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- Eriksson, Martin, 1970, et al.
(författare)
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A phylogenetic approach to detect selection on the target site of the antifouling compound irgarol in tolerant periphyton communities
- 2009
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 11, s. 2065-2077
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Tidskriftsartikel (refereegranskat)abstract
- Using DNA sequence data for phylogenetic assessment of toxicant targets is a new and promising approach to study toxicant-induced selection in communities. Irgarol 1051 is a photosystem (PS) II inhibitor used in antifouling paint. It inhibits photosynthesis through binding to the D1 protein in PS II, which is encoded by the psbA gene found in genomes of chloroplasts, cyanobacteria and cyanophages. psbA mutations that alter the target protein can confer tolerance to PS II inhibitors. We have previously shown that irgarol induces community tolerance in natural marine periphyton communities and suggested a novel tolerance mechanism, involving the amino acid sequence of a turnover-regulating domain of D1, as contributive to this tolerance. Here we use a large number of psbA sequences of known identity to assess the taxonomic affinities of psbA sequences from these differentially tolerant communities, by performing phylogenetic analysis. We show that periphyton communities have high psbA diversity and that this diversity is adversely affected by irgarol. Moreover, we suggest that within tolerant periphyton the novel tolerance mechanism is present among diatoms only, whereas some groups of irgarol-tolerant cyanobacteria seem to have other tolerance mechanisms. However, it proved difficult to identify periphyton psbA haplotypes to the species or genus level, which indicates that the genomic pool of the attached, periphytic life forms is poorly studied and inadequately represented in international sequence databases. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.
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| 2. |
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| 3. |
- Hassellöv, Martin, 1970, et al.
(författare)
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REACH missar nano!
- 2009
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Ingår i: Miljöforskning. ; 2009:3-4
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 4. |
- Callaghan, Terry, et al.
(författare)
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Multi-Decadal Changes in Tundra Environments and Ecosystems : Synthesis of the International Polar Year-Back to the Future Project (IPY-BTF)
- 2011
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Ingår i: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 40:6, s. 705-716
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the responses of tundra systemsto global change has global implications. Most tundraregions lack sustained environmental monitoring and oneof the only ways to document multi-decadal change is toresample historic research sites. The International PolarYear (IPY) provided a unique opportunity for such researchthrough the Back to the Future (BTF) project (IPY project#512). This article synthesizes the results from 13 paperswithin this Ambio Special Issue. Abiotic changes includeglacial recession in the Altai Mountains, Russia; increasedsnow depth and hardness, permafrost warming, andincreased growing season length in sub-arctic Sweden;drying of ponds in Greenland; increased nutrient availabilityin Alaskan tundra ponds, and warming at mostlocations studied. Biotic changes ranged from relativelyminor plant community change at two sites in Greenland tomoderate change in the Yukon, and to dramatic increasesin shrub and tree density on Herschel Island, and in subarcticSweden. The population of geese tripled at one sitein northeast Greenland where biomass in non-grazed plotsdoubled. A model parameterized using results from a BTFstudy forecasts substantial declines in all snowbeds andincreases in shrub tundra on Niwot Ridge, Colorado overthe next century. In general, results support and provideimproved capacities for validating experimental manipulation,remote sensing, and modeling studies.
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| 5. |
- Eriksson, Martin, 1970, et al.
(författare)
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Community-Level Analysis of psbA Gene Sequences and Irgarol Tolerance in Marine Periphyton
- 2009
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Ingår i: Applied and Environmental Microbiology. - Washington, D.C. : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 75:4, s. 897-906
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Tidskriftsartikel (refereegranskat)abstract
- This study analyzes psbA gene sequences, predicted D1 protein sequences, species relative abundance, and pollution-induced community tolerance in marine periphyton communities exposed to the antifouling compound Irgarol 1051. The mechanism of action of Irgarol is the inhibition of photosynthetic electron transport at photosystem II by binding to the D1 protein. The metagenome of the communities was used to produce clone libraries containing fragments of the psbA gene encoding the D1 protein. Community tolerance was quantified with a short-term test for the inhibition of photosynthesis. The communities were established in a continuous flow of natural seawater through microcosms with or without added Irgarol. The selection pressure from Irgarol resulted in an altered species composition and an inducted community tolerance to Irgarol. Moreover, there was a very high diversity in the psbA gene sequences in the periphyton, and the composition of psbA and D1 fragments within the communities was dramatically altered by increased Irgarol exposure. Even though tolerance to this type of compound in land plants often depends on a single amino acid substitution (Ser(264)-> Gly) in the D1 protein, this was not the case for marine periphyton species. Instead, the tolerance mechanism likely involves increased degradation of D1. When we compared sequences from low and high Irgarol exposure, differences in nonconserved amino acids were found only in the so-called PEST region of D1, which is involved in regulating its degradation. Our results suggest that environmental contamination with Irgarol has led to selection for high-turnover D1 proteins in marine periphyton communities at the west coast of Sweden.
