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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. |
- Carninci, P, et al.
(författare)
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The transcriptional landscape of the mammalian genome
- 2005
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 309:5740, s. 1559-1563
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Tidskriftsartikel (refereegranskat)abstract
- This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5′ and 3′ boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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| 4. |
- Haas, Brian J., et al.
(författare)
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Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
- 2009
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 461:7262, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
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| 5. |
- Baxter, Charles J, et al.
(författare)
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The metabolic response of heterotrophic Arabidopsis cells to oxidative stress
- 2007
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Ingår i: Plant Physiology. - Rockville, USA : American Society of Plant Biologists. - 0032-0889 .- 1532-2548. ; 143:1, s. 312-25
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Tidskriftsartikel (refereegranskat)abstract
- To cope with oxidative stress, the metabolic network of plant cells must be reconfigured either to bypass damaged enzymes or to support adaptive responses. To characterize the dynamics of metabolic change during oxidative stress, heterotrophic Arabidopsis (Arabidopsis thaliana) cells were treated with menadione and changes in metabolite abundance and (13)C-labeling kinetics were quantified in a time series of samples taken over a 6 h period. Oxidative stress had a profound effect on the central metabolic pathways with extensive metabolic inhibition radiating from the tricarboxylic acid cycle and including large sectors of amino acid metabolism. Sequential accumulation of metabolites in specific pathways indicated a subsequent backing up of glycolysis and a diversion of carbon into the oxidative pentose phosphate pathway. Microarray analysis revealed a coordinated transcriptomic response that represents an emergency coping strategy allowing the cell to survive the metabolic hiatus. Rather than attempt to replace inhibited enzymes, transcripts encoding these enzymes are in fact down-regulated while an antioxidant defense response is mounted. In addition, a major switch from anabolic to catabolic metabolism is signaled. Metabolism is also reconfigured to bypass damaged steps (e.g. induction of an external NADH dehydrogenase of the mitochondrial respiratory chain). The overall metabolic response of Arabidopsis cells to oxidative stress is remarkably similar to the superoxide and hydrogen peroxide stimulons of bacteria and yeast (Saccharomyces cerevisiae), suggesting that the stress regulatory and signaling pathways of plants and microbes may share common elements.
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| 7. |
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| 8. |
- Pietras, Alexander, et al.
(författare)
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HIF-2 alpha maintains an undifferentiated state in neural crest-like human neuroblastoma tumor-initiating cells
- 2009
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 106:39, s. 16805-16810
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Tidskriftsartikel (refereegranskat)abstract
- High hypoxia-inducible factor-2 alpha (HIF-2 alpha) protein levels predict poor outcome in neuroblastoma, and hypoxia dedifferentiates cultured neuroblastoma cells toward a neural crest-like phenotype. Here, we identify HIF-2 alpha as a marker of normoxic neural crest-like neuroblastoma tumor-initiating/stem cells (TICs) isolated from patient bone marrows. Knockdown of HIF-2 alpha reduced VEGF expression and induced partial sympathetic neuronal differentiation when these TICs were grown in vitro under stem cell-promoting conditions. Xenograft tumors of HIF-2 alpha-silenced cells were widely necrotic, poorly vascularized, and resembled the bulk of tumor cells in clinical neuroblastomas by expressing additional sympathetic neuronal markers, whereas control tumors were immature, well-vascularized, and stroma-rich. Thus, HIF-2 alpha maintains an undifferentiated state of neuroblastoma TICs. Because low differentiation is associated with poor outcome and angiogenesis is crucial for tumor growth, HIF-2 alpha is an attractive target for neuroblastoma therapy.
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| 9. |
- Reynolds, Ben C., et al.
