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6,171 results for “mutant”
Linked collectors and determiners for: The structure of the cataract causing P 23 T mutant of human gamma-D crystallin.
Natural history specimen data linked to collectors and determiners held within, "The structure of the cataract causing P 23 T mutant of human gamma-D crystallin". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/4caaf0c8-bd51-4d80-86ba-5544792d65ce">https://bionomia.net/dataset/4caaf0c8-bd51-4d80-86ba-5544792d65ce</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/4caaf0c8-bd51-4d80-86ba-5544792d65ce">https://gbif.org/dataset/4caaf0c8-bd51-4d80-86ba-5544792d65ce</a>. Formatted as a Frictionless Data package.
Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST
<div> <div> <div> <div> <p>Lysosomal storage diseases (LSDs) comprise ~50 monogenic disorders marked by the buildup of cellular material in lysosomes, yet systematic global molecular phenotyping of proteins and lipids is lacking. We present a nanoflow-based multi-omic single-shot technology (nMOST) workflow that quantifies HeLa cell proteomes and lipidomes from over two dozen LSD mutants. Global cross-correlation analysis between lipids and proteins identified autophagy defects, notably the accumulation of ferritinophagy substrates and receptors, especially in NPC1-/- and NPC2-/- mutants, where lysosomes accumulate cholesterol. Autophagic and endocytic cargo delivery failures correlated with elevated lyso-phosphatidylcholine species and multi-lamellar structures visualized by cryo-electron tomography. Loss of mitochondrial cristae, MICOS-complex components, and OXPHOS components rich in iron-sulfur cluster proteins in NPC2-/- cells was largely alleviated when iron was provided through the transferrin system. This study reveals how lysosomal dysfunction affects mitochondrial homeostasis and underscores nMOST as a valuable discovery tool for identifying molecular phenotypes across LSDs.</p> </div> </div> </div> </div>
Original data sets of a DEER/PELDOR ring test of four doubly spin-labelled mutants of the protein YopO
<p>The dataset is discussed in manuscript "Benchmark test and guidelines for DEER/PELDOR experiments on nitroxide-labeled biomolecules" by Olav Schiemann, Caspar A. Heubach, Dinar Abdullin, Katrin Ackermann, Mykhailo Azarkh, Elena Bagryanskaya, Malte Drescher, Burkhard Endeward, Jack H. Freed, Laura Galazzo, Daniella Goldfarb, Tobias Hett, Laura Esteban Hofer, Luis Fábregas Ibáñez, Eric J. Hustedt, Svetlana Kucher, Ilya Kuprov, Janet E. Lovett, Andreas Meyer, Sharon Ruthstein, Sunil Saxena, Stefan Stoll, Christiane Timmel, Marilena Di Valentin, Hassane S. Mchaourab, Thomas F. Prisner, Bela E. Bode, Enrica Bordignon, Marina Bennati, Gunnar Jeschke. It was generated in a ring test by seven laboratories. The authors names of individual data are not assigned on purpose, rather data sets are referred to by laboratory identifiers A, B, C, D, E, F, G. The Supplementary Information for the above mentioned manuscript, which contains a link to this dataset, describes how the samples were prepared and how the measurements were performed.</p>
Screen of Arabidopsis mutants homologous to Cowpea GWAS peaks
<p>This dataset was collected for T-DNA insertion mutants of Arabidopsis that were selected based on the sequence homology with the candidate genes in cowpea (<em>Vigna unguiculata</em>) identified through GWAS for drought induced changes in growth, evapotranspiration and photosynthetic efficiency. The T-DNA insertion lines were germinated on agar plates and transferred to soil - where the seedlings were exposed to drought stress (10% soil water-holding capacity). </p>
Structural variants of calreticulin mutants associated with essential thrombocythemia
<p>Video S1. CALRwt molecular simulation with Ca2+ ions binding to the structure. This movie shows the dynamics of Ca2+ ions over the 40 ns and how they rapidly bind to the CALRwt structure. Most of the ions bind to the C-terminal part of CALRwt, where the majority of the negative residues are located. The binding of Ca2+ ions creates an interaction between residues that can induce specific folding. In this example, residues E407 and E416 interact with a calcium ion and fold, as shown at the end of the movie.</p> <p>Video S2. CALRwt molecular simulation with calcium ions binding to the structure. This movie shows the dynamics of CALRwt and Ca2+ ions over 400 ns and how ions are rapidly bound to the CALRwt structure. Most of the ions bind to the C-terminal region of CALRwt, where the majority of the negative residues are located. The binding of calcium ions creates an interaction between residues that can induce specific folding (a specific example of fold is shown on Video S1). On this full movie, we are able to see the unfolding of the N-terminal region of the helix and the stabilization of the C- terminal region thanks to calcium binding.</p> <p>Video S3. CALRwt molecular simulation with Na+ ions. This movie shows the dynamics of CALRwt with Na+ ions. The absence of binding from calcium ions leaves the structure free of any external constraint, especially for the C-terminal region. The latter appears to be flexible but this region is in fact quite stable at the local level and has its own dynamics, unstructured slightly the C-terminal of the helix.