TY - JOUR TI - Germ‐line transformation of the Australian sheep blowfly Lucilia cuprina AU - Heinrich, J. C. AU - Li, X. AU - Henry, R. A. AU - Haack, N. AU - Stringfellow, L. AU - Heath, A. C. G. AU - Scott, M. J. T2 - Insect Molecular Biology AB - Abstract The Australian sheep blowfly, Lucilia cuprina , is the most important economic insect pest for the sheep industries in Australia and New Zealand. piggyBac ‐mediated germ‐line transformation of L. cuprina was achieved with a helper plasmid that had the Drosophila melanogaster hsp70 promoter controlling expression of the transposase and a piggyBac vector with an EGFP marker gene. Two transformant lines were obtained, at a frequency of approximately 1–2% per fertile G 0 . One of these lines has a single copy of the transgene, the other most likely has four copies. This is the first report of germ‐line transformation of L. cuprina and is an important step towards the generation of engineered strains that would be suitable for male‐only release eradication/suppression programmes. DA - 2002/2// PY - 2002/2// DO - 10.1046/j.0962-1075.2001.00301.x VL - 11 IS - 1 SP - 1-10 J2 - Insect Molecular Biology LA - en OP - SN - 0962-1075 1365-2583 UR - http://dx.doi.org/10.1046/j.0962-1075.2001.00301.x DB - Crossref 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 - Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3 AU - Zhao, Yunde AU - Hull, Anna K. AU - Gupta, Neeru R. AU - Goss, Kendrick A. AU - Alonso, José AU - Ecker, Joseph R. AU - Normanly, Jennifer AU - Chory, Joanne AU - Celenza, John L. T2 - Genes & Development DA - 2002/// PY - 2002/// VL - 16 IS - 23 SP - 3100-3112 ER - TY - JOUR TI - Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth AU - Friedrichsen, Danielle M. AU - Nemhauser, Jennifer AU - Muramitsu, Takamichi AU - Maloof, Julin N. AU - Alonso, José AU - Ecker, Joseph R. AU - Furuya, Masaki AU - Chory, Joanne T2 - Genetics DA - 2002/// PY - 2002/// VL - 162 IS - 3 SP - 1445-1456 ER - TY - JOUR TI - NPSN11 is a cell plate-associated SNARE protein that interacts with the syntaxin KNOLLE AU - Zheng, Haiyan AU - Bednarek, Sebastian Y. AU - Sanderfoot, Anton A. AU - Alonso, Jose AU - Ecker, Joseph R. AU - Raikhel, Natasha V. T2 - Plant physiology DA - 2002/// PY - 2002/// VL - 129 IS - 2 SP - 530-539 ER - TY - JOUR TI - De-Etiolated 1 and Damaged DNA Binding Protein 1 Interact to Regulate< i> Arabidopsis Photomorphogenesis AU - Schroeder, Dana F. AU - Gahrtz, Manfred AU - Maxwell, Bridey B. AU - Cook, R. Kimberley AU - Kan, Jack M. AU - Alonso, José M. AU - Ecker, Joseph R. AU - Chory, Joanne T2 - Current Biology DA - 2002/// PY - 2002/// VL - 12 IS - 17 SP - 1462-1472 ER - TY - JOUR TI - A role for peroxisomes in photomorphogenesis and development of Arabidopsis AU - Hu, Jianping AU - Aguirre, Maria AU - Peto, Charles AU - Alonso, José AU - Ecker, Joseph AU - Chory, Joanne T2 - Science DA - 2002/// PY - 2002/// VL - 297 IS - 5580 SP - 405-409 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 - SEUSS, a member of a novel family of plant regulatory proteins, represses floral homeotic gene expression with LEUNIG. AU - Franks, R.G. AU - Wang, C. AU - Levin, J.Z. AU - Liu, Z. AU - Development DA - 2002/1// PY - 2002/1// VL - 129 IS - 1 SP - 253–263 UR - http://europepmc.org/abstract/med/11782418 ER - TY - JOUR TI - SEUSS, a member of a novel family of plant regulatory proteins, represses floral homeotic gene expression with LEUNIG AU - Franks, R.G. AU - Wang, C. AU - Levin, J.Z. AU - Liu, Z. T2 - Development DA - 2002/// PY - 2002/// VL - 129 IS - 1 SP - 253-263 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0036333380&partnerID=MN8TOARS ER - TY - JOUR TI - Conservation strategies for Pinus maximinoi based on provenance, RAPD and allozyme information AU - Dvorak, W. S. AU - Hamrick, J. L. AU - Furman, B. J. AU - Hodge, G. R. AU - Jordan, A. P. T2 - Forest Genetics DA - 2002/// PY - 2002/// VL - 9 IS - 4 SP - 263 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 - Trends in reproductive performance in Southeastern Holstein and Jersey DHI herds AU - Washburn, SP AU - Silvia, WJ AU - Brown, CH AU - McDaniel, BT AU - McAllister, AJ T2 - JOURNAL OF DAIRY SCIENCE AB - Trends in average days open and services per conception from 1976 to 1999 were examined in 532 Holstein and 29 Jersey herds from 10 Southeastern states. Three-year averages for eight intervals (time) were calculated (first: 1976 to 1978; eighth: 1997 to 1999). Milk, fat, fat-corrected milk, and number of cows increased across time. Herds of both breeds had linear, quadratic, and cubic effects of time on days open and services per conception. For 1976 to 1978, respective averages of days open and services per conception were 122 +/- 2.8 d and 1.91 +/- 0.08 for Jerseys, 124 +/- 0.7 d and 1.91 +/- 0.02 for Holsteins. Days open increased nonlinearly to 152 +/- 2.8 d for Jerseys and 168 +/- 0.7 d for Holsteins by 1997 to 1999, resulting in a breed x time interaction. Services per conception also increased nonlinearly, reaching 2.94 +/- 0.04 services for both breeds in 1994 to 1996, changing only slightly after 1996. Fat-corrected milk and number of cows had small but significant effects. Five subregions (one to three states) differed in mean days open and services per conception, but changes in those measures across time among subregions were similar. Days to first service increased by 16 (Holsteins) and 18 d (Jerseys) during the last five 3-yr periods, associated with increasing days open. Estrus detection rates generally declined from 1985 to 1999, associated inversely with services per conception. Reduced reproductive performance in Southeastern dairy herds is of concern. Multiple strategies are needed to attenuate further declines. DA - 2002/1// PY - 2002/1// DO - 10.3168/jds.S0022-0302(02)74073-3 VL - 85 IS - 1 SP - 244-251 SN - 0022-0302 KW - Holstein KW - Jersey KW - reproduction KW - days open 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 - Identification and characterization of Leuconostoc fallax strains isolated from an industrial sauerkraut fermentation AU - Barrangou, R AU - Yoon, SS AU - Breidt, F AU - Fleming, HP AU - Klaenhammer, TR T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT Lactic acid bacterial strains were isolated from brines sampled after 7 days of an industrial sauerkraut fermentation, and six strains were selected on the basis of susceptibility to bacteriophages. Bacterial growth in cabbage juice was monitored, and the fermentation end products were identified, quantified, and compared to those of Leuconostoc mesenteroides . Identification by biochemical fingerprinting, endonuclease digestion of the 16S-23S intergenic transcribed spacer region, and sequencing of variable regions V1 and V2 of the 16S rRNA gene indicated that the six selected sauerkraut isolates were Leuconostoc fallax