multiple-gene approach is based on sampling more than 80,000 publicly available tylenchid EST sequences to identify phylum-wide orthologues. Bayesian inference, minimum evolution, maximum likelihood and protein distance methods were employed for phylogenetic reconstruction and hypothesis tests were constructed to elucidate differential selective pressures across the phylogeny for each gene. Our results place M. incognita and M. javanica as sister taxa, with M. arenaria as the next closely related nematode. Significant differences in selective pressure were revealed for some genes under some hypotheses, though all but one gene are exclusively under purifying selection, indicating conservation across the orthologous groups. This EST-based multi-gene analysis is a first step towards accomplishing genome-wide coverage for tylenchid evolutionary analyses. DA - 2005/9// PY - 2005/9// DO - 10.1016/j.ympev.2005.03.016 VL - 36 IS - 3 SP - 536-545 SN - 1095-9513 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-21744452353&partnerID=MN8TOARS KW - Bayesian KW - Caenorhabditis elegans KW - COG KW - cyst nematode KW - orthologues KW - root-knot nematode ER - TY - JOUR TI - Organ-specific roles for transcription factor NF-kappa B in reovirus-induced apoptosis and disease AU - Sherry, B. T2 - Journal of Clinical Investigation DA - 2005/// PY - 2005/// VL - 115 IS - 9 SP - 2341-2350 ER - TY - JOUR TI - Olanzapine versus risperidone in newly admitted acutely ill psychotic patients AU - Kraus, JE AU - Sheitman, BB AU - Cook, A AU - Reviere, R AU - Lieberman, JA T2 - JOURNAL OF CLINICAL PSYCHIATRY AB - Risperidone and olanzapine are the 2 most widely prescribed second-generation anti-psychotics. The purpose of this study was to compare the efficacy of risperidone and olanzapine using duration of hospitalization as the primary outcome measure. This outcome was selected as it is an indirect measure of how well patients are responding to the medication and represents a "real world" endpoint relevant to practicing hospital psychiatrists.The study was done at a large state psychiatric hospital in North Carolina from 2001 to 2003. Subjects were eligible for inclusion if they required treatment with an antipsychotic (e.g., positive symptoms) and were able to provide informed consent. Eighty-five patients entered the study and were randomly assigned to risperidone (N = 40) or olanzapine (N = 45) as their initial antipsychotic. Treatment was naturalistic, and dosing was based on the discretion of the treating physician.There was no significant difference in the mean durations of hospitalization for the risperidone group (7.9 days) as compared to the olanzapine group (8.1 days). There were no significant differences in the demographics of either treatment group, but, during the study, risperidone-treated patients used more antihistamines (chi(2) = 4.0, p = .05). Eighty percent of each group (N = 36, olanzapine; N = 32, risperidone) remained on the study medication at discharge.Risperidone and olanzapine were equally efficacious, suggesting that measures other than "efficacy" (e.g., side effects, cost) should be considered when determining overall "effectiveness" of treatment. DA - 2005/12// PY - 2005/12// DO - 10.4088/JCP.v66n1211 VL - 66 IS - 12 SP - 1564-1568 SN - 1555-2101 ER - TY - JOUR TI - NMR studies on Fraser fir Abies fraseri (Pursh) Poir. Lignins (vol 59, 488, 2005) AU - Balakshin, MY AU - Capanema, EA AU - Goldfarb, B AU - Frampton, J AU - Kadla, JF T2 - HOLZFORSCHUNG AB - Abstracting & Indexing DA - 2005/// PY - 2005/// DO - 10.1515/hf.2005.112 VL - 59 IS - 6 SP - 706-706 SN - 1437-434X ER - TY - JOUR TI - Methodology for isolation and phenotypic characterization of feline small intestinal leukocytes AU - Howard, KE AU - Fisher, IL AU - Dean, GA AU - Burkhard, MJ T2 - JOURNAL OF IMMUNOLOGICAL METHODS AB - Critical assessment of intestinal immune responses requires the ability to characterize leukocytes from different anatomic locations as leukocytes from inductive sites such as Peyer's patches and lymphoid follicles vary significantly from their effector counterparts, intraepithelial lymphocytes (IEL) and lamina propria lymphocytes (LPL). This study describes (1) methods developed to isolate specific intestinal leukocyte populations with high yield and purity, (2) difficulties encountered in establishing a panel of monoclonal antibodies to assess phenotype, and (3) the phenotypic characterization of effector and inductive sites in the feline small intestine. We found that the phenotypic distribution of feline intestinal leukocytes was similar to that found in other species such as humans, macaques and mice. The majority of IEL were CD5(+) T-cells with less than 7% B-cells. CD8(+) T-cells comprised approximately 60% of the IEL with roughly half displaying CD8alphaalpha homodimers. Approximately 10% of IEL were CD4(+) T-cells. In the LPL, CD4(+) T-cells predominated at 42%, with 33% CD8(+) T-cells and 10% B-cells. As would be expected, B-cells predominated in Peyer's patches with 40% B-cells, 28% CD4(+) T-cells and 20% CD8(+) T-cells. Increased MHCII expression was found in the Peyer's patches as compared to the IEL and LPL. B7.1 expression was significantly higher in mucosal leukocyte populations as compared to organized lymphoid tissue in the periphery with expression detected on 65% of IEL and 53% of LPL. Plasma cells were found in all regions of small intestine examined with greater numbers in lamina propria and Peyer's patches. Lymphoblasts were only identified in inductive tissue. In general, no differences were found between the phenotype of mucosal leukocyte populations from specific pathogen free or random source cats. However, the percentage of CD4(+) CD25(+) T-cells was significantly greater in both IEL and LPL from random source animals. This study provides techniques and a baseline from which future studies of the feline intestinal immune system can be conducted. DA - 2005/7// PY - 2005/7// DO - 10.1016/j.jim.2005.04.019 VL - 302 IS - 1-2 SP - 36-53 SN - 1872-7905 KW - feline KW - small intestine KW - IEL KW - LPL KW - Peyer's patches KW - phenotype ER - TY - JOUR TI - Genotypic probabilities for pairs of inbred relatives AU - Liu, W. L. AU - Weir, B. S. T2 - Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences DA - 2005/// PY - 2005/// VL - 360 IS - 1459 SP - 1379-1385 ER - TY - JOUR TI - Conjugated linoleic acid evokes de-lipidation through the regulation of genes controlling lipid metabolism in adipose and liver tissue AU - House, RL AU - Cassady, JP AU - Eisen, EJ AU - McIntosh, MK AU - Odle, J T2 - OBESITY REVIEWS AB - Conjugated linoleic acid (CLA) is a unique lipid that elicits dramatic reductions in adiposity in several animal models when included at < or = 1% of the diet. Despite a flurry of investigations, the precise mechanisms by which conjugated linoleic acid elicits its dramatic effects in adipose tissue and liver are still largely unknown. In vivo and in vitro analyses of physiological modifications imparted by conjugated linoleic acid on protein and gene expression suggest that conjugated linoleic acid exerts its de-lipidating effects by modulating energy expenditure, apoptosis, fatty acid oxidation, lipolysis, stromal vascular cell differentiation and lipogenesis. The purpose of this review shall be to examine the recent advances and insights into conjugated linoleic acid's effects on obesity and lipid metabolism, specifically focused on changes in gene expression and physiology of liver and adipose tissue. DA - 2005/8// PY - 2005/8// DO - 10.1111/j.1467-789X.2005.00198.x VL - 6 IS - 3 SP - 247-258 SN - 1467-789X KW - adipocyte KW - adipose tissue KW - CLA KW - de-lipidation KW - lipid metabolism KW - liver tissue KW - obesity ER - TY - JOUR TI - Characterization and enzymatic degradation of Sup35NM, a yeast prion-like protein AU - Chen, CY AU - Rojanatavorn, K AU - Clark, AC AU - Shih, JCH T2 - PROTEIN SCIENCE AB - Transmissible spongiform encephalopathies (TSEs) are believed to be caused by an unconventional infectious agent, the prion protein. The pathogenic and infectious form of prion protein, PrPSc, is able to aggregate and form amyloid fibrils, very stable and resistant to most disinfecting processes and common proteases. Under specific conditions, PrPSc in bovine spongiform encephalopathy (BSE) brain tissue was found degradable by a bacterial keratinase and some other proteases. Since this disease-causing prion is infectious and dangerous to work with, a model or surrogate protein that is safe is needed for the in vitro degradation study. Here a nonpathogenic yeast prion-like protein, Sup35NM, cloned and overexpressed in E. coli, was purified and characterized for this purpose. Aggregation and deaggregation of Sup35NM were examined by electron microscopy, gel electrophoresis, Congo red binding, fluorescence, and Western blotting. The degradation of Sup35NM aggregates by keratinase and proteinase K under various conditions was studied and compared. These results will be of value in understanding the mechanism and optimization of the degradation process. DA - 2005/9// PY - 2005/9// DO - 10.1110/ps.041234405 VL - 14 IS - 9 SP - 2228-2235 SN - 1469-896X KW - BSE KW - prion KW - PrPSc KW - Sup35NM KW - yeast prion KW - prion surrogate protein KW - enzymatic degradation ER - TY - JOUR TI - Bartonella quintana in Cynomolgus Monkey (Macaca fascicularis) AU - O'Rourke, Laurie G. AU - Pitulle, Christian AU - Hegarty, Barbara C. AU - Kraycirik, Sharon AU - Killary, Karen A. AU - Grosenstein, Paul AU - Brown, James W. AU - Breitschwerdt, Edward B. T2 - Emerging Infectious Diseases AB - We identified a Bartonella quintana strain by polymerase chain reaction amplification, cloning, and sequencing of DNA extracted from lysed erythrocytes and cultured colonies grown from peripheral blood collected from a captive-bred cynomolgus monkey (Macaca fascicularis). This report describes naturally acquired B. quintana infection in a nonhuman primate. DA - 2005/12// PY - 2005/12// DO - 10.3201/eid1112.030045 VL - 11 IS - 12 SP - 1931–1934 SN - 1080-6040 1080-6059 UR - http://dx.doi.org/10.3201/eid1112.030045 ER - TY - JOUR TI - Bartonella henselae in porpoise blood AU - Maggi, R. G. AU - Harms, C. A. AU - Hohn, A. A. AU - Pabst, D. A. AU - McLellan, W. A. AU - Walton, W. J. AU - Rotstein, D. S. AU - Breitschwerdt, E. B. T2 - Emerging Infectious Diseases DA - 2005/// PY - 2005/// VL - 11 IS - 12 SP - 1894-1898 ER - TY - JOUR TI - Anaplasma phagocytophilum infection (granulocytic anaplasmosis) in a dog from Vancouver Island AU - Lester, S. J. AU - Breitschwerdt, E. B. AU - Collis, C. D. AU - Hegarty, B. C. T2 - Canadian Veterinary Journal DA - 2005/// PY - 2005/// VL - 46 IS - 9 SP - 825-827 ER - TY - JOUR TI - The Dog as a Sentinel for Human Infection: Prevalence of Borrelia burgdorferi C6 Antibodies in Dogs from Southeastern and Mid-Atlantic States AU - Duncan, Ashlee W. AU - Correa, Maria T. AU - Levine, Jay F. AU - Breitschwerdt, Edward B. T2 - Vector-Borne and Zoonotic Diseases AB - Lyme disease is the most frequently reported human vector-associated disease in the United States. Infection occurs after the bite of an Ixodid tick that is infected with Borrelia burgdorferi. Dogs have often been reported to serve as effective sentinel animals to assess the risk of human B. burgdorferi infection. Based on published data of human Lyme disease case numbers and our clinical impressions, we hypothesized that canine exposure to B. burgdorferi would be lower in North Carolina when compared to the exposure in Virginia, Maryland, and Pennsylvania. To address this hypothesis, we evaluated B. burgdorferi exposure status utilizing a specific and sensitive C6 peptide-based enzyme-linked immunosorbent assay. Our convenience sample included 1,666 canine serum samples submitted to the Vector-Borne Disease Diagnostic Laboratory from North Carolina (n = 987), Virginia (n = 472), Maryland (n = 167), and Pennsylvania (n = 40). Comparisons among states were made using the Chisquare test or the Fisher's exact test; p-values were adjusted for multiple comparisons using the Bonferroni correction. A Chi-square test for trend was used to determine if there was an increase in the frequency of seroreactors associated with the geographical origin of the samples. The proportion of seroreactive dogs in North Carolina was markedly lower (p < 0.008) than that observed in dogs from Virginia, Maryland, and Pennsylvania. These results support the hypothesis that B. burgdorferi transmission seems to occur infrequently in North Carolina dogs as compared to dogs residing in other southeastern and mid-Atlantic states. Furthermore, they support the utility of dogs as a sentinel to characterize the risk of B. burgdorferi transmission to humans in a defined geographical location. DA - 2005/6// PY - 2005/6// DO - 10.1089/vbz.2005.5.101 VL - 5 IS - 2 SP - 101-109 J2 - Vector-Borne and Zoonotic Diseases LA - en OP - SN - 1530-3667 1557-7759 UR - http://dx.doi.org/10.1089/vbz.2005.5.101 DB - Crossref KW - Borrelia burgdorferi C6 KW - dogs KW - lyme disease ER - TY - JOUR TI - Structural analysis of divalent metals binding to the Bacillus subtilis response regulator Spo0F: the possibility for In vitro metalloregulation in the initiation of sporulation AU - Kojetin, DJ AU - Thompson, RJ AU - Benson, LM AU - Naylor, S AU - Waterman, J AU - Davies, KG AU - Opperman, CH AU - Stephenson, K AU - Hoch, JA AU - Cavanagh, J T2 - BIOMETALS DA - 2005/10// PY - 2005/10// DO - 10.1007/s10534-005-4303-8 VL - 18 IS - 5 SP - 449-466 SN - 1572-8773 KW - metal binding KW - NMR spectroscopy KW - response regulator KW - sporulation KW - two-component signal transduction ER - TY - JOUR TI - Regulation of biosynthetic genes and antioxidant properties of vitamin B-6 vitamers during plant defense responses AU - Denslow, SA AU - Walls, AA AU - Daub, ME T2 - PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY AB - Vitamin B6, an essential cofactor in enzymatic reactions, has only recently been linked to cellular oxidative stress. We investigated the role of this vitamin as an antioxidant in oxidative responses linked to plant defense. B6 vitamers effectively quenched superoxide and had antioxidant activity when assayed in vitro. The de novo B6 biosynthetic genes (PDX1 and PDX2) were identified in Nicotiana tabacum cv. ‘Burley 21’ and their transcript abundance was assayed during defense responses. PDX1 and PDX2 transcript levels decreased following inoculation with the incompatible pathogen Pseudomonas syringae pv. phaseolicola and transiently increased in response to salicylic acid and methyl jasmonate. Excess vitamin B6 in tobacco leaves interfered with the development of a hypersensitive response caused by P. syringae pv. phaseolicola and increased disease severity caused by the compatible bacterium P. syringae pv. tabaci. Our findings indicate that during plant defense responses, vitamin B6 functions and its synthesis is regulated in a manner consistent with this vitamin's activity as an antioxidant and modulator of active oxygen species in vivo. DA - 2005/6// PY - 2005/6// DO - 10.1016/j.pmpp.2005.09.004 VL - 66 IS - 6 SP - 244-255 SN - 0885-5765 KW - vitamin B-6 KW - pyridoxine KW - antioxidant KW - plant defense KW - PDX1 KW - PDX2 KW - SOR1 KW - SNO KW - SNZ KW - Nicotiana tabacum cv. 'Burley 21' KW - Pseudomonas syringae pv. phaseolicola KW - Pseudomonas syringae pv. tabaci ER - TY - JOUR TI - Production of a thermostable archaeal superoxide reductase in plant cells AU - Im, YJ AU - Ji, MK AU - Lee, AM AU - Boss, WF AU - Grunden, AM T2 - FEBS LETTERS AB - Pyrococcus furiosus superoxide reductase (SOR) is a thermostable archaeal enzyme that reduces superoxide without producing oxygen. When produced as a fusion protein with the green fluorescent protein in plant cells, P. furiosus SOR is located in the cytosol and nucleus. The recombinant SOR enzyme retains its function and heat stability when assayed in vitro. Importantly, expressing SOR in plant cells enhances their survival at high temperature indicating that it functions in vivo. The archaeal SOR provides a novel mechanism to reduce superoxide and demonstrates the potential for using archaeal genes to alter eukaryotic metabolism. DA - 2005/10/24/ PY - 2005/10/24/ DO - 10.1016/j.febslet.2005.09.015 VL - 579 IS - 25 SP - 5521-5526 SN - 1873-3468 KW - archaeal KW - heat-stress KW - hyperthermophile KW - plant KW - reactive oxygen species KW - superoxide dismutase KW - superoxide reductase ER - TY - JOUR TI - Prediction of loblolly pine wood properties using transmittance near-infrared spectroscopy AU - Sykes, R AU - Li, BL AU - Hodge, G AU - Goldfarb, B AU - Kadla, J AU - Chang, HM T2 - CANADIAN JOURNAL OF FOREST RESEARCH AB - Near-infrared (NIR) spectroscopy is a rapid nondestructive technique that has been used to characterize chemical and physical properties of a wide range of materials. In this study, transmittance NIR spectra from thin wood wafers cut from increment cores were used to develop calibration models for the estimation of α-cellulose content, average fiber length, fiber coarseness, and lignin content in the laboratory. Eleven-year-old trees from two sites were sampled using 12-mm increment cores. Earlywood and latewood of ring 3 and ring 8 from these samples were analyzed in the laboratory using microanalytical methods for α-cellulose content, average fiber length, fiber coarseness, and lignin content. NIR calibrations and laboratory measurements based on one site were generally reliable, with coefficients of determination (R 2 ) ranging from 0.54 to 0.88 for average fiber length and α-cellulose content, respectively. Predicting ring 8 properties using ring 3 calibration equations showed potential for predicting α-cellulose content and fiber coarseness, with R 2 values of approximately 0.60, indicating the potential for early selection. Predicting the wood properties using the calibration equations from one site to predict another showed moderate success for α-cellulose content (R 2 = 0.64) and fiber coarseness (R 2 = 0.63), but predictions for fiber length were relatively poor (R 2 = 0.43). Prediction of lignin content using transmittance NIR spectroscopy was not as reliable in this study, partially because of low variation in lignin content in these wood samples and large errors in measuring lignin content in the laboratory. DA - 2005/10// PY - 2005/10// DO - 10.1139/X05-161 VL - 35 IS - 10 SP - 2423-2431 SN - 1208-6037 ER - TY - JOUR TI - Positive assortative mating with family size as a function of predicted parental breeding values AU - Lstiburek, M AU - Mullin, TJ AU - Mackay, TFC AU - Huber, D AU - Li, B T2 - GENETICS AB - While other investigations have described benefits of positive assortative mating (PAM) for forest tree breeding, the allocation of resources among mates in these studies was either equal or varied, using schemes corresponding only to parental rank (i.e., more resources invested in higher-ranking parents). In this simulation study, family sizes were proportional to predicted midparent BLUP values. The distribution of midparent BLUP values was standardized by a constant, which was varied to study the range of distributions of family size. Redistributing progenies from lower- to higher-ranking families to a point where an equal number of progenies were still selected out of each family to the next generation caused minimal change in group coancestry and inbreeding in the breeding population (BP), while the additive genetic response and variance in the BP were both greatly enhanced. This generated additional genetic gains for forest plantations by selecting more superior genotypes from the BP (compared to PAM with equal family sizes) for production of improved regeneration materials. These conclusions were verified for a range of heritability under a polygenic model and under a mixed-inheritance model with a QTL contributing to the trait variation. DA - 2005/11// PY - 2005/11// DO - 10.1534/genetics.105.041723 VL - 171 IS - 3 SP - 1311-1320 SN - 1943-2631 ER - TY - JOUR TI - Multistate molecular information storage using S-acetylthio-derivatized dyads of triple-decker sandwich coordination compounds AU - Lysenko, AB AU - Malinovskii, VL AU - Padmaja, K AU - Wei, LY AU - Diers, , JR AU - Bocian, DF AU - Lindsey, JS T2 - JOURNAL OF PORPHYRINS AND PHTHALOCYANINES AB - An approach toward molecular information storage employs redox-active molecules attached to an electroactive surface. The chief advantages of such molecular capacitors include higher charge density and more versatile synthetic design than is afforded by typical semiconductor charge-storage materials. An architecture containing two triple-decker sandwich coordination complexes and an S-acetylthiomethyl-terminated tether has been designed for multibit storage. Each triple decker is composed of two phthalocyanines, one porphyrin, and two europium atoms. The oxidation potentials of each triple decker are tuned through the use of different substituents on the phthalocyanines (t-butyl, methyl, H ) and porphyrins (pentyl, p-tolyl). Interleaving of the four cationic oxidation states of each triple decker potentially affords eight distinct oxidation states. Two dyads were examined in solution and in self-assembled monolayers (SAMs) on a Au surface. One dyad exhibited eight distinct states in solution and in the SAM, thus constituting a molecular octal counter. The potentials ranged from −0.1-+1.3 V in solution and +0.1-+1.6 V in the SAM. Taken together, this approach provides a viable means of achieving multibit information storage at relatively low potential. DA - 2005/// PY - 2005/// DO - 10.1142/S1088424605000617 VL - 9 IS - 7 SP - 491-508 SN - 1099-1409 KW - memory KW - charge storage KW - capacitor KW - redox-active KW - triple decker KW - lanthanide KW - porphyrin KW - phthalocyanine KW - dyad KW - self-assembled monolayer KW - SAM KW - multibit KW - counter KW - octal ER - TY - JOUR TI - Isolation of bacteriophages from Bartonella vinsonii subsp berkhoffii and the characterization of Pap31 gene sequences from bacterial and phage DNA AU - Maggi, RG AU - Breitschwerdt, EB T2 - JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY AB - Bacteriophages enhance bacterial survival, facilitate bacterial adaptation to new environmental conditions, assist in the adaptation to a new host species, and enhance bacterial evasion or inactivation of host defense mechanisms. We describe the detection and purification of a novel tailed bacteriophage from <i>Bartonella vinsonii </i>subsp.<i> berkhoffii</i>, which was previously described as a bacteriophage-negative species. We also compare <i>B. vinsonii </i>subsp.<i> berkhoffi </i>Pap31 bacteriophage gene sequences to <i>B. henselae </i>(Houston I), and <i>B. quintana</i> (Fuller) bacteriophage Pap31 sequences. Negative staining electron microscopy of log phase culturesof <i>B. vinsonii </i>subsp.<i> berkhoffii </i>identifiedbacteriophages, possessing a 50-nm icosahedric head diameter and a 60- to 80-nm contractile tail. Sequence analysis of the bacteriophage Pap31 gene from<i> B. vinsonii </i>subsp.<i> berkhoffii</i> showed three consensus sequences and a 12-bp insertion when compared with Pap31 gene sequences from <i>B. henselae (</i>Houston I) and <i>B. quintana (</i>Fuller) bacteriophages. Isolation of <i>B. vinsonii </i>subsp.