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  • Sanli, Kemal, et al. (författare)
  • Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities
  • 2015
  • Ingår i: Frontiers in Microbiology. - 1664-302X. ; 6:1192
  • Tidskriftsartikel (refereegranskat)abstract
    • Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.
  • Nilsson, R. Henrik, 1976-, et al. (författare)
  • Mycobiome diversity: high-throughput sequencing and identification of fungi.
  • 2019
  • Ingår i: Nature reviews. Microbiology. - 1740-1534. ; 17, s. 95-109
  • Forskningsöversikt (refereegranskat)abstract
    • Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
  • Gustafsson, Jon Petter, et al. (författare)
  • Towards a consistent geochemical model for prediction of uranium(VI) removal from groundwater by ferrihydrite
  • 2009
  • Ingår i: Applied Geochemistry. - Oxford : Pergamon Press. - 0883-2927. ; 24:3, s. 454-462
  • Tidskriftsartikel (refereegranskat)abstract
    • Uranium(VI), which is often elevated in granitoidic groundwaters, is known to adsorb strongly to Fe (hydr)oxides under certain conditions. This process can be used in water treatment to remove U(VI). To develop a consistent geochemical model for U(VI) adsorption to ferrihydrite, batch experiments were performed and previous data sets reviewed to optimize a set of surface complexation constants using the 3-plane CD-MUSIC model. To consider the effect of dissolved organic matter (DOM) on U(VI) speciation, new parameters for the Stockholm Humic Model (SHM) were optimized using previously published data. The model, which was constrained from available X-ray absorption fine structure (EXAFS) spectroscopy evidence, fitted the data well when the surface sites were divided into low- and high-affinity binding sites. Application of the model concept to other published data sets revealed differences in the reactivity of different ferrihydrites towards U(VI). Use of the optimized SHM parameters for U(VI)-DOM complexation showed that this process is important for U(VI) speciation at low pH. However in neutral to alkaline waters with substantial carbonate present, Ca–U–CO3 complexes predominate. The calibrated geochemical model was used to simulate U(VI) adsorption to ferrihydrite for a hypothetical groundwater in the presence of several competitive ions. The results showed that U(VI) adsorption was strong between pH 5 and 8. Also near the calcite saturation limit, where U(VI) adsorption was weakest according to the model, the adsorption percentage was predicted to be >80%. Hence U(VI) adsorption to ferrihydrite-containing sorbents may be used as a method to bring down U(VI) concentrations to acceptable levels in groundwater.
  • Khalaf, Hazem, et al. (författare)
  • Diastereomers of the Brominated Flame Retardant 1,2-dibromo-4-(1,2 dibromoethyl)cyclohexane Induce Androgen Receptor Activation in the HepG2 Hepatocellular Carcinoma Cell Line and the LNCaP Prostate Cancer Cell Line
  • 2009
  • Ingår i: Journal of Environmental Health Perspectives. - National Institute of Environmental Health Science. - 0091-6765. ; 117:12, s. 1853-1859
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Reported incidences of prostate cancer and masculinization of animals indicate a release of compounds with androgenic properties into the environment. Large numbers of environmental pollutants have been screened to identify such compounds; however, not until recently was 1,2-dibromo-4-(1,2-dibromoethyl)cyclohex​ane (TBECH) identified as the first potent activator of the human androgen receptor (hAR). TBECH has been found in beluga whales and bird eggs and has also been found to be maternally transferred in zebrafish.Objectives: In the present study we investigated interaction energies between TBECH diastereomers (α, β, γ, and δ) and the hAR, and their ability to activate the receptor and induce prostate-specific antigen (PSA) expression in vitro.Methods: We performed computational modeling to determine interaction energies between the ligand and the AR ligand-binding site, and measured in vitro competitive binding assays for AR by polarization fluorometry analysis. We used enzyme-linked immunosorbent assays to determine PSA activity in LNCaP and HepG2 cells.Results: We found the γ and δ diastereomers to be more potent activators of hAR than the α and β diastereomers, which was confirmed in receptor binding studies. All TBECH diastereomers induced PSA expression in LNCaP cells even though the AR present in these cells is mutated (T877A). Modeling studies of LNCaP AR revealed that TBECH diastereomers bound to the receptor with a closer distance to the key amino acids in the ligand-binding domain, indicating stronger binding to the mutated receptor.Conclusions: The present study demonstrates the ability of TBECH to activate the hAR, indicating that it is a potential endocrine disruptor.
