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2,137 results for “wild-type”
Paternal effects in a wild-type zebrafish implicate a role of sperm-derived small RNAs
<p>While the importance of maternal effects has long been appreciated, a growing body of evidence now points to the paternal environment having an important influence on offspring phenotype. Indeed, research on rodent models suggests that paternal stress leaves an imprint on the behaviour and physiology of offspring via non-genetic information carried in the spermatozoa, however fish have been understudied with regard to these sperm-mediated effects. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors (conspecific-derived alarm cue, chasing, and bright light) before mating and assessing the behavioural and endocrine responses of their offspring, including their behavioural response to conspecific-derived alarm cue. We found that after males are exposed to stress, their larval offspring show weakened responses to stressors. Small RNA sequencing subsequently revealed that the levels of several small noncoding RNAs, including microRNAs, PIWI-interacting RNAs, and tRNA-derived small RNAs, were altered in the spermatozoa of stressed fathers, suggesting that stress-induced alterations to the spermatozoal RNA landscape may contribute to shaping offspring phenotype. The work demonstrates that paternal stress should not be overlooked as a source of phenotypic variation and that spermatozoal small RNAs may be important intergenerational messengers in fish.</p>
Cofactor specificity of the tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter oxydans: Studies of wild-type and mutants forms.
<p>Here we present the results regarding the characterization of the kinetics parameters for NAD and NADP of the 6-phosphogluconate dehydrogenase from Gluconobacter oxydans at different concentrations of 6PG.</p> <p>The raw data of kinetic parameters for NAD or NADP at different 6PG concentrations are represented in kcat and KM, with the units s-1 and µM, respectively. Al the rest values as an efficient constant are represented in s-1µM-1. </p> <p>Also, we included the kinetic characterizations of the mutants Go6PGDH-R31L, Go6PGDH-R31V, and Go6PGDH-D30N. The CSV files contain four columns. 1. NAD or NADP concentration in µM; 2. enzyme activity in U/mg; 3. Standard deviation and 4. The number of independent experiments. </p> <p> </p> <p> </p> <p> </p>
Competitive growth experiments with a high-lipid Chlamydomonas reinhardtii mutant strain and its wild-type to predict industrial and ecological risks
<p>Key microalgal species are currently being exploited as biomanufacturing platforms using mass cultivation systems. The opportunities to enhance productivity levels or produce non-native compounds are increasing as genetic manipulation and metabolic engineering tools are rapidly advancing. Regardless of the end product, there are both environmental and industrial risks associated to open pond cultivation of mutant microalgal strains. A mutant escape could be detrimental to local biodiversity and increase the risk of algal blooms. Similarly, if the cultivation pond is invaded by a wild-type microalgae or the mutant reverts to wild-type phenotypes, productivity could be impacted. To investigate these potential risks, a response surface methodology was applied to determine the competitive outcome of two <em>Chlamydomonas reinhardtii</em> strains, a wild-type (CC-124) and a high-lipid accumulating mutant (CC-4333), grown in mixotrophic conditions, with differing levels of nitrogen and initial wild-type to mutant ratios. Results of the growth experiments show that mutant cells have double the exponential growth rate of the wild-type in monoculture. However, due to a slower transition from lag phase to exponential phase, mutant cells are outcompeted by the wild-type in every co-culture treatment. This suggests that, under the conditions tested, outdoor cultivation of the <em>C. reinhardtii</em> cell wall-deficient mutant strains does not carry a significant environmental risk to its wild-type in an escape scenario. Furthermore, lipid results show the mutant strain accumulates over 200% more TAGs per cell, at 50 mg/L NH<sub>4</sub>Cl, compared to the wild-type, therefore, the fragility of the mutant strain could impact on overall industrial productivity.</p>
