TY - CONF TI - 'Using Maple to grade Maple' assessment software from North Carolina State University AU - Kaltofen, Erich AU - McLean, Michael AU - Norris, Larry C2 - 2002/// C3 - Proceedings 2002 Maple Workshop DA - 2002/// PB - Waterloo Maple Inc. With Dmitriy Morozov, John May and William Turner ER - TY - CONF TI - Algorithms for computing the sparsest shifts of polynomials via the Berlekamp/Massey algorithm AU - Giesbrecht, Mark AU - Kaltofen, Erich AU - Lee, Wen-shin T2 - ISSAC 02: International symposium on symbolic and algebraic computation AB - As a sub-procedure our algorithm executes the Berlekamp/Massey algorithm on a sequence of large integers or polynomials. We give a fraction-free version of the Berlekamp/Massey algorithm, which does not require rational numbers or functions and GCD operations on the arising numerators and denominators. The relationship between the solution of Toeplitz systems, Pade approximations, and the Euclidean algorithm is classical. Fraction-free versions [3] can be obtained from the subresultant PRS algorithm [2]. Dornstetter [6] gives an interpretation of the Berlekamp/Massey algorithm as a partial extended Euclidean algorithm. We map the subresultant PRS algorithm onto Dornstetter's formulation. We note that the Berlekamp/Massey algorithm is more efficient than the classical extended Euclidean algorithm. C2 - 2002/// C3 - Proceedings of the 2002 international symposium on Symbolic and algebraic computation - ISSAC '02 CY - Lille, France DA - 2002/// PY - 2002/7// DO - 10.1145/780506.780519 PB - ACM Press SN - 1581134843 9781581134841 UR - http://dx.doi.org/10.1145/780506.780519 ER - TY - JOUR TI - Discussion on the meeting on 'Statistical modelling and analysis of genetic data' AU - Balding, D.J. AU - Carothers, A.D. AU - Marchini, J.L. AU - Cardon, L.R. AU - Vetta, A. AU - Griffiths, B. AU - Weir, B.S. AU - Hill, W.G. AU - Goldstein, D. AU - Strimmer, K. AU - Myers, S. AU - Beaumont, M.A. AU - Glasbey, C.A. AU - Mayer, C.D. AU - Richardson, S. AU - Marshall, C. AU - Durrett, R. AU - Nielsen, R. AU - Visscher, P.M. AU - Knott, S.A. AU - Haley, C.S. AU - Ball, R.D. AU - Hackett, C.A. AU - Holmes, S. AU - Husmeier, D. AU - Jansen, R.C. AU - ter Braak, CJF AU - Maliepaard, CA AU - Boer, MP AU - Joyce, P AU - Li, N AU - Stephens, M AU - Marcoulides, GA AU - Drezner, Z AU - Mardia, K AU - McVean, G AU - Meng, XL AU - Ochs, MF AU - Pagel, M AU - Sha, N AU - Vannucci, M AU - Sillanpaa, MJ AU - Sisson, S AU - Yandell, BS AU - Jin, CF AU - Satagopan, JM AU - Gaffney, PJ AU - Zeng, ZB AU - Broman, KW AU - Speed, TP AU - Fearnhead, P AU - Donnelly, P AU - Larget, B AU - Simon, DL AU - Kadane, JB AU - Nicholson, G AU - Smith, AV AU - Jonsson, F AU - Gustafsson, O AU - Stefansson, K AU - Donnelly, P AU - Parmigiani, G AU - Garrett, ES AU - Anbazhagan, R AU - Gabrielson, E T2 - Journal of the Royal Statistical Society: Series B (Statistical Methodology) AB - Journal of the Royal Statistical Society: Series B (Statistical Methodology)Volume 64, Issue 4 p. 737-775 Discussion on the meeting on ‘Statistical modelling and analysis of genetic data’ First published: 23 October 2002 https://doi.org/10.1111/1467-9868.00359Citations: 11Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume64, Issue4October 2002Pages 737-775 RelatedInformation DA - 2002/10// PY - 2002/10// DO - 10.1111/1467-9868.00359 VL - 64 IS - 4 SP - 737-775 SN - 1369-7412 1467-9868 UR - http://dx.doi.org/10.1111/1467-9868.00359 ER - TY - JOUR TI - Coinfection with Three Ehrlichia Species in Dogs from Thailand and Venezuela with Emphasis on Consideration of 16S Ribosomal DNA Secondary Structure AU - Suksawat, J. AU - Pitulle, C. AU - Arraga-Alvarado, C. AU - Madrigal, K. AU - Hancock, S. I. AU - Breitschwerdt, E. B. T2 - Journal of Clinical Microbiology DA - 2002/10/1/ PY - 2002/10/1/ DO - 10.1128/JCM.40.10.3887.2002-a VL - 40 IS - 10 SP - 3887-3887 J2 - Journal of Clinical Microbiology LA - en OP - SN - 0095-1137 UR - http://dx.doi.org/10.1128/JCM.40.10.3887.2002-a DB - Crossref ER - TY - JOUR TI - Investigation of the phylogenetic relationships within the genus Bartonella based on comparative sequence analysis of the rnpB gene, 16S rDNA and 23S rDNA. AU - Pitulle, Christian AU - Strehse, Christoph AU - Brown, James W AU - Breitschwerdt, Edward B T2 - International Journal of Systematic and Evolutionary Microbiology AB - A variety of genes and analytical methods have been applied to the study of phylogenetic relationships within the genus Bartonella, but so far the results have been inconsistent. While previous studies analysed single protein-encoding genes, we have analysed an alignment containing the sequences of three important phylogenetic markers, RNase P RNA, 16S rRNA and 23S rRNA, merged by catenation, to determine the phylogenetic relationships within the genus Bartonella. The dataset described here comprises 13 different Bartonella strains, including the seven strains that are known to be human pathogens. A variety of algorithms have been used to construct phylogenetic trees based on the combined alignment and, for comparison purposes, each individual gene. Trees generated from the catenated alignment are more consistent (independent of algorithm) and robust (higher bootstrap support). It is suggested that a phylogenetic analysis incorporating the RNase P RNA, 16S rRNA and 23S rRNA be used to study the phylogenetic relationships within the genus Bartonella. DA - 2002/11/1/ PY - 2002/11/1/ DO - 10.1099/00207713-52-6-2075 VL - 52 IS - 6 SP - 2075-2080 LA - en OP - SN - 1466-5026 1466-5034 UR - http://dx.doi.org/10.1099/00207713-52-6-2075 DB - Crossref ER - TY - CONF TI - LINBOX: A GENERIC LIBRARY FOR EXACT LINEAR ALGEBRA AU - Dumas, J. G. AU - Gautier, T. AU - Giesbrecht, M. AU - Giorgi, P. AU - Hovinen, B. AU - Kaltofen, E. AU - Saunders, B. D. AU - Turner, W. J. AU - Villard, G. T2 - Proceedings of the First International Congress of Mathematical Software AB - Black box techniques [12] are enabling exact linear algebra computations of a scale well beyond anything previously possible. The development of new and interesting algorithms has proceeded apace for the past two decades. It is time for the dissemination of these algorithms in an easily used software library so that the mathematical community may readily take advantage of their power. LinBox is that library. In this paper, we describe the design of this generic library, sketch its current range of capabilities, and give several examples of its use. The examples include a solution of Trefethen’s “Hundred Digit Challenge” problem #7 [14] and the computation of all the homology groups of simplicial complexes using the Smith normal form [8]. Exact black box methods are currently successful on sparse matrices with hundreds of thousands of rows and columns and having several million nonzero entries. The main reason large problems can be solved by black box methods is that they require much less memory in general than traditional eliminationbased methods do. This fact is widely used in the numerical computation area. We refer for instance to the templates for linear system solution and eigenvalue problems [2,1]. This has also led the computer algebra community to a considerable interest in black box methods. Since Wiedemann’s seminal paper [16], many developments have been proposed especially to adapt Krylov or Lanczos methods to fast exact algorithms. We refer to [5] and references therein for a review of problems and solutions. LinBox supplies efficient black box solutions for a variety of problems including linear equations and matrix normal forms with the guiding design principle of re-usability. The most essential and driving design criterion for LinBox is that it is generic with respect to the domain of computation. This is because there are many and various representations of finite fields each of which is advantageous to use for some algorithm under some circumstance. The integral and rational number capabilities depend heavily on modular C2 - 2002/7// C3 - Mathematical Software DA - 2002/7// DO - 10.1142/9789812777171_0005 PB - WORLD SCIENTIFIC SN - 9789812380487 9789812777171 UR - http://dx.doi.org/10.1142/9789812777171_0005 DB - Crossref ER - TY - CONF TI - An output-sensitive variant of the baby steps/giant steps determinant algorithm AU - Kaltofen, Erich T2 - the 2002 international symposium AB - In the first of 2000, two new algorithms were discovered for the efficient computation of the determinant of a (dense) matrix with integer entries. Suppose that the dimension of the matrix is n x n and that the maximum bit length of all entries is b. The algorithm by [10] requires (n3.5b2.5)1+o(1) fixed precision, that is, bit operations. Here and in the following we use the exponent +o(1) to capture missing polylogarithmic factors O((log n)C1(log b)C2), where C1, C2 are constants (soft-O). As it has turned out an algorithm in [15], which in turn is based on one by [31] and which uses the baby steps/giant steps algorithm design technique, can be adapted to the dense integer matrix determinant problem and then has bit complexity (n3.5b)1+o(1) [20, Section 2]. Both algorithms use randomization and the algorithm in [10] is Monte Carlo--always fast and probably correct--and the one in [20] is Las Vegas--always correct and probably fast. Both algorithms can be speeded by asymptotically fast subcubic matrix multiplication algorithms a la Strassen [8, 7, 14]. By blocking [6, 16, 29, 30] the baby steps/giant steps algorithm can be further improved, which yields the currently fastest known algorithms [20, Section 3] of bit complexity (n3+1/3b)1+o(1), that without subcubic matrix multiplication and without the FFT-based polynomial half GCD procedures a la Knuth [23; 2, Chapter 8], and of bit complexity n2.698b1+o(1) with subcubic matrix multiplication and FFT-based polynomial GCD procedures. C2 - 2002/// C3 - Proceedings of the 2002 international symposium on Symbolic and algebraic computation - ISSAC '02 DA - 2002/// DO - 10.1145/780506.780524 PB - ACM Press SN - 1581134843 UR - http://dx.doi.org/10.1145/780506.780524 DB - Crossref ER - TY - JOUR TI - Short communication Effect of maize rhizodeposits on soil microbial community structure E. Benizri, O. Dedourge, C. Dibattista-Leboeuf, S. Piutti, C. Nguyen and A. Guckert (France).................. 261 AU - Larsen, KS AU - Jonasson, S AU - Denmark, A Michelsen AU - Dromph, KM AU - Denmark, S Vestergaard AU - Salamanca, EF AU - Raubuch, M T2 - Applied Soil Ecology DA - 2002/// PY - 2002/// VL - 21 SP - 289{\k{a}}290 ER - TY - JOUR TI - Tracking historic migrations of the Irish potato famine pathogen, Phytophthora infestans AU - Ristaino, Jean Beagle T2 - Microbes and infection DA - 2002/// PY - 2002/// VL - 4 IS - 13 SP - 1369-1377 ER - TY - JOUR TI - Effect of synthetic and organic soil fertility amendments on southern blight, soil microbial communities, and yield of processing tomatoes T2 - Phytopathology DA - 2002/// PY - 2002/// VL - 92 IS - 2 SP - 181-189 ER - TY - JOUR TI - Organic and synthetic fertility amendments influence soil microbial, physical and chemical properties on organic and conventional farms T2 - Applied Soil Ecology DA - 2002/// PY - 2002/// VL - 19 IS - 2 SP - 147-160 ER - TY - JOUR TI - Influences of organic and synthetic soil fertility amendments on nematode trophic groups and community dynamics under tomatoes T2 - Applied soil ecology DA - 2002/// PY - 2002/// VL - 21 IS - 3 SP - 233-250 ER - TY - CONF TI - Genetic structure of Phytophthora infestans populations from Costa Rica. Estructura genética de las poblaciones de Phytophthora infestans de Costa Rica. AU - Gómez-Alpı́zar, Luis Enrique AU - Cafe-Filho, AC AU - Ristaino, Jean Beagle C2 - 2002/// C3 - Annual Meeting of the American Phytopathological Society, Milwaukee, WI, US, July 27-31, 2002. DA - 2002/// VL - 92 SP - S30 M1 - 6 ER - TY - JOUR TI - Effie A. Southworth, First woman Plant Pathologists hired at USDA AU - Ristaino, Jean AU - Peterson, Paul T2 - The plant Health Instructor DA - 2002/// PY - 2002/// VL - 10 SP - 1094 ER - TY - JOUR TI - Effect of synthetic and organic soil fertility amendments on southern blight, soil microbial communities, and yield of processing tomatoes T2 - Phytopathology DA - 2002/// PY - 2002/// VL - 92 IS - 2 SP - 181-189 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0036164806&partnerID=MN8TOARS ER - TY - JOUR TI - When a day makes a difference. Interpreting data from endoplasmic reticulum-targeted green fluorescent protein fusions in cells grown in suspension culture AU - Persson, S. AU - Love, J. AU - Tsou, P. L. AU - Robertson, D. AU - Thompson, William AU - Boss, W. F. T2 - Plant Physiology DA - 2002/// PY - 2002/// DO - 10.1104 VL - 128 IS - 2 SP - 341–344 ER - TY - JOUR TI - The North Carolina Premium Fraser Fir Seed Cooperative AU - Frampton, J. AU - McKinney, D. T2 - Limbs & Needles DA - 2002/// PY - 2002/// VL - 29 IS - 2 SP - 10-13 ER - TY - JOUR TI - Developing firs adapted to North Carolina: a research overview AU - Frampton, J. T2 - Conifer Quarterly DA - 2002/// PY - 2002/// VL - 19 IS - 2 SP - 78-79 ER - TY - JOUR TI - Christmas tree production in Western Australia AU - Frampton, J. T2 - American Christmas Tree Journal DA - 2002/// PY - 2002/// VL - 46 IS - 2 SP - 6-9 ER - TY - JOUR TI - Seedling vs clonal testing options for loblolly pine AU - Isik, F. AU - Li, B. AU - Frampton, J. AU - Goldfarb, G. T2 - Proc. of Silviculture and Genetic Impact on productivity of southern pine forests. IEG-40 Meeting DA - 2002/// PY - 2002/// ER - TY - JOUR TI - Evolutionary genomics of maize AU - Buckler, E. AU - Doebley, J. AU - Gaut, B. AU - Goodman, M. AU - Kresovich, S. AU - Muse, S. AU - Weir, B. T2 - Maize Genetics Cooperation Newsletter DA - 2002/// PY - 2002/// IS - 76 SP - 86 ER - TY - JOUR TI - Isolation, identification and detection of undescribed RNA sweetpotato viruses AU - Moyer, JW AU - Abad, JA AU - New, J AU - Bell, J T2 - PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON SWEETPOTATO: FOOD AND HEALTH FOR THE FUTURE DA - 2002/// PY - 2002/// DO - 10.17660/actahortic.2002.583.13 IS - 583 SP - 121-127 SN - 0567-7572 KW - sweetpotato virus detection KW - potyviruses KW - sweetpotato feathery mottle virus KW - sweetpotato chlorotic stunt virus KW - sweetpotato virus G KW - sweetpotato mild mottle virus KW - dsRNA KW - RT-PCR cloning ER - TY - PAT TI - High density non-volatile memory device AU - Bocian, D. F. AU - Kuhr, W. G. AU - Lindsey, J. S. C2 - 2002/// DA - 2002/// PY - 2002/// ER - TY - JOUR TI - What is your neurological diagnosis? AU - Higgins, MA AU - Sharp, NJH T2 - JOURNAL OF THE AMERICAN VETERINARY MEDICAL ASSOCIATION DA - 2002/11/1/ PY - 2002/11/1/ DO - 10.2460/javma.2002.221.1253 VL - 221 IS - 9 SP - 1253-1255 SN - 0003-1488 ER - TY - JOUR TI - The nature of quantitative genetic variation for Drosophila longevity AU - MacKay, T. F. C. T2 - Mechanisms of Ageing and Development AB - Longevity is a typical quantitative trait: the continuous variation in life span observed in natural populations is attributable to genetic variation at multiple quantitative trait loci (QTL), environmental sensitivity of QTL alleles, and truly continuous environmental variation. To begin to understand the genetic architecture of longevity at the level of individual QTL, we have mapped QTL for Drosophila life span that segregate between two inbred strains that were not selected for longevity. A mapping population of 98 recombinant inbred lines (RIL) was derived from these strains, and life span of virgin male and female flies measured under control culture conditions, chronic heat and cold stress, heat shock and starvation stress, and high and low density larval environments. The genotypes of the RIL were determined for polymorphic roo transposable element insertion sites, and life span QTL were mapped using composite interval mapping methods. A minimum of 19 life span QTL were detected by recombination mapping. The life span QTL exhibited strong genotype by sex, genotype by environment, and genotype by genotype (epistatic) interactions. These interactions complicate mapping efforts, but evolutionary theory predicts such properties of segregating QTL alleles. Quantitative deficiency mapping of four longevity QTL detected in the control environment by recombination mapping revealed a minimum of 11 QTL in these regions. Clearly, longevity is a complex quantitative trait. In the future, linkage disequilibrium mapping can be used to determine which candidate genes in a QTL region correspond to the genetic loci affecting variation in life span, and define the QTL alleles at the molecular level. DA - 2002/// PY - 2002/// DO - 10.1016/S0047-6374(01)00330-X VL - 123 IS - 2-3 SP - 95-104 ER - TY - JOUR TI - Genetic diversity and selection in the maize starch pathway AU - Whitt, , SR AU - Wilson, LM AU - Tenaillon, MI AU - Gaut, BS AU - Buckler, ES T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Maize is both phenotypically and genetically diverse. Sequence studies generally confirm the extensive genetic variability in modern maize is consistent with a lack of selection. For more than 6,000 years, Native Americans and modern breeders have exploited the tremendous genetic diversity of maize (Zea mays ssp. mays) to create the highest yielding grain crop in the world. Nonetheless, some loci have relatively low levels of genetic variation, particularly loci that have been the target of artificial selection, like c1 and tb1. However, there is limited information on how selection may affect an agronomically important pathway for any crop. These pathways may retain the signature of artificial selection and may lack genetic variation in contrast to the rest of the genome. To evaluate the impact of selection across an agronomically important pathway, we surveyed nucleotide diversity at six major genes involved in starch metabolism and found unusually low genetic diversity and strong evidence of selection. Low diversity in these critical genes suggests that a paradigm shift may be required for future maize breeding. Rather than relying solely on the diversity within maize or on transgenics, future maize breeding would perhaps benefit from the incorporation of alleles from maize's wild relatives. DA - 2002/10/1/ PY - 2002/10/1/ DO - 10.1073/pnas.202476999 VL - 99 IS - 20 SP - 12959-12962 SN - 0027-8424 ER - TY - JOUR TI - High-throughput transgene copy number estimation by competitive PCR AU - Callaway, AS AU - Abranches, R AU - Scroggs, J AU - Allen, GC AU - Thompson, WF T2 - PLANT MOLECULAR BIOLOGY REPORTER DA - 2002/9// PY - 2002/9// DO - 10.1007/BF02782462 VL - 20 IS - 3 SP - 265-277 SN - 0735-9640 KW - competitive KW - copy number KW - high throughput KW - PCR KW - quantitative KW - transgenic ER - TY - CHAP TI - Empty cages: animal rights and vivsection AU - Gilland, T. AU - Regan, T. T2 - Animal experimentation: Good or bad? (Debating matters) CN - HV4918 .A65 2002 PY - 2002/// SP - 19-36 PB - London: Hodder & Stoughton SN - 0340857331 ER - TY - JOUR TI - Synthesis of perylene-porphyrin dyads for light-harvesting studies AU - Loewe, RS AU - Tomizaki, KY AU - Chevalier, F AU - Lindsey, JS T2 - JOURNAL OF PORPHYRINS AND PHTHALOCYANINES AB - The spectral coverage of porphyrin-based light-harvesting arrays can be enhanced through the use of suitable accessory pigments. Perylene-monoimide dyes can serve as valuable accessory pigments with porphyrins. To investigate the choice of perylene-monoimide and the effects of molecular architecture on light-harvesting efficacy, five perylene-porphyrin dyads were prepared. Each dyad employs a diphenylethyne linker that bridges the perylene N-imide site and the porphyrin meso-position. Three dyads incorporate a mono-phenoxy perylene at the o-, m-, or p-position of the meso-aryl group on the porphyrin. The two remaining dyads incorporate a perylene-monoimide (bearing zero or three phenoxy substituents) at the p-position of the meso-aryl group on the porphyrin. The introduction of phenoxy groups on the perylenes increases the solubility, a key requirement for use in light-harvesting arrays. The long-wavelength absorption band of the perylene shifts from 506 nm to 532 or 533 nm upon substitution with one or three phenoxy groups, respectively. The synthesis of the dyads entails Pd -mediated coupling of a bromo-perylene and an ethynyl porphyrin, or the mixed-aldehyde condensation with a perylene-aldehyde, mesitaldehyde, and pyrrole. Five perylene-monoimide dyes bearing an ethyne or bromo substituent at the p-position of the N-aryl unit were developed for this modular chemistry. Each perylene-porphyrin dyad exhibits efficient energy transfer from the excited perylene to the ground-state porphyrin. DA - 2002/// PY - 2002/// DO - 10.1142/S1088424602000774 VL - 6 IS - 9-10 SP - 626-642 SN - 1099-1409 KW - perylene KW - porphyrin KW - perylene-monoimide KW - light-harvesting KW - energy transfer KW - ethyne ER - TY - JOUR TI - Synthesis and excited-state photodynamics of perylene-porphyrin dyads. 4. Ultrafast charge separation and charge recombination between tightly coupled units in polar media AU - Kirmaier, C AU - Yang, SI AU - Prathapan, S AU - Miller, MA AU - Diers, , JR AU - Bocian, DF AU - Lindsey, JS AU - Holten, D T2 - RESEARCH ON CHEMICAL INTERMEDIATES DA - 2002/// PY - 2002/// DO - 10.1163/15685670260469384 VL - 28 IS - 7-9 SP - 719-740 SN - 0922-6168 ER - TY - PAT TI - Substrates carrying polymers of linked sandwich coordination compounds and methods of use thereof AU - Li, J. AU - Gryko, D. AU - Lindsey, J. S. C2 - 2002/// DA - 2002/// PY - 2002/// ER - TY - JOUR TI - Pulping and bleaching of partially CAD-deficient wood AU - Dimmel, DR AU - MacKay, JJ AU - Courchene, CE AU - Kadla, JF AU - Scott, JT AU - DM O'Malley, AU - McKeand, SE T2 - JOURNAL OF WOOD CHEMISTRY AND TECHNOLOGY AB - ABSTRACT Mutant loblolly pine trees that are partially deficient in cinnamyl alcohol dehydrogenase (CAD) have been studied as a possible new source of pulpwood. Young (4- and 6-year-old) partially CAD-deficient pine trees are ˜20% more easily delignified (pulping and bleaching) and provide similar pulp yields to that of similarly aged normal pines grown on the same plots. Bleached pulp from a 6-year-old partially CAD-deficient pine tree displayed better strength properties than the same age normal pine tree; this probably reflects the milder pulping conditions needed in the case of the partially CAD-deficient tree. Studies also were conducted on a limited number of 14-year-old trees from a different genetic background. In contrast to the results with young trees, no real differences in ease of delignification, pulp yields, bleached pulp strength properties, and wood specific gravities were observed with the 14-year-old trees. There would likely be no penalty if partially CAD-deficient trees were used for lumber products. The rapid growth of partially CAD-deficient trees could make them a valuable pulpwood. DA - 2002/// PY - 2002/// DO - 10.1081/WCT-120016260 VL - 22 IS - 4 SP - 235-248 SN - 0277-3813 KW - pulping KW - bleaching KW - kraft KW - lignin KW - cinnamyl alcohol dehydrogenase KW - CAD-deficient KW - loblolly pine KW - mutant ER - TY - JOUR TI - Nematode gene sequences, update for June 2002 AU - McCarter, J.P. AU - Clifton, S.W. AU - Bird, D.McK. AU - Waterston, R.H. T2 - Journal of Nematology DA - 2002/// PY - 2002/// VL - 34 IS - 2 SP - 71-74 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0036618995&partnerID=MN8TOARS ER - TY - JOUR TI - Dorsal laminectomy for caudal cervical spondylomyelopathy: Postoperative recovery and long-term follow-up in 20 dogs AU - De Risio, L. AU - Munana, K. AU - Murray, M. AU - Olby, N. AU - Sharp, N. J. H. AU - Cuddon, P. T2 - Veterinary Surgery AB - Objective— To evaluate the postoperative morbidity and long‐term outcome of dogs after dorsal laminectomy for caudal cervical spondylomyelopathy (CCSM). Study design— Retrospective study. Sample population— Twenty dogs with CCSM. Methods— Medical records of dogs treated by dorsal laminectomy for CCSM at North Carolina State University and Colorado State University between 1989 and 1999 were reviewed. Information on signalment, onset, progression and duration of clinical signs, diagnostic testing, sites of dorsal laminectomy, postoperative complications, length of hospitalization, and the ambulatory status on discharge was recorded. A minimum follow‐up of 7 months was required for inclusion in the study. Neurologic status was graded (0 to 5) preoperatively, 2 days after surgery, and at the time of the study (final score). Improvement or worsening of the neurologic status was assessed by comparison of different scores for each dog. Additional follow‐up information was obtained by means of a detailed telephone questionnaire directed at both the owner and referring veterinarian. Results— Mean duration of clinical signs before surgery was 4.9 months. At admission, 15 dogs were ambulatory and 5 were nonambulatory. Neurologic status worsened in 70% of dogs 2 days after surgery but improved in all but 1 dog over the long term. Mean time to optimal recovery was 3.6 months. Long‐term follow‐up ranged from 7 months to 9 years (mean ± SD, 3.2 ± 2.4 years). Four dogs had confirmed recurrence; 2 other dogs may have had recurrence. Conclusions— Dorsal cervical laminectomy is an effective treatment for CCSM in those dogs with dorsal compression or multiple sites of involvement. Clinical relevance— Although most dogs' neurologic status transiently worsened after surgery, long‐term outcome and recurrence rates were comparable to those seen with other surgical techniques for CCSM. DA - 2002/// PY - 2002/// DO - 10.1053/jvet.2002.34673 VL - 31 IS - 5 SP - 418-427 ER - TY - JOUR TI - Brassinosteroid signal transduction: Clarifying the pathway from ligand perception to gene expression AU - Clouse, SD T2 - MOLECULAR CELL AB - Recent genetic screens for novel components of brassinosteroid signaling have revealed proteins with cell surface, cytoplasmic, and nuclear localization that function as either positive activators or negative regulators of the brassinosteroid response. Initial microarray experiments have expanded the number of known brassinosteroid-regulated genes, providing a useful resource for better understanding terminal events in signal transduction. DA - 2002/11// PY - 2002/11// DO - 10.1016/S1097-2765(02)00744-X VL - 10 IS - 5 SP - 973-982 SN - 1097-2765 ER - TY - JOUR TI - Synthesis of perylene-porphyrin building blocks and rod-like oligomers for light-harvesting applications AU - Loewe, RS AU - Tomizaki, K AU - Youngblood, WJ AU - Bo, ZS AU - Lindsey, JS T2 - JOURNAL OF MATERIALS CHEMISTRY AB - We present the synthesis of four perylene–porphyrin building blocks for use in Glaser, Sonogashira, or Suzuki polymerizations. The building blocks bear synthetic handles (4-ethynylphenyl, 4-iodophenyl, bromo) at the trans (5,15) meso-positions of a zinc porphyrin and contain two or four perylene-monoimide dyes attached at the 3,5-positions of the non-linking meso-aryl rings of the porphyrin. Each perylene-monoimide bears three 4-tert-butylphenoxy substituents (at the 1-, 6-, and 9-positions) and two isopropyl groups (on the N-aryl unit) for increased solubility. In each case the intervening linker is a diarylethyne unit that bridges the N-imide position of the perylene and the meso-position of the porphyrin. The perylene–porphyrin building blocks were prepared by (1) reaction of a diperylene-dipyrromethane with an aldehyde yielding a trans-A2B2-porphyrin, (2) reaction of a diperylene-aldehyde with a dipyrromethane yielding a trans-A2B2-porphyrin, and (3) reaction of a diperylene-dipyrromethane with a dipyrromethane-dicarbinol yielding a trans-AB2C-porphyrin or ABCD-porphyrin. The building blocks were subjected to Glaser, Sonogashira, or Suzuki coupling conditions in an effort to prepare oligomers containing porphyrins joined via 4,4′-diphenylbutadiyne (dpb), 4,4′-diphenylethyne (dpe), or 1,4-phenylene linkers (p), respectively. Each porphyrin in the backbone bears two or four pendant perylene-monoimide dyes. The Glaser and Sonogashira reactions afforded a distribution of oligomers, whereas the Suzuki reaction was unsuccessful. The oligomers were soluble in solvents such as toluene, THF, or CHCl3 enabling routine handling. The use of perylenes results in (1) increased light-harvesting efficiency particularly in the green spectral region where porphyrins are relatively transparent and (2) greater solubility than is achieved with the use of porphyrins alone. The soluble perylene–porphyrin oligomers are attractive for use as light-harvesting materials in molecular-based solar cells. DA - 2002/// PY - 2002/// DO - 10.1039/b205680a VL - 12 IS - 12 SP - 3438-3451 SN - 1364-5501 ER - TY - JOUR TI - Randomized COMparison of platelet inhibition with abciximab, TiRofiban and eptifibatide during percutaneous