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39 results for “Molecular processes”
Liquid Chromatography - Tandem Mass Spectrometry (LC-MS/MS) and Gas Chromatography - Mass Spectrometry (GC-MS) Reference Libraries from Global Natural Products Social Molecular Networking (GNPS) and National Institute of Standards and Technology (NIST) WebBook Processed for Spectral Library Matching
<div>In order to obtain a high-quality LC-MS/MS reference database for spectral library matching, we selected 22 high-quality GNPS tandem mass spectrometry databases generated under the positive ion mode. Further preprocessing similar to Huber et al involving mass-to-charge (m/z) and intensity filtering yields the database found in the file LCMS_GNPS_reference_library.csv which contains 14,705 electrospray ionization (ESI) mass spectra, each of which corresponds to a unique compound. The NIST WebBook database was used to construct GC-MS database contained in the file GCMS_NIST_WebBook.csv. This database contains 23,721 electron ionization (EI) mass spectra, each of which corresponds to a unique non-hyphenated Chemical Abstract Service (CAS) Registry Number.</div> <div> </div> <div>Both LC-MS/MS and GC-MS databases are organized into three columns: one for the identifier, one for the m/z values, and one for the intensity values. For example, if spectrum A has 20 ion fragments, then there will be 20 rows corresponding to spectrum A in the corresponding database with the identifier A repeated 20 times with the corresponding m/z and intensity values.</div>
Tissue microarray data and processing scripts for The molecular consequences of androgen activity in the human breast
<p>This repository contains raw and processed data from the CODEX imaging dataset in this publication.</p> <p>The RAW data tables provide the resulting nuclei and membrane staining signals obtained from the nuclei segmentation described in the Methods.</p> <p>The processed data file provides the clustered and annotated version described in Methods.</p> <p>The repository also contains two scripts describing the processing of snRNA-seq and snATAC-seq data.</p>
A human genome editing-based MLL-AF4 acute lymphoblastic leukemia model recapitulates key cellular and molecular leukemogenic features. (Processed data)
<p>The prognosis of infant B-cell acute lymphoblastic leukemia (iB-ALL) remains dismal, especially in patients harboring the MLL-AF4 (KTM2A-AFF1) rearrangement, which arises prenatally in early hematopoietic stem/progenitor cells (HSPCs) and accounts for 80% of iB-ALL and 10% of non-infant cases. MLL-AF4+ B-ALL shows a bimodal localization of the MLL gene breakpoint within the MLL break cluster region, and two subgroups of patients based on the gene expression pattern of the HOXA/MEIS cluster have been identified. The pathogenic mechanisms in MLL- AF4+ B-ALL are challenging to study functionally due to the absence of faithful human cellular models recapitulating the disease phenotype and latency. Here, we assess the molecular contribution and leukemogenic capacity of MLL breakpoints occurring in either intron 10 (MLL i10 , centromeric) or intron 12 (MLL i12 , telomeric) in ontogenically-different human HSPCs sourced prenatally (fetal liver) and neonatally (cord blood). CRISPR-Cas9-induced MLL-AF4 (MA) targeting either MLL i10 (M i10 A) or MLL i12 (M i12 A) causes MA-driven in vitro myeloid immortalization in both fetal liver- and cord blood-CD34+ HSPCs. The centromeric location of the MLL breakpoint, but not the cellular ontogeny, determined the expression of HOXA/MEIS1 genes in MLL-edited cells. Centromeric MLL breakpoints endowed enhanced myeloid clonogenic replating to MLL- edited CD34+ HSPCs. The cellular ontogeny and the location of the MLL breakpoint also influenced the capacity of MLL-edited CD34+ HSPCs to initiate pro-B-ALL in vivo, which faithfully recapitulated the molecular, transcriptomic and methylome profiles of patients with primary MA+ iB-ALL. Our data provide key insights into the cellular and molecular leukemogenic determinants of MA+ iB-ALL. This dataset contains processed RNAseq and DNA methylation data from the abovementioned study.</p>
Supporting molecular simulations data for "A combined molecular dynamics and experimental study of two-step process enabling low-temperature formation of phase-pure α-FAPbI3"
<p>Supplementary data for "A combined molecular dynamics and experimental study of two-step process enabling low-temperature formation of phase-pure α-FAPbI3: <a href="https://doi.org/10.1126/sciadv.abe3326">10.1126/sciadv.abe3326</a>"</p>
