1,510 Hits in 6.8 sec

The use of genomics in microbial vaccine development

Stefania Bambini, Rino Rappuoli
2009 Drug Discovery Today  
The availability of complete genome sequences, together with the progression of high-throughput technologies such as functional and structural genomics, has led to a new paradigm in vaccine development  ...  Vaccination is one of the most effective tools for the prevention of infectious diseases.  ...  Acknowledgements We are grateful to Isabel Delany and Maurizio Comanducci for critical reading, to Giorgio Corsi for artwork and to Catherine Mallia for manuscript editing.  ... 
doi:10.1016/j.drudis.2008.12.007 pmid:19150507 pmcid:PMC7108364 fatcat:q2mrqum2enccthsgby42kxgj3q

Proteinaceous effector discovery and characterization in filamentous plant pathogens

Claire Kanja, Kim E. Hammond‐Kosack
2020 Molecular plant pathology  
of the effectors of filamentous plant pathogens and identification of their host targets.  ...  The purpose of this review is to give a chronological perspective on the evolution of the methodologies used in effector discovery from physical isolation and in silico predictions, to functional characterization  ...  Originally identified as an immune mechanism in bacteria and archaea, the CRISPR-Cas9 system is used as a genome-editing tool in plants and animals, and was adapted by Nødvig et al. (2015) for use in  ... 
doi:10.1111/mpp.12980 pmid:32767620 fatcat:cb5ehk47hbed5hgdbhp7x7qeta

Identification of novel vaccine candidates againstAcinetobacter baumanniiusing reverse vaccinology

Ming-Hsien Chiang, Wang-Chou Sung, Shu-Pei Lien, Ying-Zih Chen, Annie Fei-yun Lo, Jui-Hsin Huang, Shu-Chen Kuo, Pele Chong
2015 Human Vaccines & Immunotherapeutics  
After excluding those antigens have been used as vaccine candidates reported by the in silico search-engines of PubMed and Google Scholar, 13 proteins could potentially be vaccine candidates.  ...  proteins, 77 genes were identified and selected for further studies.  ...  Funding This work was supported by the grants from Ministry of Science and Technology (NSC 101-2321-B-400-020-MY2) and National Health Research Institutes, Taiwan, ROC.  ... 
doi:10.1080/21645515.2015.1010910 pmid:25751377 pmcid:PMC4514290 fatcat:basa3t74jzf2loq67yfy43jjoi

Studying Salmonellae and Yersiniae Host–Pathogen Interactions Using Integrated 'Omics and Modeling [chapter]

Charles Ansong, Brooke L. Deatherage, Daniel Hyduke, Brian Schmidt, Jason E. McDermott, Marcus B. Jones, Sadhana Chauhan, Pep Charusanti, Young-Mo Kim, Ernesto S. Nakayasu, Jie Li, Afshan Kidwai (+10 others)
2012 Current Topics in Microbiology and Immunology  
The metabolic complexity of these organisms facilitates robust lifestyles both outside of and within animal hosts.  ...  Salmonella and Yersinia are two distantly related genera containing species with wide host-range specificity and pathogenic capacity.  ...  The Host-Pathogen Interface The interplay between effector proteins secreted by the pathogen and host cells exposed to these effector proteins are relevant to infection in many Enteropathogens and as such  ... 
doi:10.1007/82_2012_247 pmid:22886542 pmcid:PMC6197062 fatcat:selfq5rs4nfibd6mgq2ugplmra

Identification of genomic loci associated with genotypic and phenotypic variation among Pseudomonas aeruginosa clinical isolates from pneumonia

Cristina S. Mesquita, Pedro Soares-Castro, Alberta Faustino, Hugo M. Santos, José L. Capelo, Pedro Santos
2019 Microbial Pathogenesis  
Secretome analysis identified signatures features with unknown function as potential novel pathogenic (e.g. a MATE-protein in HB13, a protease in HB15) and antibiotic resistance (a HlyD-like secretion  ...  protein in HB13) determinants.  ...  Supplementary Material A contains the detailed protocol, parameters and in silico tools used for peptide identification and analysis.  ... 
doi:10.1016/j.micpath.2019.103702 pmid:31472259 fatcat:oieg6pjtuvhnlgpszxgu5s3veu

Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches

Sidra Aslam, Sajjad Ahmad, Fatima Noor, Usman Ali Ashfaq, Farah Shahid, Abdur Rehman, Muhammad Tahir ul Qamar, Eid A. Alatawi, Fahad M. Alshabrmi, Khaled S. Allemailem
2021 Biology  
system chaperone Scc2, CT847 family type III secretion system effector, hypothetical protein CTDEC_0668, and CHLPN 76kDa-like protein.  ...  An in silico vaccine was developed using carefully selected epitopes (11 CTL, 2 HTL & 10 LBL) and then docked with the MHC molecules (MHC I & MHC II) and human TLR4.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biology10100997 pmid:34681096 fatcat:mlflnwql7fbstldw2ndj7couoi

Modeling-Enabled Systems Nutritional Immunology

Meghna Verma, Raquel Hontecillas, Vida Abedi, Andrew Leber, Nuria Tubau-Juni, Casandra Philipson, Adria Carbo, Josep Bassaganya-Riera
2016 Frontiers in Nutrition  
This review highlights the fundamental role of nutrition in the maintenance of health, the immune response, and disease prevention.  ...  The review sets an unconventional path to apply complex science methodologies to nutritional immunology research, discovery, and development through "use cases" centered around the impact of nutrition  ...  Case Study One of the "use cases" that explains the success of in silico experimentation is the identification of lanthionine synthetase component cyclase-like 2 protein (LANCL2) and its application as  ... 
doi:10.3389/fnut.2016.00005 pmid:26909350 pmcid:PMC4754447 fatcat:3xomgnn7pzhavmlrcqruyvgwta

Identification and characterization of putative Aeromonas spp. T3SS effectors

Luiz Thiberio Rangel, Jeremiah Marden, Sophie Colston, João Carlos Setubal, Joerg Graf, Johann Peter Gogarten, Luis Caetano Martha Antunes
2019 PLoS ONE  
The results of this study demonstrate the utility of our approach, combining a novel in silico search method with in vivo experimental validation, and will be useful in future research aimed at identifying  ...  We experimentally validated our in silico findings by assessing the cytotoxicity of representative effectors in Saccharomyces cerevisiae BY4741, with 15 out of 21 assayed proteins eliciting a cytotoxic  ...  An example of these challenges are two effectors, AexT and AexU, in Aeromonas, which share one domain with a second domain being completely novel [29, 30] .  ... 
doi:10.1371/journal.pone.0214035 pmid:31163020 pmcid:PMC6548356 fatcat:mpwpz3ckvvaypphvczksswhjym

T-cell dependent immunogenicity of protein therapeutics: Preclinical assessment and mitigation

Vibha Jawa, Leslie P. Cousens, Michel Awwad, Eric Wakshull, Harald Kropshofer, Anne S. De Groot
2013 Clinical Immunology  
While in silico tools have dramatically improved over time, and consideration of epitope "off-rate" or peptide "residence time" on the MHC molecule is probably within reach of future generations of algorithms  ...  Application of in silico tools reduces downstream in vitro testing dramatically, typically by at least 20-fold [98] , and provides an opportunity in early development to modify a protein to decrease its  ... 
doi:10.1016/j.clim.2013.09.006 pmid:24263283 fatcat:unpdy2qv2fdhbnxko4rkmsvhqy

Pro-Inflammatory Cytokines in Sepsis: Biological Studies and Prospects From In Silico Research

Andréia Patrícia Gomes, Paulo Sergio Balbino Miguel
2015 Biological Systems Open Access  
Acknowledgement The authors are grateful to CNPq (National Council for Scientific and Technological Development), FAPEMIG (Foundation for Research Support of the State of Minas Gerais) and FADIP (Faculdade  ...  We hope that the in silico approach will allow for a better understanding of the mechanisms that enable perspectives that promote advances in the identification of sepsis biomarkers, with the goal of earlier  ...  The pathophysiology and diagnosis of sepsis, its management and prognostic prediction are in fact, great challenges [8] .  ... 
doi:10.4172/2329-6577.1000158 fatcat:khi4kpqv6vfznfmf7ztl5gkmki

Plants versus Fungi and Oomycetes: Pathogenesis, Defense and Counter-Defense in the Proteomics Era

