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89 results for “FRAGMENT ANALYSIS”
Fig. 2 in Landscape Ecological Analysis Of Taurkalne Forest Tract Fragmentation
Fig. 2. Road network length (km) by category.
PanDDA analysis of NUDT7 screened against DSPL and OxXChem fragment libraries
<p><strong><a href="https://www.thesgc.org/scientists/groups/oxford">SGC Oxford</a> has performed a crystallographic fragment screen on the human peroxisomal coenzyme A diphosphatase NUDT7 (<a href="http://www.uniprot.org/uniprot/P0C024">UniProtKB - P0C024</a>). All structures with clearly identifiable ligands were deposited in the <a href="http://www.wwpdb.org/">Protein Data Bank</a> under Group Deposition ID G_1002045. The final structures and the relevant PanDDA event maps can be found at the <a href="https://www.thesgc.org/fragment-screening">SGC fragment screening website</a>. This work is part of the <a href="https://www.thesgc.org/tep">Target Enabling Package (TEP)</a> program at SGC and the complete TEP for NUDT7 is will also be available on ZENODO shortly.</strong></p> <p> </p> <p><em><strong>Experiment</strong></em></p> <p>Crystals were prepared at the <a href="http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html">XChem </a>facility of the <a href="http://www.diamond.ac.uk">Diamond Light Source</a> (DLS). Briefly, crystals were soaked overnight with two fragment libraries; the Diamond- SGC Poised Library set (Cox et al., 2016) and the <a href="https://xchem.github.io/oxxchem/">OxXChem</a> set with nominal fragment concentrations of 100 mM, with DMSO at 30% v/v. Additionally, a series of follow-up compounds based on an initial fragment hit was synthesized and soaked overnight with nominal compound concentrations of 30 mM, with DMSO at 30% v/v. All datasets were collected at <a href="http://www.diamond.ac.uk/Beamlines/Mx.html">MX beamlines at DLS</a>. Autoprocessed datasets were analysed by Pan-Dataset Density Analysis (PanDDA) (Pearce et al., 2017). All ligands that were clearly identifiable in PanDDA event maps were modelled, refined and deposited into the PDB.</p> <p> </p> <p><em><strong>Content</strong></em></p> <p>This repository contains:</p> <ul> <li>all results from the PanDDA analysis, including ground-state-mean maps and PanDDA event & Z-maps for all ligand bound structures</li> <li>MTZ and AIMLESS logfiles from auto-processing</li> <li>PDB, CIF & PNG files of all the soaked compounds</li> <li>final refine.pdb and refine.mtz filess of all ligand bound structures</li> <li>all data belonging to an individual crystal can be found in <em>processed_datasets/<crystal_ID></em></li> </ul> <p> </p> <p><em><strong>References</strong></em></p> <p>Cox, O. B. et al. A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Chem. Sci. 7, 2322–2330 (2016).</p> <p>Pearce, N. M. et al. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun 8, (2017).</p>
PanDDA analysis of NUDT5 screened against DSPi poised fragment library
<p><strong>A crystallographic fragment screen on the human ADP-sugar pyrophosphatase NUDT5 (UniProtKB - Q9UKK9) has been performed at the Structural Genomics Consortium (SGC). All structures with clearly identifiable ligands were deposited in the <a href="http://www.wwpdb.org/">Protein Data Bank</a> under Group Deposition ID </strong> <strong>G_1002057. The final structures and the relevant PanDDA event maps can be found at the <a href="https://www.thesgc.org/fragment-screening">SGC fragment screening website</a>. </strong></p> <p> </p> <p><em><strong>Experiment</strong></em></p> <p>The experiment has been performed at the XChem facility at the Diamond Light Source. NUDT5 crystals were soaked with concentrated solutions (500 mM) of fragments from DSPi poised fragment library at 10% v/v for 30 minutes. All datasets were collected at I04-1 at DLS. Autoprocessed datasets were analysed by Pan-Dataset Density Analysis (PanDDA) (Pearce et al., 2017). All ligands that were clearly identifiable in PanDDA event maps were modelled, refined and deposited into the PDB.</p> <p> </p> <p><em><strong>Content</strong></em></p> <p>This repository contains:</p> <ul> <li>all results from the PanDDA analysis, including ground-state-mean maps and PanDDA event & Z-maps for all ligand bound structures</li> <li>MTZ and AIMLESS logfiles from auto-processing</li> <li>PDB, CIF & PNG files of all the soaked compounds</li> <li>final refine.pdb and refine.mtz filess of all ligand bound structures</li> <li>all data belonging to an individual crystal can be found in <em>processed_datasets/<crystal_ID</em></li> </ul> <p><em><strong>References</strong></em></p> <p>Cox, O. B. et al. A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Chem. Sci. 7, 2322–2330 (2016).</p> <p>Pearce, N. M. et al. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun 8, (2017).</p>
PanDDA analysis of DCP2B screened against DSPL/DSi Poised, OxXChem fragment libraries and initial follow up chemistry
