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Topic: Epitopes

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	CIDRAP >> Report may spur quest for more versatile flu vaccines
		Epitopes that different strains have in common could, scientists believe, be used to make a vaccine that would protect against multiple strains and could be used for years.
		The lack of H5N1 epitope data is not surprising, given the recent emergence of the virus and the special biosecurity measures required for studying it, the researchers say.
		Antibody epitopes were identified from only 5 of the 10 viral proteins—most of them from hemagglutinin, neuraminidase, and M2—whereas T cell epitopes from all 10 proteins were identified.
	www.cidrap.umn.edu /cidrap/content/influenza/panflu/news/jan0307epitopes.html (1231 words)

	Antibody and T Cell Epitopes of Influenza A
		The Immune Epitope Database and Analysis Resource (IEDB) was recently developed to capture epitope related data, and is publicly available at www.immuneepitope.org.
		While antibody epitopes were described mostly in mouse and rabbit, T cell epitopes were studied in mouse and also humans.
		For complete description of the study, see "Ab and T cell epitopes of influenza A virus, knowledge and opportunities." Following are the results of the study.
	immuneepitope.org /export/doc/influenza/index.html (758 words)

	BioMed Central \| Full text \| Bcipep: A database of B-cell epitopes
		These epitopes can be classified into two categories; i) conformational/discontinuous epitope, where residues are distantly separated in the sequence and brought into physical proximity by protein folding and, ii) linear/continuous epitope, comprised of a single continuous stretch of amino acids within a protein sequence that can react with anti-protein antibodies [2,3].
		A number of vaccines based on B-cell epitopes are currently under clinical phase trials against viruses [5], bacteria [6] and cancer [7].
		These epitopes are also important for allergy research and in determining cross-reactivity of IgE-type epitopes of allergens [8].
	www.biomedcentral.com /1471-2164/6/79 (3109 words)

	Technologiestiftung Berlin / News / Diagnosis and prediction of tumour aggressiveness by oligoclonal antibodies ...
		The antigenic sequences of the epitopes have been chosen among the most highly conserved both in human and mouse, permitting a wider application for animal model research.
		The selection of these epitopes has also been made to guarantee the maximum specificity and efficiency and the minimum cross-reactivity of the oligoclonal antibody with the various glycosilated isoforms of cytoplasmic clusterin and to obtain highly specific and selective antibodies for the non-glycosilated nuclear isoform.
		Moreover, the manufacturing of oligoclonal antibodies, based on the selection of very short antigenic epitopes (synthesised on solid phase), permits the determination of a small repertoire of antibodies that are comparable to monoclonal antibodies, considering the characteristics of specificity and affinity.
	www.technologiestiftung-berlin.de /indexx.php/1947.html (810 words)

	Database of Structurally inferred Antigenic Epitopes in Proteins - [Background]
		Antigenic determinants, or epitopes, are particular surface areas of a protein that are specifically recognized by immunoglobulin molecules.
		Linear epitopes are continuous amino acid sequences of five to ten residues.
		After denaturation or digestion into small fragments, the peptides corresponding to the amino acid sequences of the conformational epitopes can no longer bind the antibody (some conformational epitopes were found to be composed of a number of linear epitopes).
	www.rostlab.org /services/epitome/background.html (409 words)

	BioPortfolio News : SARS coronavirus genome epitopes identified as potential markers for viral infection
		"Epitopes at the N-terminus of the membrane protein and the C-terminus of nucleocapsid protein elicited strong antibody responses.
		Epitopes on the spike protein were only moderately immunogenic but the effects were persistent.
		The authors concluded, "Important epitopes of the SARS-CoV genome that may serve as potential markers for the viral infection are identified.
	www.bioportfolio.com /July_06/13_07_2006/SARS_coronavirus_genome.html (407 words)

	Antigens - Immunogenicity - Epitopes
		Epitopes which are present on proteins, carbohydrates and lipids are candidates for binding, even if the epitope is a small molecule such as a nitrophenyl ring.
		In addition, the epitopes tend to be mobile - that is, the "better" epitopes are discrete antigen regions which exhibit a fair amount of molecular movement (the statistical probability of an epitope to assume an appropriate site-fitting shape increases if the region is moving rather than static).
		A conformational epitope is one which represents a discrete folded region of polypeptide or polysaccharide which forms due to the secondary and/or tertiary folding characteristics of the protein or polysaccharide.
	micronet.im.ac.cn /vdu.old/imlect6.htm (2017 words)