strains. Random amplification of polymorphic DNA fingerprints indicated that the strains were distinct from one another. The growth and fermentation patterns of the L. fallax isolates were highly similar to those of L. mesenteroides . The final pH of cabbage juice fermentation was 3.6, and the main fermentation end products were lactic acid, acetic acid, and mannitol for both species. However, none of the L. fallax strains exhibited the malolactic reaction, which is characteristic of most L. mesenteroides strains. These results indicated that in addition to L. mesenteroides , a variety of L. fallax strains may be present in the heterofermentative stage of sauerkraut fermentation. The microbial ecology of sauerkraut fermentation appears to be more complex than previously indicated, and the prevalence and roles of L. fallax require further investigation. DA - 2002/6// PY - 2002/6// DO - 10.1128/AEM.68.6.2877-2884.2002 VL - 68 IS - 6 SP - 2877-2884 SN - 0099-2240 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 - JOUR TI - A genetic attack on the defense complex AU - Gibson, G T2 - BIOESSAYS AB - An increasing number of "non-model" organisms are becoming accessible to genetic analysis in the field, as evolutionary biologists develop dense molecular genetic maps. Peichel et al.'s recent study(1) provides a microsatellite-based map for threespine stickleback fish (Gasterosteus aculeatus), and the first evidence for QTL affecting feeding morphology and defensive armor. This species has undergone rapid and parallel morphological and behavioral evolution, and there is now hope that some of the genes responsible for the divergence may soon be identified. DA - 2002/6// PY - 2002/6// DO - 10.1002/bies.10104 VL - 24 IS - 6 SP - 487-489 SN - 1521-1878 ER - TY - JOUR TI - Long-term manipulations of intact microbial mat communities in a greenhouse collaboratory: Simulating Earth's present and past field environments AU - Bebout, BM AU - Carpenter, SP AU - Des Marais, DJ AU - Discipulo, M AU - Embaye, T AU - Garcia-Pichel, F AU - Hoehler, TM AU - Hogan, M AU - Jahnke, LL AU - Keller, RM AU - Miller, , SR AU - Prufert-Bebout, LE AU - Raleigh, C AU - Rothrock, M AU - Turk, K T2 - ASTROBIOLOGY AB - Photosynthetic microbial mat communities were obtained from marine hypersaline saltern ponds, maintained in a greenhouse facility, and examined for the effects of salinity variations. Because these microbial mats are considered to be useful analogs of ancient marine communities, they offer insights about evolutionary events during the >3 billion year time interval wherein mats co-evolved with Earth's lithosphere and atmosphere. Although photosynthetic mats can be highly dynamic and exhibit extremely high activity, the mats in the present study have been maintained for >1 year with relatively minor changes. The major groups of microorganisms, as assayed using microscopic, genetic, and biomarker methodologies, are essentially the same as those in the original field samples. Field and greenhouse mats were similar with respect to rates of exchange of oxygen and dissolved inorganic carbon across the mat-water interface, both during the day and at night. Field and greenhouse mats exhibited similar rates of efflux of methane and hydrogen. Manipulations of salinity in the water overlying the mats produced changes in the community that strongly resemble those observed in the field. A collaboratory testbed and an array of automated features are being developed to support remote scientific experimentation with the assistance of intelligent software agents. This facility will permit teams of investigators the opportunity to explore ancient environmental conditions that are rare or absent today but that might have influenced the early evolution of these photosynthetic ecosystems. DA - 2002/// PY - 2002/// DO - 10.1089/153110702762470491 VL - 2 IS - 4 SP - 383-402 SN - 1531-1074 KW - microbial mat KW - biogeochemistry KW - biomarkers ER - TY - JOUR TI - Marker-assisted selection for resistance to black shank disease in tobacco AU - Johnson, ES AU - Wolff, MF AU - Wernsman, EA AU - Rufty, RC T2 - PLANT DISEASE AB - Bulked segregant (BSA) and random amplified polymorphic DNA (RAPD) analyses were used to identify markers linked to the dominant black shank resistance gene, Ph, from flue-cured tobacco (Nicotiana tabacum) cv. Coker 371-Gold. Sixty RAPD markers, 54 in coupling and 6 in repulsion phase linkage to Ph, were identified in a K 326-derived BC1F1 (K 326-BC1F1) doubled haploid (DH) population. Thirty RAPD markers, 26 in coupling and 4 in repulsion phase linkage to Ph, were used to screen 149 K 326-BC2F1 haploid plants. Complete linkage between the 26 coupling phase markers and Ph was confirmed by screening 149 K 326-BC2F1 DH lines produced from the haploid plants in black shank nurseries. RAPD markers OPZ-5770 in coupling and OPZ-7370 in repulsion phase linkage were used to select plants homozygous for the Ph gene for further backcrossing to the widely grown flue-cured cultivar K 326. Black shank disease nursery evaluation of 11 K 326-BC4S1 lines and their testcross hybrids to a susceptible tester confirmed linkage between Ph and OPZ-5770. The results demonstrated the efficiency of marker-assisted selection for Ph using a RAPD marker linked in coupling and repulsion. Complete linkage between 26 RAPD markers and the Ph gene was confirmed in the K 326-BC5 generation, and RAPD phenotypes were stable across generations and ploidy levels. These RAPD markers are useful in marker-assisted selection for Ph, an important black shank resistance gene in tobacco. DA - 2002/12// PY - 2002/12// DO - 10.1094/PDIS.2002.86.12.1303 VL - 86 IS - 12 SP - 1303-1309 SN - 1943-7692 KW - bulked segregant and RAPD analyses KW - disease resistance genes KW - Phytophthora parasitica var. nicotianae 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 - Food research trends - 2003 and beyond AU - Mermelstein, N. H. AU - Fennema, O. R. AU - Batt, C. A. AU - Goff, H. D. AU - Griffiths, M. W. AU - Hoover, D. G. AU - Hsieh, F. H. AU - Juneja, V. K. AU - Kroger, M. AU - Lund, D. B. AU - Miller, D. D. AU - Min, D. B. AU - Murphy, P. A. AU - Palumbo, S. A. AU - Rao, M. A. AU - Ryser, E. T. AU - Klaenhammer, T. AU - al, T2 - Food Technology DA - 2002/// PY - 2002/// VL - 56 IS - 12 SP - 30- ER - TY - JOUR TI - Divergence time and evolutionary rate estimation with multilocus data AU - Thorne, JL AU - Kishino, H T2 - SYSTEMATIC BIOLOGY AB - Bayesian methods for estimating evolutionary divergence times are extended to multigene data sets, and a technique is described for detecting correlated changes in evolutionary rates among genes. Simulations are employed to explore the effect of multigene data on divergence time estimation, and the methodology is illustrated with a previously published data set representing diverse