<p><strong><a href="https://www.thesgc.org/scientists/groups/oxford">SGC Oxford</a> has performed a crystallographic fragment screen, and initial follow up chemistry on the </strong><strong>Human m7GpppN-mRNA Hydrolase (DCP2/NUDT20, <a href="https://www.uniprot.org/uniprot/Q8IU60">UniProtKB - QIU60</a>). All structures with clearly identifiable ligands were deposited in the <a href="http://www.wwpdb.org/">Protein Data Bank</a> under Group Deposition ID G_1002061, the corresponding apo structures are deposited under Group Deposition ID G_1002062. </strong></p> <p><em><strong>Experiment</strong></em></p> <p>Crystals were prepared at the <a href="http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html">XChem </a>facility of the <a href="http://www.diamond.ac.uk">Diamond Light Source</a> (DLS). Briefly, crystals were soaked overnight with two fragment libraries; the Diamond- SGC Poised Library set (Cox et al., 2016) and the <a href="https://xchem.github.io/oxxchem/">OxXChem</a> set with nominal fragment concentrations of 100 mM, with DMSO at 20% v/v. Additionally, a series of follow-up compounds based on an initial fragment hit was synthesized and soaked overnight with nominal compound concentrations of 10-200 mM, with DMSO at 20% v/v. All datasets were collected at <a href="http://www.diamond.ac.uk/Beamlines/Mx.html">MX beamlines at DLS</a>. Autoprocessed datasets were analysed by Pan-Dataset Density Analysis (PanDDA) (Pearce et al., 2017). All ligands that were clearly identifiable in PanDDA event maps were modelled, refined and deposited into the PDB.</p> <p><em><strong>Content</strong></em></p> <p>This repository contains:</p> <p><em><strong>Modelled Data</strong></em></p> <ul> <li>Organised by crystal identifier, each folder contains: <ul> <li>Autoprocessing data from Diamond Light Source automated pipelines (including MTZ)</li> <li>PDB, CIF & PNG files of all the soaked compounds</li> <li>PanDDA event maps</li> <li>Final refine.pdb and refine.mtz files of all ligand bound structure <ul> <li>Superposed structures (refine.pdb)</li> <li>Separated bound & ground states (refine.split.bound.pdb & refine.split.ground.pdb)</li> </ul> </li> </ul> </li> </ul> <p><em><strong>PanDDA Analysis Data</strong></em></p> <ul> <li>This is split into two directories. This split is only due to technical limitations at the time of preparation of the data, and the timeliness of the data. <ul> <li>All results from the PanDDA analysis, including ground-state-mean maps and PanDDA event & Z-maps for all ligand bound structures. </li> </ul> </li> </ul>
PanDDA analysis of PTP1B re-screened against fragment libraries at RT
<p>PTP1B re-screened against multiple fragment libraries with RT crystallography</p>
Tropical bat ectoparasitism in continuous versus fragmented forests: A gap analysis and preliminary meta-analysis
<p><span>Tropical regions are experiencing rapid rates of forest fragmentation, which can have several effects on wildlife, including altered parasite dynamics. Bats are a useful host group to consider these effects of fragmentation because they are abundant in the tropics, serve important ecological roles, and harbour many parasites. Nevertheless, research on the effects of fragmentation on bat ectoparasites is still limited. To help guide ongoing and future research efforts, this study had two objectives: (1) conduct a gap analysis to characterize the state of currently available research on fragmentation effects on bat ectoparasites, and (2) conduct a preliminary meta-analysis to identify current trends. We systematically highlighted several research gaps: studies comparing the effects of fragmented versus continuous forests on ectoparasites are limited and have primarily been conducted in the Neotropics, with a focus on bats in the superfamily Noctilionidea (especially frugivorous phyllostomids). Our preliminary meta-analysis suggested that ectoparasite prevalence (but not the mean or variance in intensity) was higher in fragments than in continuous forests. Moreover, prevalence increased with increasing roost duration, and mean intensity was higher for bats with higher wing aspect ratios. Intensity variance was affected by an interaction between forest type and wing aspect ratio, such that variance increased for bats with high wing aspect ratios in continuous forests but decreased in fragments. These results suggest that fragmentation can shape aspects of bat ectoparasitism and could have implications for the ecology, health, and conservation of bats in fragmented landscapes. However, existing research gaps could bias our current understanding of habitat change and bat health, and future research should thus investigate these effects in the Paleotropics and with other bat families. </span><span><br></span></p>
Tropical bat ectoparasitism in continuous versus fragmented forests: A gap analysis and preliminary meta-analysis
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K.107 Fragment of Práḥ Thãt Khnai Van : Transcription, translation and analysis
<p><a href="https://siddham.network/inscription/k107/">K.107</a> Fragment of Práḥ Thãt Khnai Van : Transcription, translation and analysis</p> <p><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Inscriptions+--+Cambodia">Inscriptions -- Cambodia</a><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Inscriptions.">Inscriptions. </a><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Cambodia.">Cambodia. </a></p> <p> </p>
