Genetics - 2008

Li, F., Schiemann, A. H., & Scott, M. J. (2008). Incorporation of the Noncoding <i>roX</i> RNAs Alters the Chromatin-Binding Specificity of the <i>Drosophila</i> MSL1/MSL2 Complex. Molecular and Cellular Biology, 28(8), 2850–2850. https://doi.org/10.1128/MCB.00309-08

Scott, M. J., & Li, F. (2008). How do ncRNAs guide chromatin-modifying complexes to specific locations within the nucleus? RNA Biology, 5(1), 13–16. https://doi.org/10.4161/rna.5.1.5943

Olby, N. J., Harris, T., Mehta, P. M., Breen, M., Thomas, R., Myers, R., & Nielsen, D. (2008). Linkage Analysis in American Staffordshire Terriers with Hereditary Cerebellar Cortical Degeneration. Journal of Veterinary Internal Medicine, 22(3), 723–724.

Nielsen, D. M., Suchindran, S., & Smith, C. P. (2008). Does strong linkage disequilibrium guarantee redundant association results? Genetic Epidemiology, 32(6), 546–552. https://doi.org/10.1002/gepi.20328

Leivar, P., Monte, E., Al-Sady, B., Carle, C., Storer, A., Alonso, J. M., … Quail, P. H. (2008). The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. The Plant Cell Online, 20(2), 337–352. https://doi.org/10.1105/tpc.107.052142

Hu, J., Mitchum, M. G., Barnaby, N., Ayele, B. T., Ogawa, M., Nam, E., … Ecker, J. R. (2008). Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis. The Plant Cell Online, 20(2), 320–336. https://doi.org/10.1105/tpc.107.057752

Zou, W., & Zeng, Z.-B. (2008). Statistical Methods for Mapping Multiple QTL. International Journal of Plant Genomics, 2008, 1–8. https://doi.org/10.1155/2008/286561

Tanurdzic, M., Vaughn, M. W., Jiang, H., Lee, T.-J., Slotkin, R. K., Sosinski, B., … Martienssen, R. A. (2008). Epigenomic Consequences of Immortalized Plant Cell Suspension Culture. PLoS Biology, 6(12), e302. https://doi.org/10.1371/journal.pbio.0060302

Conkling, M. A., Song, W., & Mendu, N. (2008). Methods and compositions for protein production in tobacco plants with reduced nicotine.

Klaenhammer, T., Azcarate-Peril, A., & Altermann, E. (2008). Lactobacillus acidophilus nucleic acids and uses thereof.

Klaenhammer, T. R., Altermann, E., & Russell, W. M. (2008). Lactobacillus acidophilus nucleic acid sequences encoding protease homologues and uses therefore.

Klaenhammer, T. R., Altermann, E., Barrangou, R., Russell, W. M., & Duong, T. (2008). Lactobacillus acidophilus nucleic acid sequences encoding carbohydrate utilization-related proteins and uses therefor.

Konstantinov, S. R., Smidt, H., Vos, W. M., Bruijns, S. C. M., Singh, S. K., Valence, F., … Kooyk, Y. (2008). S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(49), 19474–19479. https://doi.org/10.1073/pnas.0810305105

Tanurdzic, M., Vaughn, M. W., Jiang, H., Lee, T. J., Slotkin, R. K., Sosinski, B., … Martienssen, R. A. (2008). [Review of Epigenomic consequences of immortalized plant cell suspension culture]. PLoS Biology, 6(12), 2880–2895.

Powers, J. G., Sit, T. L., Heinsohn, C., George, C. G., Kim, K.-H., & Lommel, S. A. (2008). The Red clover necrotic mosaic virus RNA-2 encoded movement protein is a second suppressor of RNA silencing. VIROLOGY, 381(2), 277–286. https://doi.org/10.1016/j.virol.2008.09.004

Franco Garcia, A. A., Wang, S., Melchinger, A. E., & Zeng, Z.-B. (2008). Quantitative Trait Loci Mapping and The Genetic Basis of Heterosis in Maize and Rice. GENETICS, 180(3), 1707–1724. https://doi.org/10.1534/genetics.107.082867

Gibson, G., & Reed, L. K. (2008). Cryptic genetic variation. Current Biology, 18(21), R989–990.

