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666 results for “translocation”
ERK KTR translocation after pulsatile optoFGFR stimulation. Dataset for Nalecz-Jawecki et al.
<p>Quantified microscopic data: Single cell measurements of ERK activity reporter (ERK KTR) translocation after stimulation of optoFGFR with 100 ms blue (470 nm) light pulses in random points of time. Dataset used in Nałęcz-Jawecki et al. to quantify information transmission rate throught the MAPK/ERK pathway. Preprint available at BioArxiv: https://doi.org/10.1101/2022.03.17.484713.</p> <p>UPDATE: v1.1 contains one experiment file mising in v1.0</p>
Input Files for Peptide Translocation Across Phospholipid Membranes Using Various Collective Variables and Martini Coarse-Grained Simulations
<p>Input files for publication: Ivo Kabelka, Radim Brožek, and Robert Vácha: Selecting Collective Variables and Free Energy Methods for Peptide Translocation Across Membranes, Journal of Chemical Information and Modeling, submitted</p>
Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish
<p>Variation in the composition of skin-associated microbiomes has been attributed to host species, geographic location, and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (<em>Cyprinus</em> <em>carpio</em>) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch, and growth, but not temperature gain while basking, sex, personality, or colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared to the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organisation (richness and composition of fish-associated microbial communities).</p>
Unravelling the mystery of endemic versus translocated populations of the endangered Australian lungfish (Neoceratodus forsteri)
<p><strong>RADseq dataset of the Australian lungfish (</strong><em><strong>Neoceratodus forsteri).</strong></em></p> <p>The dataset is constituted of 100 samples and 5,196 nuclear SNPs. There are five populations each with 20 samples. IDs: BUR (Burnett River), MRY (Mary River), TIN (Tinana River), NPD (North Pine River), BNE (Brisbane River).</p> <p>The dataset is in VCF format.</p> <p> </p> <p><strong>Scripts for statistical calculations and demographic simulations.</strong></p>
Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers
<p>Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start-sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and 2-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/sec for surprising distances on extended linear DNA. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.</p>
Data from: Feather corticosterone is lower in translocated and historical populations of the endangered Laysan duck (Anas laysanensis)
<p>Identifying reliable bioindicators of population status is a central goal of conservation physiology. Physiological stress measures are often used as metrics of individual health and can assist in managing endangered species if linked to fitness traits. We analysed feather corticosterone, a cumulative physiological stress metric, of individuals from historical, translocated, and source populations of an endangered endemic Hawaiian bird, the Laysan duck (<em>Anas laysanensis</em>). We hypothesised that feather corticosterone would reflect the improved reproduction and survival rates observed in populations translocated to Midway and Kure Atolls from Laysan Island. We also predicted less physiological stress in historical Laysan birds collected before ecological conditions deteriorated and the population bottleneck. All hypotheses were supported: we found lower feather corticosterone in the translocated populations and historical samples than in those from recent Laysan samples. This suggests that current Laysan birds are experiencing greater physiological stress than historical Laysan and recently translocated birds. Our initial analysis suggests that feather corticosterone may be an indicator of population status and could be used as a non-invasive physiological monitoring tool for this species with further validation. Furthermore, these preliminary results, combined with published demographic data, suggest that current Laysan conditions may not be optimal for this species.</p>
Using species distribution models and decision tools to direct surveys and identify potential translocation sites for a critically endangered species
<p>Aim: Occurrence records for cryptic species are typically limited or highly uncertain, leaving their distributions poorly resolved and hampering conservation. This can apply to well‐studied species, and increased survey effort and/or novel methods are required to improve distribution data. Here, we paired species distribution modelling (SDM) with decision tools to direct surveys for the critically endangered Leadbeater's possum (Gymnobelideus leadbeateri) outside its current restricted range. We also assessed survey areas for their suitability to host translocations.</p> <p>Location: Victoria, Australia.</p> <p>Method: We used both recent and historic records (now out of range and spatially uncertain) of Leadbeater's possum to build SDMs using MaxEnt. The SDMs informed an initial multi‐criteria decision analysis (MCDA) that enabled prioritization of 80 survey sites across seven forest patches (13–145 km outside the known range), which we surveyed using camera traps. Site and vegetation data were used in a post‐survey MCDA to rank their potential translocation suitability.</p> <p>Results: The SDM predictions were consistent with the species' ecology, identifying cold areas with high rainfall that had not recently burnt as suitable. The spatial uncertainty of records did not exert a strong influence on either model predictions or the ranking of patches for surveys. Camera trap surveys yielded records of 19 native species, with Leadbeater's possum detected in only one survey patch, 13 km outside of its previously known range. The post‐survey MCDA identified three forest patches as potentially suitable for conservation translocations, and these priorities were not sensitive to the decision criteria used.</p> <p>Main conclusions: The approach outlined here prioritized survey effort over a large area, resulting in detection of Leadbeater's possum in one new patch. The potential translocation sites identified could present an important risk‐spreading measure for the species given the threat posed by bushfire. Combining SDMs and decision tools can help target surveys and guide subsequent conservation strategies.</p>
Predicting harvest impact and establishment success when translocating highly mobile and endangered species