Multiscale analysis of canopy arthropod diversity in a volcanically fragmented landscape
<p><strong>Dataset and code associated with the article "Multiscale analysis of canopy arthropod diversity in a volcanically fragmented landscape" (Tielens et al 2019, Ecosphere).</strong></p> <p><strong>Article abstract:</strong></p> <p>Habitat fragmentation resulting in habitat loss and increased isolation is a dominant driver of global species declines. Habitat isolation and connectivity vary across scales, and understanding how con- nectivity affects biodiversity can be challenging because the relevant scale depends on the taxa involved. A multiscale analysis can provide insight in biodiversity patterns across spatial scale when information on dispersal ability is not available, in particular for community-level studies focusing on multiple taxa. In this study, we examine the relationship between arthropod diversity, patch area, and connectivity using a mul- tiscale approach. We make use of a natural experiment on Hawai'i Island, where historic volcanic activity has transformed contiguous native forests to lava matrix and discrete forest patches. This landscape of patches has persisted for 150 yr, and we selected 10,000 ha consisting of 863 patches to analyze landscape connectivity using a graph theory approach. We collected arthropod samples from Metrosideros polymor- pha tree canopies in 34 forest patches during multiple years. We analyzed the relationship of arthropod diversity with area, as well as with connectivity across increasing scales, or dispersal threshold distances. In contrast to well-established ecological theory as well as prior work on birds and fungi in this system, we did not find support for a canonical species–area relationship. Next, we calculated connectivity across spa- tial scales and found lower Shannon diversity with higher connectivity at small scales, but no effect at increased dispersal threshold distances. We examined the landscape structure and found all habitat patches connected into three subnetworks at a 350 m threshold distance. All patches were connected at 700 m threshold distance, indicating structural dispersal limitation only at small scales. Our findings sug- gest that canopy arthropods are not dispersal limited at scales shown to impact both soil fungi and birds in this system. Instead, Hawaiian canopy arthropods may perceive the landscape as a connected area where discrete forest patches and the early-successional matrix contribute resources that vary spatially with regard to habitat quality. We argue for the utility of multiscale approaches, and the importance of examin- ing maintenance of biodiversity in fragmented landscapes that persist for hundreds of years.</p>
Data from: Comparative analysis of adaptive and neutral markers of Drosophila mediopunctata populations dispersed among forest fragments
Comparison of adaptive and neutral genetic markers is a valuable approach to characterize the evolutionary consequences of populations living in environments threatened by anthropogenic disturbances, such as forest fragmentation. Shifts in allele frequencies, low genetic variability, and a small effective population size can be considered clear signs of forest fragmentation effects (due to genetic drift) over natural populations, while adaptive responses correlate with environmental variables. Brazilian Atlantic Forest had its landscape drastically reduced and fragmented. Now, several forest remnants are isolated from each other by urban and crop areas. We sampled Drosophila mediopunctata populations from eight forest remnants dispersed on two adjacent geomorphological regions, which are physiognomic and climatically quite distinct. Microsatellite data of inversion‐free chromosomes (neutral genetic marker) indicate low structuration among populations suggesting that they were panmictic and greatly influenced by gene flow. Moreover, significant differences in chromosomal inversion frequencies (adaptive genetic marker) among populations and their correlations with climatic and geographical variables indicate that genetic divergence among populations could be an adaptive response to their environment. Nonetheless, we observed a significant difference in inversion frequencies of a population in two consecutive years that may be associated with edge and demographic effects. Also, it may be reflecting seasonal changes of inversion frequencies influenced by great temperature variation due to edge effects. Moreover, the forest fragment size does not affect genetic variation of neutral markers. Our data indicate that despite oscillations in chromosomal inversion frequencies, D. mediopunctata populations from Brazilian Atlantic Forest and their divergence may be driven by adaptive factors to local differences, perhaps because it is a small flying insect easily carried by the wind increasing its migration rates.
