Genetics - 2003

Zeng, Z.-B. (2003). Quantitative Trait Loci Mapping. In D. Cooper (Ed.), Nature encyclopedia of the human genome. New York: Nature Publishing Group.

Alonso, J. M., Stepanova, A. N., Leisse, T. J., Kim, C. J., Chen, H., Shinn, P., … Ecker, J. R. (2003). Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science, 301(5633), 653–657. https://doi.org/10.1126/science.1086391

Alonso, J. M., & Stepanova, A. N. (2003). T-DNA mutagenesis in Arabidopsis. Methods in Molecular Biology (Clifton, N.J.), 236, 177–188. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0-1542548233&partnerID=MN8TOARS

Ullah, H., Chen, J.-G., Temple, B., Boyes, D. C., Alonso, J. M., Davis, K. R., … Jones, A. M. (2003). The β-subunit of the Arabidopsis G protein negatively regulates auxin-induced cell division and affects multiple developmental processes. The Plant Cell Online, 15(2), 393–409.

Lariguet, P., Boccalandro, H. E., Alonso, J. M., Ecker, J. R., Chory, J., Casal, J. J., & Fankhausera, C. (2003). The Balance between phytochrome kinase substrate1 and PKS2 Provides Homeostasis for Phytochrome A Signaling in Arabidopsis. The Plant Cell Online.

Catalá, R., Santos, E., Alonso, J. M., Ecker, J. R., Martínez-Zapater, J. M., & Salinas, J. (2003). Mutations in the Ca2+/H+ transporter CAX1 increase CBF/DREB1 expression and the cold-acclimation response in Arabidopsis. The Plant Cell Online, 15(12), 2940–2951.

Monte, E., Alonso, J. M., Ecker, J. R., Zhang, Y., Li, X., Young, J., … Quail, P. H. (2003). Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways. The Plant Cell Online, 15(9), 1962–1980.

Larkin, R. M., Alonso, J. M., Ecker, J. R., & Chory, J. (2003). GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science, 299(5608), 902–906.

Alonso, J. M. (2003). Genome-wide insertional mutagenesis of Arabidopsis thaliana (vol 301, pg 653, 2003). Science, 301(5641), 1849.

Alonso, J. M., Stepanova, A. N., Leisse, T. J., Kim, C. J., Chen, H., Shinn, P., … Cheuk, R. (2003). Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science, 301(5633), 653–657.

Alonso, J. M., Stepanova, A. N., Solano, R., Wisman, E., Ferrari, S., Ausubel, F. M., & Ecker, J. R. (2003). Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 100(5), 2992–2997. https://doi.org/10.1073/pnas.0438070100

Michael, T. P., Salome, P. A., Hannah, J. Y., Spencer, T. R., Sharp, E. L., McPeek, M. A., … McClung, C. R. (2003). Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science, 302(5647), 1049–1053.

Strand, Å., Asami, T., Alonso, J., Ecker, J. R., & Chory, J. (2003). Chloroplast to nucleus communication triggered by accumulation of Mg-protoporphyrinIX. Nature, 421(6918), 79–83.

Lariguet, P., Boccalandro, H. E., Alonso, J. M., Ecker, J. R., Chory, J., Casal, J. J., & Fankhauser, C. (2003). A growth regulatory loop that provides homeostasis to phytochrome A signaling. The Plant Cell Online, 15(12), 2966–2978.

Mackey, D., Belkhadir, Y., Alonso, J. M., Ecker, J. R., & Dangl, J. L. (2003). < i> Arabidopsis</i> RIN4 Is a Target of the Type III Virulence Effector AvrRpt2 and Modulates RPS2-Mediated Resistance. Cell, 112(3), 379–389.

Conkling, M. A., Song, W., & Mendu, N. (2003). Regulation of quinolate phosphoribosyl transferase expression. Washington, DC: U.S. Patent and Trademark Office.

