Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

On Brucella pathogenesis: looking for the unified challenge in systems and synthetic biology.

ABSTRACT: Brucellosis is a zoonotic infection transmitted to humans from infected animals and is one of the widely spread zoonoses. Recently, six species were recognized within the genus Brucella wherein B. melitensis, B. suis and B. abortus are considered virulent for humans. While these species differ phenotypically by their pattern of metabolic activities, there has been an imperative need to understand pathogenesis of Brucella species. It has been foreseen that creating a human vaccine for Brucellosis would entail decreased dose of antibiotics. However the emerging role of Brucella pathogenesis still centers on isolation of the organism and various diagnostic tests thereby leading to varying strategies of treatment cycle. In view of disease heterogeneity, we focus systems and synthetic biology challenges that might improve our understanding the Brucella pathogenesis.

SUBMITTER: Chiliveru S

PROVIDER: S-EPMC4427581 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

On Brucella pathogenesis: looking for the unified challenge in systems and synthetic biology.

Chiliveru Srikanth S Appari Mahesh M Suravajhala Prashanth P

Systems and synthetic biology 20141221 1-2

Brucellosis is a zoonotic infection transmitted to humans from infected animals and is one of the widely spread zoonoses. Recently, six species were recognized within the genus Brucella wherein B. melitensis, B. suis and B. abortus are considered virulent for humans. While these species differ phenotypically by their pattern of metabolic activities, there has been an imperative need to understand pathogenesis of Brucella species. It has been foreseen that creating a human vaccine for Brucellosis ...[more]

PMID: 25972991

Similar Datasets

Looking at COVID-19 from a Systems Biology Perspective.

Project description:The sudden outbreak and worldwide spread of the SARS-CoV-2 pandemic pushed the scientific community to find fast solutions to cope with the health emergency. COVID-19 complexity, in terms of clinical outcomes, severity, and response to therapy suggested the use of multifactorial strategies, characteristic of the network medicine, to approach the study of the pathobiology. Proteomics and interactomics especially allow to generate datasets that, reduced and represented in the forms of networks, can be analyzed with the tools of systems biology to unveil specific pathways central to virus-human host interaction. Moreover, artificial intelligence tools can be implemented for the identification of druggable targets and drug repurposing. In this review article, we provide an overview of the results obtained so far, from a systems biology perspective, in the understanding of COVID-19 pathobiology and virus-host interactions, and in the development of disease classifiers and tools for drug repurposing.

| S-EPMC8961533 | biostudies-literature

Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

Project description:Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

| S-EPMC3972654 | biostudies-literature

Protein assembly systems in natural and synthetic biology.

Project description:The traditional view of protein aggregation as being strictly disease-related has been challenged by many examples of cellular aggregates that regulate beneficial biological functions. When coupled with the emerging view that many regulatory proteins undergo phase separation to form dynamic cellular compartments, it has become clear that supramolecular assembly plays wide-ranging and critical roles in cellular regulation. This presents opportunities to develop new tools to probe and illuminate this biology, and to harness the unique properties of these self-assembling systems for synthetic biology for the purposeful manipulation of biological function.

| S-EPMC7099826 | biostudies-literature

Synthetic Biology: Engineering Living Systems from Biophysical Principles.

Project description:Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties.

| S-EPMC5376109 | biostudies-literature

Genome-scale engineering for systems and synthetic biology.

Project description:Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targeted gene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering.

| S-EPMC3564264 | biostudies-other

Combining systems and synthetic biology for in vivo enzymology.

Project description:Enzymatic parameters are classically determined in vitro, under conditions that are far from those encountered in cells, casting doubt on their physiological relevance. We developed a generic approach combining tools from synthetic and systems biology to measure enzymatic parameters in vivo. In the context of a synthetic carotenoid pathway in Saccharomyces cerevisiae, we focused on a phytoene synthase and three phytoene desaturases, which are difficult to study in vitro. We designed, built, and analyzed a collection of yeast strains mimicking substantial variations in substrate concentration by strategically manipulating the expression of geranyl-geranyl pyrophosphate (GGPP) synthase. We successfully determined in vivo Michaelis-Menten parameters (KM, Vmax, and kcat) for GGPP-converting phytoene synthase from absolute metabolomics, fluxomics and proteomics data, highlighting differences between in vivo and in vitro parameters. Leveraging the versatility of the same set of strains, we then extracted enzymatic parameters for two of the three phytoene desaturases. Our approach demonstrates the feasibility of assessing enzymatic parameters directly in vivo, providing a novel perspective on the kinetic characteristics of enzymes in real cellular conditions.

| S-EPMC11535393 | biostudies-literature

Multiscale Mathematical Modeling in Systems Biology: A Framework to Boost Plant Synthetic Biology.

