236 research outputs found
Functional profiling of single-nucleotide polymorphisms associated with bipolar disorder
No full textThe SLiMDisc server: short, linear motif discovery in proteins
No full textShort, linear motifs (SLiMs) play a critical role in many biological processes, particularly in protein-protein interactions. Overrepresentation of convergent occurrences of motifs in proteins with a common attribute (such as similar subcellular location or a shared interaction partner) provides a feasible means to discover novel occurrences computationally. The SLiMDisc (Short, Linear Motif Discovery) web server corrects for common ancestry in describing shared motifs, concentrating on the convergently evolved motifs. The server returns a listing of the most interesting motifs found within unmasked regions, ranked according to an information content-based scoring scheme. It allows interactive input masking, according to various criteria. Scoring allows for evolutionary relationships in the data sets through treatment of BLAST local alignments. Alongside this ranked list, visualizations of the results improve understanding of the context of suggested motifs, helping to identify true motifs of interest. These visualizations include alignments of motif occurrences, alignments of motifs and their homologues and a visual schematic of the top-ranked motifs. Additional options for filtering and/or re-ranking motifs further permit the user to focus on motifs with desired attributes. Returned motifs can also be compared with known SLiMs from the literature. SLiMDisc is available at: http://bioware.ucd.ie/ approximately slimdisc/
Demographic history has shaped the strongly differentiated corkwing wrasse populations in Northern Europe
No full textUnderstanding the biological processes involved in genetic differentiation and divergence between populations within species is a pivotal aim in evolutionary biology. One particular phenomenon that requires clarification is the maintenance of genetic barriers despite the high potential for gene flow in the marine environment. Such patterns have been attributed to limited dispersal or local adaptation, and to a lesser extent to the demographic history of the species. The corkwing wrasse (Symphodus melops) is an example of a marine fish species where regions of particular strong divergence are observed. One such genetic break occurred at a surprisingly small spatial scale (FST ~0.1), over a short coastline (<60 km) in the North Sea-Skagerrak transition area in southwestern Norway. Here, we investigate the observed divergence and purported reproductive isolation using genome resequencing. Our results suggest that historical events during the post-glacial recolonization route can explain the present population structure of the corkwing wrasse in the northeast Atlantic. While the divergence across the break is strong, we detected ongoing gene flow between populations over the break suggesting recent contact or negative selection against hybrids. Moreover, we found few outlier loci and no clear genomic regions potentially being under selection. We concluded that neutral processes and random genetic drift e.g., due to founder events during colonization have shaped the population structure in this species in Northern Europe. Our findings underline the need to take into account the demographic process in studies of divergence processes.freebayes - ALL.VAR - SNP dataset of the corkwing wrasse in Northern Europe
Parameters:
Q40
DP4_30
max_miss_5
AA
MAC3
sort
Southern population: EG*, AR*, TV*, GF*
Western population: SM*, NH*, ST*
British Isles population: ARD*
Funding provided by: Norges ForskningsrådCrossref Funder Registry ID: Award Number: 234328Funding provided by: Norges ForskningsrådCrossref Funder Registry ID: Award Number: 280453Funding provided by: Svenska Forskningsrådet FormasCrossref Funder Registry ID:Sixty-five corking wrasses were sampled from eight coastal locations from three regions: the British Isles, western and southern Scandinavia (Table 1). Samples from southern Norway were collected by beach seine, while those from the west coast of Norway, Sweden and the British Isles were collected by fish pots, as described in (Blanco Gonzalez et al., 2016). Muscle tissues were taken from fresh or frozen specimens and stored in 96% ethanol prior to DNA extraction. Total genomic DNA was extracted with the DNeasy kit (Qiagen) or the E.Z.N.A. Tissue DNA kit (Omega Bio-Tek) and resuspending the DNA in TE buffer. The extractions were analyzed with Qubit (Thermo Fisher Scientific) for assessment of the DNA quality and concentration. After normalization to 1,200 ng with Qiagen EB buffer (10 mM Tris-cl; pH = 8.0) the samples were fragmented to ~350 bp using a Covaris S220 (Life Technologies). Library construction was performed using the Illumina TruSeq DNA PCR Free protocol and checked on Bioanalyser High sensitivity chip and Tapestation (both Agilent) followed by Kapa Biosystems qPCR assay for Illumina libraries quantification.