Baxter, S. W., Papa, R., Chamberlain, N., Humphray, S. J., Joron, M., Morrison, C., … Jiggins, C. D. (2008). Convergent Evolution in the Genetic Basis of Mullerian Mimicry in Heliconius Butterflies. GENETICS, 180(3), 1567–1577. https://doi.org/10.1534/genetics.107.082982

Choi, S. C., Redelings, B. D., & Thorne, J. L. (2008). Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 363(1512), 3931–3939. https://doi.org/10.1098/rstb.2008.0167

Fernandes, A. D., & Atchley, W. R. (2008). Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative. BIOINFORMATICS, 24(19), 2177–2183. https://doi.org/10.1093/bioinformatics/btn395

Opperman, C. H., Bird, D. M., Williamson, V. M., Rokhsar, D. S., Burke, M., Cohn, J., … Windham, E. (2008). Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(39), 14802–14807. https://doi.org/10.1073/pnas.0805946105

Xiang, Q.-Y., Thorne, J. L., Seo, T.-K., Zhang, W., Thomas, D. T., & Ricklefs, R. E. (2008). Rates of nucleotide substitution in Cornaceae (Cornales)-Pattern of variation and underlying causal factors. MOLECULAR PHYLOGENETICS AND EVOLUTION, 49(1), 327–342. https://doi.org/10.1016/j.ympev.2008.07.010

Vitale, A., & Boston, R. S. (2008). [Review of Endoplasmic reticulum quality control and the unfolded protein response: Insights from plants]. TRAFFIC, 9(10), 1581–1588. https://doi.org/10.1111/j.1600-0854.2008.00780.x

Prugnolle, F., Mcgee, K., Keebler, J., & Awadalla, P. (2008). Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents. BMC Evolutionary Biology, 8.

Yamamoto, A., Zwarts, L., Callaerts, P., Norga, K., Mackay, T. F. C., & Anholt, R. R. H. (2008). Neurogenetic networks for startle-induced locomotion in Drosophila melanogaster. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(34), 12393–12398. https://doi.org/10.1073/pnas.0804889105

Ascencio-Ibanez, J. T., Sozzani, R., Lee, T. J., Chu, T. M., Wolfinger, R. D., Cella, R., & Hanley-Bowdoin, L. (2008). [Review of Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection]. Plant Physiology, 148(1), 436–454.

Propper, C., Moore, G. A., Mills-Koonce, W. R., Halpern, C. T., Hill-Soderlund, A. L., Calkins, S. D., … Cox, M. (2008). [Review of Gene-environment contributions to the development of infant vagal reactivity: The interaction of dopamine and maternal sensitivity]. CHILD DEVELOPMENT, 79(5), 1377–1394. https://doi.org/10.1111/j.1467-8624.2008.01194.x

Klaenhammer, T. R., Altermann, E., Pfeiler, E., Buck, B. L., Goh, Y.-J., O'Flaherty, S., … Duong, T. (2008, September). Functional genomics of probiotic Lactobacilli. JOURNAL OF CLINICAL GASTROENTEROLOGY, Vol. 42, pp. S160–S162. https://doi.org/10.1097/MCG.0b013e31817da140

Weber, A. L., Briggs, W. H., Rucker, J., Baltazar, B. M., Jesus Sanchez-Gonzalez, J., Feng, P., … Doebley, J. (2008). The Genetic Architecture of Complex Traits in Teosinte (Zea mays ssp parviglumis): New Evidence From Association Mapping. GENETICS, 180(2), 1221–1232. https://doi.org/10.1534/genetics.108.090134

Smith, C. A., Robertson, D., Yates, B., Nielsen, D. M., Brown, D., Dean, R. A., & Payne, G. A. (2008). The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus. Current Genetics, 54(5), 241–269. https://doi.org/10.1007/s00294-008-0215-9

Mohamadzadeh, M., & Klaenhammer, T. R. (2008). Specific Lactobacillus species differentially activate Toll-like receptors and downstream signals in dendritic cells. EXPERT REVIEW OF VACCINES, 7(8), 1155–1164. https://doi.org/10.1586/14760584.7.8.1155

Papa, R., Morrison, C. M., Walters, J. R., Counterman, B. A., Chen, R., Halder, G., … McMillan, W. O. (2008). Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies. BMC GENOMICS, 9. https://doi.org/10.1186/1471-2164-9-345

Rollmann, S. A., Zwarts, L., Edwards, A. C., Yamamoto, A., Callaerts, P., Norga, K., … Anholt, R. R. H. (2008). Pleiotropic effects of Drosophila neuralized on complex behaviors and brain structure. GENETICS, 179(3), 1327–1336. https://doi.org/10.1534/genetics.108.088435

Durmaz, E., Miller, M. J., Azcarate-Peril, M. A., Toon, S. P., & Klaenhammer, T. R. (2008, August). Genome sequence and characteristics of Lrm1, a prophage from industrial Lactobacillus rhamnosus strain M1. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol. 74, pp. 4601–4609. https://doi.org/10.1128/AEM.00010-08

Azcarate-Peril, M. A., Altermann, E., Goh, Y. J., Tallon, R., Sanozky-Dawes, R. B., Pfeiler, E. A., … Klaenhammer, T. R. (2008, August). Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol. 74, pp. 4610–4625. https://doi.org/10.1128/AEM.00054-08

Dhandaydham, M., Charles, L., Zhu, H., Starr, J. L., Huguet, T., Cook, D. R., … Opperman, C. (2008). Characterization of root-knot nematode resistance in Medicago truncatula. Journal of Nematology, 40(1), 46–54.

