| 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. |
- 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. |
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| 4. |
- 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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| 5. |
- Jones, Owen R., et al.
(författare)
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Senescence rates are determined by ranking on the fast-slow life-history continuum
- 2008
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Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 11:7, s. 664-673
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analyses of survival senescence by using life tables have identified generalizations including the observation that mammals senesce faster than similar-sized birds. These generalizations have been challenged because of limitations of life-table approaches and the growing appreciation that senescence is more than an increasing probability of death. Without using life tables, we examine senescence rates in annual individual fitness using 20 individual-based data sets of terrestrial vertebrates with contrasting life histories and body size. We find that senescence is widespread in the wild and equally likely to occur in survival and reproduction. Additionally, mammals senesce faster than birds because they have a faster life history for a given body size. By allowing us to disentangle the effects of two major fitness components our methods allow an assessment of the robustness of the prevalent life-table approach. Focusing on one aspect of life history - survival or recruitment - can provide reliable information on overall senescence.
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| 6. |
- Volkmann, Jens, et al.
(författare)
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Long-Term Effects of Pallidal or Subthalamic Deep Brain Stimulation on Quality of Life in Parkinson's Disease
- 2009
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Ingår i: Movement Disorders. - : Wiley. - 0885-3185. ; 24:8, s. 1154-1161
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Tidskriftsartikel (refereegranskat)abstract
- We assessed the effects of deep brain stimulation of the subthalamic nucleus (STN-DBS) or internal pallidum (GPi-DBS) on health-related quality of life (HrQoL) in patients with advanced Parkinson's disease participating in a previously reported multicenter trial. Sickness Impact Profile (SIP) questionnaires were available for analysis in a Subgroup of n = 20/20 patients with GPi-DBS and n = 45/49 patients with STN-DBS at baseline, 6 and 36 months. The SIP provides a physical dimension and a psychosocial dimension sum score and 12 category scores: Alertness/Intellectual Behavior (AIB), Ambulation (A), Body Care and Movement (BCM), Communication (C), Eating (E), Emotional Behavior (EB), Home Management (HM), Mobility (M), Recreation and Pastimes (RP), Sleep and Rest (SR), Social Interaction (SI), and Work (W). Motor functioning was assessed by means of the Unified Parkinson's Disease Rating Scale and diaries. At 6 months significant improvements in off-period motor symptoms and activities of daily living were paralleled by significant reductions in the total, physical, and psychosocial SIP score in both treatment groups. At 3 years, sustained improvements were observed in the physical dimension score, BCM, E, M, RP after STN-DBS and M, SI after GPi-DBS. All other SIP subscores approached baseline values, but were still the same or better (except C) whereas motor functioning remained stable after 36 months. STN-DBS and GPi-DBS led to significant early improvements in HrQoL. Despite sustained motor improvements many of these initial benefits were lost after 3 years. This may reflect either progression of the disease or adaptive changes in the subjective perception of health-related wellbeing over time. (C) 2009 Movement Disorder Society
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| 7. |
- Abreu, Paulo Cesar, et al.
(författare)
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Importance of biofilm as food source for shrimps (Farafantepenaeus paulensis) evaluated by stable isotopes (∂13C and ∂15N)
- 2007
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Ingår i: Journal of Experimental Marine Biology and Ecology. - : Elsevier BV. - 0022-0981. ; 347:1-2, s. 88-96
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Tidskriftsartikel (refereegranskat)abstract
- Abstract The contribution of biofilm and artificial feeds for the growth of the pink shrimp Farfantepenaeus paulensis reared in tanks and net cages were evaluated by using stable isotope (δ13C and δ15N) analysis. In the net cage experiment, mass balance and mixing equations showed that the biofilm contribution to shrimp growth was over 49% of carbon and 70% of nitrogen. These data suggest that the artificial feed offered in this experiment, although ingested, was not properly incorporated in the shrimp tissue. In contrast, biofilm growing in tanks contributed little to the nitrogen incorporated by the shrimp (maximum of 29%). In this experiment, shrimp presented an unusually large isotope fractionation. These results imply that the shrimp are selectively ingesting some items from the biofilm, or differentially assimilate specific items of the artificial feed, due to differential digestibility. The hypothesis of selective feeding of biofilm microorganisms was corroborated in the experiment with net cages, where shrimp preferentially consumed centric diatoms. This study also demonstrated that shrimp biofilm consumption and the presence of artificial feed largely influenced biofilm formation. The consumption of centric diatoms by shrimp seem to stimulate biofilm chlorophyll-a, while biofilm δ15N values measured in tanks indicate that microorganisms present in the biofilm absorbs nitrogen released by artificial feed after its decomposition.
