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846 results for “homologs”
A Cambrian spiny stem mollusc and the deep homology of lophotrochozoan scleritomes
<p>Molluscs encompass enormous disparity, including familiar clams and snails alongside aculiferans (chitons and vermiform aplacophorans) with complex multicomponent skeletons. Palaeozoic fossils trace crown molluscs to forms exhibiting a combination of biomineralised shells and sclerites. We describe a shell-less, Cambrian stem mollusc, Shishania aculeata, with conical, hollow organic sclerites and a smooth ventral girdle, broad foot, and mantle cavity. The sclerites have a microstructure of narrow canals consistent with the impressions of chaetal microvilli found in annelids and brachiopods. Shishania sclerites provide a morphological steppingstone between typical chaetae and the external organic part of aculiferan sclerites that encloses a mineralised body. This discovery reinforces a common origin of lophotrochozoan chaetae and the biomineralized aculiferan sclerites, suggesting the mollusc ancestor was densely covered with hollow organic chaetae.</p>
Saccharomyces cerevisiae IRC7 homology model
<p><strong>IRC7 homology model for S. cerevisiae.</strong></p> <p>IRC7 was modelled using the structures for <em>Escherichia coli</em> Cystathionine beta-lyase (PDB accession: 1CL2) and <em>Trichomonas vaginalis </em>Methionine Gamma-Lyase (PDB accession: 1E5F) as comparative references. The A and B chains of 1CL2 were superposed to 1E5F. The sequences for IRC7, 1CL2 and 1E5F were aligned with clustalx. Ten models were generated with UCSF Modeller v9.15 and evaluated with PROCHECK. The best model is uploaded here and is also available at the Protein Model DataBase (accession: PM0081794).</p>
Homology model based on 1JXX
<p>Homology model based on 1JXX</p> <p>starting sequence: SVCCPSLVARTNYNVCRLPGTEAALCATFTGCIIIPGATCGGDYAN</p> <p>Swiss Model online 24-11-2019</p>
Primary data for manuscript provisionally titled, "Fluorination-homologation of the biomass derivative Cyrene"
<p>Primary NMR FID files and HRMS data collected for compounds described in the manuscript, "Fluorination-homologation of the biomass derivative Cyrene."</p> <p>This material can be opened and processed using Topspin or Spinworks programs. </p>
Calponin-Homology Domain mediated bending of membrane associated actin filaments
<p><span>This dataset contains data from experiments described in </span>'Palani S, Ghosh S, Ivorra-Molla E, Clarke S, Suchenko A, Balasubramanian MK, Köster DV. 2021. Calponin-homology domain mediated bending of membrane associated actin filaments. <i>Elife</i> <b>10</b>. doi:10.7554/eLife.61078'. This dataset consists of fluorescence microscopy images obtained by total internal reflection fluorescence (TIRF) microscopy. Using an <em>in vitro</em> approach, we studied the effect of the IQGAP protein fragment Rng2(1-189) on the geometry of actin filaments when tethered to supported lipid bilayers all reconstituted from purified proteins. The main findings are that Rng2(1-189) bends actin filaments into tight rings when tethered to supported lipid bilayers.</p>
Fig. 14. Thoopterus nigrescens AMNH 196442 in Element Homology and the Evolution of Dental Formulae in Megachiropteran Bats (Mammalia: Chiroptera: Pteropodidae)
Fig. 14. Thoopterus nigrescens AMNH 196442
Fig. 15. Nyctimene major AMNH 159295 in Element Homology and the Evolution of Dental Formulae in Megachiropteran Bats (Mammalia: Chiroptera: Pteropodidae)
Fig. 15. Nyctimene major AMNH 159295,
Fig. 11. Thoopterus nigrescens AMNH 196442 in Element Homology and the Evolution of Dental Formulae in Megachiropteran Bats (Mammalia: Chiroptera: Pteropodidae)
Fig. 11. Thoopterus nigrescens AMNH 196442
Fig. 10. Cynopterus brachyotis AMNH 222764 in Element Homology and the Evolution of Dental Formulae in Megachiropteran Bats (Mammalia: Chiroptera: Pteropodidae)
Fig. 10. Cynopterus brachyotis AMNH 222764
