| 1. |
- 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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| 2. |
- 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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| 3. |
- Lewis, Margaret E., et al.
(författare)
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Patterns of change in in the Plio-Pleistocene carnivorans of eastern Africa: Implications for hominin evolution
- 2007
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Ingår i: Hominin environments in the East African Pliocene: An assessment of the faunal evidence. - New York : Springer-Verlag New York. ; , s. 77-105
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Bokkapitel (refereegranskat)abstract
- This paper uses changes in origination and extinction rates and species richness of eastern African carnivorans through time to discuss issues related to the evolution of hominin behavior. To address the question of which taxa were most likely to have had competitive interactions with hominins, modern carnivorans were sorted into size classes based on shifts in behavior, ecology, and body mass. Four size classes were created, among which the two largest (21.5–100 kg and >100 kg) include those taxa whose behavior is most relevant to the evolution of hominin dietary behavior. Fossil taxa were then assigned to these size classes. A summary of the temporal range and reconstructed behavior and ecology of fossil members of the two largest size classes is presented. We discuss the relevance of each taxon to reconstructing hominin behavior and suggest that hominins must have evolved not only successful anti-predator strategies, but also successful strategies to avoid kleptoparasitism before carcass-based resources could become an important part of the diet. Although hominins were unlikely to have been top predators upon first entrance into the carnivore guild, effective anti-predator/anti-kleptoparasitism strategies in combination with the eventual evolution of active hunting would have increased the rank of hominin species within the guild. While the appearance of stone tools at 2.6 Ma has no apparent effect upon carnivorans, the appearance of Homo ergaster after 1.8 Ma may have been at least partly responsible for the decrease in the carnivoran origination rate and the increase in the extinction rate at this time. The behavior of H. ergaster , climate change, and concomitant changes in prey species richness may have caused carnivoran species richness to drop precipitously after 1.5 Ma. In this situation, even effective kleptoparasitism by H. ergaster may have been enough to drive local populations of carnivorans that overlapped with hominins in dietary resources to extinction. Possibly as a result, the modern guild, which evolved within the last few hundred thousand years, is composed primarily of generalists. Although the impact of H. sapiens on the carnivoran guild cannot be assessed due to a lack of carnivoran fossils from this time period, one might not consider the modern carnivore guild to be complete until the appearance of our species approximately 200,000 years ago.
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| 4. |
- 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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| 5. |
- 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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| 6. |
- Werdelin, Lars, et al.
(författare)
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New species of Crocuta from the Early Pliocene of Kenya, with an overview of early Pliocene hyenas of eastern Africa
- 2008
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Ingår i: Journal of Vertebrate Paleontology. - 0272-4634 .- 1937-2809. ; 28, s. 1162-1170
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Tidskriftsartikel (refereegranskat)abstract
- A new species of Crocuta (spotted hyenas), Crocuta eturono n. sp., from the Early Pliocene of the Turkana Basin, Kenya is described. The species has been recovered from LO6S, a site in the Kataboi Member of the Nachukui Formation, on the western side of Lake Turkana. The site is dated to >3.4 Ma. The new species differs from all previously identified species of Crocuta in its length proportions of the cheek teeth, having a very long m1 and short p3 and p4. The species is also tentatively identified from the Tulu Bor Member of the Koobi Fora Formation, east side of Lake Turkana. The new species provides information for a discussion of the structure of the hyena guild in eastern Africa 4–3 Ma. Three groups of taxa are identified with distinct distributions. It is hypothesized that specific ecomorphologies of each group account for these distinctions.
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| 7. |
- Werdelin, Lars, et al.
(författare)
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Plio-Pleistocene Carnivora of eastern Africa: species richness and turnover patterns
- 2005
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Ingår i: Zoological Journal of the Linnean Society. - 0024-4082 .- 1096-3642. ; 144, s. 121-144
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents an up-to-date and detailed overview of the Plio-Pleistocene fossil record of Carnivora in eastern Africa. Major events in the carnivoran lineages present in the region are discussed and stratigraphic ranges of all species-level taxa are provided. The compiled data are used for quantitative analyses of species richness and turnover. Sampling is considered to be adequate for the interval 3.6–1.5 Mya, and poorer in the half-million-year time slices before and after this interval. Species richness peaks around 3.6–3.0 Mya and declines gradually from that time until the end of the time period analysed. Calculation of origination and extinction rates indicate that there are two peaks of origination: at 3.9–3.3 Mya (although the earlier half of this interval is biased through poor sampling) and at 2.1–1.8 Mya. The origination rate is zero in the interval 3.0–2.4 Mya. The extinction rate peaks at around 3.0 Mya after which it falls slightly, remaining nearly constant until 1.8 Mya, after which it increases considerably. The data support the hypothesis that the modern carnivoran guild of eastern Africa originated relatively recently, mostly within the last million years. There is no support in these data for a turnover pulse in Carnivora between 3 and 2 Mya.
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