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321 results for “Xenopus”
Supporting data for "Unveiling Vertebrate Development Dynamics in Frog Xenopus laevis using Micro-CT Imaging"
<p>The dataset contains X-ray Micro Computed Tomography data of Xenopus laevis frog. There are twenty datasets of ten individual animals. Each animal was CT scanned twice – once as a native scan to visualize the hard tissues, and once contrast-stained to visualize the soft tissues. The datasets include nine developmental stages (NF44-45, NF52, NF53, NF54, NF57, NF59, NF62, NF66 and adult). There are two adults, one male and one female. The CT data (in 8bit .tiff format compressed as .tar.gz files) are supported by .stl files created from each dataset. The database also includes .stl files of selected structures of interest (body, skeleton, skull, brain and guts of individual animals).</p>
Data to "The olfactory network of larval Xenopus laevis regenerates accurately after olfactory nerve transection"
<p>This record contains analysis scripts (written in Matlab) as well as raw and processed data to reproduce the results shown in:</p> <p>Hawkins S. J., Gärtner Y., Offner T., Weiss L., Maiello G., Hassenklöver T., and Manzini I. (under review) The olfactory network of larval <em>Xenopus laevis</em> regenerates accurately after olfactory nerve transection. </p>
Gene-level counts according to their poly(A) length and additional uridine modifications in several stages of zebrafish, Xenopus, and mouse embryos
<p>This HDF5 file contains the processed data of primary poly(A) tail length analyses for the TAIL-seq runs used for Chang and Yeo et al. (2018; doi:10.1016/j.molcel.2018.03.004). The read count tables are stored under the two-level group structure of the run identifier as the first level and the sample identifier as the second level. A dataset at a leaf node is an unsigned integer array of the read count numbers by the length of poly(A) in rows and the length of U tails following after poly(A) in columns.</p> <p>Please refer to the <a href="https://data.mendeley.com/datasets/tzc5wwczyg/1">supplementary data page</a> of the original paper for more information about the experimental design.</p> <p> </p>
Xenopus tissue data for testing segmentation models
<pre>This dataset is of xenopus tissue imaged with the following settings and it comes with a trained UNET model for performing the segmentation of such tissues. In order to use the segmentation model please install the vollseg-napari plugin from the napari hub and the model will be automatically downloaded for usage. Dataset was acquired by Mari Tolonen and Jakub Sedzinski, (0000-0002-4395-9022,0000-0002-1788-0329) at the university of Copenhagen and the model was trained by Varun Kapoor at Kapoorlabs. A Z projection of 21 Z slices acquired by the ImageJ Z Projection plugin was performed on the original acquired data. ObjectiveSettings ID="Objective:0" Medium="Water" RefractiveIndex="1.333"</pre> <pre>LensNA="1.2000000000000002" Model="C-Apochromat 40x/1.2 W AutoCorr M27" NominalMagnification="40.0"</pre> <pre>Physical Size X="0.6918881841365326" Physical Size X Unit="µm" </pre> <pre>Physical Size Y="0.6918881841365326" Physical Size Y Unit="µm" </pre> <pre>Physical Size Z="2.0" Physical Size Z Unit="µm"</pre> <pre>Time interval frames 1-160: 182 sec Time interval frames 161-262: 283 sec</pre> <pre>SignificantBits="8" Type="uint8"></pre> <pre>Channel AcquisitionMode="LaserScanningConfocalMicroscopy" ExcitationWavelength="488.0" ExcitationWavelengthUnit="nm" Fluor="EGFP"</pre>
Fig. 4 in Breeding and rearing the Critically Endangered Lake Oku Clawed Frog (Xenopus longipes Loumont and Kobel 1991)
Fig. 4. Monthly water temperatures (circles) and pH (triangles) recorded from the shoreline of Lake Oku between 2008/2009 and 2013. Error bars represent SEM.
Fig. 1 in Breeding and rearing the Critically Endangered Lake Oku Clawed Frog (Xenopus longipes Loumont and Kobel 1991)
Fig. 1. Male (top) and female (bottom) adults of Xenopus longipes in the collection at ZSL London Zoo (ZIMS ID 7441).
Fig. 3. Aquarium for X. longipes, set within a in Breeding and rearing the Critically Endangered Lake Oku Clawed Frog (Xenopus longipes Loumont and Kobel 1991)
Fig. 3. Aquarium for X. longipes, set within a custom built, centrally filtered system (inset photograph) at ZSL London Zoo. Life support system and sump not shown – see text for details.
