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In silico vaccine

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https://www.readbyqxmd.com/read/28717032/th17-mediated-cross-protection-against-pneumococcal-carriage-by-vaccination-with-a-variable-antigen
#1
Kirsten Kuipers, Wouter S P Jong, Christa E van der Gaast-de Jongh, Diane Houben, Fred van Opzeeland, Elles Simonetti, Saskia van Selm, Ronald de Groot, Marije I Koenders, Taj Azarian, Elder Pupo, Peter van der Ley, Jeroen D Langereis, Aldert Zomer, Joen Luirink, Marien I de Jonge
Serotype-specific protection against a Streptococcus pneumoniae is an important limitation of the current polysaccharide-based vaccines. To prevent serotype replacement, reduce transmission and limit emergence of new variants, it is essential to induce broad protection and restrict pneumococcal colonization. In this study, we used a prototype vaccine formulation consisting of LPS-detoxified outer membrane vesicles (OMVs) from Salmonella Typhimurium displaying the variable N-terminus of PspA (α1α2) for intranasal vaccination, which induced strong Th17 immunity associated with substantial reduction of pneumococcal colonization...
July 17, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28674640/in-silico-prediction-and-modeling-of-the-entamoeba-histolytica-proteins-serine-rich-entamoeba-histolytica-protein-and-29%C3%A2-kda-cysteine-rich-protease
#2
Kumar Manochitra, Subhash Chandra Parija
BACKGROUND: Amoebiasis is the third most common parasitic cause of morbidity and mortality, particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence there arises a necessity for a better diagnostic approach. Serine-rich Entamoeba histolyticaprotein (SREHP), peroxiredoxin and Gal/GalNAc lectin are pivotal in E. histolyticavirulence and are extensively studied as diagnostic and vaccine targets. For elucidating the cellular function of these proteins, details regarding their respective quaternary structures are essential...
2017: PeerJ
https://www.readbyqxmd.com/read/28661444/glycosylation-of-recombinant-antigenic-proteins-from-mycobacterium-tuberculosis-in-silico-prediction-of-protein-epitopes-and-ex-vivo-biological-evaluation-of-new-semi-synthetic-glycoconjugates
#3
Teodora Bavaro, Sara Tengattini, Luciano Piubelli, Francesca Mangione, Roberta Bernardini, Vincenzina Monzillo, Sandra Calarota, Piero Marone, Massimo Amicosante, Loredano Pollegioni, Caterina Temporini, Marco Terreni
Tuberculosis is still one of the most deadly infectious diseases worldwide, and the use of conjugated antigens, obtained by combining antigenic oligosaccharides, such as the lipoarabinomannane (LAM), with antigenic proteins from Mycobacterium tuberculosis (MTB), has been proposed as a new strategy for developing efficient vaccines. In this work, we investigated the effect of the chemical glycosylation on two recombinant MTB proteins produced in E. coli with an additional seven-amino acid tag (recombinant Ag85B and TB10...
June 29, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28660200/a-fast-and-inexpensive-protocol-for-empirical-verification-of-neutralizing-epitopes-in-microbial-toxins-and-enzymes
#4
Christine N Vuong, Wen-Ko Chou, Vivek A Kuttappan, Billy M Hargis, Lisa R Bielke, Luc R Berghman
In vivo targeting of peptides to antigen-presenting cells by use of agonistic anti-CD40 monoclonal antibodies has been used successfully as an immune response enhancing strategy. When tested in chickens, the antibody-guided platform was capable of inducing specific IgG production within 1 week postimmunization. However, use of this method beyond its initial conception as a vaccine delivery tool has not been fully exploited. In this study, Clostridium perfringens alpha-toxin was used as a model microbial toxin for epitope mapping by using the antibody-guided immunization method to generate a panel of antibodies against specific, regions of the toxin in an attempt to identify crucial determinants on the toxin which, once bound, would hinder downstream toxicity...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/28651021/natural-immune-response-to-plasmodium-vivax-alpha-helical-coiled-coil-protein-motifs-and-its-association-with-the-risk-of-p-vivax-malaria
#5
Nora Céspedes, Connie S N Li Wai Suen, Cristian Koepfli, Camila T França, Ingrid Felger, Issa Nebie, Myriam Arévalo-Herrera, Ivo Mueller, Giampietro Corradin, Sócrates Herrera
Protein α-helical coiled coil structures are known to induce antibodies able to block critical functions in different pathogens. In a previous study, a total of 50 proteins of Plasmodium vivax erythrocytic asexual stages containing α-helical coiled coil structural motifs were identified in silico, and the corresponding peptides were chemically synthesized. A total of 43 peptides were recognized by naturally acquired antibodies in plasma samples from both Papua New Guinea (PNG) and Colombian adult donors. In this study, the association between IgG antibodies to these peptides and clinical immunity was further explored by measuring total IgG antibody levels to 24 peptides in baseline samples from a longitudinal study of children aged 1-3 years (n = 164) followed for 16 months...