	Research - Coeliac disease: A food induced disorder. Exploration and exploitation of Tcell stimulatory gluten peptides
		Quantify and characterise the adult and paediatric T cell responses directed at the gluten peptides identified.
		Formal evidence that the T cell epitopes are associated with the toxicity of gluten will be provided by conducting peptide feeding trials in human coeliac volunteers.
		The specificity of T cell transfectants and monoclonal antibodies recognising the major gluten epitopes will be compared.
	ec.europa.eu /research/quality-of-life/ka1/volume2/qlk1-2000-00657.htm (547 words)

	Molecular approaches to identifying allergenic epitopes. (Site not responding. Last check: )
		Conformational epitopes appear to play a significant role in mediating clinical reactions of aeroallergens and linear epitopes play a major role in the etiology of allergic reactions to foods.
		This dichotomy in the type of epitope that mediates clinical symptoms is believed to be due to the fact that food allergens must survive the GI tract to provoke allergic reactions whereas aeroallergens can be introduced intact to the nasal mucosa and lung epithelium.
		The structure of the allergenic proteins appears to play a significant role in defining those regions that become epitopes and which epitopes are immunodominant in an allergic patient population.
	www.aaccnet.org /meetings/2001/Abstracts/a01ma158.htm (217 words)

	Biacore - Biacore Life Sciences > Technology > Introduction > Data from an interaction
		Complex formation can be monitored as each component is incorporated into a multimolecular complex.
		The ability of different antibodies to bind simultaneously to an antigen can be used to map epitopes on the antigen.
		Copyright © 2007 General Electric Company - All rights reserved
	www.biacore.se /lifesciences/technology (382 words)

	PubMed medline query
		The identification of T-cell epitopes of these allergens is a prerequisite for the design of immunotherapeutic strategies based on peptide vaccination or modified allergens with conserved T-cell epitopes.
		All TCCs were mapped for epitope specificities using 178 overlapping dodecapeptides representing the primary structures of two isoforms of Phl p 5 (Phl p 5a and Phl p 5b).
		Epitope recognition pattern could not be correlated with special HLA class II haplotypes.
	www.personal.uni-jena.de /~i6maud/muller01.html (340 words)

	Epitope Information \| Business.com
		Home » Directory » Pharmaceuticals & Biotechnology » Epitope, Inc.
		Epitope, Inc., through its biotechnology develops diagnostic tests and devices for the detection of Human immunodeficiency virus (HIV).
		Other business products and services to help grow and manage your business
	rd.business.com /index.asp?epm=s.1&bdcq=Epitopes&bdcr=1&bdcu=http://www.business.com/directory/pharmaceuticals_and_biotechnology/epitope,_inc/index.asp?partner=2662601&bdcp=&partner=2662601&bdcs=nwuuid-2662601-322B8AA9-F817-834B-D94D-FBA1CFFA7526-ym (101 words)

	The Human Prion Protein Residue 129 Polymorphism Lies Within a Cluster of Epitopes for T Cell Recognition - Health - ...
		Interestingly, clusters of epitopes were focused around the area of the polymorphic residue 129, previously identified as an indicator of susceptibility to prion disease, and in the C-terminal region.
		Interestingly, 8 of the 10 epitopes predicted by TEPITOPE from the human PrP 129 M sequence were represented among the 13 peptides that elicited responses in vitro.
		The importance of defining T cell epitopes in self- proteins that are used as human vaccines was dramatically illustrated when 6% of patients with Alzheimer disease in a clinical trial of Aβ vaccination developed meningoencephalitis driven by T cell invasion of the central nervous system (20).
	www.redorbit.com /news/health/736518/the_human_prion_protein_residue_129_polymorphism_lies_within_a/index.html?source=r_health (6075 words)

