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32 results for “structure alignments”
Data from: Effects of mis-alignment between dispersal traits and landscape structure on dispersal success in fragmented landscapes
Dispersal is fundamental to population dynamics and hence extinction risk. The dispersal success of animals depends on the biophysical structure of their environments and their biological traits; however, comparatively little is known about how evolutionary trade-offs among suites of biological traits affect dispersal potential. We developed a spatially explicit agent-based simulation model to evaluate the influence of trade-offs among a suite of biological traits on the dispersal success of vagile animals in fragmented landscapes. We specifically chose traits known to influence dispersal success: speed of movement, perceptual range, risk of predation, need to forage during dispersal, and amount of suitable habitat required for successful settlement in a patch. Using the metric of relative dispersal success rate, we assessed how the costs and benefits of evolutionary investment in these biological traits varied with landscape structure. In heterogeneous environments with low habitat availability and scattered habitat patches, individuals with more equal allocation across the trait spectrum dispersed most successfully. Our analyses suggest that the dispersal success of animals in heterogeneous environments is highly dependent on hierarchical interactions between trait trade-offs and the geometric configurations of the habitat patches in the landscapes through which they disperse. In an applied sense, our results indicate potential for ecological mis-alignment between species' evolved suites of dispersal-related traits and altered environmental conditions as a result of rapid global change. In many cases identifying the processes that shape patterns of animal dispersal, and the consequences of abiotic changes for these processes, will require consideration of complex relationships among a range of organism-specific and environmental factors.
Stockholm sequence-structure alignments for 9 Bacteroides sRNAs
<p>Sequence alignment supporting the manuscript "Comparative genomics provides structural and functional insights into Bacteroides RNA biology".</p>
VCF of structural variant calls of Nanopore data aligned to dm6 reference genome
<p>Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of the <em>dl</em>-<em>49</em> <em>chrX</em> inversion in <em>D</em>. <em>melanogaster</em>. We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs are completely suppressed within 500 kb of inversion breakpoints, are severely reduced within 2 Mb of an inversion breakpoint, and increase above wildtype levels 2–4 Mb from the breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, occur at wild-type levels near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break location or frequency. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation.</p>
Data from: Effects of mis-alignment between dispersal traits and landscape structure on dispersal success in fragmented landscapes
Open the record for dataset details and reuse information.
VCF of structural variant calls of Nanopore data aligned to dm6 reference genome
Open the record for dataset details and reuse information.
Presence of Pain Shows Greater Effect Than Tendon Structural Alignment During Landing Dynamics
ClinicalTrials.gov study NCT06829056. IPD Sharing: NO. Countries: 1. Publications: 0.
Bioinspired structural hydrogels with highly ordered hierarchical orientations by flow-induced alignment of nanofibrils
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Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell
GEO Series GSE303560. Candida albicans SC5314. 20 samples. Type: Expression profiling by high throughput sequencing.
Alignments from: Gene lack of expression of embryogenesis related factors correlates with structural reduction in the holoendoparasitic Angiosperm Pilostyles boyacensis (Apodanthaceae)
<p>These files are the alignments used in the work "Gene loss expression in the early embryogenesis network correlates with structural reduction in the holoendoparasitic angiosperm <em>Pilostyles boyacensis </em>(Apodanthaceae)".</p> <p>Nucleotide alignments for the AGO, AP2-ERF, HD-ZIP-III and IV, PIN, RLK-CR4, RLK-RPK2, and WOX gene families. Coding sequences were download from the following databases: TAIR database (Poole, 2007), Phytozome v13) (Goodstein et al., 2012), Cucurbit Genomics Database (Zheng et al., 2019), OneKP database (Carpenter et al., 2019). Also, new data generated for <em>P. boyacensis</em> and deposited in Genbank with the codes OR296323-OR296355.</p> <p>The codes of sequences are in Appendix 1 of "Gene loss expression in the early embryogenesis network correlates with structural reduction in the holoendoparasitic angiosperm <em>Pilostyles boyacensis</em> (Apodanthaceae). The symbol # indicates a numeric or alphanumeric code associated with the gene according to the nomenclature of each base. Alignments were performed using the RevTrans platform (Wernersson and Pedersen, 2003), which translates the sequences into amino acids, aligns them using MAFFT with its automatic parameters, and then generates the corresponding matrix in nucleotides.</p>
Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell [RNA004]
GEO Series GSE304703. synthetic construct. 4 samples. Type: Other.
Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell [nanopore_DRS]
GEO Series GSE304702. Candida albicans; synthetic construct. 35 samples. Type: Other.
Direct RNA sequencing and signal alignment reveal RNA structure ensembles in a eukaryotic cell
GEO Series GSE309111. synthetic construct. 8 samples. Type: Other.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.