plant taxa. The fact that evolutionary rates and times are confounded when sequence data are compared is emphasized and the importance of fossil information for disentangling rates and times is stressed. DA - 2002/// PY - 2002/// DO - 10.1080/10635150290102456 VL - 51 IS - 5 SP - 689-702 SN - 1076-836X KW - Markov chain Monte Carlo KW - Metropolis-Hastings algorithm KW - molecular clock KW - phylogeny ER - TY - JOUR TI - Discovering lactic acid bacteria by genomics AU - Klaenhammer, T. AU - Altermann, E. AU - Arigoni, F. AU - Bolotin, A. AU - Breidt, F. AU - Broadbent, J. AU - Cano, R. AU - Chaillou, S. AU - Deutscher, J. AU - Gasson, M. AU - Van De Guchte, M. AU - Guzzo, J. AU - Hartke, A. AU - Hawkins, T. AU - Hols, P. AU - Hutkins, R. AU - Kleerebezem, M. AU - Kok, J. AU - al., T2 - Antonie Van Leeuwenhoek AB - This review summarizes a collection of lactic acid bacteria that are now undergoing genomic sequencing and analysis. Summaries are presented on twenty different species, with each overview discussing the organisms fundamental and practical significance, environmental habitat, and its role in fermentation, bioprocessing, or probiotics. For those projects where genome sequence data were available by March 2002, summaries include a listing of key statistics and interesting genomic features. These efforts will revolutionize our molecular view of Gram-positive bacteria, as up to 15 genomes from the low GC content lactic acid bacteria are expected to be available in the public domain by the end of 2003. Our collective view of the lactic acid bacteria will be fundamentally changed as we rediscover the relationships and capabilities of these organisms through genomics. DA - 2002/// PY - 2002/// DO - 10.1007/978-94-017-2029-8_3 VL - 82 IS - 1-4 SP - 29-58 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 - 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. 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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 - 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 - Unusual genetic architecture of natural variation affecting drug resistance in Drosophila melanogaster AU - Carrillo, R AU - Gibson, G T2 - GENETICAL RESEARCH AB - Naturally occurring genetic variation was quantified for survival time of adult Drosophila melanogaster exposed to chronic ingestion of the drugs nicotine, caffeine, dopamine, tyramine and octopamine. Responses to nicotine, tyramine and octopamine were genetically correlated in both sexes, whereas caffeine response correlated with starvation resistance. However, there is also genetic variation that is specific for each of the drugs. Females tended to be more resistant than males to nicotine and caffeine but sex-by-genotype interactions were also seen for these drugs and for the response to dopamine. An unusual and complex genetic architecture was observed in crosses between lines with different responses to caffeine ingestion. Additive and dominance components were clearly seen from the analysis of F1 individuals, but increased female resistance to caffeine in backcross generations and increased male sensitivity in F2 generations confused the interpretation of possible epistatic contributions. DA - 2002/12// PY - 2002/12// DO - 10.1017/S0016672302005888 VL - 80 IS - 3 SP - 205-213 SN - 0016-6723 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 - 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 - 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 - Overexpression of peptidases in Lactococcus and evaluation of their release from leaky cells AU - Tuler, TR AU - Callanan, MJ AU - Klaenhammer, TR T2 - JOURNAL OF DAIRY SCIENCE AB - Walker and Klaenhammer (2001) developed a novel expression system in Lactococcus lactis that facilitated the release of beta-galactosidase (117 kDa monomer) without the need for secretion or export signals. The system is based on the controlled expression of integrated prophage holin and lysin cassettes via a lactococcal bacteriophage phi31 transcriptional activator (Tac31A) that resides on a high-copy plasmid. Approximately 85% of beta-galactosidase activity was detected in the supernatant of leaky lactococci without evidence of hindered growth, cell lysis, or membrane damage. The objective of this study was to determine if intracellular peptidases were externalized from leaky lactococci. Five L. lactis peptidases (PepA, PepC, PepN, PepO and PepXP) and two Lactobacillus helveticus peptidases (PepN and PepO) were cloned and overexpressed on two high-copy vectors. The lactococcal peptidases were also cloned into the high-copy vector that contained the Tac31A transcriptional activator to determine if they were externalized from the leaky prophage-containing L. lactis subsp. lactis strain NCK203. Two of the lactococcal peptidases (PepA and PepO) required an additional strong promoter (Lactobacillus paracasei P144) and optimized assay conditions to detect enzyme activity. Results showed different levels of enzymatic overexpression associated with the cellular fraction (2 to 250-fold increases in activity) and negligible amounts of activity present within the supernatant fraction (0 to 6% of total peptidase activity). The lactococcal phage-based protein release mechanism did not facilitate the externalization of the lactococcal peptidases investigated in this study. DA - 2002/10// PY - 2002/10// DO - 10.3168/jds.S0022-0302(02)74326-9 VL - 85 IS - 10 SP - 2438-2450 SN - 1525-3198 KW - leaky Lactococcus KW - peptidase ER - TY - JOUR TI - Molecular evolution and structure-function relationships of the superoxide dismutase gene families in angiosperms and their relationship to other eukaryotic and prokaryotic superoxide dismutases AU - Fink, RC AU - Scandalios, JG T2 - ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS AB - This study assesses whether the phylogenetic relationships between SODs from different organisms could assist in elucidating the functional relationships among these enzymes from evolutionarily distinct species. Phylogenetic trees and intron positions were compared to determine the relationships among these enzymes. Alignment of Cu/ZnSOD amino acid sequences indicates high homology among plant sequences, with some features that distinguish chloroplastic from cytosolic Cu/ZnSODs. Among eukaryotes, the plant SODs group together. Alignment of the Mn and FeSOD amino acid sequences indicates a higher degree of homology within the group of MnSODs (>70%) than within FeSODs (approximately 60%). Tree topologies are similar and reflect the taxonomic classification of the corresponding species. Intron number and position in the Cu/Zn Sod genes are highly conserved in plants. Genes encoding cytosolic SODs have seven introns and genes encoding chloroplastic SODs have eight introns, except the chloroplastic maize Sod1, which has seven. In