| 1. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Birney, Ewan, et al.
(författare)
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Prepublication data sharing
- 2009
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 461:7261, s. 168-170
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Tidskriftsartikel (refereegranskat)abstract
- Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.
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| 3. |
- Mikkelsen, Tarjei S, et al.
(författare)
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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7141, s. 167-177
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Tidskriftsartikel (refereegranskat)abstract
- We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
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| 4. |
- Miller, Paul, et al.
(författare)
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Exploring climatic and biotic controls on Holocene vegetation change in Fennoscandia
- 2008
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Ingår i: Journal of Ecology. - : Wiley. - 1365-2745 .- 0022-0477. ; 96:2, s. 247-259
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Tidskriftsartikel (refereegranskat)abstract
- # 1. We investigated the potential drivers of Holocene vegetation changes recorded at four Scandinavian pollen sites, two in Sweden and two in Finland, at a time when they were largely free of anthropogenic influence. # 2. We used the generalized dynamic vegetation model LPJ-GUESS forced with climate anomaly output from an atmospheric general circulation model to simulate tree species dynamics from 10 000 years ago to the present. The model results were compared to high-resolution pollen accumulation rates gathered at the sites. # 3. Our results indicate that both the observed northern distributional limits of temperate trees, and the limits of Pinus sylvestris and Alnus incana at the tree line, are a result of millennial variations in summer and winter temperatures. The simulation of several distinct trends in species occurrence observed in the pollen record indicates that a time lag due to the slow spreading of species need not be invoked for most species. # 4. Sensitivity studies indicate that competition, natural disturbance and the magnitude of interannual variability play key roles in determining the biomass, establishment and even the presence of species near their bioclimatic limits. However, neither disturbance due to fire nor limits on establishment due to drought were likely to have been major determinants of the observed trends on the timescales considered. # 5. We were unable to limit the modelled occurrence of Picea abies at the study sites to the periods at which it was observed in the pollen records, indicating that we have still not completely understood the driving or limiting factors for Holocene changes in Picea abies abundance. # 6. Synthesis. This study shows that by combining quantitative vegetation reconstructions with a modern, process-based dynamic vegetation model, we may gain new insights into the potential biotic and abiotic drivers of Holocene vegetation dynamics, and their relative importance. This knowledge will be crucial in enabling us to assess more confidently the response of northern European vegetation to future climate change.
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| 5. |
- 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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| 6. |
- Arneth, Almut, et al.
(författare)
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CO2 inhibition of terrestrial isoprene production stabilises tropospheric oxidation capacity
- 2007
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Ingår i: Geophysical Research Letters. - 1944-8007. ; 34, L18813:18
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Tidskriftsartikel (refereegranskat)abstract
- [1] Isoprene is the dominant volatile organic compound produced by the terrestrial biosphere and fundamental for atmospheric composition and climate. It constrains the concentration of tropospheric oxidants, affecting the lifetime of other reduced species such as methane and contributing to ozone production. Oxidation products of isoprene contribute to aerosol growth. Recent consensus holds that emissions were low during glacial periods ( helping to explain low methane concentrations), while high emissions ( contributing to high ozone concentrations) can be expected in a greenhouse world, due to positive relationships with temperature and terrestrial productivity. However, this response is offset when the recently demonstrated inhibition of leaf isoprene emissions by increasing atmospheric CO2 concentration is accounted for in a process-based model. Thus, isoprene may play a small role in determining pre-industrial tropospheric OH concentration and glacial-interglacial methane trends, while predictions of high future tropospheric O-3 concentrations partly driven by isoprene emissions may need to be revised.
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| 7. |
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| 8. |
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| 9. |
- Chen, Kang, et al.
(författare)
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Immunoglobulin D enhances immune surveillance by activating antimicrobial, proinflammatory and B cell-stimulating programs in basophils
- 2009
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Ingår i: Nature Immunology. - : Springer Science and Business Media LLC. - 1529-2908 .- 1529-2916. ; 10:8, s. 121-889
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Tidskriftsartikel (refereegranskat)abstract
- Immunoglobulin D (IgD) is an enigmatic antibody isotype that mature B cells express together with IgM through alternative RNA splicing. Here we report active T cell-dependent and T cell-independent IgM-to-IgD class switching in B cells of the human upper respiratory mucosa. This process required activation-induced cytidine deaminase (AID) and generated local and circulating IgD-producing plasmablasts reactive to respiratory bacteria. Circulating IgD bound to basophils through a calcium-mobilizing receptor that induced antimicrobial, opsonizing, inflammatory and B cell-stimulating factors, including cathelicidin, interleukin 1 (IL-1), IL-4 and B cell-activating factor (BAFF), after IgD crosslinking. By showing dysregulation of IgD class-switched B cells and 'IgD-armed' basophils in autoinflammatory syndromes with periodic fever, our data indicate that IgD orchestrates an ancestral surveillance system at the interface between immunity and inflammation.
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| 10. |
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