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6,171 results for “mutant”
Heat stress induced nitric oxide (DAF-FM-DA) response in respiratory growing Wild-type, atg32∆ and spe1∆ mutant yeast with and without spermidine addition
Open the record for dataset details and reuse information.
chr2 of mutant genomes used in Rodriguez-Carballo et al. 2020
<p>chr2 of mutant genomes used in Rodriguez-Carballo et al. 2020. Built from chr2 of mm10 (UCSC) and modified with information from sanger sequencing.</p>
Data from: Ovarian BDNF promotes survival, migration, and attachment of tumor precursors originated from p53 mutant fallopian tube epithelial cells
<p class="CxSpFirst"><span>High-grade serous ovarian carcinoma (HGSOC) is the most lethal gynecological malignancy. New evidence supports a hypothesis that HGSOC can originate from fallopian tube epithelium (FTE). It is unclear how genetic alterations and pathophysiological processes drive the progression of FTE tumor precursors into widespread HGSOCs. In this study, we uncovered that brain-derived neurotrophic factor (BDNF) in the follicular fluid stimulates the tropomyosin receptor kinase B (TrkB)-expressing FTE cells to promote their survival, migration, and attachment. Using <i>in vitro</i> and <i>in vivo</i> models, we further identified that the acquisition of common TP53 gain-of-function (GOF) mutations in FTE cells led to enhanced BDNF/TrkB signaling comparing to that of FTE cells with <i>TP53</i> loss-of-function (LOF) mutations. Different mutant p53 proteins can either increase TrkB transcription or enhance TrkB endocytic recycling. Our findings have demonstrated possible interplays between genetic alterations in FTE tumor precursors (i.e., p53 gain-of-function mutations) and pathophysiological processes (i.e., the release of follicular fluid upon ovulation) during the initiation of HGSOC from the fallopian tube. Our data revealed molecular events underlying the link between HGSOC tumorigenesis and ovulation, a physiological process that has been associated with risk factors of HGSOC. </span></p>
Data from: The dynamic transmission of positional information in stau-mutants during Drosophila embryogenesis.
It has been suggested that Staufen (Stau) is key in controlling the variability of the posterior boundary of the Hb anterior domain (xHb). However, its underlying mechanism is elusive. Here, we quantified the dynamic 3D expression of segmentation genes in Drosophila embryos. With improved control of measurement errors, we show xHb of stau- mutants reproducibly moves posteriorly by 10% of the embryo length (EL) to the wild type (WT) position in the nuclear cycle (nc) 14, and its variability at short time windows is comparable as that of the WT. Moreover, for stau- mutants, the upstream Bicoid (Bcd) gradients show equivalent relative intensity noise to that of the WT in nc12-nc14, and the downstream Even-skipped (Eve) and cephalic furrow (CF) show the same positional errors as the WT. Our results indicate that threshold-dependent activation and self-organized filtering are not mutually exclusive but could both be implemented in early Drosophila embryogenesis.