Mn Sod genes the number and position of introns are highly conserved among plant species, but not among nonplant species. The link between the phylogenetic relationships and SOD functions remains unclear. Our findings suggest that the 5' region of these genes played a pivotal role in the evolution of function of these enzymes. Nevertheless, the system of SODs is highly structured and it is critical to understand the physiological differences between the SODs in response to different stresses in order to compare their functions and evolutionary history. DA - 2002/3/1/ PY - 2002/3/1/ DO - 10.1006/abbi.2001.2739 VL - 399 IS - 1 SP - 19-36 SN - 1096-0384 KW - SOD,superoxide dismutase protein or isozyme KW - Sod, superoxide dismutase gene or transcript KW - molecular evolution KW - phylogenetic tree KW - gene structure and function KW - Zea mays L. (maize) KW - antioxidant genes KW - oxidative stress KW - reactive oxygen species (ROS) ER - TY - JOUR TI - Lactococcus lactis lytic bacteriophages of the p335 group are inhibited by overexpression of a truncated CI repressor AU - Durmaz, E AU - Madsen, SA AU - Israelsen, H AU - Klaenhammer, TR T2 - JOURNAL OF BACTERIOLOGY AB - ABSTRACT Phages of the P335 group have recently emerged as important taxa among lactococcal phages that disrupt dairy fermentations. DNA sequencing has revealed extensive homologies between the lytic and temperate phages of this group. The P335 lytic phage φ31 encodes a genetic switch region of c I and cro homologs but lacks the phage attachment site and integrase necessary to establish lysogeny. When the putative c I repressor gene of phage φ31 was subcloned into the medium-copy-number vector pAK80, no superinfection immunity was conferred to the host, Lactococcus lactis subsp. lactis NCK203, indicating that the wild-type CI repressor was dysfunctional. Attempts to clone the full-length c I gene in Lactococcus in the high-copy-number shuttle vector pTRKH2 were unsuccessful. The single clone that was recovered harbored an ochre mutation in the c I gene after the first 128 amino acids of the predicted 180-amino-acid protein. In the presence of the truncated CI construct, pTRKH2::CI-per1, phage φ31 was inhibited to an efficiency of plaquing (EOP) of 10 −6 in NCK203. A pTRKH2 subclone which lacked the DNA downstream of the ochre mutation, pTRKH2::CI-per2, confirmed the phenotype and further reduced the φ31 EOP to <10 −7 . Phage φ31 mutants, partially resistant to CI-per, were isolated and showed changes in two of three putative operator sites for CI and Cro binding. Both the wild-type and truncated CI proteins bound the two wild-type operators in gel mobility shift experiments, but the mutated operators were not bound by the truncated CI. Twelve of 16 lytic P335 group phages failed to form plaques on L. lactis harboring pTRKH2::CI-per2, while 4 phages formed plaques at normal efficiencies. Comparisons of amino acid and DNA level homologies with other lactococcal temperate phage repressors suggest that evolutionary events may have led to inactivation of the φ31 CI repressor. This study demonstrated that a number of different P335 phages, lytic for L. lactis NCK203, have a common operator region which can be targeted by a truncated derivative of a dysfunctional CI repressor. DA - 2002/12// PY - 2002/12// DO - 10.1128/JB.184.23.6532-6543.2002 VL - 184 IS - 23 SP - 6532-6543 SN - 0021-9193 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 - Catalase gene expression in response to auxin-mediated developmental signals AU - Guan, LQM AU - Scandalios, JG T2 - PHYSIOLOGIA PLANTARUM AB - The effect of auxin on maize catalase gene expression was examined at several different developmental stages during embryo and seedling development. All three catalase genes and their respective proteins were induced by both natural and synthetic auxin in immature embryos. Total catalase (CAT) activity increased dramatically in response to high concentrations of auxin, with CAT-2, which is not normally expressed at this stage, being the isozyme most responsible for the increase. Cat1 transcript accumulated to high levels at 2-8 h after auxin treatment, while Cat2 and Cat3 transcripts increased dramatically, but only after 12 h. In CAT-2 null mutant lines, the CAT-1 isozyme compensated for the missing CAT-2 activity and was the major isozyme responsible for the observed increase in total CAT activity. Auxin treatment mimics the germination process (i.e. induces germination) in immature embryos. Thus, the observed early induction of CAT-1 and the later increase of CAT-2 during the germination process may be due, in part, to changes in auxin content. In germinating embryos, auxin also induces total CAT activity and Cat transcript accumulation, although to a lesser extent. Auxin also induces Cat1 transcript accumulation in young leaves. The involvement of ROS in the auxin response is discussed. DA - 2002/2// PY - 2002/2// DO - 10.1034/j.1399-3054.2002.1140215.x VL - 114 IS - 2 SP - 288-295 SN - 1399-3054 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 - 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 - Estimation of effective population size of HIV-1 within a host: A pseudomaximum-likelihood approach AU - Seo, T. K. AU - Thorne, J. L. AU - Hasegawa, M. AU - Kishino, H. T2 - Genetics DA - 2002/// PY - 2002/// VL - 160 IS - 4 SP - 1283-1293 ER - TY - JOUR TI - Environment dependence of mutational parameters for viability in Drosophila melanogaster AU - Fry, J. D. AU - Heinsohn, S. L. T2 - Genetics DA - 2002/// PY - 2002/// VL - 161 IS - 3 SP - 1155-1167 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 - 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 - 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 - Effects of nitrogen availability on pigmentation and carbon assimilation in the cyanobacterium Synechococcus sp strain SH-94-5 AU - Miller, , SR AU - Martin, M AU - Touchton, J AU - Castenholz, RW T2 - ARCHIVES OF MICROBIOLOGY DA - 2002/5// PY - 2002/5// DO - 10.1007/s00203-002-0404-8 VL - 177 IS - 5 SP - 392-400 SN - 1432-072X KW - chlorophyll KW - cyanobacteria KW - nitrogen starvation KW - pigmentation-photosynthesis KW - Synechococcus KW - UV radiation 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 - Relationships of productive life evaluations with changes in evaluations for yields AU - Abdallah, JM AU - McDaniel, BT AU - Tabbaa, MJ T2 - JOURNAL OF DAIRY SCIENCE AB - The objective of this work was to investigate the relationships of productive life with changes in bull evaluations for yield traits. Two datasets were analyzed. In the first, predicted differences for change in milk yield from first to second lactation of daughters of artificial insemination (AI) Holstein bulls used widely in the southeastern United States were available from a previous study. These were correlated