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  • 1
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    Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers [Genetics] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-10-12
    Description: To catalog protein-altering mutations that may drive the development of prostate cancers and their progression to metastatic disease systematically, we performed whole-exome sequencing of 23 prostate cancers derived from 16 different lethal metastatic tumors and three high-grade primary carcinomas. All tumors were propagated in mice as xenografts, designated the LuCaP series, to model phenotypic variation, such as responses to cancer-directed therapeutics. Although corresponding normal tissue was not available for most tumors, we were able to take advantage of increasingly deep catalogs of human genetic variation to remove most germline variants. On average, each tumor genome contained ∼200 novel nonsynonymous variants, of which the vast majority was specific to individual carcinomas. A subset of genes was recurrently altered across tumors derived from different individuals, including TP53, DLK2, GPC6, and SDF4. Unexpectedly, three prostate cancer genomes exhibited substantially higher mutation frequencies, with 2,000–4,000 novel coding variants per exome. A comparison of castration-resistant and castration-sensitive pairs of tumor lines derived from the same prostate cancer highlights mutations in the Wnt pathway as potentially contributing to the development of castration resistance. Collectively, our results indicate that point mutations arising in coding regions of advanced prostate cancers are common but, with notable exceptions, very few genes are mutated in a substantial fraction of tumors. We also report a previously undescribed subtype of prostate cancers exhibiting “hypermutated” genomes, with potential implications for resistance to cancer therapeutics. Our results also suggest that increasingly deep catalogs of human germline variation may challenge the necessity of sequencing matched tumor-normal pairs.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Agriculture: Feeding the future (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-07-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McCouch, Susan -- Baute, Gregory J -- Bradeen, James -- Bramel, Paula -- Bretting, Peter K -- Buckler, Edward -- Burke, John M -- Charest, David -- Cloutier, Sylvie -- Cole, Glenn -- Dempewolf, Hannes -- Dingkuhn, Michael -- Feuillet, Catherine -- Gepts, Paul -- Grattapaglia, Dario -- Guarino, Luigi -- Jackson, Scott -- Knapp, Sandra -- Langridge, Peter -- Lawton-Rauh, Amy -- Lijua, Qui -- Lusty, Charlotte -- Michael, Todd -- Myles, Sean -- Naito, Ken -- Nelson, Randall L -- Pontarollo, Reno -- Richards, Christopher M -- Rieseberg, Loren -- Ross-Ibarra, Jeffrey -- Rounsley, Steve -- Hamilton, Ruaraidh Sackville -- Schurr, Ulrich -- Stein, Nils -- Tomooka, Norihiko -- van der Knaap, Esther -- van Tassel, David -- Toll, Jane -- Valls, Jose -- Varshney, Rajeev K -- Ward, Judson -- Waugh, Robbie -- Wenzl, Peter -- Zamir, Daniel -- England -- Nature. 2013 Jul 4;499(7456):23-4. doi: 10.1038/499023a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cornell University, Ithaca, New York, USA. mccouch@cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23823779" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization/genetics ; Agriculture/economics/*methods/*trends ; Biodiversity ; Biological Specimen Banks ; Breeding ; Crops, Agricultural/genetics ; Food Supply/*statistics & numerical data ; Genes, Plant ; Humans ; Phenotype ; Seeds/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Increasing CO2 threatens human nutrition (2014)
    Nature Publishing Group (NPG)
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    Publication Date: 2014-05-09
    Description: Dietary deficiencies of zinc and iron are a substantial global public health problem. An estimated two billion people suffer these deficiencies, causing a loss of 63 million life-years annually. Most of these people depend on C3 grains and legumes as their primary dietary source of zinc and iron. Here we report that C3 grains and legumes have lower concentrations of zinc and iron when grown under field conditions at the elevated atmospheric CO2 concentration predicted for the middle of this century. C3 crops other than legumes also have lower concentrations of protein, whereas C4 crops seem to be less affected. Differences between cultivars of a single crop suggest that breeding for decreased sensitivity to atmospheric CO2 concentration could partly address these new challenges to global health.