</p> <p>Video S4. CALRm class A molecular simulation. This movie shows the dynamics of CALRm class A over 400ns. The C-terminal region of the structure is quite flexible at first and interacts with the N-terminal region after several ns. This interaction locally constrains the structure around residues 400-404, stabilizing an unstructured structure for this region.</p> <p>Video S5. CALRm class B molecular simulation. This movie shows the dynamics of CALRm class B over 400ns. The first and last helices move away from their initial position with great flexibility of the coiled regions between the helices. The first helix interacts closely with the second helix and forms a specific T-shaped fold which stabilize the whole structure.</p> <p>Video S6. CALRm class C molecular simulation. This movie shows the dynamics of CALRm class C over 400ns. Extremities are highly flexible but the helix remains stable. This high flexibility allow the C- terminal region to have some interaction with the helix at some frames</p> <p>Video S7. CALRm class D molecular simulation. This movie shows the dynamics of CALRm class D over 400ns. The C-terminal region appears to be flexible, but the helix remains stable the whole simulation.</p> <p>Video S8. CALRm class E molecular simulation. This movie shows the dynamics of CALRm class E over 400ns. This movie shows the dynamics of CALRm class E and calcium ions over 400 ns and how ions are rapidly bound to the CALRwt structure. Most of the ions bind to the C-terminal region of CALRm class E, where the majority of the negative residues are located. The N-terminal region of the helix is being unstructured and the C-terminal region is stabilized with calcium ions. This simulation of CALRm class E is very similar to the simulation of CALRwt.</p> <p>Video S9. Dimeric form of CALRm class A molecular simulation. This movie shows the dynamics of two CALRm class A monomers forming a dimer through disulphide bonds. Both chains seem to repulse each other due to electrostatic charges, but disulphide bonds maintain the dimeric form, otherwise both chains would have been separated.</p> <p>Video S10. Dimeric form of CALRm class A with broken disulphide bonds molecular simulation. This movie shows the dynamics of two CALRm class A monomers and their attempt to form a dimer with broken disulfide bonds. As each monomer repels each other, the dimeric form cannot be stable without any disulfide bonds. This is demonstrated by the separation of each chain from each other.</p> <p>Video S11. Dimeric form of CALRm class B molecular simulation. This movie shows the dynamics of two CALRm class B monomers forming a dimer through disulphide bonds. Both chains are interacting together to form a specific shape, similar to the simulation of the monomer of class B. This interaction implies that even without any disulphide bonds, the dimeric form of class B could be stable, contrary to class A.</p> <p>Video S12. Dimeric form of CALRm class B molecular simulation. It is an interesting replicate of the same system than Video S11. Helices are also well maintained.</p> <p>Video S13. Dimeric form of CALRm class C molecular simulation. This movie shows the dynamics of two CALRm class C monomers forming a dimer through disulphide bonds. Both chains seem to repulse each other due to electrostatic charges, but disulphide bonds maintain the dimeric form, otherwise both chains would have been separated.</p> <p>Video S14. Dimeric form of CALRm class E molecular simulation. This movie shows the dynamics of two CALRm class E monomers and their attempt to form a dimer without any disulphide bonds. Chains repel and are moving away from each other after several ns, indicating the inability for class E to form a dimer.</p> <p>Video S15. Dimeric form of CALRwt molecular simulation. This movie shows the dynamics of two CALRwt monomers and their attempt to form a dimer. Some interactions occur between the N- terminus of each chain, but this is not sufficient and the chains move away from each other. Subsequently, the dynamics of each chain resembles the dynamics of the CALRwt monomer simulated with sodium ions (Video S2). CALRwt is not able to be stable as dimer.</p> <p>Video S16. Dimeric form of CALRm class D molecular simulation. This movie shows the dynamics of two CALRm class D monomers and their attempt to form a dimer without any disulphide bonds. Both chains are separated very quickly which indicate that they can not be stable as dimer.</p>
Data from: A caste differentiation mutant elucidates the evolution of socially parasitic ants
