| 1. |
- Bensch, Staffan, et al.
(författare)
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Contaminations contaminate common databases
- 2021
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Ingår i: Molecular Ecology Resources. - : Wiley-Blackwell. - 1755-098X .- 1755-0998. ; 21:2, s. 355-362
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Tidskriftsartikel (refereegranskat)abstract
- The polymerase chain reaction (PCR) is a very powerful method to detect and identify pathogens. The high sensitivity of the method, however, comes with a cost; any of the millions of artificial DNA copies generated by PCR can serve as a template in a following experiment. If not identified as contaminations, these may result in erroneous conclusions on the occurrence of the pathogen, thereby inflating estimates of host range and geographic distribution. In the present paper, we evaluate whether several published records of avian haemosporidian parasites, in either unusual host species or geographical regions, might stem from PCR contaminations rather than novel biological findings. The detailed descriptions of these cases are shedding light upon the steps in the work process that might lead to PCR contaminations. By increasing the awareness of this problem, it will aid in developing procedures that keep these to a minimum. The examples in the present paper are from haemosporidians of birds, however the problem of contaminations and suggested actions should apply generally to all kinds of PCR-based identifications, not just of parasites and pathogens.
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| 2. |
- Op De Beeck, Michiel, et al.
(författare)
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Fenton reaction facilitates organic nitrogen acquisition by an ectomycorrhizal fungus
- 2018
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Ingår i: New Phytologist. - : Wiley-Blackwell. - 0028-646X. ; 218:1, s. 335-343
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Tidskriftsartikel (refereegranskat)abstract
- Boreal trees rely on their ectomycorrhizal fungal symbionts to acquire growth-limiting nutrients, such as nitrogen (N), which mainly occurs as proteins complexed in soil organic matter (SOM). The mechanisms for liberating this N are unclear as ectomycorrhizal fungi have lost many genes encoding lignocellulose-degrading enzymes present in their saprotrophic ancestors. We hypothesized that hydroxyl radicals (bullOH), produced by the ectomycorrhizal fungus Paxillus involutus during growth on SOM, are involved in liberating organic N. Paxillus involutus was grown for 7 d on N-containing or N-free substrates that represent major organic compounds of SOM. bullOH production, ammonium assimilation, and proteolytic activity were measured daily. bullOH production was strongly induced when P. involutus switched from ammonium to protein as the main N source. Extracellular proteolytic activity was initiated shortly after the oxidation. Oxidized protein substrates induced higher proteolytic activity than unmodified proteins. Dynamic modeling predicted that bullOH production occurs in a burst, regulated mainly by ammonium and ferric iron concentrations. We propose that the production of bullOH and extracellular proteolytic enzymes are regulated by similar nutritional signals. Oxidation works in concert with proteolysis, improving N liberation from proteins in SOM. Organic N mining by ectomycorrhizal fungi has, until now, only been attributed to proteolysis.
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| 3. |
- Marcer, Arnald, et al.
(författare)
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Quality issues in georeferencing : From physical collections to digital data repositories for ecological research
- 2021
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Ingår i: Diversity and Distributions. - : Wiley-Blackwell. - 1366-9516 .- 1472-4642. ; 27:3, s. 564-567
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Tidskriftsartikel (refereegranskat)abstract
- Natural history collections constitute an enormous wealth of information of Life on Earth. It is estimated that over 2 billion specimens are preserved at institutions worldwide, of which less than 10% are accessible via biodiversity data aggregators such as GBIF. Moreover, they are a very important resource for eco-evolutionary research, which greatly depends on knowing the precise location where the specimens were collected in order to characterize the environment in which they lived. Yet, only about 55% of the accessible records are georeferenced and only 31% have coordinate uncertainty information, which is critical for conducting rigorous studies. The awareness of this gap of knowledge which hinders the enormous potential of such data in research led to the organization of a workshop which brought together key players in georeferencing of natural history collections. The discussion and outcomes of this workshop are here presented.
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| 4. |
- Toskas, Konstantinos, et al.