coronary intervention in acute coronary syndromes - The COMPARE trial T2 - Circulation (New York, N.Y. : 1950) DA - 2002/// PY - 2002/// VL - 106 IS - 12 SP - 1470-1476 ER - TY - JOUR TI - Naturally OccurringEhrlichia chaffeensisInfection in Two Prosimian Primate Species: Ring-tailed Lemurs (Lemur catta) and Ruffed Lemurs (Varecia variegata) AU - Williams, Cathy V. AU - Van Steenhouse, Jan L. AU - Bradley, Julie M. AU - Hancock, Susan I. AU - Hegarty, Barbara C. AU - Breitschwerdt, Edward B. T2 - Emerging Infectious Diseases AB - A naturally occurring infection of Ehrlichia chaffeensis in lemurs is described. DNA of Ehrlichia chaffeensis was identified by polymerase chain reaction in peripheral blood from six of eight clinically ill lemurs. Organisms were cultured from the blood of one lemur exhibiting clinical and hematologic abnormalities similar to those of humans infected with E. chaffeensis. DA - 2002/12// PY - 2002/12// DO - 10.3201/eid0812.020085 VL - 8 IS - 12 SP - 1497-1500 J2 - Emerg. Infect. Dis. OP - SN - 1080-6040 1080-6059 UR - http://dx.doi.org/10.3201/eid0812.020085 DB - Crossref ER - TY - JOUR TI - Mutations in the gravity persistence signal loci in arabidopsis disrupt the perception and/or signal transduction of gravitropic stimuli AU - Wyatt, SE AU - Rashotte, AM AU - Shipp, MJ AU - Robertson, D AU - Muday, GK T2 - PLANT PHYSIOLOGY AB - Gravity plays a fundamental role in plant growth and development, yet little is understood about the early events of gravitropism. To identify genes affected in the signal perception and/or transduction phase of the gravity response, a mutant screen was devised using cold treatment to delay the gravity response of inflorescence stems of Arabidopsis. Inflorescence stems of Arabidopsis show no response to gravistimulation at 4 degrees C for up to 3 h. However, when gravistimulated at 4 degrees C and then returned to vertical at room temperature (RT), stems bend in response to the previous, horizontal gravistimulation (H. Fukaki, H. Fujisawa, M. Tasaka [1996] Plant Physiology 110: 933-943). This indicates that gravity perception, but not the gravitropic response, occurs at 4 degrees C. Recessive mutations were identified at three loci using this cold effect on gravitropism to screen for gravity persistence signal (gps) mutants. All three mutants had an altered response after gravistimulation at 4 degrees C, yet had phenotypically normal responses to stimulations at RT. gps1-1 did not bend in response to the 4 degrees C gravity stimulus upon return to RT. gps2-1 responded to the 4 degrees C stimulus but bent in the opposite direction. gps3-1 over-responded after return to RT, continuing to bend to an angle greater than wild-type plants. At 4 degrees C, starch-containing statoliths sedimented normally in both wild-type and the gps mutants, but auxin transport was abolished at 4 degrees C. These results are consistent with GPS loci affecting an aspect of the gravity signal perception/transduction pathway that occurs after statolith sedimentation, but before auxin transport. DA - 2002/11// PY - 2002/11// DO - 10.1104/pp.102.010579 VL - 130 IS - 3 SP - 1426-1435 SN - 1532-2548 ER - TY - JOUR TI - Molecular evidence supporting Ehrlichia canis-like infection in cats AU - Breitschwerdt, EB AU - Abrams-Ogg, ACG AU - Lappin, MR AU - Bienzle, D AU - Hancock, SI AU - Cowan, SM AU - Clooten, JK AU - Hegarty, BC AU - Hawkins, EC T2 - JOURNAL OF VETERINARY INTERNAL MEDICINE AB - Currently, the pathogenic role of Ehrlichia canis in cats has been proposed predominantly on the basis of the serologic evidence of natural infection and the infrequent detection of morulae-like structures within the cytoplasm of leukocytes in cats. The purpose of this report was to provide molecular evidence supporting E. canis-like infection in 3 cats that had clinical manifestations consistent with canine ehrlichiosis but lacked antibodies to E. canis antigens. Serum from all 3 cats contained antinuclear antibodies (ANAs). The predominant disease manifestation was polyarthritis in 1 cat and bone marrow hypoplasia or dysplasia. accompanied by pancytopenia or anemia and thrombocytopenia, in 1 cat each. The alignment of E. canis partial 16S ribosomal DNA (rDNA: 382 nucleotide positions), amplified from EDTA blood samples from each cat, was identical to each other and was identical to a canine isolate of E. canis (GenBank accession number AF373613). In 1 cat, concurrent treatment with corticosteroids may have interfered with the therapeutic effectiveness of doxycycline for the elimination of E. canis-like infection. To further define the spectrum of ehrlichiosis in cats, polymerase chain reaction (PCR) testing may be necessary until serologic testing is thoroughly validated in experimentally or naturally infected cats. In addition, until E. canis has been isolated from cats and several tissue culture isolates are available from disparate geographic regions for detailed comparative genetic study, the molecular evidence presented in this study supporting E. canis-like infection in cats must be interpreted with caution. DA - 2002/// PY - 2002/// DO - 10.1892/0891-6640(2002)016<0642:MESCII>2.3.CO;2 VL - 16 IS - 6 SP - 642-649 SN - 0891-6640 KW - antinuclear antibodies KW - leukemia KW - polyarthritis KW - thrombocytopenia ER - TY - JOUR TI - Investigation of the phylogenetic relationships within the genus Bartonella based on comparative sequence analysis of the rnpB gene, 16S rDNA and 23S rDNA AU - Pitulle, C AU - Strehse, C AU - Brown, JW AU - Breitschwerdt, EB T2 - INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY DA - 2002/11// PY - 2002/11// DO - 10.1099/ijs.0.02281-0 VL - 52 IS - 2002 Nov SP - 2075-2080 SN - 1466-5034 KW - 16S rDNA KW - 23S rDNA KW - RNase P RNA KW - phylogeny KW - genus Bartonella ER - TY - JOUR TI - GAI homologues in the Hawaiian silversword alliance (Asteraceae-Madiinae): Molecular evolution of growth regulators in a rapidly diversifying plant lineage AU - Remington, DL AU - Purugganan, MD T2 - MOLECULAR BIOLOGY AND EVOLUTION AB - Accelerated evolution of regulatory genes has been proposed as an explanation for decoupled rates of morphological and molecular evolution. The Hawaiian silversword alliance (Asteraceae-Madiinae) has evolved drastic differences in growth form, including rosette plants, cushion plants, shrubs, and trees, since its origin approximately 6 MYA. We have isolated genes in the DELLA subfamily of putative growth regulators from 13 taxa of Hawaiian and North American Madiinae. The Hawaiian taxa contain two copies of DaGAI that form separate clades within the Madiinae, consistent with an allotetraploid origin for the silversword alliance. DaGAI retains conserved features that have previously been identified in DELLA genes. Selective constraint in the Hawaiian DaGAI copies remains strong in spite of rapid growth form divergence in the silversword alliance, although the constraint was somewhat relaxed in the Hawaiian copies relative to the North American lineages. We failed to detect evidence for positive selection on individual codons. Notably, selective constraint remained especially strong in the gibberellin-responsive DELLA region for which the gene subfamily is named, which is truncated or deleted in all identified dwarf mutants in GAI homologues in different angiosperm species. In contrast with the coding region, however, approximately 900 bp of the upstream flanking region shows variable rates and patterns of evolution, which might reflect positive selection on regulatory regions. DA - 2002/9// PY - 2002/9// DO - 10.1093/oxfordjournals.molbev.a004218 VL - 19 IS - 9 SP - 1563-1574 SN - 0737-4038 KW - Madiinae KW - silversword alliance KW - GAI KW - adaptive radiation KW - selection KW - regulatory genes ER - TY - JOUR TI - Forensic speaker identification based on spectral moments AU - Rodman, R AU - McAllister, D AU - Bitzer, D AU - Cepeda, L AU - Abbitt, P T2 - FORENSIC LINGUISTICS-THE INTERNATIONAL JOURNAL OF SPEECH LANGUAGE AND THE LAW AB - A new method for doing text-independent speaker identification geared to forensic situations is presented. By analysing ‘isolexemic’ sequences, the method addresses the issues of very short criminal exemplars and the need for open-set identification. An algorithm is given that computes an average spectral shape of the speech to be analysed for each glottal pulse period. Each such spectrum is converted to a probability density function and the first moment (i.e. the mean) and the second moment about the mean (i.e. the variance) are computed. Sequences of moment values are used as the basis for extracting variables that discriminate among speakers. Ten variables are presented all of which have sufficiently high inter- to intraspeaker variation to be effective discriminators. A case study comprising a ten-speaker database, and ten unknown speakers, is presented. A discriminant analysis is performed and the statistical measurements that result suggest that the method is potentially effective. The report represents work in progress. DA - 2002/// PY - 2002/// DO - 10.1558/sll.2002.9.1.22 VL - 9 IS - 1 SP - 22-43 SN - 1350-1771 KW - speaker identification KW - spectral moments KW - isolexemic sequences KW - glottal pulse period ER - TY - JOUR TI - Evaluation of FIV protein-expressing VEE-replicon vaccine vectors in cats AU - Burkhard, MJ AU - Valenski, L AU - Leavell, S AU - Dean, GA AU - Tompkins, WAF T2 - VACCINE AB - Venezuelan equine encephalitis (VEE) virus-replicon particles (VRP) were used to generate feline immunodeficiency virus (FIV) Gag- and ENV-expressing vaccine vectors. Serum and mucosal FIV-specific antibody was detected in cats immunized subcutaneously, once monthly for 5 months, with FIV-expressing VRP. Expansion of the CD8+ L-selectin negative phenotype and transient CD8+ noncytolytic suppressor activity were seen in cats immunized with FIV-expressing or control VRP. Despite induction of FIV-specific immune responses and nonspecific suppressor responses, all cats became infected following vaginal challenge with high dose, pathogenic cell-associated FIV-NCSU(1) although relative early maintenance of CD4+ cells was seen in FIV-immunized cats. DA - 2002/12/13/ PY - 2002/12/13/ DO - 10.1016/S0264-410X(02)00455-3 VL - 21 IS - 3-4 SP - 258-268 SN - 0264-410X KW - Venezuelan equine encephalitis (VEE) virus KW - VEE-replicon particles KW - feline immunodeficiency virus (FIV) ER - TY - JOUR TI - Differentiation of Haemobartonella canis and Mycoplasma haemofelis on the basis of comparative analysis of gene sequences AU - Birkenheuer, Adam J. AU - Breitschwerdt, Edward B. AU - Alleman, A. Rick AU - Pitulle, Christian T2 - American Journal of Veterinary Research AB - To determine whether Haemobartonella canis and Mycoplasma haemofelis (formerly known as H felis [large form]) can be differentiated by use of comparative analysis of gene sequences.Blood samples obtained from 3 dogs infected with H canis and 2 cats infected with M haemofelis.The partial 16S rDNA and ribonuclease P RNA (RNase P) genes were amplified, cloned, and sequenced in blood samples obtained from H canis-infected dogs and M haemofelis-infected cats. The DNA sequences were subjected to comparative analysis.The 16S rDNA sequences of H canis and M haemofelis were nearly identical (homology of 99.3 to 99.7%). In contrast, RNase P gene sequences had a lower degree of sequence homology between the 2 organisms (94.3 to 95.5%).Haemobartonella canis and M haemofelis are not identical organisms. Molecular differentiation of H canis and M haemofelis is more clearly evident by use of comparative analysis of RNase P gene sequences than by comparative analysis of 16S rDNA gene sequences. DA - 2002/10// PY - 2002/10// DO - 10.2460/ajvr.2002.63.1385 VL - 63 IS - 10 SP - 1385-1388 J2 - American Journal of Veterinary Research LA - en OP - SN - 0002-9645 UR - http://dx.doi.org/10.2460/ajvr.2002.63.1385 DB - Crossref ER - TY - JOUR TI - Brassinosteroids - Plant counterparts to animal steroid hormones? AU - Clouse, SD T2 - VITAMINS AND HORMONES - ADVANCES IN RESEARCH AND APPLICATIONS, VOL 65 AB - Brassinosteroids are polyhydroxylated derivatives of common plant membrane sterols such as campesterol. They occur throughout the plant kingdom and have been shown by genetic and biochemical analyses to be essential for normal plant growth and development. Numerous reviews have detailed the recent progress in our understanding of the biosynthesis, physiological responses, and molecular modes of action of brassinosteroids. It is clear that like their animal steroid counterparts, brassinosteroids have a defined receptor, can regulate the expression of specific genes, and can orchestrate complex physiological responses involved in growth. This review summarizes the current status of BR research, pointing out where appropriate the similarities and differences between the mechanism of action of brassinosteroids and the more thoroughly studied animal steroid hormones. DA - 2002/// PY - 2002/// DO - 10.1016/S0083-6729(02)65065-4 VL - 65 SP - 195-223 SN - 0083-6729 ER - TY - JOUR TI - BhuR, a virulence-associated outer membrane protein of Bordetella avium, is required for the acquisition of iron from heme and hemoproteins AU - Murphy, ER AU - Sacco, RE AU - Dickenson, A AU - Metzger, DJ AU - Hu, Y AU - Orndorff, PE AU - Connell, TD T2 - INFECTION AND IMMUNITY AB - ABSTRACT Iron (Fe) is an essential element for most organisms which must be obtained from the local environment. In the case of pathogenic bacteria, this fundamental element must be acquired from the fluids and tissues of the infected host. A variety of systems have evolved in bacteria for efficient acquisition of host-bound Fe. The gram-negative bacterium Bordetella avium , upon colonization of the avian upper respiratory tract, produces a disease in birds that has striking similarity to whooping cough, a disease caused by the obligate human pathogen Bordetella pertussis . We describe a B. avium Fe utilization locus comprised of bhuR and six accessory genes ( rhuIR and bhuSTUV ). Genetic manipulations of B. avium confirmed that bhuR , which encodes a putative outer membrane heme receptor, mediates efficient acquisition of Fe from hemin and hemoproteins (hemoglobin, myoglobin, and catalase). BhuR contains motifs which are common to bacterial heme receptors, including a consensus FRAP domain, an NPNL domain, and two TonB boxes. An N-terminal 32-amino-acid segment, putatively required for rhuIR -dependent regulated expression of bhuR , is present in BhuR but not in other bacterial heme receptors. Two forms of BhuR were observed in the outer membrane of B. avium : a 91-kDa polypeptide consistent in size with the predicted mature protein and a smaller 82-kDa polypeptide which lacks the 104 amino acids found at the N terminus of the 91-kDa form. A mutation in hemA was engineered in B. avium to demonstrate that the bacterium transports heme into the cytoplasm in a BhuR-dependent manner. The role of BhuR in virulence was established in turkey poults by use of a competitive-infection model. DA - 2002/10// PY - 2002/10// DO - 10.1128/IAI.70.10.5390-5403.2002 VL - 70 IS - 10 SP - 5390-5403 SN - 0019-9567 ER - TY - JOUR TI - Acidolysis of intermediates used in the preparation of core-modified porphyrinic macrocycles AU - Chevalier, F AU - Geier, GR AU - Lindsey, JS T2 - JOURNAL OF PORPHYRINS AND PHTHALOCYANINES AB - The stability towards acidolysis of intermediates used in the preparation of core-modified porphyrinic macrocycles was examined. Experiments were performed using analogs of 5-phenyldipyrromethane in which one of the two pyrrole rings was modified (XPM). The XPMs utilized in these studies had X = 2-furyl (OPM), 2-thienyl (SPM), 2-selenyl (SePM), or 3-pyrrolyl ( NC PPM). The XPMs possess a potentially labile linkage to a heteroatom-modified ring as well as a potentially labile linkage to a pyrrole ring. The stability of the two types of linkages was examined under acid catalysis conditions commonly used in the preparation of porphyrinic macrocycles. The methodology employed enabled characterization of the stability of the XPM (GC analysis), the yield of porphyrin (UV-vis absorption), and the composition of porphyrinic species (laser-desorption mass spectrometry, LD-MS) formed upon acidolysis of the XPM. These experiments showed that (1) the linkage to the heteroatom-modified ring is fairly stable in the presence of a linkage to pyrrole, and (2) the linkage to pyrrole is much more stable in the XPMs than is the case in 5-phenyldipyrromethane. Additional experiments with analogs of 5-phenyldipyrromethane having both rings modified ( X 2 M ), where X = 2- furyl ( O 2 M ), 2- thienyl ( S 2 M ), or 2- selenyl ( Se 2 M ) confirmed that linkages to furyl, thienyl, and selenyl rings are stable towards acidolysis. Taken together, the observations concerning stability of various linkages provide a foundation for understanding the types and yields of core-modified porphyrinic macrocycles formed in reactions with reactants that are not direct precursors to the isolated products. DA - 2002/// PY - 2002/// DO - 10.1142/S108842460200021X VL - 6 IS - 3 SP - 186-197 SN - 1088-4246 KW - dipyrromethane KW - core-modified porphyrin KW - acid catalysis KW - oxaporphyrin KW - thiaporphyrin KW - selenaporphyrin ER - TY - JOUR TI - A Monte Carlo EM algorithm for generalized linear mixed models with flexible random effects distribution AU - Chen, J. L. AU - Zhang, D. W. AU - Davidian, M. T2 - Biostatistics (Oxford, England) DA - 2002/// PY - 2002/// VL - 3 IS - 3 SP - 347-360 ER - TY - JOUR TI - Synthesis and photophysical properties of light-harvesting arrays comprised of a porphyrin bearing multiple perylene-monoimide accessory pigments AU - Tomizaki, K AU - Loewe, RS AU - Kirmaier, C AU - Schwartz, JK AU - Retsek, JL AU - Bocian, DF AU - Holten, D AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - We present the synthesis and characterization of new light-harvesting arrays containing two, four, or eight perylene-monoimide accessory pigments attached to a zinc porphyrin. Each perylene is substituted with one or three 4-tert-butylphenoxy substituents. A 4,3‘- or 4,2‘-diarylethyne linker joins the perylene N-imide position and the porphyrin meso-position, affording divergent or convergent architectures, respectively. The architectures are designed to provide high solubility in organic media and facile perylene-to-porphyrin energy transfer, while avoiding charge-transfer quenching of the excited porphyrin product. For the array containing four perylenes per porphyrin in both nonpolar (toluene) and polar (benzonitrile) media and for the array containing eight perylenes per porphyrin in toluene, the photoexcited perylene-monoimide dye (PMI*) decays rapidly (∼3.5 ps) and predominantly (≥90%) by energy transfer to the zinc porphyrin to form the excited zinc porphyrin (Zn*), which has excited-state characteristics (lifetime, fluorescence yield) comparable (within ∼10%) to those of the isolated chromophore. For the array containing eight perylenes in benzonitrile, PMI* decays ∼80% by energy transfer (forming Zn*) and ∼20% by hole transfer (forming PMI- Zn+); Zn* subsequently decays ∼20% by electron transfer (also forming PMI- Zn+) and ∼80% by the normal routes open to the porphyrin monomer (intersystem crossing, internal conversion, fluorescence). In addition to rapid and efficient perylene-to-porphyrin energy transfer, the broad blue-green to yellow absorption of the perylene dyes complements the blue absorption of the porphyrin, resulting in excellent light harvesting across a significant spectral region. Collectively, the work described herein identifies multiperylene−porphyrin arrays that exhibit suitable photochemical properties for use as motifs in larger light-harvesting systems. DA - 2002/9/6/ PY - 2002/9/6/ DO - 10.1021/jo0258002 VL - 67 IS - 18 SP - 6519-6534 SN - 1520-6904 ER - TY - JOUR TI - Origin of the black shank resistance gene, Ph, in tobacco cultivar Coker 371-gold AU - Johnson, ES AU - Wolff, MF AU - Wernsman, EA AU - Atchely, WR AU - Shew, HD T2 - PLANT DISEASE AB - Flue-cured tobacco (Nicotiana tabacum) cultivar Coker 371-Gold (C 371-G) possesses a dominant gene, Ph, that confers high resistance to black shank disease, caused by race 0 of the soil-borne pathogen Phytophthora parasitica var. nicotianae. The origin of this gene is unknown. Breeding lines homozygous for the Ph gene were hybridized with NC 1071 and L8, flue-cured and burley genotypes known to possess qualitative resistance genes from Nicotiana plumbaginifolia and N. longiflora, respectively. The F1 hybrids were out-crossed to susceptible testers and the progenies evaluated in field black shank nurseries and in greenhouse disease tests with P. parasitica var. nicotianae race 0. Results showed that Ph was allelic to Php from N. plumbaginifolia in NC 1071. Testcross populations of hybrids between burley lines homozygous for Ph and L8, possessing Phl from N. longiflora, showed that Ph and Phl integrated into the same tobacco chromosome during interspecific transfer. Nevertheless, the two loci were estimated to be 3 cM apart. Random amplified polymorphic DNA (RAPD) analyses of the testcross progenies confirmed that recombination between the two loci was occurring. Forty-eight RAPD markers linked to Ph in doubled haploid lines were used in cluster analyses with multiple accessions of N. longiflora and N. plumbaginifolia, breeding lines L8, NC 1071, and DH92-2770-40, and cultivars K 326, Hicks, and C 371-G. A cladogram or region tree confirmed the data obtained from field and greenhouse trials, that Ph, transferred from C 371-G to DH92-2770-40, and Php in NC 1071 were allelic and originated from N. plumbaginifolia. DA - 2002/10// PY - 2002/10// DO - 10.1094/PDIS.2002.86.10.1080 VL - 86 IS - 10 SP - 1080-1084 SN - 0191-2917 KW - disease resistance genes KW - gene phylogeny ER - TY - JOUR TI - Nitrogen nutrition of hedged stock plants of Loblolly Pine. II. Influence of carbohydrate and nitrogen status on adventitious rooting of stem cuttings AU - Rowe, DB AU - Blazich, FA AU - Goldfarb, B AU - Wise, FC T2 - NEW FORESTS DA - 2002/7// PY - 2002/7// DO - 10.1023/A:1020555013964 VL - 24 IS - 1 SP - 53-65 SN - 0169-4286 KW - conifer KW - mineral nutrition KW - Pinaceae KW - Pinus taeda KW - vegetative propagation ER - TY - JOUR TI - Interferon regulatory factor-1, interferon-beta, and reovirus-induced myocarditis AU - Azzam-Smoak, K AU - Noah, DL AU - Stewart, MJ AU - Blum, MA AU - Sherry, B T2 - VIROLOGY AB - Viral myocarditis is an important human disease, and reovirus-induced myocarditis in mice provides an excellent model to study direct viral damage to the heart. Previously, we showed that reovirus induction of and sensitivity to interferon-beta (IFN-beta) is an important determinant of viral pathogenicity in the heart and that the transcription factor interferon regulatory factor-3 (IRF-3) is required for reovirus induction of IFN-beta in primary cardiac myocyte cultures. Given several lines of evidence suggesting a possible distinctive environment for IRFs in the heart, we have now focused on IRF-1. Previous studies demonstrated that viruses, double-stranded-RNA (dsRNA), and IFN-alpha/beta can each induce IRF-1 and that IRF-1 plays a role in dsRNA, but perhaps not viral, induction of IFN-alpha/beta. Importantly, none of these studies used a virus with a dsRNA genome (such as reovirus), none of them used a highly differentiated nonlymphoid cell type, and none of them addressed whether viral induction of IRF-1 is direct or is mediated through viral induction of IFN-beta. Indeed, as recently as this year it has been assumed that viral induction of IRF-1 is direct. Here, we found that reovirus induced IRF-1 in primary cardiac myocyte cultures, but that IRF-1 was not required for reovirus induction of IFN-beta. Surprisingly, we found that reovirus failed to induce IRF-1 in the absence of the IFN-alpha/beta response. This provides the first evidence that viruses may not induce IRF-1 directly. Finally, nonmyocarditic reovirus strains induced more cardiac lesions in mice deficient for IRF-1 than they did in wildtype mice, directly demonstrating a protective role for IRF-1. Together, the results indicate that while IRF-1 is downstream of the IFN-beta response, it plays an important protective role against viral myocarditis. DA - 2002/6/20/ PY - 2002/6/20/ DO - 10.1006/viro.2002.1470 VL - 298 IS - 1 SP - 20-29 SN - 0042-6822 KW - reovirus KW - double-stranded RNA (dsRNA) KW - viral myocarditis KW - cardiac myocytes KW - interferon (IFN) KW - interferon regulatory factor (IRF) ER - TY - JOUR TI - Influences of organic and synthetic soil fertility amendments on nematode trophic groups and community dynamics under tomatoes AU - Bulluck, LR AU - Barker, KR AU - Ristaino, JB T2 - APPLIED SOIL ECOLOGY AB - Research was conducted to examine the effects of organic and synthetic soil amendments and tillage on nematode communities in field soils planted to tomato (Lycopersicon esculentum) at two locations. The experimental design was a replicated split plot with chisel-plow tillage and bare-soil or chisel-plow tillage and surface mulch with wheat straw as main plots, and soil amendments of synthetic fertilizer, composted cotton-gin trash, swine manure, or a rye-vetch green manure as subplots. Tillage did not affect free-living or plant-parasitic nematode community dynamics, but soil amendments had a large impact on nematode community structure and diversity. Populations of bacterivorous nematodes mainly in the Rhabditidae and Cephalobidae, and fungivorous nematodes were greater after planting in soils amended with swine manure, composted cotton-gin trash, or rye-vetch, than in soils amended with synthetic fertilizer at both locations. Populations of nematodes in these trophic groups decreased through time in each year. Populations of Meloidogyne incognita in soil were not affected by soil amendments, but increased through time at each location. Root-gall indices were lower in plots containing swine manure or cotton-gin trash than in those with synthetic fertilizer or rye-vetch during the second season. The combined nematode maturity index values were greater at planting in soils amended with rye-vetch or fertilizer than in soils with swine manure and composted cotton-gin trash. Shannon’s diversity index decreased over time for both years at one location, regardless of soil amendment. At the second location, the Shannon’s diversity index decreased only in the second year. Use of descriptive indices, including the Enrichment index, structure index, and channel index provided useful information about the effects of organic amendments on the structure of nematode communities in tomato field soils. DA - 2002/// PY - 2002/// DO - 10.1016/S0929-1393(02)00089-6 VL - 21 IS - 3 SP - 233-250 SN - 1873-0272 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0036784082&partnerID=MN8TOARS KW - food web KW - maturity index KW - nematode ecology KW - organic amendments KW - trophic dynamics ER - TY - JOUR TI - Genetic improvement of Virginia pine planting stock for Christmas tree production in South Carolina AU - Knoth, J AU - Frampton, J AU - Moody, R T2 - HORTTECHNOLOGY AB - Twenty open-pollinated families from a virginia pine ( Pinus virginiana ) seed orchard in South Carolina were planted and managed as Christmas trees at three sites. Retail value and related traits were assessed once the tests reached marketable size (4 years in the field). All traits assessed (except survival) proved to 1) be under a moderate degree of genetic control (family mean heritability = 0.68 for retail value) and 2) have a large range among open-pollinated family means ($11.42/tree to $22.00/tree, retail value) suggesting that they will response well to the traditional tree improvement approach of selection, breeding and testing. The retail value of the best five families tested averaged an increase of $3.47/tree or 20.7% more than the average. At a 6 × 6 ft (1.8 m) spacing [1,210 trees/acre (2,990 trees/ha)], these families would produce an increase in revenue of almost $4,200/acre ($10,387/ha). Much of this increase in value is a result of reducing the cull rate from 14.5% to 8.1%. Survival, height, crown density and straightness of these five families also exceeded the average of the 20 families tested. DA - 2002/// PY - 2002/// DO - 10.21273/horttech.12.4.675 VL - 12 IS - 4 SP - 675-678 SN - 1943-7714 KW - Pinus virginiana KW - choose and cut KW - heritability KW - gain KW - correlation KW - quality KW - crown density KW - retail value ER - TY - JOUR TI - Expression of the Drosophila gene disconnected using the UAS/GAL4 system AU - Robertson, LK AU - Dey, BK AU - Campos, AR AU - Mahaffey, JW T2 - GENESIS AB - genesisVolume 34, Issue 1-2 p. 103-106 UAS LinesFree Access Expression of the drosophila gene disconnected using the UAS/GAL4 system Lisa K. Robertson, Lisa K. Robertson Department of Genetics, North Carolina State University, Raleigh, North Carolina, USASearch for more papers by this authorBijan K. Dey, Bijan K. Dey Department of Biology, McMaster University, Hamilton, Ontario, CanadaSearch for more papers by this authorAna Regina Campos, Ana Regina Campos Department of Biology, McMaster University, Hamilton, Ontario, CanadaSearch for more papers by this authorJames W. Mahaffey, Corresponding Author James W. Mahaffey [email protected] Department of Genetics, North Carolina State University, Raleigh, North Carolina, USADepartment of Genetics, North Carolina State University, Campus Box 7614, Raleigh, NC 27695-7614Search for more papers by this author Lisa K. Robertson, Lisa K. Robertson Department of Genetics, North Carolina State University, Raleigh, North Carolina, USASearch for more papers by this authorBijan K. Dey, Bijan K. Dey Department of Biology, McMaster University, Hamilton, Ontario, CanadaSearch for more papers by this authorAna Regina Campos, Ana Regina Campos Department of Biology, McMaster University, Hamilton, Ontario, CanadaSearch for more papers by this authorJames W. Mahaffey, Corresponding Author James W. Mahaffey [email protected] Department of Genetics, North Carolina State University, Raleigh, North Carolina, USADepartment of Genetics, North Carolina State University, Campus Box 7614, Raleigh, NC 27695-7614Search for more papers by this author First published: 12 September 2002 https://doi.org/10.1002/gene.10123Citations: 8AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat LITERATURE CITED Brand AH, Perrimon N. 1993. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118: 401–415. Freeman M. 1996. Reiterative use of the EGF receptor triggers differentiation of all cell types in the Drosophila eye. Cell 87: 651–60. Glossop NRJ, Shepherd D. 1998. Disconnected mutants show disruption to the central projections of proprioceptive neurons in Drosophila melanogaster. J Neurobiol 36: 337–347. Hardin PE, Hall JC, Rosbash M. 1992. Behavioral and molecular analysis suggest that circadian output is disrupted by disconnected mutants in D. melanogaster. EMBO J 11: 1–6. Heilig JS, Freeman M, Laverty T, Lee KJ, Campos AR, Rubin GM, Steller H. 1991. Isolation and characterization of the disconnected gene of Drosophila melanogaster. EMBO J 10: 809–815. Helfrich-Forster C. 1998. Robust circadian rhythmicity of Drosophila melanogaster requires the presence of lateral neurons: a brain-behavioral study of disconnected mutants. J Comp Physiol [A] 182: 435–453. Lee KJ, Freeman M, Steller H. 1991. Expression of the disconnected gene during development of Drosophila melanogaster. EMBO J 10: 817–826. Lyko F, Ramsahoye BH, Kashevsky H, Tudor M, Mastrangelo MA, Orr-Weaver TL, Jaenisch R. 1999. Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in Drosophila. Nat Genet 23: 363–366. Mahaffey JW, Griswold CM, Cao QM. 2001. The Drosophila genes disconnected and disco-related are redundant with respect to larval head development and accumulation of mRNAs from deformed target genes. Genetics 157: 225–236. Pederson JD, Kiehart DP, Mahaffey JW. 1996. The Role of HOM-C Genes in Segmental Transformations: Reexamination of the Drosophila Sex combs reduced embryonic phenotype. Dev Biol 180: 131–142. Rubin GM, Spradling AC. 1982. Genetic transformation of Drosophila with transposable element vectors. Science 218: 348–353. Sanson B, White P, Vincent JP. 1996. Uncoupling cadherin-based adhesion from wingless signalling in Drosophila. Nature 383: 627–630. Steller H, Fischbach KF, Rubin GM. 1987. Disconnected: a locus required for neuronal pathway formation in the visual system of Drosophila. Cell 50: 1139–1153. Surdej P, Got C, Miassod R. 1990. Developmental expression pattern of a 800-kb DNA continuum cloned from the Drosophila X chromosome 14B-1415B region. Biological Cell 68: 105–118. Tautz D, Pfeifle C. 1989. A non-radioactive in situ hybridization method for the localization of specific RNAs in Drosophila embryos reveals translational control of the segmentation gene hunchback. Chromosoma 98: 81–85. Yoffe KB, Manoukian AS, Wilder EL, Brand AH, Perrimon N. 1995. Evidence for engrailed-independent wingless autoregulation in Drosophila. Dev Biol 170: 636–650. Citing Literature Volume34, Issue1-2Special Issue: GAL4/UAS in Drosophila September ‐ October 2002Pages 103-106 ReferencesRelatedInformation DA - 2002/// PY - 2002/// DO - 10.1002/gene.10123 VL - 34 IS - 1-2 SP - 103-106 SN - 1526-954X ER - TY - JOUR TI - Evolution of duplicated alpha-tubulin genes in ciliates AU - Israel, R. L. AU - Pond, S. L. K. AU - Muse, S. V. AU - Katz, L. A. T2 - Evolution AB - Ciliates provide a powerful system to analyze the evolution of duplicated alpha-tubulin genes in the context of single-celled organisms. Genealogical analyses of ciliate alpha-tubulin sequences reveal five apparently recent gene duplications. Comparisons of paralogs in different ciliates implicate differing patterns of substitutions (e.g., ratios of replacement/synonymous nucleotides and radical/conservative amino acids) following duplication. Most substitutions between paralogs in Euplotes crassus, Halteria grandinella and Paramecium tetraurelia are synonymous. In contrast, alpha-tubulin paralogs within Stylonychia lemnae and Chilodonella uncinata are evolving at significantly different rates and have higher ratios of both replacement substitutions to synonymous substitutions and radical amino acid changes to conservative amino acid changes. Moreover, the amino acid substitutions in C. uncinata and S. lemnae paralogs are limited to short stretches that correspond to functionally important regions of the alpha-tubulin protein. The topology of ciliate alpha-tubulin genealogies are inconsistent with taxonomy based on morphology and other molecular markers, which may be due to taxonomic sampling, gene conversion, unequal rates of evolution, or asymmetric patterns of gene duplication and loss. DA - 2002/// PY - 2002/// DO - 10.1111/j.0014-3820.2002.tb01425.x VL - 56 IS - 6 SP - 1110-1122 ER - TY - JOUR TI - Effects of diverse acid catalysts on the reaction course in the two-step one-flask synthesis of meso-tetraphenylporphyrin AU - Geier, GR AU - Lindsey, JS T2 - JOURNAL OF PORPHYRINS AND PHTHALOCYANINES AB - A set of 45 acids or acid combinations was examined in the condensation of pyrrole + benzaldehyde (10 mM each in CH 2 Cl 2 ) leading to meso-tetraphenylporphyrin (TPP). Initial screening experiments identified suitable acid catalysts and the optimal concentration (in terms of TPP formation) for each acid. Subsequent experiments followed the time course of reactions using the best conditions identified in the screening experiments. The reaction course was followed by monitoring reactions from 1 min to 24 h for the yield of TPP (by UV-vis and HPLC), the yields of N-confused tetraphenylporphyrin and tetraphenylsapphyrin (by HPLC), the quantity of unreacted benzaldehyde (by TLC), and the oligomer composition (by laser desorption mass spectrometry). Diverse acids (Brønsted or Lewis; soluble or insoluble) were found to provide yields of TPP ranging up to ~50%. Only 10 acids gave no TPP. In addition, N-confused tetraphenylporphyrin was found to be a ubiquitous byproduct, whereas tetraphenylsapphyrin was not widely observed. MgBr 2 -etherate and CuCl 2 each catalyzed porphyrinogen formation and resulted in porphyrin metalation following oxidation and neutralization of the reaction mixture, thereby providing direct, one-flask syntheses of magnesium and copper porphyrins. Observations concerning the reaction course obtained from prior studies of TFA or BF 3 -etherate catalysis have been found to be quite general across a broad range of acid catalysts. Collectively, these results show that many acids have potential utility in porphyrin syntheses. DA - 2002/// PY - 2002/// DO - 10.1142/S1088424602000208 VL - 6 IS - 3 SP - 159-185 SN - 1088-4246 KW - porphyrin KW - tetraphenylporphyrin KW - acid catalysis KW - Bronsted acid KW - Lewis acid KW - N-confused tetraphenylporphyrin KW - tetraphenylsapphyrin KW - pyrromethane KW - mass spectrometry ER - TY - JOUR TI - Constitutive expression of a celery mannitol dehydrogenase in tobacco enhances resistance to the mannitol-secreting fungal pathogen Alternaria alternata AU - Jennings, DB AU - Daub, ME AU - Pharr, DM AU - Williamson, JD T2 - PLANT JOURNAL AB - Our previous observation that host plant extracts induce production and secretion of mannitol in the tobacco pathogen Alternaria alternata suggested that, like their animal counterparts, plant pathogenic fungi might produce the reactive oxygen quencher mannitol as a means of suppressing reactive oxygen-mediated plant defenses. The concurrent discovery that pathogen attack induced mannitol dehydrogenase (MTD) expression in the non-mannitol-containing host tobacco suggested that plants, unlike animals, might be able to counter this fungal suppressive mechanism by catabolizing mannitol of fungal origin. To test this hypothesis, transgenic tobacco plants constitutively expressing a celery Mtd cDNA were produced and evaluated for potential changes in resistance to both mannitol- and non-mannitol-secreting pathogens. Constitutive expression of the MTD transgene was found to confer significantly enhanced resistance to A. alternata, but not to the non-mannitol-secreting fungal pathogen Cercospora nicotianae. These results are consistent with the hypothesis that MTD plays a role in resistance to mannitol-secreting fungal plant pathogens. DA - 2002/10// PY - 2002/10// DO - 10.1046/j.1365-313X.2001.01399.x VL - 32 IS - 1 SP - 41-49 SN - 0960-7412 KW - antioxidant KW - disease resistance KW - hydroxyl radical KW - mannitol KW - reactive oxygen ER - TY - JOUR TI - Bartonella henselae and Bartonella elizabethae as Potential Canine Pathogens AU - Mexas, A. M. AU - Hancock, S. I. AU - Breitschwerdt, E. B. T2 - Journal of Clinical Microbiology AB - ABSTRACT Bartonella henselae or Bartonella elizabethae DNA from EDTA-anticoagulated blood samples obtained from four dogs was amplified and sequenced. The results showed that B. elizabethae should be added to the list of Bartonella species (i.e., B. vinsonii subsp. berkhoffii , B. henselae , and B. clarridgeiae ) that are currently recognized as infectious agents in dogs. Furthermore, these results may have potential zoonotic implications, particularly if dogs can serve as a previously unrecognized reservoir for B. henselae . Although the clinical relevance of these observations remains to be determined, it is possible that molecular diagnostic techniques such as PCR may help to implicate a spectrum of Bartonella spp. as a cause of or a cofactor in chronic canine and human diseases of poorly defined causation. DA - 2002/12/1/ PY - 2002/12/1/ DO - 10.1128/JCM.40.12.4670-4674.2002 VL - 40 IS - 12 SP - 4670-4674 J2 - Journal of Clinical Microbiology LA - en OP - SN - 0095-1137 UR - http://dx.doi.org/10.1128/jcm.40.12.4670-4674.2002 DB - Crossref ER - TY - JOUR TI - Arabidopsis mutants reveal multiple roles for sterols in plant development AU - Clouse, SD T2 - PLANT CELL AB - The molecular genetic, and biochemical analysis of sterol-deficient mutants in Arabidopsis strongly suggests an essential role for sterols in regulating multiple events in plant development, independent of their conversion to brassinosteroids (BRs). Embryogenesis, cell elongation, vascular DA - 2002/9// PY - 2002/9// DO - 10.1105/tpc.140930 VL - 14 IS - 9 SP - 1995-2000 SN - 1040-4651 ER - TY - JOUR TI - 17 beta-estradiol is a hormonal regulator of mirex tumor promotion sensitivity in mice AU - Porter, KL AU - Chanda, S AU - Wang, HQ AU - Gaido, KW AU - Smart, RC AU - Robinette, CL T2 - TOXICOLOGICAL SCIENCES AB - Mirex, an organochlorine pesticide, is a potent non-phorbol ester tumor promoter in mouse skin. Previous studies have shown that female mice are 3 times more sensitive to mirex tumor promotion than male mice and that ovariectomized (OVX) female mice are resistant to mirex promotion, suggesting a role for ovarian hormones in mirex promotion. To determine whether the ovarian hormone 17-β estradiol (E2) is responsible for the sensitivity of female mice to mirex promotion, female mice were initiated with DMBA; 2 weeks later groups of mice were OVX and implants, with or without E2, were surgically implanted subcutaneously. These mice were treated topically twice weekly with mirex for 26 weeks. E2 implanted OVX mice demonstrated high normal physiologic levels of serum E2 throughout the tumor promotion experiment. E2 implants restored by 80% the intact mirex-sensitive phenotype to the OVX mice. Consistent with a role for E2 and ERα and ERβ, treatment of DMBA-initiated female mice with topical ICI 182,780, an estrogen-receptor antagonist, reduced mirex tumor multiplicity by 30%. However, in cells co-transfected with ERα or ERβ and estrogen-responsive promoter reporter, mirex did not stimulate promoter reporter activity, suggesting that the promotion effect of mirex is downstream of ERα/β. Finally, a tumor promotion study was conducted to determine whether E2 implants could increase the sensitivity of male mice to mirex promotion. E2 implants in male mice did increase sensitivity to mirex promotion; however, the implants did not produce the full female sensitivity to mirex tumor promotion. Collectively, these studies indicate that E2 is a major ovarian hormone responsible for mirex tumor promotion sensitivity in female mice. DA - 2002/9// PY - 2002/9// DO - 10.1093/toxsci/69.1.42 VL - 69 IS - 1 SP - 42-48 SN - 1096-6080 KW - mirex KW - skin KW - 17 beta-estradiol KW - tumor promotion KW - endocrine ER - TY - JOUR TI - Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species AU - Wu, RL AU - Ma, CX AU - Painter, I AU - Zeng, ZB T2 - THEORETICAL POPULATION BIOLOGY AB - With the advent of new molecular marker technologies, it is now feasible to initiate genome projects for outcrossing plant species, which have not received much attention in genetic research, despite their great agricultural and environmental value. Because outcrossing species typically have heterogeneous genomes, data structure for molecular markers representing an entire genome is complex: some markers may have more alleles than others, some markers are codominant whereas others are dominant, and some markers are heterozygous in one parent but fixed in the other parent whereas the opposite can be true for other markers. A major difficulty in analyzing these different types of marker at the same time arises from uncertainty about parental linkage phases over markers. In this paper, we present a general maximum-likelihood-based algorithm for simultaneously estimating linkage and linkage phases for a mixed set of different marker types containing fully informative markers (segregating 1:1:1:1) and partially informative markers (or missing markers, segregating 1:2:1, 3:1, and 1:1) in a full-sib family derived from two outbred parent plants. The characterization of linkage phases is based on the posterior probability distribution of the assignment of alternative alleles at given markers to two homologous chromosomes of each parent, conditional on the observed phenotypes of the markers. Two- and multi-point analyses are performed to estimate the recombination fraction and determine the most likely linkage phase between different types of markers. A numerical example is presented to demonstrate the statistical properties of the model for characterizing the linkage phase between markers. DA - 2002/5// PY - 2002/5// DO - 10.1006/tpbi.2002.1577 VL - 61 IS - 3 SP - 349-363 SN - 1096-0325 KW - EM algorithm KW - linkage phase KW - outcrossing species KW - partially informative marker KW - posterior probability KW - recombination fraction ER - TY - JOUR TI - Recovery and sequence validation of the histological signal following in situ RT-PCR localization of plant gene transcripts AU - Koltai, H AU - Bird, DM T2 - PLANT MOLECULAR BIOLOGY REPORTER DA - 2002/12// PY - 2002/12// DO - 10.1007/BF02772126 VL - 20 IS - 4 SP - 391-397 SN - 0735-9640 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-4544341383&partnerID=MN8TOARS KW - functional genomics KW - in situ RT-PCR KW - Medicago truncatula KW - nodule KW - signal specificity KW - transcription ER - TY - JOUR TI - Organic and synthetic fertility amendments influence soil microbial, physical and chemical properties on organic and conventional farms AU - Bulluck, LR AU - Brosius, M AU - Evanylo, GK AU - Ristaino, JB T2 - APPLIED SOIL ECOLOGY AB - Field experiments were conducted to examine the effects of organic and synthetic soil fertility amendments on soil microbial communities and soil physical and chemical properties at three organic and three conventional vegetable farms in Virginia and Maryland in 1996 and 1997. Two treatments, including either an alternative organic soil amendment (composted cotton-gin trash, composted yard waste, or cattle manure) or synthetic soil amendment (fertilizer) were applied to three replicated plots at each grower field location. Production history and time affected propagule densities of Trichoderma species which remained higher in soils from organic farms. Propagule densities of Trichoderma species, thermophilic microorganisms, and enteric bacteria were also detected in greater numbers in soils amended with alternative than synthetic amendments, whereas propagule densities of Phytophthora and Pythium species were lower in soils amended with alternative than synthetic fertility amendments. Concentrations of Ca, K, Mg, and Mn were higher in soils amended with alternative than synthetic fertility amendments. Canonical correlations and principle component analyses indicated significant correlation between these soil chemical factors and the biological communities. First-order canonical correlations were more negative in fields with a conventional history, and use of synthetic fertilizers, whereas canonical correlations were more positive in fields with a history of organic production and alternative soil amendments. In the first year, yields of corn or melon were not different in soil amended with either synthetic or organic amendments at four of six farms. In the second year, when all growers planted tomatoes, yields were higher on farms with a history of organic production, regardless of soil amendment type. Alternative fertility amendments, enhanced beneficial soil microorganisms reduced pathogen populations, increased soil organic matter, total carbon, and cation exchange capacity (CEC), and lowered bulk density thus improving soil quality. DA - 2002/2// PY - 2002/2// DO - 10.1016/S0929-1393(01)00187-1 VL - 19 IS - 2 SP - 147-160 SN - 1873-0272 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0036160296&partnerID=MN8TOARS KW - soil chemical and physical factors KW - organic agriculture KW - sustainable agriculture KW - soil microbial communities ER - TY - JOUR TI - Feline ehrlichiosis. The genetic identification of the agent in Avo cats AU - Beaufils, J. P. AU - Breitschwerdt, E. AU - Hancock, S. I. AU - Hegarty, B. C. AU - Martin-Granel, J. AU - Jumelle, P. AU - Barbault-Jumelle, M. AU - Blavier, A. T2 - Pratique Medicale et Chirurgicale de L'animal de Compagnie DA - 2002/// PY - 2002/// VL - 37 IS - 3 SP - 235-238 ER - TY - CHAP TI - Combinatorial use of short probes for differential gene expression profiling AU - Warren, L. L. AU - Liu, B. H. T2 - Algorithms in bioinformatics: First International Workshop, WABI 2001, Aarhus, Denmark, August 28-31, 2001 proceedings A2 - O. Gascuel, A2 - Moret, B.M.E. CN - R858 .A2 A44 2001 PY - 2002/// VL - 2452 SP - 477-490 PB - Berlin; New York: Springer SN - 3540425160 ER - TY - JOUR TI - Weakly coupled molecular photonic wires: Synthesis and excited-state energy-transfer dynamics AU - Ambroise, A AU - Kirmaier, C AU - Wagner, RW AU - Loewe, RS AU - Bocian, DF AU - Holten, D AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Molecular photonic wires, which absorb light and undergo excited-state energy transfer, are of interest as biomimetic models for photosynthetic light-harvesting systems and as molecular devices with potential applications in materials chemistry. We describe the stepwise synthesis of four molecular photonic wires. Each wire consists of an input unit, transmission element, and output unit. The input unit consists of a boron-dipyrrin dye or a perylene-monoimide dye (linked either at the N-imide or the C9 position); the transmission element consists of one or three zinc porphyrins affording short or long wires, respectively; and the output unit consists of a free base (Fb) porphyrin. The components in the arrays are joined in a linear architecture via diarylethyne linkers (an ethynylphenyl linker is attached to the C9-linked perylene). The wires have been examined by static absorption, static fluorescence, and time-resolved absorption spectroscopy. Each wire (with the exception of the C9-linked perylene wire) exhibits a visible absorption spectrum that is the sum of the spectra of the component parts, indicating the relatively weak electronic coupling between the components. Excitation of each wire at the wavelength where the input unit absorbs preferentially (typically 480-520 nm) results in emission almost exclusively from the Fb porphyrin. The static emission and time-resolved data indicate that the overall rate constants and quantum efficiencies for end-to-end (i.e., input to output) energy transfer are as follows: perylene-(N-imide)-linked short wire, (33 ps)(-1) and >99%; perylene-(C9)-linked short wire, (26 ps)(-1) and >99%; boron-dipyrrin-based long wire, (190 ps)(-1) and 81%; perylene-(N-imide)-linked long wire, (175 ps)(-1) and 86%. Collectively, the studies provide valuable insight into the singlet-singlet excited-state energy-transfer properties in weakly coupled molecular photonic wires. DA - 2002/5/31/ PY - 2002/5/31/ DO - 10.1021/jo025561i VL - 67 IS - 11 SP - 3811-3826 SN - 1520-6904 ER - TY - JOUR TI - The role of weed hosts and tobacco thrips, Frankliniella fusca, in the epidemiology of Tomato spotted wilt virus AU - Groves, RL AU - Walgenbach, JF AU - Moyer, JW AU - Kennedy, GG T2 - PLANT DISEASE AB - Wild plant species were systematically sampled to characterize reproduction of thrips, the vector of Tomato spotted wilt virus (TSWV), and natural sources TSWV infection. Thrips populations were monitored on 28 common perennial, biennial, and annual plant species over two noncrop seasons at six field locations across North Carolina. Sonchus asper, Stellaria media, and Taraxacum officianale consistently supported the largest populations of immature TSWV vector species. The tobacco thrips, Frankliniella fusca, was the most abundant TSWV vector species collected, comprising over 95% of vector species in each survey season. Perennial plant species (i.e., Plantago rugelii and Taraxacum officianale) were often only locally abundant, and many annual species (Cerastium vulgatum, Sonchus asper, and Stellaria media) were more widely distributed. Perennial species, including P. rugelii and Rumex crispus, remained TSWV infected for 2 years in a small-plot field test. Where these perennial species are locally abundant, they may serve as important and long-lasting TSWV inoculum sources. In random surveys across 12 locations in North Carolina, TSWV infection was documented by double antibody sandwich enzyme-linked immunosorbent assay in 35 of 72 (49%) common perennial (N = 10), biennial (N = 4), and annual (N = 21) plant species across 18 plant families. Estimated rates of TSWV infection were highest in Cerastium vulgatum (4.2%), Lactuca scariola (1.3%), Molluga verticillata (4.3%), Plantago rugelii (3.4%), Ranunculus sardous (3.6%), Sonchus asper (5.1%), Stellaria media (1.4%), and Taraxacum officianale (5.8%). Nine plant species were determined to be new host recordings for TSWV infection, including Cardamine hirsuta, Eupatorium capillifolium, Geranium carolinianum, Gnaphalium purpureum, Linaria canadense, Molluga verticillata, Pyrrhopappus carolinianus, Raphanus raphanistrum, and Triodanis perfoliata. Our findings document the relative potential of a number of common annual, biennial, and perennial plant species to act as important reproductive sites for F. fusca and as acquisition sources of TSWV for spread to susceptible crops. DA - 2002/6// PY - 2002/6// DO - 10.1094/PDIS.2002.86.6.573 VL - 86 IS - 6 SP - 573-582 SN - 1943-7692 KW - Frankliniella occidentalis KW - Thrips tabaci ER - TY - JOUR TI - Expression of the high capacity calcium-binding domain of calreticulin increases bioavailable calcium stores in plants AU - Wyatt, SE AU - Tsou, PL AU - Robertson, D T2 - TRANSGENIC RESEARCH DA - 2002/2// PY - 2002/2// DO - 10.1023/A:1013917701701 VL - 11 IS - 1 SP - 1-10 SN - 1573-9368 KW - Arabidopsis KW - calreticulin KW - calcium-binding KW - calcium storage KW - endoplasmic reticulum KW - environmental stress ER - TY - JOUR TI - Comparison of electron-transfer and charge-retention characteristics of porphyrin-containing self-assembled monolayers designed for molecular information storage AU - Roth, KM AU - Gryko, DT AU - Clausen, C AU - Li, JZ AU - Lindsey, JS AU - Kuhr, WG AU - Bocian, DF T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - The redox kinetics for a variety of porphyrin-containing self-assembled monolayers (SAMs) on Au are reported. The measurements probe both the rate of electron-transfer (k0) for oxidation (in the presence of applied potential) and the rate of charge dissipation after the applied potential is disconnected (characterized by a charge-retention half-life (t1/2)). The porphyrins include (1) monomeric Zn complexes that contain phenylmethylene linkers wherein the number of methylene spacers varies from 0 to 3, (2) monomeric Zn complexes that contain different ethynylphenyl-derived linkers, and (3) a triple-decker lanthanide sandwich complex with a phenylethynylphenyl linker. The k0 values for all the porphyrin SAMs are in the range of 104−105 s-1. The k0 values for the monomeric ethynylphenyl-linked porphyrin SAMs are generally faster than those for the monomeric phenylmethylene-linked SAMs. The rates for the latter SAMs decrease as the number of methylene spacers increases. The rates for the triple-decker SAM are generally slower than those for the monomers. The trends observed in the k0 values are paralleled in the t1/2 values, that is, porphyrin SAMs that exhibit relatively faster electron-transfer rates also exhibit faster charge-dissipation rates (shorter t1/2 values). However, the charge-dissipation rates (no applied potential) are approximately 6 orders of magnitude slower than the electron-transfer rates (applied potential). Both the k0 and t1/2 values for the porphyrin SAMs are sensitive to the surface coverage of the molecules. The rates for both processes decrease as the monolayers become more densely packed. This behavior is attributed to exclusion of solvent/counterions and space-charge effects. The effect of surface coverage on rates can overshadow differences that result from differences in linker type/length. Collectively, the studies help to delineate the molecular design features that could be manipulated to control the redox processes in porphyrin SAMs. The understanding of these processes is essential for the successful implementation of molecules as the active media in information-storage elements. DA - 2002/8/29/ PY - 2002/8/29/ DO - 10.1021/jp025850a VL - 106 IS - 34 SP - 8639-8648 SN - 1520-6106 ER - TY - JOUR TI - Comparison of Serological Detection Methods for Diagnosis of Ehrlichia canis Infections in Dogs AU - Belanger, M. AU - Sorenson, H. L. AU - France, M. K. AU - Bowie, M. V. AU - Barbet, A. F. AU - Breitschwerdt, E. B. AU - Alleman, A. R. T2 - Journal of Clinical Microbiology AB - ABSTRACT We determined the value of four serological assays for the diagnosis of canine monocytic ehrlichiosis by comparing them to the indirect fluorescent-antibody assay “gold standard.” The specificity of Dip-S-Ticks was significantly lower than that of all of the other tests evaluated. The sensitivity of Dip-S-Ticks was significantly higher than that of Snap3Dx or the Snap Canine Combo. The sensitivity of the rMAP2 enzyme-linked immunosorbent assay (ELISA) was significantly higher than that of the Snap Canine Combo. The accuracy levels of the rMAP2 ELISA, Snap3Dx, Dip-S-Ticks, and Snap Canine Combo were 97.0, 89.8, 85.1, and 82.9%, respectively. DA - 2002/9/1/ PY - 2002/9/1/ DO - 10.1128/JCM.40.9.3506-3508.2002 VL - 40 IS - 9 SP - 3506-3508 J2 - Journal of Clinical Microbiology LA - en OP - SN - 0095-1137 UR - http://dx.doi.org/10.1128/jcm.40.9.3506-3508.2002 DB - Crossref ER - TY - JOUR TI - CCAAT/enhancer binding protein-beta is a mediator of keratinocyte survival and skin tumorigenesis involving oncogenic Ras signaling AU - Zhu, SY AU - Yoon, K AU - Sterneck, E AU - Johnson, PF AU - Smart, RC T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - The basic leucine zipper transcription factor CCAAT/enhancer binding protein-beta (C/EBPbeta) is expressed in many cell types, including keratinocytes. C/EBPbeta activity can be increased by phosphorylation through pathways stimulated by oncogenic Ras, although the biological implications of Ras-C/EBPbeta signaling are not currently understood. We report here that C/EBPbeta-nullizygous mice are completely refractory to skin tumor development induced by a variety of carcinogens and carcinogenesis protocols, including 7,12-dimethylbenz[a]anthracene-initiation/12-O-tetradecanoylphorbol 13-acetate promotion, that produce tumors containing oncogenic Ras mutations. No significant differences in TPA-induced epidermal keratinocyte proliferation were observed in C/EBPbeta-null versus wild-type mice. However, apoptosis was significantly elevated (17-fold) in the epidermal keratinocytes of 7,12-dimethylbenz[a]anthracene-treated C/EBPbeta-null mice compared with wild-type mice. In v-Ha-ras transgenic mice, C/EBPbeta deficiency also led to greatly reduced skin tumor multiplicity and size, providing additional evidence for a tumorigenesis pathway linking Ras and C/EBPbeta. Oncogenic Ras potently stimulated C/EBPbeta to activate a C/EBP-responsive promoter-reporter in keratinocytes and mutating an ERK1/2 phosphorylation site (T188) in C/EBPbeta abolished this Ras effect. Finally, we observed that C/EBPbeta participates in oncogenic Ras-induced transformation of NIH 3T3 cells. These findings indicate that C/EBPbeta has a critical role in Ras-mediated tumorigenesis and cell survival and implicate C/EBPbeta as a target for tumor inhibition. DA - 2002/1/8/ PY - 2002/1/8/ DO - 10.1073/pnas.012437299 VL - 99 IS - 1 SP - 207-212 SN - 0027-8424 ER - TY - JOUR TI - An experiment planner for performing successive focused grid searches with an automated chemistry workstation AU - Dixon, JM AU - Du, H AU - Cork, DG AU - Lindsey, JS T2 - CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS AB - Automated chemistry workstations equipped for parallel and adaptive experimentation can provide a significant impact in chemistry research, particularly for exploring search spaces as part of optimization studies. A traditional method of investigating a search space involves generation of a response surface upon examination of a regular grid of points (e.g., as in a full factorial design). Such experimental approaches are compatible with parallel experimentation but are not adaptive in directing the search toward favorable regions of the search space. We have developed an algorithm wherein a succession of grid searches is performed in a search space. The location of the optimal response obtained in one search cycle constitutes the location about which a subsequent more fine-grained search is performed. In this manner, a sequential iterative optimization can be achieved: one cycle is comprised of a set of parallel reactions followed by data evaluation, and multiple cycles occur until one of several user-defined termination criteria is satisfied. In successive cycles, the number of levels on each dimension can be decremented and the range of each dimension can be decreased by a defined “shrinkage” factor. The resulting successive focused grid search (SFGS) affords a breadth-first then in-depth study. We have developed an experimental planner that enables the SFGS algorithm to be implemented on an automated chemistry workstation. Options are available for adjusting the scope of experimentation to conserve material resources (e.g., solvent, reagents, reactants) or to curtail the duration of experimentation. Collectively, the SFGS module enables parallel adaptive experimentation and affords a comprehensive response surface that is fine-grained in the region of optimal response. DA - 2002/5/28/ PY - 2002/5/28/ DO - 10.1016/S0169-7439(02)00009-6 VL - 62 IS - 2 SP - 115-128 SN - 1873-3239 KW - grid search KW - factorial design KW - automated chemistry workstation KW - parallel experimentation KW - adaptive experimentation ER - TY - JOUR TI - An approach for parallel and adaptive screening of discrete compounds followed by reaction optimization using an automated chemistry workstation AU - Du, H AU - Lindsey, JS T2 - CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS AB - The challenge of finding appropriate reagents, catalysts, or cocatalysts for chemical reactions is typically met with a strategy of surveying broadly to identify a good starting point (i.e., a hit) from which an in-depth optimization can be performed. We have developed an approach for experiment planning that enables this two-tiered strategy to be implemented on an automated chemistry workstation. One experiment-planning module (Parascreen) for screening discrete substances to identify hits is linked to a second module (Multidirectional search, MDS) for optimization of each hit compound. The screening module has been constructed through modification of an experiment-planning module for performing grid searches. Each candidate is examined over a range of concentrations. Two levels of decision-making are performed. (1) Local evaluation: Yield-versus-time data from a given reaction are examined in a pattern-matching procedure to assess whether monitoring should be continued or terminated. (2) Global evaluation: When a user-defined threshold (e.g., yield) is reached, the candidate is flagged as a hit; any experiments at higher concentration of the same candidate are deleted. Each of the hit compounds is subjected to identification of refined conditions by means of an MDS optimization. Each module alone enables parallel adaptive experimentation. Several issues for automated use of two different modules in succession have been addressed. This two-tiered approach of breadth-first screening followed by in-depth optimization of hits enables autonomous experimentation using an automated chemistry workstation. DA - 2002/5/28/ PY - 2002/5/28/ DO - 10.1016/S0169-7439(02)00012-6 VL - 62 IS - 2 SP - 159-170 SN - 0169-7439 KW - multidirectional search KW - automated chemistry workstation KW - parallel experimentation KW - adaptive experimentation ER - TY - JOUR TI - A two-tiered strategy for simplex and multidirectional optimization of reactions with an automated chemistry workstation AU - Matsumoto, T AU - Du, H AU - Lindsey, JS T2 - CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS AB - A two-tiered strategy for optimizing reaction conditions has been developed for use with an automated chemistry workstation capable of parallel adaptive experimentation. In tier one, a broad survey of conditions is performed in parallel. In tier two, the promising region identified in the first tier is used as the starting point for in-depth searches. The search strategies employed in tier two include the composite-modified Simplex (CMS), multidirectional search (MDS), and parallel Simplex search (PSS) methods. Accordingly, this two-tiered strategy has been integrated into the CMS, MDS, and PSS experiment-planning modules. Each of these methods requires an initial user-defined simplex to explore reaction conditions. The breadth-first survey avoids the lengthy experimentation that occurs when the initial simplex is located far from the optimal region, and also diminishes the possibility of trapping in local maxima. Thus, the two-tiered strategy (breadth-first, depth-second) enables the optimal region to be reached rapidly. DA - 2002/5/28/ PY - 2002/5/28/ DO - 10.1016/S0169-7439(02)00011-4 VL - 62 IS - 2 SP - 149-158 SN - 0169-7439 KW - simplex KW - composite-modified simplex KW - multidirectional search KW - automated chemistry workstation KW - parallel experimentation KW - adaptive experimentation ER - TY - JOUR TI - A revised classification scheme for genetically diverse populations of Heterodera glycines AU - Niblack, T. L. AU - Arelli, P. R. AU - Noel, G. R. AU - Opperman, C. H. AU - Ore, J. H. AU - Schmitt, D. P. AU - Shannon, J. G. AU - Tylka, G. L. T2 - Journal of Nematology DA - 2002/// PY - 2002/// VL - 34 IS - 4 SP - 279-288 ER - TY - JOUR TI - A parallel simplex search method for use with an automated chemistry workstation AU - Matsumoto, T AU - Du, H AU - Lindsey, JS T2 - CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS AB - The Simplex method, an inherently serial means of optimization, can be used to search for improved conditions for chemical reactions. We have developed an automated chemistry workstation equipped for parallel adaptive experimentation. To exploit the capabilities of the workstation and thereby optimize reaction conditions in a more expedient manner, we have developed an experiment-planning module for performing Simplex searches in parallel. The parallel Simplex search (PSS) module enables multiple composite modified Simplex (CMS) searches to be performed in a concurrent manner. Features have been incorporated for two applications. (1) Multiple concurrent simplex searches in one search space, enabling optimization of conditions for one reaction. The use of Simplex searches starting from several points in a search space reduces the possibility of falsely concluding that a local maximum is the global maximum. (2) Concurrent investigation of multiple search spaces with one Simplex search per space, enabling optimization of conditions for each member of a set of catalysts or set of reactants for a given reaction. This latter feature is useful for combinatorial chemistry applications. All individual Simplex searches in a PSS study must employ the same experimental template. The PSS module includes options to define conditions for simplex moves as well as specifying initial points in the search space. Provisions are included for stop criteria, termination of an individual Simplex search, and global termination of multiple Simplex searches. The PSS method provides a parallel yet adaptive means for identifying improved conditions for chemical reactions. DA - 2002/5/28/ PY - 2002/5/28/ DO - 10.1016/S0169-7439(02)00010-2 VL - 62 IS - 2 SP - 129-147 SN - 0169-7439 KW - simplex KW - composite modified simplex KW - automated chemistry workstation KW - parallel experimentation ER - TY - JOUR TI - Two E2F elements regulate the proliferating cell nuclear antigen promoter differently during leaf development AU - Egelkrout, EM AU - Mariconti, L AU - Settlage, SB AU - Cella, R AU - Robertson, D AU - Hanley-Bowdoin, L T2 - PLANT CELL AB - E2F transcription factors regulate genes expressed at the G1/S boundary of the cell division cycle in higher eukaryotes. Although animal E2F proteins and their target promoters have been studied extensively, little is known about how these factors regulate plant promoters. An earlier study identified two E2F consensus binding sites in the promoter of a Nicotiana benthamiana gene encoding proliferating cell nuclear antigen (PCNA) and showed that the proximal element (E2F2) is required for the full repression of PCNA expression in mature leaves. In this study, we examined the distal element (E2F1) and how it interacts with the E2F2 site to regulate the PCNA promoter. Gel shift assays using plant nuclear extracts or purified Arabidopsis E2F and DP proteins showed that different complexes bind to the two E2F sites. Mutation of the E2F1 site or both sites differentially altered PCNA promoter function in transgenic plants. As reported previously for the E2F2 mutation, the E2F1 and E2F1+2 mutations partially relieved the repression of the PCNA promoter in mature leaves. In young tissues, the E2F1 mutation resulted in a threefold reduction in PCNA promoter activity, whereas the E2F1+2 mutation had no detectable effect. The activity of E2F1+2 mutants was indistinguishable from that of E2F2 mutants. These results demonstrate that both E2F elements contribute to the repression of the PCNA promoter in mature leaves, whereas the E2F1 site counters the repression activity of the E2F2 element in young leaves. DA - 2002/12// PY - 2002/12// DO - 10.1105/tpc.006403 VL - 14 IS - 12 SP - 3225-3236 SN - 1040-4651 ER - TY - JOUR TI - Transcriptional and posttranscriptional regulation of Arabidopsis TCH4 expression by diverse stimuli. Roles of cis regions and brassinosteroids AU - Iliev, EA AU - Xu, W AU - Polisensky, DH AU - Oh, MH AU - Torisky, RS AU - Clouse, SD AU - Braam, J T2 - PLANT PHYSIOLOGY AB - The Arabidopsis TCH4 gene is up-regulated in expression by diverse environmental and hormonal stimuli. Because TCH4 encodes a xyloglucan endotransglucosylase/hydrolase, this change in expression may reflect a recruitment of cell wall-modifying activity in response to environmental stress and growth. How diverse stimuli lead to the common response of TCH4 expression regulation is not known. Here, we show that induction of expression by the diverse stimuli of touch, darkness, cold, heat, and brassinosteroids (BRs) is conferred to reporter genes by the same 102-bp 5'-untranscribed TCH4 region; this result is consistent with the idea that shared regulatory elements are employed by diverse stimuli. Distal regions influence magnitude and kinetics of expression and likely harbor regulatory elements that are redundant with those located more proximal to the transcriptional start site. Substitution of the proximal regulatory region sequences in the context of distal elements does not disrupt inducible expression. TCH4 expression induction is transcriptional, at least in part because 5'-untranscribed sequences are sufficient to confer this regulation. However, 5'-untranslated sequences are necessary and sufficient to confer the marked transience of TCH4 expression, most likely through an effect on mRNA stability. Perception of BR is not necessary for TCH4::GUS induction by environmental stimuli because regulation is intact in the BR-insensitive mutant, bri1-2. The full response to auxin, however, requires the functioning of BRI1. Developmental expression of TCH4 is unlikely to be meditated by BR because TCH4::GUS is expressed in BR perception and biosynthetic mutants bri1-2 and det2-1, respectively. DA - 2002/10// PY - 2002/10// DO - 10.1104/pp.008680 VL - 130 IS - 2 SP - 770-783 SN - 0032-0889 ER - TY - JOUR TI - The hepatic endothelial carcinogen riddelliine induces endothelial apoptosis, mitosis, S phase, and p53 and hepatocytic vascular endothelial growth factor expression after short-term exposure AU - Nyska, A AU - Moomaw, CR AU - Foley, JF AU - Maronpot, RR AU - Malarkey, DE AU - Cummings, CA AU - Peddada, S AU - Moyer, CF AU - Allen, DG AU - Travlos, G AU - Chan, PC T2 - TOXICOLOGY AND APPLIED PHARMACOLOGY AB - Riddelliineis a naturally occurring pyrrolizidine alkaloid found in certain poisonous rangeland plants of the western United States. In National Toxicology Program 2-year studies, riddelliine induced high incidences of hemangiosarcoma in the liver of F344/N rats (both sexes) and B6C3F1 mice (males). To understand this pathogenesis, we tested short-term effects of riddelliine. Three groups (control; 1.0 mg/kg/day, high dose used in the 2-year study; and 2.5 mg/kg/day) of seven male F344/N rats per group were terminated after 8 consecutive doses and 30 doses (6 weeks, excluding weekends). Serum vascular endothelial growth factor (VEGF), histological, immunohistochemical [factor VIII-related antigen/von Willebrand factor (fVIII-ra/vWf)], VEGF, VEGF receptor-2 (VEGFR2), glutathione S-transferase-π, S-phase (BrdU), p53, apoptosis, and ultrastructural evaluations were performed on the liver. Following 8 doses of 1.0 and 2.5 mg/kg/day, increased numbers of apoptotic and S-phase nuclei appeared in hepatocytes and endothelial cells. Following 30 doses of 1.0 and 2.5 mg/kg/day, hepatocytes exhibited reduced mitosis, fewer S-phase nuclei, increased hypertrophy, and fatty degeneration, while endothelial cells showed karyomegaly, cytomegaly, decreased apoptosis, more S-phase nuclei, and p53 positivity. Hepatocytes of treated animals expressed higher VEGF immunopositivity. That altered endothelial cells were fVIII-ra/vWf and VEGFR2 positive confirmed their identity. These changes may have promoted hemangiosarcoma development upon long-term exposure through endothelial adduct formation, apoptosis, proliferation of endothelial cells having undamaged and/or damaged DNA, and mutation. Endothelial proliferation may also have been promoted through endothelial arrest at S phase, which was associated with endothelial karyo- and cytomegaly, resulting in hepatocytic hypoxia, triggering VEGF induction. DA - 2002/11/1/ PY - 2002/11/1/ DO - 10.1006/taap.2002.9485 VL - 184 IS - 3 SP - 153-164 SN - 1096-0333 KW - pyrrolizidine alkaloid KW - endothelium KW - hemangiosarcoma KW - cytotoxicity KW - vascular endothelial growth factor KW - VEGFR2 KW - BrdU KW - factor VIII-related antigen KW - von Willebrand factor KW - p53 ER - TY - JOUR TI - The cost of inbreeding in Arabidopsis AU - Bustamante, CD AU - Nielsen, R AU - Sawyer, SA AU - Olsen, KM AU - Purugganan, MD AU - Hartl, DL T2 - NATURE DA - 2002/4/4/ PY - 2002/4/4/ DO - 10.1038/416531a VL - 416 IS - 6880 SP - 531-534 SN - 0028-0836 ER - TY - JOUR TI - The complex genetic architecture of Drosophila life span AU - Leips, J AU - Mackay, TFC T2 - EXPERIMENTAL AGING RESEARCH AB - Continuous phenotypic variation in life span results from segregating genetic variation at multiple loci, the environmental sensitivity of expression of these loci, and the history of environmental variation experienced by the organism throughout its life. We have mapped quantitative trait loci (QTL) that produce variation in the life span of mated Drosophila melanogaster using a panel of recombinant inbred lines (RIL) that were backcrossed to the parental strains from which they were derived. Five QTL were identified that influence mated life span, three were male-specific, one was female-specific, and one affected life span in both sexes. The additive allelic effects and dominance of QTL were highly sex-specific. One pair of QTL also exhibited significant epistatic effects on life span. We summarize all of the QTL mapping data for Drosophila life span, and outline future prospects for disentangling the genetic and environmental influences on this trait. DA - 2002/// PY - 2002/// DO - 10.1080/03610730290080399 VL - 28 IS - 4 SP - 361-390 SN - 1096-4657 ER - TY - JOUR TI - Synthesis and electronic properties of regioisomerically pure oxochlorins AU - Taniguchi, M AU - Kim, HJ AU - Ra, DY AU - Schwartz, JK AU - Kirmaier, C AU - Hindin, E AU - Diers, , JR AU - Prathapan, S AU - Bocian, DF AU - Holten, D AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - We describe a two-step conversion of C-alkylated zinc chlorins to zinc oxochlorins wherein the keto group is located in the reduced ring (17-position) of the macrocycle. The transformation proceeds by hydroxylation upon exposure to alumina followed by dehydrogenation with DDQ. The reactions are compatible with ethyne, iodo, ester, trimethylsilyl, and pentafluorophenyl groups. A route to a spirohexyl-substituted chlorin/oxochlorin has also been developed. Representative chlorins and oxochlorins were characterized by static and time-resolved absorption spectroscopy and fluorescence spectroscopy, resonance Raman spectroscopy, and electrochemistry. The fluorescence quantum yields of the zinc oxochlorins (Phi(f) = 0.030-0.047) or free base (Fb) oxochlorins (Phi(f) = 0.13-0.16) are comparable to those of zinc tetraphenylporphyrin (ZnTPP) or free base tetraphenylporphyrin (FbTPP), respectively. The excited-state lifetimes of the zinc oxochlorins (tau = 0.5-0.7 ns) are on average 4-fold lower than that of ZnTPP, and the lifetimes of the Fb oxochlorins (tau = 7.4-8.9 ns) are approximately 40% shorter than that of FbTPP. Time-resolved absorption spectroscopy of a zinc oxochlorin indicates the yield of intersystem crossing is >70%. Resonance Raman spectroscopy of copper oxochlorins show strong resonance enhancement of the keto group upon Soret excitation but not with Q(y)()-band excitation, which is attributed to the location of the keto group in the reduced ring (rather than in the isocyclic ring as occurs in chlorophylls). The one-electron oxidation potential of the zinc oxochlorins is shifted to more positive potentials by approximately 240 mV compared with that of the zinc chlorin. Collectively, the fluorescence yields, excited-state lifetimes, oxidation potentials, and various spectral characteristics of the chlorin and oxochlorin building blocks provide the foundation for studies of photochemical processes in larger architectures based on these chromophores. DA - 2002/10/18/ PY - 2002/10/18/ DO - 10.1021/jo025843i VL - 67 IS - 21 SP - 7329-7342 SN - 0022-3263 ER - TY - JOUR TI - Single-Tube Nested PCR for Detection of Tritrichomonasfoetus in Feline Feces AU - Gookin, J. L. AU - Birkenheuer, A. J. AU - Breitschwerdt, E. B. AU - Levy, M. G. T2 - Journal of Clinical Microbiology AB - ABSTRACT Tritrichomonas foetus , a venereal pathogen of cattle, was recently identified as an inhabitant of the large intestine in young domestic cats with chronic diarrhea. Recognition of the infection in cats has been mired by unfamiliarity with T . foetus in cats as well as misdiagnosis of the organisms as Pentatrichomonas hominis or Giardia sp. when visualized by light microscopy. The diagnosis of T . foetus presently depends on the demonstration of live organisms by direct microscopic examination of fresh feces or by fecal culturing. As T . foetus organisms are fastidious and fragile, routine flotation techniques and delayed examination and refrigeration of feces are anticipated to preclude the diagnosis in numerous cases. The objective of this study was to develop a sensitive and specific PCR test for the diagnosis of feline T . foetus infection. A single-tube nested PCR was designed and optimized for the detection of T . foetus in feline feces by using a combination of novel (TFITS-F and TFITS-R) and previously described (TFR3 and TFR4) primers. The PCR is based on the amplification of a conserved portion of the T . foetus internal transcribed spacer (ITS) region (ITS1 and ITS2) and the 5.8S rRNA gene. The absolute detection limit of the single-tube nested PCR was 1 organism, while the practical detection limit was 10 organisms per 200 mg of feces. Specificity was examined by using P . hominis , Giardia lamblia, and feline genomic DNA. Our results demonstrate that the single-tube nested PCR is ideally suited for (i) diagnostic testing of feline fecal samples that are found negative by direct microscopy and culturing and (ii) definitive identification of microscopically observable or cultivated organisms. DA - 2002/11/1/ PY - 2002/11/1/ DO - 10.1128/JCM.40.11.4126-4130.2002 VL - 40 IS - 11 SP - 4126-4130 J2 - Journal of Clinical Microbiology LA - en OP - SN - 0095-1137 UR - http://dx.doi.org/10.1128/jcm.40.11.4126-4130.2002 DB - Crossref ER - TY - JOUR TI - Registration of 'NC Hulless' oat AU - Murphy, JP AU - Navarro, RA AU - Leath, S AU - Bowman, DT T2 - CROP SCIENCE AB - Crop ScienceVolume 42, Issue 1 p. 311-311 Registration of Cultivars Registration of ‘NC Hulless’ Oat J.P. Murphy, Corresponding Author J.P. Murphy njpm@unity.ncsu.edu Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695-7629Corresponding author (njpm@unity.ncsu.edu)Search for more papers by this authorR.A. Navarro, R.A. Navarro Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695-7629Search for more papers by this authorS. Leath, S. Leath USDA-ARS, Dep. of Plant Pathology, North Carolina State Univ., Raleigh, NC, 27695-7629Search for more papers by this authorD.T. Bowman, D.T. Bowman Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695-7629Search for more papers by this author J.P. Murphy, Corresponding Author J.P. Murphy njpm@unity.ncsu.edu Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695-7629Corresponding author (njpm@unity.ncsu.edu)Search for more papers by this authorR.A. Navarro, R.A. Navarro Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695-7629Search for more papers by this authorS. Leath, S. Leath USDA-ARS, Dep. of Plant Pathology, North Carolina State Univ., Raleigh, NC, 27695-7629Search for more papers by this authorD.T. Bowman, D.T. Bowman Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695-7629Search for more papers by this author First published: 01 January 2002 https://doi.org/10.2135/cropsci2002.3110 Research supported in part by grants from the North Carolina Small Grains Growers Association, Inc. and the USDA-ARS. Registration by CSSA. Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Volume42, Issue1January–February 2002Pages 311-311 RelatedInformation DA - 2002/// PY - 2002/// DO - 10.2135/cropsci2002.0311 VL - 42 IS - 1 SP - 311-311 SN - 0011-183X ER - TY - JOUR TI - Performance differences and genetic parameters for four coastal provenances of loblolly pine in the southeastern United States AU - Sierra-Lucero, V. AU - Mckeand, S. E. AU - Huber, D. A. AU - Rockwood, D. L. AU - White, T. L. T2 - Forest Science DA - 2002/// PY - 2002/// VL - 48 IS - 4 SP - 732-742 ER - TY - JOUR TI - Host DNA replication is induced by geminivirus infection of differentiated plant cells AU - Nagara, S AU - Hanley-Bowdoin, L AU - Robertson, D T2 - PLANT CELL AB - The geminivirus Tomato golden mosaic virus (TGMV) replicates in differentiated plant cells using host DNA synthesis machinery. We used 5-bromo-2-deoxyuridine (BrdU) incorporation to examine DNA synthesis directly in infected Nicotiana benthamiana plants to determine if viral reprogramming of host replication controls had an impact on host DNA replication. Immunoblot analysis revealed that up to 17-fold more BrdU was incorporated into chromosomal DNA of TGMV-infected versus mock-infected, similarly treated healthy leaves. Colocalization studies of viral DNA and BrdU demonstrated that BrdU incorporation was specific to infected cells and was associated with both host and viral DNA. TGMV and host DNA synthesis were inhibited differentially by aphidicolin but were equally sensitive to hydroxyurea. Short BrdU labeling times resulted in some infected cells showing punctate foci associated with host DNA. Longer periods showed BrdU label uniformly throughout host DNA, some of which showed condensed chromatin, only in infected nuclei. By contrast, BrdU associated with viral DNA was centralized and showed uniform, compartmentalized labeling. Our results demonstrate that chromosomal DNA is replicated in TGMV-infected cells. DA - 2002/12// PY - 2002/12// DO - 10.1105/tpc.005777 VL - 14 IS - 12 SP - 2995-3007 SN - 1040-4651 ER - TY - JOUR TI - Heterologous array analysis in Pinaceae: hybridization of Pinus taeda cDNA arrays with cDNA from needles and embryogenic cultures of P-taeda, P-sylvestris or Picea abies AU - Zyl, L AU - Arnold, S AU - Bozhkov, P AU - Chen, YZ AU - Egertsdotter, U AU - MacKay, J AU - Sederoff, RR AU - Shen, J AU - Zelena, L AU - Clapham, DH T2 - COMPARATIVE AND FUNCTIONAL GENOMICS AB - Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few conifer cDNA libraries have been sequenced. Because of the high level of sequence conservation between Pinus and Picea we have investigated the use of arrays from one genus for studies of gene expression in the other. The partial cDNAs from 384 identifiable genes expressed in differentiating xylem of Pinus taeda were printed on nylon membranes in randomized replicates. These were hybridized with labelled cDNA from needles or embryogenic cultures of Pinus taeda, P. sylvestris and Picea abies, and with labelled cDNA from leaves of Nicotiana tabacum. The Spearman correlation of gene expression for pairs of conifer species was high for needles (r(2) = 0.78 - 0.86), and somewhat lower for embryogenic cultures (r(2) = 0.68 - 0.83). The correlation of gene expression for tobacco leaves and needles of each of the three conifer species was lower but sufficiently high (r(2) = 0.52 - 0.63) to suggest that many partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous probing was further used to identify tissue-specific gene expression over species boundaries. To evaluate the significance of differences in gene expression, conventional parametric tests were compared with permutation tests after four methods of normalization. Permutation tests after Z-normalization provide the highest degree of discrimination but may enhance the probability of type I errors. It is concluded that arrays of cDNA from loblolly pine are useful for studies of gene expression in other pines or spruces. DA - 2002/8// PY - 2002/8// DO - 10.1002/cfg.199 VL - 3 IS - 4 SP - 306-318 SN - 1532-6268 KW - cDNA array KW - conifer KW - normalization KW - functional genomics KW - pine KW - spruce ER - TY - JOUR TI - Heterobilharzia americana infection in a dog AU - Flowers, , JR AU - Hammerberg, B AU - Wood, SL AU - Malarkey, DE AU - Dam, GJ AU - Levy, MG AU - McLawhorn, LD