Processed data supporting the manuscript "Cutting the sap: first molecular phylogeny of twig-girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviors contributed to morphological evolution"
<div><strong>Processed data supporting the manuscript: </strong>Cutting the sap: first molecular phylogeny of twig-girdler longhorn beetles (Coleoptera: Cerambycidae: Lamiinae: Onciderini) suggests shifts in host plant attack behaviors contributed to morphological evolution</div> <div> </div> <div><strong>By:</strong> Diego de S. Souza 1, 2, Rowan L. K. French 3, José O. Silva Júnior 4, Eugenio H. Nearns 5, Luciane Marinoni 4, Ian P. Swift 6, Kelly B. Miller 7, Felix A. H. Sperling 2 & Marcela L. Monné 1</div> <div> </div> <div>1 Department of Entomology, National Museum, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.</div> <div>2 Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.</div> <div>3 Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.</div> <div>4 Department of Zoology, Federal University of Paraná, Curitiba, Paraná, Brazil.</div> <div>5 National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.</div> <div>6 California State Collection of Arthropods, Sacramento, California, USA.</div> <div>7 Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA.</div> <div> </div> <div>Corresponding author: Diego de S. Souza, dsouza@fieldmuseum.org. Current affiliation: Field Museum of Natural History, Chicago, Illinois, USA.</div> <div> </div> <div> </div> <div><strong>List of Contents: </strong></div> <div> </div> <div><strong>Onciderini_concat_matrix.phy</strong></div> <div>Concatenated matrix (cox1, Wg and CPS) used for the phylogenetic analyses of Onciderini (Coleoptera: Cerambycidae: Lamiinae: Onciderini). </div> <div> </div> <div><strong>PartitionFinder_AICc_best_scheme.txt</strong></div> <div>Results from PartitionFinder v2.1.1, containing the best partitioning scheme for the concatenated matrix of Onciderini, identified using the corrected Akaike Information Criterion (AICc), with model definitions for use in the phylogenetic analyses.</div> <div> </div> <div><strong>RAxML_Onciderini_concat_matrix (zip file)</strong></div> <div>- Onciderini_concat_matrix.phy: concatenated matrix (cox1, Wg and CPS) used in the RAxML phylogenetic analyses of Onciderini (Coleoptera: Cerambycidae: Lamiinae: Onciderini).</div> <div>- Partitions_AICc_RAxML.txt: partitioning scheme used in the RAxML analysis as predefined by PartitionFinder v2.1.1 using the corrected Akaike Information Criterion (AICc).</div> <div>- RAxML_bestTree.Onciderini_concat_matrix_ML: best-scoring maximum likelihood tree inferred by RAxML for the concatenated matrix of Onciderini.</div> <div>- RAxML_bipartitions.Onciderini_concat_matrix_final: bipartitions (clades) of the maximum likelihood tree inferred by RAxML with support values estimated from 1,000 pseudoreplicates.</div> <div>- RAxML_bipartitionsBranchLabels.Onciderini_concat_matrix_final: final maximum likelihood tree inferred by RAxML for the concatenated matrix of Onciderini, with labeled branches showing bootstrap support values.</div> <div>- RAxML_bootstrap.Onciderini_concat_matrix_bootstrap: bootstrap trees generated from a non-parametric bootstrap analysis in RAxML based on 1,000 pseudoreplicates.</div> <div>- RAxML_info.Onciderini_concat_matrix_bootstrap: log file containing details of the bootstrap analysis, including the settings and parameters used in the non-parametric bootstrap runs in RAxML.</div> <div>- RAxML_info.Onciderini_concat_matrix_final: log file summarizing the RAxML analysis, including settings and convergence statistics for the final maximum likelihood tree.</div> <div>- RAxML_info.Onciderini_concat_matrix_ML: log file containing details of the maximum likelihood tree search, including the parameters and models applied during the maximum likelihood analysis conducted by RAxML.</div> <div>- RAxML_log.Onciderini_concat_matrix_ML: log file of the maximum likelihood tree search for the concatenated matrix of Onciderini.</div> <div>- RAxML_parsimonyTree.Onciderini_concat_matrix_ML: parsimony starting tree used by RAxML during the maximum likelihood analysis for the concatenated matrix of Onciderini.</div> <div>- RAxML_result.Onciderini_concat_matrix_ML: maximum likelihood tree inferred by RAxML from the concatenated matrix of Onciderini, summarizing the tree topology and likelihood score for the best tree obtained.</div> <div> </div> <div><strong>BI_AICc_Onciderini_concat_matrix (zip file)</strong></div> <div>- BI_AICc_Onciderini_concat_matrix.nex: nexus file containing the concatenated matrix of Onciderini used for Bayesian Inference (BI), including the best-fit model scheme identified by PartitionFinder and MCMC parameters for running the analysis in MrBayes.