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293 results for “protein kinase”
Data from: Evolution of the leucine-rich repeat receptor-like protein kinase gene family: Ancestral copy number and functional divergence of BAM1 and BAM2 in Brassicaceae
Gene duplication allows for functional divergence and innovation that provide selective advantages. However, in flowering plants genetic studies have revealed that single-gene mutations affecting one of two or more closely related paralogs often fail to cause detectable morphological defects, suggesting functional redundancy. Flowering plants have hundreds of genes encoding leucine-rich repeat receptor-like protein kinases (LRR-RLKs), several of which play important roles in anther development but little is known about their evolutionary history and possible functional divergence. We investigated the evolutionary relationship of the LRR-RLK gene family by phylogenetic analysis and found that these closely related paralogs resulted from multiple duplication events, such as the one resulting in BAM1 and BAM2. We further used qRT-PCR to verify gene expression changes in immature anthers from the bam1/bam2 single and double mutants compared with wild type providing strong evidence that the BAM1 and BAM2 genes have evolved different functions, with differential effects on anther gene expression. Moreover, careful examination of anther development in bam1 and bam2 single mutants revealed previously unrecognized extra cell division in tapetum cell layers. Thus our results from phylogenetic, molecular and morphological analyses uncover sequence and functional differences between paralogs whose single mutants lack obvious fertility defects, effectively revealing functional divergence of duplicate genes.
Data from: High cell density upregulates calcium oscillation by increasing calcium store content via basal mitogen-activated protein kinase activity
Calcium releases of non-excitable cells are generally a combination of oscillatory and non-oscillatory patterns, and factors affecting the calcium dynamics are still to be determined. Here we report the influence of cell density on calcium increase patterns of clonal cell lines. The majority of HeLa cells seeded at 1.5 x 104/cm2 showed calcium oscillations in response to histamine and ATP, whereas cells seeded at 0.5 x 104/cm2 largely showed transient and sustained calcium increases. Cell density also affected the response of HEK293 cells to ATP in a similar manner. High cell density increased the basal activity of the mitogen-activated protein (MAP) kinase and calcium store content, and both calcium oscillation and calcium store content were down-regulated by a MAP kinase inhibitor, U0126. Thus, MAP kinase-mediated regulation of calcium store likely underlie the effect of cell density on calcium oscillation. Calcium increase patterns of HeLa cells were conserved at any histamine concentrations tested, whereas the overexpression of histamine H1 receptor, which robustly increased histamine-induced inositol phospholipid hydrolysis, converted calcium oscillations to sustained calcium increases only at high histamine concentrations. Thus, the consequence of modulating inositol phospholipid metabolism was distinct from that of changing cell density, suggesting the effect of cell density is not attributed to inositol phospholipid metabolism. Collectively, our results propose that calcium increase patterns of non-excitable cells reflect calcium store, which is regulated by the basal MAP kinase activity under the influence of cell density.