<p>Harvesting individuals for translocations can negatively impact source populations, a critical challenge for species reduced to small populations. Consequently, translocation cohorts often remain small, reducing the establishment probability at the destination. Balancing the potential benefits and risks of such translocations is further complicated by philopatry and natural metapopulation dynamics if the target species is highly mobile. These challenges highlight the importance of translocation feasibility assessments, but such assessments often remain qualitative to date. The critically endangered Kuaka (Whenua Hou Diving Petrel; Pelecanoides whenuahouensis) is a philopatric, highly mobile seabird that could benefit from conservation translocations, but only one small population remains. Through expert elicitations with a user-friendly Shiny app, we developed a novel metapopulation extension to an integrated population model fitted to long-term data, allowing us to simultaneously project harvest impact on the source and establishment of destination populations under alternative translocation scenarios, while accounting for philopatry and metapopulation dynamics. Establishment of a destination population without excessive impact on the source was possible, but subject to uncertainty about philopatry and metapopulation dynamics. Accounting for juveniles returning to the source post-translocations reduced impact on the source, but also decreased establishment at the destination. Natural movements of adults and juveniles between source and destination populations were predicted to modulate effects of different harvest intensities. Synthesis and application: Using state-of-the art integrated population models and expert elicitations, we illustrate how translocation feasibility can be evaluated transparently and quantitatively, even when targeting endangered, philopatric, and highly mobile species. Our approach is a considerable improvement on current qualitative feasibility assessments. However, we also illustrate that, ultimately, the favoured translocation strategy depends on balancing biological and other fundamental objectives inherent to translocations. Therefore, the ideal strategy cannot be determined solely mathematically, and feasibility assessments should incorporate explicit value statements. Our methodology is applicable to any future translocation scenario.</p>
Figure 3 in Intraspecific variation in Gyrodactylus mediotorus and G. crysoleucas (Gyrodactylidae) from Nearctic shiners (Leuciscidae): evidence for ongoing speciation, host-switching, and parasite translocation
Figure 3. Bayesian inference (BI) phylogram of Gyrodactylus spp. parasitizing Nearctic Cypriniformes based on sequences of the ITS regions (927 bp). Values above branches indicate posterior probabilities (PP) from BI analyses and bootstrap support (BS) from ML. Values below 0.80 (BI) and 70 (ML) are shown as dashes.
Figure 2 in Intraspecific variation in Gyrodactylus mediotorus and G. crysoleucas (Gyrodactylidae) from Nearctic shiners (Leuciscidae): evidence for ongoing speciation, host-switching, and parasite translocation
Figure 2. Photomicrographs (A–C) and line drawings (B–D) of Gyrodactylus mediotorus King, Marcogliese, Forest, McLaughlin and Bentzen, 2013 from the blacktail shiner, Cyprinella venusta (A–B) and from the sand shiner, Notropis cf. stramineus (Guadalupe River) (C–D).
Figure 1 in Intraspecific variation in Gyrodactylus mediotorus and G. crysoleucas (Gyrodactylidae) from Nearctic shiners (Leuciscidae): evidence for ongoing speciation, host-switching, and parasite translocation
Figure 1. Photomicrographs (A) and line drawings (B) of Gyrodactylus crysoleucas from the blacktail shiner, Cyprinella venusta.
colorSV translocation call sets on COLO829 and HCC1395
<p>Translocation call sets generated by colorSV (v0.1.0) on the COLO829 and HCC1395 cell lines as described in the <a href="https://doi.org/10.1101/2024.07.29.605160">colorSV paper</a>.</p>
Fig. 7 in Altered parasite community structure in an endangered marsupial following translocation
Fig. 7. Mean trypanosome prevalence over time (with 95% CI) in translocated and resident woylies within Dryandra. TRAN: time of translocation.
Fig. 6 in Altered parasite community structure in an endangered marsupial following translocation
Fig. 6. Non-metric multidimensional scaling plots showing convergence of parasite community composition in translocated (TYPE T) and resident (TYPE R) woylie groups following translocation. Boxes on the left depict both groups at all time points prior to and including the point of translocation; boxes on the right depict both groups six months after translocation.
Fig. 5 in Altered parasite community structure in an endangered marsupial following translocation
Fig. 5. Overall parasite infracommunity richness in (A) translocated and (B) resident woylies over time. TRAN: time of translocation; Error bars represent one standard error.
Fig. 2 in Altered parasite community structure in an endangered marsupial following translocation
Fig. 2. The overall effect of site on mean faecal egg counts (above solid line) and parasite prevalence (below solid horizontal line) for each parasite taxon in (A) translocated and (B) resident woylies. Error bars represent 95% CI.
Fig. 3 in Altered parasite community structure in an endangered marsupial following translocation
Fig. 3. The effect of time since translocation (model coefficients for all sites combined) on mean faecal egg counts (above solid horizontal line) and parasite prevalence (below solid horizontal line) for each parasite taxon in translocated and resident woylies. Left of the dashed vertical line indicates a negative effect, right of the line indicates a positive effect; Error bars represent 95% CI.
Fig. 4 in Altered parasite community structure in an endangered marsupial following translocation
Fig. 4. Significant changes to mean strongyle egg counts (A) and flea prevalence (B) over time. TRAN: time of translocation; Boxplots (A) are delimited by the first (lower) and third (upper) quartile with the median represented by the thick horizontal line; whiskers represent the 1.5 interquartile range; solid black dots represent outliers; Error bars (B) represent 95% CI.
Fig. 1 in Altered parasite community structure in an endangered marsupial following translocation
Fig. 1. Map (from Northover et al., 2019) illustrating the study sites within south-western Australia, including Walcott and Warrup East in relation to Perup Sanctuary (box, right), and Dryandra, situated roughly 250 km north-east of the Upper Warren region.
Fig. 1. A in Translocation a potential corridor for equine piroplasms in Cape mountain zebra (Equus zebra zebra)
Fig. 1. A map of south-western South Africa, showing the localities of the 3 reserves from which samples were obtained (black circles) namely Mountain Zebra National Park (MZNP), De Hoop Nature Reserve (DHNR) and Karoo National Park (KNP). The grey diamonds show other known municipal nature reserves and national parks which contain Cape Mountain zebra sourced from Cradock, Eastern Cape, South Africa.
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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.