<i> berkhoffii</i> bacteriophages containing a Pap31 gene suggests that this heme-binding protein gene might play an important role in bacterial virulence through the genetic exchange of DNA within this subspecies. Defining phage-associated genes may also contribute to the enhanced understanding of the evolutionary relationships among members of the genus <i>Bartonella</i>. DA - 2005/// PY - 2005/// DO - 10.1159/000088145 VL - 9 IS - 1 SP - 44-51 SN - 1660-2412 KW - alpha-proteobacteria KW - virus KW - canine KW - pathogen KW - phage-associated protein KW - Bartonella ER - TY - JOUR TI - Interaction of Arabidopsis BRASSINOSTEROID-INSENSITIVE 1 receptor kinase with a homolog of mammalian TGF-beta receptor interacting protein AU - Ehsan, H AU - Ray, WK AU - Phinney, B AU - Wang, XF AU - Huber, SC AU - Clouse, SD T2 - PLANT JOURNAL AB - Brassinosteroids (BRs) regulate multiple aspects of plant growth and development and require an active BRASSINOSTEROID-INSENSITIVE 1 (BRI1) receptor serine/threonine kinase for hormone perception and signal transduction. In mammals, the transforming growth factor-beta (TGF-beta) family of polypeptides modulate numerous aspects of development and are perceived at the cell surface by a complex of type I and type II TGF-beta receptor serine/threonine kinases. TGF-beta receptor interacting protein (TRIP-1) is a cytoplasmic substrate of the TGF-beta type II receptor kinase and plays a role in TGF-beta signaling. TRIP-1 is a WD domain protein that also functions as an essential subunit of the eIF3 eukaryotic translation initiation factor in animals, yeast and plants. We previously cloned putative TRIP-1 homologs from bean and Arabidopsis and found that transgenic Arabidopsis plants expressing antisense TRIP-1 RNA exhibited a broad range of developmental defects including some morphological characteristics that resemble the phenotype of BR-deficient and -insensitive mutants. We now show that the BRI1 kinase domain phosphorylates Arabidopsis TRIP-1 on three specific sites in vitro (Thr-14, Thr-89 and either Thr-197 or Ser-198). Co-immunoprecipitation experiments using antibodies against TRIP-1, BRI1 and various fusion proteins strongly suggest that TRIP-1 and BRI1 also interact directly in vivo. These findings support a role for TRIP-1 in the molecular mechanisms of BR-regulated plant growth and development, possibly as a cytoplasmic substrate of the BRI1 receptor kinase. DA - 2005/7// PY - 2005/7// DO - 10.1111/j.1365-313X.2005.02448.x VL - 43 IS - 2 SP - 251-261 SN - 1365-313X KW - brassinosteroids KW - BRI1 KW - BAK1 KW - TRIP-1 KW - receptor kinase KW - TGF-beta ER - TY - JOUR TI - Inheritance and chromosomal assignment of powdery mildew resistance genes in two winter wheat germplasm lines AU - Srnic, G AU - Murphy, JP AU - Lyerly, JH AU - Leath, S AU - Marshall, DS T2 - CROP SCIENCE AB - Powdery mildew of wheat ( Triticum aestivum L.), caused by Blumeria graminis DC f. sp. tritici Em. Marchal, occurs annually in eastern North America resulting in reduced grain yield and end‐use quality in susceptible cultivars. The objectives of this study were to determine the inheritance, chromosomal location, and linkage with molecular markers of powdery mildew resistance genes in the two recently released germplasm lines NC96BGTA4 and NC99BGTAG11. Between 99 and 194 F 2:3 progenies plus parents in two populations, ‘Saluda’ × NC96BGTA4 and Saluda × NC99BGTAG11, were evaluated in greenhouse and field nurseries for reaction to powdery mildew infection. Results indicated that the germplasm lines each contained a different, partially dominant, major resistance gene. The two segregating populations were subjected to amplified fragment length polymorphism (AFLP) and simple sequence repeat, or microsatellite (SSR) analyses. Both resistance genes were located on the long arm of chromosome 7A. The most likely locus order indicated that the resistance gene in NC96BGTA4 was flanked by the SSR loci Xbarc292 and Xwmc525 The resistance gene in NC99BGTAG11 was most likely flanked by the AFLP markers XE38M54‐196 and XE36M55‐126 , and the SSR loci Xgwm332 and Xwmc525 Both genes mapped to a chromosome arm that contains the powdery mildew resistance loci Pm1 and Pm9 The resistance genes in the two germplasms are different from the Pm1a allele. Our mapping results suggested that the resistance genes were not alleles at the Pm1 or Pm9 loci, but further allelism tests are necessary to determine the relationships both between the two genes themselves and between the two genes and named Pm loci on chromosome 7AL. DA - 2005/// PY - 2005/// DO - 10.2135/cropsci2004.0530 VL - 45 IS - 4 SP - 1578-1586 SN - 1435-0653 ER - TY - JOUR TI - Imine-substituted dipyrromethanes in the synthesis of porphyrins bearing one or two meso substituents AU - Taniguchi, M AU - Balakumar, A AU - Fan, DZ AU - McDowell, BE AU - Lindsey, JS T2 - JOURNAL OF PORPHYRINS AND PHTHALOCYANINES AB - 5,15-substituted porphyrins are valuable compounds in bioorganic and materials chemistry. A new synthesis has been developed that employs 1,9-diformylation of a dipyrromethane, conversion of the diformyldipyrromethane to the bis(imino) derivative, and reaction of the bis(imino)dipyrromethane + a dipyrromethane to give the zinc-porphyrin bearing trans-AB-substituents. 1,9-diformylation was achieved via Vilsmeier reaction. Imination was achieved by treatment of the 1,9-diformyldipyrromethane with excess amine under neat conditions at room temperature. The porphyrin-forming reaction was carried out over 2 h in refluxing ethanol containing zinc acetate exposed to air. Oxidation of the intermediate porphyrinogen occurs aerobically. A complex composed of two bis(imino)dipyrromethanes and two zinc atoms was observed to form reversibly during the course of the reaction. A set of zinc-porphyrins with trans-AB-, A 2 -, or A-substituents has been prepared in yields of ~30% (without detectable scrambling) with straightforward purification. The reaction is applicable to A/B substituent combinations of aryl/aryl, aryl/alkyl, and aryl/H. DA - 2005/// PY - 2005/// DO - 10.1142/S1088424605000678 VL - 9 IS - 8 SP - 554-574 SN - 1099-1409 KW - dipyrromethane KW - pyrrole KW - imine KW - Schiff's base KW - porphyrin KW - aerobic oxidation KW - dipyrrin KW - self-assembly KW - zinc ER - TY - JOUR TI - Evolutionary and ecological genomics of arabidopsis AU - Shimizu, KK AU - Purugganan, MD T2 - PLANT PHYSIOLOGY AB - Why are some plants self-pollinating? What determines the timing of flowering and germination? Why do resistant and susceptible alleles of pathogen-resistant genes coexist in populations? These are just a few questions traditionally asked in the domain of ecology and evolutionary biology, and DA - 2005/6// PY - 2005/6// DO - 10.1104/pp.105.061655 VL - 138 IS - 2 SP - 578-584 SN - 1532-2548 ER - TY - JOUR TI - Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system AU - Diener, S. E. AU - Houfek, T. D. AU - Kalat, S. E. AU - Windham, D. E. AU - Burke, M. AU - Opperman, C. AU - Dean, R. A. T2 - BMC Bioinformatics DA - 2005/// PY - 2005/// VL - 6 ER - TY - JOUR TI - Summary of IEG-40 meeting: Silviculture and genetic impacts on productivity of southern pine forests AU - McKeand, S. E. AU - Allen, H. L. T2 - Southern Journal of Applied Forestry DA - 2005/// PY - 2005/// VL - 29 IS - 2 SP - 61 ER - TY - JOUR TI - Structural control of the photodynamics of boron-dipyrrin complexes AU - Kee, HL AU - Kirmaier, C AU - Yu, LH AU - Thamyongkit, P AU - Youngblood, WJ AU - Calder, ME AU - Ramos, L AU - Noll, BC AU - Bocian, DF AU - Scheidt, WR AU - Birge, RR AU - Lindsey, JS AU - Holten, D T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - Boron−dipyrrin chromophores containing a 5-aryl group with or without internal steric hindrance toward aryl rotation have been synthesized and then characterized via X-ray diffraction, static and time-resolved optical spectroscopy, and theory. Compounds with a 5-phenyl or 5-(4-tert-butylphenyl) group show low fluorescence yields (∼0.06) and short excited-singlet-state lifetimes (∼500 ps), and decay primarily (>90%) by nonradiative internal conversion to the ground state. In contrast, sterically hindered analogues having an o-tolyl or mesityl group at the 5-position exhibit high fluorescence yields (∼0.9) and long excited-state lifetimes (∼6 ns). The X-ray structures indicate that the phenyl or 4-tert-butylphenyl ring lies at an angle of ∼60° with respect to the dipyrrin framework whereas the angle is ∼80° for mesityl or o-tolyl groups. The calculated potential energy surface for the phenyl-substituted complex indicates that the excited state has a second, lower energy minimum in which the nonhindered aryl ring rotates closer to the mean plane of the dipyrrin, which itself undergoes some distortion. This relaxed, distorted excited-state conformation has low radiative probability as well as a reduced energy gap from the ground state supporting a favorable vibrational overlap factor for nonradiative deactivation. Such a distorted conformation is energetically inaccessible in a complex bearing the sterically hindered o-tolyl or mesityl group at the 5-position, leading to a high radiative probability involving conformations at or near the initial Franck−Condon form of the excited state. These combined results demonstrate the critical role of aryl-ring rotation in governing the excited-state dynamics of this class of widely used dyes. DA - 2005/11/3/ PY - 2005/11/3/ DO - 10.1021/jp0525078 VL - 109 IS - 43 SP - 20433-20443 SN - 1520-5207 ER - TY - JOUR TI - Stringhalt associated with a pasture infested with Hypochoeris radicata AU - Gardner, S. Y. AU - Cook, A. G. AU - Jortner, B. S. AU - Troan, B. V. AU - Sharp, N. J. H. AU - Campbell, N. B. AU - Brownie, C. F. T2 - Equine Veterinary Education AB - Equine Veterinary EducationVolume 17, Issue 3 p. 118-122 Stringhalt associated with a pasture infested with Hypochoeris radicata S. Y. Gardner, Corresponding Author S. Y. Gardner Department of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USADepartment of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USASearch for more papers by this authorA. G. Cook, A. G. Cook Departments of Large Animal Clinical Sciences, Virginia Maryland Regional College of Veterinary Medicine, Virginia-Tech and University of Maryland, Blacksburg, Virginia 24061, USA Davie County Large Animal Hospital, 928 Farmington Rd, Mocksville, North Carolina 27028, USASearch for more papers by this authorB. S. Jortner, B. S. Jortner Biomedical Sciences and Pathobiology, Virginia Maryland Regional College of Veterinary Medicine, Virginia-Tech and University of Maryland, Blacksburg, Virginia 24061, USASearch for more papers by this authorB. V. Troan, B. V. Troan Department of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USASearch for more papers by this authorN. J. H. Sharp, N. J. H. Sharp Department of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USA Animal Critical Care Group, 1410 Boundary Road, Burnaby, British Columbia V5K 4V3, CanadaSearch for more papers by this authorN. B. Campbell, N. B. Campbell Department of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USASearch for more papers by this authorC. F. Brownie, C. F. Brownie Department of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USASearch for more papers by this author S. Y. Gardner, Corresponding Author S. Y. Gardner Department of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USADepartment of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USASearch for more papers by this authorA. G. Cook, A. G. Cook Departments of Large Animal Clinical Sciences, Virginia Maryland Regional College of Veterinary Medicine, Virginia-Tech and University of Maryland, Blacksburg, Virginia 24061, USA Davie County Large Animal Hospital, 928 Farmington Rd, Mocksville, North Carolina 27028, USASearch for more papers by this authorB. S. Jortner, B. S. Jortner Biomedical Sciences and Pathobiology, Virginia Maryland Regional College of Veterinary Medicine, Virginia-Tech and University of Maryland, Blacksburg, Virginia 24061, USASearch for more papers by this authorB. V. Troan, B. V. Troan Department of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USASearch for more papers by this authorN. J. H. Sharp, N. J. H. Sharp Department of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USA Animal Critical Care Group, 1410 Boundary Road, Burnaby, British Columbia V5K 4V3, CanadaSearch for more papers by this authorN. B. Campbell, N. B. Campbell Department of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USASearch for more papers by this authorC. F. Brownie, C. F. Brownie Department of Clinical Sciences, Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, North Carolina 27606, USASearch for more papers by this author First published: 05 January 2010 https://doi.org/10.1111/j.2042-3292.2005.tb00349.xCitations: 9 AboutPDF ToolsExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Citing Literature Volume17, Issue3June 2005Pages 118-122 RelatedInformation DA - 2005/// PY - 2005/// DO - 10.1111/j.2042-3292.2005.tb00349.x VL - 17 IS - 3 SP - 118-122 ER - TY - JOUR TI - Strategies and case studies for incorporating ecophysiology into southern pine tree improvement programs AU - Martin, T. A. AU - Dougherty, P. M. AU - McKeand, S. E. T2 - Southern Journal of Applied Forestry DA - 2005/// PY - 2005/// VL - 29 IS - 2 SP - 70-79 ER - TY - JOUR TI - Risk assessment with current deployment strategies for fusiform rust-resistant loblolly and slash pines AU - Bridgwater, F. AU - Kubisiak, T. AU - Byram, T. AU - McKeand, S. T2 - Southern Journal of Applied Forestry DA - 2005/// PY - 2005/// VL - 29 IS - 2 SP - 80-87 ER - TY - JOUR TI - Relative pathogenicity of Cryphonectria cubensis on Eucalyptus clones differing in their resistance to C-cubensis AU - Heerden, SW AU - Amerson, HV AU - Preisig, O AU - Wingfield, BD AU - Wingfield, MJ T2 - PLANT DISEASE AB - Cryphonectria cubensis causes a destructive canker disease of Eucalyptus species. Management of this disease is primarily through breeding and selection of disease resistant trees. One means of selecting such trees is by artificial inoculation with the pathogen. In routine screening trials in South Africa, an isolate of C. cubensis, considered to be highly pathogenic, has been used for such inoculations. Although the most resistant clones under natural conditions are the same as those detected in inoculation trials, a question has arisen whether all clones respond similarly to different C. cubensis isolates. Thus, a trial consisting of five clones, known to differ in susceptibility to infection by C. cubensis, was established. These trees were inoculated with nine South African C. cubensis isolates previously shown to differ in pathogenicity. Inoculations showed a significant isolate × clone interaction as well as an “apparent immunity” for one clone × isolate interaction, providing evidence highly suggestive of a vertical resistance component in the pathosystem. Disease screening in this pathosystem has traditionally relied on a single pathogen isolate; however, considering data presented here, future reliance on a single isolate may be inadequate. DA - 2005/6// PY - 2005/6// DO - 10.1094/PD-89-0659 VL - 89 IS - 6 SP - 659-662 SN - 1943-7692 KW - gene-for-gene resistance KW - host-pathogen interaction ER - TY - JOUR TI - Planting nonlocal seed sources of loblolly pine: Managing benefits and risks AU - Lambeth, C. AU - McKeand, S. AU - Rousseau, R. AU - Schmidtling, R. T2 - Southern Journal of Applied Forestry DA - 2005/// PY - 2005/// VL - 29 IS - 2 SP - 96-104 ER - TY - JOUR TI - Networks of coevolving sites in structural and functional domains of serpin proteins AU - Buck, MJ AU - Atchley, WR T2 - MOLECULAR BIOLOGY AND EVOLUTION AB - Amino acids do not occur randomly in proteins; rather, their occurrence at any given site is strongly influenced by the amino acid composition at other sites, the structural and functional aspects of the region of the protein in which they occur, and the evolutionary history of the protein. The goal of our research study is to identify networks of coevolving sites within the serpin proteins (serine protease inhibitors) and classify them as being caused by structural-functional constraints or by evolutionary history. To address this, a matrix of pairwise normalized mutual information (NMI) values was computed among amino acid sites for the serpin proteins. The NMI matrix was partitioned into orthogonal patterns of amino acid variability by factor analysis. Each common factor pattern was interpreted as having phylogenetic and/or structural-functional explanations. In addition, we used a bootstrap factor analysis technique to limit the effects of phylogenetic history on our factor patterns. Our results show an extensive network of correlations among amino acid sites in key functional regions (reactive center loop, shutter, and breach). Additionally, we have discovered long-range coevolution for packed amino acids within the serpin protein core. Lastly, we have discovered a group of serpin sites which coevolve in the hydrophobic core region (s5B and s4B) and appear to represent sites important for formation of the “native” instead of the “latent” serpin structure. This research provides a better understanding on how protein structure evolves; in particular, it elucidates the selective forces creating coevolution among protein sites. DA - 2005/7// PY - 2005/7// DO - 10.1093/molbev/msi157 VL - 22 IS - 7 SP - 1627-1634 SN - 1537-1719 KW - serpin KW - factor analysis KW - coevolution KW - covariation KW - protein structure KW - mutual information ER - TY - JOUR TI - Mist level influences vapor pressure deficit and gas exchange during rooting of juvenile stem cuttings of loblolly pine AU - LeBude, A. V. AU - Goldfarb, B. AU - Blazich, F. A. AU - Frampton, J. AU - Wise, F. C. T2 - HortScience DA - 2005/// PY - 2005/// VL - 40 IS - 5 SP - 1448-1456 ER - TY - JOUR TI - Identification and characterization of endoplasmic reticulum-associated degradation proteins differentially affected by endoplasmic reticulum stress AU - Kirst, ME AU - Meyer, DJ AU - Gibbon, BC AU - Jung, R AU - Boston, RS T2 - PLANT PHYSIOLOGY AB - Abstract The disposal of misfolded proteins from the lumen of the endoplasmic reticulum (ER) is one of the quality control mechanisms present in the protein secretory pathway. Through ER-associated degradation, misfolded substrates are targeted to the cytosol where they are degraded by the proteasome. We have identified four maize (Zea mays) Der1-like genes (Zm Derlins) that encode homologs of Der1p, a yeast (Saccharomyces cerevisiae) protein implicated in ER-associated degradation. Zm Derlins are capable of functionally complementing a yeast Der1 deletion mutant. Such complementation indicates that the Der1p function is conserved among species. Zm Derlin genes are expressed at low levels throughout the plant, but appear prevalent in tissues with high activity of secretory protein accumulation, including developing endosperm cells. Expression of three of the four Zm Derlin genes increases during ER stress, with Zm Derlin1-1 showing the strongest induction. Subcellular fractionation experiments localized Zm Derlin proteins to the membrane fraction of microsomes. In maize endosperm, Zm Derlin proteins were found primarily associated with ER-derived protein bodies regardless of the presence of an ER stress response. DA - 2005/5// PY - 2005/5// DO - 10.1104/pp.105.060087 VL - 138 IS - 1 SP - 218-231 SN - 1532-2548 ER - TY - JOUR TI - Genetics and genomics of Drosophila mating behavior AU - Mackay, TFC AU - Heinsohn, SL AU - Lyman, RF AU - Moehring, AJ AU - Morgan, TJ AU - Rollmann, SM T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - The first steps of animal speciation are thought to be the development of sexual isolating mechanisms. In contrast to recent progress in understanding the genetic basis of postzygotic isolating mechanisms, little is known about the genetic architecture of sexual isolation. Here, we have subjected Drosophila melanogaster to 29 generations of replicated divergent artificial selection for mating speed. The phenotypic response to selection was highly asymmetrical in the direction of reduced mating speed, with estimates of realized heritability averaging 7%. The selection response was largely attributable to a reduction in female receptivity. We assessed the whole genome transcriptional response to selection for mating speed using Affymetrix GeneChips and a rigorous statistical analysis. Remarkably, >3,700 probe sets (21% of the array elements) exhibited a divergence in message levels between the Fast and Slow replicate lines. Genes with altered transcriptional abundance in response to selection fell into many different biological process and molecular function Gene Ontology categories, indicating substantial pleiotropy for this complex behavior. Future functional studies are necessary to test the extent to which transcript profiling of divergent selection lines accurately predicts genes that directly affect the selected trait. DA - 2005/5/3/ PY - 2005/5/3/ DO - 10.1073/pnas.0501986102 VL - 102 SP - 6622-6629 SN - 0027-8424 ER - TY - JOUR TI - Geminivirus C3 protein: Replication enhancement and protein interactions AU - Settlage, SB AU - See, RG AU - Hanley-Bowdoin, L T2 - JOURNAL OF VIROLOGY AB - ABSTRACT Most dicot-infecting geminiviruses encode a replication enhancer protein (C3, AL3, or REn) that is required for optimal replication of their small, single-stranded DNA genomes. C3 interacts with C1, the essential viral replication protein that initiates rolling circle replication. C3 also homo-oligomerizes and interacts with at least two host-encoded proteins, proliferating cell nuclear antigen (PCNA) and the retinoblastoma-related protein (pRBR). It has been proposed that protein interactions contribute to C3 function. Using the C3 protein of Tomato yellow leaf curl virus , we examined the impact of mutations to amino acids that are conserved across the C3 protein family on replication enhancement and protein interactions. Surprisingly, many of the mutations did not affect replication enhancement activity of C3 in tobacco protoplasts. Other mutations either enhanced or were detrimental to C3 replication activity. Analysis of mutated proteins in yeast two-hybrid assays indicated that mutations that inactivate C3 replication enhancement activity also reduce or inactivate C3 oligomerization and interaction with C1 and PCNA. In contrast, mutated C3 proteins impaired for pRBR binding are fully functional in replication assays. Hydrophobic residues in the middle of the C3 protein were implicated in C3 interaction with itself, C1, and PCNA, while polar resides at both the N and C termini of the protein are important for C3-pRBR interaction. These experiments established the importance of C3-C3, C3-C1, and C3-PCNA interactions in geminivirus replication. While C3-pRBR interaction is not required for viral replication in cycling cells, it may play a role during infection of differentiated cells in intact plants. DA - 2005/8// PY - 2005/8// DO - 10.1128/jvi.79.15.9885-9895.2005 VL - 79 IS - 15 SP - 9885-9895 SN - 1098-5514 ER - TY - JOUR TI - Functional genomic characterization of delipidation elicited by trans-10, cis-12-conjugated linoleic acid (t10c12-CLA) in a polygenic obese line of mice AU - House, RL AU - Cassady, JP AU - Eisen, EJ AU - Eling, TE AU - Collins, JB AU - Grissom, SF AU - Odle, J T2 - PHYSIOLOGICAL GENOMICS AB - Gene expression was measured during t10c12-CLA-induced body fat reduction in a polygenic obese line of mice. Adult mice ( n = 185) were allotted to a 2 × 2 factorial experiment consisting of either nonobese (ICR-control) or obese (M16-selected) mice fed a 7% fat, purified diet containing either 1% linoleic acid (LA) or 1% t10c12-CLA. Body weight (BW) by day 14 was 12% lower in CLA- compared with LA-fed mice ( P < 0.0001). By day 14, t10c12-CLA reduced weights of epididymal, mesenteric, and brown adipose tissues, as a percentage of BW, in both lines by 30, 27, and 58%, respectively, and increased liver weight/BW by 34% ( P < 