Dataset (IX) related to publication: Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors
<p>Well-tempered metadynamics simulation data of compounds <strong>1 </strong>and<strong> 2</strong> of the related to the publication Pantsar et al.: <em>Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors.</em></p> <p>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files).</p> <p>All datasets related to this publication:</p> <p><a href="https://doi.org/10.5281/zenodo.4568113">https://doi.org/10.5281/zenodo.4568113</a>(compound <strong>1</strong>; dataset: I)</p> <p><a href="https://doi.org/10.5281/zenodo.4572444">https://doi.org/10.5281/zenodo.4572444</a> (compound <strong>1</strong>; dataset: II)</p> <p><a href="https://doi.org/10.5281/zenodo.4561797">https://doi.org/10.5281/zenodo.4561797</a>(compound <strong>2</strong>; dataset: III)</p> <p><a href="https://doi.org/10.5281/zenodo.4563896">https://doi.org/10.5281/zenodo.4563896</a> (compound <strong>2</strong>; dataset: IV)</p> <p><a href="https://doi.org/10.5281/zenodo.5563359">https://doi.org/10.5281/zenodo.5563359</a> (<strong>SB203580</strong>; dataset: V)</p> <p><a href="https://doi.org/10.5281/zenodo.5563655">https://doi.org/10.5281/zenodo.5563655</a> (<strong>SB203580</strong>; dataset: VI)</p> <p><a href="https://doi.org/10.5281/zenodo.5564118%20">https://doi.org/10.5281/zenodo.5564118 </a>(compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VII)</p> <p><a href="https://doi.org/10.5281/zenodo.5564208%20">https://doi.org/10.5281/zenodo.5564208 </a>(compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VIII)</p> <p><a href="https://doi.org/10.5281/zenodo.5564586">https://doi.org/10.5281/zenodo.5564586</a> (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: IX)</p> <p><a href="https://doi.org/10.5281/zenodo.5570882">https://doi.org/10.5281/zenodo.5570882</a> (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: X)</p> <p><a href="https://doi.org/10.5281/zenodo.5571352">https://doi.org/10.5281/zenodo.5571352</a> (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: XI)</p> <p>The datasets include original Desmond raw-trajectories (datasets I–VIII), PDB-coordinates for the energy minimized metastable state derived structures (datasets II, IV and VI) and raw-trajectories of the well-tempered metadynamics simulations (dataset IX–XI).</p>
Dataset (X) related to publication: Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors
<p>Well-tempered metadynamics simulation data of compounds <strong>1 </strong>and<strong> 2</strong> of the related to the publication Pantsar et al.: <em>Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors.</em></p> <p>Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files).</p> <p>All datasets related to this publication:</p> <p><a href="https://doi.org/10.5281/zenodo.4568113">https://doi.org/10.5281/zenodo.4568113</a>(compound <strong>1</strong>; dataset: I)</p> <p><a href="https://doi.org/10.5281/zenodo.4572444">https://doi.org/10.5281/zenodo.4572444</a> (compound <strong>1</strong>; dataset: II)</p> <p><a href="https://doi.org/10.5281/zenodo.4561797">https://doi.org/10.5281/zenodo.4561797</a>(compound <strong>2</strong>; dataset: III)</p> <p><a href="https://doi.org/10.5281/zenodo.4563896">https://doi.org/10.5281/zenodo.4563896</a> (compound <strong>2</strong>; dataset: IV)</p> <p><a href="https://doi.org/10.5281/zenodo.5563359">https://doi.org/10.5281/zenodo.5563359</a> (<strong>SB203580</strong>; dataset: V)</p> <p><a href="https://doi.org/10.5281/zenodo.5563655">https://doi.org/10.5281/zenodo.5563655</a> (<strong>SB203580</strong>; dataset: VI)</p> <p><a href="https://doi.org/10.5281/zenodo.5564118%20">https://doi.org/10.5281/zenodo.5564118 </a>(compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VII)</p> <p><a href="https://doi.org/10.5281/zenodo.5564208%20">https://doi.org/10.5281/zenodo.5564208 </a>(compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VIII)</p> <p><a href="https://doi.org/10.5281/zenodo.5564586">https://doi.org/10.5281/zenodo.5564586</a> (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: IX)</p> <p><a href="https://doi.org/10.5281/zenodo.5570882">https://doi.org/10.5281/zenodo.5570882</a> (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: X)</p> <p><a href="https://doi.org/10.5281/zenodo.5571352">https://doi.org/10.5281/zenodo.5571352</a> (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: XI)</p> <p>The datasets include original Desmond raw-trajectories (datasets I–VIII), PDB-coordinates for the energy minimized metastable state derived structures (datasets II, IV and VI) and raw-trajectories of the well-tempered metadynamics simulations (dataset IX–XI).</p>