<div> <div> <div> <div> <p>Most ant species have two distinct female castes – queens and workers – yet the developmental and genetic mechanisms that produce these alternative phenotypes remain poorly understood. Working with the clonal raider ant, <em>Ooceraea</em> <em>biroi</em>, we discovered a variant strain that expresses queen-like traits in individuals that would normally become workers. The variants show changes in morphology, behavior, and fitness that cause them to rely on workers in wild-type (WT) colonies for survival. Overall, they resemble the queens of many obligately parasitic ants that have evolutionarily lost the worker caste and live inside colonies of closely related hosts. <br><br>To understand the genetic basis of this variant strain, which we term the queen-like mutants (QLM), we re-analyzed published PacBio and Hi-C data (McKenzie and Kronauer 2018) using the Falcon pipeline. </p> </div> </div> </div> </div>
The 400 ns molecular dynamic (MD) trajectories for the wild type and mutant forms of the S. tuberosum eIF4E1 and eIF4E2
<p>Truncated from the N termini models of the wild type and mutant forms of the S. tuberosum eIF4E1 and eIF4E2. <br> The molecular dynamic (MD) trajectories with 400-ns length for each wild type and mutant forms of the eIF4E in the water environment according to the standard MD procedure.</p>
Kinetic in support of "Pre-Steady-State Kinetic Characterization of an Antibiotic-Resistant Mutant of Staphylococcus aureus DNA Polymerase PolC"
<p>These are KinTek Explorer mechanism files containing the data and analysis described in the manuscript "Pre-Steady-State Kinetic Characterization of an Antibiotic-Resistant Mutant of Staphylococcus aureus DNA Polymerase PolC" (bioRxiv 2022.10.04.510889; doi: https://doi.org/10.1101/2022.10.04.510889). </p>
The cell-associated magnesium content is affected in Salmonella mutants defective for SigmaS/RpoS and O-antigen synthesis
<p>In many Gram-negative bacteria, the stress sigma factor of RNA polymerase, σS/RpoS, remodels global gene expression to reshape the physiology of quiescent cells and ensure their survival under non-optimal growth conditions. In the foodborne pathogen <i>Salmonella enterica</i> serovar Typhimurium, σS is also required for biofilm formation and virulence. </p><p>Our recent work has shown that a Δ<i>rpoS</i> mutation reduces the magnesium content of <i>Salmonella</i> (Metaane et al. 2022, PLoS ONE 17(3): e0265511). The O-antigen of LPS is a Mg2+ reservoir that can be used under magnesium deprivation. </p><p>We show here that eventhough the cell-associated magnesium content is affected when <i>Salmonella</i> lacks the entire O-antigen, an effect of the Δ<i>rpoS</i> mutation can be still observed. </p><p>We have also shown that the amount of intracellular free Mg2+ is slightly reduced in the Δ<i>rpoS</i> mutant compared to the wild-type strain (Metaane et al 2023, PLoS ONE 18(9): e0291736). </p><p><strong>This work was supported by the French National Research Agency (ANR-19-CE44-0005-01, PERIOMET project).</strong> </p>
Data underlying the article: 3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors
<p>This repository contains the datasets and results supporting the conclusions of the manuscript "<strong>3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors</strong>". </p> <p>Publicly available data is not included in this repository. The source code to generate the results gathered here can be found on GitHub (https://github.com/CDDLeiden/3ddpd). </p>
A Study of Dabrafenib in Combination With Trametinib in Chinese Patients With BRAF V600E Mutant Metastatic NSCLC
ClinicalTrials.gov study NCT04452877. IPD Sharing: YES. Countries: 1. Publications: 1.
A Study of Binimetinib and Encorafenib in Advanced BRAF Mutant Cancers
ClinicalTrials.gov study NCT03843775. IPD Sharing: YES. Countries: 1. Publications: 1.
Milademetan Plus Quizartinib Combination Study in FLT3-ITD Mutant Acute Myeloid Leukemia (AML)
ClinicalTrials.gov study NCT03552029. IPD Sharing: YES. Countries: 1. Publications: 1.
Treatment of CD79B Mutant Relapsed/Refractory Diffuse Large B-Cell Lymphoma With Bruton Tyrosine Kinase Inhibitor Zanubrutinib
ClinicalTrials.gov study NCT05068440. IPD Sharing: YES. Countries: 1. Publications: 0.
DS-1205c With Gefitinib for Metastatic or Unresectable Epidermal Growth Factor Receptor (EGFR)-Mutant Non-Small Cell Lung Cancer
ClinicalTrials.gov study NCT03599518. IPD Sharing: YES. Countries: 1. Publications: 1.
DS-1205c With Osimertinib for Metastatic or Unresectable Epidermal Growth Factor Receptor (EGFR)-Mutant Non-Small Cell Lung Cancer
ClinicalTrials.gov study NCT03255083. IPD Sharing: YES. Countries: 1. Publications: 2.
Study Assessing the Efficacy and Safety of Alpelisib Plus Fulvestrant or Letrozole, Based on Prior Endocrine Therapy, in Patients With PIK3CA Mutant, HR+, HER2- Advanced Breast Cancer Who Have Progres
ClinicalTrials.gov study NCT03056755. IPD Sharing: YES. Countries: 19. Publications: 4.
Phenotypic measurements of STERILE APETALA mutants in Mimulus verbenaceus
Open the record for dataset details and reuse information.
Whole genome sequence data of Mycobacterium tuberculosis and Mycolicibacterium smegmatis mutants of the riboflavin biosynthetic pathway- Part 1
Open the record for dataset details and reuse information.
Population dynamics of C. elegans and C. briggsae dormancy mutants
Open the record for dataset details and reuse information.
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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.