Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN

He, Yongqun; Xiang, Zuoshuang

doi:10.1186/1745-7580-6-s1-s5

Cited by 46 publications

(43 citation statements)

References 32 publications

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“…61,65 In another time-series study, results of systems biology analysis of Brucella and bovine host gene expression data 61,65 were combined with reverse vaccinology 62 to identify effective candidate subunit vaccines protective against virulent challenge in the mouse model. 66 These studies provide provocative examples in support of using systems biology to more effectively integrate and exploit data for model development, for causal discovery, for the prediction of biological activities, for improving the design of in vitro and in vivo experiments, for finding biomarkers for enhanced brucellosis diagnosis, and for druggable targets for more effective treatment of brucellosis.…”

Section: Brucella Pathogenesismentioning

confidence: 99%

“…6,8,13,16,18,32,53e60 This broad spectrum of data sets was analyzed to identify candidate genes and biomarkers of Brucella and hosts, 61 to analyze 62 and predict Brucella antigenic proteins, to identify subunit vaccines, 63 to understand gene regulatory networks, 54 and to characterize the stringent Brucella stress response 64 and modulation of host responses. 53 Time-series studies of in vitro or in vivo experimental infection data were performed with a systems-based perspective of complex biological organizations to categorize the interactions of individual proteins within Brucellaehost proteine protein networks.…”

Section: Systems Biology and Omics Analysis Of Brucella And Hostsmentioning

confidence: 99%

See 1 more Smart Citation

Pathogenesis and Immunobiology of Brucellosis

Figueiredo

Ficht

Rice‐Ficht

et al. 2015

The American Journal of Pathology

379

270

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This review of Brucellaehost interactions and immunobiology discusses recent discoveries as the basis for pathogenesis-informed rationales to prevent or treat brucellosis. Brucella spp., as animal pathogens, cause human brucellosis, a zoonosis that results in worldwide economic losses, human morbidity, and poverty. Although Brucella spp. infect humans as an incidental host, 500,000 new human infections occur annually, and no patient-friendly treatments or approved human vaccines are reported. Brucellae display strong tissue tropism for lymphoreticular and reproductive systems with an intracellular lifestyle that limits exposure to innate and adaptive immune responses, sequesters the organism from the effects of antibiotics, and drives clinical disease manifestations and pathology. Stealthy brucellae exploit strategies to establish infection, including i) evasion of intracellular destruction by restricting fusion of type IV secretion systemdependent Brucella-containing vacuoles with lysosomal compartments, ii) inhibition of apoptosis of infected mononuclear cells, and iii) prevention of dendritic cell maturation, antigen presentation, and activation of naive T cells, pathogenesis lessons that may be informative for other intracellular pathogens. Data sets of next-generation sequences of Brucella and host time-series global expression fused with proteomics and metabolomics data from in vitro and in vivo experiments now inform interactive cellular pathways and gene regulatory networks enabling full-scale systems biology analysis. The newly identified effector proteins of Brucella may represent targets for improved, safer brucellosis vaccines and therapeutics. It is noteworthy that long ago in his publication Epidemics, Hippocrates described brucellosis-type syndromes in humans living in the Mediterranean littoral. Many centuries later, British physician, David Bruce, and Greek physician, Themistokles Zammit, in 1886 would discover the causative agent, Micrococcus melitensis, of brucellosis and would identify milk products of goats as the source of infection for military troops on the island of Malta. Even after more than a century of extensive research, Brucella spp. are still serious animal pathogens that cause brucellosis, a zoonosis that results in substantial economic losses, human morbidity, and perpetuates poverty worldwide.1 These Gram-negative bacteria infect a diverse array of land and aquatic mammals,

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Section: Brucella Pathogenesismentioning

confidence: 99%

Section: Systems Biology and Omics Analysis Of Brucella And Hostsmentioning

confidence: 99%

Pathogenesis and Immunobiology of Brucellosis

Figueiredo

Ficht

Rice‐Ficht

et al. 2015

The American Journal of Pathology

379

270

View full text Add to dashboard Cite

show abstract

“…The Vaxign execution pipeline is able to predict antigen cellular localization, adhesion, epitope binding to MHC class I and class II, and sequence similarities to human, mouse and/or pig proteins. Vaxign has successfully been tested in prediction of vaccine candidates for many different pathogens such as Brucella [5-7] , uropathogenic E. coli [4], Francisella [8], Streptococcus agalactiae [9] and human herpes simplex virus [10]. The experimental verification of Vaxign-predicted results [7] confirms the accuracy of the Vaxign vaccine candidate prediction.…”

Section: Progresses and Challengesmentioning

confidence: 94%

Ontology-supported research on vaccine efficacy, safety and integrative biological networks

2014

Expert Review of Vaccines

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Summary While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including the Vaccine Ontology, Ontology of Adverse Events, and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network (“OneNet”) Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms.

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“…However, one plausible theory is that to compensate for these changes in gene expression, Rev 1 may have up-regulated other pathways, such as those involved in the _ oxidation of fatty acids and protein synthesis, to generate more reducing equivalents, ultimately for use in the production of ATP. These alterations would compensate for the energy loss due to misregulation of iron metabolism (72,95).…”

Section: Wwwintechopencommentioning

confidence: 99%

“…Such a global characterization would not have been possible by using time consuming and traditional biochemical approaches. The era of post-genomic technology offers new and exciting opportunities to understand the complete biology of different Brucella species (93,95,96).…”

Section: Wwwintechopencommentioning

confidence: 99%