Fig. 2 in Breeding and rearing the Critically Endangered Lake Oku Clawed Frog (Xenopus longipes Loumont and Kobel 1991)
Fig. 2. Keratinized nuptial pads on the inside surfaces of the front limbs of male (A and C) and cloaca of a female X. longipes (B); note the cloacal papillae, which are absent in male frogs.
Fig. 5 in Breeding and rearing the Critically Endangered Lake Oku Clawed Frog (Xenopus longipes Loumont and Kobel 1991)
Fig. 5. Gosner stage progression of the most rapidly developing X. longipes tadpole. Hatching to metamorphosis took 193 days, but smaller tadpoles had only reached stage 35 by this point.
Tracking cells in Xenopus tissue with TrackMate-MorphoLibJ
<p>Tracking cells in Xenopus tissue with TrackMate-MorphoLibJ.</p> <p>For more details see https://imagej.net/plugins/trackmate/trackmate-morpholibj</p> <p>Image courtesy of Jakub Sedzinski.</p> <p> </p> <p> </p>
Data from: Dynamic effects of thermal acclimation on chytridiomycosis infection intensity and transmission potential in Xenopus laevis
Open the record for dataset details and reuse information.
Monitoring the compaction of single DNA molecules in Xenopus egg extract in real time
Open the record for dataset details and reuse information.
Does the spatial sorting of dispersal traits affect the phenotype of the non-dispersing stages of the invasive frog Xenopus laevis through coupling?
<p>Over ten weeks, we surveyed the development of <em>X. laevis</em> tadpoles in the French invasive range by conducting experiments in outdoor mesocosms and in laboratory microcosms, from free-swimming larvae to metamorphosis. We tested the effect of the location of the parental pond in the colonised range (core or periphery) on morphological traits related to dispersal (SVL and hind limb length), time to metamorphosis (development) and survival to metamorphosis. This excel spreadsheet contains the metadata and data spreadsheets used in the analysis. In addition to the first metadata sheet, the file contains nine additional sheets each containing data used in the separate analysis as outlined in the manuscript. </p>
Thyroid hormone induces DNA demethylation in Xenopus tadpole brain
<p>Thyroid hormone (T3) plays pivotal roles in vertebrate development, acting via nuclear receptors (TRs) that regulate gene transcription by promoting posttranslational modifications to histones. Methylation of cytosine residues in DNA also modulates gene transcription, and our recent finding of predominant DNA demethylation in the brain of Xenopus tadpoles at metamorphosis, a T3-dependent developmental process, caused us to hypothesize that T3 induces these changes in vivo. Treatment of pre-metamorphic tadpoles with T3 for 24 or 48 hr increased immunoreactivity in several brain regions for the DNA demethylation intermediates 5-hydroxymethylcytosine (5-hmC) and 5-carboxylcytosine, and the methylcytosine dioxygenase ten-eleven translocation 3 (TET3). Thyroid hormone treatment induced locus-specific DNA demethylation in proximity to known T3 response elements within the DNA methyltransferase 3a and Krüppel-like factor 9 genes, analyzed by 5-hmC immunoprecipitation and methylation sensitive restriction enzyme digest. Chromatin-immunoprecipitation (ChIP) assay showed that T3 induced TET3 recruitment to these loci. Furthermore, the mRNAs for several genes encoding DNA demethylation enzymes were induced by T3 in a time-dependent manner in tadpole brain. A TR ChIP-sequencing experiment identified putative TR binding sites at several of these genes, and we provide multiple lines of evidence to support that tet2 contains a bona fide T3 response element. Our findings show that T3 can promote DNA demethylation in developing tadpole brain, in part by promoting TET3 recruitment to discrete genomic regions, and by inducing genes that encode DNA demethylation enzymes.</p>
Figure 10. Lepidepecreoides xenopus K.H in The Lysianassoid Amphipod Genera Lepidepecreoides and Lepidepecreum in Southern Waters (Crustacea: Lysianassidae: Tryphosinae)
Figure 10. Lepidepecreoides xenopus K.H. Barnard. Whole figure: paratype
Data for: New insights into Xenopus sex chromosome genomics from the Marsabit clawed frog, X. borealis
<p><span>In many groups, sex chromosomes change frequently but the drivers of their rapid evolution are varied and often poorly characterized. With an aim of further understanding sex chromosome turnover, we investigated the polymorphic sex chromosomes of the Marsabit clawed frog, <em>Xenopus borealis,</em> using genomic data and a new chromosome-scale genome assembly. We confirmed previous findings that 54.1 Mb of chromosome 8L is sex-linked in animals from east Kenya and a lab strain, but most (or all) of this region is not sex-linked in natural populations from west Kenya. Previous work suggests possible degeneration of the Z chromosomes in the east population because many sex-linked transcripts of this female heterogametic population have female-biased expression, and we therefore expected this chromosome to not be present in the west population. In contrast, our simulations support a model where the sex-linked portion of the Z chromosome from the east acquired autosomal segregation in the west, and where the W chromosome from the east was lost in the west. These recent changes are consistent with the hot potato model, wherein sex chromosome turnover is favoured by natural selection if it purges a (minimally) degenerate sex-specific sex chromosome, but counterintuitively suggest natural selection failed to purge a Z chromosome that has signs of more advanced and possibly more ancient regulatory degeneration. These findings highlight complex evolutionary dynamics of young, rapidly evolving <em>Xenopus</em> sex chromosomes, and set the stage for mechanistic work aimed at pinpointing additional sex-determining genes in this group.</span></p>
Observations of invertebrate predation on Xenopus mellotropicalis frogs.