2017: PloS One
https://www.readbyqxmd.com/read/28646586/vaccine-candidate-discovery-for-the-next-generation-of-malaria-vaccines
#6
REVIEW
James Tuju, Gathoni Kamuyu, Linda M Murungi, Faith H A Osier
Although epidemiological observations, IgG passive transfer studies and experimental infections in humans all support the feasibility of developing highly effective malaria vaccines, the precise antigens that induce protective immunity remain uncertain. Here, we review the methodologies applied to vaccine candidate discovery for Plasmodium falciparum malaria from the pre- to post- genomic era. Probing of genomic and/or cDNA libraries with antibodies of defined specificities or functional activity predominated the former, while reverse vaccinology encompassing high throughput in silico analyses of genomic, transcriptomic or proteomic parasite datasets is the mainstay of the latter...
June 24, 2017: Immunology
https://www.readbyqxmd.com/read/28638312/in-silico-signature-prediction-modeling-in-cytolethal-distending-toxin-producing-escherichia-coli-strains
#7
Maryam Javadi, Mana Oloomi, Saeid Bouzari
In this study, cytolethal distending toxin (CDT) producer isolates genome were compared with genome of pathogenic and commensal Escherichia coli strains. Conserved genomic signatures among different types of CDT producer E. coli strains were assessed. It was shown that they could be used as biomarkers for research purposes and clinical diagnosis by polymerase chain reaction, or in vaccine development. cdt genes and several other genetic biomarkers were identified as signature sequences in CDT producer strains...
June 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28588634/in-silico-identification-of-epitopes-from-house-cat-and-dog-proteins-as-peptide-immunotherapy-candidates-based-on-human-leukocyte-antigen-binding-affinity
#8
H N Tipu, D Ahmed, S A H Gardezi
The objective of this descriptive study was to determine Felis domesticus (cat) and Canis familiaris (dog) protein epitopes that bind strongly to selected HLA class II alleles to identify synthetic vaccine candidate epitopes and to identify individuals/populations who are likely to respond to vaccines. FASTA amino acid sequences of experimentally validated allergenic proteins of house cat and dog were identified using International Union of Immunological Societies (IUIS) allergen nomenclature database. NetMHCII 2...
2017: Iranian journal of veterinary research
https://www.readbyqxmd.com/read/28584981/immunoinformatics-as-a-tool-for-new-antifungal-vaccines
#9
Rupanjali Chaudhuri, Srinivasan Ramachandran
Immunoinformatics aids in screening for vaccine candidates, which can be experimentally tested for their efficacy. This chapter describes methods to use immunoinformatics to screen fungal vaccines candidates. Surface-localized molecules called adhesins could elicit immune response and serve as efficient vaccine candidates. The screening process is patterned on two steps, namely, a First Layer screen mostly used for value addition and prioritization based on characteristics of known antigens and a Second Layer highly focussed on core immunoinformatics analysis involving the binding and interactions of the molecules of the immune system...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28570984/in-silico-identification-of-vaccine-candidates-against-klebsiella-oxytoca
#10
Sandipan Talukdar, Udeshna Bayan, Kandarpa Kr Saikia
Klebsiella oxytoca causes several diseases in immunocompromised as well as healthy individuals. Increasing resistance to a number of antibiotics makes treatment options limited. Prevention using vaccine could be an important solution to get rid of infections caused by Klebsiella oxytoca. In recent time, genome based approaches have contributed significantly in vaccine development. Our aim was to identify the most conserved and immunogenic antigens that can be considered as potential vaccine candidates. KEGG database was used to find out pathways unique to the bacteria...
