Substitutional Analysis on Influenza PeB Binding
Ontology highlight
ABSTRACT:
ORGANISM(S): unidentified influenza virus
PROVIDER: GSE78700 | GEO | 2016/02/27
SECONDARY ACCESSION(S): PRJNA313235
REPOSITORIES: GEO
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Project description:In search for peptides with higher or special binding affinity and for further understanding of the mode of action, a full substitutional analysis of peptide PeB using microarrays was performed. Thus, 152 PeB mutant variants were generated. In each of them, the full-length sequence was preserved except for only one amino acid from the eight loop-forming amino acids of the original PeB peptide (ARDFYDYDVFYYAMD) which was substituted with the 19 remaining natural amino acids. To assess binding, influenza material was labeled with a protein reacting fluorophore. Microarray-based substitutional analysis of peptide PeB was performed using a PepStar® peptide library spotted on glass slides by JPT Peptide Technologies. The slides were used without additional treatment. For the labeling of proteins with a fluorescent dye, Dyomics DY-634 (λex = 635 nm, λem = 654 nm, Fluoro-spin 634 Kit (emp Biotech) was used, according to the manufacturer´s instructions. The following materials were labeled: NewYork H3N2, Aichi H3N2, Victoria H3N2 and California H1N1. Labeled analytes were incubated several hours or overnight at indicated concentrations using Femtotip buffer (FTP)30 (20 mM Tris, 30% glycerol, 3% polyvinylpyrrolidon 90, 0.1% Tween 20, pH 8.4) for dilution. The slides were washed twice in FTP and twice in ultrapure water and subsequently dried under a stream of nitrogen. Experiments were performed in triplicates using glycans (2,3'-/2,6'-sialyllactose) and proteins (Anti-H1/Anti-H3 antibodies, fetuin) as positive and negative controls.
2016-02-27 | E-GEOD-78700 | biostudies-arrayexpress
Project description:We are studying new ways to look for abnormal areas/tissues of the colon during a colonoscopy. The current scopes used for colonoscopies are very good. But if the area doesn’t look different to the naked eye, then the scope can’t improve on that. We are using special stains or dyes and special scopes to see abnormal areas that are hard to see with the naked eye. The stain or dye is "fluorescent", meaning it glows when special light is used in the colonoscopy scope.
You are being asked to let us spray a peptide with a fluorescent tag onto your colon. Peptides are small chains of amino acids (the building blocks that make up proteins) linked together. The peptide we use has 7 amino acids attached to a fluorescent tag ("FIT C" or Fluoresceinisothiocyanate). FITC is used by eye doctors to examine your eyes (the yellow eye drops).
We are testing this "fluorescent peptide" to see if it will stick if there are any abnormal areas. If the peptide "sticks", it will "glow" when a special light in the scope is used. In this study, we will apply the fluorescent peptide to your colon by using a spray tube that fits in the colonoscope.
This is a phase IB study. This means that although we have applied the peptide to 25 people in our first research study, we still need to learn more about "fluorescent peptide" in people. The Food and Drug Administration (FDA) has not approved this agent, but is allowing us to test it in this study. The main goal of this study is to see if the peptide "glows" well and if we can take pictures of areas that do glow.
This is a research study of the peptide and our ability to see it "glow or fluoresce". Being in this study and applying the peptide won’t change how our biopsies are taken or how your colonoscopy is done.
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Project description:The Proline-rich Antimicrobial Peptide (PrAMP) apidaecin (Api) inhibits translation by binding in the ribosomal nascent peptide exit tunnel, trapping release factors RF1 or RF2, and arresting ribosomes at stop codons. To explore the extent of sequence variations of the native 18-amino acid Api that allows it to preserve its activity, we screened a library of synthetic mutant Api genes expressed in bacterial cells, resulting in nearly 350,000 peptide variants with multiple substitutions. By applying orthogonal negative and positive selection strategies, we identified a number of multi-substituted Api variants capable of arresting ribosomes at stop codons. Our findings underscore the critical contribution of specific amino acid residues of the peptide for its on-target function while significantly expanding the variety of PrAMPs acting on the terminating ribosome. Additionally, some of the tested synthesized multi-substituted Api variants exhibit improved antibacterial activity compared to that of the wild type PrAMP and may constitute the starting point to develop clinically useful antimicrobials.
