Mathematical Methods for Inferring Regulatory Networks Interactions: Application to Genetic Regulation

2004 ◽  
Vol 52 (4) ◽  
pp. 391-400 ◽  
Author(s):  
J. Aracena ◽  
J. Demongeot
Keyword(s):  
Regulatory Networks ◽  
Genetic Regulation ◽  
Mathematical Methods

scholarly journals The HrpG/HrpX Regulon of Xanthomonads—An Insight to the Complexity of Regulation of Virulence Traits in Phytopathogenic Bacteria

2021 ◽  
Vol 9 (1) ◽  
pp. 187
Author(s):  
Doron Teper ◽  
Sheo Shankar Pandey ◽  
Nian Wang
Keyword(s):  
Regulatory Network ◽  
Regulatory Networks ◽  
Focal Point ◽  
Genetic Regulation ◽  
Transcriptional Regulators ◽  
Secretion System ◽  
In Planta ◽  
Type 3 Secretion System ◽  
Type 3 ◽  
Made In

Bacteria of the genus Xanthomonas cause a wide variety of economically important diseases in most crops. The virulence of the majority of Xanthomonas spp. is dependent on secretion and translocation of effectors by the type 3 secretion system (T3SS) that is controlled by two master transcriptional regulators HrpG and HrpX. Since their discovery in the 1990s, the two regulators were the focal point of many studies aiming to decipher the regulatory network that controls pathogenicity in Xanthomonas bacteria. HrpG controls the expression of HrpX, which subsequently controls the expression of T3SS apparatus genes and effectors. The HrpG/HrpX regulon is activated in planta and subjected to tight metabolic and genetic regulation. In this review, we cover the advances made in understanding the regulatory networks that control and are controlled by the HrpG/HrpX regulon and their conservation between different Xanthomonas spp.

scholarly journals Dissipativity and Error Feedback Controller Design of Time-Delay Genetic Regulatory Networks

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Yonggang Ma ◽  
Junmei Liu ◽  
Jiao Ai
Keyword(s):  
Time Delay ◽  
Regulatory Networks ◽  
Controller Design ◽  
Estimation Error ◽  
Rapid Development ◽  
Genetic Regulation ◽  
Genetic Regulatory Networks ◽  
Error Feedback ◽  
Attraction Set ◽  
Parameter Dependent

Genetic regulatory networks (GRNs) play an important role in the development and evolution of the biological system. With the rapid development of DNA technology, further research on GRNs becomes possible. In this paper, we discuss a class of time-delay genetic regulatory networks with external inputs. Firstly, under some reasonable assumptions, using matrix measures, matrix norm inequalities, and Halanay inequalities, we give the global dissipative properties of the solution of the time-delay genetic regulation networks and estimate the parameter-dependent global attraction set. Secondly, an error feedback control system is designed for the time-delay genetic control networks. Furthermore, we prove that the estimation error of the model is asymptotically stable. Finally, two examples are used to illustrate the validity of the theoretical results.

Systems Biology and Infectious Diseases

2009 ◽  
pp. 377-402 ◽  
Author(s):  
Alia Benkahla ◽  
Lamia Guizani-Tabbane ◽  
Ines Abdeljaoued-Tej ◽  
Slimane Ben Miled ◽  
Koussay Dellagi
Keyword(s):  
Immune Response ◽  
Systems Biology ◽  
Molecular Biology ◽  
Infected Cell ◽  
Regulatory Networks ◽  
Interdisciplinary Approach ◽  
Biochemical Networks ◽  
Mathematical Methods ◽  
Meaningful Information ◽  
Models And Modelling

This chapter reports a variety of molecular biology informatics and mathematical methods that model the cell response to pathogens. The authors first outline the main steps of the immune response, then list the high throughput biotechnologies, generating a wealth of information on the infected cell and some of the immune-related databases; and finally explain how to extract meaningful information from these sources. The modelling aspect is divided into modelling molecular interaction and regulatory networks, through dynamic Boolean and Bayesian models, and modelling biochemical networks and regulatory networks, through Differential/Difference Equations. The interdisciplinary approach explains how to construct a model that mimics the cell’s dynamics and can predict the evolution and the outcome of infection.

scholarly journals Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria

2020 ◽  
Vol 8 (3) ◽  
pp. 384 ◽  
Author(s):  
Marta Robledo ◽  
Natalia I. García-Tomsig ◽  
José I. Jiménez-Zurdo
Keyword(s):  
Stress Responses ◽  
Regulatory Networks ◽  
Transcriptional Control ◽  
Genetic Regulation ◽  
Regulation Of Gene Expression ◽  
Nodule Development ◽  
Nitrogen Fixing ◽  
Endosymbiotic Bacteria ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