0.0001). Total RNA was isolated and pooled (4 pools per tissue per day) from epididymal adipose ( days 5 and 14) of the obese mice to analyze gene expression profiles using Agilent mouse oligo microarray slides representing >20,000 genes. Numbers of genes differentially expressed by greater than or equal to twofold in epididymal adipose ( days 5 and 14) were 29 and 125, respectively. It was concluded that, in adipose tissue, CLA increased expression of uncoupling proteins (1 and 2), carnitine palmitoyltransferase system, tumor necrosis factor-α ( P < 0.05), and caspase-3 but decreased expression of peroxisome proliferator-activated receptor-γ, glucose transporter-4, perilipin, caveolin-1, adiponectin, resistin, and Bcl-2 ( P < 0.01). In conclusion, this experiment has revealed candidate genes that will be useful in elucidating mechanisms of adipose delipidation. DA - 2005/5/11/ PY - 2005/5/11/ DO - 10.1152/physiolgenomics.00244.2004 VL - 21 IS - 3 SP - 351-361 SN - 1531-2267 KW - apoptosis KW - cell biology KW - gene expression KW - lipid metabolism KW - obesity ER - TY - JOUR TI - Conversion of nicotine to nornicotine in Nicotiana tabacum is mediated by CYP82E4, a cytochrome P450 monooxygenase AU - Siminszky, B. AU - Gavilano, L. AU - Bowen, S. W. AU - Dewey, R. E. T2 - Proceedings of the National Academy of Sciences of the United States of America DA - 2005/// PY - 2005/// DO - 10.1073/pnas.050658102 VL - 102 IS - 41 SP - 14919-14924 ER - TY - JOUR TI - Comparative plant genomics. Frontiers and prospects AU - Caicedo, AL AU - Purugganan, MD T2 - PLANT PHYSIOLOGY AB - Comparative methods have long been the cornerstone of studies that draw inferences about function and evolution at various levels of biological organization. The availability of whole-genome sequences as well as other genomic resources (e.g. microarray methods, expressed sequence tag [EST] libraries DA - 2005/6// PY - 2005/6// DO - 10.1104/pp.104.900148 VL - 138 IS - 2 SP - 545-547 SN - 1532-2548 ER - TY - JOUR TI - Cloning and characterisation of genes encoding two transforming growth factor-beta-like ligands from the hookworm, Ancylostoma caninum AU - Freitas, TC AU - Arasu, P T2 - INTERNATIONAL JOURNAL FOR PARASITOLOGY AB - To elucidate the role of transforming growth factor beta (TGF-beta) signalling in the arrest/reactivation pathway of the Ancylostoma caninum hookworm, two parasite-encoded TGF-beta-like ligands were cloned and characterised. Ac-dbl-1 showed 60% amino acid identity to the Caenorhabditis elegansdbl-1 gene, which regulates growth while Ac-daf-7 showed 46% amino acid identity to Ce-daf-7 which regulates arrested development. Exon/intron organisation of the genes for Ac-dbl-1 and Ac-daf-7 were different from that of the corresponding C. elegans genes with nine and 10 exons, respectively, and introns ranging in size from 56 to 2,556 bp. Based on real-time reverse transcriptase (RT)-PCR, Ac-dbl-1 and Ac-daf-7 were expressed in all stages tested, i.e. egg, first/second stage larvae (L1/L2), infective third stage larvae (iL3), serum-stimulated third stage larvae (ssL3), and male and female adult worms. Expression of Ac-dbl-1 peaked in the adult male stage suggesting a similar role to Ce-dbl-1 in regulating male tail patterning. Ac-daf-7 expression was at a maximum in the arrested iL3 and reactivated ssL3 stages, which differs from that of Ce-daf-7 expression and may be unique to parasitic nematodes that have an obligate requirement to undergo developmental arrest. In support of the PCR results, antibodies to the A. caninum TGF-beta-like ligands detected proteins in iL3, ssL3, and adult worm extracts. Immunofluorescent studies showed that Ac-daf-7 is expressed in the anterior region of the iL3 similar to Ce-daf-7, which is localised to the ASI chemosensory neurons. DA - 2005/12// PY - 2005/12// DO - 10.1016/j.ijpara.2005.07.005 VL - 35 IS - 14 SP - 1477-1487 SN - 0020-7519 KW - Ancylostoma caninum KW - TGF-beta KW - dbl-1 KW - daf-7 KW - development ER - TY - JOUR TI - Adaptive radiation and regulatory gene evolution in the Hawaiian silversword alliance (Asteraceae) AU - Purugganan, M. D. AU - Robichaux, R. H. T2 - Annals of the Missouri Botanical Garden DA - 2005/// PY - 2005/// VL - 92 IS - 1 SP - 28-35 ER - TY - JOUR TI - The rb7 matrix attachment region increases the likelihood and magnitude of transgene expression in tobacco cells: A flow cytometric study AU - Halweg, C AU - Thompson, WF AU - Spiker, S T2 - PLANT CELL AB - Many studies in both plant and animal systems have shown that matrix attachment regions (MARs) can increase expression of transgenes in whole organisms or cells in culture. Because histochemical assays often indicate variegated transgene expression, a question arises: Do MARs increase transgene expression by increasing the percentage of cells expressing the transgene (likelihood), by increasing the level of expression in expressing cells (magnitude), or both? To address this question, we used flow cytometry to measure green fluorescent protein (GFP) expression in individual tobacco (Nicotiana tabacum) cells from lines transformed by Agrobacteriumtumefaciens. We conclude that MAR-mediated overall increases in transgene expression involve both likelihood and magnitude. On average, cell lines transformed with the Rb7 MAR-containing vector expressed GFP at levels 2.0- to 3.7-fold higher than controls. MAR lines had fewer nonexpressing cells than control lines (10% versus 45%), and the magnitude of GFP expression in expressing cells was greater in MAR lines by 1.9- to 2.9-fold. We also show that flow cytometry measurements on cells from isogenic lines are consistent with those from populations of independently transformed cell lines. By obviating the need to establish isogenic lines, this use of flow cytometry could greatly simplify the evaluation of MARs or other sequence elements that affect transgene expression. DA - 2005/2// PY - 2005/2// DO - 10.1105/tpc.104.028100 VL - 17 IS - 2 SP - 418-429 SN - 1532-298X ER - TY - JOUR TI - The CTB1 gene encoding a fungal polyketide synthase is required for cercosporin biosynthesis and fungal virulence of Cercospora nicotianae AU - Choquer, M AU - Dekkers, KL AU - Chen, HQ AU - Cao, LH AU - Ueng, PP AU - Daub, ME AU - Chung, KR T2 - MOLECULAR PLANT-MICROBE INTERACTIONS AB - Cercosporin is a light-activated, non-host-selective toxin produced by many Cercospora fungal species. In this study, a polyketide synthase gene (CTB1) was functionally identified and molecularly characterized to play a key role in cercosporin biosynthesis by Cercospora nicotianae. We also provide conclusive evidence to confirm the crucial role of cercosporin in fungal pathogenesis. CTB1 encoded a polypeptide with a deduced length of 2,196 amino acids containing a keto synthase (KS), an acyltransferase (AT), a thioesterase/claisen cyclase (TE/CYC), and two acyl carrier protein (ACP) domains, and had high levels of similarity to many fungal type I polyketide synthases. Expression of a 6.8-kb CTB1 transcript was highly regulated by light and medium composition, consistent with the conditions required for cercosporin biosynthesis in cultures. Targeted disruption of CTB1 resulted in the loss of both CTB1 transcript and cercosporin biosynthesis in C. nicotianae. The ctb1-null mutants incited fewer necrotic lesions on inoculated tobacco leaves compared with the wild type. Complementation of ctb1-null mutants with a full-length CTB1 clone restored wild-type levels of cercosporin production as well as the ability to induce lesions on tobacco. Thus, we have demonstrated conclusively that cercosporin is synthesized via a polyketide pathway, and cercosporin is an important virulence factor in C. nicotianae. The results also suggest that strategies that avoid the toxicity of cercosporin will be useful in reduction of disease incidence caused by Cercospora spp. DA - 2005/5// PY - 2005/5// DO - 10.1094/MPMI-18-0468 VL - 18 IS - 5 SP - 468-476 SN - 1943-7706 KW - gene disruption KW - pathogenicity KW - perylenequinone ER - TY - JOUR TI - Stumping height, crown position, and age of parent tree influence rooting of stem cuttings of fraser fir AU - Rosier, C. L. AU - Frampton, J. AU - Goldfarb, B. AU - Wise, F. C. AU - Blazich, F. A. T2 - HortScience DA - 2005/// PY - 2005/// VL - 40 IS - 3 SP - 771-777 ER - TY - JOUR TI - Solving the protein sequence metric problem AU - Atchley, WR AU - Zhao, JP AU - Fernandes, AD AU - Druke, T T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Biological sequences are composed of long strings of alphabetic letters rather than arrays of numerical values. Lack of a natural underlying metric for comparing such alphabetic data significantly inhibits sophisticated statistical analyses of sequences, modeling structural and functional aspects of proteins, and related problems. Herein, we use multivariate statistical analyses on almost 500 amino acid attributes to produce a small set of highly interpretable numeric patterns of amino acid variability. These high-dimensional attribute data are summarized by five multidimensional patterns of attribute covariation that reflect polarity, secondary structure, molecular volume, codon diversity, and electrostatic charge. Numerical scores for each amino acid then transform amino acid sequences for statistical analyses. Relationships between transformed data and amino acid substitution matrices show significant associations for polarity and codon diversity scores. Transformed alphabetic data are used in analysis of variance and discriminant analysis to study DNA binding in the basic helix-loop-helix proteins. The transformed scores offer a general solution for analyzing a wide variety of sequence analysis problems. DA - 2005/5/3/ PY - 2005/5/3/ DO - 10.1073/pnas.0408677102 VL - 102 IS - 18 SP - 6395-6400 SN - 1091-6490 KW - basic helix-loop-helix KW - molecular evolution KW - multivariate statistics KW - amino acid attributes KW - factor analysis ER - TY - JOUR TI - Sequence signatures and the probabilistic identification of proteins in the Myc-Max-Mad network AU - Atchley, WR AU - Fernandes, AD T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Accurate identification of specific groups of proteins by their amino acid sequence is an important goal in genome research. Here we combine information theory with fuzzy logic search procedures to identify sequence signatures or predictive motifs for members of the Myc-Max-Mad transcription factor network. Myc is a well known oncoprotein, and this family is involved in cell proliferation, apoptosis, and differentiation. We describe a small set of amino acid sites from the N-terminal portion of the basic helix-loop-helix (bHLH) domain that provide very accurate sequence signatures for the Myc-Max-Mad transcription factor network and three of its member proteins. A predictive motif involving 28 contiguous bHLH sequence elements found 337 network proteins in the GenBank NR database with no mismatches or misidentifications. This motif also identifies at least one previously unknown fungal protein with strong affinity to the Myc-Max-Mad network. Another motif found 96% of known Myc protein sequences with only a single mismatch, including sequences from genomes previously not thought to contain Myc proteins. The predictive motif for Myc is very similar to the ancestral sequence for the Myc group estimated from phylogenetic analyses. Based on available crystal structure studies, this motif is discussed in terms of its functional consequences. Our results provide insight into evolutionary diversification of DNA binding and dimerization in a well characterized family of regulatory proteins and provide a method of identifying signature motifs in protein families. DA - 2005/5/3/ PY - 2005/5/3/ DO - 10.1073/pnas.0408964102 VL - 102 IS - 18 SP - 6401-6406 SN - 0027-8424 KW - Myc KW - predictive motif KW - transcription factor KW - oncoprotein KW - molecular evolution ER - TY - JOUR TI - Predicted genetic gains and testing efficiency from two loblolly pine clonal trials AU - Isik, F AU - Goldfarb, B AU - LeBude, A AU - Li, BL AU - McKeand, S T2 - CANADIAN JOURNAL OF FOREST RESEARCH AB - Clonal field trials were established at two sites using rooted cuttings from 450 clones of eight full-sib families of loblolly pine (Pinus taeda L.). Height, survival, fusiform rust infection (caused by Cronartium quercuum (Berk) Miyabe ex Shirai f.sp. fusiforme), bole straightness, and diameter were measured after four growing seasons. There were significant differences among full-sib families and among clones within families for all traits studied. Moderately high within-family repeatabilities of clone means (0.50 to 0.75) for growth traits and a very high within-family repeatability of clone means (0.94) for fusiform rust infection were estimated. When the best eight clones were selected regardless of family structure, the volume yield was 52% greater than that of the unimproved seedlings at two sites. Selection of the best two clones from each of four families produced only slightly lower estimated genetic gains than the above scenario. The probability of fusiform rust infection ranged from 0.08 to 0.93 among clones at the South Carolina site. Predicted genetic gain for rust resistance was relatively insensitive to selection intensity, as there were numerous clones with high apparent resistance. The number of ramets per clone necessary to reliably characterize performance on one site was estimated to be between four and six. These results contribute to estimates of the gains available from clonal forestry and will help guide clonal testing and selection programs. Implementation of clonal forestry and cost issues are discussed. DA - 2005/7// PY - 2005/7// DO - 10.1139/X05-064 VL - 35 IS - 7 SP - 1754-1766 SN - 1208-6037 ER - TY - JOUR TI - Pre-existing immunity to pathogenic Listeria monocytogenes does not prevent induction of immune responses to feline immunodeficiency virus by a novel recombinant Listeria monocytogenes vaccine AU - Stevens, R AU - LaVoy, A AU - Nordone, S AU - Burkhard, M AU - Dean, GA T2 - VACCINE AB - Listeria monocytogenes is an attractive biologic vaccine vector against HIV because it induces a strong cell mediated immune response, can be delivered by mucosal routes, can be readily manipulated to express viral antigens, and is easy and inexpensive to produce. Proof of concept studies have been performed using HIV Gag expressing recombinant L. monocytogenes in the mouse. Here we report the development and validation of recombinant L. monocytogenes to be evaluated in the FIV/cat model of HIV. Using a simplified approach to introduce individual and polyprotein FIV gag genes, we show that recombinant L. monocytogenes containing the entire gag expresses the full-length Gag polyprotein in a soluble secreted form. A DNA vaccine plasmid (pND14-Lc-env) that replicates in Gram positive bacteria and contains the FIV SU (gp100) and the ectodomain of TM (gp40) in a eukaryotic expression cassette was transfected into LM-gag to create LM-gag/pND14-Lc-env. After infection of target cells with LM-gag/pND14-Lc-env in vitro, both FIV Gag and Env proteins were detected in soluble cell lysates. Whether previous exposure to L. monocytogenes affects the immunogenicity of LM-gag/pND14-Lc-env was determined in cats infected with wild-type L. monocytogenes orally and/or subcutaneously. After a single oral dose of LM-gag/pND14-Lc-env, cats with existing anti-L. monocytogenes immune responses developed anti-FIV Gag IgA titers in vaginal secretions, saliva, and feces. Similarly, FIV Gag and Env specific IFN-γ ELISPOT responses were measurable in spleen and lymph node but at a statistically higher frequency in cats exposed to a single subcutaneous dose of wild-type L. monocytogenes versus cats exposed both subcutaneously and orally. The FIV/cat model will provide a useful challenge system to determine whether recombinant L. monocytogenes can protect against a lentivirus in its natural host after challenge by the routes common to HIV transmission. DA - 2005/2/10/ PY - 2005/2/10/ DO - 10.1016/j.vaccine.2004.09.033 VL - 23 IS - 12 SP - 1479-1490 SN - 1873-2518 KW - Listeria monocytogenes KW - feline immunodeficiency virus KW - HIV ER - TY - JOUR TI - PowerMarker: an integrated analysis environment for genetic marker analysis AU - Liu, KJ AU - Muse, SV T2 - BIOINFORMATICS AB - PowerMarker delivers a data-driven, integrated analysis environment (IAE) for genetic data. The IAE integrates data management, analysis and visualization in a user-friendly graphical user interface. It accelerates the analysis lifecycle and enables users to maintain data integrity throughout the process. An ever-growing list of more than 50 different statistical analyses for genetic markers has been implemented in PowerMarker.www.powermarker.net DA - 2005/5/1/ PY - 2005/5/1/ DO - 10.1093/bioinformatics/bti282 VL - 21 IS - 9 SP - 2128-2129 SN - 1460-2059 ER - TY - PCOMM TI - Potential limitations of the 16S-23S rRNA intergenic region for molecular detection of Bartonella species - Authors' reply AU - Breitschwerdt, E. B. AU - Maggi, R. G. DA - 2005/// PY - 2005/// SP - 4922 ER - TY - JOUR TI - Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins AU - Houston, N. L. AU - Fan, C. Z. AU - Xiang, Q. Y. AU - Schulze, J. M. AU - Jung, R. AU - Boston, R. S. T2 - Plant Physiology AB - Abstract Protein disulfide isomerases (PDIs) are molecular chaperones that contain thioredoxin (TRX) domains and aid in the formation of proper disulfide bonds during protein folding. To identify plant PDI-like (PDIL) proteins, a genome-wide search of Arabidopsis (Arabidopsis thaliana) was carried out to produce a comprehensive list of 104 genes encoding proteins with TRX domains. Phylogenetic analysis was conducted for these sequences using Bayesian and maximum-likelihood methods. The resulting phylogenetic tree showed that evolutionary relationships of TRX domains alone were correlated with conserved enzymatic activities. From this tree, we identified a set of 22 PDIL proteins that constitute a well-supported clade containing orthologs of known PDIs. Using the Arabidopsis PDIL sequences in iterative BLAST searches of public and proprietary sequence databases, we further identified orthologous sets of 19 PDIL sequences in rice (Oryza sativa) and 22 PDIL sequences in maize (Zea mays), and resolved the PDIL phylogeny into 10 groups. Five groups (I–V) had two TRX domains and showed structural similarities to the PDIL proteins in other higher eukaryotes. The remaining five groups had a single TRX domain. Two of these (quiescin-sulfhydryl oxidase-like and adenosine 5′-phosphosulfate reductase-like) had putative nonisomerase enzymatic activities encoded by an additional domain. Two others (VI and VIII) resembled small single-domain PDIs from Giardia lamblia, a basal eukaryote, and from yeast. Mining of maize expressed sequence tag and RNA-profiling databases indicated that members of all of the single-domain PDIL groups were expressed throughout the plant. The group VI maize PDIL ZmPDIL5-1 accumulated during endoplasmic reticulum stress but was not found within the intracellular membrane fractions and may represent a new member of the molecular chaperone complement in the cell. DA - 2005/// PY - 2005/// DO - 10.1104/pp.104.056507 VL - 137 IS - 2 SP - 762-778 ER - TY - JOUR TI - PhotochemCAD 2: A Refined Program with Accompanying Spectral Databases for Photochemical Calculations AU - Dixon, JM AU - Taniguchi, M AU - Lindsey, JS T2 - PHOTOCHEMISTRY AND PHOTOBIOLOGY DA - 2005/// PY - 2005/// DO - 10.1562/2004-11-06-TSN-361.1 VL - 81 IS - 1 SP - 212-213 SN - 1751-1097 ER - TY - JOUR TI - Modeling quantitative trait loci and interpretation of models AU - Zeng, ZB AU - Wang, T AU - Zou, W T2 - GENETICS AB - A quantitative genetic model relates the genotypic value of an individual to the alleles at the loci that contribute to the variation in a population in terms of additive, dominance, and epistatic effects. This partition of genetic effects is related to the partition of genetic variance. A number of models have been proposed to describe this relationship: some are based on the orthogonal partition of genetic variance in an equilibrium population. We compare a few representative models and discuss their utility and potential problems for analyzing quantitative trait loci (QTL) in a segregating population. An orthogonal model implies that estimates of the genetic effects are consistent in a full or reduced model in an equilibrium population and are directly related to the partition of the genetic variance in the population. Linkage disequilibrium does not affect the estimation of genetic effects in a full model, but would in a reduced model. Certainly linkage disequilibrium would complicate the detection of QTL and epistasis. Using different models does not influence the detection of QTL and epistasis. However, it does influence the estimation and interpretation of genetic effects. DA - 2005/3// PY - 2005/3// DO - 10.1534/genetics.104.035857 VL - 169 IS - 3 SP - 1711-1725 SN - 0016-6731 ER - TY - JOUR TI - Model systems in agriculture: Lessons from worms AU - Bird, D.M. T2 - Annals of Applied Biology AB - Genomic tools are expanding the utility of organisms originally developed as models for biomedical research as a means to address complex agricultural problems. Conversely, agricultural pests are serving as models to help unravel questions of basic biology. Examples from C. elegans and root-knot nematode of this two-way exchange are discussed. DA - 2005/// PY - 2005/// DO - 10.1111/j.1744-7348.2005.040066.x VL - 146 IS - 2 SP - 147-154 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-16444385698&partnerID=MN8TOARS ER - TY - JOUR TI - Investigating hookworm genomes by comparative analysis of two Ancylostoma species AU - Mitreva, M. AU - McCarter, J. P. AU - Arasu, P. AU - Hawdon, J. AU - Martin, J. AU - Dante, M. AU - Wylie, T. AU - Xu, J. AU - Stajich, J. E. AU - Kapulkin, W. AU - Clifton, S. W. AU - Waterston, R. H. AU - Wilson, R. K. T2 - BMC Genomics DA - 2005/// PY - 2005/// VL - 6 ER - TY - JOUR TI - In vivo processing and isolation of furin protease-sensitive alphavirus glycoproteins: a new technique for producing mutations in virus assembly AU - Nelson, S AU - Hernandez, R AU - Ferreira, D AU - Brown, DT T2 - VIROLOGY AB - Sindbis virus particles are composed of three structural proteins (Capsid/E2/E1). In the mature virion the E1 glycoprotein is organized in a highly constrained, energy-rich conformation. It is hypothesized that this energy is utilized to drive events that deliver the viral genome to the cytoplasm of a host cell. The extraction of the E1 glycoprotein from virus membranes with detergent results in disulfide-bridge rearrangement and the collapse of the protein to a number of low-energy, non-native configurations. In a new approach to the production of membrane-free membrane glycoproteins, furin protease recognition motifs were installed at various positions in the E1 glycoprotein ectodomain. Proteins containing the furin-sensitive sites undergo normal folding and assembly in the endoplasmic reticulum and only experience the consequence of the mutation during transport to the cell surface. Processing by furin in the Golgi results in the release of the protein from the membrane. Processing of the proteins also impacts the envelopment of the nucleocapsid in the modified plasma membrane. This technique provides a unique method for studying the mechanism of virus assembly and protein structure without altering crucial early events in protein assembly, folding, and maturation. DA - 2005/2/20/ PY - 2005/2/20/ DO - 10.1016/j.virol.2004.12.013 VL - 332 IS - 2 SP - 629-639 SN - 0042-6822 KW - alphavirus KW - Sindbis KW - membrane