Alonso, J. M., & Stepanova, A. N. (2003). T-DNA mutagenesis in Arabidopsis. In Plant Functional Genomics (pp. 177–187). https://doi.org/10.1385/1-59259-413-1:177

Holl, J. W., & Robison, O. W. (2003). Results from nine generations of selection for increased litter size in swine. Journal of Animal Science, 81(3), 624–629. https://doi.org/10.2527/2003.813624x

Liu, K. J., Goodman, M., Muse, S., Smith, J. S., Buckler, E., & Doebley, J. (2003). Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics, 165(4), 2117–2128.

Wiegmann, B. M., Yeates, D. K., Thorne, J. L., & Kishino, H. (2003). Time flies, a new molecular time-scale for brachyceran fly evolution without a clock. Systematic Biology, 52(6), 745–756.

Norga, K. K., Gurganus, M. C., Dilda, C. L., Yamamoto, A., Lyman, R. F., Patel, P. H., … Bellen, H. J. (2003). Quantitative analysis of bristle number in Drosophila mutants identifies genes involved in neural development. CURRENT BIOLOGY, 13(16), 1388–1397. https://doi.org/10.1016/S0960-9822(03)00546-3

Baas, T. J., Goodwin, R. N., Christian, L. L., Johnson, R. K., Robison, O. W., Mabry, J. W., … Berger, P. J. (2003). Design and standards for genetic evaluation of swine seedstock populations. Journal of Animal Science, 81(10), 2409–2418. https://doi.org/10.2527/2003.81102409x

Ventura, M., Canchaya, C., Meylan, V., Klaenhammer, T. R., & Zink, R. (2003). Analysis, characterization, and loci of the tuf genes in Lactobacillus and Bifidobacterium species and their direct application for species identification. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 69(11), 6908–6922. https://doi.org/10.1128/AEM.69.11.6908-6922.2003

Dillon, J. G., Miller, SR, & Castenholz, R. W. (2003). UV-acclimation responses in natural populations of cyanobacteria (Calothrix sp.). ENVIRONMENTAL MICROBIOLOGY, 5(6), 473–483. https://doi.org/10.1046/j.1462-2920.2003.00435.x

Flint-Garcia, S. A., Thornsberry, J. M., & Buckler, E. S. (2003). [Review of Structure of linkage disequilibrium in plants]. ANNUAL REVIEW OF PLANT BIOLOGY, 54, 357–374. https://doi.org/10.1146/annurev.arplant.54.031902.134907

Russell, W. M., & Klaenhammer, T. R. (2003). Polynucleotide encoding a Lactobacillus gasseri beta-glucuronidase polypeptide. Washington, DC: U.S. Patent and Trademark Office.

Mahmoud, T. H., McCuen, B. W., Hao, Y., Moon, S. J., Tatebayashi, M., Stinnett, S., … Wong, F. (2003). Lensectomy and vitrectomy decrease the rate of photoreceptor loss in rhodopsin P347L transgenic pigs. GRAEFES ARCHIVE FOR CLINICAL AND EXPERIMENTAL OPHTHALMOLOGY, 241(4), 298–308. https://doi.org/10.1007/s00417-003-0637-5

Lu, Z., Breidt, F., Fleming, H. P., Altermann, E., & Klaenhammer, T. R. (2003). Isolation and characterization of a Lactobacillus plantarum bacteriophage, Phi JL-1, from a cucumber fermentation. INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY, 84(2), 225–235. https://doi.org/10.1016/S0168-1605(03)00111-9

Xie, J. H., Wehner, T. C., Wollenberg, K., Purugganan, M. D., & Conkling, M. A. (2003). Intron and polypeptide evolution of conserved NPA to NPA motif regions in plant aquaporins. Journal of the American Society for Horticultural Science, 128(4), 591–597.

Scholl, E. H., Thorne, J. L., McCarter, J. P., & Bird, D. M. (2003). Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. Genome Biology, 4(6), R39–1.

