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- Gantner, S, et al.
(författare)
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Novel primers for 16S rRNA-based archaeal community analyses in environmental samples
- 2011
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Ingår i: Journal of Microbiological Methods. - : Elsevier BV. - 0167-7012 .- 1872-8359. ; 84:1, s. 12-18
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Tidskriftsartikel (refereegranskat)abstract
- Next generation sequencing technologies for in depth analyses of complex microbial communities rely on rational primer design based on up-to-date reference databases. Most of the 16S rRNA-gene based analyses of environmental Archaea community composition use PCR primers developed from small data sets several years ago, making an update long overdue. Here we present a new set of archaeal primers targeting the 16S rRNA gene designed from 8500 aligned archaeal sequences in the SILVA database. The primers 340F-1000R showed a high archaeal specificity (<1% bacteria amplification) covering 93 and 97% of available sequences for Crenarchaeota and Euryarchaeota respectively. In silico tests of the primers revealed at least 38% higher coverage for Archaea compared to other commonly used primers. Empirical tests with clone libraries confirmed the high specificity of the primer pair to Archaea in three biomes: surface waters in the Arctic Ocean, the pelagic zone of a temperate lake and a methanogenic bioreactor. The clone libraries featured both Euryarchaeota and Crenarchaeota in variable proportions and revealed dramatic differences in the archaeal community composition and minimal phylogenetic overlap between samples.
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- Grubisic, Lorena M., et al.
(författare)
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Lake bacterioplankton dynamics over diurnal timescales
- 2017
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Ingår i: Freshwater Biology. - : Blackwell Publishing. - 0046-5070 .- 1365-2427. ; 62:1, s. 191-204
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Tidskriftsartikel (refereegranskat)abstract
- 1. Planktonic bacterial community dynamics over short timescales can be of great importance for food webs and ecosystem functioning but are rarely described when microbial community and composition are assessed. To study the significance of such dynamics we sampled the surface water at the deepest point of a mesotrophic lake (Lake Erken, Sweden) every third hour over two days. 2. By combining 454 pyrosequencing of 16S rRNA genes with bromodeoxyuridine immunocapturing of DNA, replicating populations were identified and compared to the community retrieved from total DNA samples. This comparison revealed a significant difference between the actively replicating and total community. 3. The high-frequency diurnal sampling was compared to a year-long survey conducted in the same lake in order to compare the diurnal and seasonal variation in bacterioplankton community composition. At the diurnal-scale, the variation was significantly higher in the replicating than in the total community. However, variation in both active and total diurnal community was significantly lower than the variation in the seasonal total community. 4. Our analysis revealed pronounced short-term dynamics of individual bacterial populations uncoupled from the diurnal light cycle. For example, the proliferating fraction of the most abundant bacterial tribe (LD12) followed a cyclic pattern that covaried with viral abundance. This implies that environmental factors other than light may act as important drivers of microbial community composition, at least in mesotrophic Lake Erken.
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- Krebs, Alice, et al.
(författare)
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Template for the Description of Cell-Based Toxicological Test Methods to Allow Evaluation and Regulatory Use of the Data
- 2019
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Ingår i: Altex. - : ALTEX Edition. - 1868-596X .- 1868-8551. ; 36:4, s. 682-699
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Only few cell-based test methods are described by Organisation for Economic Co-operation and Development (OECD) test guidelines or other regulatory references (e.g., the European Pharmacopoeia). The majority of toxicity tests still falls into the category of non-guideline methods. Data from these tests may nevertheless be used to support regulatory decisions or to guide strategies to assess compounds (e.g., drugs, agrochemicals) during research and development if they fulfill basic requirements concerning their relevance, reproducibility and predictivity. Only a method description of sufficient clarity and detail allows interpretation and use of the data. To guide regulators faced with increasing amounts of data from non-guideline studies, the OECD formulated Guidance Document 211 (GD211) on method documentation for the purpose of safety assessment. As GD211 is targeted mainly at regulators, it leaves scientists less familiar with regulation uncertain as to what level of detail is required and how individual questions should be answered. Moreover, little attention was given to the description of the test system (i.e., cell culture) and the steps leading to it being established in the guidance. To address these issues, an annotated toxicity test method template (ToxTemp) was developed (i) to fulfill all requirements of GD211, (ii) to guide the user concerning the types of answers and detail of information required, (iii) to include acceptance criteria for test elements, and (iv) to define the cells sufficiently and transparently. The fully annotated ToxTemp is provided here, together with reference to a database containing exemplary descriptions of more than 20 cell-based tests.
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