with predicted transmitting abilities (PTA) of productive life from May 2000 USDA sire evaluations. Based on bulls with at least 10 daughters (n = 560) the correlation of PTA productive life with predicted differences for the change in milk yield was 0.30. The correlation increased to 0.36 for bulls with at least 50 daughters (n = 319) and to 0.40 for bulls with at least 75 daughters (n = 284). The second analysis included data on 1831 AI sampled Holstein bulls evaluated by USDA between July 1989 and May 2000. Changes in PTA yields were calculated as PTA from evaluations based on first and second records of daughters minus those from first-record evaluations. Correlation analyses showed that PTA yields from first-record evaluation and changes in PTA yields were positively associated with productive life. Regression coefficients on changes in PTA yields were all positive indicating that increases in PTA for yield traits as daughters aged corresponded with longer productive life. Using changes in AI bull evaluations for yields could improve prediction of productive life for little cost. DA - 2002/3// PY - 2002/3// DO - 10.3168/jds.s0022-0302(02)74123-4 VL - 85 IS - 3 SP - 677-681 SN - 0022-0302 KW - correlations KW - predicted transmitting abilities KW - productive life ER - TY - JOUR TI - Proven and young Holstein: Bulls compared for daughter yields, productive life, somatic cell score, and inbreeding AU - Abdallah, JM AU - McDaniel, BT T2 - JOURNAL OF DAIRY SCIENCE AB - The objective of this study was to compare daughters of proven (progeny-tested) and young sampling bulls available for use at the same time for yield traits, productive life, somatic cell score, and inbreeding. Data were from USDA sire evaluations of July 1989 through July 1994. Proven bulls used between 1989 and 1994 were identified based on the change in number of daughters. Young bulls were identified based on age and date a bull first entered artificial insemination. Young bulls were classified into two categories: one included all young bulls available in one year and the other included the top 50% on parent average for milk. Daughter deviations for yields, productive life and somatic cell scores, and average inbreeding were obtained from May 2000 evaluation. Daughter deviation milk was not different between proven and top 50% young bulls but was lower for all young bulls. Young bulls (all and top 50%) exceeded proven bulls in daughter deviation fat and protein. Progeny of proven bulls had favorably higher productive life in most years but unfavorably higher somatic cell score than progeny of young bulls. Inbreeding was consistently higher for daughters of young bulls than for those of proven bulls. Results indicate that young bulls were competitive with proven bulls. Use of young bulls from among the top 50% should result in equal or higher genetic progress in yields compared to contemporaries by proven bulls. DA - 2002/3// PY - 2002/3// DO - 10.3168/jds.s0022-0302(02)74121-0 VL - 85 IS - 3 SP - 665-669 SN - 0022-0302 KW - daughter deviations KW - proven bulls KW - young bulls ER - TY - JOUR TI - Prediction of most recent evaluations of Holstein bulls from first available pedigree information AU - Abdallah, JM AU - McDaniel, BT T2 - JOURNAL OF DAIRY SCIENCE AB - The objectives of this study were to predict most recent evaluations of young bulls entering artificial insemination (AI) sampling programs from pedigree information available at time of sampling and investigate whether prediction equations differ among AI organizations. Data were pedigree information and most recent USDA evaluations on bulls entering AI sampling programs from 1989 through 1994. Pedigree information included earliest available parent average, predicted transmitting abilities (PTA) of sire, dam, and maternal grand sire. Most recent evaluations were from May 2000 evaluations and included PTA and daughter yield deviations for milk, fat, and protein. Regression coefficients on PTA of sire and PTA of dam were less than the expected coefficient of 0.50. Accuracy of prediction as determined by R-square values was less than 12%. Inclusion of PTA of maternal grand sire after PTA of sire and dam increased the accuracy of prediction by less than 1%, but regression coefficients on PTA of maternal grand sire differed from 0. Regressions on parent average were not different among AI organizations for prediction of PTA and daughter yield deviations. Partial regression coefficients on PTA of sire differed among AI organizations for prediction of fat and protein but did not differ for milk. Coefficients on PTA of dam did not differ among organizations. These results indicate that AI organizations put different emphasis on PTA of sire in selection of sons for fat and protein. DA - 2002/3// PY - 2002/3// DO - 10.3168/jds.s0022-0302(02)74122-2 VL - 85 IS - 3 SP - 670-676 SN - 0022-0302 KW - genetic evaluations KW - pedigree selection KW - prediction 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 - Heritability of changes in genetic evaluations of dairy bulls from first to later records of daughters AU - Abdallah, JM AU - McDaniel, BT T2 - JOURNAL OF DAIRY SCIENCE AB - Objectives of this study were to investigate changes in predicted transmitting abilities (PTA) of yields from evaluations based on first records to evaluations based on first and later records of daughters and determine whether these changes are heritable. Data were USDA sire evaluations of July 1989 through May 2000 on Holstein bulls in standard progeny testing programs. Changes in PTA for milk, fat, and protein from evaluations based on first records of daughters to evaluations on first and second were obtained on 2001 bulls. These were divided into two sets: subset 1 (n = 889) included bulls first evaluated before 1995 and subset 2 (n = 1112) included bulls first evaluated in 1995 and later. Changes in PTA from first-record evaluation to most recent evaluation (May 2000) were obtained on 2524 bulls first evaluated in 1995 or later. Mean changes in PTA for bulls first evaluated in 1995 and later were smaller than mean changes for bulls evaluated earlier but standard deviations were similar. Regressions of changes in PTA on changes in parent average showed that a change of 1.0 kg in parent average resulted in 1.1 to 1.2 kg change in PTA. Heritabilities estimated with animal model ranged from 0.14 to 0.23 for changes from first-record evaluation to evaluation on first and second, and 0.27 to 0.35 for changes from first-record evaluation to most recent evaluation. Heritabilities of this magnitude allow for identifying bulls that decrease in PTA. DA - 2002/4// PY - 2002/4// DO - 10.3168/jds.S0022-0302(02)74154-4 VL - 85 IS - 4 SP - 951-957 SN - 0022-0302 KW - change in evaluations KW - heritability ER - TY - JOUR TI - Distribution of strains of Staphylococcus