scholarly journals Mapping polyclonal antibody responses to bacterial infection using next generation phage display

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Ibrahim A. Naqid ◽  
Jonathan P. Owen ◽  
Ben C. Maddison ◽  
Anastasios Spiliotopoulos ◽  
Richard D. Emes ◽  
...  
Keyword(s):  
Phage Display ◽  
Bacterial Infection ◽  
Polyclonal Antibody ◽  
Antibody Responses ◽  
Next Generation

Development and Application of Computational Methods in Phage Display Technology

2020 ◽  
Vol 26 (42) ◽  
pp. 7672-7693 ◽  
Author(s):  
Bifang He ◽  
Anthony Mackitz Dzisoo ◽  
Ratmir Derda ◽  
Jian Huang
Keyword(s):  
Phage Display ◽  
Computational Methods ◽  
Peptide Ligands ◽  
Next Generation ◽  
Phage Display Technology ◽  
Next Generation Sequencing Technology ◽  
Screening Experiments ◽  
Display Technology ◽  
Comprehensive Search ◽  
Generation Sequencing

Background: Phage display is a powerful and versatile technology for the identification of peptide ligands binding to multiple targets, which has been successfully employed in various fields, such as diagnostics and therapeutics, drug-delivery and material science. The integration of next generation sequencing technology with phage display makes this methodology more productive. With the widespread use of this technique and the fast accumulation of phage display data, databases for these data and computational methods have become an indispensable part in this community. This review aims to summarize and discuss recent progress in the development and application of computational methods in the field of phage display. Methods: We undertook a comprehensive search of bioinformatics resources and computational methods for phage display data via Google Scholar and PubMed. The methods and tools were further divided into different categories according to their uses. Results: We described seven special or relevant databases for phage display data, which provided an evidence-based source for phage display researchers to clean their biopanning results. These databases can identify and report possible target-unrelated peptides (TUPs), thereby excluding false-positive data from peptides obtained from phage display screening experiments. More than 20 computational methods for analyzing biopanning data were also reviewed. These methods were classified into computational methods for reporting TUPs, for predicting epitopes and for analyzing next generation phage display data. Conclusion: The current bioinformatics archives, methods and tools reviewed here have benefitted the biopanning community. To develop better or new computational tools, some promising directions are also discussed.

scholarly journals Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Aleksandar Antanasijevic ◽  
Leigh M. Sewall ◽  
Christopher A. Cottrell ◽  
Diane G. Carnathan ◽  
Luis E. Jimenez ◽  
...  
Keyword(s):  
High Resolution ◽  
Polyclonal Antibody ◽  
Vaccine Development ◽  
Mutational Analysis ◽  
Rhesus Macaques ◽  
Antibody Responses ◽  
Glycosylation Sites ◽  
High Resolution Analysis ◽  
Resolution Analysis ◽  
Resolution Mapping

AbstractEngineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate the immunogenicity of several stabilized BG505 SOSIP constructs both as free trimers and presented on a nanoparticle. We applied a cryoEM-based method for high-resolution mapping of polyclonal antibody responses elicited in immunized animals (cryoEMPEM). Mutational analysis coupled with neutralization assays were used to probe the neutralization potential at each epitope. We demonstrate that cryoEMPEM data can be used for rapid, high-resolution analysis of polyclonal antibody responses without the need for monoclonal antibody isolation. This approach allowed to resolve structurally distinct classes of antibodies that bind overlapping sites. In addition to comprehensive mapping of commonly targeted neutralizing and non-neutralizing epitopes in BG505 SOSIP immunogens, our analysis revealed that epitopes comprising engineered stabilizing mutations and of partially occupied glycosylation sites can be immunogenic.

scholarly journals Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

10.3791/56981 ◽  
2018 ◽  
Author(s):  
Maria Felicia Soluri ◽  
Simone Puccio ◽  
Giada Caredda ◽  
Giorgio Grillo ◽  
Vito Flavio Licciulli ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Phage Display ◽  
Next Generation ◽  
Library Construction ◽  
Generation Sequencing

scholarly journals A Next Generation Bivalent Human Ad5 COVID-19 Vaccine Delivering Both Spike and Nucleocapsid Antigens Elicits Th1 Dominant CD4+, CD8+ T-cell and Neutralizing Antibody Responses