	PepSpots!" - Epitope Mapping - JPT Peptide Technologies GmbH
		Mapped epitopes can be functionally characterized by rapid determination of key residues playing a definite role in the binding process.
		These important questions are answered by performing a substitutional analysis: each amino acid of the mapped epitope is substituted by all 20 L-amino acids to provide detailed information on the mode of peptide binding.
		Identification of distinct antibody epitopes and mimotopes from a peptide array of 5520 randomly generated sequences, Reineke et al., J. Immun.
	www.jpt.com /products/peptide_arrays/pepspots.htm (431 words)

	COMMENTARIES
		The new formed structures, denominated oxidation-specific epitopes, are recognized by the immune system and have been shown to activate T cells and trigger immune responses, leading to generation of antibodies.
		It has been shown that EO6 binds to the PC epitopes on both oxLDL and apoptotic cells, blocks their binding to macrophage scavenger receptors (SR) CD36 and SR-B1 and inhibits cellular uptake.
		These results might be explained by cross reactivity between PC epitopes on oxLDL and those on the polysaccharide capsule of the bacteria.
	www.athero.org /commentaries/comm396.asp (1724 words)

	Research - EU Research strategy to infectious diseases - EPI-VAC
		The aim of this project is to select peptide epitopes that mimic neutralisation-sensitive domains of HIV-1 envelope and may function as candidate HIV-1 vaccines.
		The main objective of this proposal is to select peptide epitopes that mimic neutralisation sensitive regions of HIV-1 envelope and may function as candidate HIV-1 vaccines.
		Furthermore, the peptide epitopes will be subjected to an in vitro affinity maturation by using extensive structural analysis and site-directed mutagenesis to improve their immunological fitness.
	ec.europa.eu /research/health/poverty-diseases/projects/88_en.htm (1421 words)

	New details on how the immune system recognizes influenza
		The analysis drew upon a much larger effort called the Immune Epitope Database and Analysis Resources Program, which began in 2004 after NIAID awarded LIAI a $25 million contract to create a single repository of immune epitopes from critical disease-causing microbes, including agents that might be used in a bioterrorist attack.
		One of their main goals was to determine how conserved, or similar, epitopes are between different strains of bird and human influenza viruses.
		Most of the influenza virus epitopes in the database are those recognized by a type of immune cell known as a T cell; far fewer are recognized by B cells, a type of white blood cell that produces infection-fighting antibodies.
	www.eurekalert.org /pub_releases/2007-01/nioa-ndo122706.php (1057 words)

	CTLPred: A SVM & ANN Based CTL epitope Prediction method
		The identification of CTL epitopes is backbone for subunit vaccine designs.In the past, large number of computational tools had been developed for identification of T cell epitopes.
		The data of the CTL epitopes have been obtained from MHCBN database version 1.1., a comprehensive database of MHC binding and non-binding peptides.The MHC class I alleles mostly bind to peptides of 9 amino acids, thus we have chosen the 9 amino acid long epitopes from extracted data of CTL epitopes.
		During the preprocessing of the data all the duplicate and epitopes with non-natural amino acids are removed from the dataset of CTL epitopes.
	www.imtech.res.in /raghava/ctlpred/algo.html (1473 words)

	P4: "Analysis of B cell epitopes of allergenic proteins"
		As IgE-antibodies (and antibodies obtained by natural forms of immunization in general) predominantly recognize conformational epitopes (Laver et al., 1990) the correct folding of the allergenic protein is an important prerequisite.
		Such anti-sera in general do recognize all aspects of the protein including denatured and linear epitopes because the mixture of protein and adjuvant that is used for injection is usually partly denatured.
		Exchanges key amino acids (lys, arg) within the presumed epitope structures by in vitro mutagenesis of the enolases and testing the recombinant proteins in IgE immunoblots should clarify whether the predicted regions are responsible for the formation of cross-reactive epitopes.
	www.natur.sbg.ac.at /allergy/allergy1-17.htm (1554 words)

	LIAI completes world's most comprehensive analysis on influenza virus data
		Antibody and T cell epitopes are small sites on a virus that are the targets of the immune response, and they are critical for developing therapies and vaccines to combat infectious disease.
		However, it remains to be seen whether these epitopes are similar enough to enable the successful development of a highly cross reactive influenza vaccine that would protect against many viruses.
		And, in fact, the study found only one epitope that has been published, which appears to be an ideal candidate for creating a multi-strain influenza vaccine.
	www.eurekalert.org /pub_releases/2007-01/ljif-lcw122606.php (1128 words)