T2 - JOURNAL OF THE AMERICAN VETERINARY MEDICAL ASSOCIATION AB - A 7-year-old castrated male Golden Retriever cross was evaluated because of intermittent blood-tinged diarrhea, severe weight loss, anorexia, and lethargy of 2 months' duration; the dog was unresponsive to antimicrobial and standard anthelmintic treatment. Results of fecal flotations for parasite ova were negative. Alkaline phosphatase, aspartate aminotransferase, and alanine aminotransferase activities and total protein and globulin conentrations were greater than reference ranges. Biopsy specimens were obtained during laparotomy and examination revealed multiple granulomatous lesions with helminth ova nidi in the intestine, pancreas, liver, and mesenteric lymph node. Saline solution direct smear and saline solution sedimentation of feces yielded trematode ova that were morphologically consistent with Heterobilharzia americana. Identification was confirmed when miracidia were hatched from these ova and produced characteristic cercariae from infected snails. An antigen capture ELISA, typically used for the diagnosis of schistosomiasis in humans, was performed, and schistosome circulating anodic antigen was detected. Treatment with 30 mg of praziquantel/kg (14 mg/lb) of body weight stopped ova shedding, removed detectable circulating antigens, and caused the dog's body weight and attitude to return to normal. Although this is the first report of canine heterobilharziasis in North Carolina, it suggests that heterobilharziasis is underdiagnosed in dogs that have contact with water frequented by raccoons. Inappropriate diagnostic procedures can foil accurate detection of this parasitic disease. DA - 2002/1/15/ PY - 2002/1/15/ DO - 10.2460/javma.2002.220.193 VL - 220 IS - 2 SP - 193-196 SN - 0003-1488 ER - TY - JOUR TI - Efficient energy transfer and electron transfer in an artificial photosynthetic antenna-reaction center complex AU - Kodis, G AU - Liddell, PA AU - Garza, L AU - Clausen, PC AU - Lindsey, JS AU - Moore, AL AU - Moore, TA AU - Gust, D T2 - JOURNAL OF PHYSICAL CHEMISTRY A AB - A highly efficient functional mimic of a photosynthetic antenna−reaction center complex has been designed, synthesized, and studied spectroscopically. The antenna, consisting of four covalently linked zinc tetraarylporphyrins, (PZP)3−PZC, has been coupled to a free-base porphyrin−fullerene artificial photosynthetic reaction center, P−C60, to form a (PZP)3−PZC−P−C60 hexad. As revealed by time-resolved absorption and emission studies in 2-methyltetrahydrofuran solution at ambient temperature, excitation of a peripheral zinc porphyrin moiety is followed by singlet−singlet energy transfer to the central zinc porphyrin to give (PZP)3−1PZC−P−C60 with a time constant of 50 ps. The excitation is passed on to the free-base porphyrin in 32 ps to produce (PZP)3−PZC−1P−C60, which decays by electron transfer to the fullerene with a time constant of 25 ps. The resulting (PZP)3−PZC−P•+−C60•- charge-separated state is generated with a quantum yield of 0.98 based on light absorbed by the porphyrin antenna. Direct excitation of the free-base porphyrin moiety or the fullerene also generates this state with a yield near unity. Thermodynamically favorable migration of positive charge into the zinc porphyrin array transforms the initial state into a long-lived ((PZP)3−PZC)•+−P−C60•- charge-separated state with a time constant of 380 ps. The final charge-separated state, formed in high yield (∼0.90), decays to the ground state with a lifetime of 240 ns. In benzonitrile, the lifetime is 25 μs. A previous hexad, which differs from the current hexad solely in the nature of the free-base porphyrin, gave a charge-separated state with a lower yield (0.69) and a shorter lifetime (1.3 ns). The difference in performance is attributed to differences in electronic composition (a2u versus a1u HOMO), conformation, and oxidation potential (1.05 versus 0.84 V) between the meso-tetraarylporphyrin and the β-octaalkylporphyrin of the current and former hexads, respectively. These results can be explained on the basis of an understanding of factors that affect through-bond energy-transfer and electron-transfer processes. The results demonstrate that it is possible to design and prepare synthetic, porphyrin-based antenna−reaction center complexes that mimic the basic photochemical functions of natural photosynthetic light-harvesting antennas and reaction centers in simple, structurally well-defined constructs. DA - 2002/3/14/ PY - 2002/3/14/ DO - 10.1021/jp012133s VL - 106 IS - 10 SP - 2036-2048 SN - 1520-5215 ER - TY - JOUR TI - Effects of nursery characteristics on field survival and growth of loblolly pine rooted cuttings AU - Frampton, J. AU - Isik, F. AU - Goldfarb, B. T2 - Southern Journal of Applied Forestry DA - 2002/// PY - 2002/// VL - 26 IS - 4 SP - 207-213 ER - TY - JOUR TI - Diallel analysis of sweetpotatoes for resistance to sweetpotato virus disease AU - Mwanga, ROM AU - Yencho, CGC AU - Moyer, JW T2 - EUPHYTICA DA - 2002/// PY - 2002/// DO - 10.1023/A:1020828421757 VL - 128 IS - 2 SP - 237-248 SN - 0014-2336 KW - general combining ability KW - heritability KW - Ipomoea batatas KW - Sweetpotato chlorotic stunt virus KW - Sweetpotato feathery mottle virus KW - Sweetpotato virus disease ER - TY - JOUR TI - Design, synthesis, and characterization of prototypical multistate counters in three distinct architectures AU - Schweikart, KH AU - Malinovskii, VL AU - Diers, , JR AU - Yasseri, AA AU - Bocian, DF AU - Kuhr, WG AU - Lindsey, JS T2 - JOURNAL OF MATERIALS CHEMISTRY AB - The storage of multiple bits of information in distinct molecular oxidation states is anticipated to afford extraordinarily high memory densities. Among redox-active molecules, lanthanide porphyrinic triple-decker complexes are attractive candidates for such molecular information storage elements because they provide at least four cationic states over a modest potential range. Our approach toward a molecular multistate counter involves covalently linking two triple deckers with interleaving oxidation potentials to achieve a commensurate increase in the number of oxidation states within a single dyad. We report the design and synthesis of five dyads comprised of triple-decker complexes of the form (Pc)Ln(Pc)Ln(Por) or (Por1)Ln(Pc)Ln(Por2), where Pc = phthalocyaninato, Por = porphyrinato, and Ln = Ce or Eu. The dyads were prepared in a modular building-block fashion by Pd-mediated coupling of an iodophenyl-triple decker and an ethynylphenyl-triple decker. The different dyad architectures examined include a vertical architecture with one linker (V1), a horizontal architecture with one linker (H1), and a horizontal architecture with two linkers (H2). In each dyad, one or two S-acetylthiomethyl groups incorporated on the porphyrinic moiety of the triple decker enables attachment to an electroactive surface viain situ cleavage of the protected thiol linker(s). Three dyads (Dyad1–3) have the V1 architecture but different compositions of triple deckers; three dyads (Dyad3–5) have identical composition but different architectures (V1, H1, H2) for comparison of the properties in self-assembled monolayers (SAMs) on gold. The SAM of each dyad exhibits robust reversible electrochemical behavior; the redox waves are essentially the sum of the waves of the component triple deckers. In contrast, mixtures of the component triple decker monomers form poor quality SAMs with inferior electrochemical characteristics. Accordingly, all three dyad architectures are viable constructs for assembling a multistate counter. DA - 2002/// PY - 2002/// DO - 10.1039/b108520d VL - 12 IS - 4 SP - 808-828 SN - 0959-9428 ER - TY - JOUR TI - Use of vagal nerve stimulation as a treatment for refractory epilepsy in dogs AU - Munana, KR AU - Vitek, SM AU - Tarver, WB AU - Saito, M AU - Skeen, TM AU - Sharp, NJH AU - Olby, NJ AU - Haglund, MM T2 - JOURNAL OF THE AMERICAN VETERINARY MEDICAL ASSOCIATION AB - To evaluate safety and efficacy of vagal nerve stimulation in dogs with refractory epilepsy.Placebo-controlled, double-masked, crossover study.10 dogs with poorly controlled seizures.A programmable pacemaker-like device designed to deliver intermittent stimulation to the left cervical trunk of the vagus was surgically implanted in each dog. Dogs were assigned randomly to two 13-week test periods, 1 with nerve stimulation and 1 without nerve stimulation. Owners recorded data on seizure frequency, duration, and intensity, as well as adverse effects.No significant difference in seizure frequency, duration, or severity was detected between overall 13-week treatment and control periods. During the final 4 weeks of the treatment period, a significant decrease in mean seizure frequency (34.4%) was detected, compared with the control period. Complications included transient bradycardia, asystole, and apnea during intraoperative device testing, and seroma formation, subcutaneous migration of the generator, and transient Horner's syndrome during the 14-day period between surgery and suture removal. No adverse effects of stimulation were detected, and most owners were satisfied with the treatment.Vagal nerve stimulation is a potentially safe approach to seizure control that appears to be efficacious in certain dogs and should be considered a possible treatment option when antiepileptic medications are ineffective. DA - 2002/10/1/ PY - 2002/10/1/ DO - 10.2460/javma.2002.221.977 VL - 221 IS - 7 SP - 977-983 SN - 0003-1488 ER - TY - JOUR TI - The role of interferon regulatory factors in the cardiac response to viral infection AU - Sherry, B T2 - VIRAL IMMUNOLOGY AB - Reovirus-induced murine myocarditis provides an excellent model for the human disease. Cardiac tissue damage varies between reovirus strains, and is caused by a direct viral cytopathogenic effect. One determinant of virus-induced cardiac tissue damage is the cardiac interferon-beta (IFN-beta) response to viral infection. Nonmyocarditic reoviruses induce more IFN-beta and/or are more sensitive to the antiviral effects of IFN-beta in cardiac cells than myocarditis reoviruses. The roles of interferon regulatory factors (IRFs) in the cardiac response to viral infection are reviewed, and results suggest possible cardiac-specific variations in IRF-3 and IRF-1 function. In addition, data are presented indicating that the role of IRF-2 in regulation of IFN-beta expression is cell type-specific and differs between skeletal and cardiac muscle cells. Together, results suggest that the heart may provide a unique environment for IRF function, critical for protection against virus-induced cardiac damage. DA - 2002/// PY - 2002/// DO - 10.1089/088282402317340206 VL - 15 IS - 1 SP - 17-28 SN - 1557-8976 ER - TY - JOUR TI - Resistance to sweetpotato chlorotic stunt virus and sweetpotato feathery mottle virus is mediated by two separate recessive genes in sweetpotato AU - Mwanga, R. O. M. AU - Kriegner, A. AU - Cervantes-Flores, J. C. AU - Zhang, D. P. AU - Moyer, J. W. AU - Yencho, G. C. T2 - Journal of the American Society for Horticultural Science DA - 2002/// PY - 2002/// VL - 127 IS - 5 SP - 798-806 ER - TY - JOUR TI - Quantitative trait loci analysis of growth response to varying nitrogen sources in Arabidopsis thaliana AU - Rauh, BL AU - Basten, C AU - Buckler, ES T2 - THEORETICAL AND APPLIED GENETICS DA - 2002/4// PY - 2002/4// DO - 10.1007/s00122-001-0815-y VL - 104 IS - 5 SP - 743-750 SN - 0040-5752 KW - quantitative trait mapping KW - QTL x environment interaction KW - Arabidopsis KW - nitrogen utilization KW - roots ER - TY - JOUR TI - Probing electronic communication in covalently linked multiporphyrin arrays. A guide to the rational design of molecular photonic devices AU - Holten, D AU - Bocian, DF AU - Lindsey, JS T2 - ACCOUNTS OF CHEMICAL RESEARCH AB - Understanding electronic communication among the constituents in multicomponent macromolecular architectures is essential for the rational design of molecular devices for photonic, electronic, or optoelectronic applications. This Account describes studies aimed at understanding the mechanisms of electronic communication in porphyrin-based architectures that undergo excited-state energy migration and ground-state hole/electron hopping. Porphyrins are ideal building blocks for such constructs owing to their attractive and versatile physical properties and amenability to synthetic control. These properties have permitted the creation of covalently linked multiporphyrin arrays wherein the rates of excited-state energy migration and ground-state hole/electron hopping can be tuned over a wide range. DA - 2002/1// PY - 2002/1// DO - 10.1021/ar970264z VL - 35 IS - 1 SP - 57-69 SN - 1520-4898 ER - TY - JOUR TI - Phytophthora infestans populations from tomato and potato in North Carolina differ in genetic diversity and structure AU - Wangsomboondee, T AU - Groves, CT AU - Shoemaker, PB AU - Cubeta, MA AU - Ristaino, JB T2 - PHYTOPATHOLOGY AB - Phytophthora infestans causes a destructive disease on tomato and potato. In North Carolina (NC) potatoes are mostly grown in the east, whereas tomatoes are grown in the mountainous areas in the western part of the state. Five genotypes of P. infestans were identified from 93 and 157 isolates collected from tomato and potato over a 5 year period between 1993 and 1998. All isolates collected from potato in eastern NC were the US-8 genotype, whereas only a single isolate was the US-1 genotype. Tuber blight was found on immature daughter tubers in a single field in 1997, however infection on mature tubers was not observed. Within potato fields, a range of sensitivity to metalaxyl was observed among isolates but all were either intermediate or highly resistant to the fungicide. In contrast, isolates from tomatoes included previously reported US-7 and US-8 genotypes and two new genotypes called US-18 and US-19 (A2 mating type, allozyme genotype Gpi 100/100 and Pep 92/100). These genotypes had unique restriction fragment length polymorphism banding patterns, were sensitive to metalaxyl, and have not been reported elsewhere. All genotypes, with the exception of the US-1, were the Ia mitochondrial haplotype. Thus, isolates of P. infestans from tomato were more genetically diverse over time in NC than those from potato and include two new genotypes that are sensitive to metalaxyl. DA - 2002/11// PY - 2002/11// DO - 10.1094/PHYTO.2002.92.11.1189 VL - 92 IS - 11 SP - 1189-1195 SN - 0031-949X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0036827876&partnerID=MN8TOARS KW - epidemiology KW - Irish potato famine KW - population genetics ER - TY - JOUR TI - PCR-based single-strand conformation polymorphism (SSCP) analysis to clone nine aquaporin genes in cucumber AU - Xie, J. H. AU - Wehner, T. C. AU - Conkling, M. A. T2 - Journal of the American Society for Horticultural Science DA - 2002/// PY - 2002/// VL - 127 IS - 6 SP - 925-930 ER - TY - JOUR TI - Linking molecular insight and ecological research AU - Jackson, RB AU - Linder, CR AU - Lynch, M AU - Purugganan, M AU - Somerville, S AU - Thayer, SS T2 - TRENDS IN ECOLOGY & EVOLUTION AB - Significant environmental challenges, including the genetic and physiological effects of environmental pollutants, the rapid spread of diseases and invasive species, the release of transgenic organisms and global climate change, affect our daily lives and the sustainability of ecosystems. Managing these environmental problems will require new approaches that span the biology of genes, organisms, populations, communities and ecosystems. In parallel with these practical concerns is the basic need to study gene functions in their natural context. The Arabidopsis 2010 project, for example, seeks to understand the functions of all 25 000 Arabidopsis genes within a decade but, to do so, we must also understand the role of the environment in determining gene function. A new priority is evident – understanding the interplay of molecular mechanisms with organismal and ecosystem biology. Combining genomic and ecological research perspectives will answer crucial unresolved questions, but will require significant new multidisciplinary resources, infrastructure and training. DA - 2002/9// PY - 2002/9// DO - 10.1016/S0169-5347(02)02571-5 VL - 17 IS - 9 SP - 409-414 SN - 1872-8383 ER - TY - JOUR TI - Insulin-like growth factor-1 inscribes a gene expression profile for angiogenic factors and cancer progression in breast epithelial cells AU - Oh, J. S. AU - Kucab, J. E. AU - Bushel, P. R. AU - Martin, K. AU - Bennett, L. AU - Collins, J. AU - Diaugustine, R. P. AU - Barrett, J. C. AU - Afshari, C. A. AU - Dunn, S. E. T2 - Neoplasia DA - 2002/// PY - 2002/// DO - 10.1038/sj/neo/7900229 VL - 4 IS - 3 SP - 204-217 ER - TY - JOUR TI - Functional expression and cellular localization of cercosporin-resistance proteins fused with the GFP in Cercospora nicotianae AU - Chung, KR AU - Ehrenshaft, M AU - Daub, ME T2 - CURRENT GENETICS DA - 2002/6// PY - 2002/6// DO - 10.1007/s00294-002-0289-8 VL - 41 IS - 3 SP - 159-167 SN - 0172-8083 KW - photosensitizer KW - singlet oxygen KW - fungi KW - pyridoxine ER - TY - JOUR TI - Differential Top10 promoter regulation by six tetracycline analogues in plant cells AU - Love, J AU - Allen, GC AU - Gatz, C AU - Thompson, WF T2 - JOURNAL OF EXPERIMENTAL BOTANY AB - The effects of five tetracycline analogues, anhydrotetracycline, doxycycline, minocycline, oxytetracycline, and tetracycline, on Top10 promoter activity in NT1 tobacco tissue culture cells have been analysed. The concentration that repressed Top10 promoter activity, the level of transgene repression and the kinetics of transgene de‐repression were determined for each analogue, and could not be predicted from in vitro binding affinity to the tetracycline repressor or from comparison with animal cells. Doxycycline had the most potent effect on the Top10 promoter and completely inhibited transgene expression at 4 nmol l–1. Tetracycline was the most versatile of the analogues tested; tetracycline inhibited the Top10 promoter at 10 nmol l–1 and was easily washed out to restore Top10‐driven expression in 12–24 h. A study was also made of the suitability for plant research of a novel tetracycline analogue, GR33076X. In animal cells, GR33076X de‐repressed Top10 promoter activity in the presence of inhibitory concentrations of anhydrotetracycline. In NT1, it is shown that GR 33076X can antagonize repression of the Top10 promoter in the presence of tetracycline, but not of anhydrotetracycline or of doxycycline. Different tetracycline analogues can therefore be used to regulate the Top10 promoter in plant cells and this property may be exploited in planning an optimum course of transgene regulation. DA - 2002/9// PY - 2002/9// DO - 10.1093/jxb/erf050 VL - 53 IS - 376 SP - 1871-1877 SN - 1460-2431 KW - tetracycline analogues KW - tobacco KW - Top10 promoter activity KW - tissue culture ER - TY - JOUR TI - Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway AU - Olsen, K. M. AU - Womack, A. AU - Garrett, A. R. AU - Suddith, J. I. AU - Purugganan, M. D. T2 - Genetics DA - 2002/// PY - 2002/// VL - 160 IS - 4 SP - 1641-1650 ER - TY - JOUR TI - Consensus statement on ehrlichial disease of small animals from the infectious disease study group of the ACVIM AU - Neer, TM AU - Breitschwerdt, EB AU - Greene, RT AU - Lappin, MR T2 - JOURNAL OF VETERINARY INTERNAL MEDICINE AB - Within the past several decades, the number of Ehrlichia spp. recognized to infect cats, dogs, and human beings has expanded substantially. The recent application of advanced techniques in molecular biology has changed how ehrlichiosis is diagnosed and has provided new tools for the assessment of treatment. As these techniques are applied, the numerous questions that relate to the management of dogs and cats with ehrlichiosis ultimately will be answered. We hope this consensus statement will assist veterinarians in the management of their patients. DA - 2002/// PY - 2002/// DO - 10.1892/0891-6640(2002)016<0309:CSOEDO>2.3.CO;2 VL - 16 IS - 3 SP - 309-315 SN - 1939-1676 ER - TY - JOUR TI - Characterization of charge storage in redox-active self-assembled monolayers AU - Roth, KM AU - Lindsey, JS AU - Bocian, DF AU - Kuhr, WG T2 - LANGMUIR AB - Self-assembled monolayers (SAMs) of thiol-derivatized alkyl ferrocenes and Zn tetraarylporphyrins on a gold surface have been characterized under open circuit conditions using fluorescence imaging microscopy and a variety of electrochemical methods. The fluorescence of the neutral form of the Zn tetraarylporphyrin SAM and the electrode cell potential are monitored simultaneously after oxidation of the SAM and subsequent establishment of an open circuit condition. These experiments capitalize on the fact that the neutral Zn tetraarylporphyrin SAM is fluorescent whereas emission from the oxidized Zn tetraarylporphyrin SAM is quenched. Accordingly, the fluorescence recovery after disconnection from an oxidizing potential provides an independent measure of the change in oxidation state of the porphyrin SAM as a function of time after the cell is open-circuited. This measurement demonstrates that the porphyrin SAM remains oxidized for an extended period (hundreds of seconds) even though the electrochemical cell potential decays rapidly to the open circuit potential (OCP). Cyclic voltammetry was used to confirm the electrochemical properties of the redox SAMs and to determine the surface coverage of the redox-active molecules. A new method, designated open circuit potential amperometry, was used to read the charge of the oxidized SAM at the OCP after charging currents have decayed away. Additionally, open circuit potential voltammetry yields a sigmoidal response with a characteristic half-wave potential identical to that observed with cyclic voltammetry, indicative of a Nernstian process. Collectively, these studies show that the electrochemical cell discharges to the OCP quickly, that the SAM remains oxidized under these conditions, and that these methods can be used to quantitatively determine the amount of stored charge in the SAM. DA - 2002/5/14/ PY - 2002/5/14/ DO - 10.1021/la025525e VL - 18 IS - 10 SP - 4030-4040 SN - 0743-7463 ER - TY - JOUR TI - Capacitance and conductance characterization of ferrocene-containing self-assembled monolayers on silicon surfaces for memory applications AU - Li, QL AU - Mathur, G AU - Homsi, M AU - Surthi, S AU - Misra, V AU - Malinovskii, V AU - Schweikart, KH AU - Yu, LH AU - Lindsey, JS AU - Liu, ZM AU - Dabke, RB AU - Yasseri, A AU - Bocian, DF AU - Kuhr, WG T2 - APPLIED PHYSICS LETTERS AB - Self-assembled monolayers of 4-ferrocenylbenzyl alcohol attached to silicon provided the basis for electrolyte-molecule-silicon capacitors. Characterization by conventional capacitance and conductance techniques showed very high capacitance and conductance peaks near ∼0.6 V associated with charging and discharging of electrons into and from discrete levels in the monolayer owing to the presence of the redox-active ferrocenes. The reversible charge trapping of these molecules suggest their potential application in memory devices. Due to the molecular scalability and low-power operation, molecular-silicon hybrid devices may be strong candidates for next-generation electronic devices. DA - 2002/8/19/ PY - 2002/8/19/ DO - 10.1063/1.1500781 VL - 81 IS - 8 SP - 1494-1496 SN - 0003-6951 ER - TY - JOUR TI - A single domestication for maize shown by multilocus microsatellite genotyping AU - Matsuoka, Y AU - Vigouroux, Y AU - Goodman, MM AU - Sanchez, GJ AU - Buckler, E AU - Doebley, J T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of diversity in maize, several authors have proposed that maize landraces were the products of multiple independent domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, that challenge the multiple-origins hypothesis. Instead, our results indicate that all maize arose from a single domestication in southern Mexico about 9,000 years ago. Our analyses also indicate that the oldest surviving maize types are those of the Mexican highlands with maize spreading from this region over the Americas along two major paths. Our phylogenetic work is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. We also found only modest evidence for postdomestication gene flow from teosinte into maize. DA - 2002/4/30/ PY - 2002/4/30/ DO - 10.1073/pnas.052125199 VL - 99 IS - 9 SP - 6080-6084 SN - 0027-8424 ER - TY - JOUR TI - A geminivirus replication protein interacts with a protein kinase and a motor protein that display different expression patterns during plant development and infection AU - Kong, LJ AU - Hanley-Bowdoin, L T2 - PLANT CELL AB - The geminivirus protein AL1 initiates viral DNA replication, regulates its own expression, and induces plant gene transcription. To better understand how AL1 interacts with host proteins during these processes, we used yeast two-hybrid library screening and a baculovirus protein interaction system to identify plant proteins that interact with AL1. These studies identified a Ser/Thr kinase, a kinesin, and histone H3 as AL1 partners. The kinase is autophosphorylated and can phosphorylate common kinase substrates in vitro. The kinesin is phosphorylated in insect cells by a cyclin-dependent kinase. Immunostaining of Nicotiana benthamiana and Arabidopsis showed that kinase protein levels and subcellular location are regulated during plant development and geminivirus infection. By contrast, the kinesin is ubiquitous even though it is associated with the spindle apparatus in mitotic cells. Together, our results establish that AL1 interacts with host proteins involved in plant cell division and development. Possible functions of these host factors in healthy and geminivirus-infected plants are discussed. DA - 2002/8// PY - 2002/8// DO - 10.1105/tpc.003681 VL - 14 IS - 8 SP - 1817-1832 SN - 1532-298X ER - TY - JOUR TI - The Potato virus Y (MNR)-N-S Nlb-replicase is the elicitor of a veinal necrosis-hypersensitive response in root knot nematode resistant tobacco AU - Fellers, JP AU - Tremblay, D AU - Handest, MF AU - Lommel, SA T2 - MOLECULAR PLANT PATHOLOGY AB - Summary A root knot nematode resistance gene in Nicotiana tabacum , Rk , providing resistance to the nematode parasite Meloidogyne incognita is tightly linked to, or is a pleiotropic gene with a veinal necrosis systemic hypersensitive response to infection by Potato virus Y (PVY) M s N r . The single PVY M s N r open reading frame was sequenced and found to have 89% protein identity to PVY N. Individual PVY M s N r polypeptides were deduced and the corresponding cDNA were cloned into a Potato virus X (PVX) based expression vector and used as templates for in vitro transcriptions. Infected plant sap, from N. benthamiana inoculated with infectious RNA, was used to inoculate both root knot nematode (RKN) resistant and susceptible tobacco lines. Lines were then evaluated for the induction of the hypersensitive response. The PVY M s N r NIb‐replicase protein was found to induce a hypersensitive response 10 days post inoculation in nematode resistant tobacco. None of the other PVX/PVY M s N r constructs induced a hypersensitive response. The NIb‐replicase of PVY N, which shares 93% identity to PVY M s N r , did not induce a hypersensitive response when expressed from the PVX vector. This confirmed that the PVY M s N r NIb‐replicase is the elicitor of PVY M s N r veinal necrosis on RKN plants and thus the first report of a Potyvirus replicase functioning as an avirulence factor. DA - 2002/5// PY - 2002/5// DO - 10.1046/j.1364-3703.2002.00106.x VL - 3 IS - 3 SP - 145-152 SN - 1464-6722 ER - TY - JOUR TI - Sp3 represses gene expression via the titration of promoter-specific transcription factors AU - Kennett, SB AU - Moorefield, KS AU - Horowitz, JM T2 - JOURNAL OF BIOLOGICAL CHEMISTRY AB - We have determined previously that Sp3 encodes three distinct gene products as follows: a full-length protein (Sp3) that is an activator of transcription and two isoforms (M1 and M2) derived via internal translational initiation that function as transcriptional repressors. To identify amino acids and functions required for transcriptional repression, we employed PCR-directed mutagenesis to create a panel of mutated M2 proteins. Biochemical and functional analyses of these mutated proteins indicate that functions encoded by the M2 carboxyl terminus, such as DNA binding activity and the capacity to form multimeric complexes, are not required or sufficient for transcriptional repression. Instead, a 93-amino acid portion of the trans-activation domain was shown to be the minimal portion of M2 required to block Sp-dependent gene expression. Transcriptional analysis of three Sp-dependent promoters showed that mutations sustained by many M2 proteins result in promoter-specific effects. Regions of M2 required for physical interactions with five TATA box-associated factors (TAFIIs) were mapped, and mutations that disrupt the interaction of M2 with two of these proteins, TAFII70 and TAFII40, were identified. We conclude that Sp3- mediated transcriptional repression is due, at least in part, to competition for promoter-specific transcription factors. We have determined previously that Sp3 encodes three distinct gene products as follows: a full-length protein (Sp3) that is an activator of transcription and two isoforms (M1 and M2) derived via internal translational initiation that function as transcriptional repressors. To identify amino acids and functions required for transcriptional repression, we employed PCR-directed mutagenesis to create a panel of mutated M2 proteins. Biochemical and functional analyses of these mutated proteins indicate that functions encoded by the M2 carboxyl terminus, such as DNA binding activity and the capacity to form multimeric complexes, are not required or sufficient for transcriptional repression. Instead, a 93-amino acid portion of the trans-activation domain was shown to be the minimal portion of M2 required to block Sp-dependent gene expression. Transcriptional analysis of three Sp-dependent promoters showed that mutations sustained by many M2 proteins result in promoter-specific effects. Regions of M2 required for physical interactions with five TATA box-associated factors (TAFIIs) were mapped, and mutations that disrupt the interaction of M2 with two of these proteins, TAFII70 and TAFII40, were identified. We conclude that Sp3- mediated transcriptional repression is due, at least in part, to competition for promoter-specific transcription factors. TATA box-associated factors glutathione S-transferase dihydrofolate reductase hemagglutinin 6-(2-deoxy-β-d-ribofuranosyl)-3,4-dihydro-8H-pyrimido-[4,5-c][1,2]oxazin-7-one triphosphate Sp1 is the founding member of a family of five transcription factors, Sp1–5, that govern the expression of a wide variety of mammalian genes (for review, see Ref. 1Phillipsen S. Suske G. Nucleic Acids Res. 1991; 27: 2991-3000Crossref Scopus (537) Google Scholar). Sp1 encodes a ubiquitously expressed nuclear phosphoprotein that has been divided into five sub-domains based upon their respective functions (2Pascal E. Tjian R. Genes Dev. 1991; 5: 1646-1656Crossref PubMed Scopus (356) Google Scholar, 3Courey A.J. Tjian R. Cell. 1988; 55: 887-898Abstract Full Text PDF PubMed Scopus (1079) Google Scholar). The Sp1trans-activation domain is composed of three sub-domains termed A–C, each of which is capable of stimulating transcription if tethered to DNA via a DNA-binding domain. Sub-domains A and B are composed by serine- and threonine-rich regions as well as glutamine-rich regions. The glutamine-rich portions of A and B are believed to be required for trans-activation, whereas the function(s) of the serine/threonine-rich sub-regions is(are) less well understood. Domain C carries a number of charged amino acids and weakly stimulates transcription in the absence of domains A or B. Carboxyl-terminal to the domain C is a region featuring three Cys2-His2 zinc “fingers” required for sequence-specific DNA binding to GC-rich promoter elements. A carboxyl-terminal domain, termed D, facilitates protein multimerization and is essential for synergistic trans-activation of promoters with multiple Sp-binding sites. Sp1 associates with a large number of transcription-associated proteins, including components of the basal transcription complex (e.g.hTAFII130/dTAFII110 and hTAFII55; Refs. 4Chiang C.