| 1. |
- Quaglia, Federica, et al.
(författare)
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DisProt in 2022 : improved quality and accessibility of protein intrinsic disorder annotation
- 2022
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 50:D1, s. D480-D487
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Tidskriftsartikel (refereegranskat)abstract
- The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.
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| 2. |
- Szabó, Katalin É., et al.
(författare)
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Sequential colonization of river periphyton analysed by microscopy and molecular fingerprinting
- 2008
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Ingår i: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 53:7, s. 1359-1371
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Tidskriftsartikel (refereegranskat)abstract
- 1. An artificial glass substratum was incubated in the River Danube for a period of 28 days in order to detect the sequential colonization of microorganisms.2. Light and fluorescent microscopy showed that microalgae and the picoalgal fraction on the slides increased rapidly over the first 2 weeks of colonization. Diatoms were numerically the most abundant component of the periphyton and their species richness and diversity increased rapidly in the early phase of colonization whereas diversity subsequently increased moderately.3. Evenness of the diatom community was initially high, lower in the intermediate phase and again higher later on. Succession involving early, intermediate and late colonizer species was observed. Community composition during the first 5 days of colonization was very different from later stages whereas there were only minor changes subsequently.4. Molecular community analysis by means of terminal restriction fragment length polymorphism analysis of PCR amplified 16S rRNA and 18S rRNA genes pointed to even larger differences between the composition of samples obtained early and late in the period.5. The number of 18S rRNA and 16S rRNA terminal restriction fragments (T-RF-s) was variable over the colonization period and the fragment patterns of both the bacterial and eukaryotic portion of the microbial community were variable, with most T-RF-s unique to a single sample, suggesting a wide diversity and dynamic properties of periphytic organisms.
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| 3. |
- Szabó-Taylor, Katalin É., et al.
(författare)
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Composition and dynamics of microeukaryote communities in the River Danube
- 2010
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Ingår i: Fottea. - 1802-5439. ; 10:1, s. 99-113
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Tidskriftsartikel (refereegranskat)abstract
- The diversity of microeukaryote communities inhabiting rivers is still poorly known. Here, we have analyzed the periphytic and planktonic microeukaryote communities present in one section of the River Danube by two different methods: 18S rRNA-based terminal restriction fragment length polymorphism with fragment sequencing and microscopical analysis of the phytoplankton and periphyton. Both data sets were then related to environmental variables. Molecular fingerprinting revealed diverse communities with fluctuating composition, with the majority of sequences affiliated to the groups Bacillariophyta, Synurophyceae and Chlorophyceae. This was in accordance with microscopical data. The total number of detected T-RFs during the study period was 145, with more than half of the T-RFs being restricted to either plankton or periphyton. This suggests that the likely different natural selection regimes experienced by microeukaryotes in these two environments may promote the presence of different lineages in each of them. Significant correlations were found between phytoplankton chlorophyll a content, phosphorus content, temperature, and the T RFLP pattern of the planktonic microeukaryotic community, suggesting that the former environmental factors are especially important in structuring the planktonic microeukaryote communities in the River Danube. These data, together with earlier studies suggest that molecular methods are an invaluable addition in pursuit of the better understanding of the diversity and fluctuation of freshwater microeukaryotic communities.
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