2020 ◽  
Author(s):  
Adrian Rice ◽  
Mohit Verma ◽  
Annie Shin ◽  
Lise Zakin ◽  
Peter Sieling ◽  
...  
Keyword(s):  
T Cell ◽  
Cell Surface ◽  
Immune Responses ◽  
Cd8 T Cell ◽  
Surface Expression ◽  
Antibody Responses ◽  
Cell Surface Expression ◽  
Clinical Testing ◽  
Next Generation ◽  
Cell Responses

ABSTRACTIn response to the health crisis presented by the COVID-19 pandemic, rapid development of safe and effective vaccines that elicit durable immune responses is imperative. Recent reports have raised the concern that antibodies in COVID-19 convalescent patients may not be long lasting and thus even these individuals may require vaccination. Vaccine candidates currently in clinical testing have focused on the SARS-CoV-2 wild type spike (S) protein (S-WT) as the major antigen of choice and while pre-clinical and early clinical testing have shown that S elicits an antibody response, we believe the optimal vaccine candidate should be capable of inducing robust, durable T-cell responses as well as humoral responses. We report here on a next generation bivalent human adenovirus serotype 5 (hAd5) vaccine capable of inducing immunity in patients with pre-existing adenovirus immunity, comprising both an S sequence optimized for cell surface expression (S-Fusion) and a conserved nucleocapsid (N) antigen designed to be transported to the endosomal subcellular compartment, with the potential to generate durable immune protection. Our studies suggest that this bivalent vaccine is optimized for immunogenicity as evidenced by the following findings: (i) The optimized S-Fusion displayed improved S receptor binding domain (RBD) cell surface expression compared to S-WT where little surface expression was detected; (ii) the expressed RBD from S-Fusion retained conformational integrity and recognition by ACE2-Fc; (iii) the viral N protein modified with an enhanced T-cell stimulation domain (ETSD) localized to endosomal/lysosomal subcellular compartments for MHC I/II presentation; and (iv) these optimizations to S and N (S-Fusion and N-ETSD) generated enhanced de novo antigen-specific B cell and CD4+ and CD8+ T-cell responses in antigen-naive pre-clinical models. Both the T-cell and antibody immune responses to S and N demonstrated a T-helper 1 (Th1) bias. The antibody responses were neutralizing as demonstrated by two independent SARS-CoV-2 neutralization assays. Based on these findings, we are advancing this next generation bivalent hAd5 S-Fusion + N-ETSD vaccine as our lead clinical candidate to test for its ability to provide robust, durable cell-mediated and humoral immunity against SARS-CoV-2 infection. Further studies are ongoing to explore utilizing this vaccine construct in oral, intranasal, and sublingual formulations to induce mucosal immunity in addition to cell-mediated and humoral immunity. The ultimate goal of an ideal COVID-19 vaccine is to generate long-term T and B cell memory.

scholarly journals 1337. Development, Maintenance, and Application of Opsonophagocytic Assays to Measure Functional Antibody Responses to Support a 20 Valent Pneumococcal Conjugate Vaccine

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S484-S484
Author(s):  
Ingrid L Scully ◽  
Mark W Cutler ◽  
Seema Gangolli ◽  
Todd Belanger ◽  
David Cooper ◽  
...  
Keyword(s):  
Quality Control ◽  
Antibody Responses ◽  
Antibody Activity ◽  
Pneumococcal Vaccines ◽  
Next Generation ◽  
High Quality ◽  
Assay Performance ◽  
Control Serum ◽  
Serological Data ◽  
Over Time