Dowd, P. F., Zuo, W. N., Gillikin, J. W., Johnson, E. T., & Boston, R. S. (2003). Enhanced resistance to Helicoverpa zea in tobacco expressing an activated form of maize ribosome-inactivating protein. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 51(12), 3568–3574. https://doi.org/10.1021/jf0211433

Conkling, M. A., Song, W., & Mendu, N. (2003). Regulation of quinolate phosphoribosyl transferase expression by transformation with a tobacco quinolate phosphoribosyl transferase nucleic acid. Washington, DC: U.S. Patent and Trademark Office.

Lawton-Rauh, A., Robichaux, R. H., & Purugganan, M. D. (2003). Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae). MOLECULAR ECOLOGY, 12(5), 1301–1313. https://doi.org/10.1046/j.1365-294X.2003.01814.x

Morgan, T. J., Garland, T., & Carter, P. A. (2003). Ontogenies in mice selected for high voluntary wheel-running activity. I. Mean ontogenies. EVOLUTION, 57(3), 646–657. https://doi.org/10.1111/j.0014-3820.2003.tb01556.x

Shepard, K. A., & Purugganan, M. D. (2003). Molecular population genetics of the Arabidopsis CLAVATA2 region: The genomic scale of variation and selection in a selfing species. Genetics, 163(3), 1083–1095.

Hsieh, W. P., Chu, T. M., Wolfinger, R. D., & Gibson, G. (2003). Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles. Genetics, 165(2), 747–757.

Gibson, G. (2003, October). Microarray analysis - Genome-scale hypothesis scanning. PLOS BIOLOGY, Vol. 1, pp. 28–29. https://doi.org/10.1371/journal.pbio.0000015

Purugganan, M., & Gibson, G. (2003, May). Merging ecology, molecular evolution, and functional genetics. MOLECULAR ECOLOGY, Vol. 12, pp. 1109–1112. https://doi.org/10.1046/j.1365-294X.2003.01851.x

Miller, SR. (2003). Evidence for the adaptive evolution of the carbon fixation gene rbcL during diversification in temperature tolerance of a clade of hot spring cyanobacteria. MOLECULAR ECOLOGY, 12(5), 1237–1246. https://doi.org/10.1046/j.1365-294X.2003.01831.x

Riley, R. M., Jin, W., & Gibson, G. (2003). Contrasting selection pressures on components of the Ras-mediated signal transduction pathway in Drosophila. MOLECULAR ECOLOGY, 12(5), 1315–1323. https://doi.org/10.1046/j.1365-294X.2003.01741.x

Barrangou, R., Altermann, E., Hutkins, R., Cano, R., & Klaenhammer, T. R. (2003). Functional and comparative genomic analyses of an operon involved in fructooligosaccharide utilization by Lactobacillus acidophilus. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100(15), 8957–8962. https://doi.org/10.1073/pnas.1332765100

Dworkin, I., Palsson, A., Birdsall, K., & Gibson, G. (2003). Evidence that Egfr contributes to cryptic genetic variation for photoreceptor determination in natural populations of Drosophila melanogaster. CURRENT BIOLOGY, 13(21), 1888–1893. https://doi.org/10.1016/j.cub.2003.10.001

Mankin, S. L., Allen, G. C., Phelan, T., Spiker, S., & Thompson, W. F. (2003). Elevation of transgene expression level by flanking matrix attachment regions (MAR) is promoter dependent: a study of the interactions of six promoters with the RB7 3 ' MAR. TRANSGENIC RESEARCH, 12(1), 3–12. https://doi.org/10.1023/A:1022194120518

Jaenicke-Despres, V., Buckler, E. S., Smith, B. D., Gilbert, M. T. P., Cooper, A., Doebley, J., & Paabo, S. (2003). Early allelic selection in maize as revealed by ancient DNA. SCIENCE, 302(5648), 1206–1208. https://doi.org/10.1126/science.1089056