Genome annotations of Drosophila melanogaster and Drosophila simulans wild-type strains from long read sequencing assemblies
<p>Genome assemblies were performed for eight wild-type strains of Drosophila melanogaster and Drosophila simulans from Oxford Nanopore long read sequencing (please refer to Mohamed et al. Cells 2020 (doi:10.3390/cells9081776)). Assemblies were deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB50024 (<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEBxxxx">https://www.ebi.ac.uk/ena/browser/view/</a>PRJEB50024).</p> <p>Transposable Element annotations: we used RepeatMasker 4.1.0 (<a href="http://repeatmasker.org/">http://repeatmasker.org/</a>) -species Drosophila, followed by OneCodeToFindThemAll (Bailly-Bechet et al. 2014) with default parameters.</p> <p>Gene annotations: We retrieved gtf files from FlyBase : <a>ftp.flybase.net/genomes/D</a><a>rosophila_melanogaster/dmel_r6,46_FB2022_03/gft/dmel-all-r6.46.gtf.gz</a> and <a>ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/gtf/dsim-all-</a><a>r2,02.gtf.gz</a>. The corresponding fasta files were also downloaded from FlyBase: <a>ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6,46_FB2022_03/</a><a>fasta</a><a>/dmel-all-</a><a>chromosome-</a><a>r6.46.</a><a>fasta</a><a>.gz</a> and <a>ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/</a><a>fasta</a><a>/dsim-all-</a><a>chromosome-</a><a>r2,02.</a><a>fasta</a><a>.gz</a>. We used Liftoff (Shumate and Salzberg, 2020) to lift over gene annotations from the references to our genome assemblies. We used -flank 0.2 and only kept the “gene” and “exon” terms.</p>
ATXN1 N-terminal region explains the binding differences of wild-type and expanded forms
<p>Additional file 12 of the publication "<strong>ATXN1 N-terminal region explains the binding differences of wild-type and expanded forms</strong>". Each PDB file describes the docking of wt/expanded ATXN1 with an interactor.</p>
SAXS data of GDAP1 delta303-358 wild-type protein
<p>SEC-SAXS data of GDAP1 delta303-358 wild-type protein. The compressed files contain a directory containing the buffer and sample frames. The directory should open in ATSAS chromixs for data reduction.</p>
RNA-seq based analysis of gene expression in thyroids of wild-type and Keap1 knockdown mice after exposure to excess iodide.
<p>C57BL/6J Keap1flox/flox mice were developed by Prof. Masayuki Yamamoto (DOI: 10.1016/j.bbrc.2005.10.185). These mice express lower levels of Keap1 because of the loxP site insertions (DOI: 10.1128/MCB.01591-09) and are designated as Keap1KD. 3-4 months old WT and Keap1KD mice fed a standard diet (KLIBA NAFAG 3242, Switzerland) containing 1.5 mg/kg sodium iodine were given normal tap water with or without 0.05% sodium iodide (Sigma, St Louis, MO, USA) for 7 days. Hence, the following groups of mice were included:</p> <p>WT mice on control water (n=8)-designated as wt in the file</p> <p>WT mice exposed to excess iodide (WT-IOD, n=6)- designated as wti in the file</p> <p>Keap1KD mice on control water (n=8)- designated as kp in the file</p> <p> and Keap1KD mice exposed to excess iodide (Keap1KD-IOD, n=6)- designated as kpI in the file. </p> <p> Mice were maintained in the animal facility of the Department of Physiology at the University of Lausanne in temperature-, light-, and humidity-controlled rooms with a 12-hour light/dark cycle. All animal procedures were in accordance with Swiss legislature and the study was approved by the Canton of Vaud SCAV.</p> <p>RNA from individual mouse thyroids was prepared as previously described (DOI: 10.1007/978-1-4939-3756-1_25) and was submitted to Alithea Genomics (Switzerland). The bulk RNA barcoding and sequencing (BRB-seq) libraries were generated and sequenced as described previously (DOI: 10.1186/s13059-019-1671-x) to a depth of approximately 1.2 million raw reads per sample.</p> <p>This research was funded by the Swiss National Science Foundation Research Grants 310030_212558, IZCOZ0_205415 and IZCOZ0_177070</p> <p></p> <p></p>
Study of Oral cMET Inhibitor INC280 in Patients With EGFR Wild-type (wt), Advanced Non-small Cell Lung Cancer (NSCLC) (Geometry Mono-1)
ClinicalTrials.gov study NCT02414139. IPD Sharing: YES. Countries: 20. Publications: 3.
