| 1. |
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| 2. |
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| 3. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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A software pipeline for processing and identification of fungal ITS sequences
- 2009
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Ingår i: Source Code for Biology and Medicine. - 1751-0473. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region for use in BLAST-based similarity searches in the International Nucleotide Sequence Databases. These searches are time-consuming and regularly require a significant amount of manual intervention and complementary analyses. We here present software - in the form of an identification pipeline for large sets of fungal ITS sequences - developed to automate the BLAST process and several additional analysis steps. The performance of the pipeline was evaluated on a dataset of 350 ITS sequences from fungi growing as epiphytes on building material. Results The pipeline was written in Perl and uses a local installation of NCBI-BLAST for the similarity searches of the query sequences. The variable subregion ITS2 of the ITS region is extracted from the sequences and used for additional searches of higher sensitivity. Multiple alignments of each query sequence and its closest matches are computed, and query sequences sharing at least 50 % of their best matches are clustered to facilitate the evaluation of hypothetically conspecific groups. The pipeline proved to speed up the processing, as well as enhance the resolution, of the evaluation dataset considerably, and the fungi were found to belong chiefly to the Ascomycota, with Penicillium and Aspergillus as the two most common genera. The ITS2 was found to indicate a different taxonomic affiliation than did the complete ITS region for 10 % of the query sequences, though this figure is likely to vary with the taxonomic scope of the query sequences. Conclusions The present software readily assigns large sets of fungal query sequences to their respective best matches in the international sequence databases and places them in a larger biological context. The output is highly structured to be easy to process, although it still needs to be inspected and possibly corrected for the impact of the incomplete and sometimes erroneously annotated fungal entries in these databases. The open source pipeline is available for UNIX-type platforms, and updated releases of the target database are made available biweekly. The pipeline is easily modified to operate on other molecular regions and organism groups.
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| 4. |
- Hallenberg, Nils, 1947, et al.
(författare)
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Pseudolagarobasidium (Basidiomycota): on the reinstatement of a genus of parasitic, saprophytic, and endophytic resupinate fungi
- 2008
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Ingår i: Botany. - 1916-2804. ; 86:11, s. 1319-1325
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Tidskriftsartikel (refereegranskat)abstract
- The small resupinate genus Pseudolagarobasidium (Polyporales, Basidiomycota) presently comprises less than five species, all of which were described from tropical to subtropical regions, and two of which are root parasites on leguminous trees. The genus has recently been synonymized with Radulodon on morphological grounds, and the present study evaluates this proposal in a molecular context. Pseudolagarobasidium was found to constitute a well supported, monophyletic group excluding Radulodon and this synonymy is rejected. The ecological range of the genus spans saprotrophy to parasitism, and this study presents evidence that at least one lineage in Pseudolagarobasidium is endophytic in the cacao tree (Theobroma cacao L.). Key words: Polyporales, Radulodon, phylogeny, plant interactions. Résumé: Le Pseudolagarobasidium (Polyporales, Basidiomycota) constitue un genre de petits champignons résupinés qui comporte actuellement cinq espèces, toutes décrites à partir de régions tropicales ou subtropicales, incluant deux espèces parasites des racines d'arbres de la famille des légumineuses. On en a récemment établi la synonymie avec le genre Radulodon sur la base morphologique, mais les auteurs utilisent ici l'approche moléculaire. On constate que le genre Pseudolagarobasidium constitue un groupe monophylétique robuste excluant les Radulodon ce qui conduit au rejet de cette synonymie. L'amplitude écologique du genre va du saprophytisme au parasitisme, et on présente des preuves qu'au moins une lignée est un endophyte du cacaoyer (Theobroma cacao L.). Mots-clés : Polyporales, Radulon, phylogénie, interactions végétales.
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| 8. |
- Mamontov, Eugen, 1955
(författare)
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Homeorhesis and evolutionary properties of living systems: From ordinary differential equations to the active-particle generalized kinetics theory
- 2006
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Ingår i: 10th Evolutionary Biology Meeting at Marseilles, 20-22 September 2006, Marseilles, France.