Ascenzi, R., Ulker, B., Todd, J. J., Sowinski, D. A., Schimeneck, C. R., Allen, G. C., … Thompson, W. F. (2003). Analysis of trans-silencing interactions using transcriptional silencers of varying strength and targets with and without flanking nuclear matrix attachment regions. TRANSGENIC RESEARCH, 12(3), 305–318. https://doi.org/10.1023/A:1023310118231

Roberts, R. J., Belfort, M., Bestor, T., Bhagwat, A. S., Bickle, T. A., Bitinaite, J., … Xu, S. Y. (2003). A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. NUCLEIC ACIDS RESEARCH, 31(7), 1805–1812. https://doi.org/10.1093/nar/gkg274

Hasegawa, M., Thorne, J. L., & Kishino, H. (2003). [Review of Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution]. GENES & GENETIC SYSTEMS, 78(4), 267–283. https://doi.org/10.1266/ggs.78.267

Gibson, G. (2003, December 2). Population genomics: Finding the dispatch variants of mass disruption. CURRENT BIOLOGY, Vol. 13, pp. R901–R903. https://doi.org/10.1016/j.cub.2003.11.008

Lawton-Rauh, A. (2003). [Review of Evolutionary dynamics of duplicated genes in plants]. MOLECULAR PHYLOGENETICS AND EVOLUTION, 29(3), 396–409. https://doi.org/10.1016/j.ympev.2003.07.004

Anholt, R. R. H., Dilda, C. L., Chang, S., Fanara, J. J., Kulkarni, N. H., Ganguly, I., … Mackay, T. F. C. (2003). The genetic architecture of odor-guided behavior in Drosophila: epistasis and the transcriptome. NATURE GENETICS, 35(2), 180–184. https://doi.org/10.1038/ng1240

Visser, J. A. G. M., Hermisson, J., Wagner, G. P., Meyers, L. A., Bagheri, H. C., Blanchard, J. L., … Whitlock, M. C. (2003). Perspective: Evolution and detection of genetic robustness. EVOLUTION, 57(9), 1959–1972. https://doi.org/10.1554/02-750R

Squire, T. L., Lowe, M. E., Bauer, V. W., & Andrews, M. T. (2003). Pancreatic triacylglycerol lipase in a hibernating mammal. II. Cold-adapted function and differential expression. PHYSIOLOGICAL GENOMICS, 16(1), 131–140. https://doi.org/10.1152/physiolgenomics.00168.2002

Andrus, J. M., Bowen, S. W., Klaenhammer, T. R., & Hassan, H. M. (2003). Molecular characterization and functional analysis of the manganese-containing superoxide dismutase gene (sodA) from Streptococcus thermophilus AO54. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 420(1), 103–113. https://doi.org/10.1016/j.abb.2003.09.007

Tao, Y., Zeng, Z. B., Li, J., Hartl, D. L., & Laurie, C. C. (2003). Genetic dissection of hybrid Incompatibilities between Drosophila simulansand D. mauritiana. II. Mapping hybrid male sterility loci on the third chromosome. Genetics, 164(4), 1399–1418.

De Luca, M., Roshina, N. V., Geiger-Thornsberry, G. L., Lyman, R. F., Pasyukova, E. G., & Mackay, T. F. C. (2003). Dopa decarboxylase (Ddc) affects variation in Drosophila longevity. NATURE GENETICS, 34(4), 429–433. https://doi.org/10.1038/ng1218

Du, C. G., Buckler, E., & Muse, S. (2003, April). Development of a maize molecular evolutionary genomic database. COMPARATIVE AND FUNCTIONAL GENOMICS, Vol. 4, pp. 246–249. https://doi.org/10.1002/cfg.282

Morgan, T. J., Garland, T., Irwin, B. L., Swallow, J. G., & Carter, P. A. (2003). The mode of evolution of molecular markers in populations of house mice under artificial selection for locomotor behavior. JOURNAL OF HEREDITY, 94(3), 236–242. https://doi.org/10.1093/jhered/esg021