aureus isolated from milk of cows in North Carolina AU - Smith, P. AU - Spooner, C. AU - Lyman, R. AU - George, C. AU - Kloos, W. AU - Anderson, K. T2 - Annual Meeting, National Mastitis Council, Inc DA - 2002/// PY - 2002/// VL - 41 IS - 2002 SP - 233-234 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 - Microarrays in ecology and evolution: a preview AU - Gibson, G T2 - MOLECULAR ECOLOGY AB - Microarray technology provides a new tool with which molecular ecologists and evolutionary biologists can survey genome-wide patterns of gene expression within and among species. New analytical approaches based on analysis of variance will allow quantification of the contributions of among individual variation, genotype, sex, microenvironment, population structure, and geography to variation in gene expression. Applications of this methodology are reviewed in relation to studies of mechanisms of adaptation and divergence; delineation of developmental and physiological pathways and networks; characterization of quantitative genetic parameters at the level of transcription ('quantitative genomics'); molecular dissection of parasitism and symbiosis; and studies of the diversification of gene content. Establishment of microarray resources is neither prohibitively expensive nor technologically demanding, and a commitment to development of gene expression profiling methods for nonmodel organisms could have a tremendous impact on molecular and genetic research at the interface of organismal and population biology. DA - 2002/1// PY - 2002/1// DO - 10.1046/j.0962-1083.2001.01425.x VL - 11 IS - 1 SP - 17-24 SN - 1365-294X KW - cDNA microarray KW - gene expression profiling KW - parasitism KW - population structure KW - quantitative genomics KW - symbiosis KW - variation ER - TY - JOUR TI - Conservation and regeneration of transgenic lines of swine by semen cryopreservation and artificial insemination AU - Sommer, J. R. AU - Collins, E. B. AU - Neiding, T. AU - Rozeboom, K. AU - Wong, F. AU - Petters, R. M. T2 - Lab Animal DA - 2002/// PY - 2002/// VL - 31 IS - 1 SP - 25-31 ER - TY - JOUR TI - Roles of gene transcription and PKA subtype activation in maturation of murine oocytes AU - Rodriguez, K. F. AU - Petters, R. M. AU - Crosier, A. E. AU - Farin, C. E. T2 - Reproduction (Cambridge, England) AB - The aims of this study were to examine the role of transcription and the coincident involvement of type I and type II protein kinase A (PKA) in the resumption of meiosis in murine cumulus-oocyte complexes (COCs) using the transcriptional inhibitors 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) and alpha-amanitin. The first series of experiments was designed to: (i) characterize the role of transcription in gonadotrophin-mediated and spontaneous maturation of murine oocytes; (ii) examine the roles of specific gonadotrophins (FSH versus hCG) and cumulus cells in transcriptionally mediated oocyte maturation; and (iii) determine the reversibility of the transcriptional arrest of meiosis. In the presence of FSH, transcriptional inhibitors arrested germinal vesicle breakdown (GVBD) (DRB: 2 +/- 2% and control: 76 +/- 2%; alpha-amanitin: 4 +/- 4% and control: 70 +/- 4%). Furthermore, cumulus cells were required for transcriptional inhibitors to arrest GVBD (DRB with cumulus cells: 0 +/- 15%; DRB without cumulus cells: 94 +/- 13%; alpha-amanitin with cumulus cells: 15 +/- 2%; alpha-amanitin without cumulus cells: 99 +/- 2%). Thus, in mice, FSH-mediated GVBD uses a transcriptional mechanism, which probably occurs within the cumulus cell compartment. In a second series of experiments, the role of transcription in mediating the resumption of meiosis after activation of either type I or type II PKA was examined. Activation of type I PKA in murine COCs resulted in an arrest of GVBD that was independent of a transcriptional event (with DRB: 7 +/- 9% GVBD; without DRB: 11 +/- 9% GVBD). In contrast, activation of type II PKA resulted in a resumption of meiosis, which required the occurrence of gene transcription (with DRB: 12 +/- 9% GVBD; without DRB: 80 +/- 9% GVBD). As FSH binding to cumulus cells activates the PKA second messenger system, our results indicate that, in cultured murine COCs, FSH binding to cumulus cells results in the activation of type II PKA, which, in turn, mediates a downstream transcriptional event required for the initiation of GVBD. DA - 2002/// PY - 2002/// DO - 10.1530/rep.0.1230799 VL - 123 IS - 6 SP - 799-806 ER - TY - JOUR TI - Isolation and characterization of bacteriophages from fermenting sauerkraut AU - Yoon, SS AU - Barrangou-Poueys, R AU - Breidt, F AU - Klaenhammer, TR AU - Fleming, HP T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT This paper presents the first report of bacteriophage isolated from commercial vegetable fermentations. Nine phages were isolated from two 90-ton commercial sauerkraut fermentations. These phages were active against fermentation isolates and selected Leuconostoc mesenteroides and Lactobacillus plantarum strains, including a starter culture. Phages were characterized as members of the Siphoviridae and Myoviridae families. All Leuconostoc phages reported previously, primarily of dairy origin, belonged to the Siphoviridae family. DA - 2002/2// PY - 2002/2// DO - 10.1128/AEM.68.2.973-976.2002 VL - 68 IS - 2 SP - 973-976 SN - 0099-2240 ER - TY - JOUR TI - Expression of antisense RNA targeted against Streptococcus thermophilus bacteriophages AU - Sturino, JM AU - Klaenhammer, TR T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT Antisense RNA complementary to a putative helicase gene ( hel3.1 ) of a cos -type Streptococcus thermophilus bacteriophage was used to impede the proliferation of a number of cos -type S. thermophilus bacteriophages and one pac -type bacteriophage. The putative helicase gene is a component of the Sfi21-type DNA replication module, which is found in a majority of the S. thermophilus bacteriophages of industrial importance. All bacteriophages that strongly hybridized a 689-bp internal hel3.1 probe were sensitive to the expression of antisense hel3.1 RNA. A 40 to 70% reduction in efficiency of plaquing (EOP) was consistently observed, with a concomitant decrease in plaque size relative to that of the S. thermophilus parental strain. When progeny were released, the burst size was reduced. Growth curves of S. thermophilus NCK1125, in the presence of variable levels of bacteriophage κ3, showed that antisense hel3.1 conferred protection, even at a multiplicity of infection of approximately 1.0. When the hel3.1 antisense RNA cassette was expressed in cis from the κ3-derived phage-encoded resistance (PER) plasmid pTRK690:: ori3.1 , the EOP for bacteriophages sensitive to PER and antisense targeting was reduced to between 10 −7 and 10 −8 , beyond the resistance conferred by the PER element