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| 6. |
- Mamontov, Eugen, 1955, et al.
(författare)
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What stochastic mechanics are relevant to the study of living systems?
- 2005
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Ingår i: Proceedings of the Latvian Academy of Sciences. Section B: Natural, Exact and Applied Sciences. - Riga, Latvia : Latvian Academy of Sciences. - 1407-009X. ; 59:6, s. 255-262
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Tidskriftsartikel (refereegranskat)abstract
- Biologists have identified many features of living systems which cannot be studied by application of fundamental statistical mechanics (FSM). The present work focuses on some of these features. By discussing all the basic approaches of FSM, the work formulates the extension of the kinetic-theory paradigm (based on the reduced one-particle distribution function) that possesses all the considered properties of the living systems. This extension appears to be a model within the generalized-kinetic theory developed by N. Bellomo and his co-authors. In connection with this model, the work also stresses some other features necessary for making the model relevant to living systems. An example is discussed, which is a generalized kinetic equation coupled with the probability-density equation which represents the varying component content of a living system. The work also suggests directions for future research.
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| 7. |
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| 8. |
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| 9. |
- Andersson, Magnus, et al.
(författare)
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A proposed time-resolved X-ray scattering approach to track local and global conformational changes in membrane transport proteins
- 2008
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 16:1, s. 21-28
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Tidskriftsartikel (refereegranskat)abstract
- Time-resolved X-ray scattering has emerged as a powerful technique for studying the rapid structural dynamics of small molecules in solution. Membrane-protein-catalyzed transport processes frequently couple large-scale conformational changes of the transporter with local structural changes perturbing the uptake and release of the transported substrate. Using light-driven halide ion transport catalyzed by halorhodopsin as a model system, we combine molecular dynamics simulations with X-ray scattering calculations to demonstrate how small-molecule time-resolved X-ray scattering can be extended to the study of membrane transport processes. In particular, by introducing strongly scattering atoms to label specific positions within the protein and substrate, the technique of time-resolved wide-angle X-ray scattering can reveal both local and global conformational changes. This approach simultaneously enables the direct visualization of global rearrangements and substrate movement, crucial concepts that underpin the alternating access paradigm for membrane transport proteins.
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| 10. |
- Mamontov, Eugen, 1955
(författare)
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Ordinary differential equation system for population of individuals and the corresponding probabilistic model
- 2008
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Ingår i: Mathl. Computer Modelling. - : Elsevier BV. - 0895-7177.
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Tidskriftsartikel (refereegranskat)abstract
- The key model for particle populations in statistical mechanics is the Bogolyubov–Born– Green–Kirkwood–Yvon (BBGKY) equation chain. It is derived mainly from the Hamilton ordinary differential equation (ODE) system for the vectors of the particle states in the particle position-momentum phase space. Many problems beyond physics or chemistry, for instance, in the living-matter sciences (biology, medicine, ecology, and scoiology) make it necessary to extend the notion of a particle to an individual, or active particle. This challenge is met by the generalized kinetic theory. It implements the extension by extending the phase space from the space of the position-momentum vectors to more rich spaces formed by the state vectors with the entries which need not be limited to the entries of the position and momentum: they include other scalar variables (e.g., those associated with modelling homeorhesis or other features inherent to the individuals). One can assume that the dynamics of the state vector in the extended space, i.e. the states of the individuals (rather than common particles) is also described by an ODE system. The latter, however, need not be the Hamilton one. The question is how one can derive the analogue of the BBGKY paradigm for the new settings. The present work proposes an answer to this question. It applies a very limited number of carefully selected tools of probability theory and common statistical mechanics. It in particular uses the well-known feature that the maximum number of the individuals which can mutually interact simultaneously is bounded by a fixed value of a few units. The present approach results in the finite system of equations for the reduced many-individual distribution functions thereby eliminating the so-called closure problem inevitable in the BBGKY theory. The thermodynamic-limit assumption is not needed either. The system includes consistently derived terms of all of the basic types known in kinetic theory, in particular, both the “mean-field” and scattering-integral terms, and admits the kinetic equation of the form allowing a direct chemical-reaction reading. The present approach can deal with Hamilton’s equation systems which are nonmonogenic and not treated in statistical mechanics. The proposed modelling suggests the basis of the generalized kinetic theory and may serve as the stochastic mechanics of population of individuals.
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