Helicos direct RNA sequencing of FPA mutants and overexpressors
<p>Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat receptor (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, controlling their functional expression and impacting immunity. Using long-read nanopore direct RNA sequencing we resolve the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.</p>
Arabidopsis ovule primordium stages 0-I to 2-II, wild-type Col_0, Ws-4 and botero (bot1-7) mutant
<p>This image resource describes the development of ovule primordia from stages 0-I to 2-I in 3D and at cellular resolution. The images were segmented using ImarisCell (BitplaneAG) and annotated as described in the associated manuscript Hernandez-Lagana et al. https://www.biorxiv.org/content/10.1101/2020.07.30.226670v3</p>
chr2 of Inv(CS65_SB7)lacZ mutant genome used in Bolt et al. 2021
<p>chr2 of Inv(CS65_SB7)lacZ mutant genome used in Bolt et al. 2021 under the name ‘inv2’. It is an inversion of 961058bp. At the position of the centromeric breakpoint, there is loxP site, beta-globin promoter, lacZ, SV40 polyA signal, and left IRDR of the Sleeping Beauty Transposon. At the telomeric breakpoint there is a loxP site and the R-IRDR of Sleeping Beauty. The fasta was built from chr2 of mm10 (<a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm10/chromosomes/chr2.fa.gz">http://hgdownload.soe.ucsc.edu/goldenPath/mm10/chromosomes/chr2.fa.gz</a>).</p>
Mass spectrometry data of Chalmydomonas reinhardtii central pair mutants
<p>The following data includes the mass spectrometry results from 5 different strains of Chlamydomonas reinhardtii. The first strain is CC-124 or more commonly referred to as the wild type strain. The second strain is a mutant that lacks the central pair <em>pf15</em>. Other central pair mutants are <em>pf16</em>, <em>pf6</em> and <em>cpc1</em>.</p> <p>All strains were cultured under identical conditions and the doublet microtubules were purified and treated twice with NaCl before mass spectrometry. Biological triplicates were performed on each strain for mass spectrometry.</p>
RNA sequencing data from the guts of Drosophila wildtype and CG3740/nazo double mutant 20-day-old males
<p>Lipid dyshomeostasis has been implicated in a variety of diseases ranging from obesity to neurodegenerative disorders such as Neurodegeneration with Brain Iron Accumulation (NBIA). Here, we uncover the physiological role of Nazo, the Drosophilamelanogaster homolog of the NBIA-mutated protein – c19orf12, whose function has been elusive. Ablation of Drosophila c19orf12 homologs leads to dysregulation of multiple lipid metabolism genes. nazo mutants exhibit markedly reduced gut lipid droplet and whole-body triglyceride contents. Consequently, they are sensitive to starvation and oxidative stress. Nazo is required for maintaining normal levels of Perilipin-2, an inhibitor of the lipase – Brummer. Concurrent knockdown of Brummer or overexpression of Perilipin-2 rescues the nazo phenotype, suggesting that this defect, at least in part, may arise from diminished Perilipin-2 on lipid droplets leading to aberrant Brummer-mediated lipolysis. Our findings potentially provide novel insights into the role of c19orf12 as a possible link between lipid dyshomeostasis and neurodegeneration, particularly in the context of NBIA.</p>
Wheat Enhanced Disease Resistance EMS-Mutants Include Lesion-mimics With Adult Plant Resistance to Stripe Rust
<h3>The datasets for '<strong>Wheat Enhanced Disease Resistance EMS-Mutants Include Lesion-mimics With Adult Plant Resistance to Stripe Rust</strong>'.</h3> <p> </p> <p><strong>Main datasets</strong></p> <ul> <li>Kr620_GATK.zip</li> <li>Kr620_QTLseq.zip</li> </ul> <p><strong>Kr620_GATK.zip</strong> includes vcf files generated by mapping wild type Kronos and resistant or susceptible Kr620 into the Kronos genome. <strong>Kr620_QTLseq.zip </strong>includes the bulk segregation analysis outputs using QTL-seq. </p>
Negative Stain Electron Microscopy Datasets for alphaB-crystallin NT-IXI perturbed mutants in fibrillar and cage-like morphologies
<p>Negative stain datasets for alphaB-crystallin NT-AXA mutant. Contains two datasets, one for the fibrillar morphology (93 micorgraphs) and another for the cage-like morphology (119 micrographs)</p> <p>Images were taken on a Thermo Fisher Tecnai T-12 microscope equipped with a BM-Eagle detector at a calibrated pixel size of 4.37<span>Å/px</span></p>
Output files from tauRAMD simulations for the dissociation of ligands from T4 lysozyme mutants