Whole-genome resequencing was conducted on the Illumina HiSeq platform, generating 2 × 125 bp paired-end reads to an average depth of ~9.16× per sample (595× in total across the 65 sample libraries). The mean read insert size across samples was 347 (range: 246–404). Reads were mapped to the corkwing wrasse reference genome assembly (Mattingsdal et al., 2018) using bwa-mem (v0.7.5a; Li & Durbin, 2009) followed by duplicate removal by Picard (http://broadinstitute.github.io/picard/). Single nucleotide polymorphisms (SNPs) were called across all samples with freebayes (v1.0.2-33; Garrison & Marth, 2012), using the following quality control criteria: (a) quality >40; (b) minimum and maximum read depth of ×4 and ×30; (c) maximum 5% missing genotypes; (d) minimum minor allele count of 3 (MAF >2%). Two data sets were made: (a) all SNPs with ancestral states and (b) a thinned data set keeping random SNPs equally spaced by 10,000 bp and excluding rare variants (MAF >2%, thinned with "–bp-space 10,000").
The ancestral allele states were inferred using whole-contig alignments between the corkwing and ballan wrasse (L. bergylta) genome assemblies (Lie et al., 2018; Mattingsdal et al., 2018) constructed by last (v923; Frith, Hamada, & Horton, 2010); both species are members of the Labridae family. First, the genomes were indexed specifying the "YASS" and "R11" options, optimizing for long and weak similarities and masking low-complexity regions. Then, a pairwise genome-wide alignment between corkwing- and ballan wrasses was made, setting minimum E-value to 0.05 and maximum matches per query position = 100. The "last-split" function was run twice to ensure 1-1 alignments. The multiple alignments were converted to bam format and SNP positions in the corkwing wrasse genome used to extract "genotypes" in the corkwing and ballan wrasse alignment using samtools and bcftools (Li et al., 2009). The inferred ancestral states were manually controlled and plink v1.90b3.40 (Purcell et al., 2007) was used to annotate the ancestral state as the reference allele. Missing data were imputed and phased using beagle default settings (Browning & Browning, 2013). To elucidate demographic relationships between the populations, we searched for identical-by-decent (IBD) haplotypes inferred by beagle (Browning & Browning, 2013), which accounts for haplotype phase uncertainty
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
No full textMultidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line resources are available for revealing globular domains in sequences, there has hitherto been no comprehensive collection of small functional sites/motifs comparable to the globular domain resources, yet these are as important for the function of multidomain proteins. Short linear peptide motifs are used for cell compartment targeting, protein-protein interaction, regulation by phosphorylation, acetylation, glycosylation and a host of other post-translational modifications. ELM, the Eukaryotic Linear Motif server at http://elm.eu.org/, is a new bioinformatics resource for investigating candidate short non-globular functional motifs in eukaryotic proteins, aiming to fill the void in bioinformatics tools. Sequence comparisons with short motifs are difficult to evaluate because the usual significance assessments are inappropriate. Therefore the server is implemented with several logical filters to eliminate false positives. Current filters are for cell compartment, globular domain clash and taxonomic range. In favourable cases, the filters can reduce the number of retained matches by an order of magnitude or more
The ELM server: A new source for revealing short functional sites in modular eukaryotic proteins. Nucleic Acids Res., 31(13):3625-30.
No full textMultidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line resources are available for revealing globular domains in sequences, there has hitherto been no comprehensive collection of small functional sites/motifs comparable to the globular domain resources, yet these are as important for the function of multidomain proteins. Short linear peptide motifs are used for cell compartment targeting, protein-protein interaction, regulation by phosphorylation, acetylation, glycosylation and a host of other post-translational modifications. ELM, the Eukaryotic Linear Motif server at http://elm.eu.org/, is a new bioinformatics resource for investigating candidate short non-globular functional motifs in eukaryotic proteins, aiming to fill the void in bioinformatics tools. Sequence comparisons with short motifs are difficult to evaluate because the usual significance assessments are inappropriate. Therefore the server is implemented with several logical filters to eliminate false positives. Current filters are for cell compartment, globular domain clash and taxonomic range. In favourable cases, the filters can reduce the number of retained matches by an order of magnitude or more
CAGE17-2 Cruise Report: Gas hydrate deposits and methane seepages in Storfjordrenna, Northern Flank of Olga Basin, and West Sentralbanken (Barents Sea): Biogeochemical and biological investigations
No full textThe main goal of CAGE 17-2 AMGG cruise was to study the gas-hydrate-bearing system and methane emission off south and east of Spitsbergen in Storfjordrenna and the northern flank of Olga Basin (named here Olga craters) respectively, and in the West Sentralbanken.
We addressed this through a comprehensive scientific program comprising dives with the MISO-Tow Cam adapted to the multicorer frame from UiT-NPI (TowCam/Multicorer, TCM), methane measurements in sediments, water column, and in air, sediment coring (multicorer + gravity corer), water column and sediment biogeochemistry, microbiology, micropaleontology, and bathymetric mapping.
Cruise CAGE 17-2 was also hosting this year’s AMGG research school cruise with masters, PhD and post-doc students participating.
