| 1. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
- 2012
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 4, s. 37-63
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Tidskriftsartikel (refereegranskat)abstract
- Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
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| 2. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Top 50 most wanted fungi
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 12, s. 29-40
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Tidskriftsartikel (refereegranskat)abstract
- Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond “Fungi”. There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more.
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| 4. |
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| 5. |
- Sharif, Hanan, et al.
(författare)
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A monoclonal antibody-based sandwich ELISA for measuring canine Thymidine kinase 1 protein and its role as biomarker in canine lymphoma
- 2023
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Ingår i: Frontiers in Veterinary Science. - : Frontiers Media SA. - 2297-1769. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Dogs play an important role in society, which increased during the covid epidemics. This has led to a much higher workload for the veterinarians. Therefore, there is a need for efficient diagnostic tools to identify risk of malignant diseases. Here the development of a new test that can solve some of these problems is presented. It is based on serum Thymidine Kinase 1 (TK1), which is a biomarker for cell proliferation and cell lysis.Methods: Anti-TK1 monoclonal antibodies were produced against two different epitopes, the active site of the TK1 protein and the C-terminal region of canine TK1. The antibodies were developed with hybridoma technology and validated using dot blot, Quartz Crystal Microbalance (QCM) technology, western blots, immunoprecipitation (IP), and enzyme-linked immunosorbent assay (ELISA). Clinical evaluation of Canine TK1 ELISA was done by using sera from 131 healthy dogs and 93 dogs with lymphoma. The two selected Anti-TK1 monoclonal antibodies have Kd values in the range of 10(-9) M and further analysis with dot and western blots confirmed the high affinity binding of these antibodies. A sandwich Canine TK1 ELISA was developed using the anti-TK1 antibodies, and TK1 concentrations in serum samples were determined using dog recombinant TK1 as a standard.Results: Serum TK1 protein levels were significantly higher in dogs with lymphoma compared to those in healthy dogs (p < 0.0001). Receiver operating curve analysis showed that the canine TK1-ELISA obtain a sensitivity of 0.80, at a specificity of 0.95. Moreover, the Canine TK1 ELISA has a positive predictive value (PPV) of 97%, and the negative predictive value (NPV) of 83%, reflecting the proportion of test results that are truly positive and negative. Furthermore, Canine TK1 ELISA had significantly higher capacity to differentiate dogs with T-cell lymphoma from those with B-cell lymphoma compared to earlier used TK1 activity assays.Discussion: These results demonstrate that the Canine TK1 ELISA can serve as an efficient tool in the diagnosis and management of dogs with lymphomas.
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| 6. |
- Eklöf, Johan S., 1978-, et al.
(författare)
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Effects of seasonal spawning closures on pike (Esox lucius L.) and perch (Perca fluviatilis L.) catches and coastal food webs in the western Baltic Sea
- 2023
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Ingår i: Fisheries Research. - : Elsevier BV. - 0165-7836 .- 1872-6763. ; 263
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Tidskriftsartikel (refereegranskat)abstract
- Marine protected areas have become one of the main tools in the battle to curb marine biodiversity loss and habitat degradation. Yet, implementation of permanent fishery closures has often generated resource user conflicts that ultimately undermine conservation goals. Here we assessed the influence of an alternative and often more accepted measure – seasonal fish spawning closures – on large predatory fish and coastal food webs in the western Baltic Sea (Sweden). In spring 2017, we conducted a multivariable field survey in 11 seasonal closures and 11 paired references areas open to fishing. In each area, pike was sampled through angling, and perch and mesopredators through gillnet surveys. To assess trophic cascades, we measured zooplankton abundance and loss of tethered gammarids from predation. Catches per unit effort of northern pike (Esox lucius) – the main target species in recreational fisheries – were ca. 2.5 times higher per unit effort in closures than reference areas; an effect that may be caused by higher abundance and/or higher catchability of pike in the absence of fishing. Catch and weight per unit effort of the more common predator European perch (Perca fluviatilus), and the mesopredators roach (Rutilus rutilus) and three-spined stickleback (Gasterosteus aculeatus) in survey nets were, however, unaffected by closures. Moreover, a previously hypothesized trophic cascade from perch to zooplankton via three-spined stickleback was supported by the analyses, but appeared independent of closures. Yet, predation risk for tethered gammarid amphipods (a prey of stickleback and an important grazer on macroalgae) was three times higher in fished areas than in closures; a cascading closure effect that may potentially be caused by small predatory fish being less active in protected areas to avoid pike predation. Overall, our results suggest that spawning closures impact pike abundance and/or behavior and could help limit the effects of fishing, but that more research is needed to disentangle i) what mechanism(s) that underlie the protection effect on pike catches, ii) the apparently weaker closure impacts on other fish species, as well as iii) the potential for cascading effects on lower trophic levels. Therefore, new seasonal spawning closures should be implemented in addition to (and not instead of) much-needed permanent closures, which have well-known effects on the wider ecosystem.