2024-06-18 | GSE269894 | GEO
Project description:The lantibiotic mersacidin is an antimicrobial peptide of 20 amino acids that is produced by Bacillus sp. strain HIL Y-85,54728. Lantibiotics are antibiotics containing nonproteinogenic amino acids like lanthionine and/or 3-methyllanthionine. Mersacidin interferes with cell wall biosynthesis by targeting the peptidoglycan precursor lipid II and inhibits the growth of MRSA and other gram-positive bacteria. Therefore, mersacidin could be a lead substance for the development of new antibacterial agents. The clinical VISA isolates S. aureus 137/93A and its spontaneous mutant S. aureus 137/93G show reduced sensitivity towards mersacidin. This phenotype could not be traced to factors being responsible for vancomycinresistance (i.e. the thickened cell wall). Here, we focussed on the comparative transcriptome analysis of S. aureus 137/93A and S. aureus SG511 (sensitive strain) via full genome S. aureus microarrays to identify genes involved in the reduced sensitivity towards mersacidin.
2009-01-17 | GSE12016 | GEO
Project description:modENCODE_submission_3227 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP86(official name : OP86 genotype : unc119(ed3);wgIs86(peb-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The PEB-1::EGFP fusion protein is expressed in the correct peb-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PEB-1 transcription factor. made_by : R Waterston ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs86(peb-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene peb-1; Strain OP86(official name : OP86 genotype : unc119(ed3);wgIs86(peb-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The PEB-1::EGFP fusion protein is expressed in the correct peb-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PEB-1 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius
2013-07-11 | E-GEOD-48699 | biostudies-arrayexpress
Project description:Sepsis is an exaggerated immune response upon infection with lipopolysaccharide (LPS) as the main causative agent. LPS-induced activation and apoptosis of endothelial cells (EC) can lead to organ dysfunction and finally organ failure. We have previously demonstrated that the first twenty amino acids of the Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) are sufficient to inhibit EC apoptosis. To identify genes whose regulation by LPS is affected by this N-terminal APEX1 peptide, EC were transduced with an expression vector for the APEX1 peptide or an empty control vector and treated with LPS. Following RNA deep sequencing, genes upregulated in LPS-treated EC expressing the APEX1 peptide were identified bioinformatically.
2021-09-20 | E-MTAB-10936 | biostudies-arrayexpress
Project description:Genome-wide binding of SoxN in wild type embryos: SoxNDam (DamID, stage 8-11), SoxND1 (ChIP, stage 8-11), SoxND2 (ChIP, stage 8-11), SoxNPA179 Early (ChIP, stage 7-10), and SoxNPA179 Late (ChIP, stage 11-13). One DamID experiment, four ChIP experiments. Three biological replicates per experiment. Two conditions: Dam (control) vs SoxNDam (sample) for DamID, anti-M-NM-2gal (control, 40-1a antibody from DSHB) vs anti-SoxN (sample, either SoxND1, SoxND2 or SoxNPA179 antibody) for ChIP. The only commercially available antibody is the anti-BetaGal. All the anti-SoxN antibodies are home-made. anti-BetaGal: Developmental Studies Hybridoma Bank (DSHB), 40-1a, mouse, monoclonal (http://dshb.biology.uiowa.edu/beta-galactosidase_2) SoxND1: polyclonal antiserum raised in rabbit immunized with a protein fragment corresponding to amino acids 2-92 of SoxN. Produced by the modENCODE consortium (http://www.modencode.org/). SoxND2: polyclonal antiserum raised in rabbit immunized with a protein fragment corresponding to amino acids 317-417 of SoxN. Produced by the modENCODE consortium (http://www.modencode.org/). SoxNPA179: affinity purified polyclonal antibody raised in rabbit immunized with a small peptide corresponding to amino acids 506-521 of SoxN. Commisioned by our lab and produced by Eurogentec (http://www.eurogentec.com/eu-home.html).
2014-04-23 | E-GEOD-47337 | biostudies-arrayexpress
Project description:Prp45 is a budding yeast NineTeen-Complex associated factor, which plays a role in pre-mRNA splicing. prp45(1-169) is a temperature-sensitive truncation allele expressing only the first 169 amino acids (the full-length protein consists of 379 amino acids). RNA-seq analysis was performed to determine changes in transcription and splicing in cells with prp45(1-169) allele prepared by the CRISPR/Cas9 method as a scarless truncation, i.e. with no tags and with preserved endogenous 3' UTR. Total RNA was isolated by combining phenol-chlorophorm extraction with MasterPure Yeast RNA Purification Kit (Epicentre). Ribodepletion, library preparation and sequencing were performed by BGI Genomics.
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