-
Konferensbidrag (refereegranskat)abstract
- Advanced generalized-kinetic-theory (GKT) models for biological systems are developed for populations of active (or living) particles [1]-[5]. These particles are described with both the stochastic variables common in kinetic theory (such as time, the particle random location and velocity) and the stochastic variables related to the internal states of an active particle. Evolution of these states represents biological, ecological, or social properties of the particle behavior. Paper [6] analyzes a number of the well-known statistical-mechanics approaches and shows that the active-particle GKT (APGKT) is the only treatment capable of modelling living systems. Work [2] summarizes the significance of the notion of an active particle in kinetic models. This notion draws attention to the features distinguishing living matter from nonliving matter. They are discussed by many authors (e.g., [7]-[15], [1]-[3], [6], [16]-[18]). Work [11] considers a lot of differences between living and nonliving matters, and the limitations of the modelling approaches developed for nonliving matter. Work [6] mainly focuses on the comparison of a few theoretical mechanics treatments in terms of the key living-matter properties formulated in [15]. One of the necessary properties of the evolution of living systems is homeorhesis. It is, loosely speaking, a peculiar qualitative and quantitative insensitivity of a living system to the exogenous signals acting on it. The earlier notion, homeostasis, was introduced by W. B. Cannon in 1926 who discussed the phenomenon in detail later [7]. Homeorhesis introduced by C. H. Waddington [8, p. 32] generalizes homeostasis and is well known in biology [8], [9], [12]. It is an inherent part of mathematical models for oncogeny (e.g., [16]-[18], [6, Appendix]). Homeorhesis is also discussed in [3, Section 4] in connection with APGKT. Homeorhesis is documented in ecology (e.g., [11], [13, the left column on p. 675]) where it is one of the key notions of the strong Gaia theory, a version of the Gaia theory (e.g., [14, Chapter 8]). The strong Gaia theory “states that the planet with its life, a single living system, is regulated in certain aspects by that life” [14, p. 124]. The very origin of the name “Gaia” is related to homeorhesis or homeostasis [14, p. 118]. These notions are also used in psychology and sociology. If evolution of a system is not homeorhetic, the system can not be living. Work [6, Appendix] derives a preliminary mathematical formulation of homeorhesis in terms of the simplest dynamical systems, i.e. ordinary differential equations (ODEs). The present work complements, extended, and further specify the approach of [6, Appendix]. The work comprises the two main parts. The first part develops the sufficient conditions for ODE systems to describe homeorhesis, and suggests a fairly general structure of the ODE model. It regards homeorhesis as piecewise homeostasis. The model can be specified in different ways depending on specific systems and specific purposes of the analysis. An example of the specification is also noted (the PhasTraM nonlinear reaction-diffusion model for hyperplastic oncogeny [16]-[18]). The second part of the work discusses implementation of the above homeorhesis ODE model in terms of a special version [3] of APGKT (see above). The key feature of this version is that the components of a living population need not be discrete: the subdivision into the components is described with a general, continuous-discrete probability distribution (see also [6]). This enables certain properties of living matter noted in [15]. Moreover, the corresponding APGKT model presents a system of, firstly, a generalized kinetic equation for the conditional distribution function conditioned by the internal states of the population and, secondly, Ito's stochastic differential equations for these states. This treatement employs the results on nonstationary invariant diffusion stochastic processes [19]. The second part of the work also stresses that APGKT is substantially more important for the living-matter analysis than in the case of nonliving matter. One of the reasons is certain limitations in experimental sampling of the living-system modes presented with stochastic processes. A few directions for future research are suggested as well. REFERENCES: [1] Bellomo, N., Bellouquid, A. and Delitala, M., 2004, Mathematical topics on the modelling complex multicellular systems and tumor immune cells competition, Math. Models Methods Appl. Sci., 14, 1683-1733. [2] Bellomo, N., 2006, New hot Paper Comments, Essential Science Indicators, http://www.esi-topics.com/nhp/2006 /may- 06-NicolaBellomo.html. [3] Willander, M., Mamontov, E. and Chiragwandi, Z., 2004, Modelling living fluids with the subdivision into the components in terms of probability distributions, Math. Models Methods Appl. Sci. 14, 1495-1520. [4] Bellomo, N. and Maini, P.K., 2005, Preface and the Special Issue “Multiscale Cancer Modelling-A New Frontier in Applied Mathematics”, Math. Models Methods Appl. Sci., 15, iii-viii. [5] De Angelis, E. and Delitala, M., 2006, Modelling complex systems in applied sciences: Methods and tools of the mathematical kinetic theory for active particles. Mathl Comput. Modelling, 43, 1310-1328. [6] Mamontov, E., Psiuk-Maksymowicz, K. and Koptioug, A., 2006, Stochastic mechanics in the context of the properties of living systems, Mathl Comput. Modelling, Article in Press, 13 pp. [7] Cannon, W.B., 1932, The Wisdom of the Body (New York: Norton). [8] Waddington, C.H., 1957, The Strategy of the Genes. A Discussion of Some Aspects of Theoretical Biology (London, George Allen and Unwin). [9] Waddington, C.H., 1968, Towards a theoretical biology, Nature, 218, 525-527. [10] Cotnoir, P.