| 1. |
- 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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| 2. |
- Andersson, Jan O., et al.
(författare)
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A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution
- 2007
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 8, s. 51-
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Forskningsöversikt (refereegranskat)abstract
- Background: Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey project resulting in 2341 expressed sequence tags (EST) corresponding to 853 unique clones, 5275 genome survey sequences (GSS), and eleven finished contigs from the diplomonad fish parasite Spironucleus salmonicida (previously described as S. barkhanus). Results: The analyses revealed a compact genome with few, if any, introns and very short 3′ untranslated regions. Strikingly different patterns of codon usage were observed in genes corresponding to frequently sampled ESTs versus genes poorly sampled, indicating that translational selection is influencing the codon usage of highly expressed genes. Rigorous phylogenomic analyses identified 84 genes - mostly encoding metabolic proteins - that have been acquired by diplomonads or their relatively close ancestors via lateral gene transfer (LGT). Although most acquisitions were from prokaryotes, more than a dozen represent likely transfers of genes between eukaryotic lineages. Many genes that provide novel insights into the genetic basis of the biology and pathogenicity of this parasitic protist were identified including 149 that putatively encode variant-surface cysteine-rich proteins which are candidate virulence factors. A number of genomic properties that distinguish S. salmonicida from its human parasitic relative G. lamblia were identified such as nineteen putative lineage-specific gene acquisitions, distinct mutational biases and codon usage and distinct polyadenylation signals. Conclusion: Our results highlight the power of comparative genomic studies to yield insights into the biology of parasitic protists and the evolution of their genomes, and suggest that genetic exchange between distantly-related protist lineages may be occurring at an appreciable rate in eukaryote genome evolution.
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| 3. |
- Andersson, Jan O., et al.
(författare)
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Evolution of four gene families with patchy phylogenetic distributions : influx of genes into protist genomes
- 2006
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Ingår i: BMC Evolutionary Biology. - 1471-2148. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Lateral gene transfer (LGT) in eukaryotes from non-organellar sources is a controversial subject in need of further study. Here we present gene distribution and phylogenetic analyses of the genes encoding the hybrid-cluster protein, A-type flavoprotein, glucosamine-6-phosphate isomerase, and alcohol dehydrogenase E. These four genes have a limited distribution among sequenced prokaryotic and eukaryotic genomes and were previously implicated in gene transfer events affecting eukaryotes. If our previous contention that these genes were introduced by LGT independently into the diplomonad and Entamoeba lineages were true, we expect that the number of putative transfers and the phylogenetic signal supporting LGT should be stable or increase, rather than decrease, when novel eukaryotic and prokaryotic homologs are added to the analyses. RESULTS: The addition of homologs from phagotrophic protists, including several Entamoeba species, the pelobiont Mastigamoeba balamuthi, and the parabasalid Trichomonas vaginalis, and a large quantity of sequences from genome projects resulted in an apparent increase in the number of putative transfer events affecting all three domains of life. Some of the eukaryotic transfers affect a wide range of protists, such as three divergent lineages of Amoebozoa, represented by Entamoeba, Mastigamoeba, and Dictyostelium, while other transfers only affect a limited diversity, for example only the Entamoeba lineage. These observations are consistent with a model where these genes have been introduced into protist genomes independently from various sources over a long evolutionary time. CONCLUSION: Phylogenetic analyses of the updated datasets using more sophisticated phylogenetic methods, in combination with the gene distribution analyses, strengthened, rather than weakened, the support for LGT as an important mechanism affecting the evolution of these gene families. Thus, gene transfer seems to be an on-going evolutionary mechanism by which genes are spread between unrelated lineages of all three domains of life, further indicating the importance of LGT from non-organellar sources into eukaryotic genomes.
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| 4. |
- Andersson, Jan O, et al.
(författare)
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Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids.
- 2005
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Ingår i: Mol Biol Evol. - 0737-4038. ; 22:1, s. 85-90
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Tidskriftsartikel (refereegranskat)abstract
- Rare evolutionary events, such as lateral gene transfers and gene fusions, may be useful to pinpoint, and correlate the timing of, key branches across the tree of life. For example, the shared possession of a transferred gene indicates a phylogenetic relationship among organismal lineages by virtue of their shared common ancestral recipient. Here, we present phylogenetic analyses of prolyl-tRNA and alanyl-tRNA synthetase genes that indicate lateral gene transfer events to an ancestor of the diplomonads and parabasalids from lineages more closely related to the newly discovered archaeal hyperthermophile Nanoarchaeum equitans (Nanoarchaeota) than to Crenarchaeota or Euryarchaeota. The support for this scenario is strong from all applied phylogenetic methods for the alanyl-tRNA sequences, whereas the phylogenetic analyses of the prolyl-tRNA sequences show some disagreements between methods, indicating that the donor lineage cannot be identified with a high degree of certainty. However, in both trees, the diplomonads and parabasalids branch together within the Archaea, strongly suggesting that these two groups of unicellular eukaryotes, often regarded as the two earliest independent offshoots of the eukaryotic lineage, share a common ancestor to the exclusion of the eukaryotic root. Unfortunately, the phylogenetic analyses of these two aminoacyl-tRNA synthetase genes are inconclusive regarding the position of the diplomonad/parabasalid group within the eukaryotes. Our results also show that the lineage leading to Nanoarchaeota branched off from Euryarchaeota and Crenarchaeota before the divergence of diplomonads and parabasalids, that this unexplored archaeal diversity, currently only represented by the hyperthermophilic organism Nanoarchaeum equitans, may include members living in close proximity to mesophilic eukaryotes, and that the presence of split genes in the Nanoarchaeum genome is a derived feature.
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| 5. |
- Boukhelifa, Malika, et al.