glycoproteins KW - form protease KW - virus assembly ER - TY - JOUR TI - Geographic distribution of babesiosis among dogs in the United States and association with dog bites: 150 cases (2000-2003) AU - Birkenheuer, Adam J. AU - Correa, Maria T. AU - Levy, Michael G. AU - Breitschwerdt, Edward B. T2 - Journal of the American Veterinary Medical Association AB - To identify the geographic distribution of babesiosis among dogs in the United States and determine, for dogs other than American Pit Bull Terriers (APBTs), whether infection was associated with a recent dog bite.Retrospective study.150 dogs.Canine blood samples submitted to the North Carolina State University Vector-Borne Disease Diagnostic Laboratory between May 2000 and October 2003 for which results of a Babesia-specific polymerase chain reaction assay were positive were identified, and breed and geographic origin of dogs from which samples were obtained were recorded. History and hematologic abnormalities for dogs that were not APBTs were recorded, and possible associations with a recent dog bite were examined.Dogs positive for Babesia DNA were located in 29 states and 1 Canadian province (Ontario). Babesia gibsoni was the most commonly detected species, with B gibsoni DNA detected in blood samples from 131 of 144 (91%) dogs. Of the 131 dogs positive for B gibsoni DNA, 122 (93%) were APBTs. Of the 10 dogs positive for Babesia canis vogeli DNA, 6 were Greyhounds. In dogs other than APBTs, there was an association between having recently been bitten by another dog, particularly an APBT, and infection with B gibsoni.Results document an expansion of the known geographic range for babesiosis among dogs in the United States. Testing for babesiosis should be pursued in dogs with clinicopathologic abnormalities consistent with immune-mediated hemolytic anemia or thrombocytopenia, particularly if there is a history of a recent dog bite. DA - 2005/9// PY - 2005/9// DO - 10.2460/javma.2005.227.942 VL - 227 IS - 6 SP - 942-947 J2 - Journal of the American Veterinary Medical Association LA - en OP - SN - 0003-1488 UR - http://dx.doi.org/10.2460/javma.2005.227.942 DB - Crossref ER - TY - JOUR TI - Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid AU - Kirst, M AU - Basten, CJ AU - Myburg, AA AU - Zeng, ZB AU - Sederoff, RR T2 - GENETICS AB - Species diversity may have evolved by differential regulation of a similar set of genes. To analyze and compare the genetic architecture of transcript regulation in different genetic backgrounds of Eucalyptus, microarrays were used to examine variation in mRNA abundance in the differentiating xylem of a E. grandis pseudobackcross population [E. grandis x F(1) hybrid (E. grandis x E. globulus)]. Least-squares mean estimates of transcript levels were generated for 2608 genes in 91 interspecific backcross progeny. The quantitative measurements of variation in transcript abundance for specific genes were mapped as expression QTL (eQTL) in two single-tree genetic linkage maps (F(1) hybrid paternal and E. grandis maternal). EQTL were identified for 1067 genes in the two maps, of which 811 were located in the F(1) hybrid paternal map, and 451 in the E. grandis maternal map. EQTL for 195 genes mapped to both parental maps, the majority of which localized to nonhomologous linkage groups, suggesting trans-regulation by different loci in the two genetic backgrounds. For 821 genes, a single eQTL that explained up to 70% of the transcript-level variation was identified. Hotspots with colocalized eQTL were identified in both maps and typically contained genes associated with specific metabolic and regulatory pathways, suggesting coordinated genetic regulation. DA - 2005/4// PY - 2005/4// DO - 10.1534/genetics.104.039198 VL - 169 IS - 4 SP - 2295-2303 SN - 1943-2631 ER - TY - JOUR TI - Differences in wood density and growth of fertilized and nonfertilized loblolly pine associated with a mutant gene, cad-n1 AU - Yu, Q AU - McKeand, SE AU - Nelson, CD AU - Li, B AU - Sherrill, , JR AU - Mullin, TJ T2 - CANADIAN JOURNAL OF FOREST RESEARCH AB - A rare mutant allele (cad-n1) of the cad gene in loblolly pine (Pinus taeda L.) causes a deficiency in the production of cinnamyl alcohol dehydrogenase (CAD). Effects associated with this allele were examined by comparing wood density and growth traits of cad-n1 heterozygous trees with those of wild-type trees in a 10-year-old open-pollinated family trial growing under two levels of fertilization in Scotland County, North Carolina. In all, 200 trees were sampled, with 100 trees for each fertilizer treatment. Wood density measurements were collected from wood cores at breast height using X-ray densitometry. We found that the substitution of a cad-n1 for a wild-type allele (Cad) was associated with a significant effect on wood density. The cad-n1 heterozygotes had a significantly higher wood density (+2.6%) compared with wild-type trees. The higher density was apparently due to the higher percentage of latewood in the heterozygotes. The fertilization effect was highly significant for both growth and wood density traits. This study indicates that the cad-n1 allele could be a valuable gene to the pulp and paper industry for the purpose of enhancing pulp yields by increasing wood density. DA - 2005/7// PY - 2005/7// DO - 10.1139/X05-103 VL - 35 IS - 7 SP - 1723-1730 SN - 1208-6037 ER - TY - JOUR TI - Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays AU - Wadenback, J. AU - Clapham, D. H. AU - Craig, D. AU - Sederoff, R. AU - Peter, G. F. AU - Von Arnold, S. AU - Egertsdotter, U. T2 - BMC Genomics DA - 2005/// PY - 2005/// VL - 6 IS - 61 ER - TY - JOUR TI - Cloning and expression of feline interleukin 15 AU - Dean, GA AU - Barger, A AU - LaVoy, A T2 - CYTOKINE AB - A cDNA encoding feline interleukin 15 (IL15) was cloned from the lymph node of a cat infected with feline infectious peritonitis virus. The cDNA is 486 bp in length and encodes a protein of 162 amino acids. Recombinant protein was readily expressed as a GST fusion in Escherichia coli and purified by glutathione affinity chromatography. Expression of recombinant protein in mammalian cells was only accomplished by eliminating the 5′ and 3′ UTR, replacing the IL15 signal peptide with the tissue plasminogen activator signal peptide, and adding 3′ sequence to disrupt presumptive secondary structure of the mRNA. Biologically active feline IL15 was expressed in HEK293T cells and was shown to sustain primary feline lymphocytes, a feline T cell line, and mouse CTLL-2 cells. Proliferation of CTLL-2 cells was induced by the recombinant protein in a dose-dependent manner. Monoclonal and polyclonal antibodies against human IL15 recognized feline IL15 in immunofluorescence and Western blot assays. Additionally, feline IL15 was detectable using a commercially available human IL15 ELISA kit. DA - 2005/1/21/ PY - 2005/1/21/ DO - 10.1016/j.cyto.2004.09.012 VL - 29 IS - 2 SP - 77-83 SN - 1096-0023 KW - feline KW - feline immunodeficiency virus KW - interleukin 15 ER - TY - JOUR TI - Cell wall localization of Red clover necrotic mosaic virus movement protein is required for cell-to-cell movement AU - Tremblay, D AU - Vaewhongs, AA AU - Turner, KA AU - Sit, TL AU - Lommel, SA T2 - VIROLOGY AB - The Red clover necrotic mosaic virus movement protein (MP) is essential for cell-to-cell movement. Eight previously characterized alanine-scanning mutants of the MP were fused to the green fluorescent protein (GFP) and expressed from viral infectious transcripts. Inoculated plants were assayed for movement and intracellular accumulation of MP by confocal laser-scanning microscopy. A strict correlation was observed between the targeting to the cell wall (presumably the plasmodesmata) and cell-to-cell movement. Complementation of dysfunctional MP mutants with either wild-type MP or other null mutants in some cases rescued intracellular targeting and movement. The data suggest the presence of distinct domains in the MP for virus movement (near residues 27–31), complementarity (near residues 122 and 128), and intracellular localization (near residue 161). These data support a model of MP interacting cooperatively with itself to bind viral RNA, localize to and modify plasmodesmata and effect virus movement. DA - 2005/3/1/ PY - 2005/3/1/ DO - 10.1016/j.virol.2004.12.019 VL - 333 IS - 1 SP - 10-21 SN - 0042-6822 KW - RCNMV movement protein KW - plasmodesmata KW - GFP KW - intracellular localization KW - viral movement KW - confocal microscopy ER - TY - JOUR TI - Bartonella species as a potential cause of epistaxis in dogs AU - Breitschwerdt, EB AU - Hegarty, BC AU - Maggi, R AU - Hawkins, E AU - Dyer, P T2 - JOURNAL OF CLINICAL MICROBIOLOGY AB - Infection with a Bartonella species was implicated in three cases of epistaxis in dogs, based upon isolation, serology, or PCR amplification. These cases, in conjunction with previously published reports, support a potential role for Bartonella spp. as a cause of epistaxis in dogs and potentially in other animals, including humans. DA - 2005/5// PY - 2005/5// DO - 10.1128/JCM.43.5.2529-2533.2005 VL - 43 IS - 5 SP - 2529-2533 SN - 1098-660X ER - TY - JOUR TI - Autochthonous visceral leishmaniasis in dogs in North America AU - Schantz, Peter M. AU - Steurer, Francis J. AU - Duprey, Zandra H. AU - Kurpel, Katherine P. AU - Barr, Stephen C. AU - Jackson, Joan E. AU - Breitschwerdt, Edward B. AU - Levy, Michael G. AU - Fox, J. C. T2 - Journal of the American Veterinary Medical Association DA - 2005/4// PY - 2005/4// DO - 10.2460/javma.2005.226.1316 VL - 226 IS - 8 SP - 1316-1322 J2 - Journal of the American Veterinary Medical Association LA - en OP - SN - 0003-1488 UR - http://dx.doi.org/10.2460/javma.2005.226.1316 DB - Crossref ER - TY - JOUR TI - A compact all-carbon tripodal tether affords high coverage of porphyrins on silicon surfaces AU - Padmaja, K AU - Wei, LY AU - Lindsey, JS AU - Bocian, DF T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Redox-active molecules designed to give high charge density on electroactive surfaces are essential for applications in molecular information storage. To achieve a small molecular footprint and thereby high surface charge density, a compound consisting of a triallyl tripod attached via a p-phenylene unit to a porphyrin (1) has been synthesized. The zinc chelate of 1 (Zn-1) was attached to Si(100). Electrochemical measurements indicate that the molecular footprint (75 Å) in the monolayer is only ∼50% larger than the minimum achievable, indicating high surface coverage. IR spectroscopy indicates that the bands due to the ν(CC) (1638 cm-1) and γ(CH) (915 cm-1) vibrations present in the solid sample (KBr pellet) are absent from the spectra of the monolayers of Zn-1, consistent with saturation of the double bond in each of the three legs of the tripod upon the hydrosilylation process accompanying attachment. Comparison of the relative intensities of the in-plane (998 cm-1) versus out-of-plane (797 cm-1) porphyrin modes indicates the average tilt angle (α) of the porphyrin ring with respect to the surface normal is ∼46°, a value also observed for analogous porphyrins tethered to Si(100) via monopodal carbon linkers. Accordingly, the higher packing densities afforded by the compact tripodal linker are not due to a more upright orientation on the surface. The charge-retention half-lives (t1/2) for the first oxidation state of the Zn-1 monolayers increase from 10 to 50 s at low surface coverage (1−5 × 10-11 mol·cm-2) to near 200 s at saturation coverage (∼2 × 10-10 mol·cm-2). Taken together, the high surface charge density (despite the lack of upright orientation) of the triallyl-tripodal porphyrin makes this construct a viable candidate for molecular information storage applications. DA - 2005/9/30/ PY - 2005/9/30/ DO - 10.1021/jo0510078 VL - 70 IS - 20 SP - 7972-7978 SN - 0022-3263 ER - TY - JOUR TI - 1,9-bis(N,N-dimethylaminomethyl)dipyrromethanes in the synthesis of porphyrins bearing one or two meso substituents AU - Fan, DZ AU - Taniguchi, M AU - Yao, Z AU - Dhanalekshmi, S AU - Lindsey, JS T2 - TETRAHEDRON AB - A synthesis of 5,15-disubstituted zinc-porphyrins has been developed that employs condensation of a 1,9-bis(N,N-dimethylaminomethyl)dipyrromethane+a dipyrromethane in refluxing ethanol containing zinc acetate followed by oxidation with DDQ. The N,N-dimethylaminomethylation of the dipyrromethane was achieved via Eschenmoser's reagent (N,N-dimethylmethyleneammonium iodide) in CH2Cl2 at room temperature. The synthesis is compatible with diverse substituents (e.g., alkyl, aryl, ester, acetal) and enables rapid synthesis of trans-AB-, A2-, and A-porphyrins. The synthesis of >40 zinc porphyrins has been surveyed; 13 zinc porphyrins were isolated in yields of 5–20% without detectable scrambling. DA - 2005/10/24/ PY - 2005/10/24/ DO - 10.1016/j.tet.2005.08.028 VL - 61 IS - 43 SP - 10291-10302 SN - 0040-4020 KW - dipyrromethane KW - aminomethylation KW - porphyrin KW - zinc ER - TY - JOUR TI - Vernalization sensitivity in Arabidopsis thaliana (brassicaceae): The effects of latitude and FLC variation AU - Stinchcombe, , JR AU - Caicedo, AL AU - Hopkins, R AU - Mays, C AU - Boyd, EW AU - Purugganan, MD AU - Schmitt, J T2 - AMERICAN JOURNAL OF BOTANY AB - Latitudinal variation in climate is predicted to select for latitudinal differentiation in sensitivity to the environmental cues that signal plants to flower at the appropriate time for a given climate. In Arabidopsis thaliana, flowering is promoted by exposure to cold temperatures (vernalization), and several vernalization pathway loci are known. To test whether natural variation in vernalization sensitivity could account for a previously observed latitudinal cline in flowering time in A. thaliana, we exposed 21 European accessions to 0, 10, 20, or 30 d of vernalization and observed leaf number at flowering under short days in a growth chamber. We observed a significant latitudinal cline in vernalization sensitivity: southern accessions were more sensitive to vernalization than northern accessions. In addition, accessions that were late flowering in the absence of vernalization were more sensitive to vernalization cues. Allelic variation at the flowering time regulatory gene FLC was not associated with mean vernalization sensitivity, but one allele class exhibited greater variance in vernalization sensitivity. DA - 2005/10// PY - 2005/10// DO - 10.3732/ajb.92.10.1701 VL - 92 IS - 10 SP - 1701-1707 SN - 1537-2197 KW - Brassicaceae KW - ecological genomics KW - FLC KW - flowering time KW - FRI KW - latitudinal cline KW - vernalization ER - TY - JOUR TI - Polygenic mutation in Drosophila melanogaster: Mapping spontaneous mutations affecting sensory bristle number AU - Mackay, TFC AU - Lyman, RF AU - Lawrence, F T2 - GENETICS AB - Our ability to predict long-term responses to artificial and natural selection, and understand the mechanisms by which naturally occurring variation for quantitative traits is maintained, depends on detailed knowledge of the properties of spontaneous polygenic mutations, including the quantitative trait loci (QTL) at which mutations occur, mutation rates, and mutational effects. These parameters can be estimated by mapping QTL that cause divergence between mutation-accumulation lines that have been established from an inbred base population and selected for high and low trait values. Here, we have utilized quantitative complementation to deficiencies to map QTL at which spontaneous mutations affecting Drosophila abdominal and sternopleural bristle number have occurred in 11 replicate lines during 206 generations of divergent selection. Estimates of the numbers of mutations were consistent with diploid per-character mutation rates for bristle traits of 0.03. The ratio of the per-character mutation rate to total mutation rate (0.023) implies that >2% of the genome could affect just one bristle trait and that there must be extensive pleiotropy for quantitative phenotypes. The estimated mutational effects were not, however, additive and exhibited dependency on genetic background consistent with diminishing epistasis. However, these inferences must be tempered by the potential for epistatic interactions between spontaneous mutations and QTL affecting bristle number on the deficiency-bearing chromosomes, which could lead to overestimates in numbers of QTL and inaccurate inference of gene action. DA - 2005/8// PY - 2005/8// DO - 10.1534/genetics.104.032581 VL - 170 IS - 4 SP - 1723-1735 SN - 1943-2631 ER - TY - JOUR TI - Interaction between the alpha-T catenin gene (VR22) and APOE in Alzheimer's disease AU - Martin, ER AU - Bronson, PG AU - Li, YJ AU - Wall, N AU - Chung, RH AU - Schmechel, DE AU - Small, G AU - Xu, PT AU - Bartlett, J AU - Schnetz-Boutaud, N AU - Haines, JL AU - Gilbert, , JR AU - Pericak-Vance, MA T2 - JOURNAL OF MEDICAL GENETICS AB - APOE is the only gene that has been consistently replicated as a risk factor for late onset Alzheimer's disease. Several recent studies have identified linkage to chromosome 10 for both risk and age of onset, suggesting that this region harbours genes that influence the development of the disease. A recent study reported association between single nucleotide polymorphisms (SNPs) in the VR22 gene (CTNNA3) on chromosome 10 and plasma levels of Abeta42, an endophenotype related to Alzheimer's disease.To assess whether polymorphisms in the VR22 gene are associated with Alzheimer's disease in a large sample of Alzheimer's disease families and an independent set of unrelated cases and controls.Several SNPs showed association in either the family based or case-control analyses (p<0.05). The most consistent findings were with SNP6, for which there was significant evidence of association in both the families and the unrelated cases and controls. Furthermore, there was evidence of significant interaction between APOE-4 and two of the VR22 SNPs, with the strongest evidence of association being concentrated in individuals carrying APOE-4.This study suggests that VR22 or a nearby gene influences susceptibility to Alzheimer's disease, and the effect is dependent on APOE status. DA - 2005/10// PY - 2005/10// DO - 10.1136/jmg.2004.029553 VL - 42 IS - 10 SP - 787-792 SN - 0022-2593 ER - TY - JOUR TI - Evaluation of endogenous reference genes for real-time PCR quantification of gene expression in Ancylostoma caninum AU - Trivedi, S AU - Arasu, P T2 - MOLECULAR AND BIOCHEMICAL PARASITOLOGY DA - 2005/10// PY - 2005/10// DO - 10.1016/j.molbiopara.2005.05.011 VL - 143 IS - 2 SP - 241-244 SN - 1872-9428 KW - Ancylostoma hookworms KW - real-time PCR KW - validation KW - reference gene ER - TY - JOUR TI - Diminished expression of C/EBP alpha in skin carcinomas is linked to oncogenic Ras and reexpression of C/EBP alpha in carcinoma cells inhibits proliferation AU - Shim, M. AU - Powers, K. L. AU - Ewing, S. J. AU - Zhu, S. AU - Smart, R. C. T2 - Cancer Research DA - 2005/// PY - 2005/// VL - 65 IS - 3 SP - 861–867 ER - TY - JOUR TI - Synthesis and film-forming properties of ethynylporphyrins AU - Liu, ZM AU - Schmidt, I AU - Thamyongkit, P AU - Loewe, RS AU - Syomin, D AU - Diers, , JR AU - Zhao, Q AU - Misra, V AU - Lindsey, JS AU - Bocian, DF T2 - CHEMISTRY OF MATERIALS AB - Thermal treatment of ethynyl porphyrin monomers on a surface has been found to yield robust porphyrin films. The scope of this in situ polymerization has been surveyed by the synthesis and characterization of a collection of 20 zinc porphyrins bearing diverse patterns of 1−4 ethyne (or protected ethyne) groups and a variety of nonlinking substituents. Films have been prepared on Si(100), SiO2, Au(111), and glass. The films prepared on Si(100) have been examined by electrochemical methods, which indicate that surface coverages 50-fold greater than those of saturation-coverage monolayers are achievable, although the coverage varies appreciably (10-fold) among the survey group of molecules under a controlled set of film-forming conditions. Variation in these conditions affords control over the number of layers in the film (from a few to tens or more). The electrochemical characteristics of the multilayer films further indicate that the redox thermodynamics are of comparable homogeneity to those of monolayers. Examination of the films by FTIR and resonance Raman spectroscopy indicates the absence of an ethynyl or ethenyl linkage between the porphyrins. SEM analysis indicates the porphyrin polymer films range in thickness from tens to hundreds of nanometers. The in situ polymerization technique not only enables control over the thickness of the porphyrin polymer film but also sidesteps solubility problems that typically result upon solution polymerization. The ability to access the porphyrins in the films electrochemically to form porphyrin cation radicals affords increased surface charge density versus that with a monolayer, suggesting the application of the porphyrin films as materials for electrically addressable, molecular-based information storage. DA - 2005/7/12/ PY - 2005/7/12/ DO - 10.1021/cm047858y VL - 17 IS - 14 SP - 3728-3742 SN - 1520-5002 ER - TY - JOUR TI - Sumoylation of internally initiated Sp3 isoforms regulates transcriptional repression via a Trichostatin A-insensitive mechanism AU - Spengler, ML AU - Kennett, SB AU - Moorefield, KS AU - Simmons, SO AU - Brattain, MG AU - Horowitz, JM T2 - CELLULAR SIGNALLING AB - Sp3 is a ubiquitously expressed member of the Sp family of transcription factors that encodes three proteins, Sp3, M1 and M2, with differing capacities to stimulate or repress transcription. As part of ongoing efforts to study the functions of Sp3 isoforms, we employed a yeast “two-hybrid” screen to identify Sp3-binding proteins. This screen resulted in the identification of Ubc9, a SUMO-1 conjugating enzyme, as an M2-binding protein, and consistent with these results sequence analyses identified consensus sumoylation motifs within several Sp family members. Western blots probed with anti-Sp3 detected a high molecular weight Sp3 isoform that is stabilized by a SUMO-1 hydrolase inhibitor, and this protein is also bound by anti-SUMO-1 antiserum. Transient transfection assays with epitope-tagged-SUMO-1 and GFP-SUMO-1 fusion proteins confirmed that Sp3, M1 and M2 proteins are sumoylated in vivo. Substitution of arginine for lysine at one putative site of sumoylation, lysine551, blocked sumoylation of all Sp3 isoforms in vivo and led to a marginal increase in Sp3-mediated trans-activation in insect and mammalian cells. In contrast, introduction of this amino acid substitution within M1 converted it into a potent transcriptional trans-activator. We conclude that Sp3 isoforms are sumoylated in vivo and this post-translational modification plays an important role in the regulation of Sp3-mediated transcription. DA - 2005/2// PY - 2005/2// DO - 10.1016/j.cellsig.2004.06.007 VL - 17 IS - 2 SP - 153-166 SN - 1873-3913 KW - sumoylation KW - trichostatin A KW - SP3 KW - PML KW - transcriptional regulation KW - trans-activation KW - trans-repression ER - TY - JOUR TI - Solution STM images of porphyrins on HOPG reveal that subtle differences in molecular structure dramatically alter packing geometry AU - Zou, ZQ AU - Wei, LY AU - Chen, F AU - Liu, ZM AU - Thamyongkit, P AU - Loewe, RS AU - Lindsey, JS AU - Mohideen, U AU - Bocian, DF T2 - JOURNAL OF PORPHYRINS AND PHTHALOCYANINES AB - Solution STM images are reported for free-base octaethylporphyrin ( H 2 OEP ) and the Cu ( II ) and Zn ( II ) chelates ( CuOEP and ZnOEP ) on HOPG in 1,2-dichlorobenzene solution under ambient conditions. H 2 OEP and CuOEP each form a quasi-square lattice, whereas ZnOEP forms a quasi-hexagonal lattice on the surface. The binary mixture of any two of the porphyrins forms a well-ordered two-layer