-A., 1981, La compétence environnementale: Une affaire d’adaptation. Séminaire en écologie behaviorale, Univeristé du Québec, Montralé. Available online at: http://pac.cam.org/culture.doc . [11] O’Neill, R.V., DeAngelis, D.L., Waide, J.B. and Allen, T.F.H., 1986, A Hierarchical Concept of Ecosystems, Princeton: Princeton Univ. Press). [12] Sauvant, D., 1992, La modélisation systémique en nutrition, Reprod. Nutr. Dev., 32, 217-230. [13] Christensen, N.L., Bartuska, A.M., Brown, J.H., Carpenter, S., D'Antonio, C., Francis, R., Franklin, J.F., MacMahon, J.A., Noss, R.F., Parsons, D.J., Peterson, C.H., Turner, M.G. and Woodmansee, R.G., 1996, The Report of the Ecological Society of America Committee on the Scientific Basis for Ecosystem Management, Ecological Applications, 6, 665-691. Available online at: http://www.esa.org/pao/esaPositions/Papers/ReportOfSBEM.php. [14] Margulis, L., 1998, Symbiotic Planet. A New Look at Evolution (Amherst: Sciencewriters). [15] Hartwell, L.H., Hopfield, J.J., Leibler, S. and Murray, A.W., 1999, From molecular to modular cell biology, Nature, 402, C47-C52. [16] Mamontov, E., Koptioug, A.V. and Psiuk-Maksymowicz, K., 2006, The minimal, phase-transition model for the cell- number maintenance by the hyperplasia-extended homeorhesis, Acta Biotheoretica, 54, 44 pp., (no. 2, May-June, accepted). [17] Psiuk-Maksymowicz, K. and Mamontov, E., 2005, The time-slices method for rapid solving the Cauchy problem for nonlinear reaction-diffusion equations in the competition of homeorhesis with genotoxically activated hyperplasia, In: European Conference on Mathematical and Theoretical Biology - ECMTB05 (July 18-22, 2005) Book of Abstracts, Vol.1 (Dresden: Center for Information Services and High Performance Computing, Dresden Univ. Technol.), p. 429 (http://www.ecmtb05.org/). [18] Psiuk-Maksymowicz, K. and Mamontov, E., 2006, The homeorhesis-based modelling and fast numerical analysis for oncogenic hyperplasia under radiation therapy, submitted. [19] Mamontov, E., 2005, Nonstationary invariant distributions and the hydrodynamic-style generalization of the Kolmogorov-forward/Fokker-Planck equation, Appl. Math. Lett. 18 (9) 976-982.
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| 9. |
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| 10. |
- 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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| 11. |
- Bienert, Gern, 2008, et al.
(författare)
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A subgroup of plant aquaporins facilitate the bi-directional diffusion of As(OH)3 and Sb(OH)3 across membranes
- 2008
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 6:26
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Tidskriftsartikel (refereegranskat)abstract
- Background Arsenic is a toxic and highly abundant metalloid that endangers human health through drinking water and the food chain. The most common forms of arsenic in the environment are arsenate (As(V)) and arsenite (As(III)). As(V) is a non-functional phosphate analog that enters the food chain via plant phosphate transporters. Inside cells, As(V) becomes reduced to As(III) for subsequent extrusion or compartmentation. Although much is known about As(III) transport and handling in microbes and mammals, the transport systems for As(III) have not yet been characterized in plants. Results Here we show that the Nodulin26-like Intrinsic Proteins (NIPs) AtNIP5;1 and AtNIP6;1 from Arabidopsis thaliana, OsNIP2;1 and OsNIP3;2 from Oryza sativa, and LjNIP5;1 and LjNIP6;1 from Lotus japonicus are bi-directional As(III) channels. Expression of these NIPs sensitized yeast cells to As(III) and antimonite (Sb(III)), and direct transport assays confirmed their ability to facilitate As(III) transport across cell membranes. On medium containing As(V), expression of the same NIPs improved yeast growth, probably due to increased As(III) efflux. Our data furthermore provide evidence that NIPs can discriminate between highly similar substrates and that they may have differential preferences in the direction of transport. A subgroup of As(III) permeable channels that group together in a phylogenetic tree required N-terminal truncation for functional expression in yeast. Conclusion This is the first molecular identification of plant As(III) transport systems and we propose that metalloid transport through NIPs is a conserved and ancient feature. Our observations are potentially of great importance for improved remediation and tolerance of plants, and may provide a key to the development of low arsenic crops for food production.
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| 12. |
- Sandström, Olof, et al.