(författare)
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PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons
- 2022
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:34
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Tidskriftsartikel (refereegranskat)abstract
- How neurons can maintain cellular identity over an entire life span remains largely unknown. Here, we show that maintenance of identity in differentiated dopaminergic and serotonergic neurons is critically reliant on the Polycomb repressive complex 2 (PRC2). Deletion of the obligate PRC2 component, Eed, in these neurons resulted in global loss of H3K27me3, followed by a gradual activation of genes harboring both H3K27me3 and H3K9me3 modifications. Notably, H3K9me3 was lost at these PRC2 targets before gene activation. Neuronal survival was not compromised; instead, there was a reduction in subtype-specific gene expression and a progressive impairment of dopaminergic and serotonergic neuronal function, leading to behavioral deficits characteristic of Parkinson's disease and anxiety. Single-cell analysis revealed subtype-specific vulnerability to loss of PRC2 repression in dopamine neurons of the substantia nigra. Our study reveals that a PRC2-dependent nonpermissive chromatin state is essential to maintain the subtype identity and function of dopaminergic and serotonergic neurons.
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| 5. |
- Chapman, Lesley M, et al.
(författare)
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A crowdsourced set of curated structural variants for the human genome
- 2020
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Ingår i: PLoS Computational Biology. - : Public Library of Science (PLoS). - 1553-7358. ; 16:6
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Tidskriftsartikel (refereegranskat)abstract
- A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs) is more challenging. In this study, we manually curated 1235 SVs, which can ultimately be used to evaluate SV callers or train machine learning models. We developed a crowdsourcing app - SVCurator - to help GIAB curators manually review large indels and SVs within the human genome, and report their genotype and size accuracy. SVCurator displays images from short, long, and linked read sequencing data from the GIAB Ashkenazi Jewish Trio son [NIST RM 8391/HG002]. We asked curators to assign labels describing SV type (deletion or insertion), size accuracy, and genotype for 1235 putative insertions and deletions sampled from different size bins between 20 and 892,149 bp. 'Expert' curators were 93% concordant with each other, and 37 of the 61 curators had at least 78% concordance with a set of 'expert' curators. The curators were least concordant for complex SVs and SVs that had inaccurate breakpoints or size predictions. After filtering events with low concordance among curators, we produced high confidence labels for 935 events. The SVCurator crowdsourced labels were 94.5% concordant with the heuristic-based draft benchmark SV callset from GIAB. We found that curators can successfully evaluate putative SVs when given evidence from multiple sequencing technologies.
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| 6. |
- Eisen, Katherine E., et al.
(författare)
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An analytical pipeline to support robust research on the ecology, evolution, and function of floral volatiles
- 2022
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Ingår i: Frontiers in Ecology and Evolution. - : Frontiers Media S. A.. - 2296-701X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Research on floral volatiles has grown substantially in the last 20 years, which has generated insights into their diversity and prevalence. These studies have paved the way for new research that explores the evolutionary origins and ecological consequences of different types of variation in floral scent, including community-level, functional, and environmentally induced variation. However, to address these types of questions, novel approaches are needed that can handle large sample sizes, provide quality control measures, and make volatile research more transparent and accessible, particularly for scientists without prior experience in this field. Drawing upon a literature review and our own experiences, we present a set of best practices for next-generation research in floral scent. We outline methods for data collection (experimental designs, methods for conducting field collections, analytical chemistry, compound identification) and data analysis (statistical analysis, database integration) that will facilitate the generation and interpretation of quality data. For the intermediate step of data processing, we created the R package bouquet, which provides a data analysis pipeline. The package contains functions that enable users to convert chromatographic peak integrations to a filtered data table that can be used in subsequent statistical analyses. This package includes default settings for filtering out non-floral compounds, including background contamination, based on our best-practice guidelines, but functions and workflows can be easily customized as necessary. Next-generation research into the ecology and evolution of floral scent has the potential to generate broadly relevant insights into how complex traits evolve, their genomic architecture, and their consequences for ecological interactions. In order to fulfill this potential, the methodology of floral scent studies needs to become more transparent and reproducible. By outlining best practices throughout the lifecycle of a project, from experimental design to statistical analysis, and providing an R package that standardizes the data processing pipeline, we provide a resource for new and seasoned researchers in this field and in adjacent fields, where high-throughput and multi-dimensional datasets are common.