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| 7. |
- Niemi, Niklas, et al.
(författare)
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Influence of reed beds (Phragmites australis) and submerged vegetation on pike (Esox lucius)
- 2023
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Ingår i: Fisheries Research. - : Elsevier BV. - 0165-7836 .- 1872-6763. ; 261
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Tidskriftsartikel (refereegranskat)abstract
- Eutrophication and reduced grazing have led to an expansion of the common reed (Phragmites australis) in archipelago areas in the Baltic Sea, while at the same time the composition of submerged vegetation has changed. Although reed is important as nursery habitat for many fish species, extensive emergent vegetation may reduce biodiversity and abundance of predatory fish. Pike (Esox lucius) is a predatory fish whose larvae and young-of-the-year find both food and shelter in reed but use different micro-habitats during different life-stages. Here we investigate the influence of reed and submerged vegetation on abundance and body size of adult pike during the spawning season. We predicted that coastal bays with extensive but heterogeneous reed beds with higher cover of submerged vegetation would have more and larger pike than bays with smaller, homogenous reed belts or with less submerged vegetation. To test these predictions, we estimated abundance and size-structure of adult pike from catches in angling fishing among 22 bays in the Stockholm archipelago at the Swedish Baltic Sea coast. Our analyses show that catches of adult pike were positively associated with both extensive reed beds and cover of rooted submerged vegetation. However, pike size was not correlated with any vegetation variable, but instead increased with wave exposure and bay area. Our study suggests that reed beds and submerged vegetation are important for adult pike during the spawning season, and even the most extensive reed beds had no evident negative effect on pike populations. We could not see any clear relationship between emergent reed habitat and cover of submerged vegetation among the studied bays, and conclude that to maintain pike population during the spawning season it is important that coastal bays have sufficient amounts of both reed beds and rooted submerged vegetation.
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| 8. |
- Sanli, Kemal, et al.
(författare)
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Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities
- 2015
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 6:1192
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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.
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| 9. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
- 2013
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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| 10. |
- Blanck, Hans, 1950, et al.
(författare)
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A retrospective analysis of contamination and periphyton PICT patterns for the antifoulant irgarol 1051, around a small marina on the Swedish west coast
- 2009
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Ingår i: Marine Pollution Bulletin. - : Elsevier BV. - 0025-326X .- 1879-3363. ; 58, s. 230-237
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Tidskriftsartikel (refereegranskat)abstract
- Irgarol is a triazine photosystem II (PSII) inhibitor that has been used in Sweden as an antifouling ingredient since the 1990s. Early microcosm studies indicated that periphyton was sensitive to irgarol at concentrations regularly found in harbours and marinas. However, field studies of irgarol effects on the Swedish west coast in 1994, using the pollution-induced community tolerance (PICT) approach, failed to detect any effects of the toxicant in the field. A PICT study involves sampling of replicate communities in a gradient of contamination, and a comparison of their community tolerance levels, with an increase being an indication that sensitive species have been eliminated and replaced by more tolerant ones. Typically, short-term assays are used to quantify the community tolerance levels. Later PICT studies in the same area over a 10 year period demonstrate that irgarol tolerance levels have increased, although the contamination pattern has been stable. Our results support the hypothesis that that the PICT potential was low initially, due to a small differential sensitivity between the community members, and that a persistent selection pressure was required to favour and enrich irgarol-tolerant species or genotypes. © 2008 Elsevier Ltd. All rights reserved.
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