structure on the HOPG surface, with one species occupying the bridge sites of the array of the other species. All of the mixed adlayers exhibit a quasi-hexagonal lattice with a higher packing density than the single-component adlayers. Collectively, these observations indicate that the structure of the adlayers is controlled by a complex interplay of substrate-molecule and molecule-molecule interactions. DA - 2005/// PY - 2005/// DO - 10.1142/S1088424605000484 VL - 9 IS - 6 SP - 387-392 SN - 1099-1409 KW - solution STM KW - porphyrin KW - HOPG KW - self-assembly KW - adlayer ER - TY - JOUR TI - Single amino acid insertions at the junction of the Sindbis virus e2 transmembrane domain and endodomain disrupt virus envelopment and alter infectivity AU - Hernandez, R. AU - Ferreira, D. AU - Sinodis, C. AU - Litton, K. AU - Brown, D. T. T2 - Journal of Virology DA - 2005/// PY - 2005/// DO - 10.1128/JVI.79.7682-7697.2005 VL - 79 IS - 12 SP - 7682-7697 ER - TY - JOUR TI - Phylogenetic analysis of the spirochetes Borrelia parkeri and Borrelia turicatae and the potential for tick-borne relapsing fever in Florida AU - Schwan, TG AU - Raffel, SJ AU - Schrumpf, ME AU - Policastro, PF AU - Rawlings, JA AU - Lane, RS AU - Breitschwerdt, EB AU - Porcella, SF T2 - JOURNAL OF CLINICAL MICROBIOLOGY AB - Isolates of Borrelia turicatae, Borrelia parkeri, and the Florida canine borrelia (FCB) were examined to further phylogenetically characterize the identities of these spirochetes in the United States. DNA sequences of four chromosomal loci (the 16S rRNA gene, flaB, gyrB, and glpQ) were determined for eight isolates of B. turicatae and six isolates of B. parkeri, which grouped the spirochetes into two distinct but closely related taxa (>98% sequence identity) separate from Borrelia hermsii. The FCB was clearly separated with the group identified as B. turicatae, confirming this bacterium as a relapsing fever spirochete. Therefore, the potential for tick-borne relapsing fever in humans and other animals exists in Florida and future efforts are needed to determine the enzootic hosts and distribution of this spirochete in the southeastern United States. Analysis of plasmids demonstrated both linear and circular forms in B. turicatae but only linear plasmids in B. parkeri, which should be of interest to investigators concerned with plasmid diversity and evolution within this group of spirochetes. DA - 2005/8// PY - 2005/8// DO - 10.1128/JCM.43.8.3851-3859.2005 VL - 43 IS - 8 SP - 3851-3859 SN - 1098-660X ER - TY - JOUR TI - Novel chemically modified liquid medium that will support the growth of seven Bartonella species AU - Maggi, Ricardo AU - Duncan, A. W. AU - Breitschwerdt, Edward T2 - Journal of Clinical Microbiology AB - ABSTRACT Bacteria of the genus Bartonella , a member of the Alphaproteobacteria , are fastidious, gram-negative, aerobic bacilli that comprise numerous species, subspecies, and subtypes. In human and veterinary medicine, species isolation remains a vital component of the diagnostic and therapeutic management of Bartonella infection. We describe a novel, chemically modified, insect-based liquid culture medium that supports the growth of at least seven Bartonella species. This medium will also support cocultures consisting of different Bartonella species, and it facilitated the primary isolation of Bartonella henselae from blood and aqueous fluid of naturally infected cats. This liquid growth medium may provide an advantage over conventional direct blood agar plating for the diagnostic confirmation of bartonellosis. DA - 2005/// PY - 2005/// DO - 10.1128/JCM.43.6.2651-2655.2005 VL - 43 IS - 6 SP - 2651–2655 ER - TY - JOUR TI - Matrix attachment regions and regulated transcription increase and stabilize transgene expression AU - Abranches, R AU - Shultz, RW AU - Thompson, WF AU - Allen, GC T2 - PLANT BIOTECHNOLOGY JOURNAL AB - Transgene silencing has been shown to be associated with strong promoters, but it is not known whether the propensity for silencing is caused by the level of transcription, or some other property of the promoter. If transcriptional activity fosters silencing, then transgenes with inducible promoters may be less susceptible to silencing. To test this idea, a doxycycline-inducible luciferase transgene was transformed into an NT1 tobacco suspension culture cell line that constitutively expressed the tetracycline repressor. The inducible luciferase gene was flanked by tobacco Rb7 matrix attachment regions (MAR) or spacer control sequences in order to test the effects of MARs in conjunction with regulated transcription. Transformed lines were grown under continuous doxycycline (CI), or delayed doxycycline induction (DI) conditions. Delayed induction resulted in higher luciferase expression initially, but continued growth in the presence of doxycycline resulted in a reduction of expression to levels similar to those found in continuously induced lines. In both DI and CI treatments, the Rb7 MAR significantly reduced the percentage of silenced lines and increased transgene expression levels. These data demonstrate that active transcription increases silencing, especially in the absence of the Rb7 MAR. Importantly, the Rb7 MAR lines showed higher expression levels under both CI and DI conditions and avoided silencing that may occur in the absence of active transcription such as what would be expected as a result of condensed chromatin spreading. DA - 2005/9// PY - 2005/9// DO - 10.1111/j.1467-7652.2005.00144.x VL - 3 IS - 5 SP - 535-543 SN - 1467-7644 KW - PTGS KW - TGS KW - RNAi KW - MARs KW - transgene expression KW - induction ER - TY - JOUR TI - Identification and characterization of cowpea aphid-borne mosaic virus as the second virus from mixed-infected Crotalaria juncea plants in Nigeria AU - Ladipo, J. L. AU - Lommel, S. A. AU - Barnett, O. W. T2 - Zeitschrift fur Pflanzenkrankheiten und Pflanzenschutz DA - 2005/// PY - 2005/// VL - 112 IS - 3 SP - 222-228 ER - TY - JOUR TI - Genetic effects of rooting loblolly pine stem cuttings from a partial diallel mating design AU - Baltunis, BS AU - Huber, DA AU - White, TL AU - Goldfarb, B AU - Stelzer, HE T2 - CANADIAN JOURNAL OF FOREST RESEARCH-REVUE CANADIENNE DE RECHERCHE FORESTIERE AB - More than 239 000 stem cuttings from nearly 2200 clones of loblolly pine (Pinus taeda L.) were set in five rooting trials to estimate genetic parameters associated with rooting. Overall rooting success across the five trials was 43%, and significant seasonal effects were observed. Differences among clones within full-sib families accounted for approximately 10%–17% of the total variation. On the binary scale, individual-tree narrow-sense heritability (ĥ 2 0.1 ) ranged from 0.075 to 0.089 for rooting across the five separate settings, while broad-sense heritability (Ĥ 2 0.1 ) ranged from 0.15 to 0.22. Narrow- and broad-sense heritability estimates on the observed binary scale were transformed to their underlying normal scale (ĥ 2 N , Ĥ 2 N ). When all of the data from the five trials were analyzed together, ĥ 2 N (±SE) was 0.081 (0.027), Ĥ 2 N was 0.16 (0.013), the type B additive correlation was 0.68 (0.23), and the type B dominance correlation was 0.61 (0.27). Narrow-sense family mean heritability was 0.83 (0.24), while broad-sense clonal mean heritability was 0.82 (0.074). These moderate to high family and clonal mean heritabilities, moderate type B correlations, and substantial among-family and among-clone genetic variation indicate the potential for increasing rooting efficiency by selecting good rooting families and clones or culling poor rooters. DA - 2005/5// PY - 2005/5// DO - 10.1139/X05-038 VL - 35 IS - 5 SP - 1098-1108 SN - 0045-5067 ER - TY - JOUR TI - Gene expression profiles associated with the transition to parasitism in Ancylostoma caninum larvae AU - Moser, J. M. AU - Freitas, T. AU - Arasu, P. AU - Gibson, G. T2 - Molecular and Biochemical Parasitology DA - 2005/// PY - 2005/// DO - 10.1016/j.molbiopran.2005.04.012 VL - 143 IS - 1 SP - 39-48 ER - TY - JOUR TI - Characterization and comparative analysis of Arabidopsis phosphatidylinositol phosphate 5-kinase 10 reveals differences in Arabidopsis and human phosphatidylinositol phosphate kinases AU - Perera, IY AU - Davis, AJ AU - Galanopilou, D AU - Im, YJ AU - Boss, WF T2 - FEBS LETTERS AB - Arabidopsis phosphatidylinositol phosphate (PtdInsP) kinase 10 ( At PIPK10; At4g01190) is shown to be a functional enzyme of the subfamily A, type I At PtdInsP kinases. It is biochemically distinct from At PIPK1 (At1g21980), the only other previously characterized At PtdInsP kinase which is of the B subfamily. At PIPK10 has the same K m , but a 10‐fold lower V max than At PIPK1 and it is insensitive to phosphatidic acid. At PIPK10 transcript is most abundant in inflorescence stalks and flowers, whereas At PIPK1 transcript is present in all tissues. Comparative analysis of recombinant At PIPK10 and At PIPK1 with recombinant Hs PIPKIα reveals that the Arabidopsis enzymes have roughly 200‐ and 20‐fold lower V max / K m , respectively. These data reveal one explanation for the longstanding mystery of the relatively low phosphatidylinositol‐(4,5)‐bisphosphate:phosphatidylinositol‐4‐phosphate ratio in terrestrial plants. DA - 2005/6/20/ PY - 2005/6/20/ DO - 10.1016/j.febslet.2005.05.018 VL - 579 IS - 16 SP - 3427-3432 SN - 1873-3468 KW - phosphatidylinositol phosphate kinase KW - lipid kinase KW - Arabidopsis ER - TY - JOUR TI - Basal and reovirus-induced beta interferon (IFN-beta) and IFN-beta-stimulated gene expression are cell type specific in the cardiac protective response AU - Stewart, MJ AU - Smoak, K AU - Blum, MA AU - Sherry, B T2 - JOURNAL OF VIROLOGY AB - ABSTRACT Viral myocarditis is an important human disease, with a wide variety of viruses implicated. Cardiac myocytes are not replenished yet are critical for host survival and thus may have a unique response to infection. Previously, we determined that the extent of reovirus induction of beta interferon (IFN-β) and IFN-β-mediated protection in primary cardiac myocyte cultures was inversely correlated with the extent of reovirus-induced cardiac damage in a mouse model. Surprisingly, and in contrast, the IFN-β response did not determine reovirus replication in skeletal muscle cells. Here we compared the IFN-β response in cardiac myocytes to that in primary cardiac fibroblast cultures, a readily replenished cardiac cell type. We compared basal and reovirus-induced expression of IFN-β, IRF-7 (an interferon-stimulated gene [ISG] that further induces IFN-β), and another ISG (561) in the two cell types by using real-time reverse transcription-PCR. Basal IFN-β, IRF-7, and 561 expression was higher in cardiac myocytes than in cardiac fibroblasts. Reovirus T3D induced greater expression of IFN-β in cardiac myocytes than in cardiac fibroblasts but equivalent expression of IRF-7 and 561 in the two cell types (though fold induction for IRF-7 and 561 was higher in fibroblasts than in myocytes because of the differences in basal expression). Interestingly, while reovirus replicated to equivalent titers in cardiac myocytes and cardiac fibroblasts, removal of IFN-β resulted in 10-fold-greater reovirus replication in the fibroblasts than in the myocytes. Together the data suggest that the IFN-β response controls reovirus replication equivalently in the two cell types. In the absence of reovirus-induced IFN-β, however, reovirus replicates to higher titers in cardiac fibroblasts than in cardiac myocytes, suggesting that the higher basal IFN-β and ISG expression in myocytes may play an important protective role. DA - 2005/3// PY - 2005/3// DO - 10.1128/JVI.79.5.2979-2987.2005 VL - 79 IS - 5 SP - 2979-2987 SN - 1098-5514 ER - TY - JOUR TI - Assisting Hox proteins in controlling body form: are there new lessons from flies (and mammals)? AU - Mahaffey, JW T2 - CURRENT OPINION IN GENETICS & DEVELOPMENT AB - Hox proteins regulate specific sets of target genes to give rise to morphological distinctions along the anterior–posterior body axis of metazoans. Though they have high developmental specificity, Hox proteins have low DNA binding specificity, so how they select the appropriate target genes has remained enigmatic. There is general agreement that cofactors provide additional specificity, but a comprehensive model of Hox control of gene expression has not emerged. There is now evidence that a global network of zinc finger transcription factors contributes to patterning of the Drosophila embryo. These zinc finger proteins appear to establish fields in which certain Hox proteins can function. Though the nature of these fields is uncertain at this time, it is possible that these zinc finger proteins are Hox cofactors, providing additional specificity during Hox target-gene selection. Furthermore, these zinc finger proteins are conserved, as are aspects of their anterior–posterior expression, suggesting that their roles might be conserved, as well. Perhaps this layer in the genetic control of body patterning will help bridge some of the chasms that remain in our understanding of the genetic control of pattern formation. DA - 2005/8// PY - 2005/8// DO - 10.1016/j.gde.2005.06.009 VL - 15 IS - 4 SP - 422-429 SN - 0959-437X ER - TY - JOUR TI - Anabaena sp strain PCC 7120 gene devH is required for synthesis of the heterocyst glycolipid layer AU - Ramirez, ME AU - Hebbar, PB AU - Zhou, RB AU - Wolk, CP AU - Curtis, SE T2 - JOURNAL OF BACTERIOLOGY AB - In response to deprivation for fixed nitrogen, the filamentous cyanobacterium Anabaena sp. strain PCC 7120 provides a microoxic intracellular environment for nitrogen fixation through the differentiation of semiregularly spaced vegetative cells into specialized cells called heterocysts. The devH gene is induced during heterocyst development and encodes a product with characteristics of a trans-acting regulatory protein. A devH mutant forms morphologically distinguishable heterocysts but is Fox(-), incapable of nitrogen fixation in the presence of oxygen. We demonstrate that rearrangements of nitrogen fixation genes take place normally in the devH mutant and that it is Fix(+), i.e., has nitrogenase activity under anoxic conditions. The Fox(-) phenotype was shown by ultrastructural studies to be associated with the absence of the glycolipid layer of the heterocyst envelope. The expression of glycolipid biosynthetic genes in the mutant is greatly reduced, and heterocyst glycolipids are undetectable. DA - 2005/4// PY - 2005/4// DO - 10.1128/JB.187.7.2326-2331.2005 VL - 187 IS - 7 SP - 2326-2331 SN - 1098-5530 ER - TY - JOUR TI - Tomato spotted wilt virus on potato in eastern North Carolina AU - Abad, JA AU - Moyer, JW AU - Kennedy, GG AU - Holmes, GA AU - Cubeta, MA T2 - AMERICAN JOURNAL OF POTATO RESEARCH DA - 2005/// PY - 2005/// DO - 10.1007/BF02853592 VL - 82 IS - 3 SP - 255-261 SN - 1874-9380 KW - plant virus detection KW - Tospoviruses KW - INSV KW - Solanum ER - TY - JOUR TI - Toll-like receptor expression in feline lymphoid tissues AU - Ignacio, G AU - Nordone, S AU - Howard, KE AU - Dean, GA T2 - VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY AB - Toll-like receptors (TLRs) are germline-encoded pattern recognition receptors (PRRs) that activate the innate immune system. While it is clear that TLRs are important in the immune response against pathogens, they may also be exploited by some pathogens. Our objective is to determine whether feline immunodeficiency virus (FIV) infection affects TLR expression or function thereby resulting in innate immune dysfunction. To this end, we cloned partial sequences for feline TLRs 1–3, 5–8, and developed real-time PCR assays to quantify feline TLRs 1–9. TLR expression was quantified in normal cat lymphoid tissues, purified lymphocyte subsets, and FIV-infected cell lines. Different expression patterns of TLRs were found in spleen, mesenteric lymph node, retropharyngeal lymph node, thymus, intestinal intraepithelial lymphocytes, and lamina propria lymphocytes. B lymphocytes, CD4+ T cells, and CD8+ T cells all expressed TLRs 2–5, 7–9; however, the relative levels of expression varied among lymphocyte phenotypes. Infection of cell lines with FIV resulted in altered TLR expression levels that differed depending on cell type. These results demonstrate that tissue distribution of TLRs is associated with the immunological role of a particular tissue, that lymphocytes may also express these ‘innate immune’ receptors, and that FIV infection can alter TLR expression. DA - 2005/7/15/ PY - 2005/7/15/ DO - 10.1016/j.vetimm.2005.02.022 VL - 106 IS - 3-4 SP - 229-237 SN - 1873-2534 KW - toll-like receptors KW - feline KW - feline immunodeficiency virus KW - innate immunity ER - TY - JOUR TI - The genome sequence of the rice blast fungus Magnaporthe grisea AU - Dean, RA AU - Talbot, NJ AU - Ebbole, DJ AU - Farman, ML AU - Mitchell, TK AU - Orbach, MJ AU - Thon, M AU - Kulkarni, R AU - Xu, , JR AU - Pan, HQ AU - Read, ND AU - Lee, YH AU - Carbone, I AU - Brown, D AU - Oh, YY AU - Donofrio, N AU - Jeong, JS AU - Soanes, DM AU - Djonovic, S AU - Kolomiets, E AU - Rehmeyer, C AU - Li, WX AU - Harding, M AU - Kim, S AU - Lebrun, MH AU - Bohnert, H AU - Coughlan, S AU - Butler, J AU - Calvo, S AU - Ma, LJ AU - Nicol, R AU - Purcell, S AU - Nusbaum, C AU - Galagan, JE AU - Birren, BW T2 - NATURE AB - Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation. DA - 2005/4/21/ PY - 2005/4/21/ DO - 10.1038/nature03449 VL - 434 IS - 7036 SP - 980-986 SN - 1476-4687 ER - TY - JOUR TI - Structural implications of novel diversity in eucaryal RNase P RNA AU - Marquez, S. M. AU - Harris, J. K. AU - Kelley, S. T. AU - Brown, J. W. AU - Dawson, S. C. AU - Roberts, E. C. AU - Pace, N. R. T2 - RNA DA - 2005/// PY - 2005/// VL - 11 IS - 5 SP - 739-751 ER - TY - JOUR TI - Ontogeny and kinetics of carnitine palmitoyltransferase in liver and skeletal muscle of the domestic felid (Felis domestica) AU - Lin, X AU - House, R AU - Odle, J T2 - JOURNAL OF NUTRITIONAL BIOCHEMISTRY AB - The ontogeny of carnitine palmitoyltransferase (CPT) was examined in liver and muscle throughout growth and development of the domestic felid. Homogenates from animals in six age categories (newborn, 24-h, 3-, 6- and 9-week-old, and adult) were examined. Hepatic CPT specific activity increased progressively from birth to 6 weeks and then declined slightly into adulthood, with maximal values for animals greater than 24 h of age [171 nmol/(min g wet tissue)] being 70% higher than for newborns [99 nmol/(min g wet tissue)] (P<.05). Specific activity in adults was similar to that in 6- and 9-week-old juveniles. Total hepatic CPT activity [nmol/(min liver)] increased linearly with age, but the activity expressed per kg body weight [nmol/(min kg BW)] declined after 3 weeks. In contrast, skeletal muscle CPT-specific activity remained unchanged from birth to 3 weeks and then increased significantly, with maximal values at 9 weeks being 90% greater than those for young animals (newborn to 3 weeks; P<.05), whereas specific activity in adults was 50% lower than that observed in 9-week-old animals (P<.05). Hepatic and muscle apparent Km's for carnitine averaged 440 μM and did not vary with age. Hepatic carnitine concentrations remained relatively constant during development, but were lower in adult lactating females, whereas skeletal muscle concentrations increased markedly with age. Hepatic concentrations were 20–50% higher than apparent Km's for carnitine in young and growing animals, but concentrations were similar to the apparent Km at 6 weeks and significantly lower than the apparent Km in adults. Carnitine concentrations in skeletal muscle were 37% lower than apparent Km during the neonatal period, but significantly higher in cats >3 weeks of age. We conclude that postnatal increases in CPT activity support increased capacity for fatty acid oxidation in the developing felid and that dietary carnitine may be required to maximize enzyme activity. DA - 2005/6// PY - 2005/6// DO - 10.1016/j.jnutbio.2004.12.012 VL - 16 IS - 6 SP - 331-338 SN - 1873-4847 KW - fatty acid oxidation KW - feline development KW - lipid metabolism KW - cats KW - CPT ER - TY - JOUR TI - Microclinal variation for ovariole number and body size in Drosophila melanogaster in 'Evolution Canyon' AU - Wayne, ML AU - Korol, A AU - Mackay, TFC T2 - GENETICA DA - 2005/3// PY - 2005/3// DO - 10.1007/s10709-004-5056-y VL - 123 IS - 3 SP - 263-270 SN - 1573-6857 KW - genetic variation KW - microspatial KW - population subdivision KW - selection ER - TY - JOUR TI - Matrix attachment regions increase the efficiency and stability of RNA-mediated resistance to Tomato Spotted Wilt Virus in transgenic tobacco AU - Levin, JS AU - Thompson, WF AU - Csinos, AS AU - Stephenson, MG AU - Weissinger, AK T2 - TRANSGENIC RESEARCH DA - 2005/4// PY - 2005/4// DO - 10.1007/s11248-004-5413-8 VL - 14 IS - 2 SP - 193-206 SN - 1573-9368 KW - gene silencing KW - matrix attachment regions KW - RNA-mediated virus resistance KW - Tomato Spotted Wilt Virus ER - TY - JOUR TI - Genetic interaction of the fusiform rust fungus with resistance gene Fr1 in loblolly pine AU - Kubisiak, TL AU - Amerson, HV AU - Nelson, CD T2 - PHYTOPATHOLOGY AB - We propose a method for defining DNA markers linked to Cronartium quercuum f. sp. fusiforme avirulence (Avr) genes. However, before this method can be successfully employed, a spore competition study was needed to determine the genetic composition of single pycnial drops and multiple drops on single galls when using the standard inoculation procedure, whether virulent (avr1) basidiospores ever predispose some resistant (Fr1/fr1) trees to infection by avirulent (Avr1) basidiospores, and whether avr1 and Avr1 basidiospores equally infect susceptible (fr1/fr1) trees. Results of this study suggest that multiple infections within a single gall are common using the concentrated basidiospore system, resulting on average in >4 infection events per tree. Due to multiple infections within a single gall, an individual pycnial drop cannot be assumed to consist of spores from only a single haploid pycnium. Roughly 57% of the drops harvested were found to consist of more than one haploid genotype, most likely due to the physical mixing of spores from genetically different pycnia. Most importantly, although multiple infections do occur in the formation of a single gall, there is no evidence to suggest that the genetics of the proposed gene-for-gene interaction are compromised. Only avr1 basidiospores were observed to cause infection on Fr1/fr1 trees, whereas both avr1 and Avr1 basidiospores were observed to cause infection on fr1/fr1 trees, albeit not at equal frequencies. DA - 2005/4// PY - 2005/4// DO - 10.1094/PHYTO-95-0376 VL - 95 IS - 4 SP - 376-380 SN - 0031-949X KW - gametothalli KW - infection haplotype KW - Pinus taeda ER - TY - JOUR TI - Free amino acid profiles suggest a possible role for asparagine in the control of storage-product accumulation in developing seeds of low- and high-protein soybean lines AU - Hernandez-Sebastia, C AU - Marsolais, F AU - Saravitz, C AU - Israel, D AU - Dewey, RE AU - Huber, SC T2 - JOURNAL OF EXPERIMENTAL BOTANY AB - Several approaches were taken to examine the role of N-assimilate supply in the control of soybean (Glycine max) seed composition. In the first study, developing seeds were grown in vitro with D-[U-14C]sucrose (Suc) and different concentrations of Gln. Light stimulated carbon flux into oil and protein, and was required to sustain Suc uptake and anabolic processes under conditions of elevated nitrogen supply. High Gln supply resulted in higher transcript levels of β-conglycinin and oleosin. In the second study, analyses of soluble amino acid pools in two genetically related lines, NC103 and NC106 (low- and