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Genome-Based Bioinformatic Prediction of Major Histocompatibility Complex (MHC) Epitopes

Over the last 12 years, a large amount of knowledge has been accumulated on various aspects of Major Histocompatibility Complex (MHC) molecules. In conjunction, numerous algorithms and tools have been developed to screen protein molecules for these MHC receptor sites. By combining these ...

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Identification of Protein Biomarkers in Human Serum Using iTRAQ and Shotgun Mass Spectrometry

Blood serum is one of the easiest accessible sources of biomarkers and its proteome presents a significant parcel of immune system proteins. These proteins can provide not only biological explanation but also diagnostic and drug response answers independently of the type of disease or co ...

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Preparation of the Low Molecular Weight Serum Proteome for Mass Spectrometry Analysis

The discovery of viable biomarkers or indicators of disease states is complicated by the inherent complexity of the chosen biological specimen. Every sample, whether it is serum, plasma, urine, tissue, cells, or a host of others, contains thousands of large and small components, each interac ...

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Profiling of Cytokine and Chemokine Responses Using Multiplex Bead Array Technology

Multiplex bead array technology expands upon the principles of the enzyme-linked immunosorbent assay by allowing the simultaneous quantification of a large number of cytokines and chemokines within a single sample. This allows for the researcher more freedom to investigate compl ...

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Construction and Screening of an Antigen-Derived Peptide Library Displayed on Yeast Cell Surface for CD4+ T Cell Epitope Identification

Identification of T cell epitopes is a critical, but often difficult step in studying T cell function and developing peptide-based vaccines and immunotherapies. Unlike antibodies that recognize free soluble antigens, T cell receptor (TCR) recognizes its epitope bound to major histo ...

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Identification and Quantitation of MHC Class II-Bound Peptides from Mouse Spleen Dendritic Cells by Immunoprecipitation and Mass Spectrometry Analysis

Advances in immunology and immune therapies require knowledge of antigenic peptide sequences that are presented on MHC class II and class I molecules of antigen presenting cells. The most specialized antigen presenting cells are dendritic cells (DCs). In the past, the small number of DCs that ...

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Cell-Based Arrays for the Identification of Interacting Polypeptide Domains or Epitopes

The specific regions on proteins which are responsible for protein–protein interaction are called interacting domains, or epitopes in case of antigen–antibody binding. These domains are one feature to characterize proteins and are important in clinical diagnostics and researc ...

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Whole-Cell MALDI-TOF Mass Spectrometry: A Tool for Immune Cell Analysis and Characterization

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used in proteomics. It has been recently demonstrated that MALDI-TOF MS can be used to identify and classify numerous bacterial species or subspecies. We applied MALDI-TOF MS di ...

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Enrichment and Characterization of Glycopeptide Epitopes from Complex Mixtures

Antigen posttranslational modifications, including glycosylation, are recognized by the innate and adaptive arms of the immune system. Analytical approaches, including mass spectrometry and allied techniques, have allowed advances in the enrichment and identification ...

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Chemo-Enzymatic Production of O-Glycopeptides for the Detection of Serum Glycopeptide Antibodies

Protein microarray is a highly sensitive tool for antibody detection in serum. Monitoring of patients’ antibody titers to specific antigens is increasingly employed in the diagnosis of several conditions, ranging from infectious diseases, allergies, autoimmune diseases, and ca ...

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Immunoblotting for Active Caspase-1

Immunoblotting for caspase-1 is the gold-standard method of detecting inflammasome activation. In contrast to IL-1β-based readouts, it can be used in an experimental setup independent of de novo gene expression. Here, we present protocols for the preparation and precipitation of supe ...

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ASC Speck Formation as a Readout for Inflammasome Activation

All inflammasomes require the adapter protein apoptosis associated speck-like protein containing a CARD (ASC) for the activation of caspase-1. After inflammasome activation, ASC assembles into a large protein complex, which is termed “speck”. ASC specks can be observed as they reach a si ...

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Detection of Pyroptosis by Measuring Released Lactate Dehydrogenase Activity

Pyroptosis is a form of programmed, inflammatory cell death that is dependent on the activation of a cysteine protease caspase-1. Following caspase-1 activation via inflammasomes (including NLRP3, NLRC4, Nlrp1b, and AIM2), cells lose membrane integrity and lyse, releasing lactate de ...

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Measuring Inflammasome Activation in Response to Bacterial Infection

Inflammasomes are multi-protein signaling platforms assembled in response to viral and bacterial pathogens as well as endogenous danger signals. Inflammasomes serve as activation platforms for the mammalian cysteine protease caspase-1, a central mediator of innate immunit ...

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NLRP3 Inflammasome Activation and Cytotoxicity Induced by Particulate Adjuvants

The ability of particulate materials to provoke inflammatory immune responses has been well documented. In the case of endogenous and environmental particulates, these effects can often lead to pathological disorders. In contrast, particulate adjuvants incorporated into vac ...

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Assessment of Inflammasome Activation in Primary Human Immune Cells

Inflammasomes are central regulators of inflammation, responsible for cleavage of the inactive pro-�inflammatory cytokines IL-1β and IL-18 into their biologically active counterparts. Several regulatory stages within the pathways responsible for the production of these c ...

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Assessment and Quantification of Crystal-Induced Lysosomal Damage

Lysosomes are organelles that degrade endocytosed, phagocytosed, or autophagocytosed materials. Lysosomal degradation of engulfed material is a highly controlled mechanism, which is vital in the control of infection, recycling of cellular organelles, and the breakdown of lar ...

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Activating the NLRP3 Inflammasome Using the Amyloidogenic Peptide IAPP

In addition to several other extracellular substances, phagocytosis of amyloid-forming peptides can perturb cellular homeostasis, leading to activation of the cytoplasmic innate immune receptor NLRP3. Once triggered, NLRP3 forms an inflammasome complex that ultimately c ...

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Assessing -Amyloid-Induced NLRP3 Inflammasome Activation in Primary Microglia

Senile plaques are an important histological hallmark of Alzheimer’s disease. They mainly consist of the fibrillar peptide β-amyloid (Aβ) and are surrounded by activated microglia and astrocytes. Microglia in the vicinity of senile plaques express high levels of proinflammatory c ...

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In Vivo Evaluation of Neutrophil Recruitment in Response to Sterile Particulates

Sterile particulates such as monosodium urate crystals induce inflammasome activation resulting in activation of caspase-1, secretion of IL-1α, and processing of IL-1β. Local production and activation of IL-1 leads to neutrophil recruitment in vivo. Here we describe two quick and sim ...

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