Abstract Background Opsonophagocytic assays (OPAs) are an important tool for assessing vaccine-induced functional antibody responses. OPAs are complex assays composed of many biological components (eg serum, complement sources, bacteria, and human phagocytes) which contribute to assay variability and may result in titer drift if not carefully controlled. Rigorous development and validation coupled with routine monitoring of assay performance are required to ensure that high-quality OPA serological data are consistently generated throughout the lifetime of existing and next-generation pneumococcal vaccines. Methods OPA specificity was demonstrated by competing functional antibody activity with pneumococcal polysaccharides. Assay qualification/validation assessed accuracy, precision, and sample linearity. Assay performance over time was assessed through the implementation of quality control serum data tracking systems and longterm serum proficiency panels that are routinely tested during assay performance. Human quality control sera are included on each assay plate to ensure that each plate meets pre-specified acceptance criteria. Proficiency serum panels are comprised of individual human serum samples derived from subjects immunized with pneumococcal vaccines and are used to monitor performance across a range of serological titers and over time. Results The OPAs were shown to be specific and reproducible. Monitoring of assay performance over time demonstrated that the assays are stable. For the 13 serotypes contained in 13vPnC reliable titers have been generated in over a decade of testing which is an essential prerequisite in the evaluation of next-generation pneumococcal conjugate vaccines such as 20vPnC, whose licensure depends on demonstration of non-inferiority to 13vPnC. Conclusion Maintenance and careful monitoring of high-quality assays to measure functional antibody responses, such as OPAs, is critical for the delivery of reliable serological data to support the advancement of pneumococcal vaccine programs. Pneumococcal OPAs must be rigorously maintained to ensure continuity of serological data over time and inform licensure decisions of next-generation vaccines as well as postmarketing and seroepidemiology studies. Disclosures All authors: No reported disclosures.

Screening and Identification of PLK1-Polo Box Binding Peptides by High-Throughput Sequencing of Phage-Selected Libraries

2019 ◽  
Vol 26 (8) ◽  
pp. 620-633 ◽  
Author(s):  
Nousheen Bibi ◽  
Hafsa Niaz ◽  
Ted Hupp ◽  
Mohammad Amjad Kamal ◽  
Sajid Rashid
Keyword(s):  
Next Generation Sequencing ◽  
Phage Display ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
B Lymphocyte ◽  
Fluorescent Protein ◽  
Next Generation ◽  
Peptide Phage Display ◽  
Binding Peptides ◽  
Generation Sequencing

Background: Human proteome contains a plethora of short linear peptide motifs that is crucial for signaling and other cellular processes. These motifs are difficult to identify due to lack of systematic approach for their detection. Objective: Here we demonstrate the use of peptide phage display in combination with high throughput next generation sequencing to identify enriched peptide sequences through biopanning process against polo box domain (PBD) of mitotic polo like kinase 1 (Plk1). Methods: Purified recombinant Plk1 and two unrelated controls namely B-lymphocyte antigen (CD20) and fluorescent protein (mCherry) were subjected to peptide phage display analysis. Bacterially-propagated phage DNA was amplified by PCR using triplet bar coded primers to tag the pool from each amplicon. Results: Proteomic peptide phage display along with next generation sequencing and Bioinformatics analysis demonstrated several known and putative novel interactions which were potentially related to Plk1-PBD. With our strategy, we were able to identify and characterize several Plk1-PBD binding peptides, as well as define more precisely, consensus sequences. Conclusion: We believe that this information could provide valuable tools for exploring novel interaction involved in Plk1 signaling as well as to choose peptides for Plk1 specific drug development.

scholarly journals Next Generation Sequencing Reveals the Expression of a Unique miRNA Profile in Response to a Gram-Positive Bacterial Infection

PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e57543 ◽  
Author(s):  
Nathan Lawless ◽  
Amir B. K. Foroushani ◽  
Matthew S. McCabe ◽  
Cliona O’Farrelly ◽  
David J. Lynn
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Infection ◽  
Mirna Profile ◽  
Next Generation ◽  
Gram Positive ◽  
Generation Sequencing

scholarly journals Next-Generation Phage Display: Integrating and Comparing Available Molecular Tools to Enable Cost-Effective High-Throughput Analysis

PLoS ONE ◽  
2009 ◽  
Vol 4 (12) ◽  
pp. e8338 ◽  
Author(s):  
Emmanuel Dias-Neto ◽  
Diana N. Nunes ◽  
Ricardo J. Giordano ◽  
Jessica Sun ◽  
Gregory H. Botz ◽  
...  
Keyword(s):  
Phage Display ◽  
High Throughput ◽  
Cost Effective ◽  
Next Generation ◽  
Molecular Tools ◽  
High Throughput Analysis ◽  
Throughput Analysis
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