  • Karlsson, Magnus, 1972-, et al. (författare)
  • Application of a mass-balance model to predict PCDD/F turnover in a Baltic coastal estuary
  • 2010
  • Ingår i: Estuarine, Coastal and Shelf Science. - 0272-7714 .- 1096-0015. ; 88:2, s. 209-218
  • Tidskriftsartikel (refereegranskat)abstract
    • A dynamical, process-based mass-balance model was applied to quantify the transports of polychlorinated-p-dibenzodioxins and dibenzofurans (PCDD/Fs) to, within and from the Kallrigafjarden Bay, a coastal estuary in the Baltic Sea, and to predict the PCDD/F levels in the water and sediments of the bay. Before the modelling, a one-year sampling programme was implemented in 2007-2008 to measure the flows of PCDD/Fs in tributaries entering the system, the fluxes from the adjacent sea and the levels in water, sediment and fish within the estuary. The collected data set was used as input data to the model and for validation purposes.The model was originally developed and tested for suspended particulate matter and phosphorus in Baltic coastal areas. In this work, it was run monthly without any tuning of the original model variables. The simulation results compared favourably with the field measurements of levels of 15 PCDD/F congeners in the water and sediments of the bay. The dominating fluxes of PCDD/Fs were the exchange with the adjacent sea, followed by riverine input, atmospheric deposition and sediment burial.Although the sediment-water exchange was of minor importance for the overall mass-balance due to the rapid water turnover and limited areas favourable for the long-term deposition of fine sedimentary matter, sensitivity analyses indicated that the model's predictive capability was improved with about 5% by taking the sediment burial and release into account.
  • Maddalo, Gianluca, et al. (författare)
  • Porcine P2 myelin protein primary structure and bound fatty acids determined by mass spectrometry
  • 2010
  • Ingår i: Analytical and Bioanalytical Chemistry. - 1618-2642 .- 1618-2650. ; 397:5, s. 1903-1910
  • Tidskriftsartikel (refereegranskat)abstract
    • Complementary collision-induced/electron capture dissociation Fourier-transform ion cyclotron resonance mass spectrometry was used to fully sequence the protein P2 myelin basic protein. It is an antigenic fatty-acid-binding protein that can induce experimental autoimmune neuritis: an animal model of Guillain-Barre syndrome, a disorder similar in etiology to multiple sclerosis. Neither the primary structure of the porcine variant, nor the fatty acids bound by the protein have been well established to date. A 1.8-angstrom crystal structure shows but a bound ligand could not be unequivocally identified. A protocol for ligand extraction from protein crystals has been developed with subsequent gas chromatography MS analysis allowing determination that oleic, stearic, and palmitic fatty acids are associated with the protein. The results provide unique and general evidence of the utility of mass spectrometry for characterizing proteins from natural sources and generating biochemical information that may facilitate attempts to elucidate the causes for disorders such as demyelination.
  • Posthumanistiska nyckelstexter
  • 2012
  • Samlingsverk (redaktörskap) (övrigt vetenskapligt)abstract
    • Den här boken introducerar några viktiga författare på samtidsaktuella teoriområden. Donna Haraway, Karen Barad, Rosi Braidotti, Michel Callon, Gilles Deleuze, Félix Guattari, Michel Serres och Annemarie Mol presenteras i boken, som också innehåller översatta texter av dessa namn. Boken ger en bakgrund till och en överblick över ett område i intensiv teoriutveckling. Här presenteras den så kallade materiella, posthumana eller ontologiska vändningen. Här kartläggs grunderna för olika posthumanistiska förhållningssätt till de både mänskliga och icke-mänskliga (djur, miljö, teknik) krafterna i vår värld så som de begreppsliggjorts inom filosofi, feministisk teori, kulturstudier och samhällsvetenskapliga studier av naturvetenskap, medicin och teknik. Genom lästips och en omfattande litteraturlista öppnar boken för fortsatta studier och vidare diskussioner. Avslutningsvis finns också en omfattande ordlista med viktiga nyckelbegrepp som i sig ger en introduktion till ett heterogent forskningsfält. Boken riktar sig till studenter, doktorander och andra nyfikna forskare inom olika tvärvetenskapliga eller disciplinära former av humaniora och samhällsvetenskap.POSTHUMANISTISKA NYCKELTEXTER ger i de inledande kapitlen en överblick och en introduktion till posthumanistiska studier och till materiell-semiotik. Här behandlas tankeströmningar som rör det humanas natur, humanismens etik och humanvetenskapernas framtid. Boken ger en introduktion till det som inom genusvetenskap och tekniksociologi kommit att kallas den ontologiska vändningen mot de materiaaliteter och världsliga relationer som både gör och förgör oss. Här kartläggs grunderna för posthumanistiska förhållningssätt till de både mänskliga och icke-mänskliga (djur, miljö, teknik) dimensionerna av vår värld så som de begreppsliggjorts inom filosofi, feministisk teori, kulturstudier och sociala studier av vetenskap och teknik. POSTHUMANISTISKA NYCKELTEXTER erbjuder introduktioner till viktiga författare och översättningar av nyckeltexter skrivna av Donna Haraway, Karen Barad, Rosi Braidotti, Michel Callon, Gilles Deleuze med Felix Guattari, Michel Serres och Annemarie Mol. Boken innehåller även en omfattande ordlista med viktiga nyckelbegrepp som i sig ger en introduktion till ett mångfaldigt forskningsfält.