Kim, J. K., Jang, I. C., Wu, R., Zu, W. N., Boston, R. S., Lee, Y. H., … Nahm, B. H. (2003). Co-expression of a modified maize ribosome-inactivating protein and a rice basic chitinase gene in transgenic rice plants confers enhanced resistance to sheath blight. TRANSGENIC RESEARCH, 12(4), 475–484. https://doi.org/10.1023/A:1024276127001

Remington, D. L., & Purugganan, M. D. (2003). [Review of Candidate genes, quantitative trait loci, and functional trait evolution in plants]. INTERNATIONAL JOURNAL OF PLANT SCIENCES, 164(3), S7–S20. https://doi.org/10.1086/367812

Ruzsa, S. M., & Scandalios, J. G. (2003). Altered Cu metabolism and differential transcription of Cu/ZnSod genes in a Cu/ZnSOD-deficient mutant of maize: Evidence for a Cu-responsive transcription factor. BIOCHEMISTRY, 42(6), 1508–1516. https://doi.org/10.1021/bi020551x

Liu, Y. S., Levin, J. S., Murray, J. S., Wernsman, E. A., & Weissinger, A. K. (2003). A multi-generation analysis of the stability of transgenic virus resistance in doubled-haploid tobacco lines. Molecular Breeding, 12(2), 145–156.

Gibson, G. (2003, January). Population genomics: celebrating individual expression. HEREDITY, Vol. 90, pp. 1–2. https://doi.org/10.1038/sj.hdy.6800195

Ungerer, M. C., Linder, C. R., & Rieseberg, L. H. (2003). Effects of genetic background on response to selection in experimental populations of Arabidopsis thaliana. Genetics, 163(1), 277–286.

Flint-Garcia, S. A., Jampatong, C., Darrah, L. L., & McMullen, M. D. (2003). Quantitative trait locus analysis of stalk strength in four maize populations. CROP SCIENCE, 43(1), 13–22. https://doi.org/10.2135/cropsci2003.0013

Robinson, D. M., Jones, D. T., Kishino, H., Goldman, N., & Thorne, J. L. (2003). Protein evolution with dependence among codons due to tertiary structure. MOLECULAR BIOLOGY AND EVOLUTION, 20(10), 1692–1704. https://doi.org/10.1093/molbev/msg184

Bird, D. M., Opperman, C. H., & Davies, K. G. (2003). [Review of Interactions between bacteria and plant-parasitic nematodes: now and then]. INTERNATIONAL JOURNAL FOR PARASITOLOGY, 33(11), 1269–1276. https://doi.org/10.1016/S0020-7519(03)00160-7

Moore, R. C., & Purugganan, M. D. (2003). The early stages of duplicate gene evolution. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100(26), 15682–15687. https://doi.org/10.1073/pnas.2535513100

Barrier, M., Bustamante, C. D., Yu, J. Y., & Purugganan, M. D. (2003). Selection on rapidly evolving proteins in the Arabidopsis genome. Genetics, 163(2), 723–733.

Buck, M. J., & Atchley, W. R. (2003). Phylogenetic analysis of plant basic helix-loop-helix proteins. Journal of Molecular Evolution, 56(6), 742–750. https://doi.org/10.1007/s00239-002-2449-3

Squire, T. L., & Andrews, M. T. (2003). Pancreatic triacylglycerol lipase in a hibernating mammal. I. Novel genomic organization. PHYSIOLOGICAL GENOMICS, 16(1), 119–130. https://doi.org/10.1152/physiolgenomics.00167.2002

Purugganan, M. (2003). Michael Purugganan. Nature, 421(6919), 117. https://doi.org/10.1038/421117a

Flint-Garcia, S. A., McMullen, M. D., & Darrah, L. L. (2003). Genetic relationship of stalk strength and ear height in maize. CROP SCIENCE, 43(1), 23–31. https://doi.org/10.2135/cropsci2003.0023