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| 7. |
- Fogelmark, Karl, et al.
(författare)
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Selection Shapes Transcriptional Logic and Regulatory Specialization in Genetic Networks.
- 2016
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:2
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Tidskriftsartikel (refereegranskat)abstract
- Living organisms need to regulate their gene expression in response to environmental signals and internal cues. This is a computational task where genes act as logic gates that connect to form transcriptional networks, which are shaped at all scales by evolution. Large-scale mutations such as gene duplications and deletions add and remove network components, whereas smaller mutations alter the connections between them. Selection determines what mutations are accepted, but its importance for shaping the resulting networks has been debated.
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| 8. |
- Georgakopoulos-Soares, Ilias, et al.
(författare)
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Alternative splicing modulation by G-quadruplexes
- 2022
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Alternative splicing is central to metazoan gene regulation, but the regulatory mechanisms are incompletely understood. Here, we show that G-quadruplex (G4) motifs are enriched ~3-fold near splice junctions. The importance of G4s in RNA is emphasised by a higher enrichment for the non-template strand. RNA-seq data from mouse and human neurons reveals an enrichment of G4s at exons that were skipped following depolarisation induced by potassium chloride. We validate the formation of stable RNA G4s for three candidate splice sites by circular dichroism spectroscopy, UV-melting and fluorescence measurements. Moreover, we find that sQTLs are enriched at G4s, and a minigene experiment provides further support for their role in promoting exon inclusion. Analysis of >1,800 high-throughput experiments reveals multiple RNA binding proteins associated with G4s. Finally, exploration of G4 motifs across eleven species shows strong enrichment at splice sites in mammals and birds, suggesting an evolutionary conserved splice regulatory mechanism.
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| 9. |
- Heinze, Stanley, et al.
(författare)
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A unified platform to manage, share, and archive morphological and functional data in insect neuroscience
- 2021
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Ingår i: eLife. - : eLife Sciences Publications. - 2050-084X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Insect neuroscience generates vast amounts of highly diverse data, of which only a small fraction are findable, accessible and reusable. To promote an open data culture, we have therefore developed the InsectBrainDatabase (IBdb), a free online platform for insect neuroanatomical and functional data. The IBdb facilitates biological insight by enabling effective cross-species comparisons, by linking neural structure with function, and by serving as general information hub for insect neuroscience. The IBdb allows users to not only effectively locate and visualize data, but to make them widely available for easy, automated reuse via an application programming interface. A unique private mode of the database expands the IBdb functionality beyond public data deposition, additionally providing the means for managing, visualizing, and sharing of unpublished data. This dual function creates an incentive for data contribution early in data management workflows and eliminates the additional effort normally associated with publicly depositing research data.
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| 10. |
- Johanson, Urban, et al.
(författare)
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Comparison of the complete sequence of the str operon in Salmonella typhimurium and Escherichia coli
- 1992
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Ingår i: Gene. - : Elsevier. - 0378-1119 .- 1879-0038. ; 120:1, s. 93-98
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Tidskriftsartikel (refereegranskat)abstract
- The nucleotide (nt) sequences of the str operon in Escherichia coli K-12 and Salmonella typhimurium LT2 were completed and compared at the nt and amino acid (aa) level. The order of conservation at the nt and aa level is rpsL greater than tufA greater than rpsG greater than f usA. A striking difference is that the rpsG-encoded ribosomal protein, S7, in E. coli K-12 is 23 aa longer than in S. typhimurium. The very low (0.18) codon adaptation index of this part of the E. coli K-12-encoding gene and the unusual stop codon (UGA) suggest that this is a relatively recent extension. A trend towards a higher G+C content in fusA (gene encoding elongation factor (EF)-G) and tufA (gene encoding EF-Tu) in S. typhimurium is noted. In fusA, nt substitutions at all three positions in a codon occur at a much higher frequency than expected from the number of nt substitutions in the gene, assuming they are random and independent events. An analysis of substitutions in this and other genes suggests that the triple substitutions in fusA, and some other genes, are the result of the sequential accumulation of individual mutations, probably driven by selection pressure for particular codons or aa.
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