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Antigens Involved in Adaptive Immunity

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An antigen is any substance the immune system identifies as foreign and potentially harmful to the body, prompting an immune response. Antigens have two functional properties: immunogenicity and reactivity. Immunogenicity is the ability of an antigen to stimulate a specific immune response. At the same time, reactivity describes the antigen's ability to react with the cells and antibodies produced in response to it.
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Related Experiment Video

Updated: Jul 19, 2025

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

Published on: March 25, 2014

Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn.

Anna-Maria Liebhoff^1,2, Thiagarajan Venkataraman², William R Morgenlander²

¹Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.

Biorxiv : the Preprint Server for Biology

|August 14, 2023

Summary

Researchers profiled antibody responses to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). A new method, Dolphyn, significantly improved PhIP-Seq efficiency and revealed immune responses to bacteria-infecting viruses in the gut.

Keywords:

PhIP-Seq antibody profiling gut phages peptides libraries public epitopes

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Published on: October 22, 2012

Area of Science:

Immunology
Microbiology
Bioinformatics

Background:

The gut-immune axis is crucial for health, but the antibody response to gut phages remains underexplored.
Phage Immunoprecipitation Sequencing (PhIP-Seq) is a method to profile antibody responses to phages.
Existing PhIP-Seq methods have limitations in library size and efficiency.

Approach:

Developed Dolphyn, a novel machine learning method to select optimal peptides for PhIP-Seq libraries.
Dolphyn utilizes epitope-stitching to compress proteomes, reducing the number of synthesized peptides.
Applied Dolphyn-enhanced PhIP-Seq to profile antibody responses to gut phages in healthy individuals.

Key Points:

Dolphyn improved the fraction of gut phage library peptides bound by antibodies from 10% to 31% in healthy individuals.
Dolphyn reduced the number of synthesized peptides by 78%, making PhIP-Seq more cost-effective.
Identified significant antibody responses to bacteria-infecting viruses, particularly E. coli-infecting Myoviridae, in the human gut.

Conclusions:

Dolphyn significantly enhances the efficiency and cost-effectiveness of PhIP-Seq for studying gut phages.
The human immune system actively targets bacteria-infecting viruses within the gut microbiome.
This approach facilitates broader investigation of the gut-immune axis and phage-host interactions.