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex_r1_r2_combined_consensus.tree: consensus tree from two combined independent Bayesian Inference (BI) runs based on the concatenated matrix of Onciderini, after discarding the first 25% of initial generations as burn-in.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex.run1.p: log file containing parameter values and likelihood scores from the first run of the Bayesian Inference (BI) based on the concatenated matrix of Onciderini.</div> <div>- BI_AICc_Onciderini_concat_matrix.nex.run2.p: log file containing parameter values and likelihood scores from the second run of the Bayesian Inference (BI) based on the concatenated matrix of Onciderini.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_lognormal (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_lognormal.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- BEAST2_Onciderini_BD_lognormal_run[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution.</div> <div>- TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a lognormal distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_exponential (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_exponential.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- BEAST2_Onciderini_BD_exponential_[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- TreeAnnotator_Onciderini_BD_exponential_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution.</div> <div>- TreeAnnotator_Onciderini_BD_exponential_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and an exponential distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>BEAST2_Onciderini_BD_uniform (zip file)</strong></div> <div>- BEAUTi_Onciderini_BD_uniform.xml: XML file generated by BEAUTi for running BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- BEAST2_Onciderini_BD_uniform_[1-8].log: log files from eight independent runs of BEAST2, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- TreeAnnotator_Onciderini_BD_uniform_run1-run8_consensus.out: TreeAnnotator output file combining the results of eight BEAST2 runs based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution.</div> <div>- TreeAnnotator_Onciderini_BD_uniform_run1-run8_consensus.tre: consensus tree from eight combined BEAST2 runs, based on the concatenated matrix of Onciderini, using a birth-death (BD) process model and a uniform distribution, after discarding the first 10% of initial generations as burn-in.</div> <div> </div> <div><strong>Comparative_analyses (zip file)</strong></div> <div><strong>RawData (folder):</strong> raw morphometric and girdling data, plus tree that was later pruned for downstream comparative analyses; these data were used as input for the OncidHeadDimorphism-DatasetPREP-FINAL.R data cleaning script. </div> <div>- Onciderini_BD_lognormal_run1-run8_consensus.nwk: newick version of TreeAnnotator_Onciderini_BD_lognormal_run1-run8_consensus.tre (outputted as a newick file by importing the .tre file into FigTree and exporting in newick format).</div> <div>- Measurements_Onciderini_Raw_Final.csv: individual-level raw morphometric data for Onciderini.</div> <div>- Behav_Matrix_2_states_trimmed_2022-12-15.csv: species-level data on girdling status for Onciderini species, with all Lochmaeocles species classified as girdlers (2 behavioral states across Onciderini species). </div> <div>- Matrix_3_states_trimmed_final.csv: species-level data on girdling status for Onciderini species, with all Lochmaeocles species classified as facultative girdlers (3 behavioral states across Onciderini species). </div> <div>- Matrix_2_states_trimmed_1LochGirdler_Final.csv: species-level data on girdling status for Onciderini species, with only one Lochmaeocles species (L. tessellatus) classified as a girdler (2 behavioral states across Onciderini species). </div> <div> </div> <div><strong>ProcessedData (folder): </strong>filtered data and pruned trees outputted by the OncidHeadDimorphism-DatasetPREP-FINAL.R script</div> <div>- oncid_f_36spp_clean.csv: dataset of species means and log-ratios for morphometric traits in females, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_m_42spp_clean.csv: dataset of species means and log-ratios for morphometric traits in males, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_sd_35spp_clean.csv: dataset of species means for sexual dimorphism in morphometric traits, plus girdling data; only includes species that have girdling data and are in the phylogenetic tree</div> <div>- oncid_girdlingbehav_allingroupspp_clean.csv: full dataset of girdling behavior