Accurate profiling of full length Fv in highly homologous antibody libraries using UMI tagged short reads
<p>Data consists of raw Illumina MiSeq 2x250bp reads from the Fab mini library Mix9A, and Illumina MiSeq 2x300bp reads from the Fab mini library Mix14 at 8 attomole as described in the journal publication "Accurate profiling of full length Fv in highly homologous antibody libraries using UMI tagged short reads".</p>
Mechanism of RecF-RecO-RecR cooperation in bacterial homologous recombination
<p>This repository includes the following source datasets:</p> <p><strong>1. FluorescenceAnisotropyIII.zip </strong></p> <p>This contains following files:</p> <ol> <li>The raw fluorescence anisotropy file (Excel file) showing the values for Polarization, Anisotropy, Total Intensity, Intensity (parallel) and Intensity (perpendicular) for all the samples included in the paper as separate sheets.</li> <li>The analysis files generated in the Graphpad prism.</li> <li>The details of the files.</li> </ol> <p> </p> <p><strong>2. FT-IR.zip</strong>: This contains the normalized values for the FT-IR spectroscopy of the WT RecF, WT RecR, RecF A170W and RecR A147W.</p> <p> </p> <p><strong>3. Glycerol gradient.zip</strong>: This contains the raw gel files for the three sets of independent experiments, standard protein ruler with the respective WT RecF, WT RecO and WT RecR and details regarding the loading of samples on gels.</p> <p> </p> <p><strong>4. Pull-downII.zip</strong>: This contains details of all the pull-down experiments and the raw gel files used for</p> <ol> <li>Quantification</li> <li>The major samples for all the experiments done in triplicate</li> <li>Figure preparation for paper</li> </ol> <p> </p> <p> </p>
Data for: Insect homolog of oxytocin/vasopressin associated with parenting of males but not females in a subsocial beetle
<p>Parental care is thought to evolve through modification of behavioral precursors, which predicts that the mechanistic changes occur in the genes underlying those traits. The duplicated gene system of oxytocin/vasopressin has been broadly co-opted across vertebrates to influence parenting, from a pre-duplication ancestral role in water balance. It remains unclear whether co-option of these genes for parenting is limited to vertebrates. Here, we experimentally tested for associations between <em>inotocin </em>gene expression and water balance, parental acceptance of offspring, and active parenting in the subsocial beetle <em>Nicrophorus orbicollis</em>, to test whether a single copy homologue,<em> inotocin</em>, has similarly been co-opted for parental care in a species with elaborate parenting. As expected, <em>inotocin</em> was associated with water balance in both sexes. <em>Inotocin</em> expression increased around sexual maturation in both males and females, although more clearly in males. Finally, we found that expression of inotocin was not associated with acceptance of larvae but was associated with a transition to male but not female parenting. Moreover, level of offspring provisioning behavior and gene expression were positively correlated in males but uncorrelated in females. Our results suggest a broad co-option of this system for parenting that may have existed prior to gene duplication, and that inotocin may be associated with flexibility in parenting behavior.</p>
Petascale Homology Search for Structure Prediction - MSAs
<p>Multiple sequence alignments (MSAs) of CASP15 targets used in "Petascale Homology Search for Structure Prediction" publication. </p> <p>Each MSA is constructed from a combination of different sequence databases, using different search tools, 1) ColabFoldDB (CFDB) using ColabFold search module, 2) Sequence Read Archive (SRA) using MMseqs2, and 3) UniRef30+BFD using HHblits (HH).</p> <ul> <li><strong>Queries</strong>: Regular CASP15 TS targets, excluding TBM-easy</li> <li><strong>MSAs (A3M) </strong> <ul> <li>CFDB (cfdb.tar.gz)</li> <li>SRA + CFDB (sra_cfdb.tar.gz)</li> <li>HH + CFDB (hh_cfdb.tar.gz)</li> <li>HH + SRA + CFDB (hh_sra_cfdb.tar.gz)</li> </ul> </li> </ul>
