| 1. |
- Andersson, Anders, et al.
(författare)
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Effects of Tobacco Smoke on IL-16 in CD8+ Cells from Human Airways and Blood: a Key Role for Oxygen Free Radicals?
- 2011
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Ingår i: AJP - Lung cellular and molecular physiology. - : American Physiological Society. - 1522-1504. ; 300:1
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Tidskriftsartikel (refereegranskat)abstract
- Chronic exposure to tobacco smoke leads to an increase in the frequency of infections and in CD8(+) and CD4(+)cells as well as the CD4(+) chemo-attractant cytokine IL-16 in the airways. Here, we investigated whether tobacco smoke depletes intracellular IL-16 protein and inhibits de novo production of IL-16 in CD8(+) cells from human airways and blood, while at the same time increasing extracellular IL-16 and whether oxygen free radicals (OFR) are involved. Intracellular IL-16 protein in CD8(+) cells and mRNA in all cells was decreased in bronchoalveolar lavage (BAL) samples from chronic smokers. This was also the case in human blood CD8(+) cells exposed to water-soluble tobacco smoke components in vitro; in which oxidized proteins were markedly increased. Extracellular IL-16 protein was increased in cell-free BAL fluid from chronic smokers and in human blood CD8(+) cells exposed to water-soluble tobacco smoke components in vitro. This was not observed in occasional smokers after short-term exposure to tobacco smoke. A marker of activation (CD69) was slightly increased whereas other markers of key cellular functions (membrane integrity, apoptosis and proliferation) in human blood CD8(+) cells in vitro were negatively affected by water-soluble tobacco smoke components. An OFR scavenger prevented these effects whereas a protein synthesis inhibitor, a beta-adrenoceptor, a glucocorticoid receptor agonist, a phosphodiesterase, a calcineurin phosphatase and a caspase-3 inhibitor did not. In conclusion, tobacco smoke depletes preformed intracellular IL-16 protein, inhibits its de novo synthesis and distorts key cellular functions in human CD8(+) cells. OFR may play a key role in this context.
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| 2. |
- Andersson, Magnus, et al.
(författare)
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Fiskbestånd och miljö i hav och sötvatten : Resurs- och miljööversikt 2012
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Detta är den nionde utgåvan av den samlade översikten över fisk- och kräftdjursbeståndens status i våra vatten. Kunskap om fiskbestånden och miljön är en förutsättning för att utnyttjandet av fiskresurserna skall bli bärkraftigt. För svenska vattenområden beskrivs miljöutvecklingen i ett ekosystemsperspektiv, dels för att tydliggöra fiskens ekologiska roll och beskriva yttre miljöfaktorer som påverkar fiskbestånden, dels för att belysa fiskets effekter på miljön.Fiskbestånd och miljö i hav och sötvatten är utarbetad av Sveriges lantbruksuniversitet (SLU), Institutionen för akvatiska resurser (SLU Aqua), på uppdrag av Havs- och vattenmyndigheten. Rapporten sammanfattar utveckling och beståndsstatus för de kommersiellt viktigaste fisk- och kräftdjursarterna i våra vatten. Bedömningar och förvaltningsråd är baserade på Internationella Havsforskningsrådets (ICES) rådgivning, SLU Aquas nationella och regionala provfiskedata, samt yrkesfiskets rapportering.
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| 3. |
- Mahmudi, Owais, et al.
(författare)
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Genome-wide probabilistic reconciliation analysis across vertebrates
- 2013
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 14:Suppl 15, s. S10-
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Tidskriftsartikel (refereegranskat)abstract
- Gene duplication is considered to be a major driving force in evolution that enables the genome of a species to acquire new functions. A reconciliation - a mapping of gene tree vertices to the edges or vertices of a species tree explains where gene duplications have occurred on the species tree. In this study, we sample reconciliations from a posterior over reconciliations, gene trees, edge lengths and other parameters, given a species tree and gene sequences. We employ a Bayesian analysis tool, based on the probabilistic model DLRS that integrates gene duplication, gene loss and sequence evolution under a relaxed molecular clock for substitution rates, to obtain this posterior. By applying these methods, we perform a genome-wide analysis of a nine species dataset, OPTIC, and conclude that for many gene families, the most parsimonious reconciliation (MPR) - a reconciliation that minimizes the number of duplications - is far from the correct explanation of the evolutionary history. For the given dataset, we observe that approximately 19% of the sampled reconciliations are different from MPR. This is in clear contrast with previous estimates, based on simpler models and less realistic assumptions, according to which 98% of the reconciliations can be expected to be identical to MPR. We also generate heatmaps showing where in the species trees duplications have been most frequent during the evolution of these species.
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| 4. |
- Sjöstrand, Joel, et al.
(författare)
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A Bayesian Method for Analyzing Lateral Gene Transfer
- 2014
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 63:3, s. 409-420
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Tidskriftsartikel (refereegranskat)abstract
- Lateral gene transfer (LGT)uwhich transfers DNA between two non-vertically related individuals belonging to the same or different speciesuis recognized as a major force in prokaryotic evolution, and evidence of its impact on eukaryotic evolution is ever increasing. LGT has attracted much public attention for its potential to transfer pathogenic elements and antibiotic resistance in bacteria, and to transfer pesticide resistance from genetically modified crops to other plants. In a wider perspective, there is a growing body of studies highlighting the role of LGT in enabling organisms to occupy new niches or adapt to environmental changes. The challenge LGT poses to the standard tree-based conception of evolution is also being debated. Studies of LGT have, however, been severely limited by a lack of computational tools. The best currently available LGT algorithms are parsimony-based phylogenetic methods, which require a pre-computed gene tree and cannot choose between sometimes wildly differing most parsimonious solutions. Moreover, in many studies, simple heuristics are applied that can only handle putative orthologs and completely disregard gene duplications (GDs). Consequently, proposed LGT among specific gene families, and the rate of LGT in general, remain debated. We present a Bayesian Markov-chain Monte Carlo-based method that integrates GD, gene loss, LGT, and sequence evolution, and apply the method in a genome-wide analysis of two groups of bacteria: Mollicutes and Cyanobacteria. Our analyses show that although the LGT rate between distant species is high, the net combined rate of duplication and close-species LGT is on average higher. We also show that the common practice of disregarding reconcilability in gene tree inference overestimates the number of LGT and duplication events. [Bayesian; gene duplication; gene loss; horizontal gene transfer; lateral gene transfer; MCMC; phylogenetics.].
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| 5. |
- Sjöstrand, Joel, et al.
(författare)
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DLRS : Gene tree evolution in light of a species tree
- 2012
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 28:22, s. 2994-2995
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Tidskriftsartikel (refereegranskat)abstract
- PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters.
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| 6. |
- Sjöstrand, Joel, et al.
(författare)
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GenPhyloData : realistic simulation of gene family evolution
- 2013
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Background: PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and-perhaps more interestingly-also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock. Result: Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data. Conclusion: The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.
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| 7. |
- Werner, Malin, et al.
(författare)
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Utsjöfisk
- 2011
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Ingår i: Havet. - 1654-6741. ; , s. 58-59
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Annan publikation (populärvet., debatt m.m.)
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| 8. |
- Werner, Malin, et al.
(författare)
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Utsjöfisk
- 2012
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Ingår i: Havet. - 1654-6741. ; , s. 72-
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Annan publikation (övrigt vetenskapligt/konstnärligt)
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