(författare)
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Integrated fish monitoring in Sweden
- 2003
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Ingår i: Utredningsrapport till Naturvårdsverket. ; , s. 1-32
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Rapport (övrigt vetenskapligt/konstnärligt)
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| 13. |
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| 14. |
- Nilsson, R. Henrik, 1976
(författare)
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Fungal taxonomy and systematics in the digital era, with an outlook on the cantharelloid clade (Basidiomycota)
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Fungi form a large and ubiquitous group of organisms where species identification and delimitation on morphological grounds often fall short. DNA sequences have proved an invaluable information source for these pursuits and are now routinely used in most mycological laboratories. Newl generated DNA sequences are typically compared with the entries of the large INSD sequence database for inference of taxonomic affiliations and other properties using the sequence similarity search tool BLAST. This thesis highlights some practical difficulties in using BLAST for these purposes it is for example very sensitive to the length of the sequences - and shows that improper use of BLAST appears to have had considerable repercussion on the general level of taxonomic reliability of the fungal sequences in INSD, more than 10% of which may be incorrectly identified to species level. An initiative to build a new DNA sequence database for taxonomically reliable DNA-based identification of mycorrhizal (plant-mutualistic) fungi is described. The database differs from similar initiatives in that its entries are determined to species level by pertinent experts; it allows for integrative sequence annotations, including photos and morphological descriptions; and it employs new, phylogeny-based tools for sequence identification to alleviate the concerns with simplistic, similarity-based tools as arbiters of taxonomic affiliation. That phylogenetic analyses can be beneficial also to classification and nomenclatural projects is shown in the mor enterprise, which is a weekly automaton of Agaricomycetes (mushroom-forming fungi) phylogeny. All fungal sequences from the nuclear ribosomal large subunit gene are assembled on a weekly basis; automated phylogenetic analyses are undertaken; and the resulting phylogenetic trees are displayed and analyzed for changes in clade topology and inclusiveness. The enigmatic cantharelloid clade of the Agaricomycetes is studied using a four-gene phylogenetic approach. While this heterogeneous assembly of mushroom-like, resupinate, clavarioid, and lichen-forming fungi defies any morphological attempt at indicating a close relatedness for its species, the results from the molecular analyses show that there is indeed strong evidence to support that these fungi form a monophyletic group; a restrictive circumscription of the clade to include the genera Botryobasidium, Sistotrema, Multiclavula, Membranomyces, Hydnum, Clavulina, Cantharellus, and Craterellus is advocated. Stichic basidia, and to a lesser extent parenthesome ultrastructure, are found to be characteristic of the clade, and the previously reported divergent rates of evolution for the genera Cantharellus and Craterellus are shown to be limited to the nuclear ribosomal genes. The largely resupinate, and purportedly wood-decaying, genus Sistotrema is demonstrated to hold mycorrhizal lineages, and the molecular evidence to consider the genus polyphyletic is found to be very convincing.
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| 15. |
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| 16. |
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| 17. |
- 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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| 19. |
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| 20. |
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| 21. |
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| 22. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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The ITS region as a target for characterization of fungal communities using emerging sequencing technologies
- 2009
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Ingår i: FEMS Microbiology Letters. - 0378-1097 .- 1574-6968. ; 296:1, s. 97-101
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Tidskriftsartikel (refereegranskat)abstract
- The advent of new high-throughput DNA-sequencing technologies promises to redefine the way in which fungi and fungal communities – as well as other groups of organisms – are studied in their natural environment. With read lengths of some few hundred base pairs, massively parallel sequencing (pyrosequencing) stands out among the new technologies as the most apt for large-scale species identification in environmental samples. Although parallel pyrosequencing can generate hundreds of thousands of sequences at an exceptional speed, the limited length of the reads may pose a problem to the species identification process. This study explores whether the discrepancy in read length between parallel pyrosequencing and traditional (Sanger) sequencing will have an impact on the perceived taxonomic affiliation of the underlying species. Based on all 39 200 publicly available fungal environmental DNA sequences representing the nuclear ribosomal internal transcribed spacer (ITS) region, the results show that the two approaches give rise to quite different views of the diversity of the underlying samples. Standardization of which subregion from the ITS region should be sequenced, as well as a recognition that the composition of fungal communities as depicted through different sequencing methods need not be directly comparable, appear crucial to the integration of the new sequencing technologies with current mycological praxis.
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| 23. |
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| 24. |
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| 25. |
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| 26. |
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| 27. |
- Wallensten, Anders, 1974-, et al.
(författare)
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Mounting evidence for the presence of influenza A virus in the avifauna of the Antarctic region
- 2006
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Ingår i: Antarctic Science. - New York : Cambridge University Press. - 0954-1020 .- 1365-2079. ; 18:3, s. 353-356
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Tidskriftsartikel (refereegranskat)abstract
- Penguin blood samples collected at Bird Island, sub-Antarctic South Georgia, and faecal samples taken from penguins at several localities along the Antarctic Peninsula were analysed in order to investigate if influenza A virus is present in penguin populations in the South Atlantic Antarctic region. Serology was performed on the blood samples while the faecal samples were screened by a RT-PCR method directed at the matrix protein gene for determining the presence of influenza A virus. All faecal samples were negative by PCR, but the blood samples gave serologic indications that influenza A virus is present amongst these penguin species, confirming previous studies, although the virus has still not been isolated from any bird in the Antarctic region.
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| 28. |
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| 29. |
- 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. ; 11:8, 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.
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| 30. |
- Jarvis, Åsa, et al.