high-seed protein, respectively) showed that, in the light, NC106 accumulated higher levels of Asn and several other amino acids in developing cotyledons compared with NC103, whereas at the seed coat and apoplast levels both lines were similar. In the dark, NC103 accumulated Gln, Arg, and its precursors, suggesting a reduced availability of organic acids required for amino acid interconversions, while NC106 maintained higher levels of the pyruvate-derived amino acids Val, Leu, and Ile. Comparing NC103 and NC106, differences in seed composition were reflected in steady-state transcript levels of storage proteins and the lipogenic enzyme multi-subunit acetyl CoA carboxylase. In the third study, a positive correlation (P ≤0.05) between free Asn in developing cotyledons and seed protein content at maturity was confirmed in a comparison of five unrelated field-grown cultivars. The findings support the hypothesis that high seed-protein content in soybean is determined by the capacity of the embryo to take up nitrogen sources and to synthesize storage proteins. Asn levels are probably tightly regulated in the embryo of high-protein lines, and may act as a metabolic signal of seed nitrogen status. DA - 2005/7// PY - 2005/7// DO - 10.1093/jxb/eri191 VL - 56 IS - 417 SP - 1951-1963 SN - 1460-2431 KW - amino acid profile KW - carbon partitioning KW - seed nitrogen supply KW - seed protein content KW - soybean ER - TY - CHAP TI - Experimental analysis of the q-matrix method in knowledge discovery AU - Barnes, T. AU - Bitzer, D. AU - Vouk, M. T2 - Foundations of intelligent systems: 15th international symposium, ISMIS 2005, Saratoga Springs, NY, USA, May 25-28, 2005: Proceedings AB - The q-matrix method, a new method for data mining and knowledge discovery, is compared with factor analysis and cluster analysis in analyzing fourteen experimental data sets. This method creates a matrix-based model that extracts latent relationships among observed binary variables. Results show that the q-matrix method offers several advantages over factor analysis and cluster analysis for knowledge discovery. The q-matrix method can perform fully unsupervised clustering, where the number of clusters is not known in advance. It also yields better error rates than factor analysis, and is comparable in error to cluster analysis. The q-matrix method also allows for automatic interpretation of the data sets. These results suggest that the q-matrix method can be an important tool in automated knowledge discovery. CN - [Electronic Resource] PY - 2005/// DO - 10.1007/11425274_62 VL - 3488 SP - 603-611 PB - Berlin; New York: Springer SN - 3540258787 ER - TY - JOUR TI - De novo synthesis of stable tetrahydroporphyrinic macrocycles: Bacteriochlorins and a tetradehydrocorrin AU - Kim, HJ AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Bacteriochlorins (tetrahydroporphyrins) are attractive for diverse photochemical applications owing to their strong absorption in the near-infrared spectral region, as exemplified by the bacterial photosynthetic pigment bacteriochlorophyll a, yet often are labile toward dehydrogenation to give the chlorin. Tetradehydrocorrins (ring-contracted tetrahydroporphyrins) are attractive for studies of catalysis analogous to that of vitamin B12. An eight-step synthesis toward such tetrahydroporphyrinic macrocycles begins with p-tolualdehyde and proceeds to a dihydrodipyrrin-acetal (1) bearing a geminal dimethyl group and a p-tolyl substituent. Self-condensation of 1 in CH3CN containing BF3·OEt2 at room temperature afforded a readily separable mixture of two free base bacteriochlorins and a free base B,D-tetradehydrocorrin. Each bacteriochlorin contains two geminal dimethyl groups to lock-in the bacteriochlorin hydrogenation level, p-tolyl substituents at opposing (2,12) β-positions, and the absence (H−BC) or presence (MeO−BC) of a methoxy group at the 5- (meso) position. The B,D-tetradehydrocorrin (TDC) lies equidistant between the hydrogenation levels of corrin and corrole, is enantiomeric, and contains two geminal dimethyl groups, 2,12-di-p-tolyl substituents, and an acetal group at the pyrroline−pyrrole junction. Examination of the effect of the concentrations of 1 (2.5−50 mM) and BF3·OEt2 (10−500 mM) revealed a different response surface for each of H−BC, MeO−BC, and TDC, enabling relatively selective preparation of a given macrocycle. The highest isolated yield of each was 49, 30, and 66%, respectively. The macrocycles are stable to routine handling in light and air. The bacteriochlorins display characteristic spectral features; for example, H−BC exhibits near-IR absorption (λQy = 737 nm, εQy = 130 000 M-1 cm-1) and emission (λem = 744 nm, Φf = 0.14). In summary, this simple entry to stable bacteriochlorins and tetradehydrocorrins should facilitate a wide variety of applications. DA - 2005/7/8/ PY - 2005/7/8/ DO - 10.1021/jo050467y VL - 70 IS - 14 SP - 5475-5486 SN - 0022-3263 ER - TY - JOUR TI - Virulence genes in Heterodera glycines: Allele frequencies and ror gene groups among field isolates and inbred lines AU - Dong, K AU - Barker, KR AU - Opperman, CH T2 - PHYTOPATHOLOGY AB - ABSTRACT Genetic variation in field populations of Heterodera glycines is a key issue for both resistance gene deployment and basic understanding of virulence-gene flow in populations. In this study, we examined phenotypically defined genes for virulence under selection from host resistance. We separated the most common H. glycines genotypes in the United States into two virulence groups, based on their reproductive abilities on the resistant soybean plant introduction (PI) 88788. These groups correspond to previously identified virulence genes in the nematode, as follows: the dominant gene in H. glycines to PI88788, and the recessive genes to PI90763 and Pickett/Peking. Virulence allele frequencies and virulence genotype frequencies of selected field isolates were investigated by testing the host range of single-female-derived lines, which were developed through single-female inoculation on the standard susceptible soybean 'Lee 68'. By comparing virulence genotype frequencies between the original field isolates and their single-female-derived lines, we were able to determine allele frequencies in the field populations. The results suggest that tremendous variation in H. glycines virulence genes exists among field populations. Potential mechanisms of selection which could cause virulence genotype frequency increases are discussed as related to population genetics equilibrium theory. DA - 2005/2// PY - 2005/2// DO - 10.1094/PHYTO-95-0186 VL - 95 IS - 2 SP - 186-191 SN - 1943-7684 KW - cyst nematode KW - gene frequency ER - TY - JOUR TI - Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana AU - Moore, R. C. AU - Grant, S. R. AU - Purugganan, M. D. T2 - Molecular Biology and Evolution DA - 2005/// PY - 2005/// VL - 22 IS - 1 SP - 91-103 ER - TY - JOUR TI - Accumulation and localization of aluminium in root tips of loblolly pine seedlings and the associated ectomycorrhiza Pisolithus tinctorius AU - Moyer-Henry, K AU - Silva, I AU - Macfall, J AU - Johannes, E AU - Allen, N AU - Goldfarb, B AU - Rufty, T T2 - PLANT CELL AND ENVIRONMENT AB - ABSTRACT Evidence from past studies suggests that loblolly pine may be tolerant of Al. The experiments described in this manuscript were initiated to examine Al tolerance and Al accumulation in the pine root and the degree of Al accumulation in fungal hyphae when pine roots were colonized with the ectomycorrhiza Pisolithus tinctorius . The experiments used lumogallion staining and confocal microscopy to localize Al in root and fungal structures. The results clearly showed that loblolly pine seedlings were highly resistant to Al. A decrease in primary root extension could not be detected until Al +3 activities approached 40 µ mol L −1 , and extension was suppressed only 30% at an Al +3 activity of 580 µ mol L −1 . This contrasted with the response of the Al‐sensitive ‘check’ species soybean, where primary root extension was severely restricted at Al +3 activities lower than 5 µ mol L −1 . Tissue Al measurements and lumogallion fluorescence of longitudinal sections of the pine root tip indicated that tolerance was associated with both Al exclusion from the tip region and compartmentalization of absorbed Al in peripheral cell areas outside of the meristem. In lateral roots colonized with ectomycorrhizae, lumogallion fluorescence showed that large amounts of Al accumulated at the fungal mantle and in areas with the Hartig net. At higher magnification, lumogallion indicated substantial Al accumulation inside hyphae. Little Al could be detected in lateral root cells. The results show that pine possesses multiple mechanisms that can contribute to Al tolerance in acid field soils. DA - 2005/2// PY - 2005/2// DO - 10.1111/j.1365-3040.2004.01240.x VL - 28 IS - 2 SP - 111-120 SN - 1365-3040 KW - Pisolithus tinctorius KW - confocal scanning microscopy KW - lumogallion ER - TY - JOUR TI - On the complexity of computing determinants AU - Kaltofen, E AU - Villard, G T2 - COMPUTATIONAL COMPLEXITY AB - We present new baby steps/giant steps algorithms of asymptotically fast running time for dense matrix problems. Our algorithms compute the determinant, characteristic polynomial, Frobenius normal form and Smith normal form of a dense n × n matrix A with integer entries in $$\left( {n^{3.2} \log \left\| A \right\|} \right)^{1 + o(1)} $$ and $$\left( {n^{2.697263} \log \left\| A \right\|} \right)^{1 + o(1)} $$ bit operations; here $$\left\| A \right\|$$ denotes the largest entry in absolute value and the exponent adjustment by “+o(1)” captures additional factors $$C_1 (\log n)^{C_2 } \left( {\log \log \left\| A \right\|} \right)^{C_3 } $$ for positive real constants C1, C2, C3. The bit complexity $$\left( {n^{3.2} \log \left\| A \right\|} \right)^{1 + o(1)} $$ results from using the classical cubic matrix multiplication algorithm. Our algorithms are randomized, and we can certify that the output is the determinant of A in a Las Vegas fashion. The second category of problems deals with the setting where the matrix A has elements from an abstract commutative ring, that is, when no divisions in the domain of entries are possible. We present algorithms that deterministically compute the determinant, characteristic polynomial and adjoint of A with n3.2+o(1) and O(n2.697263) ring additions, subtractions and multiplications. DA - 2005/2// PY - 2005/2// DO - 10.1007/s00037-004-0185-3 VL - 13 IS - 3-4 SP - 91-130 SN - 1420-8954 KW - integer matrix KW - matrix determinant KW - characteristic polynomial KW - Smith normal form KW - bit complexity KW - division-free complexity KW - randomized algorithm KW - multivariable control theory KW - realization KW - matrix sequence KW - block Wiedemann algorithm KW - block Lanczos algorithm ER - TY - JOUR TI - HyPhy: hypothesis testing using phylogenies AU - Pond, SLK AU - Frost, SDW AU - Muse, SV T2 - BIOINFORMATICS AB - The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution.http://www.hyphy.orgmuse@stat.ncsu.eduHyPhydocumentation and tutorials are available at http://www.hyphy.org. DA - 2005/3/1/ PY - 2005/3/1/ DO - 10.1093/bioinformatics/bti079 VL - 21 IS - 5 SP - 676-679 SN - 1460-2059 ER - TY - JOUR TI - Root-knot nematodes and bacterial Nod factors elicit common signal transduction events in Lotus japonicus AU - Weerasinghe, RR AU - Bird, DM AU - Allen, NS T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - The symbiosis responsible for nitrogen fixation in legume root nodules is initiated by rhizobial signaling molecules [Nod factors (NF)]. Using transgenically tagged microtubules and actin, we dynamically profiled the spatiotemporal changes in the cytoskeleton of living Lotus japonicus root hairs, which precede root-hair deformation and reflect one of the earliest host responses to NF. Remarkably, plant-parasitic root-knot nematodes (RKN) invoke a cytoskeletal response identical to that seen in response to NF and induce root-hair waviness and branching in legume root hairs via a signal able to function at a distance. Azide-killed nematodes do not produce this signal. A similar response to RKN was seen in tomato. Aspects of the host responses to RKN were altered or abolished by mutations in the NF receptor genes nfr1 , nfr5 , and symRK , suggesting that RKN produce a molecule with functional equivalence to NF, which we name NemF. Because the ability of RKN to establish feeding sites and reproduce was markedly reduced in the mutant lines, we propose that RKN have adapted at least part of the symbiont-response pathway to enhance their parasitic ability. DA - 2005/2/22/ PY - 2005/2/22/ DO - 10.1073/pnas.0407926102 VL - 102 IS - 8 SP - 3147-3152 SN - 0027-8424 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-14544295731&partnerID=MN8TOARS KW - cytoskeleton KW - NemF KW - rhizobia KW - actin KW - microtubule ER - TY - JOUR TI - QTL mapping and the genetic basis of adaptation: recent developments AU - Zeng, ZB T2 - GENETICA DA - 2005/2// PY - 2005/2// DO - 10.1007/s10709-004-2705-0 VL - 123 IS - 1-2 SP - 25-37 SN - 1573-6857 KW - genetic architecture KW - genetic basis of adaptation KW - genetic correlation KW - genotype by environment interaction KW - microarrays KW - QTL mapping KW - quantitative trait loci ER - TY - JOUR TI - Potential limitations of the 16S-23S rRNA intergenic region for molecular detection of Bartonella species AU - Maggi, RG AU - Breitschwerdt, EB T2 - JOURNAL OF CLINICAL MICROBIOLOGY AB - PCR targeting the 16S-23S rRNA gene intergenic transcribed spacer (ITS) region has been proposed as a rapid and reliable method for the detection of Bartonella species DNA in clinical samples. Because of variation in ITS sequences among Bartonella species, a single PCR amplification can be used to detect different species within this genus. Therefore, by targeting the ITS region, multiple PCRs or additional sample-processing steps beyond the primary amplification can be avoided when attempting to achieve molecular diagnostic detection of Bartonella species. Although PCR amplification targeting this region is considered highly sensitive, amplification specificity obviously depends on primer design. We report evidence of nonspecific PCR amplification of Mesorhizobium species with previously published primers that were designed to amplify the Bartonella consensus ITS region. Use of these or other, less species-specific, primers could lead to a false-positive diagnostic test result when evaluating clinical samples. We also report the presence of Mesorhizobium species DNA as a contaminant in molecular-grade water, a series of homologous sequences in the ITS region that are common to Bartonella and Mesorhizobium species, the amplification of Mesorhizobium DNA with unpublished primers designed in our laboratory targeting the ITS region, and the subsequent design of unambiguous ITS primers that avoid nonspecific amplification of Mesorhizobium species. Our results define some potential limitations associated with the molecular detection of Bartonella species in patient samples and indicate that primer specificity is of critical importance if the ITS region is used as a diagnostic target for detection of Bartonella species. DA - 2005/3// PY - 2005/3// DO - 10.1128/JCM.43.3.1171-1176.2005 VL - 43 IS - 3 SP - 1171-1176 SN - 1098-660X ER - TY - JOUR TI - Overexpression of the Ca2+-binding protein calreticulin in the endoplasmic reticulum improves growth of tobacco cell suspensions (Nicotiana tabacum) in high-Ca2+ medium AU - Akesson, A AU - Persson, S AU - Love, J AU - Boss, WF AU - Widell, S AU - Sommarin, M T2 - PHYSIOLOGIA PLANTARUM AB - Calreticulin (CRT) is a eukaryotic, highly conserved, Ca 2+ ‐binding protein predominantly located in the endoplasmic reticulum (ER) lumen. In addition to being involved in the regulation of cellular Ca 2+ , calreticulin is a key quality control element during protein folding in the ER lumen. Tobacco ( Nicotiana tabacum L.) suspension cells overexpressing a maize CRT (CRT1a) were used here to examine the properties of CRT in growing plant cells with respect to stress exposure. The endogenous CRT gene was induced rapidly after subculturing of the cells to new medium. In accordance, the CRT protein levels increased, peaking at days 3–4. At day 5, when the CRT transcript levels had levelled off, a further increase in endogenous CRT expression was obtained when the cells were treated with excess Ca 2+ or the N ‐linked glycosylation inhibitor tunicamycin. Whereas the response to Ca 2+ occurred within 30 min, the induction by tunicamycin took several hours to be established. Transforming tobacco cells with maize CRT1a, under a constitutive mannopine synthase promoter, resulted in a stable level of expressed CRT1a during the growth cycle compared with endogenous CRT. The CRTs showed differences in attached glycans, but both contained the high mannose‐rich‐type glycans characteristic of ER proteins. In agreement with an ER location, both tobacco CRT and the transgene product CRT1a codistributed with the ER marker NADH cytochrome c reductase after density gradient centrifugation of microsomal fractions from tobacco cells. Increased production of CRT, as was obtained in the transgenic tobacco cell lines, made cells more tolerant than wild‐type cells to high Ca 2+ during growth. These data suggest that overexpression of CRT1a in plant cells results in a more efficient calcium buffering capacity in the ER. DA - 2005/1// PY - 2005/1// DO - 10.1111/j.1399-3054.2004.00434.x VL - 123 IS - 1 SP - 92-99 SN - 1399-3054 ER - TY - PAT TI - Methods of making porphyrins and related compounds with Lewis acids C2 - 2005/// DA - 2005/// PY - 2005/// ER - TY - JOUR TI - Introduction of a third meso substituent into 5,10-diaryl chlorins and oxochlorins AU - Taniguchi, M AU - Kim, MN AU - Ra, D AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Chlorins/oxochlorins bearing distinct patterns of substituents are valuable compounds in bioorganic and materials chemistry. Treatment of a 5,10-diaryl-substituted chlorin or oxochlorin with TFA-d1 resulted in selective deuteriation of the remaining meso positions (15, 20) rather than any of the β-pyrrolic positions. Electrophilic iodination or bromination of a 5,10-diaryl-substituted chlorin proceeded with high regioselectivity, affording the 5,10-diaryl-15-halo-substituted chlorin. Iodination or bromination of a free base 5,10-diaryloxochlorin gave a mixture of products arising through halogenation at the 15-, 20-, and β-pyrrolic positions, while bromination of a zinc 5,10-diaryloxochlorin selectively gave the 5,10-diaryl-20-bromo-substituted oxochlorin. The Suzuki coupling reaction of a phenyl boronic acid derivative and a 5,10-diaryl-15-iodooxochlorin or 5,10-diaryl-20-bromooxochlorin gave the corresponding 5,10,15- or 5,10,20-triaryloxochlorin. The introduction of a third aryl substituent into the chlorin or oxochlorin causes an ∼5-nm red shift of the long wavelength Qy absorption band. Two phenylethyne-linked oxochlorin−oxochlorin dyads in distinct metalation states (zinc/free base, free base/zinc) were prepared by Sonogashira coupling reactions of a 5,10-diaryl-20-bromooxochlorin and a 10-substituted ethynylphenyl oxochlorin. This study provides access to new chlorins/oxochlorins that can be utilized in diverse applications. DA - 2005/1/7/ PY - 2005/1/7/ DO - 10.1021/jo048440m VL - 70 IS - 1 SP - 275-285 SN - 1520-6904 ER - TY - JOUR TI - Vegetative propagation of mature eastern and Carolina hemlocks by rooted softwood cuttings AU - Jetton, R. M. AU - Frampton, J. AU - Hain, F. P. T2 - HortScience DA - 2005/// PY - 2005/// VL - 40 IS - 5 SP - 1469-1473 ER - TY - JOUR TI - Phylogenetic analysis of Pasteuria penetrans by use of multiple genetic loci AU - Charles, L AU - Carbone, I AU - Davies, KG AU - Bird, D AU - Burke, M AU - Kerry, BR AU - Opperman, CH T2 - JOURNAL OF BACTERIOLOGY AB - ABSTRACT Pasteuria penetrans is a gram-positive, endospore-forming eubacterium that apparently is a member of the Bacillus-Clostridium clade. It is an obligate parasite of root knot nematodes ( Meloidogyne spp.) and preferentially grows on the developing ovaries, inhibiting reproduction. Root knot nematodes are devastating root pests of economically important crop plants and are difficult to control. Consequently, P. penetrans has long been recognized as a potential biocontrol agent for root knot nematodes, but the fastidious life cycle and the obligate nature of parasitism have inhibited progress on mass culture and deployment. We are currently sequencing the genome of the Pasteuria bacterium and have performed amino acid level analyses of 33 bacterial species (including P. penetrans ) using concatenation of 40 housekeeping genes, with and without insertions/deletions (indels) removed, and using each gene individually. By application of maximum-likelihood, maximum-parsimony, and Bayesian methods to the resulting data sets, P. penetrans was found to cluster tightly, with a high level of confidence, in the Bacillus class of the gram-positive, low-G+C-content eubacteria. Strikingly, our analyses identified P. penetrans as ancestral to Bacillus spp. Additionally, all analyses revealed that P. penetrans is surprisingly more closely related to the saprophytic extremophile Bacillus haladurans and Bacillus subtilis than to the pathogenic species Bacillus anthracis and Bacillus cereus . Collectively, these findings strongly imply that P. penetrans is an ancient member of the Bacillus group. We suggest that P. penetrans may have evolved from an ancient symbiotic bacterial associate of nematodes, possibly as the root knot nematode evolved to be a highly specialized parasite of plants. DA - 2005/8// PY - 2005/8// DO - 10.1128/JB.187.16.5700-5708.2005 VL - 187 IS - 16 SP - 5700-5708 SN - 1098-5530 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-23644445501&partnerID=MN8TOARS ER - TY - JOUR TI - In vitro selection of phage RB69 RegA RNA binding sites yields UAA repeats AU - Dean, TR AU - Allen, SV AU - Miller, ES T2 - VIROLOGY AB - The SELEX method of in vitro selection was used to isolate RNAs that bind the RB69 RegA translational repressor protein immobilized on Ni-NTA agarose. After five rounds of SELEX, the pool of selected RNA displayed striking sequence uniformity: UAAUAAUAAUAAUA was clearly enriched in the 14 nucleotides that underwent selection. Individual, cloned molecules displayed a repeating (UAA) sequence, with only two RNAs having a 3' AUG. Removing the 3' AUG slightly reduced binding in gel shift assays, moving the AUG 5' proximal of the (UAA) slightly improved binding, but (UAA)4 alone still bound the purified protein. Dissociation constants showed that RNA shortened to (UAA)3 and (UAA)2 also retained binding, whereas cytosine clearly prevented binding by RB69 RegA. Scanning of RB69 gene starts and ends with an RB69 RegA SELEX information weight matrix yielded 21 sequences as potential RegA sites. One site, on the mRNA for the pentameric (4:1) phage gp44/62 DNA polymerase clamp loader complex, has the RB69 gene 44 stop codon and 3'-adjacent gene 62 initiation codon in a sequence (GAAAUAAUAUG) that is similar to in vitro selected RNA and was shown to bind RB69 RegA. Sequences between the Shine-Dalgarno and initiation codon, which frequently contain a UAA stop codon of a 5'-adjacent gene, appear to be preferred RB69 RegA binding sites. DA - 2005/5/25/ PY - 2005/5/25/ DO - 10.1016/j.virol.2005.03.002 VL - 336 IS - 1 SP - 26-36 SN - 0042-6822 KW - RNA SELEX KW - translation repressor KW - T4-type phage ER - TY - JOUR TI - Comparative genomics of nematodes AU - Mitreva, M AU - Blaxter, ML AU - Bird, DM AU - McCarter, JP T2 - TRENDS IN GENETICS AB - Recent transcriptome and genome