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Myers, Samuel S -- Zanobetti, Antonella -- Kloog, Itai -- Huybers, Peter -- Leakey, Andrew D B -- Bloom, Arnold J -- Carlisle, Eli -- Dietterich, Lee H -- Fitzgerald, Glenn -- Hasegawa, Toshihiro -- Holbrook, N Michele -- Nelson, Randall L -- Ottman, Michael J -- Raboy, Victor -- Sakai, Hidemitsu -- Sartor, Karla A -- Schwartz, Joel -- Seneweera, Saman -- Tausz, Michael -- Usui, Yasuhiro -- 8UL1TR000170-0/TR/NCATS NIH HHS/ -- P30 ES000002/ES/NIEHS NIH HHS/ -- UL1 TR000170/TR/NCATS NIH HHS/ -- England -- Nature. 2014 Jun 5;510(7503):139-42. doi: 10.1038/nature13179. Epub 2014 May 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, 02215, USA [2] Harvard University Center for the Environment, Cambridge, Massachusetts 02138, USA. ; Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, 02215, USA. ; The Department of Geography and Environmental Development, Ben-Gurion University of the Negev, PO Box 653, Beer Sheva, Israel. ; Department of Earth and Planetary Science, Harvard University, Cambridge, Massachusetts 02138, USA. ; Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. ; Department of Plant Sciences, University of California at Davis, Davis, California 95616, USA. ; University of Pennsylvania, Department of Biology, Philadelphia, Pennsylvania 19104, USA. ; Department of Environment and Primary Industries, Horsham, Victoria 3001, Australia. ; National Institute for Agro-Environmental Sciences, Tsukuba, Ibaraki, 305-8604, Japan. ; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; United States Department of Agriculture Agricultural Research Service, Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, USA. ; School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA. ; United States Department of Agriculture Agricultural Research Service, Aberdeen, Idaho 83210, USA. ; The Nature Conservancy, Santa Fe, New Mexico 87544, USA. ; Department of Agriculture and Food Systems, Melbourne School of Land and Environment, The University of Melbourne, Creswick, Victoria 3363, Australia. ; Department of Forest and Ecosystem Science, Melbourne School of Land and Environment, The University of Melbourne, Creswick, Victoria 3363, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24805231" target="_blank"〉PubMed〈/a〉
    Keywords: Air/analysis ; Atmosphere/chemistry ; Australia ; Breeding ; Carbon Dioxide/analysis/*pharmacology ; Crops, Agricultural/*chemistry/*drug effects/metabolism ; Diet ; Edible Grain/chemistry/drug effects/metabolism ; Fabaceae/chemistry/drug effects/metabolism ; Global Health/trends ; Humans ; Iron/analysis/deficiency/metabolism ; Japan ; *Nutritional Status ; Nutritive Value/*drug effects ; Photosynthesis/drug effects ; Phytic Acid/analysis/metabolism ; Public Health/*trends ; United States ; Zinc/analysis/deficiency/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Registration of Soybean Germplasm Line LG00-3372 (2011)
    Wiley
    Details
    Publication Date: 2011-09-01
    Print ISSN: 1936-5209
    Electronic ISSN: 1940-3496
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Wiley
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  • 5
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    Registration of Soybean Germplasm Line LG00-6313 (2011)
    Wiley
    Details
    Publication Date: 2011-09-01
    Print ISSN: 1936-5209
    Electronic ISSN: 1940-3496
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Wiley
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  • 6
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    Registration of the High-Yielding Soybean Germplasm Line LG04-6000 (2012)
    Wiley
    Details
    Publication Date: 2012-05-01
    Print ISSN: 1936-5209
    Electronic ISSN: 1940-3496
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Wiley
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  • 7
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    On the formation of planetary systems via oligarchic growth in thermally evolving viscous discs (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-01