<p>The zip files contain the output files generated by tauRAMD to simulate the dissociation of ligands from T4 lysozyme (T4L) mutants.</p> <p>Directories:</p> <p>bnz-l99a-ph5: benzene bound to T4L L99A; simulations at 20 °C<br> bnz-l99a-ph5-t10: benzene bound to T4L L99A; simulations at 10 °C<br> bnz-l99a-ph5-t30: benzene bound to T4L L99A; simulations at 30 °C<br> bnz-m102a-ph5: benzene bound to T4L M102A<br> bnz-f104a-ph5: benzene bound to T4L F104A<br> ind-l99a-ph5: indole bound to T4L L99A</p> <p>Further details about the method can be found in the publication "Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations" (doi: https://doi.org/10.1016/j.crstbi.2021.04.001).</p> <p> </p>
Cleavage of SARS-CoV-2 spike protein mutants
<p class="MsoNormal"><span>Several SARS-CoV-2 variants emerged that harbor mutations in the surface unit of the viral spike (S) protein that enhance infectivity and transmissibility. Here, we analyzed whether ten naturally-occurring mutations found within the extended loop harboring the S1/S2 cleavage site of the S protein, a determinant of SARS-CoV-2 cell tropism and pathogenicity, impact S protein processing and function. None of the mutations increased but several decreased S protein cleavage at the S1/S2 site, including S686G and P681H, the latter of which is found in variants of concern B.1.1.7 (Alpha variant) and B.1.1.529 (Omicron variant). None of the mutations reduced ACE2 binding and cell-cell fusion although several modulated the efficiency of host cell entry. The effects of mutation S686G on viral entry were cell-type dependent and could be linked to the availability of cathepsin L for S protein activation. These results show that polymorphisms at the S1/S2 site can modulate S protein processing and host cell entry. </span></p>
Systematic prediction of EMS-induced mutations in a sorghum mutant population
<p>Sorghum is a next-generation crop species with tremendous potential for discovering highly desirable agronomical traits. We described an improved method for the systematic detection of EMS-induced mutations in the previous sequencing of the M3 generation of 600 sorghum BTx623 mutants. We used both SAMtools and GATK-based variant-calling algorithms to demonstrate the general utility of the method. The approach also includes a clustering algorithm for detecting likely false-negative EMS-induced mutations. We detected 3,497,654 EMS-induced single nucleotide polymorphisms (SNPs) in 30,285 distinct sorghum genes, and cataloged 10,263 high impact and 136,639 moderate impact SNPs. We also implemented a light-weight web portal for searching the mutation database for the 600 sorghum mutants.</p>
Structural Dynamics Support Electrostatic Interactions in the Active Site of Adenylate Kinase - V142G mutant
<p>Tinker MD trajectories of AdK WT and mutants as described in the paper published in ChemBioChem, e202200097.</p>
Structural Dynamics Support Electrostatic Interactions in the Active Site of Adenylate Kinase - A55G and V135G mutants
<p>Tinker MD trajectories of AdK WT and mutants as described in the paper published in ChemBioChem, e202200097.</p>
Dataset wih MD simulations of fish aquaporin - wt and different mutants.
<p>MD trajectories and final minimized structures after 100 ns MD simulation for wt, pT38, pY107, L117A, Y107A and Y107E variants of fish aquaporin.</p> <p>All simulations performed using the YASARA software (www.yasara.org). </p>
RNA-Seq data of Raji cells transduced with retrovirus expressing WT or mutant IRF4
<p>Total RNA was extracted using RNAiso Plus (TaKaRa) from Raji cells transduced with retrovirus expressing WT or mutant IRF4. RNA-seq was performed by BGI (Beijing Genomic Institute, ShenZhen, China) using the BGISEQ-500 platform, pair end 100 bases read lengths. The sequencing data were filtered with SOAPnuke (v1.5.2). The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to identify genes and differentially spliced genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI with known and novel coding transcripts included, then the expression level of gene was calculated by RSEM (v1.2.12).</p>
Dataset: Predicting T Cell Receptor Functionality against Mutant Epitopes
<p>This upload contains the Datasets and Supplementary Material for "Predicting T Cell Receptor Functionality against Mutant Epitopes" (DOI: https://doi.org/10.1101/2023.05.10.540189) by Felix Drost, Emilio Dorigatti, Adrian Straub, Philipp Hilgendorf, Karolin I. Wagner, Kersten Heyer, Marta López Montes, Bernd Bischl, Dirk H. Busch, Kilian Schober, and Benjamin Schubert.</p>
Data underlying the article: "A patient-centric knowledge graph approach to prioritize mutants for selective anti-cancer targeting"
<p>This repository contains the data and code underlying the article: "A patient-centric knowledge graph approach to prioritize mutants for selective anti-cancer targeting" available on BioRxiv. </p>
ScienceDex guides
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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.