alone (less than 10 −6 ). These results illustrate the first successful applications of antisense RNA and explosive delivery of antisense RNA to inhibit the proliferation of S. thermophilus bacteriophages. DA - 2002/2// PY - 2002/2// DO - 10.1128/AEM.68.2.588-596.2002 VL - 68 IS - 2 SP - 588-596 SN - 1098-5336 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 - A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times AU - Seo, TK AU - Thorne, JL AU - Hasegawa, M AU - Kishino, H T2 - BIOINFORMATICS AB - The high pace of viral sequence change means that variation in the times at which sequences are sampled can have a profound effect both on the ability to detect trends over time in evolutionary rates and on the power to reject the Molecular Clock Hypothesis (MCH). Trends in viral evolutionary rates are of particular interest because their detection may allow connections to be established between a patient's treatment or condition and the process of evolution. Variation in sequence isolation times also impacts the uncertainty associated with estimates of divergence times and evolutionary rates. Variation in isolation times can be intentionally adjusted to increase the power of hypothesis tests and to reduce the uncertainty of evolutionary parameter estimates, but this fact has received little previous attention.We provide approximations for the power to reject the MCH when the alternative is that rates change in a linear fashion over time and when the alternative is that rates differ randomly among branches. In addition, we approximate the standard deviation of estimated evolutionary rates and divergence times. We illustrate how these approximations can be exploited to determine which viral sample to sequence when samples representing different dates are available. DA - 2002/1// PY - 2002/1// DO - 10.1093/bioinformatics/18.1.115 VL - 18 IS - 1 SP - 115-123 SN - 1367-4803 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 - JOUR TI - Microarrays in ecology and evolution: A preview. AU - Gibson, G. T2 - Molecular Ecology DA - 2002/// PY - 2002/// VL - 11 IS - 1 SP - 17-24 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 - The evolution of developmental regulatory pathways AU - Gibson, G AU - Honeycutt, E T2 - CURRENT OPINION IN GENETICS & DEVELOPMENT AB - Evolutionary analysis of the content of developmental regulatory pathways has been advanced by the publication of pairs of complete genome sequences from representative taxonomic groups. Annotation of the fission yeast, rice, and mouse genomes confirms that most regulatory families are shared among eukaryotes but also shows that certain gene families have restricted distributions. Theoretical advances in the past few years include development of the theory of scale-free networks, which provides a new framework in which to consider the connectivity and evolution of regulatory systems, and introduction of algorithms that use comparative data to enhance detection of transcriptional regulatory motifs. DA - 2002/12// PY - 2002/12// DO - 10.1016/S0959-437X(02)00352-0 VL - 12 IS - 6 SP - 695-700 SN - 1879-0380 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 - Genetic and nutritional effects on swine excreta AU - Crocker, A. W. AU - Robison, O. W. T2 - Journal of Animal Science AB - The objective of this study was to investigate genetic and nutritional effects on swine excreta. Two studies were used. Study I was a 3 x 2 x 2 factorial design with three genetic groups, two diets, and two sexes. Genetic groups were a maternal line (WL), paternal line (BL) and their F1 progeny. Corn-soybean meal diets with either 18 or 14% CP, differing only by substitution of soybean meal for corn, were used in both studies. Study II was a 2 x 2 factorial design with two genetic groups and two diets. High testosterone (D2) and low testosterone (D1) Duroc lines were used. Solid and liquid wastes were collected for 3 d. A total of 108 pens in Study I and 50 pens in Study II were sampled twice. Total excreta were measured and samples collected for chemical analysis of N, NH3N, P, Ca, Cu, K, Zn, and Fe. Measures were adjusted for pig weight and feed disappearance. Maternal-line pigs excreted significantly less P, Ca, Cu, Zn, and Fe than F1 or BL pigs and numerically smaller quantities of all nutrients than BL pigs. In study II, differences were found between lines ofthe same breed. Line D2 pigs had greater output of P, Ca, and Cu (P< 0.05) than D1 pigs and numerically larger quantities of all other nutrients except NH3N and Fe. Pigs fed 14% CP excreted less N, NH3N, and K (P < 0.01) in both studies and excreted significantly less P in Study I. Pigs on a 14% CP diet excreted numerically smaller amounts of all nutrients in both studies except Ca in Study II. In Study I, gilts excreted smaller (P < 0.05) amounts of all nutrients than barrows. Genetic, nutritional, and gender differences influenced waste output. DA - 2002/// PY - 2002/// DO - 10.2527/2002.80112809x VL - 80 IS - 11 SP - 2809-2816 ER - TY - JOUR TI - E-coli chromosomal DNA in a transgene locus created by microprojectile bombardment in tobacco AU - Ulker, B AU - Weissinger, AK AU - Spiker, S T2 - TRANSGENIC RESEARCH DA - 2002/6// PY - 2002/6// DO - 10.1023/A:1015614220200 VL - 11 IS - 3 SP - 311-313 SN - 0962-8819 KW - DNA purity KW - E. coli chromosomal DNA KW - microprojectile bombardment KW - transformation KW - transgene locus ER - TY - JOUR TI - Characterization of six Leuconostoc fallax bacteriophages isolated from an industrial sauerkraut fermentation AU - Barrangou, R AU - Yoon, SS AU - Breidt, F AU - Fleming, HP AU - Klaenhammer, TR T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT Six bacteriophages active against Leuconostoc fallax strains were isolated from industrial sauerkraut fermentation brines. These phages were characterized as to host range, morphology, structural proteins, and genome fingerprint. They were exclusively lytic against the species L. fallax and had different host ranges among the strains of this species tested. Morphologically, three of the phages were assigned to the family Siphoviridae , and the three others were assigned to the family Myoviridae . Major capsid proteins detected by electrophoresis were distinct for each of the two morphotypes. Restriction fragment length polymorphism analysis and randomly amplified polymorphic DNA fingerprinting showed that all six phages were genetically distinct. These results revealed for the first time the existence of bacteriophages that are active against L. fallax and confirmed the presence and diversity of bacteriophages in a sauerkraut fermentation. Since a variety of L. fallax strains have been shown to be present in sauerkraut fermentation, bacteriophages active against L. fallax are likely to contribute to the microbial ecology of sauerkraut fermentation and could be