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| 8. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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Pollination of the Lady's slipper orchid (Cypripedium calceolus) in Scandinavia - taxonomic and conservational aspects
- 2009
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Ingår i: Nordic Journal of Botany. - : Wiley. - 0107-055X .- 1756-1051. ; 27:4, s. 266-273
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Tidskriftsartikel (refereegranskat)abstract
- The Lady's slipper orchid Cypripedium calceolus L. is considered one of the most beautiful orchids of Europe. Consequently, the species has suffered from over-collecting and is now critically endangered in many countries. Although pollination success is suspected to influence the long-term survival of Cypripedium calceolus, relatively little is known about the identity of its pollinators in mainland Sweden - a region that comprises the largest European populations. In order to identify which species pollinate eight representative populations in mainland Sweden, we observed and sampled visitors to flowers using a standardized protocol. Specimens were identified and any pollen smear found on their body was examined for the presence of Cypripedium pollen. Nine species were recognized as effective pollen vectors (Andrena cineraria, A. carantonica, A. haemorrohoa, A. helvola, A. nigroaenea, A. praecox, Colletes cunicularius, Lasioglossum fratellum and L. fulvicorne), four of them for the first time in Scandinavia. This is the first time that a species of Colletes is reported to carry pollen of Cypripedium in this region. All but one specimens were females. Our results suggest a taxonomically heterogeneous pollinator fauna for Cypripedium calceolus and are discussed in light of the management of this species.
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| 9. |
- Covacu, Ruxandra, et al.
(författare)
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Nitric oxide exposure diverts neural stem cell fate from neurogenesis towards astrogliogenesis
- 2006
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Ingår i: Stem Cells. - : Oxford University Press (OUP). - 1066-5099 .- 1549-4918. ; 178, s. 268-268
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Regeneration of cells in the central nervous system is a process that might be affected during neurological disease and trauma. Because nitric oxide (NO) and its derivatives are powerful mediators in the inflammatory cascade, we have investigated the effects of pathophysiological concentrations of NO on neurogenesis, gliogenesis, and the expression of proneural genes in primary adult neural stem cell cultures. After exposure to NO, neurogenesis was downregulated, and this corresponded to decreased expression of the proneural gene neurogenin-2 and beta-III-tubulin. The decreased ability to generate neurons was also found to be transmitted to the progeny of the cells. NO exposure was instead beneficial for astroglial differentiation, which was confirmed by increased activation of the Janus tyrosine kinase/signal transducer and activator of transcription transduction pathway. Our findings reveal a new role for NO during neuroinflammatory conditions, whereby its proastroglial fate-determining effect on neural stem cells might directly influence the neuroregenerative process.
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| 10. |
- Daniel, C, et al.
(författare)
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Microbial food webs in the dark: independence of Lake Plankton from recent algal production
- 2005
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Ingår i: Aquatic Microbial Ecology. - 0948-3055. ; 38:2, s. 113-123
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the development of a heterotrophic plankton food web with or without phytoplankton primary production in a long-term (>1 yr) laboratory experiment. Water from 3 Swedish lakes (humic, oligotrophic clearwater, eutrophic) was exposed to low light or kept in total darkness in triplicate 100 1 cylinders. Dissolved organic carbon (DOC) dynamics, bacterial growth and biomass of protozoans, rotifers and microcrustaceans were followed over 18 mo. In the dark treatments, no primary production was detected and DOC concentrations decreased by between 19 and 27% (1.3 to 3.2 mg C l(-1)). There was bacterial and protozoan growth in the dark during the whole experimental period. However, numbers and production of bacteria, as well as protozoan biomass, were significantly lower in darkness. Dissolved (DOM) and particulate organic matter (POM) initially present in the water (i.e. 18 mo old at the end of the experiment) helped to support substantial metazoan biomasses in dark treatments in the humic and eutrophic waters, but not in the oligotrophic clearwater lake. DOM in the humic water, thus largely of allochthonous origin, gave the highest and most prolonged support to zooplankton living in darkness. Our study indicates that a microbial food web, based on allochthonous organic matter and developing independently from phytoplankton, can act as a link to metazoan zooplankton, especially in oligotrophic humic lakes. These results confirm studies using stable C isotopes, showing a substantial incorporation of terrestrial carbon into zooplankton.
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