for 56 Onciderini species that are in the phylogenetic tree; includes separate columns for the three alternative girdling classification schemes</div> <div>- oncid_tree_behavfull_56spp.nwk: pruned phylogenetic tree for the full girdling dataset (56 species)</div> <div>- oncid_tree_f_36spp.nwk: pruned phylogenetic tree for the female morphometric dataset (36 species)</div> <div>- oncid_tree_m_42spp.nwk: pruned phylogenetic tree for the male morphometric dataset (42 species)</div> <div>- oncid_tree_mf_43spp.nwk: pruned phylogenetic tree for all species with morphometric data for males or females; used for the stochastic character map next to the heatmap plot (Fig 4)</div> <div>- oncid_tree_sd_35spp.nwk: pruned phylogenetic tree for the sexual dimorphism dataset (35 species)</div> <div> </div> <div><strong>FittedModels (folder): </strong>fitted models (mvgls, model comparison analyses, OUM models, simmaps) outputted by the OncidHeadDimorphism-Analysis-FINAL.R script </div> <div>- MacroModelFits_logRtraits_f_36spp-2024-10-12.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to female morphometric data across 100 stochastic character maps of girdling behavior</div> <div>- MacroModelFits_logRtraits_m_42spp-2024-10-12.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to male morphometric data across 100 stochastic character maps of girdling behavior</div> <div>- MacroModelFits-SDDI-35spp_2024-10-11.Rdata: summary of model comparison results for Brownian Motion (BM), single-peak Ornstein-Uhlenbeck (OU), multipeak OU (OUM), and multi-rate Brownian motion (BMM) models (univariate and multivariate) fitted to sexual dimorphism data across 100 stochastic character maps of girdling behavior</div> <div>- mvgls-results-headsize-mf-2024-10-12.Rdata: fitted mvgls regression models for male and female traits (analyzed separately)</div> <div>- mvgls-results-sddi-2024-10-12.Rdata: fitted mvgls regression models for sexual dimorphism</div> <div>- OUM_headtraits_f_36spp-2024-10-12.Rdata: fitted OUM models and summary statistics for female head traits</div> <div>- OUM_headtraits_m_42spp-2024-10-12.Rdata: fitted OUM models and summary statistics for male head traits</div> <div>- OUM-SDDI-35spp-2024-10-12.Rdata: fitted OUM models and summary statistics for sexual dimorphism in head traits</div> <div>- simmaps_ard_full_2state.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with two behavioral states (girdling or non-girdling) - all Lochmaeocles species are classified as girdlers</div> <div>- simmaps_ard_full_3state.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with three behavioral states (girdling, non-girdling, or facultative girdling)</div> <div>- simmaps_ard_full_1Loch.RDS: stochastic character maps of girdling behaviour for all 56 species with girdling data, with two behavioral states (girdling or non-girdling) - only one Lochmaeocles species (L. tessellatus) is classified as a girdler</div> <div>- simmaps_ard_m.RDS: stochastic character map for the 42 species used in the analyses of male morphometric traits</div> <div>- simmaps_ard_f.RDS: stochastic character map for the 36 species used in the analyses of female morphometric traits</div> <div>- simmaps_ard.RDS: stochastic character map for the 35 species used in the sexual dimorphism analyses; 2 behavioral states.</div> <div> </div> <div><strong>Rscripts (folder): </strong>R scripts used to process data and run phylogenetic comparative analyses of head size and girdling behavior.</div> <div>- OncidHeadDimorphism-DatasetPREP-FINAL.R: R script used to filter data and prune trees from the RawData folder for downstream phylogenetic comparative analyses; outputs of this script are in the ProcessedData folder.</div> <div>- OncidHeadDimorphism-Analysis-FINAL.R: R script used to analyze data in the ProcessedData folder to answer questions about the origin and evolution of girdling behavior and the relationship between girdling and head size or head size sexual dimorphism; fitted models outputted by this script are in the FittedModels folder</div> <div>- OncidHeadDimorphism-Plots-FINAL.R: R script used to generate plots for the manuscript<br><br></div>
Data from: Molecular and cellular processes of deafferentation after plexus injury in human dorsal root ganglia
