| 1. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 2. |
- Armstrong, Janet L., et al.
(författare)
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Interannual and Spatial Feeding Patterns of Hatchery and Wild Juvenile Pink Salmon in the Gulf of Alaska in Years of Low and High Survival
- 2008
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Ingår i: Transactions of the American Fisheries Society 2008; 137: 1299-1316.
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Tidskriftsartikel (refereegranskat)abstract
- To improve understanding of the mechanisms affecting growth and survival, we evaluated the summer diets and feeding patterns (prey composition, energy density, and stomach fullness) of hatchery and wild juvenile pink salmon Oncorhynchus gorbuscha in Prince William Sound (PWS) and the northern coastal Gulf of Alaska (CGOA). Our study (19992004) included 2 years of low (3%), mid (5%), and high (89%) survival of PWS hatchery pink salmon. Because variations in diet should affect growth and ultimately survival, we expected that the variations in diet, growth, and survival would be correlated. During August in the CGOA, pteropod-dominated diets and higher gut fullness corresponded to high survival (59%), and copepod-dominated diets and lower gut fullness corresponded to low survival (3%). Within years, no significant differences were found in diet composition or gut fullness between hatchery and wild fish or among the four PWS hatchery stocks. Diets varied by water mass (habitat) as juveniles moved from PWS to more saline habitats in the CGOA. In July, when juveniles were most abundant in PWS, their diets were dominated by pteropods and hyperiid amphipods. The diets of fish that moved to inner-shelf (i.e., the least-saline) habitat in the CGOA in July were dominated by larvaceans in low-survival years and pteropods in high-survival years. Diet quality was higher in CGOA habitats than in PWS in July. In August, fish moved to the more productive, more saline water masses in the CGOA, where large copepods and pteropods were dominant prey and diet quality was better than in PWS. Our results indicate that spatial variation in the diets of juvenile pink salmon in July and the timing of migration to the CGOA play a critical role in marine growth and survival
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| 4. |
- Ding, Li, et al.
(författare)
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Somatic mutations affect key pathways in lung adenocarcinoma
- 2008
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 455:7216, s. 1069-1075
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Tidskriftsartikel (refereegranskat)abstract
- Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.
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| 5. |
- Field, Dawn, et al.
(författare)
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The minimum information about a genome sequence (MIGS) specification.
- 2008
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Ingår i: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 26:5, s. 541-7
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Tidskriftsartikel (refereegranskat)abstract
- With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.
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| 6. |
- Guigliano, Robert P, et al.
(författare)
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Early versus delayed, provisional eptifibatide in acute coronary syndromes.
- 2009
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Ingår i: New England Journal of Medicine. - : Massachusetts Medical Society. - 0028-4793 .- 1533-4406. ; 360:21, s. 2176-2190
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Tidskriftsartikel (refereegranskat)abstract
- Background Glycoprotein IIb/IIIa inhibitors are indicated in patients with acute coronary syndromes who are undergoing an invasive procedure. The optimal timing of the initiation of such therapy is unknown. Methods We compared a strategy of early, routine administration of eptifibatide with delayed, provisional administration in 9492 patients who had acute coronary syndromes without ST-segment elevation and who were assigned to an invasive strategy. Patients were randomly assigned to receive either early eptifibatide (two boluses, each containing 180 µg per kilogram of body weight, administered 10 minutes apart, and a standard infusion 12 hours before angiography) or a matching placebo infusion with provisional use of eptifibatide after angiography (delayed eptifibatide). The primary efficacy end point was a composite of death, myocardial infarction, recurrent ischemia requiring urgent revascularization, or the occurrence of a thrombotic complication during percutaneous coronary intervention that required bolus therapy opposite to the initial study-group assignment ("thrombotic bailout") at 96 hours. The key secondary end point was a composite of death or myocardial infarction within the first 30 days. Key safety end points were bleeding and the need for transfusion within the first 120 hours after randomization. Results The primary end point occurred in 9.3% of patients in the early-eptifibatide group and in 10.0% in the delayed-eptifibatide group (odds ratio, 0.92; 95% confidence interval [CI], 0.80 to 1.06; P=0.23). At 30 days, the rate of death or myocardial infarction was 11.2% in the early-eptifibatide group, as compared with 12.3% in the delayed-eptifibatide group (odds ratio, 0.89; 95% CI, 0.79 to 1.01; P=0.08). Patients in the early-eptifibatide group had significantly higher rates of bleeding and red-cell transfusion. There was no significant difference between the two groups in rates of severe bleeding or nonhemorrhagic serious adverse events. Conclusions In patients who had acute coronary syndromes without ST-segment elevation, the use of eptifibatide 12 hours or more before angiography was not superior to the provisional use of eptifibatide after angiography. The early use of eptifibatide was associated with an increased risk of non–life-threatening bleeding and need for transfusion.
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| 12. |
- Piccolo, John, et al.
(författare)
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Seasonal distribution and size of juvenile pink salmon in the Gulf of Alaska: relating ocean habitat use to growth and survival
- 2007
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Konferensbidrag (refereegranskat)abstract
- Each year millions of wild and hatchery juvenile pink salmon enter the waters of Prince William Sound (PWS) in the northern Gulf of Alaska. By mid summer, they begin to migrate out of PWS, first into the Alaska Coastal Current (ACC), and then into Shelf waters, where they forage and grow prior to migrating offshore in the fall. Differences in feeding and growth conditions among PWS, ACC, and Shelf habitats are likely to affect growth during the first summer, and ultimately cohort survival. In July-September of 2001-2004, we collected juvenile pink salmon with a surface trawl in PWS, ACC and Shelf habitats, to determine their seasonal distribution, diet, and growth. In July of all years, catch per unit effort was relatively high in PWS and ACC habits, and low in the Shelf habitat. By August and September this pattern had reversed, with most fish being caught in the Shelf habitat. Fish from year classes that subsequently showed higher adult survivals (2002 and 2004) were larger, and they tended to migrate into Shelf habitats earlier than did those with lower adult survivals (2001 and 2003). Using thermal mark recovery of PWS hatchery cohorts, we compared the size of known-age fish in the different habitats. In three of four years, hatchery fish of the same age were significantly larger in Shelf habitats than they were in ACC or PWS habitats. In general, hatchery cohorts that had larger juveniles in late summer had higher adult survivals, but there was considerable variation in this trend both among hatcheries and among years
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| 13. |
- Richards, Stephen, et al.
(författare)
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The genome of the model beetle and pest Tribolium castaneum.
- 2008
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Ingår i: Nature. - 1476-4687. ; 452:7190, s. 949-55
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Tidskriftsartikel (refereegranskat)abstract
- Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
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| 14. |
- Sodergren, Erica, et al.
(författare)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Tidskriftsartikel (refereegranskat)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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