Estrada, J. L., Collins, B., York, A., Bischoff, S., Sommer, J., Tsai, S., … Piedrahita, J. A. (2008, June). Successful cloning of the Yucatan minipig using commercial/occidental breeds as oocyte donors and embryo recipients. CLONING AND STEM CELLS, Vol. 10, pp. 287–296. https://doi.org/10.1089/clo.2008.0005

Ehrenreich, I. M., & Purugganan, M. D. (2008). Sequence variation of microRNAs and their binding sites in Arabidopsis. PLANT PHYSIOLOGY, 146(4), 1974–1982. https://doi.org/10.1104/pp.108.116582

Azhakanandam, S., Nole-Wilson, S., Bao, F., & Franks, R. G. (2008). SEUSS and AINTEGUMENTA mediate patterning and ovule initiation during gynoecium medial domain development. PLANT PHYSIOLOGY, 146(3), 1165–1181. https://doi.org/10.1104/pp.107.114751

Ruedi, E. A., & Hughes, K. A. (2008). Natural genetic variation in complex mating behaviors of male Drosophila melanogaster. BEHAVIOR GENETICS, 38(4), 424–436. https://doi.org/10.1007/s10519-008-9204-5

Kocher, S. D., Richard, F.-J., Tarpy, D. R., & Grozinger, C. M. (2008). Genomic analysis of post-mating changes in the honey bee queen (Apis mellifera). BMC GENOMICS, 9. https://doi.org/10.1186/1471-2164-9-232

Huang, L., Heinloth, A. N., Zeng, Z. B., Paules, R. S., & Bushel, P. R. (2008). Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants. BMC Genomics, 9.

Fernandes, A. D., & Atchley, W. R. (2008). Biochemical and functional evidence of p53 homology is inconsistent with molecular phylogenetics for distant sequences. JOURNAL OF MOLECULAR EVOLUTION, 67(1), 51–67. https://doi.org/10.1007/s00239-008-9124-2

Sanders, L. R., Pate, M., & Mahaffey, J. W. (2008). The drosophila gap gene giant has an anterior segment identity function mediated through disconnected and teashirt. GENETICS, 179(1), 441–453. https://doi.org/10.1534/genetics.107.084988

Funk-Keenan, J., Haire, F., Woolard, S., & Atchley, W. R. (2008). Hepatic endopolyploidy as a cellular consequence of age-specific selection for rate of development in mice. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION, 310B(5), 385–397. https://doi.org/10.1002/jez.b.21211

Sambandan, D., Carbone, M. A., Anholt, R. R. H., & Mackay, T. E. C. (2008). Phenotypic plasticity and genotype by environment interaction for olfactory behavior in Drosophila melanogaster. GENETICS, 179(2), 1079–1088. https://doi.org/10.1534/genetics.108.086769

Need, A. C., Attix, D. K., McEvoy, J. M., Cirulli, E. T., Linney, K. N., Wagoner, A. P., … Goldstein, D. B. (2008). Failure to replicate effect of Kibra on human memory in two large cohorts of European origin. AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS, 147B(5), 667–668. https://doi.org/10.1002/ajmg.b.30658

Costa, M. D. L., Reis, P. A. B., Valente, M. A. S., Irsigler, A. S. T., Carvalho, C. M., Loureiro, M. E., … Fontes, E. P. B. (2008). A new branch of endoplasmic reticulum stress signaling and the osmotic signal converge on plant-specific asparagine-rich proteins to promote cell death. JOURNAL OF BIOLOGICAL CHEMISTRY, 283(29), 20209–20219. https://doi.org/10.1074/jbc.M802654200

Kennerly, E., Ballmann, A., Martin, S., Wolfinger, R., Gregory, S., Stoskopf, M., & Gibson, G. (2008). A gene expression signature of confinement in peripheral blood of red wolves (Canis rufus). MOLECULAR ECOLOGY, 17(11), 2782–2791. https://doi.org/10.1111/j.1365-294X.2008.03775.x

Stepanova, A. N., Robertson-Hoyt, J., Yun, J., Benavente, L. M., Xie, D.-Y., Dolezal, K., … Alonso, J. M. (2008). TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. CELL, 133(1), 177–191. https://doi.org/10.1016/j.cell.2008.01.047

Hancock, J. F., & Stuber, C. (2008). Sustaining public plant breeding to meet future national needs. HortScience, 43(2), 298–299.