CATH-KinFams: CATH Protein Kinase classification alignments and Hidden Markov Models
<p>CATH KinFams are protein kinase domain families classified according to functional similarity based on SDP. In this deposition we make available 2,210 KinFams sequence alignments alongside Hidden Markov Models built from them to be used with HMMER3.</p> <p>A concatenated library 'kinases_4.3-FF-seed.hmm' is also available to scan against the whole KinFams dataset.</p> <p>The Zenodo deposition contains:</p> <p>kinfams-cath-4.3-seed-alignments.tar.gz - KinFams FASTA file alignments with headers 'UniProt_ID/start-stop' i.e. A8XMX4/281-587</p> <p>kinfams-cath-4.3-seed-hmms.tar.gz - HMMs for each individual KinFam and concatenated in a HMM library.</p> <p>kinfams-cath-4.3-seed-mda-strings - Multi-Domain-Architecture string assignment for each sequence in the KinFams dataset.</p> <p>human_kinfams_af2_models_cif.tar.gz - Chopped mmCIF files containing Human Kinases AlphaFold2 Models.</p>
Dataset for the Tyrosine-protein kinase SYK antibody screening study
<p>This project contains the following underlying data included in a study aiming at characterizing antibodies for Tyrosine-protein kinase SYK. The study is available on Zenodo (https://doi.org/10.5281/zenodo.6566940).</p>
Mitogen Activated Protein Kinase Kinase (MEK1/2) Inhibitor Selumetinib (AZD6244 Hydrogen Sulfate) in People With Neurofibromatosis Type 1 (NF1) Mutated Gastrointestinal Stromal Tumors (GIST)
ClinicalTrials.gov study NCT03109301. IPD Sharing: Not stated. Countries: 0. Publications: 0.
Treatment of Chinese Participants With B-Cell Malignancies With BGB-16673, a Bruton Tyrosine Kinase-Targeted Protein-Degrader
ClinicalTrials.gov study NCT05294731. IPD Sharing: YES. Countries: 1. Publications: 0.
Phase 1 Trial of MSC2490484A, an Inhibitor of a DNA-dependent Protein Kinase, in Combination With Radiotherapy
ClinicalTrials.gov study NCT02516813. IPD Sharing: NO. Countries: 8. Publications: 0.
A Multicentre, Open Label, Phase 1 Trial in Japan of the Mitogen Activated Protein Extracellular Signal Regulated Kinase (MEK) Inhibitor Pimasertib Given Orally to Subjects With Solid Tumors as Monoth
ClinicalTrials.gov study NCT01668017. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: High cell density upregulates calcium oscillation by increasing calcium store content via basal mitogen-activated protein kinase activity
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Data from: Deficit of mitogen-activated protein kinase phosphatase 1 (DUSP1) accelerates progressive hearing loss
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Data from: Evolution of the leucine-rich repeat receptor-like protein kinase gene family: Ancestral copy number and functional divergence of BAM1 and BAM2 in Brassicaceae
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Data from: Prion protein inhibits fast axonal transport through a mechanism involving casein kinase 2
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Optimizing intestinal glucotonic effect via atypical protein kinase C
GEO Series GSE312264. Rattus norvegicus. 4 samples. Type: Expression profiling by high throughput sequencing.
Region-specific roles of stress-activated protein kinase MKK7 in the developing and maturing murine brain
GEO Series GSE293965. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
HOXC6 drives a therapeutically targetable pancreatic cancer growth and metastasis pathway via stimulating MSK1 kinase and suppressing PPP2R2B protein
GEO Series GSE150222. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
PrrA modulation of Mycobacterium tuberculosis response to nitric oxide is critically regulated by serine/threonine protein kinases
GEO Series GSE198999. Mycobacterium tuberculosis. 8 samples. Type: Expression profiling by high throughput sequencing.
Identification of a potent and selective chemical probe for exploring the role of Mediator complex-associated protein kinases CDK8 and CDK19 in human disease [LS-174-T]
GEO Series GSE67846. Homo sapiens. 9 samples. Type: Expression profiling by array.
Spatially resolved single-cell analysis uncovers protein kinase Cδ-expressing microglia with anti-tumor activity in glioblastoma [scRNA-seq]
GEO Series GSE298688. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
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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.