Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
99
datasets available to search
ShareScore release 0.9.0
Dataset results
99 results for “Antimicrobial peptides”
Innate immunity promotes sleep through epidermal antimicrobial peptides
<p>Wounding and infection trigger a protective innate immune response that includes the production of antimicrobial peptides in the affected tissue as well as increased sleep. Little is known, however, how peripheral wounds or innate immunity signal to the nervous system to increase sleep. We found that during <i>C. elegans</i> larval molting, an epidermal tolloid/BMP-1-like protein called NAS-38 promotes sleep. NAS-38 is negatively regulated by its thrombospondin domain and acts through its astacin protease domain to activate p38 MAP/PMK-1 kinase and TGF-β-SMAD/SMA-3-dependent innate immune pathways in the epidermis that cause STAT/STA-2 and SLC6 (solute carrier)/SNF-12-dependent expression of antimicrobial peptide (AMP) genes. We show that more than a dozen epidermal AMPs act as somnogens, signaling across tissues to promote sleep through the sleep-active RIS neuron. In the adult, epidermal injury activates innate immunity and turns up AMP production to trigger sleep, a process that requires EGFR signaling that is known to promote sleep following cellular stress. We show for one AMP, NLP-29, that it acts through the neuropeptide receptor NPR-12 in locomotion-controlling neurons that are presynaptic to RIS and that depolarize this neuron to induce sleep. Sleep in turn increases the chance of surviving injury. Thus, we found a novel mechanism by which peripheral wounds signal to the nervous system to increase protective sleep. Such a cross-tissue somnogen signaling function of AMPs might also boost sleep in other animals including humans.</p>
Data from: Evolution of defence cocktails: antimicrobial peptide combinations reduce mortality and persistent infection
The simultaneous expression of costly immune effectors such as multiple antimicrobial peptides is a hallmark of innate immunity of multicellular organisms, yet the adaptive advantage remains unresolved. Here, we test current hypotheses on the evolution of such defence cocktails. We use RNAi gene knock-down to explore, the effects of three highly expressed antimicrobial peptides, displaying different degrees of activity in vitro against Staphylococcus aureus, during an infection in the beetle Tenebrio molitor. We find that a defensin confers no survival benefit but reduces bacterial loads. A coleoptericin contributes to host survival without affecting bacterial loads. An attacin has no individual effect. Simultaneous knock-down of the defensin with the other AMPs results in increased mortality and elevated bacterial loads. Contrary to common expectations, the effects on host survival and bacterial load can be independent. The expression of multiple AMPs increases host survival and contributes to the control of persisting infections and tolerance. This is an emerging property that explains the adaptive benefit of defence cocktails.
Supplementary Information: Multimodal binding and inhibition of bacterial ribosomes by the 2 antimicrobial peptides Api137 and Api88
<div> <div>This dataset contains important data files for the MD simulation that are part of this publication.</div> <div> </div> <div>The "simulations" directory contains Gromacs parameter files (.mdp) and the run input files (.tpr) as well as the final coordinate files (.gro) of each individual production simulation.</div> <div> </div> <div>The directory "figure3" contains the raw data used to create Figure 3 in the manuscript.</div> <div> </div> <div>The subdirectory "a" contains the data for the PCA projection plot in subfigure 3a. It includes projections of the simulation ensembles of Api88 conformation I-III on to the two dominant conformational modes (.xvg) and the respective extreme conformations (.pdb). The projections of the three initial models and the optimized structure set are also included.</div> <div> </div> <div>Subdirectory "b" contains a numpy array (.npy) with the data for the correlation heatmap in subfigure 3b.</div> <div> </div> <div>Subdirectory "c" contains the results of several correlation-optimization searches. Each directory "N#_maps", where # is to be replaced by the number of structures in the set, contains the search results for N correlation-optimized structures in the Api88 trajectories in the form of a pickled python dictionary (state.pkl). The dictionary has the following keys:</div> <ul> <li>used: Already used sets of MD structures (frozenset)</li> <li>selection: Structure set selected in the last iteration (set)</li> <li>weights: weights of each structure in the selected structure set (numpy array)</li> <li>iteration: Counter of the last iteration (int)</li> </ul> <div> </div> <div>The directory "supplentary_figure_correlation_time" contains the data for a plot of the optimized correlation coefficient as a function of simulation time. The results of the optimization algorithms (as pickled python objects) are included in the subdirectories with the associated trajectory length as a name.</div> </div> <p> </p>