Homology judgements of pre-Darwinian naturalists explained by general human shape matching abilities
<p>Dataset relative to the following publication:</p> <p>Stegmann, U., & Schmidt, F. (2023). Homology judgements of pre-evolutionary naturalists explained by general human shape matching abilities. <em>Scientific Reports, 13</em>, 12269.</p> <p>Each experiment folder contains the data relative to one experiment, together with a text file with comments.</p>
Data from: Remote homolog detection places insect chemoreceptors in a cryptic protein superfamily spanning the tree of life
<p><span>Many proteins exist in the so-called "twilight zone" of sequence alignment, where low pairwise sequence identity makes it difficult to determine homology and phylogeny. As protein tertiary structure is often more conserved, recent advances in<em> ab initio </em>protein folding have made structure-based identification of putative homologs feasible. However, structural screening and phylogenetics are in their infancy, particularly for twilight zone proteins. We present a pipeline for the identification and characterization of distant homologs, and apply it to 7-transmembrane domain ion channels (7TMICs), a protein group founded by insect Odorant and Gustatory receptors. Previous sequence and limited structure-based searches identified putatively-related proteins, mainly in other animals and plants. However, very few 7TMICs have been identified in non-animal, non-plant taxa. Moreover, these proteins' remarkable sequence dissimilarity made it uncertain if disparate 7TMIC types (Gr/Or, Grl, GRL, DUF3537, PHTF and GrlHz) are homologous or convergent, leaving their evolutionary history unresolved. Our pipeline identified thousands of new 7TMICs in archaea, bacteria and unicellular eukaryotes. Using graph-based analyses and protein language models to extract family-wide signatures, we demonstrate that 7TMICs have structure and sequence similarity, supporting homology. Through sequence and structure-based phylogenetics, we classify eukaryotic 7TMICs into two families (Class-A and Class-B), which are the result of a gene duplication predating the split(s) leading to Amorphea (animals, fungi and allies) and Diaphoretickes (plants and allies). Our work reveals 7TMICs as a cryptic superfamily with origins close to the evolution of cellular life. More generally, this study serves as a methodological proof of principle for the identification of extremely distant protein homologs.</span></p>
Assess Efficacy & Safety of Selumetinib in Combination With Docetaxel in Patients Receiving 2nd Line Treatment for v-Ki-ras2 Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) Positive NSCLC
ClinicalTrials.gov study NCT01933932. IPD Sharing: YES. Countries: 26. Publications: 2.
A Study of Niraparib in Combination With Abiraterone Acetate and Prednisone Versus Abiraterone Acetate and Prednisone for the Treatment of Participants With Deleterious Germline or Somatic Homologous
ClinicalTrials.gov study NCT04497844. IPD Sharing: YES. Countries: 33. Publications: 1.
Ph I Ipilimumab Vemurafenib Combo in Patients With v-Raf Murine Sarcoma Viral Oncogene Homolog B1 (BRAF)
ClinicalTrials.gov study NCT01400451. IPD Sharing: Not stated. Countries: 1. Publications: 3.
A Study of Pembrolizumab and Olaparib for People With Metastatic Pancreatic Ductal Adenocarcinoma and Homologous Recombination Deficiency or Exceptional Treatment Response to Platinum-Based Therapy
ClinicalTrials.gov study NCT04666740. IPD Sharing: YES. Countries: 1. Publications: 1.
Pembrolizumab Activity in Patients With Homologous Recombination Competent and Deficient Tumors
ClinicalTrials.gov study NCT03274661. IPD Sharing: NO. Countries: 1. Publications: 1.
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.