projects have dramatically expanded the biological data available across the phylum Nematoda. Here we summarize analyses of these sequences, which have revealed multiple unexpected results. Despite a uniform body plan, nematodes are more diverse at the molecular level than was previously recognized, with many species- and group-specific novel genes. In the genus Caenorhabditis, changes in chromosome arrangement, particularly local inversions, are also rapid, with breakpoints occurring at 50-fold the rate in vertebrates. Tylenchid plant parasitic nematode genomes contain several genes closely related to genes in bacteria, implicating horizontal gene transfer events in the origins of plant parasitism. Functional genomics techniques are also moving from Caenorhabditis elegans to application throughout the phylum. Soon, eight more draft nematode genome sequences will be available. This unique resource will underpin both molecular understanding of these most abundant metazoan organisms and aid in the examination of the dynamics of genome evolution in animals. DA - 2005/10// PY - 2005/10// DO - 10.1016/j.tig.2005.08.003 VL - 21 IS - 10 SP - 573-581 SN - 1362-4555 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-24644458584&partnerID=MN8TOARS ER - TY - JOUR TI - Clinicopathologic findings in dogs seroreactive toBartonella henselaeantigens AU - Goodman, Robert A. AU - Breitschwerdt, Edward B. T2 - American Journal of Veterinary Research AB - To assess the potential clinical relevance of seroreactivity to Bartonella henselae antigens in dogs.40 dogs seroreactive to B henselae and 45 dogs that did not seroreact to B henselae.A case-control study was conducted. Clinical and clinicopathologic findings were extracted from medical records of each dog.Statistical differences were not detected between dogs seroreactive or nonseroreactive to B henselae when analyzed on the basis of disease category or results of hematologic, biochemical, urine, or cytologic analysis. However, seroreactivity to B henselae antigens was detected in 2 of 4 dogs with a clinical diagnosis of granulomatous meningoencephalitis, 3 of 4 dogs with immune-mediated hemolytic anemia, 3 of 4 dogs with infective endocarditis, 2 of 3 dogs with lymphoid neoplasia, and 5 of 10 dogs with polyarthritis. Additionally, seroreactivity to B henselae antigens was detected in 18 of 34 thrombocytopenic dogs and 14 of 27 dogs with neutrophilia.Significant associations were not detected between seroreactivity to B henselae and various diseases. Prospective epidemiologic studies investigating specific diseases, such as meningoencephalitis or polyarthritis, and specific hematologic abnormalities, such as immunemediated hemolytic anemia or thrombocytopenia, should be conducted to further define the potential clinical relevance of antibodies against B henselae in dogs.Bartonella organisms are increasingly reported as pathogens that induce are increasingly reported as pathogens that induce chronic infections in humans and dogs. Dogs may serve as natural candidates for future study of the disease in humans. DA - 2005/12// PY - 2005/12// DO - 10.2460/ajvr.2005.66.2060 VL - 66 IS - 12 SP - 2060-2064 J2 - American Journal of Veterinary Research LA - en OP - SN - 0002-9645 UR - http://dx.doi.org/10.2460/ajvr.2005.66.2060 DB - Crossref ER - TY - JOUR TI - pH effects on the stability and dimerization of procaspase-3 AU - Bose, K. AU - Clark, A. C. T2 - Protein Science DA - 2005/// PY - 2005/// VL - 14 IS - 1 SP - 24-36 ER - TY - JOUR TI - Site-to-site variation of synonymous substitution rates AU - Pond, SK AU - Muse, SV T2 - MOLECULAR BIOLOGY AND EVOLUTION AB - We develop a new model for studying the molecular evolution of protein-coding DNA sequences. In contrast to existing models, we incorporate the potential for site-to-site heterogeneity of both synonymous and nonsynonymous substitution rates. We demonstrate that within-gene heterogeneity of synonymous substitution rates appears to be common. Using the new family of models, we investigate the utility of a variety of new statistical inference procedures, and we pay particular attention to issues surrounding the detection of sites undergoing positive selection. We discuss how failure to model synonymous rate variation in the model can lead to misidentification of sites as positively selected. DA - 2005/12// PY - 2005/12// DO - 10.1093/molbev/msi232 VL - 22 IS - 12 SP - 2375-2385 SN - 1537-1719 KW - synonymous substitution rate KW - positive selection KW - molecular evolution KW - codon model KW - model selection ER - TY - JOUR TI - Refined synthesis of 2,3,4,5-tetrahydro-1,3,3-trimethyidipyrrin, a deceptively simple precursor to hydroporphyrins AU - Ptaszek, M AU - Bhaumik, J AU - Kim, HJ AU - Taniguchi, M AU - Lindsey, JS T2 - ORGANIC PROCESS RESEARCH & DEVELOPMENT AB - 2,3,4,5-Tetrahydro-1,3,3-trimethyldipyrrin (1) is a crucial building block in the rational synthesis of chlorins and oxochlorins. The prior five-step synthesis of 1 from pyrrole-2-carboxaldehyde (2) employed relatively simple and well-known reactions yet suffered from several drawbacks, including limited scale (≤0.5 g of 1 per run). A streamlined preparation of 1 has been developed that entails four steps: (i) nitro-aldol condensation of 2 and nitromethane under neat conditions to give 2-(2-nitrovinyl)pyrrole (3), (ii) reduction of 3 with NaBH4 to give 2-(2-nitroethyl)pyrrole (4), (iii) Michael addition of 4 with mesityl oxide under neat conditions or at high concentration to give γ-nitrohexanone-pyrrole 5, and (iv) reductive cyclization of 5 with zinc/ammonium formate to give 1. Several multistep transformations have been established, including the direct conversion of 2 → 1. The advantages of the new procedures include (1) fewer steps, (2) avoidance of several problematic reagents, (3) diminished consumption of solvents and reagents, (4) lessened reliance on chromatography, and (5) scalability. The new procedures facilitate the preparation of 1 at the multigram scale. DA - 2005/// PY - 2005/// DO - 10.1021/op050087e VL - 9 IS - 5 SP - 651-659 SN - 1520-586X ER - TY - JOUR TI - Reassembly of active caspase-3 is facilitated by the propeptide AU - Feeney, B AU - Clark, AC T2 - JOURNAL OF BIOLOGICAL CHEMISTRY AB - Changes in ionic homeostasis are early events leading up to the commitment to apoptosis. Although the direct effects of cations on caspase-3 activity have been examined, comparable studies on procaspase-3 are lacking. In addition, the effects of salts on caspase structure have not been examined. We have studied the effects of cations on the activities and conformations of caspase-3 and an uncleavable mutant of procaspase-3 that is enzymatically active. The results show that caspase-3 is more sensitive to changes in pH and ion concentrations than is the zymogen. This is due to the loss of both an intact intersubunit linker and the prodomain. The results show that, although the caspase-3 subunits reassemble to the heterotetramer, the activity return is low after the protein is incubated at or below pH 4.5 and then returned to pH 7.5. The data further show that the irreversible step in assembly results from heterotetramer rather than heterodimer dissociation and demonstrate that the active site does not form properly following reassembly. However, active-site formation is fully reversible when reassembly occurs in the presence of the prodomain, and this effect is specific for the propeptide of caspase-3. The data show that the prodomain facilitates both dimerization and active-site formation in addition to stabilizing the native structure. Overall, the results show that the prodomain acts as an intramolecular chaperone during assembly of the (pro)caspase subunits and increases the efficiency of formation of the native conformation. Changes in ionic homeostasis are early events leading up to the commitment to apoptosis. Although the direct effects of cations on caspase-3 activity have been examined, comparable studies on procaspase-3 are lacking. In addition, the effects of salts on caspase structure have not been examined. We have studied the effects of cations on the activities and conformations of caspase-3 and an uncleavable mutant of procaspase-3 that is enzymatically active. The results show that caspase-3 is more sensitive to changes in pH and ion concentrations than is the zymogen. This is due to the loss of both an intact intersubunit linker and the prodomain. The results show that, although the caspase-3 subunits reassemble to the heterotetramer, the activity return is low after the protein is incubated at or below pH 4.5 and then returned to pH 7.5. The data further show that the irreversible step in assembly results from heterotetramer rather than heterodimer dissociation and demonstrate that the active site does not form properly following reassembly. However, active-site formation is fully reversible when reassembly occurs in the presence of the prodomain, and this effect is specific for the propeptide of caspase-3. The data show that the prodomain facilitates both dimerization and active-site formation in addition to stabilizing the native structure. Overall, the results show that the prodomain acts as an intramolecular chaperone during assembly of the (pro)caspase subunits and increases the efficiency of formation of the native conformation. Apoptosis is a type of cell death that occurs in eumetazoans, is responsible for maintaining the balance between cell growth and death, and can occur via two major pathways (1Earnshaw W.C. Martins L.M. Kaufmann S.H. Annu. Rev. Biochem. 1999; 68: 383-424Crossref PubMed Scopus (2458) Google Scholar). The extrinsic pathway occurs in response to death receptor ligation (2Tewari M. Quan L.T. O'Rouke K. Desnoyers S. Zeng Z. Beidler D.R. Poirier G.G. Salvesen G.S. Dixit V.M. Cell. 1995; 81: 801-809Abstract Full Text PDF PubMed Scopus (2285) Google Scholar) and results in a cascade of limited proteolytic cleavages by upstream activator caspases that ultimately lead to the activation of the executioner caspase-3. The intrinsic pathway triggers the release of ATP and cytochrome c from the mitochondria in response to antineoplastic drugs (3Fearnhead H.O. McCurrach M.E. O'Neill J. Zhang K. Lowe S.W. Lazebnik Y.A. Genes Dev. 1997; 11: 1266-1276Crossref PubMed Scopus (61) Google Scholar), growth factor withdrawal (4Deckwerth T.L. Johnson Jr., E.M. Ann. N. Y. Acad. Sci. 1993; 679: 121-131Crossref PubMed Scopus (47) Google Scholar), or ionizing radiation (5Datta R. Banach D. Kojima H. Talanian R.V. Alnemri E.S. Wong W.W. Kufe D.W. Blood. 1996; 88: 1936-1943Crossref PubMed Google Scholar). The intrinsic pathway results in a proteolytic cascade that activates caspase-9 and, subsequently, caspase-3 (6Segal M.S. Beem E. Am. J. Physiol. 2001; 281: C1196-C1204Crossref PubMed Google Scholar). Both pathways give rise to the proteolysis of structural and protective components of the cell, which in turn leads to the coordinated disassembly of the cell (7Salvesen G.S. Dixit V.M. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 10964-10967Crossref PubMed Scopus (776) Google Scholar). A relatively well characterized event leading up to the commitment to apoptosis is the change in the ionic homeostasis of the cell. Apoptotic cells are generally characterized as having low [K+]i, normal to slightly increased [Na+]i, high [H+]i, and normal to moderately increased [Ca2+]i. The efflux of potassium (leading to the depletion of intracellular potassium) is a key early step in apoptosis (8Yu S.P. Prog. Neurobiol. (N. Y.). 2003; 70: 363-386Crossref PubMed Scopus (301) Google Scholar). Under normal conditions, [K+]i is ∼140 mm, and levels decrease to <50 mm in apoptotic cells (9Yu S.P. Canzoniero L.M.T. Choi D.W. Curr. Opin. Cell Biol. 2001; 13: 405-411Crossref PubMed Scopus (341) Google Scholar, 10Hughes Jr., F.M. Cidlowski J.A. Adv. Enzyme Regul. 1999; 39: 157-171Crossref PubMed Scopus (205) Google Scholar). The decrease in [K+]i and associated water movement are contributing factors to the change in cell volume observed during apoptosis. Normal potassium concentrations are inhibitory to apoptosis and may act by inhibiting an apoptotic nuclease, NUC18 (10Hughes Jr., F.M. Cidlowski J.A. Adv. Enzyme Regul. 1999; 39: 157-171Crossref PubMed Scopus (205) Google Scholar). In addition, normal potassium levels inhibit the cytochrome c-dependent activation of procaspase-3, but do not inhibit the activity of caspase-3 (6Segal M.S. Beem E. Am. J. Physiol. 2001; 281: C1196-C1204Crossref PubMed Google Scholar, 11Bilney A.J. Murray A.W. FEBS Lett. 1998; 424: 221-224Crossref PubMed Scopus (29) Google Scholar). Although free potassium is a major contributor to intracellular ionic strength, Hughes and Cidlowski (10Hughes Jr., F.M. Cidlowski J.A. Adv. Enzyme Regul. 1999; 39: 157-171Crossref PubMed Scopus (205) Google Scholar) showed that substitution of potassium with other monovalent ions results in similar effects. This indicates that the response is not specific to potassium cations, but is instead controlled by the ionic strength. Thus far, potassium is the only cation that has been described as having a role in the inhibition of apoptosis, although studies of the direct effects of cations on caspase-3 activation and apoptotic commitment are incomplete at best. Although the results are less clear, studies with other ions, such as magnesium, zinc, copper, and iron, show that these ions also may have a role in apoptosis in certain tissues (reviewed in Ref. 9Yu S.P. Canzoniero L.M.T. Choi D.W. Curr. Opin. Cell Biol. 2001; 13: 405-411Crossref PubMed Scopus (341) Google Scholar). In most cases, the effects of changes in ionic homeostasis occur at a stage prior to the maturation of caspase-3 and, in some cases, may result from the prevention of the formation of the apoptosome. For example, fluctuations in ion levels may inhibit the expression of caspase-9 as well as prevent the recruitment of caspase-9 to the apoptosome (6Segal M.S. Beem E. Am. J. Physiol. 2001; 281: C1196-C1204Crossref PubMed Google Scholar). Putney and co-workers (12Bian X. Hughes Jr., F.M. Huang Y. Cidlowski J.A. Putney Jr., J.W. Am. J. Physiol. 1997; 272: C1241-C1249Crossref PubMed Google Scholar) showed that Ca2+-ATPase inhibitors initiate apoptosis by decreasing [Ca2+]i, and Segal and Beem (6Segal M.S. Beem E. Am. J. Physiol. 2001; 281: C1196-C1204Crossref PubMed Google Scholar) demonstrated a 50% inhibition of caspase activity in cytosolic extracts with ∼60 mm CaCl2. However, Stennicke and Salvesen (13Stennicke H.R. Salvesen G.S. J. Biol. Chem. 1997; 272: 25719-25723Abstract Full Text Full Text PDF PubMed Scopus (481) Google Scholar) found that calcium has no effect on caspase-3 activity at 100 mm and suggested that the effects of calcium on apoptosis are unlikely to be due to an effect on caspases. In contrast, the cleavage of poly(ADP-ribose) polymerase by caspase-3 has been shown to be inhibited by zinc at concentrations as low as 0.1 mm (14Perry D.K. Smyth M.J. Stennicke H.R. Salvesen G.S. Duriez P. Poirier G.G. Hannun Y.A. J. Biol. Chem. 1997; 272: 18530-18533Abstract Full Text Full Text PDF PubMed Scopus (422) Google Scholar). This is due to a direct inactivation of caspase-3 by zinc (14Perry D.K. Smyth M.J. Stennicke H.R. Salvesen G.S. Duriez P. Poirier G.G. Hannun Y.A. J. Biol. Chem. 1997; 272: 18530-18533Abstract Full Text Full Text PDF PubMed Scopus (422) Google Scholar). Although studies of the direct effects of cations on caspase-3 activity remain incomplete, comparable studies on the activity of procaspase-3 are lacking. Until recently, procaspase-3 was thought to be enzymatically inactive; thus, studies of the effects of ions on procaspase activity were not warranted. Recently, however, it was shown by Nicholson and co-workers (15Roy S. Bayly C.I. Gareau Y. Houtzager V.M. Kargman S. Keen S.L.C. Rowland K. Seiden I.M. Thornberry N.A. Nicholson D.W. Proc. Natl. Acad. Sci. U. S. A. 2001; 98 (S. L. C.): 6132-6137Crossref PubMed Scopus (167) Google Scholar) that an uncleavable procaspase-3 mutant contains catalytic activity. In this mutant, the three processing sites (Asp9, Asp28, and Asp175) have been replaced with glutamate. Likewise, we showed previously that a procaspase-3 mutant with the processing sites replaced with alanine is active (see Fig. 1) (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar). In the maturation of procaspase-3, the cleavage at Asp175 separates the large and small subunits and results in a large increase in activity, whereas the cleavages at Asp9 and Asp28 remove the prodomain (17Denault J.-B. Salvesen G.S. Chem. Rev. 2002; 102: 4489-4499Crossref PubMed Scopus (275) Google Scholar). We further showed that the uncleavable procaspase is ∼200-fold less active than mature caspase-3 and that the lower activity is a result of a low catalytic efficiency rather than a difference in substrate binding (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar). Here, we describe the effects of physiologically relevant salts on the activity of procaspase-3 and the accompanying changes in the active-site environment. In addition, it has been noted that the procaspase-3 homodimer is more stable than the caspase-3 heterotetramer between pH 4 and 7 (18Feeney B. Pop C. Tripathy A. Clark A.C. Biochem. J. 2004; 384: 515-525Crossref PubMed Scopus (16) Google Scholar, 19Bose K. Clark A.C. Protein Sci. 2005; 14: 24-36Crossref PubMed Scopus (24) Google Scholar), although it is not clear whether this is due to the presence of the propeptide or to an intact intersubunit linker in the procaspase. Indeed, Denault and Salvesen (20Denault J.-B. Salvesen G.S. J. Biol. Chem. 2003; 278: 34042-34050Abstract Full Text Full Text PDF PubMed Scopus (102) Google Scholar) showed that the propeptide of caspase-7 plays a role in stabilizing the zymogen and alters the properties of procaspase-7 as a substrate for caspase-7. By analogy, the lower stability of caspase-3 may be due to the loss of the propeptide upon maturation. We investigated whether the prodomain or the intact intersubunit linker affects dimer stability, and we further investigated the roles that salts and pH play in the stability of the (pro)caspase-3 dimer. Based on the results, we propose a model for the salt- and propeptide-dependent assembly of the caspase subunits. Materials—Caspase-3, -6, and -7 prodomains were synthesized by the Peptide Facility at the University of North Carolina (Chapel Hill, NC). Sodium chloride, ammonium chloride, Tris base, and β-mercaptoethanol were from Fisher. Zinc chloride, magnesium chloride, dithiothreitol (DTT), 2The abbreviations used are: DTTdithiothreitolCHAPS3-[(3-cholamidopropy-l)dimethylammonio]-1-propanesulfonic acidprocaspase-3(D3A)procaspase-3(D9A,D28A,D175A)PIPES1,4-piperazinediethanesulfonic acidIMCsintramolecular chaperones. sodium citrate, and monobasic and dibasic potassium phosphate were from Sigma. Potassium chloride and sucrose were from Mallinckrodt Chemical Works. Calcium chloride was from Acros Organics. CHAPS and Ac-DEVD-7-amino-4-trifluoromethylcoumarin were from Calbiochem, and EDTA was from EM Science. dithiothreitol 3-[(3-cholamidopropy-l)dimethylammonio]-1-propanesulfonic acid procaspase-3(D9A,D28A,D175A) 1,4-piperazinediethanesulfonic acid intramolecular chaperones. Mutagenesis—A mutation was introduced into the background of pro-less caspase-3 using the template pHC329 (21Pop C. Chen Y.-R. Smith B. Bose K. Bobay B. Tripathy A. Franzen S. Clark A.C. Biochemistry. 2001; 40: 14224-14235Crossref PubMed Scopus (65) Google Scholar) and the D175A forward and reverse primers (referred to as primers 1 and 2) as described previously (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar). This generated plasmid pHC32902 and produces an uncleavable pro-less procaspase-3 with the D175A mutation. In this mutant, the N-terminal 28 amino acids were replaced previously with methionine (21Pop C. Chen Y.-R. Smith B. Bose K. Bobay B. Tripathy A. Franzen S. Clark A.C. Biochemistry. 2001; 40: 14224-14235Crossref PubMed Scopus (65) Google Scholar). Construction of plasmid pHC33209, which produces procaspase-3(D9A,D28A,D175A), was described previously (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar). The D9A,D28A double mutant was produced using the template pHC33209 and primer 1 (5′-GTGGCATTGAGACAGACAGTGGTGTTGATGATG-3′) and primer 2 (5′-CATCATCAACACCACTGTCTGTCTCAATGCCAC-3′). The resulting plasmid is called pHC33260. In this plasmid, the NheI site that was incorporated previously for screening plasmid pHC33209 was removed, and its absence was used for screening. All plasmids were sequenced (both DNA strands) to confirm the mutations. A schematic diagram of the proteins produced from these plasmids and used in the studies presented here is shown in Fig. 1. Protein Purification—Caspase-3, uncleavable procaspase-3(D9A,D28A,D175A) (called procaspase-3(D3A)) (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar), pro-less procaspase-3(D175A), and procaspase-3(D9A,D28A) were purified following overexpression in Escherichia coli as described previously (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar). Protein concentrations were determined using ϵ280 = 26,500 m–1 cm–1 (21Pop C. Chen Y.-R. Smith B. Bose K. Bobay B. Tripathy A. Franzen S. Clark A.C. Biochemistry. 2001; 40: 14224-14235Crossref PubMed Scopus (65) Google Scholar). Enzymatic Activity Versus Salt Concentration—Protein was incubated at 25 °C in buffer containing 50 mm Tris-HCl (pH 7.5) and 10 mm DTT for >1 h, and substrate (Ac-DEVD-7-amino-4-trifluoromethylcoumarin) was then added. Hydrolysis of the substrate was monitored as described previously (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar, 21Pop C. Chen Y.-R. Smith B. Bose K. Bobay B. Tripathy A. Franzen S. Clark A.C. Biochemistry. 