(författare)
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Activity and composition of ammonia oxidizing bacterial communities and emission dynamics of NH3 and N2O in a compost reactor treating organic household waste
- 2009
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Ingår i: JOURNAL OF APPLIED MICROBIOLOGY. - : Oxford University Press (OUP). - 1364-5072 .- 1365-2672. ; 106:5, s. 1502-1511
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Tidskriftsartikel (refereegranskat)abstract
- To monitor emissions of NH3 and N2O during composting and link these to ammonia oxidation rates and the community structure of ammonia oxidizing bacteria (AOB). A laboratory-scale compost reactor treating organic household waste was run for 2 months. NH3 emissions peaked when pH started to increase. Small amounts of N2O and CH4 were also produced. In total, 16% and less than 1% of the initial N was lost as NH3-N and N2O-N respectively. The potential ammonia oxidation rate, determined by a chlorate inhibition assay, increased fourfold during the first 9 days and then remained high. Initially, both Nitrosospira and Nitrosomonas populations were detected using DGGE analysis of AOB specific 16S rRNA fragments. Only Nitrosomonas europaea was detected under thermophilic conditions, but Nitrosospira populations re-established during the cooling phase. Thermophilic conditions favoured high potential ammonia oxidation rates, suggesting that ammonia oxidation contributed to reduced NH3 emissions. Small but significant amounts of N2O were emitted during the thermophilic phase. The significance of different AOBs detected in the compost for ammonia oxidation is not clear. This study shows that ammonia oxidation occurs at high temperature composting and therefore most likely reduces NH3 emissions.
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| 31. |
- Larsson, Åke, 1944, et al.
(författare)
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Kustfisk hälsa
- 2005
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Ingår i: Bottniska viken - årsrapport från den marina miljöövervakningen 2004. - 1400-2760. ; :2004, s. 24-26
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 32. |
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| 33. |
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| 34. |
- Andersson, A. F., et al.
(författare)
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Comparative analysis of human gut microbiota by barcoded pyrosequencing
- 2008
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 3:7
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Tidskriftsartikel (refereegranskat)abstract
- Humans host complex microbial communities believed to contribute to health maintenance and, when in imbalance, to the development of diseases. Determining the microbial composition in patients and healthy controls may thus provide novel therapeutic targets. For this purpose, high-throughput, cost-effective methods for microbiota characterization are needed. We have employed 454-pyrosequencing of a hyper-variable region of the 16S rRNA gene in combination with sample-specific barcode sequences which enables parallel in-depth analysis of hundreds of samples with limited sample processing. In silico modeling demonstrated that the method correctly describes microbial communities down to phylotypes below the genus level. Here we applied the technique to analyze microbial communities in throat, stomach and fecal samples. Our results demonstrate the applicability of barcoded pyrosequencing as a high-throughput method for comparative microbial ecology.
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| 35. |
- Collins, Matthew D., et al.
(författare)
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Arsenicicoccus bolidensis gen. nov., sp nov., a novel actinomycete isolated from contaminated lake sediment
- 2004
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Ingår i: INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 54, s. 605-608
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Tidskriftsartikel (refereegranskat)abstract
- An unknown Gram-positive, catalase-positive, facultatively anaerobic, non-spore-forming, coccus-shaped bacterium originating from sediment was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on ll-diaminopimelic acid (type ll-Dpm-glycine1), a complex mixture of saturated, monounsaturated and iso- and anteiso-methyl-branched, non-hydroxylated, long-chain cellular fatty acids and tetrahydrogenated menaquinones with eight isoprene units [MK-8(H4)] as the major respiratory lipoquinone. This combination of characteristics somewhat resembled members of the suborder Micrococcineae, but did not correspond to any currently described species. Comparative 16S rRNA gene sequencing confirmed that the unidentified coccus-shaped organism is a member of the Actinobacteria and represents a hitherto-unknown subline related to, albeit different from, a number of taxa including Intrasporangium, Janibacter, Terrabacter, Terracoccus and Ornithinicoccus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium originating from lake sediment be classified as a new genus and species, Arsenicicoccus bolidensis gen. nov., sp. nov. (type strain CCUG 47306T=DSM 15745T).
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| 36. |
- Mamontov, Eugen, 1955, et al.
(författare)
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Managing panic-stricken crowds: The need in quantitative models for social dynamics
- 2007
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Ingår i: Abstract Booklet, The 8th Annual Conference of the European Sociological Association.
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Konferensbidrag (refereegranskat)abstract
- Panics typically occur during disaster or social crisis. Panics in crowds in public sites (airports, hospitals, supermarkets, office buildings, air- or sea-liners, trains, stadiums, downtown areas, etc.) often cause stampedes leading to injuries or deaths. How can we best organize public events at existing sites in order to prevent the tragic outcomes? How can one design new public sites to avoid the consequences of panic? What methods and tools can be applied? These questions determine the focus of the present work. Obviously, experimental approaches are inapplicable. Intuitive problem solving does not assure specific and consistent solutions. Therefore, the work concentrates on the non-intuitive, model-based approaches. Evaluation of the model-based solutions involves quantitative characteristics, e.g., the time of the evacuation, the probability for individuals to get injured, the concentration of oxygen, etc. Subsequently, any suitable model must be quantitative. Moreover, the behaviour of crowds develops continuously in both space and time. Thus, the models must also be space-time continuous. The work analyzes these and other features of the models for social dynamics and emphasizes the key differences from the dynamical models in the natural sciences studying nonliving matter. The related application aspects and directions for future research are also discussed.
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| 37. |
- Nachin, Laurence, 1971, et al.
(författare)
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Heterodimer formation within universal stress protein classes revealed by an in silico and experimental approach.