(författare)
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The proline-rich protein palladin is a binding partner for profilin
- 2006
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Ingår i: The FEBS Journal. - : Wiley. - 1742-464X .- 1742-4658. ; 273:1, s. 26-33
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Tidskriftsartikel (refereegranskat)abstract
- Palladin is an actin-associated protein that has been suggested to play critical roles in establishing cell morphology and maintaining cytoskeletal organization in a wide variety of cell types. Palladin has been shown previously to bind directly to three different actin-binding proteins vasodilator-stimulated phosphoprotein (VASP), α-actinin and ezrin, suggesting that it functions as an organizing unit that recruits actin-regulatory proteins to specific subcellular sites. Palladin contains sequences resembling a motif known to bind profilin. Here, we demonstrate that palladin is a binding partner for profilin, interacting with profilin via a poly proline-containing sequence in the amino-terminal half of palladin. Double-label immunofluorescence staining shows that palladin and profilin partially colocalize in actin-rich structures in cultured astrocytes. Our results suggest that palladin may play an important role in recruiting profilin to sites of actin dynamics.
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| 6. |
- Dudhia, Jayesh, et al.
(författare)
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Aging enhances a mechanically-induced reduction in tendon strength by an active process involving matrix metalloproteinase activity
- 2007
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Ingår i: Aging Cell. - : Wiley. - 1474-9726 .- 1474-9718. ; 6:4, s. 547-556
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Tidskriftsartikel (refereegranskat)abstract
- Age-associated and degenerative loss of functional integrity in soft tissues develops from effects of cumulative and subtle changes in their extracellular matrix (ECM). The highly ordered tendon ECM provides the tissue with its tensile strength during loading. As age and exercise collude in the high incidence of tendinopathies, we hypothesized that aged tendons fail due to cumulative damage resulting from a combination of diminished matrix repair and fragmentation of ECM proteins induced by prolonged cyclical loading, and that this is an active cell-mediated process. We developed an equine tendon explant model to examine the effect of age on the influence of prolonged cyclical loading at physiologically relevant strain rates (5% strain, 1 Hz for 24 h) on tissue mechanical properties, loss of ECM protein and matrix metalloproteinase (MMP) expression. We show significantly diminished mechanical strength of cyclically loaded tissue compared to controls (39.7 +/- 12%, P <= 0.05) this reduction was dependent on the presence of both viable cells and metalloproteinase activity. Furthermore, tendon from older specimens was more susceptible to weakening (11-30 years, 50% P <= 0.05) compared to immature and young mature tissue (1-3 years, 34%; 4-10 years, 35%, respectively). Cyclical load also induced release of degraded cartilage oligomeric matrix protein, an integral ECM protein, an effect that could be mimicked by culture with fibronectin fragments. These findings indicate prolonged cyclical loading of physiological magnitude decreases tendon tensile strength by an active process, and that MMPs may contribute to loss of functional competence, exaggerated by age, via load-induced proteolytic disruption of the ECM.
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| 7. |
- Eriksson, Erik, et al.
(författare)
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Integrated carbon analysis of forest management practices and wood substitution
- 2007
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Ingår i: Canadian Journal of Forest Research. - 0045-5067 .- 1208-6037. ; 37:3, s. 671-681
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Tidskriftsartikel (refereegranskat)abstract
- The complex fluxes between standing and harvested carbon stocks, and the linkage between harvested biomassand fossil fuel substitution, call for a holistic, system-wide analysis in a life-cycle perspective to evaluate the impacts offorest management and forest product use on carbon balances. We have analysed the net carbon emission under alternativeforest management strategies and product uses, considering the carbon fluxes and stocks associated with tree biomass,soils, and forest products. Simulations were made using three Norway spruce (Picea abies (L.) Karst.) forest managementregimes (traditional, intensive management, and intensive fertilization), three slash management practices (no removal, removal,and removal with stumps), two forest product uses (construction material and biofuel), and two reference fossilfuels (coal and natural gas). The greatest reduction of net carbon emission occurred when the forest was fertilized, slashand stumps were harvested, wood was used as construction material, and the reference fossil fuel was coal. The lowest reductionoccurred with a traditional forest management, forest residues retained on site, and harvested biomass was used asbiofuel to replace natural gas. Product use had the greatest impact on net carbon emission, whereas forest management regime,reference fossil fuel, and forest residue usage as biofuel were less significant.
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| 8. |
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| 9. |
- Jirotka, Marina, et al.
(författare)
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Collaboration and trust in healthcare innovation : The eDiaMoND case study
- 2005
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Ingår i: Computer Supported Cooperative Work. - : Springer Science+Business Media B.V.. - 0925-9724 .- 1573-7551. ; 14:4, s. 369-398
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents findings from an investigation into requirements for collaboration in e-Science in the context of eDiaMoND, a Grid-enabled prototype system intended in part to support breast cancer screening. Detailed studies based on ethnographic fieldwork reveal the importance of accountability and visibility of work for trust and for the various forms of ‘practical ethical action’ in which clinicians are seen to routinely engage in this setting. We discuss the implications of our findings, specifically for the prospect of using distributed screening to make more effective use of scarce clinical skills and, more generally, for realising the Grid’s potential for sharing data within and across institutions. Understanding how to afford trust and to provide adequate support for ethical concerns relating to the handling of sensitive data is a particular challenge for e-Health systems and for e-Science in general. Future e-Health and e-Science systems will need to be compatible with the ways in which trust is achieved, and practical ethical actions are realised and embedded within work practices.
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| 10. |
- Karlsson, Roger, 1975, et al.
(författare)
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Chemical analysis in nanoscale surfactant networks
- 2006
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 78:17, s. 5960-5968
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Tidskriftsartikel (refereegranskat)
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