May 22, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28560699/identification-of-strategic-residues-at-the-interface-of-antigen-antibody-interactions-by-in-silico-mutagenesis
#11
Lu Xin, Hai Yu, Qiyang Hong, Xingjian Bi, Xiao Zhang, Zhiqing Zhang, Zhibo Kong, Qingbing Zheng, Ying Gu, Qinjian Zhao, Jun Zhang, Shaowei Li, Ningshao Xia
Structural information pertaining to antigen-antibody interactions is fundamental in immunology, and benefits structure-based vaccine design. Modeling of antigen-antibody immune complexes from co-crystal structures or molecular docking simulations provides an extensive profile of the epitope at the interface; however, the key amino acids involved in the interaction must be further clarified, often through the use of experimental mutagenesis and subsequent binding assays. Here, we describe an in silico mutagenesis method to identify key sites at antigen-antibody interfaces, using significant increase in pH-dependency energy among saturated point mutations...
May 30, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28558204/development-and-application-of-synthetic-affinity-ligands-for-the-purification-of-ferritin-based-influenza-antigens
#12
Shaleem I Jacob, Basmah Khogeer, Nick Bampos, Tom Sheppard, Richard Schwartz, Christopher R Lowe
A recently developed novel recombinant influenza antigen vaccine has shown great success in preclinical studies in ferrets and mice. It provides broader protection, and is efficient to manufacture compared to the conventional trivalent influenza vaccines (TIV). Each strain of the recombinant antigen has a constant self-assembled bacterial ferritin core which, if used as a target for affinity chromatography, could lead to a universal purification method. Ferritin in silico models were used to explore potential target binding sites against ligands synthesized by the four-component Ugi reaction...
June 21, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28555545/identification-of-cross-reacting-t-cell-epitopes-in-structural-and-non-structural-proteins-of-swine-and-pandemic-h1n1-influenza-a-virus-strains-in-pigs
#13
Massimiliano Baratelli, Lasse Eggers Pedersen, Ramona Trebbien, Lars Erik Larsen, Gregers Jungersen, Esther Blanco, Jens Nielsen, Maria Montoya
Heterologous protection against swine influenza viruses (SwIVs) of different lineages is an important concern for the pig industry. Cross-protection between 'avian-like' H1N1 and 2009 pandemic H1N1 lineages has been observed previously, indicating the involvement of cross-reacting T-cells. Here, reverse vaccinology was applied to identify cross-reacting MHC class I T-cell epitopes from two different SwIV H1 lineages in pigs. In silico prediction followed by in vitro and in vivo testing was used to identify SLA-1*0702 T-cell epitopes in heterologous SwIV-infected pigs...
May 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28549876/prediction-and-analysis-of-promiscuous-t-cell-epitopes-derived-from-the-vaccine-candidate-antigens-of-leishmania-donovani-binding-to-mhc-class-ii-alleles-using-in-silico-approach
#14
Manju Kashyap, Varun Jaiswal, Umar Farooq
Visceral leishmaniasis is a dreadful infectious disease and caused by the intracellular protozoan parasites, Leishmania donovani and Leishmania infantum. Despite extensive efforts for developing effective prophylactic vaccine, still no vaccine is available against leishmaniasis. However, advancement in immunoinformatics methods generated new dimension in peptide based vaccine development. The present study was aimed to identify T-cell epitopes from the vaccine candidate antigens like Lipophosphogylcan-3(LPG-3) and Nucleoside hydrolase (NH) from the L...
May 23, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28549079/computational-modeling-of-immune-system-of-the-fish-for-a-more-effective-vaccination-in-aquaculture
#15
Alice Madonia, Cristiano Melchiorri, Simone Bonamano, Marco Marcelli, Chiara Bulfon, Filippo Castiglione, Marco Galeotti, Donatella Volpatti, Francesco Mosca, Pietro-Giorgio Tiscar, Nicla Romano
Motivation: A computational model equipped with the main immunological features of the sea bass ( Dicentrarchus labrax L. ) immune system was used to predict more effective vaccination in fish. The performance of the model was evaluated by using the results of two in vivo vaccinations trials against L. anguillarum and P. damselae . Tests were performed to select the appropriate doses of vaccine and infectious bacteria to set up the model. Simulation outputs were compared with the specific antibody production and the expression of BcR and TcR gene transcripts in spleen...