The areas investigated were:
Storfjordrenna, Pingos site (ca 380 m water depth),Northern Flank of Olga Basin (ca 140 m water depth)West Sentralbanken (ca 200 m water depth)
We planned the following activities during the CAGE 17-2 cruise:
EM 302 Simrad swath bathymetry mapping to identify seabed morphology
Mapping of flare distributionsCTD stations at different water depths and in different areas for measurements ofocean water masses characteristics, andwater sampling for water/gas chemistry and microbiology investigations across methane seeps.TCM surveys (video-camera) to image seabed fluid flow expressions, sites of bacteria mats, crusts and gas bubbles.Repeated deployments with TCM to sample surficial and shallow sediments with respect to microbiology, geochemistry, biogeochemistry, and micropaleontology.Gravity corer for studying sediment biogeochemistry, biomarkers, microbiology, and foraminifera.Scrape sampling to collect rocks and crusts.Gas Chromatographer (GC) to measure methane concentration in the water and sediment samples.Flasks Restek, Electro-Polished Miniature Canister (1000 cc) for air samples.
Part of the cruise was supported by NPD, Oljedirektoratet. Special thanks to Rune Mattingsdal, NPD.
The cruise may be known as: CAGE17_
Ethics in categorizing ethnicity and disability in research with children
No full textThe use of categories is a contested subject in social sciences. The use of social categories allows researchers to explore similarities, differences, and inequalities between groups of people. However, by using social categories, researchers run the risk of essentializing differences. The aim of this article is to problematize the procedural and relational ethics of using categories in research with children. Based on two research projects studying inclusion and exclusion in physical education, we examine the ongoing ethical dilemmas of categorizing children in terms of disability and ethnic background. The reflections are grounded in intersectional and relational ethical perspectives with a focus on how power is manifested in practices and structures throughout the research process. The data consist of field notes, transcripts of interviews with children and their parents, and the authors’ reflective accounts. The results are organized into three main themes: (1) How categories frame the research in its initial phases (informed consent and voluntary participation), (2) power relationships in context (navigating meanings of categories in the interviews and the relational ethics of generational ordering in combined interviews with children and their parents), and (3) (re)constructing stories and ensuring anonymity. In the discussion, we reflect on how singling out groups of children framed the research, how categories and power relations were negotiated and navigated in interviews and fieldwork, and how, in the reporting of the results, understandings of the children and their experiences were constructed. We argue that by not reflecting on the ethics of categorizing children in research, researchers are in danger of reproducing rather than challenging social inequality and discrimination
Static Rope Rescue Operations in Western Norway: A Retrospective Analysis of 141 Missions
No full textIntroduction
The Norwegian national standard for rescuers describes medical and rescue requirements for helicopter emergency medical services (HEMS) technical crew members, but there is a lack of scientific data supporting these requirements and their safety relevance. The study aims to analyze the rescue profile of Norwegian HEMS static rope human external cargo operations, emphasizing terrain challenges and additional safety measures utilized on-site.
Methods
We conducted a retrospective descriptive analysis of static rope missions performed in daylight by 3 HEMS bases in Western Norway in the period 2015 to 2019. The analysis measures evacuation methods, terrain, on-site safety measures, and medical treatment.
Results
Out of 8352 primary HEMS and search and rescue missions, a total of 141 (2%) static rope missions were performed by the 3 HEMS bases in Western Norway. The most commonly used evacuation method was triangle harness (62%) and a static rope length of 30 m (81%). Ninety-two (65%) missions were completed in simple terrain, 38 (27%) in challenging terrain, and 11 (8%) in complex terrain. There were no reported accidents, but a small number of adverse events were registered. The most frequent medical intervention administered on-site was pain management, followed by spinal immobilization.
Conclusions
Thirty-five percent of the static rope missions performed by HEMS in Western Norway were completed in challenging or complex terrain, requiring additional safety measures on-site. The most common safety measure needed was the ability to operate in a mountain or alpine environment. Our findings support the safety relevance of a national standard for rescuers.publishedVersio
A constellation of mud volcanoes originated from a buried Arctic mega-slide, Southwestern Barents Sea
No full textGlobal estimates on the number of submarine mud volcanoes are highly uncertain, as well as their role in the deep-sea biosphere and methane budgets. Here, we report the discovery of ten Arctic mud volcanoes in the Barents Sea (440–480 m depth), where only two had been previously known. The new mud volcanoes form flat-topped mounds on the seafloor and are connected to seismic chimneys rooted within the infilling of a buried Pleistocene mega-slide scar. We suggest informally naming the area the Polaris Mud Volcano Complex. These structures have been active at least since the Late Weichselian deglaciation (< 20 ka), displaying evidence of ongoing methane-rich mud expulsion, i.e. mud pools and flows and chemosynthetic fauna. Finally, we propose a conceptual model for their formation which can be exported to other similar settings. Given the widespread occurrence of mega-slides and associated deposits along (paleo)glaciated continental margins, our findings call for a re-evaluation of mud volcanism potential in such regions
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