Project description:Global food insecurity and environmental degradation highlight the urgent need for more sustainable agricultural solutions. Plant synthetic biology emerges as a promising yet risky avenue to develop such solutions. While synthetic biology offers the potential for enhanced crop traits, it also entails risks of extensive environmental damage. This review highlights the complexities and risks associated with plant synthetic biology, while presenting the potential of multiscale mathematical modeling to assess and mitigate those risks effectively. Despite its potential, applying multiscale mathematical models in plants remains underutilized. Here, we advocate for integrating technological advancements in agricultural data analysis to develop a comprehensive understanding of crops across biological scales. By reviewing common modeling approaches and methodologies applicable to plants, the paper establishes a foundation for creating and utilizing integrated multiscale mathematical models. Through modeling techniques such as parameter estimation, bifurcation analysis, and sensitivity analysis, researchers can identify mutational targets and anticipate pleiotropic effects, thereby enhancing the safety of genetically engineered species. To demonstrate the potential of this approach, ongoing efforts are highlighted to develop an integrated multiscale mathematical model for maize (Zea mays L.), engineered through synthetic biology to enhance resilience against Striga (Striga spp.) and drought.

| S-EPMC11820955 | biostudies-literature

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering.

Project description:Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways.

| S-EPMC4874428 | biostudies-other

Systems biology approach predicts antibody signature associated with Brucella melitensis infection in humans.

Project description:A complete understanding of the factors that determine selection of antigens recognized by the humoral immune response following infectious agent challenge is lacking. Here we illustrate a systems biology approach to identify the antibody signature associated with Brucella melitensis (Bm) infection in humans and predict proteomic features of serodiagnostic antigens. By taking advantage of a full proteome microarray expressing previously cloned 1406 and newly cloned 1640 Bm genes, we were able to identify 122 immunodominant antigens and 33 serodiagnostic antigens. The reactive antigens were then classified according to annotated functional features (COGs), computationally predicted features (e.g., subcellular localization, physical properties), and protein expression estimated by mass spectrometry (MS). Enrichment analyses indicated that membrane association and secretion were significant enriching features of the reactive antigens, as were proteins predicted to have a signal peptide, a single transmembrane domain, and outer membrane or periplasmic location. These features accounted for 67% of the serodiagnostic antigens. An overlay of the seroreactive antigen set with proteomic data sets generated by MS identified an additional 24%, suggesting that protein expression in bacteria is an additional determinant in the induction of Brucella-specific antibodies. This analysis indicates that one-third of the proteome contains enriching features that account for 91% of the antigens recognized, and after B. melitensis infection the immune system develops significant antibody titers against 10% of the proteins with these enriching features. This systems biology approach provides an empirical basis for understanding the breadth and specificity of the immune response to B. melitensis and a new framework for comparing the humoral responses against other microorganisms.

| S-EPMC3189706 | biostudies-literature

Combining systems and synthetic biology for in vivo enzymology

Project description:Enzymatic parameters are classically determined in vitro, under conditions that are far from those encountered in cells, casting doubt on their physiological relevance. We developed a generic approach combining tools from synthetic and systems biology to measure enzymatic parameters in vivo. In the context of a synthetic carotenoid pathway in Saccharomyces cerevisiae, we focused on a phytoene synthase and three phytoene desaturases, which are difficult to study in vitro. We designed, built, and analyzed a collection of yeast strains mimicking substantial variations in substrate concentration by strategically manipulating the expression of geranyl-geranyl pyrophosphate (GGPP) synthase. We successfully determined in vivo Michaelis-Menten parameters (KM, Vmax and kcat) for GGPP-converting phytoene synthase from absolute metabolomics, fluxomics and proteomics data, highlighting differences between in vivo and in vitro parameters. Leveraging the versatility of the same set of strains, we then extracted enzymatic parameters for two of the three phytoene desaturases. Our approach demonstrates the feasibility of assessing enzymatic parameters directly in vivo, providing a novel perspective on the kinetic characteristics of enzymes in real cellular conditions.

| S-SCDT-10_1038-S44318-024-00251-W | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data