PanDDA analysis of JMJD2D screened against Zenobia Fragment Library
<p>De-methylase JMJD2D screened against the Zenobia Fragment Library by X-ray Crystallography.</p>
PanDDA analysis of BAZ2B screened against Zenobia Fragment Library
<p>Bromodomain BAZ2B screened against the Zenobia Fragment Library by X-ray Crystallography.</p>
Limited proteolysis fragments of full-length huntingtin with chymotrypsin – mass spectrometry analysis (2016/04/21)
<p>Open lab note book for huntingtin structure function project</p>
A new distal fibular fragment of Homo floresiensis and the first quantitative comparative analysis of proximal and distal fibular morphology in this species
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FIGURE. Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, ex-neotype, or reference strain). in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, ex-neotype, or reference strain).
FIGURE. (Continued) Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, exneotype, or reference strain). in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. (Continued) Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, exneotype, or reference strain).
PanDDA analysis of ligand screen against the NSP3 macrodomain of SARS-CoV-2: ligands from FrankenROCS fragment-linking pipeline and subsequent optimization of AVI-313
<p>This deposition contains the X-ray diffraction data used to run PanDDA in the ligand screen against the NSP3 macrodomain of SARS-CoV-2 described in Correy et al. 2024 (doi: https://doi.org/10.1101/2024.08.25.609621). Compounds were from fragment linking using FrankenROCS and subsequent optimization of AVI-313. </p> <p>frankenROCS_mac1.tar.gz contains structure factor intensities, PanDDA input/output and refined models/maps.</p> <p>frankenROCS_mac1_ligand-bound-states.tar.gz contains the ligand-bound states extracted from the multi-state PDB files.</p>
Data from: Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system
Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important role in the maintenance of these populations. A haploweb analysis of ITS2 sequences of each MLG was consistent with all of them being conspecific. Genetic differentiation was detected both between and within islands, but when a single sample per MLG was included in the analyses, the populations turned out to be nearly panmictic. These observations provide further evidence of the marked variability in reproductive strategies and genetic structure of P. damicornis throughout its geographic range; comparison with results previously obtained for the congeneric species Pocillopora meandrina underlines the importance of life history traits in shaping the genetic structure of coral populations.
Data from: Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing
High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data.
Data from: Patterns and predictors of β-diversity in the fragmented Brazilian Atlantic forest: a multiscale analysis of forest specialist and generalist birds
1. Biodiversity maintenance in human-altered landscapes (HALs) depends on the species turnover among localities, but the patterns and determinants of β-diversity in HALs are poorly known. In fact, declines, increases, and neutral shifts in β-diversity have all been documented, depending on the landscape, ecological group and spatial scale of analysis. 2. We shed some light on this controversy by assessing the patterns and predictors of bird β-diversity across multiple spatial scales considering forest specialist and habitat generalist bird assemblages. 3. We surveyed birds from 144 point counts in 36 different forest sites across two landscapes with different amount of forest cover in the Brazilian Atlantic forest. We analysed β-diversity among points, among sites, and between landscapes with multiplicative diversity partitioning of Hill numbers. We tested whether β-diversity among points was related to within-site variations in vegetation structure, and if β-diversity among sites was related to site location and/or to differences among sites in vegetation structure and landscape composition (i.e. percent forest and pasture cover surrounding each site). 4. β-diversity between landscapes was lower than among sites and among points in both bird assemblages. In forest specialist birds, the landscape with less forest cover showed the highest β-diversity among sites (bird differentiation among sites), but generalist birds showed the opposite pattern. At the local scale, however, the less forested landscape showed the lowest β-diversity among points (bird homogenisation within sites), independently of the bird assemblage. β-diversity among points was weakly related to vegetation structure, but higher β-diversity values were recorded among sites that were more isolated from each other, and among sites with higher differences in landscape composition, particularly in the less forested landscape. 5. Our findings indicate that patterns of bird β-diversity vary across scales and are strongly related to landscape composition. Bird assemblages are shaped by both environmental filtering and dispersal limitation, particularly in less forested landscapes. Conservation and management strategies should therefore prevent deforestation in this biodiversity hotspot.
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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.