responsible for some of the variability observed in this type of fermentation. DA - 2002/11// PY - 2002/11// DO - 10.1128/AEM.68.11.5452-5458.2002 VL - 68 IS - 11 SP - 5452-5458 SN - 1098-5336 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 - Population history of Manihot esculenta (Euphorbiaceae) inferred from nuclear DNA sequences AU - Olsen, KM T2 - MOLECULAR ECOLOGY AB - The nature of gene flow in plants -- including the propensity for interspecific introgression -- makes them interesting candidates for phylogeographical analysis. Plant phylogeography studies have been limited, however, by the availability of suitable intraspecific variation. In this study, DNA sequence variation from a nuclear gene [Glyceraldehyde 3-phosphate dehydrogenase; (G3pdh)] was used to examine the population history of Manihot esculenta ssp. flabellifolia and a potentially hybridizing species, M. pruinosa. These species occur in the rainforest-savanna ecotone adjoining the Amazon basin, a region believed to have undergone major habitat shifts since the Pleistocene. Geographical distributions of the G3pdh haplotypes indicate genetic isolation-by-distance across the range of M. esculenta ssp. flabellifolia. However, there is greater genetic similarity between northeastern and western populations than would be expected given the present species distribution. A nested clade analysis suggests that northeastern and western populations were connected by gene flow until relatively recently, when they became fragmented. This inferred fragmentation event is consistent with post-Pleistocene habitat shifts proposed for the Amazon basin. At the interspecific level, haplotype sharing with M. pruinosa may reflect either recent interspecific introgression or incomplete lineage sorting between these closely related species. DA - 2002/5// PY - 2002/5// DO - 10.1046/j.1365-294X.2002.01493.x VL - 11 IS - 5 SP - 901-911 SN - 0962-1083 KW - Manihot esculenta ssp KW - flabellifolia KW - Manihot pruinosa KW - nested clade analysis KW - phylogeography KW - Pleistocene KW - South America ER - TY - JOUR TI - Plasmid-borne macrolide resistance in Micrococcus luteus AU - Liebl, W AU - Kloos, WE AU - Ludwig, W T2 - MICROBIOLOGY-SGM AB - A plasmid designated pMEC2 which confers resistance to erythromycin, other macrolides, and lincomycin was detected in Micrococcus luteus strain MAW843 isolated from human skin. Curing of this approximately 4.2 kb plasmid from the host organism resulted in erythromycin sensitivity of the strain. Introduction of pMEC2 into a different M. luteus strain conferred erythromycin resistance upon this strain. Macrolide resistance in M. luteus MAW843 was an inducible trait. Induction occurred at subinhibitory erythromycin concentrations of about 0.02-0.05 micro g ml(-1). Erythromycin and oleandomycin were inducers, while spiramycin and tylosin exerted no significant inducer properties. With heterologous expression experiments in Corynebacterium glutamicum, using hybrid plasmid constructs and deletion derivatives thereof, it was possible to narrow down the location of the plasmid-borne erythromycin-resistance determinant to a region of about 1.8 kb of pMEC2. Sequence analysis of the genetic determinant, designated erm(36), identified an ORF putatively encoding a 281-residue protein with similarity to 23S rRNA adenine N(6)-methyltransferases. erm(36) was most related (about 52-54% identity) to erythromycin-resistance proteins found in high-G+C Gram-positive bacteria, including the (opportunistic) pathogenic corynebacteria Corynebacterium jeikeium, C. striatum, C. diphtheriae and Propionibacterium acnes. This is believed to be the first report of a plasmid-borne, inducible antibiotic resistance in micrococci. The possible role of non-pathogenic, saprophytic micrococci bearing antibiotic-resistance genes in the spreading of these determinants is discussed. DA - 2002/8// PY - 2002/8// DO - 10.1099/00221287-148-8-2479 VL - 148 SP - 2479-2487 SN - 1350-0872 KW - erythromycin resistance KW - erm(36) KW - induction KW - curing 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 - Gravity-stimulated changes in auxin and invertase gene expression in maize pulvinal cells AU - Long, JC AU - Zhao, W AU - Rashotte, AM AU - Muday, GK AU - Huber, SC T2 - PLANT PHYSIOLOGY AB - Maize (Zea mays) stem gravitropism involves differential elongation of cells within a highly specialized region, the stem internodal pulvinus. In the present study, we investigated factors that control gravitropic responses in this system. In the graviresponding pulvinus, hexose sugars (D-Glc and D-Fru) accumulated asymmetrically across the pulvinus. This correlated well with an asymmetric increase in acid invertase activity across the pulvinus. Northern analyses revealed asymmetric induction of one maize acid invertase gene, Ivr2, consistent with transcriptional regulation by gravistimulation. Several lines of evidence indicated that auxin redistribution, as a result of polar auxin transport, is necessary for gravity-stimulated Ivr2 transcript accumulation and differential cell elongation across the maize pulvinus. First, the auxin transport inhibitor, N-1-naphthylphthalamic acid, inhibited gravistimulated curvature and Ivr2 transcript accumulation. Second, a transient gradient of free indole-3-acetic acid (IAA) across the pulvinus was apparent shortly after initiation of gravistimulation. This temporarily free IAA gradient appears to be important for differential cell elongation and Ivr2 transcript accumulation. This is based on the observation that N-1-naphthylphthalamic acid will not inhibit gravitropic responses when applied to pulvinus tissue after the free IAA gradient peak has occurred. Third, IAA alone can stimulate Ivr2 transcript accumulation in non-gravistimulated pulvini. The gravity- and IAA-stimulated increase in Ivr2 transcripts was sensitive to the protein synthesis inhibitor, cycloheximide. Based on these results, a two-phase model describing possible relationships between gravitropic curvature, IAA redistribution, and Ivr2 expression is presented. DA - 2002/2// PY - 2002/2// DO - 10.1104/pp.010579 VL - 128 IS - 2 SP - 591-602 SN - 1532-2548 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 - Developmental evolution: Getting robust about robustness AU - Gibson, G T2 - CURRENT BIOLOGY AB - In the context of development, a process is robust if it can proceed normally despite the enormous capacity for perturbation inherent in all biological systems. A new mode of theoretical modeling of genetic networks holds great promise for increasing our understanding of both the quantitative mechanisms of robustness and its evolutionary impact. DA - 2002/5/14/ PY - 2002/5/14/ DO - 10.1016/S0960-9822(02)00855-2 VL - 12 IS - 10 SP - R347-R349 SN - 0960-9822 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 -