- 2008
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Ingår i: Journal of molecular biology. - : Elsevier BV. - 1089-8638 .- 0022-2836. ; 380:2, s. 340-50
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Tidskriftsartikel (refereegranskat)abstract
- Universal stress proteins (Usps) are found in all kingdoms of life and can be divided into four classes by phylogenic analysis. According to available structures, Usps exist as homodimers, and genetic studies show that their cellular assignments are extensive, including functions relating to stress resistance, carbon metabolism, cellular adhesion, motility, and bacterial virulence. We approached the question of how Usps can achieve such a variety of functions in a cell by using a new procedure for statistical analysis of multiple sequence alignments, based on physicochemically related values for each amino acid residue of Usp dimer interfaces. The results predicted that Usp proteins within a class may, in addition to forming homodimers, be able to form heterodimers. Using Escherichia coli Usps as model proteins, we confirmed the existence of such interactions. We especially focused on class I UspA and UspC and demonstrated that they are able to form homo- and heterodimers in vitro and in vivo. We suggest that this ability to form both homo- and heterodimers may allow for an expansion of the functional repertoire of Usps and explains why organisms usually contain multiple usp paralogues.
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| 38. |
- Carlsbecker, Annelie, et al.
(författare)
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The MADS-box gene DAL1 is a potential mediator of the juvenile-to-adult transition in Norway spruce (Picea abies)
- 2004
-
Ingår i: The Plant Journal. ; 40:4, s. 546-557
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Tidskriftsartikel (refereegranskat)abstract
- Progression through the plant life cycle involves changes in many essential features, most notably in the capacity to reproduce. The transition from juvenile vegetative and non-reproductive to an adult reproductive phase is gradual and can take many years; in the conifer Norway spruce, Picea abiea, typically 20-25 years. We present a detailed analysis of the activities of three regulatory genes with potential roles in the transition in Norway spruce: DAL1, a MADS-box gene related to the AGL6 group of genes from angiosperms, and the two LEAFY-related genes PaLFY and PaNLY. DAL1 activity is initiated in the shoots of juvenile trees at an age of 3-5 years, and then increases with age, whereas both LFY genes are active throughout the juvenile phase. The activity of DAL1 further shows a spatial pattern along the stem of the tree that parallels a similar gradient in physiolpoical and morphological features associated with maturation to the adult phase. Constitutive expression of DAL1 in transgenic Arabidopsis plants caused a dramatic attenuation of both juvenile and adult growth phases;flowers forming immediately after the embryogenic phase of development in severely affected plants. Taken together, our resulsts support the notion that DAL1 may have a regulatory role in the juvenile-to-adult transition in Norway spruce.
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| 39. |
- Knudsen, Jette, et al.
(författare)
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Diversity and distribution of floral scent
- 2006
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Ingår i: The Botanical review. - New York : The New York Botanical Garden Press. - 0006-8101 .- 1874-9372. ; 72:1, s. 1-120
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Tidskriftsartikel (refereegranskat)abstract
- A list of 1719 chemical compounds identified from headspace samples of floral scent is presented. The list has been compiled from some 270 published papers, including analyses of 991 species of flowering plants and a few gymnosperms, a sample including seed plants from 90 families and 38 orders. The compounds belong to seven major compound classes, of which the aliphatics, the benzenoids and phenylpropanoids, and, among the terpenes, the mono- and sesquiterpenes, occur in most orders of seeds plants. C5-branched compounds, irregular terpenes, nitrogen-containing compounds, and a class of miscellaneous cyclic compounds have been recorded in about two-thirds of the orders. Sulfur-containing compounds occur in a third of the orders, whereas diterpenes have been reported from three orders only. The most common single compounds in floral scent are the monoterpenes limonene, (E)-β-ocimene, myrcene, linalool, α- and β-pinene, and the benzenoids benzaldehyde, methyl 2-hydroxybenzoate (methyl salicylate), benzyl alcohol, and 2-phenyl ethanol, which occur in 54–71% of the families investigated so far. The sesquiterpene caryophyllene and the irregular terpene 6-methyl-5-hepten-2-one are also common and occur in more than 50% of the families. Orchidaceae are by far the best investigated family, followed by several families known to have many species with strongly scented flowers, such as Araceae, Arecaceae, Magnoliaceae, and Rosaceae. However, the majority of angiosperm families are still poorly investigated. Relationships between floral scent and pollination, chemistry, evolution, and phylogeny are briefly discussed. It is concluded that floral scent chemistry is of little use for phylogenetic estimates above the genus level, whereas the distribution and combinations of floral scent compounds at species and subspecific levels is a promising field of investigation for the understanding of adaptations and evolutionary processes in angiosperms.
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| 40. |
- Nilsson, R. Henrik, 1976
(författare)
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Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi.