Paternal effects in a wild-type zebrafish implicate a role of sperm-derived small RNAs
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Supplementary data for: Comparison of phenotypic and transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in wild-type and Ppara-null mouse livers
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Supplementary data for: Comparison of transcriptomic profiles between HFPO-DA and prototypical PPARa, PPARg, and cytotoxic agents in wild-type and PPARa knockout mouse hepatocytes
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Data from: Sleep, inflammation, and cognitive behavior of aged wild-type mice subjected to diffuse brain injury and aged 3xTg-AD mice as a model of Alzheimer's disease
<p>Identifying differential responses between sexes following traumatic brain injury (TBI) can elucidate the mechanisms behind disease pathology. Peripheral and central inflammation in the pathophysiology of TBI can increase sleep in male rodents, but this remains untested in females. We hypothesized that diffuse TBI would increase inflammation and sleep in males more so than in females. Diffuse TBI was induced in C57BL/6J mice and serial blood samples were collected (baseline, 1, 5, 7 days post‐injury [DPI]) to quantify peripheral immune cell populations and sleep regulatory cytokines. Brains and spleens were harvested at 7DPI to quantify central and peripheral immune cells, respectively. Mixed‐effects regression models were used for data analysis. Female TBI mice had 77%–124% higher IL‐6 levels than male TBI mice at 1 and 5DPI, whereas IL‐1β and TNF‐α levels were similar between sexes at all timepoints. Despite baseline sex differences in blood‐measured Ly6Chigh monocytes (females had 40% more than males), TBI reduced monocytes by 67% in TBI mice at 1DPI. Male TBI mice had 31%–33% more blood‐measured and 31% more spleen‐measured Ly6G+ neutrophils than female TBI mice at 1 and 5DPI, and 7DPI, respectively. Compared with sham, TBI increased sleep in both sexes during the first light and dark cycles. Male TBI mice slept 11%–17% more than female TBI mice, depending on the cycle. Thus, sex and TBI interactions may alter the peripheral inflammation profile and sleep patterns, which might explain discrepancies in disease progression based on sex.</p>
Single-Cell RNA-sequencing of neural precursor cells from an Alzheimer's mouse model, wild-type mice, and Alzheimer's mice rescued with Usp16 haploinsufficiency
<p class="MsoNormal">Alzheimer's disease (AD) is a progressive neurodegenerative disease observed with aging that represents the most common form of dementia. To date, therapies targeting end-stage disease plaques, tangles, or inflammation have limited efficacy. Therefore, we set out to identify an earlier targetable phenotype. Utilizing a mouse model of AD we found that cell intrinsic neural precursor cell (NPC) dysfunction precedes widespread inflammation and amyloid plaque pathology, making it one of the earlier defects in the evolution of the disease. We demonstrate that reversing impaired NPC self-renewal via genetic reduction of USP16, a histone modifier and critical physiological antagonist of the Polycomb Repressor Complex 1, can prevent downstream cognitive defects and decrease astrogliosis in vivo. To delineate potential self-renewal pathways that might contribute to the defect and rescue of Tg-SwDI NPCs and Tg-SwDI/<em>Usp16<sup><span>+/-</span></sup></em> NPCs, respectively, we performed single-cell RNA-seq and gene set enrichment analysis (GSEA) on lineage depleted primary FACS-sorted CD31<sup><span>-</span></sup>CD45<sup><span>-</span></sup>Ter119<sup><span>-</span></sup>CD24<sup><span>-</span></sup> NPCs from Tg-SwDI, WT, and Tg-SwDI/<em>Usp16<sup><span>+/-</span></sup></em> mice at 3-4 months and 1 year of age. Using the GSEA Hallmark gene sets, we found only three gene sets that were enriched in Tg-SwDI mice over WT mice and rescued in the Tg-SwDI/<em>Usp16<sup><span>+/-</span></sup> </em>mice at both ages: TGF-ß pathway, oxidative phosphorylation, and Myc Targets. The TGF-ß pathway consistently had the highest normalized enrichment score in pairwise comparisons between Tg-SwDI vs WT and Tg-SwDI vs Tg-SwDI/<em>Usp16<sup><span>+/-</span></sup> </em>of the three rescued pathways. These data suggest that USP16 may regulate neural precursor cell function in part through the BMP pathway.</p>
Dataset for: Conformational and Thermodynamic Differences Underlying Wild-type and Mutant YEATS Domain Specificity for Epigenetic Marks
<p>The set of molecular dynamics trajectories generated and analyzed in the paper "Conformational and Thermodynamic Differences Underlying Wild-type and Mutant YEATS Domain Specificity for Epigenetic Marks." <strong>Citations should refer directly to the manuscript. </strong> The preprint version is available at: https://doi.org/10.1101/2022.07.14.500085</p> <p>The uploaded zip file "trajectory_data.zip" contains trajectories for the (1) apo (2) h3k27ac and (3) h3k9ac systems. In each directory is a subdirectory corresponding to the wild-type, deletion, and insertion mutations. In each of those subdirectories are 10 XTC files, which correspond to the trajectories for the 10 different simulations performed for each system, along with an AMBER-formated PRMTOP file. Solvent molecules were removed from each file, and trajectories were strided such that there is one frame per 500 ps. </p>