<p><strong>Dataset of human dorsal root ganglia (DRG) images and deep learning models</strong></p> <p>Sections of six control and six plexus patient DRG were immunostained and imaged using large-field (tile) microscopy. Two staining combinations were investigated: </p> <p>- n<em>eurofilament </em>(NF), <em>fatty acid binding protein 7</em> (FABP7), and <em>clusterin (</em>APOJ)</p> <p>- n<em>eurofilament </em>(NF),<em> ionized calcium-binding adapter molecule 1 (</em>IBA1), and <em>microtubule-associated protein 2</em> (MAP2) </p> <p>NF-positive neurons were segmented with a deep learning method (<em>deepflash2</em>). FABP7 and IBA1 were segmented with a thresholding method.</p> <p>Provided are:</p> <p>- all images and corresponding segmentation masks for NF, FABP7, and IBA1 </p> <p>- images and annotated segmentation masks of NF-positive neurons (3 experts annotated the same 10 images, the estimated ground truth masks were used for training of deep learning models)</p> <p>- the deep learning model ensemble (3) for segmentation of NF-positive neurons</p> <p> </p> <p> </p>
EMD data for the paper "Impact of ad-hoc post-processing parameters on the lubricant viscosity calculated with equilibrium molecular dynamics simulations"
<p>This archive contains the post-processing data obtained from EMD simulations of <strong>2,2,4-Trimethylhexane</strong> lubricant molecule under various operating conditions. The EMD simulations were performed using LAMMPS with COMPASS force field. (See manuscript and README for details.)</p>
Multi-omic integration of DNA methylation and gene expression data reveals molecular vulnerabilities in glioblastoma (processed data)
<p>Glioblastoma multiforme (GBM) is one of the most aggressive types of cancer and exhibits profound genetic and epigenetic heterogeneity, making the development of an effective treatment a major challenge. The recent incorporation of molecular features into the diagnosis of GBM patients has led to an improved categorisation into various tumour subtypes with different prognoses and disease management. In this work, we have exploited the benefits of genome-wide multi-omic approaches to identify potential molecular vulnerabilities existing in GBM patients. Integration of gene expression and DNA methylation data from both bulk GBM and patient-derived GBM stem cell lines has revealed the presence of major sources of GBM variability, pinpointing subtype-specific tumour vulnerabilities amenable to pharmacological interventions. In this sense, inhibition of the AP1, SMAD3 and RUNX1 / RUNX2 pathways, in combination or not with the chemotherapeutic agent temozolomide, led to the subtype-specific impairment of tumour growth, particularly in the context of the aggressive, mesenchymal-like subtype. These results emphasize the involvement of these molecular pathways in the development of GBM and have potential implications for the development of personalized therapeutic approaches.</p>
Biochar mitigates microplastic-induced Destabilization of soil organic carbon via molecular Recalcitrance and microbial process regulation
Open the record for dataset details and reuse information.
Sensitive, Efficient and Portable Analysis of Molecular Exchange Processes by Hyperpolarized Ultrafast NMR
<p>Dataset for manuscript:</p> <p><a href="https://doi.org/10.1002/anie.202203957"><strong>Sensitive, Efficient and Portable Analysis of Molecular Exchange Processes by Hyperpolarized Ultrafast NMR </strong></a></p> <p> </p> <p>The uploaded archive contains:</p> <p>1. File Analysis.ipynb: Jupyter notebook with analysis and figure generation presented in the article<br> 2. UF-DEXSY experiment with mixing time 10ms: DEXSY/25<br> 3. UF-DEXSY experiment with mixing time 30ms: DEXSY/26<br> 4. UF-DEXSY experiment with mixing time 100ms: DEXSY/28<br> 5. Reference CPMG: CPMG/16<br> 6. Coil profile with yeast sample: UFProfile/4<br> 7. Coil profile with dopped water sample: UFProfile/101</p> <p> </p>
Dataset for article "Measurement report: Molecular characteristics of cloud water in southern China and insights into aqueous-phase processes from Fourier Transform Ion Cyclotron Resonance Mass Spectrometry"
<p>This dataset is the result of molecular composition of cloud water collected in southern China obtained by ESI FT-ICR MS. This dataset is for the article "Measurement report: Molecular characteristics of cloud water in southern China and insights into aqueous-phase processes from Fourier Transform Ion Cyclotron Resonance Mass Spectrometry" published in Atmospheric Chemistry and Physics by Sun et al. (2021).</p>
Exploring the Molecular Pathways of the Activation Process on PPARγ Recurrent Bladder Cancer Mutants