-M. Roeder R.G. Science. 1995; 267: 531-536Crossref PubMed Scopus (352) Google Scholar, 5Dynlacht B.D. Hoey T. Tjian R. Cell. 1991; 66: 563-576Abstract Full Text PDF PubMed Scopus (485) Google Scholar, 6Rojo-Niersbach E. Furukawa T. Tanese N. J. Biol. Chem. 2000; 274: 33778-33784Abstract Full Text Full Text PDF Scopus (31) Google Scholar, 7Gill G. Pascal E. Tseng Z.H. Tjian R. Proc. Natl. Acad. Sci. U. S. A. 1994; 91: 192-196Crossref PubMed Scopus (473) Google Scholar), sequence-specific DNA-binding proteins (e.g.E2F, YY1, p53, and AP-2; Refs. 8Pena P. Reutens A.T. Albanese C. D'Amico M. Watanabe G. Donner A. Shu I.W. Williams T. Pestell R.G. Mol. Endocrinol. 2001; 13: 1402-1416Crossref Scopus (49) Google Scholar, 9Lin S.-Y. Rhys Black A. Kostic D. Pajovic S. Hoover C.N. Azizkhan J.C. Mol. Cell. Biol. 1996; 16: 1668-1675Crossref PubMed Scopus (252) Google Scholar, 10Karlseder J. Rotheneder H. Wintersberger E. Mol. Cell. Biol. 1996; 16: 1659-1667Crossref PubMed Scopus (315) Google Scholar, 11Lee J.-S. Galvin K.M. Shi Y. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 6145-6149Crossref PubMed Scopus (276) Google Scholar, 12Gualberto A. Baldwin Jr., A.S. J. Biol. Chem. 1995; 270: 19680-19683Abstract Full Text Full Text PDF PubMed Scopus (96) Google Scholar, 13Seto E. Lewis B. Shenk T. Nature. 1993; 365: 462-464Crossref PubMed Scopus (249) Google Scholar), and transcriptional regulators (e.g. p107, HDAC-1, and VHL-1; Refs. 14Chang Y.-C. Illenye S. Heintz N.H. Mol. Cell. Biol. 2001; 21: 1121-1131Crossref PubMed Scopus (60) Google Scholar, 15Datta P.K. Raychaudhuri P. Bagchi S. Mol. Cell. Biol. 1995; 15: 5444-5452Crossref PubMed Scopus (91) Google Scholar, 16Mukhopadhyay D. Knebelmann B. Cohen H.T. Ananth S. Sukhatme V.P. Mol. Cell. Biol. 1997; 17: 5629-5639Crossref PubMed Scopus (309) Google Scholar, 17Venepally P. Waterman M.R. J. Biol. Chem. 1995; 270: 25402-25410Abstract Full Text Full Text PDF PubMed Scopus (84) Google Scholar, 18Daniel S. Kim K.-H. J. Biol. Chem. 1996; 271: 1385-1392Abstract Full Text Full Text PDF PubMed Scopus (102) Google Scholar). As might be expected given the variety of proteins with which it interacts, protein-binding sites have been identified throughout Sp1. For example, hTAFII130/dTAFII110 interact with Sp1 via itstrans-activation domain; hTAFII55 binds the Sp1 zinc fingers, and E2F requires the zinc finger and D sub-domains of Sp1 for protein-protein interactions. A wide variety of extracellular stimuli have been shown to induce gene expression via discrete promoter elements bound by Sp1 and Sp3 (17–29). Moreover, subtle mutations that negate the association of Sp1/Sp3 with their cognate binding sites completely block the induction of such genes by their respective inducing agents. Although GC-rich elements within the promoters of many Sp1/Sp3-regulated genes have been identified and their necessity for induced transcription has been noted, it remains largely unclear how extracellular stimuli activate Sp1/Sp3-dependent genes. For example, in most instances treatment of cells with inducing agents does not lead to consistent alterations in (i) the abundance or subcellular localization of Sp1/Sp3, (ii) the affinity of Sp1/Sp3 for DNA, (iii) the formation of Sp1/Sp3 multimers, nor (iv) the post-translational modification Sp1/Sp3. Instead, extracellular stimuli may activate Sp-dependent genes via alterations in protein-protein interactions. For example, transforming growth factor-β induces p15Ink4B transcription by catalyzing the formation of protein complexes between Sp1 and members of the Smad family of transcription factors (30Feng X.-H. Lin X. Derynck R. EMBO J. 2000; 19: 5178-5193Crossref PubMed Scopus (350) Google Scholar). Whether regulated interactions between Sp family members and other factors account for the induced transcription of additional Sp-dependent genes remains to be determined. Several years ago we identified two novel Sp3-derived proteins, termed M1 and M2, that arise by internal translational initiation within the region of Sp3 mRNA that encodes the Sp3 B domain (31Kennett S.B. Udvadia A.J. Horowitz J.M. Nucleic Acids Res. 1997; 25: 3110-3117Crossref PubMed Scopus (233) Google Scholar). Sp3, M1, and M2 appear to be expressed in all mammalian cells and tissues at approximately equivalent levels independent of growth status or induction by extracellular stimuli. In contrast to full-length Sp3, M1 and M2 function as potent repressors of Sp-mediated transcription, and Sp3 is at least 10-fold more sensitive to M1/M2-mediated repression than is Sp1. Given that Sp3 encodes proteins with opposing activities, we reasoned that understanding their differential regulation may shed light on mechanisms governing the activity of Sp-dependent promoters. To understand further the mechanism(s) by which M1/M2 repress transcription, we prepared a panel of M2 proteins carrying a limited number of random amino acid substitutions and examined their capacity to function as transcriptional regulators of three Sp-regulated promoters: DHFR, p21, andMDR-1. Additionally, we examined each of these mutated proteins for their capacity to bind DNA, to form multimeric complexes with Sp family members, and to bind components of the basal transcription complex. These studies have resulted in the following observations. 1) Random mutagenesis generated a panel of mutated M2 proteins that carry “loss-of-function” and “gain-of-function” mutations. 2) Many amino acid substitutions affect M2-mediated repression in a promoter-specific fashion. 3) DNA binding activity and the capacity to multimerize are not required or sufficient for M2-mediated repression. 4) The minimal region required for transcriptional repression by M2 consists of 93 amino acids of the B domain. 5) Several components of the TAFII complex bind Sp1, Sp3, and M2 in vitro. 6) The binding of two TAFII1 proteins, TAFII70 and TAFII40, is compromised in several M2 mutants. We conclude from these observations that M1/M2-mediated repression occurs at least in part via the titration of one or more transcription factors that may be required in a promoter-specific fashion. C-33A cells were obtained from the American Type Culture Collection (ATCC; Manassas, VA), and DrosophilaSchneider line-2 (SL2) cells were a gift of Dr. Cheaptip Benyajati (University of Rochester, Rochester, NY). C-33A and SL2 cells were cultured as described previously (31Kennett S.B. Udvadia A.J. Horowitz J.M. Nucleic Acids Res. 1997; 25: 3110-3117Crossref PubMed Scopus (233) Google Scholar, 32Udvadia A.J. Rogers K.T. Horowitz J.M. Cell Growth Differ. 1992; 3: 597-608PubMed Google Scholar, 33Udvadia A.J. Templeton D.J. Horowitz J.M. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 3953-3957Crossref PubMed Scopus (199) Google Scholar). Rabbit anti-Sp3 was prepared against a GST fusion protein containing the amino-terminal 300 amino acids of Sp3, and its preparation and characterization have been described (31Kennett S.B. Udvadia A.J. Horowitz J.M. Nucleic Acids Res. 1997; 25: 3110-3117Crossref PubMed Scopus (233) Google Scholar). Affinity-purified mouse anti-HA.11 antibody was obtained from a commercial supplier (Covance Research Products, Richmond, CA). pPacSp1 was obtained from Dr. Robert Tjian (University of California, Berkeley; see Ref. 3Courey A.J. Tjian R. Cell. 1988; 55: 887-898Abstract Full Text PDF PubMed Scopus (1079) Google Scholar). pPacSp3, pPacM1, pPacM2, pBSK-Sp3/flu, pCR-M1/flu, and pCR-M2/flu were prepared as described (31Kennett S.B. Udvadia A.J. Horowitz J.M. Nucleic Acids Res. 1997; 25: 3110-3117Crossref PubMed Scopus (233) Google Scholar, 33Udvadia A.J. Templeton D.J. Horowitz J.M. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 3953-3957Crossref PubMed Scopus (199) Google Scholar). Constructions employed for in vitro translation of human and DrosophilaTAFII proteins were obtained from Dr. Robert Tjian.DHFR-CAT has been described (34Swick A.G. Blake M.C. Kahn J.W. Azizkhan J.C. Nucleic Acids Res. 1989; 17: 9291-9304Crossref PubMed Scopus (91) Google Scholar). To generate aDHFR-luciferase construct, DHFR-CAT, 5′ (5′-GGAGATCTAGCGCGCGGCTGTACTAC-3′) and 3′ primers (5′-GGAAGCTTGCAGCCTGTACGCTGTGC-3′), and the PCR were employed to amplify DHFR promoter sequences. A resulting 175-bp promoter fragment was subcloned in plasmid pRL (Promega, Inc., Madison, WI). pgpLuc-B carries a 1320-bp portion of the human MDR-1promoter and was obtained from Dr. Kathleen Scotto (Memorial Sloan-Kettering Cancer Center, NY; see Ref. 35Ince T.A. Scotto K.W. J. Biol. Chem. 2001; 270: 30249-30252Abstract Full Text Full Text PDF Scopus (138) Google Scholar). p21P93-S carries a 44-bp portion of the human p21 promoter and was obtained from Dr. Xiao-Fan Wang (Duke University Medical Center; see Ref.19Datto M.B. Yu Y. Wang X.-F. J. Biol. Chem. 1995; 270: 28623-28628Abstract Full Text Full Text PDF PubMed Scopus (399) Google Scholar, 20Li J.-M. Nichols M.A. Changrasekharan S. Xiong Y. Wang X.-F. J. Biol. Chem. 1995; 270: 26750-26753Abstract Full Text Full Text PDF PubMed Scopus (231) Google Scholar, 21Biggs J.R. Kudlow J.E. Kraft A.S. J. Biol. Chem. 1996; 271: 901-906Abstract Full Text Full Text PDF PubMed Scopus (199) Google Scholar, 22Greenwel P. Inagaki Y. Hu W. Walsh M. Ramirez F. J. Biol. Chem. 1997; 272: 19738-19745Abstract Full Text Full Text PDF PubMed Scopus (173) Google Scholar). Mutagenesis of M2 was performed using methods described by Zaccolo et al. (44Zaccolo M. Williams D.M. Brown D.M. Gherardi E. J. Mol. Biol. 1996; 255: 589-603Crossref PubMed Scopus (275) Google Scholar). Reactions employed pGEX-M2 (see below) as template, 5′ (5′-CCTGACTTCATGTTGTATGAC-3′) and 3′ primers (5′-CAGTCACGATGAATTCTCGAGAATCCCTAGCTAGCGTAATCTG-3′), andTaq polymerase (Invitrogen). Three PCR cycles (92 °C for 1 min, 55 °C for 1 min, and 72 °C for 2 min) were performed in a 20-μl reaction containing 4 ng of linearized template, 0.5 μm primers, 500 μm each dNTP, and 500 μm dPTP (Amersham Biosciences). An aliquot of this reaction was subsequently employed as template for an additional 22 rounds of amplification in the absence of dPTP. PCR products were digested with DpnI, purified, and cloned in pCR-BluntII-TOPO. Expression plasmids carrying mutated M2 cDNAs were prepared by subcloning inserts from pCR-BluntII-TOPO into pPac (3Courey A.J. Tjian R. Cell. 1988; 55: 887-898Abstract Full Text PDF PubMed Scopus (1079) Google Scholar). Sequencing of M2 mutants was performed by the North Carolina State University sequencing facility using a PerkinElmer Life Sciences AB1377 sequenator or Sequenase version 2.0 DNA polymerase following a protocol supplied by the manufacturer (Amersham Biosciences). pGEX-Sp1, a bacterial expression construct that carries the Sp1 coding region fused in-frame with glutathione S-transferase (GST), has been described (36Murata Y. Kim H.G. Rogers K.T. Udvadia A.J. Horowitz J.M. J. Biol. Chem. 1994; 269: 20674-20681Abstract Full Text PDF PubMed Google Scholar). pGEX-M2 was prepared by subcloning the M2 cDNA carried by pCR-M2/flu in pGEX-2TK (Amersham Biosciences). GST-Sp3 was prepared using pBSK-Sp3/flu, 5′ (5′-GGGGGATCCGCCACCATGAATTCCGGGCCATCGCCG-3′), and 3′ primers (5′-GGAATTCCTCCATTGTCTCATTTCCAG-3′), and the PCR. A 2142-bp amplified fragment carrying the entire Sp3 cDNA was subcloned in pGEX-2TK. pGEX-FSH15 has been described previously (36Murata Y. Kim H.G. Rogers K.T. Udvadia A.J. Horowitz J.M. J. Biol. Chem. 1994; 269: 20674-20681Abstract Full Text PDF PubMed Google Scholar). To create GST expression plasmids carrying M2 cDNAs terminating at amino acids 103, 197, or 353, M2 cDNAs were amplified from pPacM2 using a 5′ primer (5′-GGGGGATCCATGGATAGTTCAGACAATTCA-3′), one of three 3′ primers (5′-CTACTAGACTCCTTGAAGTTG-3′, 5′-CTAACCAAGTGTGAGGGTTTC-3′, or 5′-TCAGTTAACAAACAAAAGGGCG-3′), and Taq polymerase. Amplified M2 cDNAs carrying premature termination codons were subcloned in pGEX-2TK. Mutated M2 GST fusion proteins were prepared by amplification from pPacM2 plasmids using 5′ (5′-GGGGGATCCATGGATAGTTCAGACAATTCA-3′) and 3′ primers (5′-GGAATTCCTCCATTGTCTCATTTCCAG-3′) andTaq polymerase. Amplified cDNAs were subcloned in pGEX-2TK. Baculovirus stocks encoding Sp1, Sp3, M1, and M2 were prepared using the PCR, appropriate primers, and pCMV4-Sp1/flu (37Udvadia A.J. Rogers K.T. Higgins P.D.R. Murata Y. Martin K.H. Humphrey P.A. Horowitz J.M. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 3265-3269Crossref PubMed Scopus (187) Google Scholar), pBSK-Sp3/flu, pCR-M1/flu, and pCR-M2/flu as substrates. Amplified cDNAs were subcloned in pFASTBacHTA and used to prepare virus stocks according to methods supplied by the manufacturer (Invitrogen). Transient transfections for transcription assays were performed by calcium phosphate precipitation as described (31Kennett S.B. Udvadia A.J. Horowitz J.M. Nucleic Acids Res. 1997; 25: 3110-3117Crossref PubMed Scopus (233) Google Scholar, 33Udvadia A.J. Templeton D.J. Horowitz J.M. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 3953-3957Crossref PubMed Scopus (199) Google Scholar). Cell extracts were prepared for analysis 48 h after transfection. The Dual-Luciferase Reporter Assay System (Promega, Inc.) was employed to quantify luciferase activity precisely as recommended by the manufacturer. Luminescence was detected in a Lumat LB 9507 luminometer (EG & G Berthold, Bad Wildbad, Germany), and results were normalized against total cell protein concentration. To prepare Drosophila SL2 extracts for Western blotting or protein/DNA binding assays, transient transfections were performed using SuperFect Transfection Reagent (Qiagen Inc., Hilden, Germany). Cell extracts were prepared 48 h after transfection. Nuclear extracts were prepared using methods described by Lee et al. (38Lee K.A. Bindereif A. Green M.R. Gene Anal. Tech. 1988; 5: 22-31Crossref PubMed Scopus (394) Google Scholar). Oligonucleotides were synthesized on an automated DNA synthesizer, deprotected, and partially purified through Sephadex G-25 spin columns. Radiolabeled probes for standard protein/DNA binding assays were prepared from the following oligonucleotides and their complements: GT box (39Kingsley C. Winoto A. Mol. Cell. Biol. 1992; 12: 4251-4261Crossref PubMed Scopus (490) Google Scholar), 5′-AGCTTCCGTTGGGGTGTGGCTTCACGTCGA-3′; p21 (19Datto M.B. Yu Y. Wang X.-F. J. Biol. Chem. 1995; 270: 28623-28628Abstract Full Text Full Text PDF PubMed Scopus (399) Google Scholar), 5′-GAGCCGGGGTCCCGCCTCCTTGAGGCGGGCCC-3′; and MDR-1 (35Ince T.A. Scotto K.W. J. Biol. Chem. 2001; 270: 30249-30252Abstract Full Text Full Text PDF Scopus (138) Google Scholar), 5′-CAGGAACAGCGCCGGGGCGTGGGCTAGC-3′. For quantitative protein/DNA binding assays, six double-stranded 60-mers were synthesized each carrying a single promoter-derived Sp-binding site flanked by common nucleotide sequences. The promoter-derived sequences utilized for these experiments are as follows: p21, 5′-CCCGCCTCCT-3′; MDR-1, 5′-CGCCGGGGCGTGGGC-3′; DHFR-1, 5′-AGGGCGTGGC-3′; DHFR-2, 5′-GAGGCGGGGC-3′; DHFR-3, 5′-GAGGCGGAGT-3′; and DHFR-4, 5′-TGGGCGGGGC-3′. Annealed and complementary oligonucleotides were radiolabeled and purified as described previously (31Kennett S.B. Udvadia A.J. Horowitz J.M. Nucleic Acids Res. 1997; 25: 3110-3117Crossref PubMed Scopus (233) Google Scholar, 32Udvadia A.J. Rogers K.T. Horowitz J.M. Cell Growth Differ. 1992; 3: 597-608PubMed Google Scholar). Protein/DNA binding assays were performed as described previously (31Kennett S.B. Udvadia A.J. Horowitz J.M. Nucleic Acids Res. 1997; 25: 3110-3117Crossref PubMed Scopus (233) Google Scholar, 32Udvadia A.J. Rogers K.T. Horowitz J.M. Cell Growth Differ. 1992; 3: 597-608PubMed Google Scholar), and complexes were visualized by autoradiography. For quantitative protein/DNA binding assays, whole cell protein extracts prepared from baculovirus-infected Sf9 cells were incubated with a radiolabeled probe derived from the c-fos gene (5′-CCCTTGCGCCACCCCTCT-3′; see Ref. 32Udvadia A.J. Rogers K.T. Horowitz J.M. Cell Growth Differ. 1992; 3: 597-608PubMed Google Scholar), and the resulting protein-DNA complexes were quantified in situ using an InstantImager (Packard Instrument Co.). Volumes of these extracts that led to half-maximal binding of this probe were then employed in assays performed in triplicate with Sp-binding sites derived from theDHFR, p21, and MDR-1 genes and quantified in situ. Whole cell or nuclear extracts were resolved on denaturing polyacrylamide gels and transferred to nitrocellulose using a semi-dry transfer apparatus. Nitrocellulose filters were incubated with 5% milk in TBS-T (2.42 g/liter Tris, 8 g/liter NaCl, pH 7.6, 1 ml/liter Tween 20) from 1 h to overnight. Primary antibodies were diluted in TBS-T (anti-Sp3 at 1:2000 and anti-HA.11 at 1:1000), incubated with filters for 1 h at room temperature, and washed with TBS-T. Filters were incubated with horseradish peroxidase-conjugated secondary antibodies diluted in TBS-T (anti-mouse, 1:10,000, Amersham Biosciences, or anti-rabbit, 1:40,000, Invitrogen) for 1 h at room temperature with gentle agitation and washed in TBS-T, and antigen-antibody complexes were detected using ECL Western blotting Detection Reagents (Amersham Biosciences). In vitro transcribed/translated proteins were produced using a coupled reticulocyte lysate system (TNT; Promega, Inc.) with T3 or T7 RNA polymerase and l-[35S]methionine (Tran35S-label; ICN). pBSK-Sp1/flu, pBSK-Sp3/flu, pCR-M2/flu, PCR-amplified mutated M2 cDNAs, and TAFIIconstructs were employed as templates for these reactions. Mutated M2 cDNAs in pPac were amplified and prepared for in vitrotranscription/translation using a 5′ T7 promoter-containing primer, a 3′ primer, and the PCR. Protein binding assays were performed as described (40Sterner J.M. Dew-Knight S. Musahl C. Kornbluth S. Horowitz J.M. Mol. Cell. Biol. 1998; 18: 2748-2757Crossref PubMed Scopus (165) Google Scholar). GST bead-bound proteins were resolved on denaturing polyacrylamide gels and visualized by autoradiography. We have shown previously that Sp1 and Sp3 stimulate transcription of theDHFR promoter and that Sp1/Sp3-mediated transcription is repressed by two isoforms of Sp3, termed M1 and M2, that arise via internal translational initiation (31Kennett S.B. Udvadia A.J. Horowitz J.M. Nucleic Acids Res. 1997; 25: 3110-3117Crossref PubMed Scopus (233) Google Scholar, 33Udvadia A.J. Templeton D.J. Horowitz J.M. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 3953-3957Crossref PubMed Scopus (199) Google Scholar, 37Udvadia A.J. Rogers K.T. Higgins P.D.R. Murata Y. Martin K.H. Humphrey P.A. Horowitz J.M. Proc. Natl. Acad. Sci. U. S. A. 1993; 90: 3265-3269Crossref PubMed Scopus (187) Google Scholar). To determine whether these results were likely to reflect a general mechanism of transcriptional regulation, we extended our analyses to thep21 and MDR-1 promoters, two well characterized Sp-dependent promoters of physiologic and therapeutic interest. The p21-luciferase construct employed in these studies includes an Sp protein-binding site that is required for transcriptional stimulation by transforming growth factor-β, calcium, or sodium butyrate, as well as a second Sp protein-binding site that is also required for induction by sodium butyrate (19Datto M.B. Yu Y. Wang X.-F. J. Biol. Chem. 1995; 270: 28623-28628Abstract Full Text Full Text PDF PubMed Scopus (399) Google Scholar, 23Nakano K. Mizuno T. Sowa Y. Orita T. Yoshino T. Okuyama Y. Fujita T. Ohtani-Fujita N. Matsukawa Y. Tokino T. Yamagishi H. Oka T. Nomura H. Sakai T. J. Biol. Chem. 1997; 272: 22199-22206Abstract Full Text Full Text PDF PubMed Scopus (372) Google Scholar, 24Discher D.J. Bishopric N.H. Wu X. Peterson C.A. Webster K.A. J. Biol. Chem. 1998; 273: 26087-26093Abstract Full Text Full Text PDF PubMed Scopus (150) Google Scholar, 25Yan G.-Z. Ziff E.B. J. Neurosci. 1997; 17: 6122-6132Crossref PubMed Google Scholar, 26Finkenzeller G. Sparacio A. Technau A. Marme D. Siemeister G. Oncogene. 1997; 15: 669-676Crossref PubMed Scopus (187) Google Scholar, 27Lin M.-C. Almus-Jacobs F. Chen H.-H. Parry G.C.N. Mackman N. Shyy J.Y.J. Chien S. J. Clin. Invest. 1997; 99: 737-744Crossref PubMed Scopus (210) Google Scholar, 28Sohm F. Gaiddon C. Antoine M. Boutillier A.-L. Loeffler J.-P. Oncogene. 1999; 18: 2762-2769Crossref PubMed Scopus (31) Google Scholar, 29Mortensen E.R. Marks P.A. Shiotani A. Merchant J.L. J. Biol. Chem. 1997; 272: 16540-16547Abstract Full Text Full Text PDF PubMed Scopus (52) Google Scholar, 41Prowse D.M. Bolgan L. Dotto G.P. J. Biol. Chem. 2001; 272: 1308-1314Abstract Full Text Full Text PDF Scopus (125) Google Scholar). TheMDR-1-luciferase construct employed includes an Sp protein-binding site that is required for induction by serum or the c-Raf kinase (42Cornwell M.M. Smith D.E. J. Biol. Chem. 1993; 268: 15347-15350Abstract Full Text PDF PubMed Google Scholar, 43Miltenberger R.J. Cortner J. Farnham P.J. J. Biol. Chem. 1993; 268: 15674-15680Abstract Full Text PDF PubMed Google Scholar). As illustrated in Fig. 1 A, the ectopic expression of Sp3 in Drosophila SL2 cells stimulated transcription of the DHFR, p21, andMDR-1 promoters to varying degrees. p21transcription was stimulated 40-fold more effectively thanMDR-1 and 12-fold more than the DHFR promoter. Analogous results were obtained for activation of each of these promoters by Sp1 (data not shown). Consistent with results reported previously for the DHFR promoter, co-expression of M1 or M2 with Sp1 or Sp3 resulted in repression of p21 andMDR-1 transcription (Fig. 1 B and data not shown). Interestingly, the sensitivity of each promoter to M1/M2-mediated repression was noted to be promoter-specific. The promoter most acutely sensitive to activation by Sp1/Sp3, p21, exhibited the least sensitivity to M1/M2-mediated repression. In turn, a promoter that is only modestly activated by Sp1/Sp3, MDR-1, exhibited the greatest sensitivity to M1/M2-mediated repression. Sensitivity ofDHFR to Sp-mediated activation and repression was noted to fall between these two extremes. Given the results presented in Fig. 1, we conclude that intrinsic differences between Sp-dependent promoters influence the degrees to which they are activated by Sp1/Sp3 and repressed by M1/M2. Because Sp proteins activated and repressed the DHFR, p21, and MDR-1to varying degrees, we wished to determine whether these effects might be accounted for by inherent differences in their capacity to bind DNA. For example, the relative sensitivity of p21 to Sp3-mediated transcription and insensitivity to M2-mediated repression might be explained if Sp3 and M2 bind the p21 promoter with substantially different affinities. To address this issue, we performed a series of quantitative protein/DNA binding assays using radiolabeled DNA probes carrying Sp-binding sites from the DHFR,p21, and MDR-1 promoters. Recombinant baculovirus stocks encoding Sp1, Sp3, M1, or M2 proteins were prepared; Sf9 cells were infected with these viruses, and protein extracts from infected cells were normalized for DNA binding activity using a well characterized Sp protein-binding site derived from the mouse c-fos promoter. The volume of each protein extract that bound 50% of the c-fos probe was then employed in protein/DNA binding assays with six Sp protein-binding sites derived from the DHFR, p21, and MDR-1promoters. Each assay was performed in triplicate and quantitatedin situ. As shown in Table I, Sp proteins bound to each probe, and the capacity of a given Sp protein to bind these DNAs varied over a 3-fold range. Interestingly, little correlation was noted between the relative capacity of Sp proteins to bind these DNAs in vitro and the efficiencies with which they activate or repress transcription in vivo. For example, Sp1 and Sp3 bound the Sp-binding site derived from the MDR-1promoter more efficiently than a site derived from the p21promoter, yet MDR-1 is activated significantly less efficiently by both proteins in vivo. Similarly, Sp protein-binding sites derived from all three promoters were bound equivalently by M2, yet their sensitivity to M2-mediated repression varies over a 13-fold range in vivo. We conclude from these studies that the relative capacity of Sp proteins to stimulate or repress transcription is not directly correlated with the efficiency with which they interact with their cognate promoter binding sitesin vitro.Table IRelative binding of recombinant Sp proteins to oligonucleotides carrying Sp-binding sites derived from three Sp-dependent promotersSp proteinPromoterp21MDR-1DHFRDHFR-1DHFR-2DHFR-3DHFR-4Sp112.52.21.813.0Sp311.22.51.91.23.0M111.51.71.20.62.1M211110.51.4Protein extracts were prepared from Sf9 cells infected with baculovirus stocks encoding Sp family members, and the volume of each extract required to bind 50% of a radiolabeled oligonucleotide probe derived from the c-fos promoter was determined. This volume of cell extract was later employed in protein/DNA binding assays with oligonucleotides derived from the DHFR, p21, andMDR-1 promoters. Binding assays were performed in triplicate and quantified in situ. DNA binding activities for each protein were normalized to the amount of binding activity detected for each protein on the p21 oligonucleotide. Open table in a new tab Protein extracts were prepared from Sf9 cells infected with b DA - 2002/3/22/ PY - 2002/3/22/ DO - 10.1074/jbc.M108661200 VL - 277 IS - 12 SP - 9780-9789 SN - 0021-9258 ER - TY - JOUR TI - Plant molecular diversity and applications to genomics AU - Buckler, ES AU - Thornsberry, JM T2 - CURRENT OPINION IN PLANT BIOLOGY AB - Surveys of nucleotide diversity are beginning to show how genomes have been shaped by evolution. Nucleotide diversity is also being used to discover the function of genes through the mapping of quantitative trait loci (QTL) in structured populations, the positional cloning of strong QTL, and association mapping. DA - 2002/4// PY - 2002/4// DO - 10.1016/S1369-5266(02)00238-8 VL - 5 IS - 2 SP - 107-111 SN - 1879-0356 ER - TY - JOUR TI - Conservation and synteny of SSR loci and QTLs for vegetative propagation in four Eucalyptus species AU - Marques, CM AU - Brondani, RPV AU - Grattapaglia, D AU - Sederoff, R T2 - THEORETICAL AND APPLIED GENETICS DA - 2002/8// PY - 2002/8// DO - 10.1007/s00122-002-0899-z VL - 105 IS - 2-3 SP - 474-478 SN - 0040-5752 KW - SSR KW - mapping KW - QTLs KW - eucalyptus KW - synteny ER - TY - JOUR TI - Association of single-nucleotide polymorphisms at the Delta locus with genotype by environment interaction for sensory bristle number in Drosophila melanogaster AU - Geiger-Thornsberry, GL AU - Mackay, TFC T2 - GENETICS RESEARCH AB - The nature of forces maintaining variation for quantitative traits can only be assessed at the level of individual genes affecting variation in the traits. Identification of single-nucleotide polymorphisms (SNPs) associated with variation in Drosophila sensory bristle number at the Delta (Dl) locus provides us with the opportunity to test a model for the maintenance of variation in bristle number by genotype by environment interaction (GEI). Under this model, genetic variation is maintained at a locus under stabilizing selection if phenotypic values of heterozygotes are more stable than homozygotes across a range of environments, and the mean allelic effect is much smaller than the standard deviation of allelic effects across environments. Homozygotes and heterozygotes for two SNPs at Dl, one affecting sternopleural and the other abdominal bristle number, were reared in five different environments. There was significant GEI for both bristle traits. Neither condition of the model was satisfied for Dl SNPs exhibiting GEI for sternopleural bristle number. Heterozygotes for the abdominal bristle number SNPs were indeed the most stable genotype for two of the three environment pairs exhibiting GEI, but the mean genotypic effect was greater than the standard deviation of effects across environments. Therefore, this mechanism of GEI seems unlikely to be responsible for maintaining the common bristle number polymorphisms at Dl. DA - 2002/6// PY - 2002/6// DO - 10.1017/S0016672302005621 VL - 79 IS - 3 SP - 211-218 SN - 1469-5073 ER - TY - JOUR TI - Synthesis and properties of weakly coupled dendrimeric multiporphyrin light-harvesting arrays and hole-storage reservoirs AU - Benites, M. D. AU - Johnson, T. E. AU - Weghorn, S. AU - Yu, L. H. AU - Rao, P. D. AU - Diers, J. R. AU - Yang, S. I. AU - Kirmaier, C. AU - Bocian, D. F. AU - Holten, D. AU - Lindsey, J. S. T2 - Journal of Materials Chemistry DA - 2002/// PY - 2002/// VL - 12 IS - 1 SP - 65-80 ER - TY - JOUR TI - Interleukin 4-producing CD4+ T cells in the skin of cats with allergic dermatitis AU - Roosje, PJ AU - Dean, GA AU - Willemse, T AU - Rutten, VPMG AU - Thepen, T T2 - VETERINARY PATHOLOGY AB - Lesional skin of cats with allergic dermatitis has a cellular infiltrate and a CD4/CD8 ratio comparable to that in humans with atopic dermatitis. CD4+ helper T cells and in particular cells belonging to the Th2 subset play an important role in disease pathogenesis in humans. We investigated the cytokine pattern of CD4+ T cells in situ, with special emphasis on the putative presence of cells producing interleukin 4 (IL4), in cats with allergic dermatitis. Immunohistochemical procedures were used to determine that CD4+ T cells in lesional and nonlesional skin of cats with allergic dermatitis can produce IL4, as occurs in humans. Lesional and nonlesional skin of cats with allergic dermatitis had significantly more IL4+ T cells (P = 0.001) than did skin of healthy control cats. Double staining indicated that all IL4+ cells were positive for pan-T or CD4 markers. Double labeling for mast cell chymase and IL4 stained primarily different cells. Western blotting demonstrated cross-reactivity between the antibody against human IL4 and a feline recombinant IL4. These results indicate that IL4 is primarily produced by CD4+ T cells and is also present in clinically uninvolved skin, indicating a role in the pathogenesis of allergic dermatitis in cats. DA - 2002/3// PY - 2002/3// DO - 10.1354/vp.39-2-228 VL - 39 IS - 2 SP - 228-233 SN - 1544-2217 KW - allergic dermatitis KW - cats KW - CD4 KW - chymase KW - immunohistochemistry KW - interleukin 4 KW - PCR KW - skin KW - T cells KW - western blotting ER - TY - JOUR TI - RNAML: A standard syntax for exchanging RNA information AU - Waugh, A AU - Gendron, P AU - Altman, R AU - Brown, JW AU - Case, D AU - Gautheret, D AU - Harvey, SC AU - Leontis, N AU - Westbrook, J AU - Westhof, E AU - Zuker, M AU - Major, F T2 - RNA AB - Analyzing a single data set using multiple RNA informatics programs often requires a file format conversion between each pair of programs, significantly hampering productivity. To facilitate the interoperation of these programs, we propose a syntax to exchange basic RNA molecular information. This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures. The syntax permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. A class-oriented approach allows us to represent data common to a given set of RNA molecules, such as a sequence alignment and a consensus secondary structure. Documentation about experiments and computations, as well as references to journals and external databases, are included in the syntax. The chief challenge in creating such a syntax was to determine the appropriate scope of usage and to ensure extensibility as new needs will arise. The syntax complies with the eXtensible Markup Language (XML) recommendations, a widely accepted standard for syntax specifications. In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation. DA - 2002/6// PY - 2002/6// DO - 10.1017/S1355838202028017 VL - 8 IS - 6 SP - 707-717 SN - 1469-9001 KW - data storage KW - file format KW - knowledge representation KW - XML ER - TY - JOUR TI - Impaired olfactory behavior in mice deficient in the a subunit of G(0) AU - Luo, AH AU - Cannon, EH AU - Wekesa, KS AU - Lyman, RF AU - Vandenbergh, JG AU - Anholt, RRH T2 - BRAIN RESEARCH AB - The ability to respond to chemical signals is essential for the survival and reproduction of most organisms. Olfactory signaling involves odorant receptor-mediated activation of G(olf), a homologue of G(s), on the dendrites of olfactory neurons. Olfactory receptor cells, however, also express Galpha(i2) and Galpha(o) on their axons, with all neurons expressing G(o) and a subset G(i2). Despite their abundance, possible contributions of G(o) and G(i2) to chemoreception remain unexplored. We investigated whether homologous recombinant mice deficient in the alpha subunit of G(o) are able to respond to odorants, whether possible olfactory impairments are dependent on genetic background, and whether formation of glomeruli in their olfactory bulbs is compromised. In an olfactory habituation/dishabituation test, G(o)-/- mice were unresponsive when exposed to odorants. Analysis of variance shows that performance of G(o)+/- mice crossed into the CD-1 background is also diminished in this test compared to their G(o)+/+ counterparts. Following food deprivation, G(o)-/- mice in the 129 Sv-ter/C57BL/6 genetic background were unable to locate a buried food pellet until they were approximately 10 weeks of age after which they performed as well as their litter mate controls. However, CD-1 G(o)-/- mice could locate a buried food pellet even when tested immediately after weaning. Despite their compromised olfactory responsiveness, histological examination did not reveal gross alterations in the olfactory bulbs of G(o)-/- mice. Thus, Galpha(o) is necessary for the expression of olfactory behavior under normal conditions and dependent on genetic background, but is not essential for the formation and maintenance of glomeruli. DA - 2002/6/21/ PY - 2002/6/21/ DO - 10.1016/S0006-8993(02)02566-0 VL - 941 IS - 1-2 SP - 62-71 SN - 0006-8993 KW - G protein KW - knock-out mouse KW - olfaction KW - chemoreception KW - behavioral genetics KW - olfactory bulb ER - TY - JOUR TI - Imaging of Pheochromocytoma in 2 dogs using p-[18F] Fluorobenzylguanidine AU - Berry, Clifford R. AU - Degrado, Timothy R. AU - Nutter, Felicia AU - Garg, Pradeep K. AU - Breitschwerdt, Edward B. AU - Spaulding, Kathy AU - Concannon, Kevin D. AU - Zalutsky, Michael R. AU - Edward Coleman, R. T2 - Veterinary Radiology and Ultrasound AB - p-[18F]Fluorobenzylguanidine ([18F]PFBG) is a norepinephrine analog that has been developed as a positron emission tomography (PET) imaging radiopharmaceutical. Myocardial sympathetic innervation, neuroendocrine structures, and tumors can be noninvasively imaged with [18F]PFBG. In this study, the uptake characteristics of [18F]PFBG were investigated in 2 dogs with a spontaneous pheochromocytoma. The extent of the pheochromocytoma was well documented in both dogs on the PET study. The standardized uptake values within the pheochromocytomas were greater than 25 by 10 min, and were 37 and 50 by 45 min in each dog. A third dog that was suspected to have an adrenal mass was also studied. In this dog, the [18F]PFBG study was normal. Surgical exploration and adrenal biopsy confirmed the [15F]PFBG imaging findings in both dogs. In each dog, there was rapid blood-pool clearance (within 10 min after intravenous administration of the [18F]PFBG), with high uptake specific within the myocardium and adrenal medulla. The results indicate that [18F]PFBG may be useful for imaging canine pheochromocytomas and aid in differentiating adrenal masses. DA - 2002/3// PY - 2002/3// DO - 10.1111/j.1740-8261.2002.tb01667.x VL - 43 IS - 2 SP - 183–186 SN - 1058-8183 1740-8261 UR - http://dx.doi.org/10.1111/j.1740-8261.2002.tb01667.x KW - canine KW - p-[F-18]fluorobenzylguanidine KW - pheochromocytoma ER - TY - JOUR TI - Glaser-mediated synthesis and photophysical characterization of diphenylbutadiyne-linked porphyrin dyads AU - Youngblood, WJ AU - Gryko, DT AU - Lammi, RK AU - Bocian, DF AU - Holten, D AU - Lindsey, JS T2 - JOURNAL OF ORGANIC CHEMISTRY AB - The Pd-mediated Glaser coupling of a zinc monoethynyl porphyrin and a magnesium monoethynyl porphyrin affords a mixture of three 4,4‘-diphenylbutadiyne-linked dyads comprised of two zinc porphyrins (Zn-pbp-Zn), two magnesium porphyrins (Mg-pbp-Mg), and one metalloporphyrin of each type (Zn-pbp-Mg). The latter is easily isolated due to the greater polarity of the magnesium versus the zinc chelate. Exposure of Zn-pbp-Mg to silica gel results in selective demetalation, affording Zn-pbp-Fb where Fb = free base porphyrin. This synthesis route employs the magnesium porphyrin as a latent form of the Fb porphyrin, thereby avoiding copper insertion during the Glaser reaction, and as a polar entity facilitating separation. The absorption spectrum of Zn-pbp-Mg or Zn-pbp-Fb is the sum of the spectra of the component parts, while in each case the fluorescence spectrum upon illumination of the Zn porphyrin is dominated by emission from the Mg or Fb porphyrin. Time-resolved absorption spectroscopy shows that the energy-transfer rate constants are (11 ps)-1 and (37 ps)-1 for Zn-pbp-Mg and Zn-pbp-Fb, respectively, corresponding to energy-transfer quantum yields of 0.995 and 0.983, respectively. The calculated Förster through-space rates are (1900 ps)-1 and (1100 ps)-1 for Zn-pbp-Mg and Zn-pbp-Fb, respectively. Accordingly, the through-bond process dominates for both dyads with a through-bond:through-space energy-transfer ratio of ≥97:1. Collectively, the studies show that the 4,4‘-diphenylbutadiynyl linker supports fast and efficient energy transfer between Zn and Mg or Fb porphyrins. DA - 2002/4/5/ PY - 2002/4/5/ DO - 10.1021/jo016150p VL - 67 IS - 7 SP - 2111-2117 SN - 1520-6904 ER - TY - JOUR TI - Deficiency of either cyclooxygenase (COX)-1 or COX-2 alters epidermal differentiation and reduces mouse skin tumorigenesis AU - Tiano, H. F. AU - Loftin, C. D. AU - Akunda, J. AU - Lee, C. A. AU - Spalding, J. AU - Sessoms, A. AU - Dunson, D. B. AU - Rogan, E. G. AU - Morham, S. G. AU - Smart, R. C. AU - al., T2 - Cancer Research DA - 2002/// PY - 2002/// VL - 62 IS - 12 SP - 3395–3401 ER - TY - JOUR TI - When a day makes a difference. Interpreting data from endoplasmic reticulum-targeted green fluorescent protein fusions in cells grown in suspension culture AU - Persson, S. AU - Love, J. AU - Tsou, P. L. AU - Robertson, D. AU - Thompson, W. F. AU - Boss, W. F. T2 - Plant Physiology AB - The stability of the self-contained structure of green fluorescent protein (GFP) has made it the most widely utilized fluorescent marker for gene expression and subcellular localization studies ([Chalfie et al., 1994][1]; [Tsien, 1998][2]; [De Giorgi et al., 1999][3]; [Haseloff et al., 1999][4]). DA - 2002/// PY - 2002/// DO - 10.1104/pp.010840 VL - 128 IS - 2 SP - 341-344 ER - TY - JOUR TI - Visceral leishmaniasis in a New York foxhound kennel AU - Gaskin, AA AU - Schantz, P AU - Jackson, J AU - Birkenheuer, A AU - Tomlinson, L AU - Gramiccia, M AU - Levy, M AU - Steurer, F AU - Kollmar, E AU - Hegarty, BC AU - Ahn, A AU - Breitschwerdt, EB T2 - JOURNAL OF VETERINARY INTERNAL MEDICINE AB - Although endemic throughout much of the world, autochthonous visceral leishmaniasis has been reported on only 3 previous occasions in North America. After diagnosis of visceral leishmaniasis in 4 foxhounds from a kennel in Dutchess County, New York (index kennel), serum and ethylenediamine-tetraacetic acid (EDTA)-anticoagulated blood were collected from the remaining 108 American or cross-bred foxhounds in the index kennel and from 30 Beagles and Basset Hounds that were periodically housed in the index kennel. Samples were analyzed for antibodies to or DNA of tickborne disease pathogens and Leishmania spp. Most dogs had antibodies to Rickettsia spp., Ehrlichia spp., Babesia spp., or some combination of these pathogens but not to Bartonella vinsonii (berkhoffi). However, DNA of rickettsial, ehrlichial, or babesial agents was detected in only 9 dogs. Visceral leishmaniasis was diagnosed in 46 of 112 (41%) foxhounds from the index kennel but was not diagnosed in any of the Beagles and Basset Hounds. A positive Leishmania status was defined by 1 or more of the following criteria: a Leishmania antibody titer > or = 1:64, positive Leishmania polymerase chain reaction (PCR), positive Leishmania culture, or identification of Leishmania amastigotes by cytology or histopathology. The species and zymodeme of Leishmania that infected the foxhounds was determined to be Leishmania infantum MON-1 by isoenzyme electrophoresis. Foxhounds that were > 18 months of age or that had traveled to the southeastern United States were more likely to be diagnosed with visceral leishmaniasis. Transmission of Leishmania spp. in kennel outbreaks may involve exposure to an insect vector, direct transmission, or vertical transmission. DA - 2002/// PY - 2002/// DO - 10.1892/0891-6640(2002)016<0034:VLIANY>2.3.CO;2 VL - 16 IS - 1 SP - 34-44 SN - 0891-6640 KW - canine KW - dogs KW - Leishmania KW - sand fly ER - TY - JOUR TI - Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system AU - Heath, LS AU - Ramakrishnan, N AU - Sederoff, RR AU - Whetten, RW AU - Chevone, BI AU - Struble, CA AU - Jouenne, VY AU - Chen, DW AU - Zyl, L AU - Grene, R T2 - COMPARATIVE AND FUNCTIONAL GENOMICS AB - Conception, design, and implementation of cDNA microarray experiments present a variety of bioinformatics challenges for biologists and computational scientists. The multiple stages of data acquisition and analysis have motivated the design of Expresso, a system for microarray experiment management. Salient aspects of Expresso include support for clone replication and randomized placement; automatic gridding, extraction of expression data from each spot, and quality monitoring; flexible methods of combining data from individual spots into information about clones and functional categories; and the use of inductive logic programming for higher-level data analysis and mining. The development of Expresso is occurring in parallel with several generations of microarray experiments aimed at elucidating genomic responses to drought stress in loblolly pine seedlings. The current experimental design incorporates 384 pine cDNAs replicated and randomly placed in two specific microarray layouts. We describe the design of Expresso as well as results of analysis with Expresso that suggest the importance of molecular chaperones and membrane transport proteins in mechanisms conferring successful adaptation to long-term drought stress. DA - 2002/6// PY - 2002/6// DO - 10.1002/cfg.169 VL - 3 IS - 3 SP - 226-243 SN - 1532-6268 KW - microarrays KW - data mining KW - experiment management systems KW - inductive logic programming KW - reactive oxygen species KW - drought stress KW - Pinus taeda KW - microarray design ER - TY - JOUR TI - Registration of NC99BGTAG11 wheat germplasm resistant to powdery mildew AU - Murphy, JP AU - Navarro, RA AU - Leath, S T2 - CROP SCIENCE AB - Crop ScienceVolume 42, Issue 4 p. 1382-1382 Registration of Germplasm Registration of NC99BGTAG11 Wheat Germplasm Resistant to Powdery Mildew J.P. Murphy, Corresponding Author J.P. Murphy njpm@unity.ncsu.edu Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695-7629Corresponding author (njpm@unity.ncsu.edu)Search for more papers by this authorR.A. Navarro, R.A. Navarro Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695-7629Search for more papers by this authorS. Leath, S. Leath USDA-ARS, Dep. Plant Pathology, North Carolina State Univ., Raleigh, NC, 27695-7629Search for more papers by this author J.P. Murphy, Corresponding Author J.P. Murphy njpm@unity.ncsu.edu Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695-7629Corresponding author (njpm@unity.ncsu.edu)Search for more papers by this authorR.A. Navarro, R.A. Navarro Dep. of Crop Science, North Carolina State Univ., Raleigh, NC, 27695-7629Search for more papers by this authorS. Leath, S. Leath USDA-ARS, Dep. Plant Pathology, North Carolina State Univ., Raleigh, NC, 27695-7629Search for more papers by this author First published: 01 July 2002 https://doi.org/10.2135/cropsci2002.1382Citations: 7 Research supported in part by the North Carolina Small Grains Growers Association, Inc. Registration by CSSA. Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume42, Issue4July–August 2002Pages 1382-1382 RelatedInformation DA - 2002/// PY - 2002/// DO - 10.2135/cropsci2002.1382 VL - 42 IS - 4 SP - 1382-1382 SN - 1435-0653 ER - TY - JOUR TI - Pioneering women in plant pathology. Part I, Effie A. Southworth, first woman plant pathologist hired at the USDA AU - Ristaino, J. B. AU - Petersen, P. T2 - From: APSNet Education Center Website. Originally published in The plant health instructor, February 1, 2002. DA - 2002/// PY - 2002/// IS - 2002 ER - TY - JOUR TI - Magnetic resonance imaging features of lissencephaly in 2 Lhasa Apsos AU - Saito, M AU - Sharp, NJH AU - Kortz, GD AU - Lahunta, A AU - Leventer, RJ AU - Tokuriki, M AU - Thrall, DE T2 - VETERINARY RADIOLOGY & ULTRASOUND AB - Two Lhasa Apsos were diagnosed with lissencephaly based on MR imaging and clinical findings. Histologic confirmation of the diagnosis was obtained in one dog. The MR imaging appearance of the brain in 2 Lhasa Apsos with lissencephaly was of a smooth cerebral surface and a thick neocortex with an absence of the corona radiata. This correlated very well with the histopathologic findings in the dog. Our findings, together with the histopathologic features reported previously, are most consistent with Lhasa Apsos having the canine equivalent of human classical lissencephaly. MR is the imaging modality of choice for antemortem diagnosis of canine lissencephaly. DA - 2002/// PY - 2002/// DO - 10.1111/j.1740-8261.2002.tb01013.x VL - 43 IS - 4 SP - 331-337 SN - 1058-8183 ER - TY - JOUR TI - Lack of teratogenicity of microcystin-LR in the mouse and toad AU - Chernoff, N AU - Hunter, ES AU - Hall, LL AU - Rosen, MB AU - Brownie, CF AU - Malarkey, D AU - Marr, M AU - Herkovits, J T2 - JOURNAL OF APPLIED TOXICOLOGY AB - Microcystin-LR (MC-LR) is a cyanobacterial toxin generated by the organism Microcystis aeruginosa. Although the hepatotoxicity of this chemical has been characterized, the potential developmental toxicity in vertebrates has not been well studied. The purpose of this study was to elucidate the effects of this toxin on the in vivo and in vitro development of mammals and the development of an Anuran (toad). Initial acute toxicity experiments with female CD-1 mice were accomplished with MC-LR administered i.p. in saline. Lethality occurred at 128 and 160 microg kg (-1) and histopathology revealed massive hepatic necrosis with diffuse hemorrhage. Developmental toxicity studies were done with MC-LR administered i.p. for 2-day periods: gestation days 7-8, 9-10 or 11-12. Doses used ranged from 2 to 128 microg kg(-1). On gestation day 17, fetuses were weighed and analyzed for gross morphological and skeletal defects. No treatment-related differences were seen in litter size, viability, weight or the incidence of anomalies. Groups of dams dosed with 32-128 microg kg(-1) on gestation days 7-8, 9-10 or 11-12 were allowed to give birth and the growth and development of their pups were followed postnatally. There were no significant effects noted in the offspring of the treated dams. Neurulation-staged CD-1 mouse conceptuses were exposed to 50-1000 nM MC-LR in whole embryo culture for 24 h. No significant increase in abnormalities or developmental delays was observed. Finally, exposure of the developing toad. Bufo arenarum was done from stage 17 (tail bud) for 10 days at concentrations of 1-20 mg l(-1). No effect on morphological development or survival was noted in any exposed groups. These data indicate that microcystin does not appear to affect development adversely in the mouse (in vivo or in vitro) or the toad at the doses and exposure parameters used. DA - 2002/// PY - 2002/// DO - 10.1002/jat.800 VL - 22 IS - 1 SP - 13-17 SN - 0260-437X KW - microcystin KW - developmental toxicology KW - mouse KW - frog KW - embryo ER - TY - JOUR TI - Isolation of a reovirus from poult enteritis and mortality syndrome and its pathogenicity in turkey poults AU - Heggen-Peay, CL AU - Qureshi, MA AU - Edens, FW AU - Sherry, B AU - Wakenell, PS AU - PH O'Connell, AU - Schat, KA T2 - AVIAN DISEASES AB - Poult enteritis and mortality syndrome (PEMS) is an acute, infectious intestinal disease of turkey poults, characterized by high mortality and 100% morbidity, that decimated the turkey industry in the mid-1990s. The etiology of PEMS is not completely understood. This report describes the testing of various filtrates of fecal material from control and PEMS-affected poults by oral inoculation into poults under experimental conditions, the subsequent isolation of a reovirus, ARV-CU98, from one of the PEMS fecal filtrates, and in vivo and in vitro studies conducted to determine the pathogenicity of ARV-CU98 in turkey poults. In order to identify a filtrate fraction of fecal material containing a putative etiologic agent, poults were challenged in two independent experiments with 220- and 100-nm filtrates of fecal material from PEMS-negative and PEMS-positive poults. The 100-nm filtrate was chosen for further evaluation because poults inoculated with this filtrate exhibited mortality and significantly lower (P ≤ 0.05) body weight and relative bursa weight, three clinical signs associated with PEMS. These results were confirmed in a third experiment with 100-nm fecal filtrates from a separate batch of PEMS fecal material. In Experiment 3, body weight and relative bursa and thymus weights were significantly lower (P ≤ 0.05) in poults inoculated with 100-nm filtrate of PEMS fecal material as compared with poults inoculated with 100-nm filtrate of control fecal material. Subsequently, a virus was isolated from the 100-nm PEMS fecal filtrate and propagated in liver cells. This virus was identified as a reovirus on the basis of cross-reaction with antisera against avian reovirus (FDO strain) as well as by electrophoretic analysis and was designated ARV-CU98. When inoculated orally into poults reared under controlled environmental conditions in isolators, ARV-CU98 was associated with a higher incidence of thymic hemorrhaging and gaseous intestines. In addition, relative bursa and liver weights were significantly lower (P ≤ 0.05) in virus-inoculated poults as compared with controls. Virus was successfully reisolated from virus-challenged poults but not from control birds. Furthermore, viral antigen was detected by immunofluorescence in liver sections from virus-challenged poults at 3 and 6 days postinfection and virus was isolated from liver at 6 days postinfection, suggesting that ARV-CU98 replicates in the liver. In addition to a decrease in liver weight, there was a functional degeneration as indicated by altered plasma alanine aminotransferase and aspartate aminotransferase activities in virus poults as compared with controls. Although this reovirus does not induce fulminating PEMS, our results demonstrated that ARV-CU98 does cause some of the clinical signs in PEMS, including intestinal alterations and significantly lower relative bursa and liver weights. ARV-CU98 may contribute directly to PEMS by affecting the intestine, bursa, and liver and may contribute indirectly by increasing susceptibility to opportunistic pathogens that facilitate development of clinical PEMS. DA - 2002/// PY - 2002/// DO - 10.1637/0005-2086(2002)046[0032:IOARFP]2.0.CO;2 VL - 46 IS - 1 SP - 32-47 SN - 0005-2086 KW - poult enteritis and mortality syndrome KW - reovirus KW - turkey KW - fecal filtrate ER - TY - JOUR TI - Isolation and identification of Mycobacterium kansasii from pleural fluid of a dog with persistent pleural effusion AU - Pressler, Barrak M. AU - Hardie, Elizabeth M. AU - Pitulle, Christian AU - Hopwood, Robin M. AU - Sontakke, Sushama AU - Breitschwerdt, Edward B. T2 - Journal of the American Veterinary Medical Association AB - A 3-year-old spayed female Whippet was examined for cough and respiratory distress. Lung lobe torsion with pleural effusion was diagnosed, and lung lobectomy was performed. Pleural effusion recurred during the following 27 months; conventional bacteriologic cultures of pleural effusion did not result in bacterial growth. A second lung lobectomy, pleuroperitoneal shunt placement. and pericardectomy were subsequently performed. Mycobacterium kansasii was eventually isolated from pleural fluid and identified by polymerase chain reaction amplification and DNA sequencing. The dog was euthanatized before therapeutic response could be evaluated. To our knowledge, this is the first report of M. kansasii infection in a dog. Additionally, this is the first report of mycobacterial isolation from pleural fluid, and one of few reports of antemortem mycobacterial isolation from a body fluid, as opposed to identification in specimens during histologic examination. Routine bacteriologic culture methods are insufficient to isolate mycobacterial agents, and special methods are indicated in dogs with persistent pleural effusion. DA - 2002/5// PY - 2002/5// DO - 10.2460/javma.2002.220.1336 VL - 220 IS - 9 SP - 1336-1340 J2 - Journal of the American Veterinary Medical Association LA - en OP - SN - 0003-1488 UR - http://dx.doi.org/10.2460/javma.2002.220.1336 DB - Crossref ER - TY - JOUR TI - Efficient matrix preconditioners for black box linear algebra AU - Chen, L AU - Eberly, W AU - Kaltofen, E AU - Saunders, BD AU - Turner, WJ AU - Villard, G T2 - LINEAR ALGEBRA AND ITS APPLICATIONS AB - The main idea of the “black box” approach in exact linear algebra is to reduce matrix problems to the computation of minimum polynomials. In most cases preconditioning is necessary to obtain the desired result. Here good preconditioners will be used to ensure geometrical/algebraic properties on matrices, rather than numerical ones, so we do not address a condition number. We offer a review of problems for which (algebraic) preconditioning is used, provide a bestiary of preconditioning problems, and discuss several preconditioner types to solve these problems. We present new conditioners, including conditioners to preserve low displacement rank for Toeplitz-like matrices. We also provide new analyses of preconditioner performance and results on the relations among