2001; 40: 14224-14235Crossref PubMed Scopus (65) Google Scholar). Salts were added to the buffer such that the final concentrations are those shown in the figures. Assays were performed in duplicate in the same buffer, and relative activity was determined versus salt concentration by comparing the initial velocity in the absence or presence of the salt. The concentration of substrate was 50 μm, and 10 nm caspase-3 or 50 nm procaspase-3 was used for each assay. Because DTT chelates Zn2+, the DTT was replaced with 20 mm β-mercaptoethanol in the assay buffer as described previously (13Stennicke H.R. Salvesen G.S. J. Biol. Chem. 1997; 272: 25719-25723Abstract Full Text Full Text PDF PubMed Scopus (481) Google Scholar). We showed previously that one can measure ∼50-fold less enzymatic activity than the maximal activity observed for procaspase-3(D3A) (or 10,000-fold less than that of mature caspase-3), establishing the sensitivity of the assay (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar). Changes in Fluorescence Emission as a Function of pH and Salt—To determine the structural effects of different cations on caspase-3 and procaspase-3, the proteins (2 μm) were incubated in 50 mm citrate (pH 3.0–6.2) or 50 mm phosphate (pH 6.0–9.0) containing NaCl, KCl, NH4Cl, MgCl2, or CaCl2 at 50–1000 mm. Samples were excited at 280 nm, and fluorescence emission was acquired between 305 and 400 nm (PTI C-61 spectrofluorometer, Photon Technology International). The average emission wavelength was then calculated at each pH as described previously (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar, 18Feeney B. Pop C. Tripathy A. Clark A.C. Biochem. J. 2004; 384: 515-525Crossref PubMed Scopus (16) Google Scholar, 22Royer C.A. Mann C.J. Matthews C.R. Protein Sci. 1993; 2: 1844-1852Crossref PubMed Scopus (177) Google Scholar) and compared with the spectra of the wild-type protein. Salt Titrations at Low pH—As described in Fig. 3, salts affected the average emission wavelength for caspase-3 but not for procaspase-3 at low pH. Because of this, we examined whether the effect was cooperative, reversible, or dependent on the protein concentration. To examine cooperativity, caspase-3 was incubated in 20 mm citrate (pH 3.0) and in the absence or presence of 2 m NaCl, KCl, NH4Cl, MgCl2, or CaCl2. Using an Olis titrator coupled to the PTI C-61 spectrofluorometer, a solution of caspase-3 in buffer containing 2 m salt was titrated into a solution of caspase-3 without salts. The solutions were mixed and incubated for 20 min between each measurement to allow equilibration. The salt-dependent conformational changes at pH 3.0 were determined by calculating the change in the fluorescence average emission wavelength (22Royer C.A. Mann C.J. Matthews C.R. Protein Sci. 1993; 2: 1844-1852Crossref PubMed Scopus (177) Google Scholar) at each concentration of salt. Reversibility was examined using 2 μm protein and a two-phase reverse titration. The first phase consisted of salt concentrations between 1000 and 250 mm, and the second phase consisted of salt concentrations between 250 and 50 mm. Two additional points were taken manually to obtain 25 and 12.5 mm salt concentrations. We observed that the data from forward or reverse titrations were superimposable, demonstrating that the transitions are reversible. The protein concentration dependence was examined by performing the titrations at several protein concentrations (2–12 μm). Reversibility of Activity as a Function of Salt and pH—To examine the reversibility of enzymatic activity following incubation at low pH as well as at high salt concentrations, both caspase-3 and procaspase-3(D3A) were dialyzed for 4 h at 25 °C in 50 mm citrate (pH 3.0) plus 1 m salt or in 50 mm Tris-HCl (pH 7.5) plus 1 m salt for monovalent cations or 0.5 m salt for divalent cations. All buffers contained 1 mm DTT. The proteins were then dialyzed for 9 h at 25 °C in 50 mm Tris-HCl (pH 7.5) and 1 mm DTT. In all cases, the volume of the dialysis buffer was >500-fold that of the protein sample. The enzymatic activity was measured in 50 mm Tris-HCl (pH 7.5), 0.1% CHAPS, 1% sucrose, and 10 mm DTT (assay buffer) (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar, 21Pop C. Chen Y.-R. Smith B. Bose K. Bobay B. Tripathy A. Franzen S. Clark A.C. Biochemistry. 2001; 40: 14224-14235Crossref PubMed Scopus (65) Google Scholar) using the substrate and protein concentrations described above. The initial velocity was compared with that of a control protein that had been stored at –20 °C (i.e. not dialyzed for 13 h). Activity as a Function of pH and Protein Concentration—The pH at which caspase-3 loses activity irreversibly was determined by dialyzing the protein (10 μm) for 4 h at 25 °C in 50 mm citrate (pH 3.0–6.0) or in 50 mm Tris-HCl (pH 6.5–7.5) containing 1 mm DTT every 0.5 pH units. Samples were then dialyzed for 9 h at 25 °C in 50 mm Tris-HCl (pH 7.5) and 1 mm DTT. The enzymatic activity was measured in assay buffer and compared with that of a control sample of caspase-3 that had been incubated for 13 h at 25 °C in 50 mm Tris-HCl (pH 7.5) and 1 mm DTT. In all cases, the volume of the dialysis buffer was >500-fold that of the protein sample. To investigate the effect of protein concentration on solubility and return of activity in the pH-dependent folding of caspase-3, protein concentrations ranging from 2 to ∼50 μm were used. Samples of caspase-3 were incubated at 25 °C in 50 mm citrate (pH 4) and 1 mm DTT for 24 h to dissociate the heterotetramer (18Feeney B. Pop C. Tripathy A. Clark A.C. Biochem. J. 2004; 384: 515-525Crossref PubMed Scopus (16) Google Scholar, 19Bose K. Clark A.C. Protein Sci. 2005; 14: 24-36Crossref PubMed Scopus (24) Google Scholar), and the protein was then refolded by dialyzing the samples against 50 mm Tris-HCl (pH 7.5) and 1 mm DTT at 25 °C for 24 h. The samples were centrifuged at 14,000 rpm at 25 °C for 5 min, and the supernatant was transferred to a new tube. The absorbance at 280 nm was compared with that at time 0. The enzymatic activity was measured in assay buffer. The final protein concentrations in the enzymatic assays were as follows: caspase-3, 10 nm; pro-less procaspase-3(D175A), 50 nm; procaspase-3(D9A,D28A), 10 nm; and procaspase-3(D3A), 50 nm. To measure the loss of enzymatic activity over time, protein (1 μm) was incubated in 50 mm Tris-HCl (pH 7.5) at 25 °C for the times indicated in Fig. 7. In separate experiments, DTT (1 or 10 mm), KCl (1 m), MgCl2 (0.5 m), or caspase-3 propeptide (15 μm) was added to the buffer. Aliquots were removed at various times, and the enzymatic activity was measured in assay buffer. The final protein concentrations were 10 nm in the assays. To examine the effect of the prodomain concentration on the return of activity, the caspase-3, -6, or -7 prodomain was added to caspase-3 or pro-less procaspase-3(D175A) at 2–200-fold excess concentrations. The (pro)caspase concentrations were 10 μm. In these experiments, the proteins were dialyzed initially in 50 mm citrate (pH 4.0) for ∼24 h at 25 °C. Following the initial dialysis, the samples were then dialyzed against 50 mm Tris-HCl (pH 7.5) for ∼24 h at 25 °C, and the enzymatic activity was measured as described above. All buffers contained 1 mm DTT. In these experiments, a dialysis membrane with an Mr 1000 cutoff was used. The final protein concentrations in the enzymatic assays were as follows: caspase-3, 10 nm; and pro-less procaspase-3(D175A), 50 nm. Activity Versus Salt Concentration—We examined the activities of caspase-3 and procaspase-3(D3A) in the presence of the monovalent cations Na+, K+, and NH+4 at concentrations up to 500 mm, and the results are shown in Fig. 2. As was observed previously (13Stennicke H.R. Salvesen G.S. J. Biol. Chem. 1997; 272: 25719-25723Abstract Full Text Full Text PDF PubMed Scopus (481) Google Scholar), the activity of caspase-3 increased slightly (∼20%) in the presence of low concentrations of Na+ (∼25 mm) (Fig. 2A). This was true also for NH+4 (∼50 mm). However, K+ had little to no effect on the activity of caspase-3. In contrast, there was no effect of Na+ or NH+4 on the activity of procaspase-3(D3A) (Fig. 2B). Unlike the activity of caspase-3, that of procaspase-3 was sensitive to the presence of K+ and decreased to ∼50% in the presence of >25 mm K+. In the presence of Mg2+, the activities of caspase-3 and procaspase-3 decreased to ∼40%, and the midpoints of the transitions were similar, ∼100 mm (Fig. 2, C and D). In addition, the activities of both proteins decreased in the presence of Ca2+ (Fig. 2, C and D). For caspase-3, the activity decreased to ∼50% between 10 and 100 mm Ca2+ and then decreased further at higher Ca2+ concentrations. For procaspase-3, the activity decreased to ∼25% in an apparent single transition, with a midpoint of ∼10 mm Ca2+. This is in contrast to results reported by Stennicke and Salvesen (13Stennicke H.R. Salvesen G.S. J. Biol. Chem. 1997; 272: 25719-25723Abstract Full Text Full Text PDF PubMed Scopus (481) Google Scholar), who observed no effect on the activity of caspase-3 at concentrations up to 100 mm. It is not clear why there is a discrepancy in the results, although the experimental conditions are similar but not identical. For these studies, our assays were carried out at 25 °C rather than at 37 °C, and our buffer contained 50 mm Tris-HCl (pH 7.5) rather than 20 mm PIPES (pH 7.2) and did not contain sucrose. In addition, the control with which the activities were compared was taken from a fresh stock of protein that had been stored at –20 °C until just prior to use. At present, it is not clear which of these parameters would result in the discrepancy. Regardless, it is interesting to note that [Ca2+]i is ∼100 nm and either increases slightly or does not change significantly, depending on the cell type, during apoptosis (9Yu S.P. Canzoniero L.M.T. Choi D.W. Curr. Opin. Cell Biol. 2001; 13: 405-411Crossref PubMed Scopus (341) Google Scholar). Thus, in the effects described here, the Ca2+ concentrations are at least 4 orders of magnitude higher than those found in apoptotic cells. Our conclusion from these studies is that, although Ca2+ does affect the activities of both caspase-3 and procaspase-3 in vitro and at high concentrations, it is unlikely that Ca2+ fluctuations in apoptotic cells directly affect the activity of either protein. However, this is not true of K+ because the concentrations used in our experiments are comparable with those found in vivo. Therefore, although the activity of caspase-3 is unaffected by changes in the levels of K+, the activity of the procaspase would be expected to increase if the efflux of potassium during apoptosis resulted in concentrations below 25 mm. Caspase-3 is known to be inactivated by micromolar concentrations of Zn2+, and it has been suggested that Zn2+ coordinates one or both catalytic residues His121 and Cys163 (14Perry D.K. Smyth M.J. Stennicke H.R. Salvesen G.S. Duriez P. Poirier G.G. Hannun Y.A. J. Biol. Chem. 1997; 272: 18530-18533Abstract Full Text Full Text PDF PubMed Scopus (422) Google Scholar). As shown in Fig. 2E, caspase-3 was completely inactivated by ∼10 mm Zn2+, in agreement with previous studies (13Stennicke H.R. Salvesen G.S. J. Biol. Chem. 1997; 272: 25719-25723Abstract Full Text Full Text PDF PubMed Scopus (481) Google Scholar, 14Perry D.K. Smyth M.J. Stennicke H.R. Salvesen G.S. Duriez P. Poirier G.G. Hannun Y.A. J. Biol. Chem. 1997; 272: 18530-18533Abstract Full Text Full Text PDF PubMed Scopus (422) Google Scholar). Surprisingly, procaspase-3(D3A) is much less sensitive to Zn2+. We observed that the procaspase was inactivated by Zn2+ concentrations between 300 and 400 μm, >3 orders of magnitude that required to inactivate caspase-3 (compare the midpoints of the curves in Fig. 2E). This is in agreement with our assertion that the catalytic residue Cys163 is less solvent-accessible in the procaspase than in the mature caspase (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar). It has been shown that ionic effects on caspase activity are due to cations rather than anions (6Segal M.S. Beem E. Am. J. Physiol. 2001; 281: C1196-C1204Crossref PubMed Google Scholar). We confirmed this by examining chloride, acetate, sulfate, and phosphate anions using the sodium or magnesium salts of each. We observed no effect on the enzymatic activity of either caspase-3 or procaspase-3(D3A) beyond those described above for the cations (data not shown). Structural Changes as a Function of pH and Salt—The active site of procaspase-3(D3A) was shown to be distinctly different from that of mature caspase-3, as evidenced in part by the differences in pH-dependent activity profiles (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar). Procaspase-3(D3A) exhibits maximal activity between pH 8.0 and 8.5, in contrast to caspase-3, which has a maximal activity between pH 7.2 and 7.8 (13Stennicke H.R. Salvesen G.S. J. Biol. Chem. 1997; 272: 25719-25723Abstract Full Text Full Text PDF PubMed Scopus (481) Google Scholar, 16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar). In addition, we examined changes in the fluorescence average emission wavelength (〈λ 〉) (Fig. 3), which report on conformational changes in the protein that result from changes in pH (16Bose K. Pop C. Feeney B. Clark A.C. Biochemistry. 2003; 42: 12298-12310Crossref PubMed Scopus (56) Google Scholar, 18Feeney B. Pop C. Tripathy A. Clark A.C. Biochem. J. 2004; 384: 515-525Crossref PubMed Scopus (16) Google Scholar). (Pro)caspase DA - 2005/12/2/ PY - 2005/12/2/ DO - 10.1074/jbc.M505834200 VL - 280 IS - 48 SP - 39772-39785 SN - 1083-351X ER - TY - JOUR TI - Positively selected sites in the Arabidopsis receptor-like kinase gene family AU - Strain, E AU - Muse, SV T2 - JOURNAL OF MOLECULAR EVOLUTION DA - 2005/9// PY - 2005/9// DO - 10.1007/s00239-004-0308-0 VL - 61 IS - 3 SP - 325-332 SN - 1432-1432 KW - receptor-like kinase KW - positive selection KW - gene family KW - leucine-rich repeat ER - TY - JOUR TI - Photoactivated perylenequinone toxins in fungal pathogenesis of plants AU - Daub, ME AU - Herrero, S AU - Chung, KR T2 - FEMS MICROBIOLOGY LETTERS AB - Several genera of plant pathogenic fungi produce photoactivated perylenequinone toxins involved in pathogenesis of their hosts. These toxins are photosensitizers, absorbing light energy and generating reactive oxygen species that damage the membranes of the host cells. Studies with toxin-deficient mutants and on the involvement of light in symptom development have documented the importance of these toxins in successful pathogenesis of plants. This review focuses on the well studied perylenequinone toxin, cercosporin, produced by species in the genus Cercospora. Significant progress has been made recently on the biosynthetic pathway of cercosporin, with the characterization of genes encoding a polyketide synthase and a major facilitator superfamily transporter, representing the first and last steps of the biosynthetic pathway, as well as important regulatory genes. In addition, the resistance of Cercospora fungi to cercosporin and to the singlet oxygen that it generates has led to the use of these fungi as models for understanding cellular resistance to photosensitizers and singlet oxygen. These studies have shown that resistance is complex, and have documented a role for transporters, transient reductive detoxification, and quenchers in cercosporin resistance. DA - 2005/11/15/ PY - 2005/11/15/ DO - 10.1016/j.femsle.2005.08.033 VL - 252 IS - 2 SP - 197-206 SN - 0378-1097 KW - plant disease KW - non-specific toxin KW - active oxygen KW - pyridoxine KW - zinc cluster transcription factor ER - TY - JOUR TI - Mixture model equations for marker-assisted genetic evaluation AU - Liu, Y AU - Zeng, ZB T2 - JOURNAL OF ANIMAL BREEDING AND GENETICS AB - Summary Marker‐assisted genetic evaluation needs to infer genotypes at quantitative trait loci (QTL) based on the information of linked markers. As the inference usually provides the probability distribution of QTL genotypes rather than a specific genotype, marker‐assisted genetic evaluation is characterized by the mixture model because of the uncertainty of QTL genotypes. It is, therefore, necessary to develop a statistical procedure useful for mixture model analyses. In this study, a set of mixture model equations was derived based on the normal mixture model and the EM algorithm for evaluating linear models with uncertain independent variables. The derived equations can be seen as an extension of Henderson's mixed model equations to mixture models and provide a general framework to deal with the issues of uncertain incidence matrices in linear models. The mixture model equations were applied to marker‐assisted genetic evaluation with different parameterizations of QTL effects. A sire‐QTL‐effect model and a founder‐QTL‐effect model were used to illustrate the application of the mixture model equations. The potential advantages of the mixture model equations for marker‐assisted genetic evaluation were discussed. The mixed‐effect mixture model equations are flexible in modelling QTL effects and show desirable properties in estimating QTL effects, compared with Henderson's mixed model equations. DA - 2005/8// PY - 2005/8// DO - 10.1111/j.1439-0388.2005.00525.x VL - 122 IS - 4 SP - 229-239 SN - 1439-0388 ER - TY - JOUR TI - Identification of significant association and gene-gene interaction of GABA receptor subunit genes in autism AU - Ma, DQ AU - Whitehead, PL AU - Menold, MM AU - Martin, ER AU - Ashley-Koch, AE AU - Mei, H AU - Ritchie, MD AU - DeLong, GR AU - Abramson, RK AU - Wright, HH AU - Cuccaro, ML AU - Hussman, JP AU - Gilbert, , JR AU - Pericak-Vance, MA T2 - AMERICAN JOURNAL OF HUMAN GENETICS AB - Autism is a common neurodevelopmental disorder with a significant genetic component. Existing research suggests that multiple genes contribute to autism and that epigenetic effects or gene-gene interactions are likely contributors to autism risk. However, these effects have not yet been identified. Gamma-aminobutyric acid (GABA), the primary inhibitory neurotransmitter in the adult brain, has been implicated in autism etiology. Fourteen known autosomal GABA receptor subunit genes were studied to look for the genes associated with autism and their possible interactions. Single-nucleotide polymorphisms (SNPs) were screened in the following genes: GABRG1, GABRA2, GABRA4, and GABRB1 on chromosome 4p12; GABRB2, GABRA6, GABRA1, GABRG2, and GABRP on 5q34-q35.1; GABRR1 and GABRR2 on 6q15; and GABRA5, GABRB3, and GABRG3 on 15q12. Intronic and/or silent mutation SNPs within each gene were analyzed in 470 white families with autism. Initially, SNPs were used in a family-based study for allelic association analysis--with the pedigree disequilibrium test and the family-based association test--and for genotypic and haplotypic association analysis--with the genotype-pedigree disequilibrium test (geno-PDT), the association in the presence of linkage (APL) test, and the haplotype family-based association test. Next, with the use of five refined independent marker sets, extended multifactor-dimensionality reduction (EMDR) analysis was employed to identify the models with locus joint effects, and interaction was further verified by conditional logistic regression. Significant allelic association was found for markers RS1912960 (in GABRA4; P = .01) and HCV9866022 (in GABRR2; P = .04). The geno-PDT found significant genotypic association for HCV8262334 (in GABRA2), RS1912960 and RS2280073 (in GABRA4), and RS2617503 and RS12187676 (in GABRB2). Consistent with the allelic and genotypic association results, EMDR confirmed the main effect at RS1912960 (in GABRA4). EMDR also identified a significant two-locus gene-gene effect model involving RS1912960 in GABRA4 and RS2351299 in GABRB1. Further support for this two-locus model came from both the multilocus geno-PDT and the APL test, which indicated a common genotype and haplotype combination positively associated with disease. Finally, these results were also consistent with the results from the conditional logistic regression, which confirmed the interaction between GABRA4 and GABRB1 (odds ratio = 2.9 for interaction term; P = .002). Through the convergence of all analyses, we conclude that GABRA4 is involved in the etiology of autism and potentially increases autism risk through interaction with GABRB1. These results support the hypothesis that GABA receptor subunit genes are involved in autism, most likely via complex gene-gene interactions. DA - 2005/9// PY - 2005/9// DO - 10.1086/433195 VL - 77 IS - 3 SP - 377-388 SN - 1537-6605 ER - TY - JOUR TI - High-diversity genes in the Arabidopsis genome AU - Cork, JM AU - Purugganan, MD T2 - GENETICS AB - High-diversity genes represent an important class of loci in organismal genomes. Since elevated levels of nucleotide variation are a key component of the molecular signature for balancing selection or local adaptation, high-diversity genes may represent loci whose alleles are selectively maintained as balanced polymorphisms. Comparison of 4300 random shotgun sequence fragments of the Arabidopsis thaliana Ler ecotype genome with the whole genomic sequence of the Col-0 ecotype identified 60 genes with putatively high levels of intraspecific variability. Eleven of these genes were sequenced in multiple A. thaliana accessions, 3 of which were found to display elevated levels of nucleotide polymorphism. These genes encode the myb-like transcription factor MYB103, a putative soluble starch synthase I, and a homeodomain-leucine zipper transcription factor. Analysis of these genes and 4-7 flanking genes in 14-20 A. thaliana ecotypes revealed that two of these loci show other characteristics of balanced polymorphisms, including broad peaks of nucleotide diversity spanning multiple linked genes and an excess of intermediate-frequency polymorphisms. Scanning genomes for high-diversity genomic regions may be useful in approaches to adaptive trait locus mapping for uncovering candidate balanced polymorphisms. DA - 2005/8// PY - 2005/8// DO - 10.1534/genetics.104.036152 VL - 170 IS - 4 SP - 1897-1911 SN - 1943-2631 ER - TY - JOUR TI - Direct synthesis of palladium porphyrins from acyldipyrromethanes AU - Sharada, DS AU - Muresan, AZ AU - Muthukumaran, K AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Palladium porphyrins are valuable photosensitizers and luminescent agents in biology and materials chemistry. New methodology is described wherein a 1-acyldipyrromethane is converted into the palladium chelate of a trans-A2B2 porphyrin via a one-flask reaction. The reaction entails self-condensation of the 1-acyldipyrromethane in refluxing ethanol containing KOH (5−10 mol equiv) and Pd(CH3CN)2Cl2 (0.6 mol equiv) exposed to air. This direct route to palladium porphyrins is more expedient than the four steps of the traditional synthesis: (1) reduction of the 1-acyldipyrromethane; (2) acid-catalyzed condensation; (3) oxidation of the porphyrinogen intermediate; and (4) metal insertion. The new synthesis requires neither acid nor DDQ and formally entails only a 2e- + 2H+ oxidation overall versus the traditional multistep synthesis which requires a 2e- + 2H+ reduction per each 1-acyldipyrromethane (4e- + 4H+ overall) followed by a 6e- + 6H+ oxidation. The analogous reaction of a 1,9-diacyldipyrromethane and a dipyrromethane also gives the palladium porphyrin. Seven palladium porphyrins have been prepared in yields of 25−57%. The direct route also can be used with Cu(OAc)2·H2O to give the copper porphyrin albeit in low yield. In summary, this methodology readily affords palladium porphyrins directly from acyldipyrromethanes. DA - 2005/4/29/ PY - 2005/4/29/ DO - 10.1021/jo050120v VL - 70 IS - 9 SP - 3500-3510 SN - 1520-6904 ER - TY - JOUR TI - The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome AU - Tsompana, M AU - Abad, J AU - Purugganan, M AU - Moyer, JW T2 - MOLECULAR ECOLOGY AB - RNA viruses are characterized by high genetic variability resulting in rapid adaptation to new or resistant hosts. Research for plant RNA virus genetic structure and its variability has been relatively scarce compared to abundant research done for human and animal RNA viruses. Here, we utilized a molecular population genetic framework to characterize the evolution of a highly pathogenic plant RNA virus [Tomato spotted wilt virus (TSWV), Tospovirus, Bunyaviridae]. Data from genes encoding five viral proteins were used for phylogenetic analysis, and for estimation of population parameters, subpopulation differentiation, recombination, divergence between Tospovirus species, and selective constraints on the TSWV genome. Our analysis has defined the geographical structure of TSWV, attributed possibly to founder effects. Also, we identify positive selection favouring divergence between Tospovirus species. At the species level, purifying selection has acted to preserve protein function, although certain amino acids appear to be under positive selection. This analysis provides demonstration of population structuring and species-wide population expansions in a multisegmented plant RNA virus, using sequence-based molecular population genetic analyses. It also identifies specific amino acid sites subject to selection within Bunyaviridae and estimates the level of genetic heterogeneity of a highly pathogenic plant RNA virus. The study of the variability of TSWV populations lays the foundation in the development of strategies for the control of other viral diseases in floral crops. DA - 2005/1// PY - 2005/1// DO - 10.1111/j.1365-294X.2004.02392.x VL - 14 IS - 1 SP - 53-66 SN - 1365-294X KW - Bunyaviridae KW - founder effect KW - mutation rate KW - population expansion KW - selection KW - TSWV ER -