	AEGiS-AIDSWeekly: HIV/AIDS Pathogenesis: Limited HIV evolution in persistently targeted CD8 epitopes in chronic ...
		Seven targeted epitopes were identified in each person.
		"Only 4 of the 14 autologous epitopes tested represented potential CTL escape variants; however, in most cases strong responses to these epitopes persisted for the 6 years of study," investigators reported.
		Scientists concluded, "These data indicate limited viral evolution within persistently targeted CD8 T-cell epitopes during the chronic phase of infection and suggest that these regions of the virus are either refractory to sequence change or that persistently activated CD8 T-cell responses in chronic infection exert little functional selection pressure."
	www.aegis.com /pubs/aidswkly/2005/AW051003.html (683 words)

	A LIMITED NUMBER OF HLA EPITOPES ARE RELATED TO ALLOGRAFT LOSS. (Site not responding. Last check: )
		The accessibility of these putative epitopes for Abs and T-cell receptors is subsequently assessed by studying the three-dimensional structure of HLA molecules with another computer program (Rasmol).
		Consequently we obtained a limited set of HLA epitopes that seem to be related to organ allograft loss.
		A detailed description of these HLA epitopes, in the context of clinical complications, may lead to an improved organ allocation strategy.
	www.a-s-t.org /abstracts98/Abs258.htm (327 words)

	Welcome to the First International Qatari Hepatitis Symposium
		Mutation within the “a” determinant epitopes of HBsAg allows the mutant virus to escape recognition by a neutralizing immune response and to continue to replicate.
		Epitope 1 was found between amino acids 121-124, while Epitope 2 was found between positions 139-147.
		Epitope mapping of anti-HBs monoclonal reagents is one tool to utilize in analyzing immunoassay reactivity.
	www.hmc.org.qa /qhs/coleman.htm (280 words)

	Carcinoembryonic Antigen Continuous Epitopes Determined by the SPOT Method
		The five major nonoverlapping epitopes (Gold 1-5) have been broadly correlated with the domain organization, but there is no precise localization of the epitopes at the sequence level.
		In an attempt to identify the peptide sequences corresponding to the five Gold epitopes on the CEA molecule, we prepared a set of 227 overlapping fifteen-mer peptides corresponding to the complete CEA sequence with the SPOT method.
		Thus, in terms of occurrence of continuous epitopes, the Ig-like domains A1, A2, A3 and B3 seem to be the most antigenic parts of CEA.
	content.karger.com /produktedb/produkte.asp?typ=pdf&file=tbi22184 (327 words)

	Virology Journal \| Full text \| Characterization of neutralizing epitopes within the major capsid protein of human ...
		Whereas the epitope of mAb H33.J3 was determined by amino acids (aa) 51–58 in the BC loop of HPV33 L1, sequences of at least two hyper variable loops, DE (aa 132–140) and FGb (aa 282–291), were found to be essential for binding of H33.B6.
		To further characterize the epitopes of HPV33-specific antibodies, hybrid virus-like particles were designed in which type-specific sequences in the major capsid protein L1 of HPV33 were replaced by corresponding amino acids of HPV16, eliminating the putative epitopes.
		The epitope recognized by the H33.B6 antibody was shown to be more complex, as exchange of loops DE or FGb resulted in the loss of reactivity.
	www.virologyj.com /content/3/1/83 (5270 words)

	Immunome Research \| Full text \| Improved method for predicting linear B-cell epitopes
		Most protein epitopes are composed of different parts of the polypeptide chain that are brought into spatial proximity by the folding of the protein.
		These epitopes are called discontinuous, but for approximately 10% of the epitopes, the corresponding antibodies are cross-reactive with a linear peptide fragment of the epitope [4].
		It consists of epitopes found in the proteins of HIV taken from the HIV Molecular Immunology Database of the Los Alamos National Laboratory [19]http://www.hiv.lanl.gov.
	www.immunome-research.com /content/2/1/2 (4209 words)

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