<p>The intricate involvement of Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) in vital processes such as glucose homeostasis and adipogenesis is well established. However, its multifaceted role in cancer, particularly in luminal bladder cancer, remains a subject of intense debate. In this context, PPARγ’s overexpression and activation have been implicated in tumorigenesis. Notably, specific gain-of-function mutations (M280I, I290M, and T475M) within PPARγ’s ligand-binding domain have been pinpointed in bladder cancer, correlating with receptor activation. Nonetheless, the underlying molecular pathways prompted by these mutations remain obscure. Here, we employed a dual-basin structure-based model (db SBM) to unveil the intricate conformational dynamics that underlie the transition between PPARγ’s inactive and active states. Additionally, we explored the effects of the M280I, I290M, and T475M mutations on this pivotal process. Our findings concur with existing literature, revealing heightened ligand-independent transcriptional activity in the I290M and T475M mutants compared to other variants. Importantly, both mutants displayed enhanced stabilization of the active state relative to the wild-type receptor, and the I290M mutation promoted a remarkably specific transition route, rendering it a prime candidate for further investigation. Electrostatic analysis pinpointed the pivotal role of residues K303 and E488 in the activation cascade of I290M. This insight was substantiated by biophysical assays, as disruption of the K303-E488 interaction curtailed the thermal stabilization characteristic of the I290M mutation. These findings designate K303 and E488 as potential targets for inhibitors aimed at modulating PPARγ activation, with promising implications for refining bladder cancer prognosis. In sum, our study highlights the remarkable predictive capabilities achieved through the integration of simulation and cheminformatics methods, validated by biochemical experiments, to gain deeper insights into molecular mechanisms of activation and identify target residues for protein modulation.</p>
Molecular and spatial signatures of human and rat corpus cavernosum physio-pathological processes at single-cell resolution
<p><span>The composition and cellular heterogeneity of the corpus cavernosum (CC) microenvironment has been characterized, but the spatial heterogeneity at the molecular level remains unexplored. In this study, we integrate single-cell RNA sequencing (scRNA-seq) and spatial transcriptome sequencing to comprehensively chart the spatial cellular landscape of human and rat CC under normal and disease conditions. We observe differences in the proportion of cell subtypes and marker genes between humans and rats. Based on the analysis of the fibroblasts (FB) niche, we also find that the enrichment scores of mechanical force signaling vary across different regions and correlate with the spatial distribution of FB subtypes. In vitro, the soft and hard extracellular matrix (ECM) induces the differentiation of FB into APO+FB and COMP+FB, respectively. In summary, our study provides a cross-species and </span><span>physio-pathological</span><span> </span><span>transcriptomic atlas of the CC, contributing to a further understanding of the molecular anatomy and regulation of penile erection.</span></p>
Molecular dynamics simulation: The process of phosphate transfer from fructose-1,6-bisphosphate to phosphoglycerate mutase 1
<p><span>Molecular dynamics (MD) simulations were performed to investigate the dynamic process of the binding and phosphorylation of PGAM1 by FBP. </span></p>
Data from: Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating
Open the record for dataset details and reuse information.
A Comparative Study of Multi-objective Optimization Methodologies for Molecular and Process Design
<p>The files contain the set of solutions generated with various multi-objective optimization methods.</p>
Multimodal Analysis for Human ex vivo Studies Shows Extensive Molecular Changes from Delays in Blood Processing
<p>This is an assembled raw data in Seurat object. Expression profiling data can be accessed from <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156989">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156989</a>.</p>
Evaluation of Half-Dose Molecular Breast Imaging With Wide Beam Reconstruction Processing
ClinicalTrials.gov study NCT01653964. IPD Sharing: NO. Countries: 1. Publications: 0.
A Lignin Molecular Brace Controls Precision Processing of Cell Wall Critical for Surface Integrity in Arabidopsis
GEO Series GSE110213. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
Multimodal Analysis for Human ex vivo Studies Shows Extensive Molecular Changes from Delays in Blood Processing
GEO Series GSE156989. Homo sapiens. 55 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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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.