May 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28536262/in-silico-and-cell-based-analyses-reveal-strong-divergence-between-prediction-and-observation-of-t-cell-recognized-tumor-antigen-t-cell-epitopes
#16
Julien Schmidt, Philippe Guillaume, Danijel Dojcinovic, Julia Karbach, George Coukos, Immanuel Luescher
Tumor exomes provide comprehensive information on mutated, overexpressed genes and aberrant splicing, which can be exploited for personalized cancer immunotherapy. Of particular interest are mutated tumor antigen T-cell epitopes, because neoepitope-specific T cells often are tumoricidal. However, identifying tumor-specific T-cell epitopes is a major challenge. A widely used strategy relies on initial prediction of human leukocyte antigen-binding peptides by in silico algorithms, but the predictive power of this approach is unclear...
July 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28534196/in-silico-analysis-of-shiga-toxins-stxs-to-identify-new-potential-vaccine-targets-for-shiga-toxin-producing-escherichia-coli
#17
Maryam Golshani, Mana Oloomi, Saeid Bouzari
Shiga toxins belong to a family of structurally and functionally related toxins serving as the main virulence factors for pathogenicity of the Shiga toxin-producing Escherichia coli (STEC) associating with Hemolytic uremic syndrome (HUS). At present, there is no effective treatment or prevention for HUS. The aim of the present study was to find conserved regions within the amino acid sequences of Stx1, Stx2 (Shiga toxin) and their variants. In this regard, In-silico identification of conformational continuous B cell and T-cell epitopes was performed in order to introduce new potential vaccine candidates...
December 2016: In Silico Pharmacology
https://www.readbyqxmd.com/read/28509875/in-silico-analysis-of-epitope-based-vaccine-candidates-against-hepatitis-b-virus-polymerase-protein
#18
Juzeng Zheng, Xianfan Lin, Xiuyan Wang, Liyu Zheng, Songsong Lan, Sisi Jin, Zhanfan Ou, Jinming Wu
Hepatitis B virus (HBV) infection has persisted as a major public health problem due to the lack of an effective treatment for those chronically infected. Therapeutic vaccination holds promise, and targeting HBV polymerase is pivotal for viral eradication. In this research, a computational approach was employed to predict suitable HBV polymerase targeting multi-peptides for vaccine candidate selection. We then performed in-depth computational analysis to evaluate the predicted epitopes' immunogenicity, conservation, population coverage, and toxicity...
May 16, 2017: Viruses
https://www.readbyqxmd.com/read/28496441/discovery-of-novel-leptospirosis-vaccine-candidates-using-reverse-and-structural-vaccinology
#19
André Alex Grassmann, Frederico Schmitt Kremer, Júlia Cougo Dos Santos, Jéssica Dias Souza, Luciano da Silva Pinto, Alan John Alexander McBride
Leptospira spp. are diderm (two membranes) bacteria that infect mammals causing leptospirosis, a public health problem with global implications. Thousands of people die every year due to leptospirosis, especially in developing countries with tropical climates. Prophylaxis is difficult due to multiple factors, including the large number of asymptomatic hosts that transmit the bacteria, poor sanitation, increasing numbers of slum dwellers, and the lack of an effective vaccine. Several leptospiral recombinant antigens were evaluated as a replacement for the inactivated (bacterin) vaccine; however, success has been limited...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28472201/predicting-hiv-1-transmission-and-antibody-neutralization-efficacy-in-vivo-from-stoichiometric-parameters
#20
Oliver F Brandenberg, Carsten Magnus, Peter Rusert, Huldrych F Günthard, Roland R Regoes, Alexandra Trkola
The potential of broadly neutralizing antibodies targeting the HIV-1 envelope trimer to prevent HIV-1 transmission has opened new avenues for therapies and vaccines. However, their implementation remains challenging and would profit from a deepened mechanistic understanding of HIV-antibody interactions and the mucosal transmission process. In this study we experimentally determined stoichiometric parameters of the HIV-1 trimer-antibody interaction, confirming that binding of one antibody is sufficient for trimer neutralization...
May 2017: PLoS Pathogens
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