| 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. |
- 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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| 3. |
- 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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| 4. |
- Shen, Li, et al.
(författare)
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An interactive 3D visualization and manipulation tool foreffective assessment of angiogenesis and arteriogenesis usingcomputed tomographic angiography
- 2005
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Ingår i: Progress in Biomedical Optics and Imaging. - : SPIE. - 1605-7422 .- 1042-4687. ; 5744:II, s. 848-858
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents IVM, an Interactive Vessel Manipulation tool that can help make effective and efficient assessmentof angiogenesis and arteriogenesis in computed tomographic angiography (CTA) studies. IVM consistsof three fundamental components: (1) a visualization component, (2) a tracing component, and (3) a measurementcomponent. Given a user-specified threshold, IVM can create a 3D surface visualization based on it. Sincevessels are thin and tubular structures, using standard isosurface extraction techniques usually cannot yieldsatisfactory reconstructions. Instead, IVM directly renders the surface of a derived binary 3D image. The imagevolumes collected in CTA studies often have a relatively high resolution. Thus, compared with more complicatedvessel extraction and visualization techniques, rendering the binary image surface has the advantages of beingeffective, simple and fast. IVM employs a semi-automatic approach to determine the threshold: a user can adjustthe threshold by checking the corresponding 3D surface reconstruction and make the choice. Typical tracingsoftware often defines ROIs on 3D image volumes using three orthogonal views. The tracing component in IVMtakes one step further: it can perform tracing not only on image slices but also in a 3D view. We observe thatdirectly operating on a 3D view can help a tracer identify ROIs more easily. After setting a threshold and tracingan ROI, a user can use IVM’s measurement component to estimate the volume and other parameters of vesselsin the ROI. The effectiveness of the IVM tool is demonstrated on rat vessel/bone images collected in a previousCTA study.
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