Editorial: Computational Systems Biology of Pathogen-Host Interactions

Durmuş, Saliha; Çakır, Tunahan; Guthke, Reinhard

doi:10.3389/fmicb.2016.00021

Cited by 35 publications

(47 citation statements)

References 8 publications

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“…There are ongoing initiatives to exploit the benefits of systems biology for a deeper understanding of pathogenicity [31][32][33] and host-pathogen interaction at a systems level has been reviewed [34,35]. Understandably, initial research focused on human pathogens.…”

Section: Systems Biologymentioning

confidence: 99%

“…In general, protein-protein interaction is the most important and most studied subject relating to the field of pathogen-host interaction [34]. Proteomic analyses attempt to reveal and quantify all proteins in a culture at a given moment under specific conditions.…”

Section: Proteomicsmentioning

confidence: 99%

“…Other approaches targeted the metabolic interactions of gut symbionts with their hosts [232][233][234][235]. Two recent reviews focus comprehensively on the systems biology of host (gut)-microbe interactions [34,236].…”

Section: Environmental Systems Biology As a Perspective For Analysis mentioning

confidence: 99%

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Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

et al. 2017

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Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features. Traditional analyses of Xanthomonas metabolism missed the Embden-Meyerhof-Parnas pathway (glycolysis) as being a route by which energy and molecular building blocks are derived from glucose. As a consequence of the emerging full picture of their metabolism process, xanthomonads were discovered to have three alternative catabolic pathways and they use an unusual and reversible phosphofructokinase as a key enzyme. In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate metabolism. This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics. Analysis of high-throughput omics data facilitates the reconstruction of organism-specific large-and genome-scale metabolic networks. Reconstructed metabolic networks are fundamental to the formulation of metabolic models that facilitate the simulation of actual metabolic activities under specific environmental conditions. SYSTEMS BIOLOGYIn recent years, systems and synthetic biology have substantially increased our understanding of many processes in life sciences at molecular and cellular levels [1][2][3]. Systems biology intends to understand the cell from a system-wide perspective. For over 100 years, life sciences have aimed at elucidating the details of molecular processes in organisms. In systems biology, scientists have started to inter-relate this data on a large scale in order to analyse the interactions of all elements [4,5], and thus initiate the decoding of entire systems, aiming at their quantitative understanding. This became possible with the development of high-throughput techniques associated with diverse computational methods and the availability of faster computing. Fundamental highthroughput methods are now routinely available in the fields of genomics, transcriptomics, metabolomics and proteomics, while additional specialized branches of omics disciplines have been developed, such as lipidomics [6][7][8], glycomics [9][10][11] and 13 C fluxomics [12,13].

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Section: Systems Biologymentioning

confidence: 99%

Section: Proteomicsmentioning

confidence: 99%

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Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

et al. 2017

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“…Moreover, the single cell information must be integrated with tissue-, organ-, organism-and maybe even the ecosystem level to obtain a complete functional understanding. Therefore, computational modeling (for recent reviews, see [130][131][132]) at multiple scales will be essential for integrating the available information. At any rate it seems safe to predict that multi-scale approaches integrating data from quite different types of techniques is a promising avenue for deciphering the role of phenotypic heterogeneity in infectious disease.…”

Section: Concluding Remarks and Future Perspectivesmentioning

confidence: 99%

Experimental approaches to phenotypic diversity in infection

Kreibich

Hardt

2015

Current Opinion in Microbiology

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“…We identified 40 and 15 death-receptor and ER genes, respectively, related to liver regeneration. We also employed the gene synergy formula (Et) (Xu et al, 2012) to analyze the interactions between the genes identified above in an effort to determine the role of death receptor and ER apoptosis pathway-related genes in rat liver regeneration (Durmuş et al, 2015;Fair and Rivas, 2015).…”

Section: Introductionmentioning

confidence: 99%

Expression profiles of the apoptosis signaling pathway mediated by death receptor and endoplasmic reticulum in rat liver regeneration

Xing

Zhu

et al. 2016

Genet. Mol. Res.

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ABSTRACT. The death receptor and endoplasmic reticulum (ER) are closely related to cell apoptosis, and it is worth studying whether the apoptosis pathways mediated by them are involved in liver regeneration. To understand the mechanism underlying death receptor-and ERmediated apoptosis during rat liver regeneration, we used the Rat Genome 230 2.0 Array to determine the changes in gene expression. We then searched the gene ontology (GO) and NCBI databases for genes associated with cell apoptosis mediated by the death receptor and ER. QIAGEN and KEGG databases were used for the related signaling pathways. We used the expression profile function to calculate the activity levels of the known apoptosis signaling pathways. The results of our study showed that the initial gene expression numbers in initiation, G0/G1 transition, cell proliferation, and redifferentiation and structural reconstruction phases were 32, 25, 44, and 29, respectively. This demonstrates that liver regeneration-related genes primarily start their expression in the initiation phase and work differently in each phase. By calculation and analysis using the gene synergy formula, it was suggested that the apoptosis signaling pathways [FAS, death receptor 3 (DR3), tumor necrosis factor receptor 1 (TNFR1), and ER] induced cell apoptosis in whole liver regeneration and anti-apoptosis pathways (DR3 and TNFR2) restrained apoptosis in the early phase of liver regeneration. In summary, these apoptosis pathways coordinated and regulated quality and quantity of the regenerating liver cells.

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Editorial: Computational Systems Biology of Pathogen-Host Interactions

Cited by 35 publications

References 8 publications

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

Experimental approaches to phenotypic diversity in infection

Expression profiles of the apoptosis signaling pathway mediated by death receptor and endoplasmic reticulum in rat liver regeneration

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