preconditioning problems and with linear algebra problems. Thus, improvements are offered for the efficiency and applicability of preconditioners. The focus is on linear algebra problems over finite fields, but most results are valid for entries from arbitrary fields. DA - 2002/3/1/ PY - 2002/3/1/ DO - 10.1016/S0024-3795(01)00472-4 VL - 343 SP - 119-146 SN - 0024-3795 KW - black box matrix KW - sparse matrix KW - structured matrix KW - Toeplitz-like matrix KW - matrix preconditioner KW - exact arithmetic KW - finite field KW - symbolic computation KW - linear system solution KW - minimal polynomial KW - characteristic polynomial KW - rank KW - determinant KW - Wiedemann algorithm KW - randomized algorithm KW - butterfly network ER - TY - JOUR TI - Effect of synthetic and organic soil fertility amendments on southern blight, soil microbial communities, and yield of processing tomatoes AU - Bulluck, LR AU - Ristaino, JB T2 - PHYTOPATHOLOGY AB - ABSTRACT Soil fertility amendments, including composted cotton-gin trash, swine manure, a rye-vetch green manure, or synthetic fertilizers, were applied to subplots and tillage on bare soil; or tillage followed by surface mulch with wheat straw were applied to main plots to determine the effect on the incidence of southern blight caused by Sclerotium rolfsii, yield of processing tomato, and soil microbial communities. The amendment-tillage interaction was significant in 1997 and disease incidence was 67% in tilled bare soil receiving synthetic fertilizers; whereas disease incidence was 3, 12, and 16% in surface-mulched plots amended with a composted cotton-gin trash, swine manure, or a rye-vetch green manure. The amendment effect was significant in 1998, and disease incidence was 61% in plots receiving synthetic fertilizer and was 23, 44, and 53% in plots receiving cotton-gin trash, swine manure, or rye-vetch green manure, respectively. In 1997, yields were highest in tilled surface-mulched plots amended with synthetic fertilizers, cotton-gin trash, or swine manure, respectively. In 1998, yields were low in all plots and there were no significant differences in yield due to treatment. Propagule densities of antagonistic soil fungi in the genus Trichoderma were highest in soils amended with composted cotton-gin trash or swine manure in both years. Propagule densities of fluorescent pseudomonads in soil were higher in plots amended with organic amendments than with synthetic fertilizers in both years. Propagules densities of enteric bacteria were elevated in soils amended with raw swine manure biosolids in both years. Our research indicates that some organic amendments, such as cotton-gin trash, reduced the incidence of southern blight in processing tomato and also enhanced populations of beneficial soil microbes. DA - 2002/2// PY - 2002/2// DO - 10.1094/PHYTO.2002.92.2.181 VL - 92 IS - 2 SP - 181-189 SN - 0031-949X KW - organic agriculture KW - sustainable agriculture ER - TY - JOUR TI - Design and synthesis of light-harvesting rods for intrinsic rectification of the migration of excited-state energy and ground-state holes AU - Loewe, RS AU - Lammi, RK AU - Diers, , JR AU - Kirmaier, C AU - Bocian, DF AU - Holten, D AU - Lindsey, JS T2 - JOURNAL OF MATERIALS CHEMISTRY AB - We present the design of molecular materials for ultimate use in solid-state solar cells. The molecular materials are semi-rigid oligomeric rods of defined length with metalloporphyrins in the backbone and a carboxy group at one end for attachment to a surface. The rods are designed to absorb visible light, and then undergo excited-state energy transfer and ground-state hole transfer in opposite directions along the length of the rod. The rational synthesis of the multiporphyrin arrays relies on joining porphyrin building blocks in an efficient and controlled manner. Several porphyrin building blocks have been synthesized that bear bromophenyl, iodophenyl, trimethylsilylethynylphenyl and/or ethynylphenyl substituents for use in a copper-free Sonogashira reaction using Pd2(dba)3 and P(o-tol)3. Competition experiments performed on equimolar quantities of an iodo-porphyrin and a bromo-porphyrin with an ethynyl-porphyrin show iodo + ethyne coupling with a low amount (35 °C) or undetectable amount (22 °C) of bromo + ethyne coupling. Efficient coupling of bromo-porphyrins with ethynyl-porphyrins was achieved using the same copper-free Sonogashira reaction conditions at higher temperature (50 °C or 80 °C). These findings allow successive coupling reactions to be achieved using substrates bearing iodo and bromo synthetic handles. Thus, a porphyrin-based tetrad (or pentad) was synthesized with a final convergent coupling of a bromo-substituted dyad (or triad) and an ethynyl-substituted dyad. A porphyrin triad was prepared by sequential iodo + ethyne coupling reactions. The triad, tetrad, and pentad each are comprised of a terminal magnesium porphyrin bearing one carboxy group (for surface attachment) and two pentafluorophenyl groups; the remaining porphyrins in each array are present as the zinc chelate. Electrochemical characterization of benchmark porphyrins indicates the presence of the desired electrochemical gradient for hole hopping in the arrays. Static absorption data indicate that the arrays are weakly coupled, while static fluorescence data indicate that the excited-state energy flows in high yield to the terminal magnesium porphyrin. Time-resolved spectroscopic analysis leads to rate constants in THF of (9 ps)−1, (15 ps)−1, and (30 ps)−1 for ZnMg dyad 20, Zn2Mg triad 13, and Zn3Mg tetrad 15, respectively, and quantum efficiencies ≥99% for energy flow to the magnesium porphyrin in each case. These design and synthesis strategies should be useful for the construction of materials for molecular-based solar cells. DA - 2002/// PY - 2002/// DO - 10.1039/b108168c VL - 12 IS - 5 SP - 1530-1552 SN - 0959-9428 ER - TY - JOUR TI - Use of bacteriophage Ba1 to identify properties associated with Bordetella avium virulence AU - Shelton, C. B. AU - Temple, L. M. AU - Orndorff, P. E. T2 - Infection and Immunity DA - 2002/// PY - 2002/// DO - 10.1128/IAI.70.3.121901224.2002 VL - 70 IS - 3 SP - 1219-1224 ER - TY - JOUR TI - Geminivirus-based vectors for gene silencing in Arabidopsis AU - Turnage, MA AU - Muangsan, N AU - Peele, CG AU - Robertson, D T2 - PLANT JOURNAL AB - Gene silencing, or RNA interference, is a powerful tool for elucidating gene function in Caenorhabditis elegans and Drosophila melanogaster. The vast genetic, developmental and sequence information available for Arabidopsis thaliana makes this an attractive organism in which to develop reliable gene-silencing tools for the plant world. We have developed a system based on the bipartite geminivirus cabbage leaf curl virus (CbLCV) that allows silencing of endogenous genes singly or in combinations in Arabidopsis. Two vectors were tested: a gene-replacement vector derived from the A component; and an insertion vector derived from the B component. Extensive silencing was produced in new growth from the A component vectors, while only minimal silencing and symptoms were seen in the B component vector. Two endogenous genes were silenced simultaneously from the A component vector and silencing of the genes was maintained throughout new growth. Because the CbLCV vectors are DNA vectors they can be inoculated directly from plasmid DNA. Introduction of these vectors into intact plants bypasses transformation and extends the kinds of silencing studies that can be carried out in Arabidopsis. DA - 2002/4// PY - 2002/4// DO - 10.1046/j.1365-313X.2002.01261.x VL - 30 IS - 1 SP - 107-114 SN - 0960-7412 KW - geminivirus KW - gene silencing KW - RNAi KW - Arabidopsis KW - cabbage leaf curl virus ER - TY - JOUR TI - Coordinate expression of the PDK4 gene: a means of regulating fuel selection in a hibernating mammal AU - Buck, MJ AU - Squire, TL AU - Andrews, MT T2 - PHYSIOLOGICAL GENOMICS AB - Hibernation in mammals requires a metabolic shift away from the oxidation of carbohydrates and toward the combustion of stored fatty acids as the primary source of energy during torpor. A key element involved in this fuel selection is pyruvate dehydrogenase kinase isoenzyme 4 (PDK4). PDK4 inhibits pyruvate dehydrogenase and thus minimizes carbohydrate oxidation by preventing the flow of glycolytic products into the tricarboxylic acid cycle. This paper examines expression of the PDK4 gene during hibernation in heart, skeletal muscle, and white adipose tissue (WAT) of the 13-lined ground squirrel, Spermophilus tridecemlineatus. During hibernation PDK4 mRNA levels increase 5-fold in skeletal muscle and 15-fold in WAT compared with summer-active levels. Similarly, PDK4 protein is increased threefold in heart, fivefold in skeletal muscle, and eightfold in WAT. High levels of serum insulin, likely to have an inhibitory effect on PDK4 gene expression, are seen during fall when PDK4 mRNA levels are low. Coordinate upregulation of PDK4 in three distinct tissues suggests a common signal that regulates PDK4 expression and fuel selection during hibernation. DA - 2002/2/11/ PY - 2002/2/11/ DO - 10.1152/physiolgenomics.00076.2001 VL - 8 IS - 1 SP - 5-13 SN - 1094-8341 KW - hibernation KW - pyruvate dehydrogenase kinase isoenzyme 4 KW - insulin KW - peroxisome proliferator-activated receptor-alpha Spermophilus tridecemlineatus ER - TY - JOUR TI - CT findings of intracranial blastomycosis in a dog AU - Saito, M AU - Sharp, NJH AU - Munana, K AU - Troan, BV AU - Tokuriki, M AU - Thrall, DE T2 - VETERINARY RADIOLOGY & ULTRASOUND AB - Computed tomography (CT) findings in a dog with intracranial blastomycosis were marked periventricular contrast enhancement of the lateral ventricles, the 3rd ventricle, and the mesencephalic aqueduct. The CT appearance correlated with the histopathologic findings, where severe ependymitis was present throughout the ventricular system and there was stenosis of the mesencephalic aqueduct due to an inflammatory infiltrate. CT is therefore recommended as a screening test for intracranial blastomycosis in dogs and also as an imaging modality for follow-up evaluation after treatment. This is particularly true in dogs with systemic or ocular blastomycosis, which appear to be at higher risk of developing CNS involvement. DA - 2002/// PY - 2002/// DO - 10.1111/j.1740-8261.2002.tb00436.x VL - 43 IS - 1 SP - 16-21 SN - 1058-8183 ER - TY - JOUR TI - Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins AU - Hall, TA AU - Brown, JW T2 - RNA AB - Although archaeal RNase P RNAs are similar in both sequence and structure to those of Bacteria rather than eukaryotes, and heterologous reconstitution between the Bacillus subtilis RNase P protein and some archaeal RNase P RNAs has been demonstrated, no archaeal protein sequences with similarity to any known bacterial RNase P protein subunit have been identified, and the density of Methanothermobacter thermoautotrophicus RNase P in Cs2SO4 (1.42 g/mL) is inconsistent with a single small bacterial-like protein subunit. Four hypothetical open reading frames (MTH11, MTH687, MTH688, and MTH1618) were identified in the genome of M. thermoautotrophicus that have sequence similarity to four of the nine Saccharomyces cerevisiae RNase P protein subunits: Pop4p, Pop5p, Rpp1p, and Rpr2p, respectively. Polyclonal antisera generated to recombinant Mth11p, Mth687p, Mth688p, and Mth1618p each recognized a protein of the predicted molecular weight in western blots of partially purified M. thermoautotrophicus RNase P, and immunoprecipitated RNase P activity from the same partially purified preparation. RNase P in Archaea is therefore composed of an RNA subunit similar to bacterial RNase P RNA and multiple protein subunits similar to those in the eukaryotic nucleus. DA - 2002/3// PY - 2002/3// DO - 10.1017/S1355838202028492 VL - 8 IS - 3 SP - 296-306 SN - 1469-9001 KW - archaebacteria KW - Methanobacterium thermoautotrophicum strain Delta H KW - Methanothermobacter thermoautotrophicus KW - ribonuclease P ER - TY - JOUR TI - Variation in Drosophila sensory bristle number at 'Evolution Canyon' AU - Lyman, RF AU - Nevo, E AU - Mackay, TFC T2 - GENETICS RESEARCH AB - ‘Evolution Canyon’ on Mount Carmel, Israel, displays highly contrasting physical and biotic environments on a micro-geographic scale, and is a natural laboratory for investigating genetic responses to variable and extreme environments across species. Samples of Drosophila melanogaster and D. simulans were collected from three sites each on the north- and south-facing slopes of the canyon along altitudinal transects, and one site on the valley floor. Numbers of abdominal and sternopleural sensory bristles were recorded for each of these subpopulations in three thermal environments. In D. simulans , sternopleural bristle number exhibited micro-geographic differentiation between the north- and south-facing slopes, while abdominal bristle number was stable across subpopulations. In D. melanogaster , the magnitudes of the difference in mean sternopleural bristle number between the north- and south-facing slopes and of mean abdominal bristle number along the altitudinal gradients were both conditional on rearing temperature. Thus, the pattern of genetic variation between sites was consistent with underlying heterogeneity of genetic mechanisms for response to the same environmental gradients between traits and sibling species. In contrast, the genetic architecture of bristle number at the level of variation within populations was very similar between species for the same bristle trait, although the two traits differed in the relative contribution of genotype by temperature and genotype by sex interaction. DA - 2002/12// PY - 2002/12// DO - 10.1017/S0016672302005876 VL - 80 IS - 3 SP - 215-223 SN - 1469-5073 ER - TY - BOOK TI - A primer of genome science AU - Gibson, G. AU - Muse, S. V. CN - QH447 .G534 2002 DA - 2002/// PY - 2002/// PB - Sunderland, MA: Sinauer SN - 0878932348 ER - TY - JOUR TI - Tracking historic migrations of the Irish potato famine pathogen, Phytophthora infestans AU - Ristaino, JB T2 - MICROBES AND INFECTION AB - The plant pathogen Phytophthora infestans causes late blight, a devastating disease on potato that led to the Irish potato famine during 1845–1847. The disease is considered a reemerging problem and still causes major epidemics on both potato and tomato crops worldwide. Theories on the origin of the disease based on an examination of the genetic diversity and structure of P. infestans populations and use of historic specimens to understand modern day epidemics are discussed. DA - 2002/11// PY - 2002/11// DO - 10.1016/S1286-4579(02)00010-2 VL - 4 IS - 13 SP - 1369-1377 SN - 1286-4579 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0036848765&partnerID=MN8TOARS KW - Phytophthora injestans KW - late blight of potatoes KW - plant disease epidemiology KW - ancient DNA ER - TY - JOUR TI - Molecular evidence on the origin and evolution of glutinous rice AU - Olsen, K. M. AU - Purugganan, M. D. T2 - Genetics DA - 2002/// PY - 2002/// VL - 162 IS - 2 SP - 941-950 ER - TY - JOUR TI - Up-regulation of phosphoinositide metabolism in tobacco cells constitutively expressing the human type I inositol polyphosphate 5-phosphatase AU - Perera, IY AU - Love, J AU - Heilmann, I AU - Thompson, WF AU - Boss, WF T2 - PLANT PHYSIOLOGY AB - To evaluate the impact of suppressing inositol 1,4,5-trisphosphate (InsP(3)) in plants, tobacco (Nicotiana tabacum) cells were transformed with the human type I inositol polyphosphate 5-phosphatase (InsP 5-ptase), an enzyme which specifically hydrolyzes InsP(3). The transgenic cell lines showed a 12- to 25-fold increase in InsP 5-ptase activity in vitro and a 60% to 80% reduction in basal InsP(3) compared with wild-type cells. Stimulation with Mas-7, a synthetic analog of the wasp venom peptide mastoparan, resulted in an approximately 2-fold increase in InsP(3) in both wild-type and transgenic cells. However, even with stimulation, InsP(3) levels in the transgenic cells did not reach wild-type basal values, suggesting that InsP(3) signaling is compromised. Analysis of whole-cell lipids indicated that phosphatidylinositol 4,5-bisphosphate (PtdInsP(2)), the lipid precursor of InsP(3), was greatly reduced in the transgenic cells. In vitro assays of enzymes involved in PtdInsP(2) metabolism showed that the activity of the PtdInsP(2)-hydrolyzing enzyme phospholipase C was not significantly altered in the transgenic cells. In contrast, the activity of the plasma membrane PtdInsP 5 kinase was increased by approximately 3-fold in the transgenic cells. In vivo labeling studies revealed a greater incorporation of (32)P into PtdInsP(2) in the transgenic cells compared with the wild type, indicating that the rate of PtdInsP(2) synthesis was increased. These studies show that the constitutive expression of the human type I InsP 5-ptase in tobacco cells leads to an up-regulation of the phosphoinositide pathway and highlight the importance of PtdInsP(2) synthesis as a regulatory step in this system. DA - 2002/8// PY - 2002/8// DO - 10.1104/pp.003426 VL - 129 IS - 4 SP - 1795-1806 SN - 1532-2548 ER - TY - JOUR TI - The genetics of plant morphological evolution AU - Shepard, KA AU - Purugganan, MD T2 - CURRENT OPINION IN PLANT BIOLOGY AB - Considerable progress has been made in identifying genes that are involved in the evolution of plant morphologies. Elements of the ABC model of flower development are conserved throughout angiosperms, and homologous MADS-box genes function in gymnosperm reproduction. Candidate gene and mapping analyses of floral symmetry, sex determination, inflorescence architecture, and compound leaves provide intriguing glimpses into the evolution of morphological adaptations. DA - 2002/2// PY - 2002/2// DO - 10.1016/S1369-5266(01)00227-8 VL - 5 IS - 1 SP - 49-55 SN - 1879-0356 ER - TY - JOUR TI - Optimization of sample size and DNA extraction methods to improve PCR detection of different propagules of Phytophthora infestans AU - Wangsomboondee, T AU - Ristaino, JB T2 - PLANT DISEASE AB - The plant pathogen Phytophthora infestans causes a destructive blight of potato tubers and foliage. A rapid polymerase chain reaction (PCR) assay has been developed for detection of P. infestans in potato tubers. In this study, the effect of method of DNA extraction on different propagule types and the minimal number of propagules of P. infestans detectable by PCR were assessed using the PINF and internal transcribed spacer (ITS)5 primers. Sensitivity of the primers for PCR was high, and DNA was detectable at concentrations as low as 10 pg/ml. Zoospores and oospores responded differently to different extraction methods, whereas all extraction methods worked equally well for sporangia. Freeze-thaw DNA lysis, in which propagules were frozen at -80°C and thawed at 65°C three times for 15 min each, or direct PCR, in which propagules were placed directly in the reaction mix, were effective methods for PCR detection of sporangia or zoospores but were not effective methods for PCR detection of DNA in oospores of P. infestans. DNA from a single sporangium or oospore could be amplified by PCR after hexadecyltrimethyl-ammonium bromide (CTAB) or NaOH lysis extraction methods, whereas DNA from a single zoospore could be amplified by CTAB or direct PCR methods. “IsoCode” Stixs, used in forensic applications, were used to collect the pathogen from leaf and tuber lesions and provided another simple method to extract template DNA. PCR detection of the pathogen in infected tubers using PINF and ITS5 primers was compared to tissue isolation or visual observation. The probability of detection of P. infestans in infected tubers at 7 days post inoculation using the PCR assay, tissue isolation, or visual observation was 0.90, 0.80, and 0.75, respectively. The PINF and ITS5 primers provide a powerful tool for rapid and sensitive detection of zoospores, sporangia, and oospores of P. infestans when used with appropriate extraction methods, and could easily be deployed to reduce spread of the pathogen in potato tubers. DA - 2002/3// PY - 2002/3// DO - 10.1094/PDIS.2002.86.3.247 VL - 86 IS - 3 SP - 247-253 SN - 1943-7692 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0036191533&partnerID=MN8TOARS ER - TY - JOUR TI - Modelling the limits on the response of net carbon exchange to fertilization in a south-eastern pine forest AU - Lai, CT AU - Katul, G AU - Butnor, J AU - Siqueira, M AU - Ellsworth, D AU - Maier, C AU - Johnsen, K AU - Mckeand, S AU - Oren, R T2 - PLANT CELL AND ENVIRONMENT AB - Abstract Using a combination of model simulations and detailed measurements at a hierarchy of scales conducted at a sandhills forest site, the effect of fertilization on net ecosystem exchange ( NEE ) and its components in 6‐year‐old Pinus taeda stands was quantified. The detailed measurements, collected over a 20‐d period in September and October, included gas exchange and eddy covariance fluxes, sampled for a 10‐d period each at the fertilized stand and at the control stand. Respiration from the forest floor and above‐ground biomass was measured using chambers during the experiment. Fertilization doubled leaf area index (LAI) and increased leaf carboxylation capacity by 20%. However, this increase in total LAI translated into an increase of only 25% in modelled sunlit LAI and in canopy photosynthesis. It is shown that the same climatic and environmental conditions that enhance photosynthesis in the September and October periods also cause an increase in respiration The increases in respiration counterbalanced photosynthesis and resulted in negligible NEE differences between fertilized and control stands. The fact that total biomass of the fertilized stand exceeded 2·5 times that of the control, suggests that the counteracting effects cannot persist throughout the year. In fact, modelled annual carbon balance showed that gross primary productivity ( GPP ) increased by about 50% and that the largest enhancement in NEE occurred in the spring and autumn, during which cooler temperatures reduced respiration more than photosynthesis. The modelled difference in annual NEE between fertilized and control stands (approximately 200 1;g 2;C 3;m −2 y −1 ) suggest that the effect of fertilization was sufficiently large to transform the stand from a net terrestrial carbon source to a net sink. DA - 2002/9// PY - 2002/9// DO - 10.1046/j.1365-3040.2002.00896.x VL - 25 IS - 9 SP - 1095-1119 SN - 1365-3040 KW - biosphere-atmosphere exchange KW - canopy carbon uptake KW - fertilization KW - net ecosystem exchange KW - turbulence modelling ER - TY - JOUR TI - Linkage mapping of sex-specific differences AU - Wu, RL AU - Ma, CX AU - Wu, SS AU - Zeng, ZB T2 - GENETICAL RESEARCH AB - Most current linkage analyses assume identical fractions of meiotic recombination between homologous marker loci of the two sexes. This assumption is not realistic, because considerable sex-related differences have been observed in recombination fraction. In this paper, a general EM-based algorithm is presented to estimate sex-specific recombination fractions for a mixed set of molecular markers segregating differently in a full-sib family derived from two heterozygous parents. The asymptotic variances of the estimates of linkage specifically for each of the parents are evaluated using a numerical analysis based on information functions. This approach will have important implications for precise gene mapping based on sex-specific linkage maps. DA - 2002/2// PY - 2002/2// DO - 10.1017/s0016672301005389 VL - 79 IS - 1 SP - 85-96 SN - 0016-6723 ER - TY - JOUR TI - Grafting Fraser fir onto rootstocks of selected Abies species AU - Hinesley, E. AU - Frampton, J. T2 - HortScience DA - 2002/// PY - 2002/// VL - 37 IS - 5 SP - 815-818 ER - TY - JOUR TI - Enabling population and quantitative genomics AU - Gibson, G AU - Mackay, TFC T2 - GENETICS RESEARCH AB - Dissection of quantitative traits to the nucleotide level requires phenotypic and genotypic analysis of traits on a genome scale. Here we discuss the set of community-wide genetic and molecular resources, including panels of specific types of inbred lines and high density resequencing and SNP detection, that will facilitate such studies. DA - 2002/8// PY - 2002/8// DO - 10.1017/S0016672302005839 VL - 80 IS - 1 SP - 1-6 SN - 1469-5073 ER - TY - JOUR TI - Brassinosteroid signaling: Novel downstream components emerge AU - Clouse, SD T2 - CURRENT BIOLOGY AB - Continued genetic screening and analysis of Arabidopsis mutants has extended our view of brassinosteroid signaling beyond hormone perception to downstream events involving a negative cytoplasmic regulator and nuclear localized positive activators of the brassinosteroid response. DA - 2002/7/23/ PY - 2002/7/23/ DO - 10.1016/S0960-9822(02)00964-8 VL - 12 IS - 14 SP - R485-R487 SN - 0960-9822 ER - TY - JOUR TI - Biodegradation of the polyketide toxin cercosporin AU - Mitchell, TK AU - Chilton, WS AU - Daub, ME T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT Cercosporin is a non-host-specific polyketide toxin produced by many species of plant pathogens belonging to the genus Cercospora . This red-pigmented, light-activated toxin is an important pathogenicity determinant for Cercospora species. In this study, we screened 244 bacterial isolates representing 12 different genera for the ability to degrade cercosporin. Cercosporin degradation was determined by screening for the presence of cleared zones surrounding colonies on cercosporin-containing culture medium and was confirmed by assaying the kinetics of degradation in liquid medium. Bacteria belonging to four different genera exhibited the cercosporin-degrading phenotype. The isolates with the greatest cercosporin-degrading activity belonged to Xanthomonas campestris pv. zinniae and X. campestris pv. pruni. Isolates of these pathovars removed over 90% of the cercosporin from culture medium within 48 h. Bacterial degradation of red cercosporin was accompanied by a shift in the color of the growth medium to brown and then green. The disappearance of cercosporin was accompanied by the appearance of a transient green product, designated xanosporic acid. Xanosporic acid and its more stable lactone derivative, xanosporolactone, are nontoxic to cercosporin-sensitive fungi and to plant tissue and are labile in the presence of light. Detailed spectroscopic analysis (to be reported in a separate publication) of xanosporolactone revealed that cercosporin loses one methoxyl group and gains one oxygen atom in the bacterial conversion. The resulting chromophore (4,9-dihydroxy-3-oxaperlylen-10H-10-one) has never been reported before but is biosynthetically plausible via oxygen insertion by a cytochrome P-450 enzyme. DA - 2002/9// PY - 2002/9// DO - 10.1128/AEM.68.9.4173-4181.2002 VL - 68 IS - 9 SP - 4173-4181 SN - 0099-2240 ER - TY - JOUR TI - Modeling epistasis of quantitative trait loci using Cockerham's model AU - Kao, C. H. AU - Zeng, Z. B. T2 - Genetics DA - 2002/// PY - 2002/// VL - 160 IS - 3 SP - 1243-1261 ER - TY - JOUR TI - Evaluation of Arachis species for resistance to tomato spotted wilt virus AU - Lyerly, J. H. AU - Stalker, H. T. AU - Moyer, J. W. AU - Hoffman, K. T2 - Peanut Science AB - Abstract Tomato spotted wilt virus (TSWV) is an important plant pathogen with a wide host range, including the domesticated peanut (Arachis hypogaea L.). After initial outbreaks on peanut during the 1980s, the virus has spread to all peanut-producing states in the U.S. TSWV is transmitted by several species of thrips which are difficult to control with insecticides; therefore, control of TSWV most likely will come from selecting resistant genotypes in breeding programs. Although moderate levels of resistance have been discovered in A. hypogaea, complete virus resistance has not been found. Several Arachis species have desirable genes for plant resistances and tolerate many disease and insect pests better than the cultivated species. The objectives of this study were to (a) evaluate TSWV disease incidence and severity in accessions of Arachis species, and (b) compare levels of TSWV resistance in diploid species to selected A. hypogaea genotypes. In this study, 46 diploid Arachis spp. accessions were evaluated in the greenhouse by artificial inoculation tests for resistance to TSWV. Nine Arachis accessions were observed with no disease symptoms when TSWV isolate 10 was used as opposed to A. hypogaea lines that ranged from moderately to highly susceptible. Additional testing with more virulent isolates identified A. diogoi accession GKP 10602 and A. correntina accession GKP 9530 as highly resistant to the virus. These two accessions are being used as parents in crossing programs to incorporate TSWV resistance genes into A. hypogaea. DA - 2002/// PY - 2002/// DO - 10.3146/pnut.29.2.0001 VL - 29 SP - 79-84 ER -