Abdelbasset El Hadrami, Ahmed F. El-Bebany, Zhen Yao, Lorne R. Adam, Ismail El Hadrami, Fouad Daayf
2012 International Journal of Molecular Sciences  
However, many challenges are encountered during in planta studies aimed at stressing details of host defenses and fungal and oomycete pathogenicity determinants during interactions.  ...  However, it is only in the last few years, with the development of new approaches, combined with bioinformatics data mining tools, gel staining, and analytical instruments, such as 2D-PAGE/nanoflow-LC-MS  ...  Resolving unambiguous identification of proteins among contrasting treatments remains an important challenge in proteomics.  ... 
doi:10.3390/ijms13067237 pmid:22837691 pmcid:PMC3397523 fatcat:6bkvhwyg4rgjbjud2frmcjfqv4

Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes

Priscila Grynberg, Roberto Coiti Togawa, Leticia Dias de Freitas, Jose Dijair Antonino, Corinne Rancurel, Marcos Mota do Carmo Costa, Maria Fatima Grossi-de-Sa, Robert N. G. Miller, Ana Cristina Miranda Brasileiro, Patricia Messenberg Guimaraes, Etienne G. J. Danchin
2020 Genes  
Among these phytoparasite-specific proteins, ca. 1000 shared the same properties as known secreted effectors involved in essential parasitic functions.  ...  In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein  ...  Jones, Catherine Wram, and Philipp H. Schiffer for providing access to the predicted proteins in Heterodera schachtii, G. pallida newton, R. similis, R. reniformis, Panagrolaimus sp.  ... 
doi:10.3390/genes11111347 pmid:33202889 fatcat:mo742dnwyrezddjgpy4eoizdfy

NovelBurkholderia malleiVirulence Factors Linked to Specific Host-Pathogen Protein Interactions

Vesna Memišević, Nela Zavaljevski, Rembert Pieper, Seesandra V. Rajagopala, Keehwan Kwon, Katherine Townsend, Chenggang Yu, Xueping Yu, David DeShazer, Jaques Reifman, Anders Wallqvist
2013 Molecular & Cellular Proteomics  
Here, we used a combined in silico, in vitro, and in vivo approach to identify B. mallei proteins required for pathogenicity.  ...  We exposed BALB/c mice to mutant strains and the wild-type strain in an aerosol challenge model using lethal B. mallei doses.  ...  Uetz and W. Nierman for helpful discussions.  ... 
doi:10.1074/mcp.m113.029041 pmid:23800426 pmcid:PMC3820922 fatcat:ouwcdxgobvelnfgwkdxd2zidbu

In Vitro and In Vivo Model Systems for Studying Enteropathogenic Escherichia coli Infections

R. J. Law, L. Gur-Arie, I. Rosenshine, B. B. Finlay
2013 Cold Spring Harbor Perspectives in Medicine  
Recent advances in in vitro and in vivo modeling of these pathogens have contributed to our knowledge of how EPEC and EHEC attach to host cells and subvert hostcell signaling pathways to promote infection  ...  Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) belong to a group of bacteria known as attaching and effacing (A/E) pathogens that cause disease by adhering to the lumenal  ...  s laboratory is supported by an operating grant from the Canadian Institute of Health Research (CIHR). Work in I.R.'  ... 
doi:10.1101/cshperspect.a009977 pmid:23457294 pmcid:PMC3579205 fatcat:vt2ov2vtzndwdn3dkieozvpafy

Plant-pathogen interactions: what is proteomics telling us?

Angela Mehta, Ana C. M. Brasileiro, Djair S. L. Souza, Eduardo Romano, Magnólia A. Campos, Maria F. Grossi-de-Sá, Marília S. Silva, Octávio L. Franco, Rodrigo R. Fragoso, Rosangela Bevitori, Thales L. Rocha
2008 The FEBS Journal  
Acknowledgements We wish to thank Dr Gilbert Engler for critical evaluation of the manuscript and English revision.  ...  In the case of pathogens, several of the proteins involved in pathogenicity are secretion proteins, which were observed in bacteria, fungi and nematodes, and were mainly identified by secretomic studies  ...  The proteomic approach is a fundamental method by which we can obtain an understanding and identification of the functions of proteins expressed in a given condition.  ... 
doi:10.1111/j.1742-4658.2008.06528.x pmid:18616468 fatcat:57yuo3xb2zewfi4epnappn5p2u
« Previous Showing results 1 — 15 out of 1,510 results