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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. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 4. |
- 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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| 5. |
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| 6. |
- Dedieu, K, et al.
(författare)
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Coupling of carbon, nitrogen and oxygen cycles in sediments from a Mediterranean lagoon: a seasonal perspective
- 2007
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Ingår i: Marine ecology progress series. - 0171-8630. ; 346, s. 45-59
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Tidskriftsartikel (refereegranskat)abstract
- Experimental data and simulations were used to investigate the seasonal coupling between carbon, nitrogen and oxygen cycles in marine sediments from a eutrophic shallow lagoon in the Mediterranean Sea area. A negative seasonal correlation was observed between oxygen consumption and coupled nitrification–denitrification rates in surface sediments. Elevated values of oxygen consumption rates were reached during warm periods (up to 87.7 mmol m–2 d–1) whereas nitrification and denitrification rates remained close to the lowest rates reported for coastal sediments (values around 0.021 to 0.35 mmol N m–2 d–1 for nitrification and 0.014 to 0.045 mmol N m–2 d–1 for denitrification). A steady-state diagenetic model closely represented the seasonal negative correlation of oxygen uptake, coupled nitrification–denitrification rates, the vertical distribution patterns of pore water oxygen and the solid phase distribution of organic carbon when nitrification inhibition by sulfide was included. Simulation adjusted to field data also highlighted the importance of oxygen penetration depth in the seasonal variation of nitrification. The modelling indicated that anaerobic metabolism was the most significant pathway (65 to 80%) during organic matter mineralization with a clear seasonal increase during warm periods. These warm periods were also characterized by the higher benthic demand of oxygen mostly used to re-oxidize the by-products from anaerobic reactions (from 57 to 82%), the other part being used for carbon mineralization.
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| 7. |
- Gilbert, F., et al.
(författare)
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Sediment reworking by marine benthic species from the Gullmar Fjord (Western Sweden): Importance of faunal biovolume
- 2007
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Ingår i: Journal of Experimental Marine Biology and Ecology. - : Elsevier BV. - 0022-0981. ; 348:1-2, s. 133-144
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Tidskriftsartikel (refereegranskat)abstract
- In order to compare and quantify sediment reworking activities by different species/functional groups of macrofauna, a laboratory experiment was carried out with species from the Gullmarsfjord (Western Sweden). Monospecific communities of Amphiura filiformis, Echinocardium cordatum, Scalibregma inflatum and Abra nitida were introduced in experimental mesocosms, with identical densities (795 ind. m(-2)), for 10 days. Sediment reworking was studied by quantifying downward and upward movements of fluorescent inert tracers (luminophores). Luminophores with different colour were initially deposited both at the sediment surface and within the sediments. Population biomass and biovolume were also determined. Surface tracers reworking coefficients ranged from 0.6 to 2.2 cm(2) y(-1) and 0.9 to 4.1 y(-1), respectively for the biodiffusive-like and non-local transports. Calculated biodiffusive-like coefficient was between 1.0 and 2.3 cm(2) y(-1) for the deep tracers. For both tracers, the E. cordatum population presented the highest reworking coefficients. Among the morphological and/or ethological parameters that could determine overall patterns of reworking and differences between species, results have shown a direct relationship between the apparent biodiffusive mixing and the biovolume of the individuals (D-b=0.35 * Biovolume). This suggests that the biovolume-of macrofauna may allow a rough estimate of the biodiffusive-like reworking intensity of particles deposited on the sediment surface. (c) 2007 Elsevier B.V. All rights reserved.
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| 8. |
- Gilbert, M. Thomas P., et al.
(författare)
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Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland
- 2008
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 320:5884, s. 1787-1789
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Tidskriftsartikel (refereegranskat)abstract
- The Paleo- Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World's northern extremes. However, their origin and genetic relationship to later cultures are unknown. We sequenced a mitochondrial genome from a Paleo- Eskimo human by using 3400- to 4500- year- old frozen hair excavated from an early Greenlandic Saqqaq settlement. The sample is distinct from modern Native Americans and Neo- Eskimos, falling within haplogroup D2a1, a group previously observed among modern Aleuts and Siberian Sireniki Yuit. This result suggests that the earliest migrants into the New World's northern extremes derived from populations in the Bering Sea area and were not directly related to Native Americans or the later Neo- Eskimos that replaced them.
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| 9. |
- Gilbert, T., et al.
(författare)
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DNA from Pre-Clovis Human Coprolites in Oregon, North America
- 2008
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 320:5877, s. 786-789
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Tidskriftsartikel (refereegranskat)abstract
- The timing of the first human migration into the Americas and its relation to the appearance of the Clovis technological complex in North America at about 11,000 to 10,800 radiocarbon years before the present ( C-14 years B. P.) remains contentious. We establish that humans were present at Paisley 5 Mile Point Caves, in south- central Oregon, by 12,300 C-14 years B. P., through the recovery of human mitochondrial DNA ( mtDNA) from coprolites, directly dated by accelerator mass spectrometry. The mtDNA corresponds to Native American founding haplogroups A2 and B2. The dates of the coprolites are > 1000 C-14 years earlier than currently accepted dates for the Clovis complex.
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| 10. |
- Albertson, F., et al.
(författare)
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Comparison of different methods to couple nonlinear source descriptions in the time domain to linear system descriptions in the frequency domain - Application to a simple valveless one-cylinder cold engine
- 2006
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Ingår i: Journal of Sound and Vibration. - : Elsevier BV. - 0022-460X .- 1095-8568. ; 291:05-mar, s. 963-985
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Tidskriftsartikel (refereegranskat)abstract
- In duct acoustics the fundamental sound generating mechanisms must often be described by nonlinear time domain models. A linear frequency domain model is in many cases sufficient for describing the sound propagation in the connected duct system. This applies both for fluid machines such as IC-engines and compressors and for musical wind instruments. Methods for coupling a nonlinear source description to a linear system description have been proposed by several authors. In this paper some of those methods are compared concerning accuracy, calculation time and the possibility to perform parametric studies. The model problem used is a simple piston-restriction system connected to a linear system with varying complexity. The piston and restriction are considered as the source part and are modelled nonlinearly.
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