<p>We report here for the first time our observations of predation events on <em>Xenopus mellotropicalis</em> frogs that illustrate the diversity of predators for that species.</p>
TAIL-seq for Xenopus laevis oocytes and embryos in various conditions (internal ID: ms97)
<p>This dataset contains the raw sequencing data from a TAIL-seq run for Xenopus laevis embryos. The cluster intensities of fluorescence signals are repacked as an HDF5 formatted file, then split into multiple parts to fit in the dataset size limitation of the Zenodo.</p>
Electrophysiological data from five species of Xenopus
<p>Across phyla, species-specific vocalizations are used by males to attract females. Functional analyses of the neural circuitry underlying behavior have been difficult, particularly in vertebrates. However, using an ex vivo brain preparation that produces fictive vocalizations, we previously identified anatomically distinct fast and slow central pattern generators (CPGs) that drive the fast and slow clicks of male courtship calls in male African clawed frogs, <em>Xenopus laevis</em>. To gain insight into the evolution of neural circuits underlying courtship calls, we extended this approach to four additional species. Here, we show that although the exact rate and duration of the clicks are unique to each species, fast and slow CPGs identified in male <em>X. laevis</em> are conserved across species. Further, we show that the development of fast CPGs depends on testosterone in a species-specific manner: testosterone facilitates the development of fast CPGs in a species with a courtship call containing fast clicks, but not in a species with a courtship call made entirely of slow clicks. Finally, we showed that, unlike other vestigial neural circuits that remain latent, the fast CPGs are not inherited by all species; rather, they are possessed only by the species that produce fast clicks. The results suggest that species-specific calls of the genus <em>Xenopus</em> have evolved by utilizing conserved fast or slow CPGs that are broadly tuned to generate fast or slow trains of clicks, the development of which appear to be regulated by a strategic expression of testosterone receptors in the brain of each species. </p>
Data from: Lower jaw modularity in the African Clawed Frog (Xenopus laevis) and Fire Salamander (Salamandra salamandra gigliolii)
<p>Modularity describes the degree to which the components of complex phenotypes vary semi-autonomously due to developmental, genetic, and functional correlations. This is a key feature underlying the potential for evolvability, as it can allow individual components to respond to different selective pressures semi-independently. The vertebrate lower jaw has become a model anatomical system for understanding modularity, but to date, most of this work has focused on the mandible of mammals and other amniotes. In contrast, modularity in the mandible of lissamphibians has been less well-studied. Here, we used geometric morphometrics to quantify the static (intraspecific) modularity patterns in <em>Xenopus laevis</em> and <em>Salamandra salamandra gigliolii.</em> We tested developmental and functional hypotheses of modularity and demonstrate that both species exhibit significant modularity. Functional modularity was supported in <em>Xenopus</em>, yet the lack of definitive support for both the developmental and functional hypotheses in <em>Salamandra</em> suggests influences on modularity are much more complex. Allometry has a small yet significant impact on lower jaw shape in both taxa and sex has a significant effect on shape in <em>Xenopus</em>. The high modularity seen in both species mimics the results of other studies on the amphibian cranium, suggesting that modularity is a ubiquitous feature of the tetrapod jaw.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.