Annotated and processed 3D confocal microscopy images of dorsal aorta in wild-type and Endoglin-deficient zebrafish embryos at 48 hpf and 72 hpf
<p>This repository contains the original 3D confocal microscopy images that were used for the analysis of vessel geometry and endothelial cell morphology in the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos at 48 hours post fertilization (hpf) and 72 hpf in the article <a href="https://www.biorxiv.org/content/10.1101/2024.02.19.580931">Novel mathematical approach to accurately quantify 3D endothelial cell morphology and vessel geometry based on fluorescently marked endothelial cell contours: Application to the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos</a>. In this article, we developed a novel mathematical approach that allows to consistently estimate 3D vessel geometry and endothelial cell surface morphology using only information from endothelial cell contours. For the article's analysis, endothelial cell contours were manually annotated on Pecam1-EGFP-labeled cell junctions. Furthermore, dorsal aorta cross-sections were outlined on Dextran Texas Red-perfused vessel lumens. Further details are provided in the article's Materials and methods section.</p> <p>This repository contains 14 images of 7 wild-type embryos, each imaged at 48hpf and 72hpf. Furthermore, 12 images of 6 Endoglin-deficient embryos, each imaged at 48hpf and 72hpf are included. These combined files (called "analysis data" in the article) are stored in "eng_wt_data.zip". Secondly, images of 2 wild-types at 72hpf with repeated cell contour annotation and outlined vessel lumens (called "validation data" in the article) are located in "wt_angiogram_data.zip". The provided files are stored in Imaris format and can be inspected using the free <a href="https://imaris.oxinst.com/imaris-viewer">Imaris Viewer software</a>.</p> <p>To allow inspection of the endothelial cell contours that we manually annotated for the article's analysis and compare them against the intermediate results of our novel mathematical approach, i.e., contour enrichments by neighboring cells, contour smoothing splines and their projections onto the estimated vessel surfaces, we imported these contours into the Imaris files. Note that the contours' coordinates in these files are slightly less precise than in our article's analysis and thus are intended for visual inspection. To exactly reproduce the results in our article, refer to the files in <a href="https://doi.org/10.5281/zenodo.10549101">our other Zenodo repository</a>.</p>
BAM files of wild-type CP-A cells and the TP53 KO CP-A clones.
<p>BAM files (alignment to hg38) of wild-type CP-A cells and the TP53 knock-out (KO) CP-A clones (2c8, 3d2, 5f4). Please refer to Figure 2. of <span>doi:</span> https://doi.org/10.1101/2024.01.24.576991.</p>
Efficacy of inhibitor on wild-type ACVR1 and R206H mutant in C2C12 cells (by DLA)
<p>There are concerns that compounds that are effective in inhibiting ALK2 by occupying its ATP-binding pocket might have reduced efficacy against mutant ALK2. That will be undesirable since the compounds should also target the mutant gain-of-function ALK2 in DIPG cells. The following experiment takes advantage of the fact that ALK2-R206H mutant confers a neofunction of being activated by Activin A (not activating towards wild-type ALK2). Therefore, using Activin A as the stimulation ligand, the effectiveness of inhibition on ALK2-R206H can be specifically determined. BMP6 which activates both wild-type ALK2 and ALK2-R206H is also included.</p>
Magnaporthe oryzae polyadenylation sites for wild-type and delta-rbp35 mutant
<p>Magnaporthe oryzae polyadenylation sites for wild-type and delta-rbp35 mutant, in 4 media: CM, MM, MM-N and MM-C</p>
Metabolic fingerprints for suboptimal mycorrhizal colonization in wild-type and the jasmonic acid deficient spr2 tomato mutant
<p>Raw data for metabolic fingerprinting of tomato roots by DLI-ESI-MS and GC-MS to examine the effect of mycorrhizal colonization on the global metabolic profile of WT and <em>spr2</em> mutant plants.</p>
Gene expression for suboptimal mycorrhizal colonization in wild-type and jasmonic acid deficient spr2 tomato mutants
<pre>Data were obtained from mycorrhizhal colonized roots of wild-type and and spr2 mutants tomato plants, at 32 and 45 days after mycorrhizhal inoculation. Amplifications were performed using SYBR Green detection chemistry and run in triplicate in 96-well reaction plates with the CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA). The data was analyzed by the delta delta ct method. </pre>
ScienceDex guides
Understand access before you commit
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.