Computational dataset, scripts and models for 'Lipid shape as a membrane activity modulator of a model antimicrobial peptide'
<p>Analysis scripts and computational models used in the manuscript 'Lipid shape as a membrane activity modulator of a model antimicrobial peptide', by Marcin Makowski, Octávio L. Franco, Nuno C. Santos and Manuel N. Melo.</p>
The lower airways microbiome and antimicrobial peptides in Idiopathic Pulmonary Fibrosis differ from Chronic Obstructive Pulmonary Disease
<p><strong>Background</strong>: The lower airways microbiome and host immune response in chronic pulmonary diseases are incompletely understood. We aimed to investigate possible microbiome characteristics and key antimicrobial peptides and proteins in idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD).</p> <p><strong>Methods</strong>: 12 IPF patients, 12 COPD patients and 12 healthy controls were sampled with oral wash (OW), protected bronchoalveolar lavage (PBAL) and right lung protected sterile brushings (rPSB). The antimicrobial peptides and proteins (AMPs), secretory leucocyte protease inhibitor (SLPI) and human beta defensins 1 and 2 (hBD-1 & hBD-2), were measured in PBAL by enzyme linked immunosorbent assay (ELISA).</p> <p>The V3V4 region of the bacterial 16S rDNA gene was sequenced. Bioinformatic analyses were performed with QIIME 2.</p> <p><strong>Results</strong>: hBD-1 levels in PBAL for IPF were lower compared with COPD. The predominant phylae in IPF were <i>Firmicutes</i>, <i>Bacteroides</i> and <i>Actinobacteria</i>; <i>Proteobacteria</i> were among top three in COPD. Differential abundance analysis at genus level showed significant differences between study groups for less abundant, mostly oropharyngeal, microbes. Alpha diversity was lower in IPF in PBAL compared to COPD (p=0.03) and controls (p=0.01), as well as in rPSB compared to COPD (p=0.02) and controls (p=0.04). Phylogenetic beta diversity showed significantly more similarity for IPF compared with COPD and controls. There were no significant correlations between alpha diversity and AMPs.</p> <p><strong>Conclusions</strong>: IPF differed in microbial diversity from COPD and controls, accompanied by differences in antimicrobial peptides. Beta diversity similarity between OW and PBAL in IPF may indicate that microaspiration contributes to changes in its microbiome<b>.</b></p>
Synergistic antimicrobial mechanism of the ultra-short antimicrobial peptide R3W4V with a tadpole-like conformation
Open the record for dataset details and reuse information.
Decorating Nanostructured Surfaces with Antimicrobial Peptides to Efficiently Fight Bacteria
<p>Data underlying the figures in the publication “Decorating Nanostructured Surfaces with Antimicrobial Peptides to Efficiently Fight Bacteria”, published in <em>ACS Appl. Bio Mater</em>., <strong>2020</strong>, 3, 3, 1533–1543.</p> <p><a href="https://pubs.acs.org/doi/10.1021/acsabm.9b01154">https://pubs.acs.org/doi/10.1021/acsabm.9b01154</a></p> <p>Table of contents:</p> <p><strong>1. Figure 1</strong>; Zip file containing the numerical data for the FCS studies of <em>Figure 1</em>.</p> <p><strong>2. Figure 2</strong>; Zip file containing the data underlying <em>Figure 2</em>.</p> <p><strong>3. Figure 3</strong>; Zip file containing the numerical data for the XPS studies of <em>Figure 3</em>.</p> <p><strong>4. Figure 4</strong>; Zip file containing the numerical data for the QCM-D studies of <em>Figure 4</em>.</p> <p><strong>5. Figure 5</strong>; Zip file containing the data underlying <em>Figure 5</em>.</p> <p><strong>6. Table 1</strong>; Zip file containing the numerical data for the FCS Fitting Parameters in <em>Table 1</em>.</p> <p><strong>5. Table 2</strong>; Zip file containing the numerical data for the Atomic concentrations calculated in <em>Table 1</em>.</p> <p> </p> <p> </p> <p> </p>
Mixed chirality α-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography
<p>The upload contains additional primary data associated with the publication <a href="https://doi.org/10.1039/D1CB00124H">https://doi.org/10.1039/D1CB00124H</a>, including raw data in the original file format whenever possible.</p> <p>Data content: HPLC-MS, CD, Vesicle leakage, Molecular Dynamics, Crystallography (primary electron density maps) and Supporting Information.</p>
Raw data for: Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides
<p>This repository contains data related to "Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides" by Pandi et al.</p> <p>Included are molecular dynamics parameter files, initial structures after system equilibration and production trajectories. For simulations of AMPs with membranes, trajectories are subsampled with 1 frame every 5 ns and final structures after 1 μs of production simulation are included.</p> <p>Contact information:<br> Name: Stefan L. Schaefer<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: stefan.schaefer@biophys.mpg.de</p>
CalcAMP: A new machine learning model for the accurate pre-diction of antimicrobial activity of peptides
<p>Datasets used for the publication: </p> <p>CalcAMP: A new machine learning model for the accurate prediction of antimicrobial activity of peptides</p>
To fold or not to fold: diastereomeric optimization of an α-helical antimicrobial peptide
<p>The upload contains additional primary data associated with the publication <a href="https://doi.org/10.1021/acs.jmedchem.3c00460">https://doi.org/10.1021/acs.jmedchem.3c00460</a>, including raw data in the original file format whenever possible.</p> <p>Data content: HPLC-MS for characterization and serum stability, HRMS, CD, Vesicle leakage, Cytotoxicity, Molecular Dynamics, Crystallography (primary electron density maps), pictures for microbiological and hemolysis assays and Supporting Information.</p>
Antimicrobial Peptides in Periodontitis
ClinicalTrials.gov study NCT02793453. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Role of Antimicrobial Peptides in Host Defense Against Vaccinia Virus
ClinicalTrials.gov study NCT00407069. IPD Sharing: YES. Countries: 1. Publications: 7.
The Role of Anti-inflammatory Cytokines and Antimicrobial Peptide LL-37 Biomarkers in the Treatment of Periodontal Disease.
ClinicalTrials.gov study NCT04404335. IPD Sharing: NO. Countries: 1. Publications: 11.
Data from: Evolution of defence cocktails: antimicrobial peptide combinations reduce mortality and persistent infection
Open the record for dataset details and reuse information.
Data from: Chronic exposure to a neonicotinoid increases expression of antimicrobial peptide genes in the bumblebee Bombus impatiens
Open the record for dataset details and reuse information.
Data from: A concise review on antimicrobial peptides for prevention and treatment of dental caries
Open the record for dataset details and reuse information.
Innate immunity promotes sleep through epidermal antimicrobial peptides
Open the record for dataset details and reuse information.
The lower airways microbiome and antimicrobial peptides in Idiopathic Pulmonary Fibrosis differ from Chronic Obstructive Pulmonary Disease
Open the record for dataset details and reuse information.
Data from: Increased survival of experimentally evolved antimicrobial peptide-resistant Staphylococcus aureus in an animal host
Antimicrobial peptides (AMPs) have been proposed as new class of antimicrobial drugs, following the increasing prevalence of bacteria resistant to antibiotics. Synthetic AMPs are functional analogues of highly evolutionarily conserved immune effectors in animals and plants, produced in response to microbial infection. Therefore, the proposed therapeutic use of AMPs bears the risk of 'arming the enemy': bacteria that evolve resistance to AMPs may be cross-resistant to immune effectors (AMPs) in their hosts. We used a panel of populations of Staphylococcus aureus that were experimentally selected for resistance to a suite of individual AMPs and antibiotics to investigate the 'arming the enemy' hypothesis. We tested whether the selected strains showed higher survival in an insect model (Tenebrio molitor) and cross-resistance against other antimicrobials in vitro. A population selected for resistance to the antimicrobial peptide iseganan showed increased in vivo survival, but was not more virulent. We suggest that increased survival of AMP-resistant bacteria almost certainly poses problems to immune-compromised hosts.
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.