- 2006
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Ingår i: 8th International Mycological Congress, Cairns, Australia.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The ever-increasing use of DNA sequences for identification purposes largely falls back on the assumption that public sequence databases contain a thorough sampling of taxonomically well-annotated sequences. Taxonomy, held by some to be an old-fashioned trade, has accordingly never been more important. emerencia does not automate the taxonomic process, but it does allow researchers to focus their efforts elsewhere than countless manual BLAST runs and arduous sieving of BLAST hit lists. The emerencia system is available on an open source basis for local installation with any organism and gene group as targets.
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| 41. |
- Nilsson, R. Henrik, 1976
(författare)
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Fungal phyloinformatics and ITS-based data mining in mycology
- 2008
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Ingår i: International Tagung der Deutschen Gesellschaft fur Mykologie 2008.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Molecular identification of fungi is discussed in the context of environmental sampling and data mining in the public sequence databases.
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| 42. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Towards an automated phylogenetic classification of homobasidiomycetes
- 2004
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Ingår i: Mycological Society of America (MSA) Meeting 2004.
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The prospects of a phylogeny-driven classification of the higher fungi are discussed, and a new software package - mor - that seeks to facilitate such classifications is presented.
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| 43. |
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| 44. |
- Riemann, Lasse, et al.
(författare)
-
Importance of Viral Lysis and Dissolved DNA for Bacterioplankton Activity in a P-Limited Estuary, Northern Baltic Sea
- 2009
-
Ingår i: MICROBIAL ECOLOGY. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 57:2, s. 286-294
-
Tidskriftsartikel (refereegranskat)abstract
- Abstract Through lysis of bacterioplankton cells, viruses mediate an important, but poorly understood, pathway of carbon and nutrients from the particulate to the dissolved form. Via this activity, nutrient-rich cell lysates may become available to noninfected cells and support significant growth. However, the nutritional value of lysates for noninfected bacteria presumably depends on the prevailing nutrient limitation. In the present study, we examined dynamics of dissolved DNA (D-DNA) and viruses along a transect in the phosphorus (P)-limited Öre Estuary, northern Baltic Sea. We found that viruses were an important mortality factor for bacterioplankton and that their activity mediated a significant recycling of carbon and especially of P. Uptake of dissolved DNA accounted for up to 70% of the bacterioplankton P demand, and about a quarter of the D-DNA pool was supplied through viral lysis of bacterial cells. Generally, the importance of viral lysates and uptake of D-DNA was highest at the estuarine and offshore stations and was positively correlated with P limitation measured as alkaline phosphatase activity. Our results highlight the importance of viral activity for the internal recycling of principal nutrients and pinpoints D-DNA as a particularly relevant compound in microbial P dynamics.
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| 45. |
- Wikström, P, et al.
(författare)
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The regulatory N-terminal region of the aromatic-responsive transcriptional activator DmpR constrains nucleotide-triggered multimerisation.
- 2001
-
Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 314:5
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Tidskriftsartikel (refereegranskat)abstract
- The transcriptional promoting activity of DmpR is under the strict control of its aromatic effector ligands that are bound by its regulatory N-terminal domain. The positive control function of DmpR resides within the central C-domain that is highly conserved among activators of sigma(54)-RNA polymerase. The C-domain mediates ATP hydrolysis and interaction with sigma(54)-RNA polymerase that are essential for open-complex formation and thus initiation of transcription. Wild-type and loss-of-function derivatives of DmpR, which are defective in distinct steps in nucleotide catalysis, were used to address the consequences of nucleotide binding and hydrolysis with respect to the multimeric state of DmpR and its ability to promote in vitro transcription. Here, we show that DmpR derivatives deleted of the regulatory N-terminal domain undergo an aromatic-effector independent ATP-binding triggered multimerisation as detected by cross-linking. In the intact protein, however, aromatic effector activation is required before ATP-binding can trigger an apparent dimer-to-hexamer switch in subunit conformation. The data suggest a model in which the N-terminal domain controls the transcriptional promoting property of DmpR by constraining ATP-mediated changes in its oligomeric state. The results are discussed in the light of recent mechanistic insights from the AAA(+) superfamily of ATPases that utilise nucleotide hydrolysis to restructure their substrates.
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| 46. |
- Bengtson, Per, et al.
(författare)
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Possible role of reactive chlorine in microbial antagonism and organic matter chlorination in terrestrial environments
- 2009
-
Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 11:6, s. 1330-1339
-
Forskningsöversikt (refereegranskat)abstract
- Several studies have demonstrated that extensive formation of organically bound chlorine occurs both in soil and in decaying plant material. Previous studies suggest that enzymatic formation of reactive chlorine outside cells is a major source. However, the ecological role of microbial-induced extracellular chlorination processes remains unclear. In the present paper, we assess whether or not the literature supports the hypothesis that extracellular chlorination is involved in direct antagonism against competitors for the same resources. Our review shows that it is by no means rare that biotic processes create conditions that render biocidal concentrations of reactive chlorine compounds, which suggest that extracellular production of reactive chlorine may have an important role in antagonistic microbial interactions. To test the validity, we searched the UniprotPK database for microorganisms that are known to produce haloperoxidases. It appeared that many of the identified haloperoxidases from terrestrial environments are originating from organisms that are associated with living plants or decomposing plant material. The results of the in silico screening were supported by various field and laboratory studies on natural chlorination. Hence, the ability to produce reactive chlorine seems to be especially common in environments that are known for antibiotic-mediated competition for resources (interference competition). Yet, the ability to produce haloperoxidases is also recorded, for example, for plant endosymbionts and parasites, and there is little or no empirical evidence that suggests that these organisms are antagonistic.