  • Le Breton, Michael, 1986-, et al. (författare)
  • Chlorine oxidation of VOCs at a semi-rural site in Beijing: significant chlorine liberation from ClNO2 and subsequent gas- and particle-phase Cl-VOC production
  • 2018
  • Ingår i: Atmospheric Chemistry and Physics. - 1680-7316. ; 18:17, s. 13013-13030
  • Tidskriftsartikel (refereegranskat)abstract
    • Nitryl chloride (ClNO2) accumulation at night acts as a significant reservoir for active chlorine and impacts the following day's photochemistry when the chlorine atom is liberated at sunrise. Here, we report simultaneous measurements of N2O5and a suite of inorganic halogens including ClNO2and reactions of chloride with volatile organic compounds (Cl-VOCs) in the gas and particle phases utilising the Filter Inlet for Gas and AEROsols time-of-flight chemical ionisation mass spectrometer (FIGAERO-ToF-CIMS) during an intensive measurement campaign 40km northwest of Beijing in May and June 2016. A maximum mixing ratio of 2900ppt of ClNO2was observed with a mean campaign nighttime mixing ratio of 487ppt, appearing to have an anthropogenic source supported by correlation with SO2, CO and benzene, which often persisted at high levels after sunrise until midday. This was attributed to such high mixing ratios persisting after numerous e-folding times of the photolytic lifetime enabling the chlorine atom production to reach 2.3 × 105moleculescm-3from ClNO2alone, peaking at 09:30LT and up to 8.4 × 105moleculescm-3when including the supporting inorganic halogen measurements. Cl-VOCs were observed in the particle and gas phases for the first time at high time resolution and illustrate how the iodide ToF-CIMS can detect unique markers of chlorine atom chemistry in ambient air from both biogenic and anthropogenic sources. Their presence and abundance can be explained via time series of their measured and steady-state calculated precursors, enabling the assessment of competing OH and chlorine atom oxidation via measurements of products from both of these mechanisms and their relative contribution to secondary organic aerosol (SOA) formation.
  • Lindh, Ingrid, et al. (författare)
  • Production of the p24 capsid protein from HIV-1 subtype C in Arabidopsis thaliana and Daucus carota using an endoplasmic reticulum-directing SEKDEL sequence in protein expression constructs
  • 2009
  • Ingår i: Protein Expression and Purification. - St. Louis : Academic Press. - 1046-5928. ; 66:1, s. 46-51
  • Tidskriftsartikel (refereegranskat)abstract
    • An optimized gene expression construct was designed in order to increase the accumulation of the HIV-1 subtype C p24 protein in Arabidopsis thaliana and carrot (Daucus carota) plants. An ER retention signal was introduced into the genetic construct generating a p24 protein containing a SEKDEL amino acid sequence at its C-terminus. Mature A. thaliana plants and carrot cells were transformed using Agrobacterium tumefaciens carrying the improved pGreen0229/p24_SEKDEL vector. Several transgenic plant lines were obtained from both plant species by growth on selective medium and confirmed by PCR. Transformed lines were analyzed for p24 protein content by western blotting using anti-p24-specific antibodies and by Southern blotting to establish the number of copies of the insert in the plant nuclear genome. To estimate the accumulation levels of p24 protein in the plants, ELISA was run using soluble plant extracts. By comparing these results with our previous findings, the ER retention signal increased the level of p24 protein 5-fold in the Arabidopsis thaliana plants. In carrot taproot, the content of p24_SEKDEL protein was approximately half of that in Arabidopsis on a fresh weight basis and was stable in planta for several months. However, on a total soluble protein basis, carrots produced considerable higher levels of the p24_SEKDEL protein than Arabidopsis.
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