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11 results for “Phage display”
Pivotal role of O-antigenic polysaccharide display in the sensitivity against phage tail-like particles in environmental Pseudomonas kin competition
<p>Environmental pseudomonads<i> </i>colonize various niches including insect and plant environments. When invading these environments, bacteria are confronted with the resident microbiota. To cope with closely related strains they deploy narrow-spectrum weaponry such as tailocins, <i>i.e</i> phage tail-like particles. Little is known about the receptors for these tailocins especially among phylogenetically closely related species. Here, we studied the interaction between an R-tailocin from <i>Pseudomonas protegens </i>CHA0 and a targeted kin, <i>Pseudomonas protegens </i>Pf-5. Using genome-wide transposon insertion sequencing, we identified that lipopolysaccharides are involved in the sensitivity of Pf-5 towards the tailocin of CHA0. By generating Pf-5 lipopolysaccharide mutants and exposing them to extracted tailocin, we specified the two O-antigenic polysaccharides (O-PS) targeted by the tailocin. We affirmed the role of these O-PS through competition assays<i> in vitro </i>as well as in insects. Further, we demonstrate that O-PS are double-edge swords that are responsible for the sensitivity of <i>P. protegens</i> towards phage tail-like particles produced by their kin, but shield bacteria from the immune system of the insect. Our results shed light on the trade-off that bacteria are confronted with, where specific O-PS decorations can both be of benefit or disadvantage depending on the host environment and its bacterial inhabitants.</p>
Flow Cytometry Data from "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing"
<p>This record contains the flow cytometry data from the manuscript "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing."</p> <p>Files are in <a href="https://docs.flowjo.com/flowjo/advanced-features/fj-acs/">Archive Cytometry Standard (ACS) format</a> . Each <code>.acs</code> file is a zip container which holds both the raw <code>.fcs</code> files and a FlowJo workspace (<code>.wsp</code>) file.</p> <p>Keywords in the workspace file identify which primary antibody (<code>primary</code>) was used and which cell genotype (<code>strain</code>) was used for each sample. The workspace also encodes the gating scheme and compensation matrix applied to each sample. Plots in the manuscript are exported from Layout views in the workspace.</p>
Molecular reshaping of phage-displayed Interleukin-2 at beta chain receptor interface to obtain potent super-agonists with improved developability profiles-primary dataset
<div class="c-message_kit__blocks c-message_kit__blocks--rich_text"> <div class="c-message__message_blocks c-message__message_blocks--rich_text"> <div class="p-block_kit_renderer"> <div class="p-block_kit_renderer__block_wrapper p-block_kit_renderer__block_wrapper--first"> </div> </div> </div> </div> <p>Interleukin-2 (IL-2) had been been engineered up to now by yeast display and in silico rational design. In this article we reshaped IL-2 interface with the IL-2 receptor beta subunit to increase binding affinity between both interacting partners, using phage display. Multiple IL-2 mutated variants were selected from large phage-displayed libraries, showing shared molecular patterns. An accumulation of negative charges in the segment 81-87 of IL-2 primary sequence was observed, as well as the strong preponderance of the replacement I92L. The first feature contributed to an optimized electrostatic complementarity between IL-2 and IL-2 receptor beta chain, resulting in higher affinity and faster association kinetics than the ones of previously reported H9 superkine retrieved from yeast display libraries. The presence of a Leu residue at position 92 was the key molecular determinant for a favourable biophysical profile characterized by high stability and production in mammalian-cell based recombinant systems, and decreased aggregation propensity. The new beta super-binders behaved as potent super agonists, both in vitro and in vivo. The latter scenario showed their better preformance when compared to both non-mutated IL-2 and H9. The current dataset contains source data for graphics showing frequency mutations and charge distribution among unselected variants contained in phage-displayed libraries and selected clones enriched after selection on immobilized beta chain. Data showing the direct comparison between different IL-2 mutated variants produced as Fc-fusion proteins are also presented. The comparison includes the results of beta chain binding assays (ELISA), proliferation and phosphorylation assays in vitro, in vivo expansion of lymphocyte populations and anti-tumor activity in animal models. Taken together, the above described data support the unique features of the new beta super-binders and their potential as immunostimulatory and anti-cancer agents.</p>
Pivotal role of O-antigenic polysaccharide display in the sensitivity against phage tail-like particles in environmental Pseudomonas kin competition
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Molecular reshaping of phage-displayed Interleukin-2 at beta chain receptor interface to obtain potent super-agonists with improved developability profiles-primary dataset
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Data from: Validation of a murine proteome-wide phage display library for identification of autoantibody specificities
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PhIP-Seq/VirScan Coronavirus phage display assay in maternal-infant dyads
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Bacterial cell surface characterization by phage display coupled to high-throughput sequencing
<p>This record contains the processed high-throughput sequencing data from the manuscript "Bacterial cell surface characterization by phage display coupled to high-throughput sequencing." Data was generated using the <a href="https://github.com/caseygrun/phage-seq">Snakemake workflows and Jupyter notebooks in this repository</a> and is intended to be analyzed further using the notebooks in that repository</p> <p>Each tarball within this record, when expanded, populates the <code>results</code> and <code>intermediate</code> directories of one of those workflows: <code>alpaca-library</code> ,<code>panning-small</code>, <code>panning-massive</code>, or <code>panning-extended</code>. Clone the <a href="https://github.com/caseygrun/phage-seq"><code>phage-seq</code> repository</a>, then download one or more of these tarballs to the corresponding directory of that directory. For example:</p> <blockquote> <pre><code>git clone https://github.com/caseygrun/phage-seq.git cd panning-extended wget https://zenodo.org/records/11246658/files/panning-extended-results.tar.gz tar vzxf panning-extended-results.tar.gz</code></pre> </blockquote> <p>More detailed instructions are included in the README for the <a href="https://github.com/caseygrun/phage-seq"><code>phage-seq</code> repository</a>.</p>
Data from: Phage display peptide libraries: deviations from randomness and correctives
Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study we implemented Next Generation Sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon overrepresentation as well as in high G phosphoramidite abundance causing amino acid distribution biases. In this study we demonstrate that the UAG overrepresentation can be attributed to the burden imposed on the phage upon the assembly of the recombinant Protein 8 subunits. This was corrected by constructing the libraries using supE44-containing bacteria which suppress the UAG driven abortive termination. We also demonstrate that the overabundance of G stems from variant synthesis-efficiency and can be corrected using compensating oligonucleotide-mixtures calibrated by Mass Spectroscopy. Construction of libraries implementing these correctives results in markedly improved libraries that display random distribution of amino acids, thus ensuring that enriched peptides obtained in biopanning represent a genuine selection event, a fundamental assumption for phage display applications.
Data from: Phage display peptide libraries: deviations from randomness and correctives
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Antigen-level resolution of commensal-specific B cell responses enabled by phage-display screening and B cell tetramers
GEO Series GSE245084. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing; Other.
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