(författare)
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An inter-laboratory comparison of Si isotope reference materials
- 2007
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Ingår i: Journal of Analytical Atomic Spectrometry. - : Royal Society of Chemistry (RSC). - 0267-9477 .- 1364-5544. ; 22:5, s. 561-568
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Tidskriftsartikel (refereegranskat)abstract
- Three Si isotope materials have been used for an inter-laboratory comparison exercise to ensure reproducibility between international laboratories investigating natural Si isotope variations using a variety of chemical preparation methods and mass spectrometric techniques. These proposed standard reference materials are (i) IRMM-018 (a SiO2 standard), (ii) Big-Batch (a fractionated SiO2 material prepared at the University of California Santa Barbara), and (iii) Diatomite (a natural diatomite sample originally deposited as marine biogenic opal). All analyses are compared with the international Si standard NBS28 (RM8546) and are in reasonable agreement (<+/- 0.22 parts per thousand. 1 sigma(SD) delta Si-30) given the different measurement techniques involved. These methods include both acid and alkaline dissolution/fusion, Si separation using cation exchange, selective co-precipitation, and gas-source versus plasma-ionization (high and low resolution) mass-spectrometric techniques. The average delta Si-30 for Diatomite, IRMM-018, and Big-Batch are + 1.26 parts per thousand, -1.65 parts per thousand and -10.48 parts per thousand, respectively, with corresponding delta Si-9 values of + 0.64 parts per thousand, -0.85 parts per thousand and -5.35 parts per thousand for the same standards, respectively. For the most fractionated standard (Big-Batch), results demonstrate a kinetic mass-dependent fractionation effect for atomic Si (i.e., delta Si-29 similar to 0.51 x delta Si-30). There is almost no statistical difference between the mean values obtained by each participating laboratory, with the notable exception of the IRMM-018 standard. This effect could be caused by heterogeneity or contamination of this standard. The results for the other two standards indicate that data sets produced using any of the methods employed in this study will have similar precision and differences are limited to 0.2 parts per thousand in mean delta Si-30 values for a given sample between laboratories, or differences of 0.13 parts per thousand. in mean delta Si-29 values.
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| 10. |
- Reynolds, Ben C., et al.
(författare)
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An inter-laboratory comparison of Si isotope reference materials
- 2007
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Ingår i: Journal of Analytical Atomic Spectrometry. - : Elsevier BV. - 0267-9477 .- 1364-5544. ; 22:5, s. 561-568
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Tidskriftsartikel (refereegranskat)abstract
- Three Si isotope materials have been used for an inter-laboratory comparison exercise to ensure reproducibility between international laboratories investigating natural Si isotope variations using a variety of chemical preparation methods and mass spectrometric techniques. These proposed standard reference materials are (i) IRMM-018 (a SiO2 standard), (ii) Big-Batch (a fractionated SiO2 material prepared at the University of California Santa Barbara), and (iii) Diatomite (a natural diatomite sample originally deposited as marine biogenic opal). All analyses are compared with the international Si standard NBS28 (RM8546) and are in reasonable agreement (<+/- 0.22 parts per thousand. 1 sigma(SD) delta Si-30) given the different measurement techniques involved. These methods include both acid and alkaline dissolution/fusion, Si separation using cation exchange, selective co-precipitation, and gas-source versus plasma-ionization (high and low resolution) mass-spectrometric techniques. The average delta Si-30 for Diatomite, IRMM-018, and Big-Batch are + 1.26 parts per thousand, -1.65 parts per thousand and -10.48 parts per thousand, respectively, with corresponding delta Si-9 values of + 0.64 parts per thousand, -0.85 parts per thousand and -5.35 parts per thousand for the same standards, respectively. For the most fractionated standard (Big-Batch), results demonstrate a kinetic mass-dependent fractionation effect for atomic Si (i.e., delta Si-29 similar to 0.51 x delta Si-30). There is almost no statistical difference between the mean values obtained by each participating laboratory, with the notable exception of the IRMM-018 standard. This effect could be caused by heterogeneity or contamination of this standard. The results for the other two standards indicate that data sets produced using any of the methods employed in this study will have similar precision and differences are limited to 0.2 parts per thousand in mean delta Si-30 values for a given sample between laboratories, or differences of 0.13 parts per thousand. in mean delta Si-29 values.
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