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| 47. |
- Boström, Björn, et al.
(författare)
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Can isotopic fractionation during respiration explain the 13C-enriched sporocarps of ectomycorrhizal and saprotrophic fungi?
- 2008
-
Ingår i: New Phytologist. - Cambridge : Cambridge University Press. - 0028-646X .- 1469-8137. ; 177:4, s. 1012-1019
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Tidskriftsartikel (refereegranskat)abstract
- • The mechanism behind the 13C enrichment of fungi relative to plant materials is unclear and constrains the use of stable isotopes in studies of the carbon cycle in soils.• Here, we examined whether isotopic fractionation during respiration contributes to this pattern by comparing δ13C signatures of respired CO2, sporocarps and their associated plant materials, from 16 species of ectomycorrhizal or saprotrophic fungi collected in a Norway spruce forest.• The isotopic composition of respired CO2 and sporocarps was positively correlated. The differences in δ13C between CO2 and sporocarps were generally small, < ±1‰ in nine out of 16 species, and the average shift for all investigated species was 0.04‰. However, when fungal groups were analysed separately, three out of six species of ectomycorrhizal basidiomycetes respired 13C-enriched CO2 (up to 1.6‰), whereas three out of five species of polypores respired 13C-depleted CO2 (up to 1.7‰; P < 0.05). The CO2 and sporocarps were always 13C-enriched compared with wood, litter or roots.• Loss of 13C-depleted CO2 may have enriched some species in 13C. However, that the CO2 was consistently 13C-enriched compared with plant materials implies that other processes must be found to explain the consistent 13C-enrichment of fungal biomass compared with plant materials.
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| 48. |
- Larsson, Åke, 1944, et al.
(författare)
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Hälsotillståndet hos abborre och tånglake
- 2007
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Ingår i: Havet 2007 - om miljötillståndet i svenska havsområden. - 1654-6741. ; 2007, s. 100-102
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Inom den nationalla marina kustfiskövervakningen har känsliga biomarkörer använts sedan 1988 för att kartlägga hälsotillståndet hos fisk. Här redovisas undersökningar på abborre och tånglake för de områden som har de längsta tidsserierna. De flesta biomarkörerna indikerar en god hälsostatus. Några erhållna mätdata talar dock för att fisken är påverkad av en ökad exponering för något eller några miljögifter. Detta kan vara tidiga tecken på på miljöförändringar som på sikt kan få allvarliga konsekvenser för fiskpopulationer i våra kustområden.
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| 49. |
- Sunhede, Stellan, 1942-
(författare)
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Vedsvampar på ek - 16. Platticka
- 2009
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Ingår i: Ekbladet. - : Ekfrämjandet. - 0283-4839. ; 24, s. 30-35
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 50. |
- Latorre-Margalef, Neus, et al.
(författare)
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Effects of influenza A virus infection on migrating mallard ducks
- 2009
-
Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 276:1659, s. 1029-1036
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Tidskriftsartikel (refereegranskat)abstract
- The natural reservoir of influenza A virus is waterfowl, particularly dabbling ducks (genus Anas). Although it has long been assumed that waterfowl are asymptomatic carriers of the virus, a recent study found that low-pathogenic avian influenza (LPAI) infection in Bewick's swans (Cygnus columbianus bewickii) negatively affected stopover time, body mass and feeding behaviour. In the present study, we investigated whether LPAI infection incurred ecological or physiological costs to migratory mallards (Anas platyrhynchos) in terms of body mass loss and staging time, and whether such costs could influence the likelihood for long-distance dispersal of the avian influenza virus by individual ducks. During the autumn migrations of 2002-2007, we collected faecal samples (n = 10 918) and biometric data from mallards captured and banded at Ottenby, a major staging site in a flyway connecting breeding and wintering areas of European waterfowl. Body mass was significantly lower in infected ducks than in uninfected ducks (mean difference almost 20 g over all groups), and the amount of virus shed by infected juveniles was negatively correlated with body mass. There was no general effect of infection on staging time, except for juveniles in September, in which birds that shed fewer viruses stayed shorter than birds that shed more viruses. LPAI infection did not affect speed or distance of subsequent migration. The data from recaptured individuals showed that the maximum duration of infection was on average 8.3 days (s.e. 0.5), with a mean minimum duration of virus shedding of only 3.1 days (s.e. 0.1). Shedding time decreased during the season, suggesting that mallards acquire transient immunity for LPAI infection. In conclusion, deteriorated body mass following infection was detected, but it remains to be seen whether this has more long-term fitness effects. The short virus shedding time suggests that individual mallards are less likely to spread the virus at continental or intercontinental scales.
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