Holmes, R. A., Boston, R. S., & Payne, G. A. (2008). [Review of Diverse inhibitors of aflatoxin biosynthesis]. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 78(4), 559–572. https://doi.org/10.1007/s00253-008-1362-0

Shimizu, K. K., Reininga, J. M., Caicedo, A. L., Mays, C. A., Moore, R. C., Olsen, K. M., … Purugganan, M. D. (2008). Darwinian selection on a selfing locus (vol 306, pg 2081, 2004). Science, Vol. 320, pp. 176–176.

Hobolth, A. (2008). A Markov chain Monte Carlo expectation maximization algorithm for statistical analysis of DNA sequence evolution with neighbor-dependent substitution rates. JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS, 17(1), 138–162. https://doi.org/10.1198/106186008X289010

Klaenhammer, T. R., Altermann, E., Buck, B. L., & Russell, W. M. (2008). Lactobacillus acidophilus nucleic acid sequences encoding cell surface protein homologues and uses therefore. Washington, DC: U.S. Patent and Trademark Office.

Aylor, D. L., & Zeng, Z. B. (2008). From classical genetics to quantitative genetics to systems biology: Modeling epistasis. PLoS Genetics, 4(3).

Kelleher, D. F., Carvalho, C. E., Doty, A. V., Layton, M., Cheng, A. T., Mathies, L. D., … Haag, E. S. (2008). Comparative genetics of sex determination: Masculinizing mutations in Caenorhabditis briggsae. GENETICS, 178(3), 1415–1429. https://doi.org/10.1534/genetics.107.073668

Idaghdour, Y., Storey, J. D., Jadallah, S. J., & Gibson, G. (2008). A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan amazighs. PLoS Genetics, 4(4).

Mohamadzadeh, M., Duong, T., Hoover, T., & Klaenhammer, T. R. (2008). [Review of Targeting mucosal dendritic cells with microbial antigens from probiotic lactic acid bacteria]. EXPERT REVIEW OF VACCINES, 7(2), 163–174. https://doi.org/10.1586/14760584.7.2.163

Harbison, S. T., & Sehgal, A. (2008). Quantitative genetic analysis of sleep in Drosophila melanogaster. GENETICS, 178(4), 2341–2360. https://doi.org/10.1534/genetics.107.081232

Ng, Y.-fai, Chan, H. H. L., Chu, P. H. W., To, C.-ho, Gilger, B. C., Petters, R. M., & Wong, F. (2008). Multifocal electroretinogram in rhodopsin P347L transgenic pigs. INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, 49(5), 2208–2215. https://doi.org/10.1167/iovs.07-1159

Kim, Y., Feng, S., & Zeng, Z.-B. (2008). Measuring and partitioning the high-order linkage disequilibrium by multiple order Markov chains. GENETIC EPIDEMIOLOGY, 32(4), 301–312. https://doi.org/10.1002/gepi.20305

Stuber, C. W., & Hancock, J. (2008). Sustaining plant breeding-national workshop. CROP SCIENCE, 48(1), 25–29. https://doi.org/10.2135/cropsci2007.07.0406spp

Velez-Zuazo, X., Ramos, W. D., Dam, R. P., Diez, C. E., Abreu-Grobois, A., & Mcmillan, W. O. (2008). Dispersal, recruitment and migratory behaviour in a hawksbill sea turtle aggregation. MOLECULAR ECOLOGY, 17(3), 839–853. https://doi.org/10.1111/j.1365-294X.2007.03635.x

Papanicolaou, A., Gebauer-Jung, S., Blaxter, M. L., McMillan, W. O., & Jiggins, C. D. (2008). ButterflyBase: a platform for lepidopteran genomics. NUCLEIC ACIDS RESEARCH, 36, D582–D587. https://doi.org/10.1093/nar/gkm853

Shimizu, K. K., Shimizu-Inatsugi, R., Tsuchimatsu, T., & Purugganan, M. D. (2008). Independent origins of self-compatibility in Arabidopsis thaliana. MOLECULAR ECOLOGY, 17(2), 704–714. https://doi.org/10.1111/j.1365-294X.2007.03605.x

Baas, T. J., Robison, O. W., Tokach, M. D., Goodwin, R., Mabry, J. W., Henry, S., … Berger, P. J. (2008, February). Untitled. https://doi.org/10.2527/jas.2007-0360