    Description: We present N -body simulations of planetary system formation in thermally evolving, viscous disc models. The simulations incorporate type I migration (including corotation torques and their saturation), gap formation, type II migration, gas accretion on to planetary cores and gas disc dispersal through photoevaporation. The aim is to examine whether or not the oligarchic growth scenario, when combined with self-consistent disc models and up-to-date prescriptions for disc-driven migration, can produce planetary systems similar to those that have been observed. The results correlate with the initial disc mass. Low-mass discs form close-packed systems of terrestrial-mass planets and super-Earths. Higher mass discs form multiple generations of planets, with masses in the range 10 m p 45 M . These planets generally type I migrate into the inner disc, because of corotation torque saturation, where they open gaps and type II migrate into the central star. Occasionally, a final generation of low- to intermediate-mass planets forms and survives due to gas disc dispersal. No surviving gas giants were formed in our simulations. Analysis shows that these planets can only survive migration if a core forms and experiences runaway gas accretion at orbital radii r 10 au prior to the onset of type II migration. We conclude that planet growth above masses m p 10 M during the gas disc lifetime leads to corotation torque saturation and rapid inward migration, preventing the formation and survival of gas giants. This result is in contrast to the success in forming gas giant planets displayed by some population synthesis models. This discrepancy arises, in part, because the type II migration prescription adopted in the population synthesis models causes too large a reduction in the migration speed when in the planet-dominated regime.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    The Genetic Architecture of Seed Composition in Soybean Is Refined by Genome-Wide Association Scans Across Multiple Populations (2014)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2014-11-15
    Description: Soybean oil and meal are major contributors to world-wide food production. Consequently, the genetic basis for soybean seed composition has been intensely studied using family-based mapping. Population-based mapping approaches, in the form of genome-wide association (GWA) scans, have been able to resolve loci controlling moderately complex quantitative traits (QTL) in numerous crop species. Yet, it is still unclear how soybean’s unique population history will affect GWA scans. Using one of the populations in this study, we simulated phenotypes resulting from a range of genetic architectures. We found that with a heritability of 0.5, ~100% and ~33% of the 4 and 20 simulated QTL can be recovered, respectively, with a false-positive rate of less than ~6 x 10 –5 per marker tested. Additionally, we demonstrated that combining information from multi-locus mixed models and compressed linear-mixed models improves QTL identification and interpretation. We applied these insights to exploring seed composition in soybean, refining the linkage group I (chromosome 20) protein QTL and identifying additional oil QTL that may allow some decoupling of highly correlated oil and protein phenotypes. Because the value of protein meal is closely related to its essential amino acid profile, we attempted to identify QTL underlying methionine, threonine, cysteine, and lysine content. Multiple QTL were found that have not been observed in family-based mapping studies, and each trait exhibited associations across multiple populations. Chromosomes 1 and 8 contain strong candidate alleles for essential amino acid increases. Overall, we present these and additional data that will be useful in determining breeding strategies for the continued improvement of soybean’s nutrient portfolio.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 9
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    Composition and fate of gas and oil released to the water column during the Deepwater Horizon oil spill [Environmental Sciences] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-12-12
    Description: Quantitative information regarding the endmember composition of the gas and oil that flowed from the Macondo well during the Deepwater Horizon oil spill is essential for determining the oil flow rate, total oil volume released, and trajectories and fates of hydrocarbon components in the marine environment. Using isobaric gas-tight samplers,...
    Keywords: Science Applications in the Deepwater Horizon Oil Spill Special Feature
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Evaluation of USDA Soybean Germplasm Accessions for Resistance to Soybean Rust in the Southern United States (2011)
    Wiley
    Details
    Publication Date: 2011-03-01
    Print ISSN: 0011-183X
    Electronic ISSN: 1435-0653
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Wiley
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