Small non-coding RNAs (sRNAs) are ubiquitous components of bacterial adaptive regulatory networks underlying stress responses and chronic intracellular infection of eukaryotic hosts. Thus, sRNA-mediated regulation of gene expression is expected to play a major role in the establishment of mutualistic root nodule endosymbiosis between nitrogen-fixing rhizobia and legume plants. However, knowledge about this level of genetic regulation in this group of plant-interacting bacteria is still rather scarce. Here, we review insights into the rhizobial non-coding transcriptome and sRNA-mediated post-transcriptional regulation of symbiotic relevant traits such as nutrient uptake, cell cycle, quorum sensing, or nodule development. We provide details about the transcriptional control and protein-assisted activity mechanisms of the functionally characterized sRNAs involved in these processes. Finally, we discuss the forthcoming research on riboregulation in legume symbionts.

scholarly journals A new paradigm for animal symmetry

2015 ◽  
Vol 5 (6) ◽  
pp. 20150032 ◽  
Author(s):  
Gábor Holló
Keyword(s):  
Regulatory Networks ◽  
Genetic Regulation ◽  
Bilateral Symmetry ◽  
Whole Body ◽  
Functional Requirements ◽  
New Paradigm ◽  
Anatomical Structures ◽  
Flexible Framework ◽  
The Difference ◽  
Biological Patterns

My aim in this article is to soften certain rigid concepts concerning the radial and bilateral symmetry of the animal body plan, and to offer a more flexible framework of thinking for them, based on recent understandings of how morphogenesis is regulated by the mosaically acting gene regulatory networks. Based on general principles of the genetic regulation of morphogenesis, it can be seen that the difference between the symmetry of the whole body and that of minor anatomical structures is only a question of a diverse timing during development. I propose that the animal genome, as such, is capable of expressing both radial and bilateral symmetries, and deploys them according to the functional requirements which must be satisfied by both the anatomical structure and body as a whole. Although it may seem paradoxical, this flexible view of symmetry, together with the idea that symmetry is strongly determined by function, bolsters the concept that the presence of the two main symmetries in the animal world is not due to chance: they are necessary biological patterns emerging in evolution.

Discrete Networks as a Suitable Approach for the Analysis of Genetic Regulation

2009 ◽  
pp. 530-540
Author(s):  
Elizabeth Santiago-Cortés
Keyword(s):  
Transcription Factors ◽  
Dynamical Systems ◽  
Regulatory Networks ◽  
Dynamical Behavior ◽  
Genetic Regulation ◽  
Genetic Regulatory Networks ◽  
Theoretical Studies ◽  
Biological Interpretation ◽  
Complex Dynamical Behavior ◽  
Discrete Networks

Biological systems are composed of multiple interacting elements; in particular, genetic regulatory networks are formed by genes and their interactions mediated by transcription factors. The establishment of such networks is critical to guarantee the reliability of transcriptional performance in any organism. The study of genetic regulatory networks as dynamical systems is a helpful methodology to understand the transcriptional behavior of the genome. From a number of theoretical studies, it is known that networks present a complex dynamical behavior that includes stability, redundancy, homeostasis, and multistationarity. In this chapter we present some particular biological processes modeled as discrete networks to show that the theoretical properties of networks have a clear biological interpretation.

Genetic Dissection of T-DNA Insertional Mutants Reveals Uncoupling of Dikaryotic Filamentation and Virulence in Sugarcane Smut Fungus

2021 ◽  
Author(s):  
Shan Lu ◽  
Feng Guo ◽  
Zhiqiang Wang ◽  
Xiaorui Shen ◽  
Yizhen Deng ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Insertional Mutagenesis ◽  
Genetic Regulation ◽  
Genetic Dissection ◽  
Opposite Mating Type ◽  
Basidiomycetous Fungus ◽  
Sporisorium Scitamineum ◽  
Type Strains ◽  
Dna Insertional Mutagenesis ◽  
Teliospore Development

The biotrophic basidiomycetous fungus Sporisorium scitamineum causing smut disease in sugarcane is characterized by a life-cycle composed of a yeast-like nonpathogenic haploid basidiosporial stage outside the plant and filamentous pathogenic dikaryotic hyphae within the plant. Under field conditions, dikaryotic hyphae are formed after mating of two opposite mating-type strains. However, the mechanisms underlying genetic regulation of filamentation and its association with pathogenicity and development of teliospores are currently unclear. This study has focused on the characterization and genetic dissection of haploid filamentous mutants derived from T-DNA insertional mutagenesis. Our results support the existence of at least three genotypes among the six haploid filamentous mutants that differentially contribute to virulence and development of the whip and teliospore, providing a novel foundation for further investigation of the regulatory networks associated with pathogenicity and teliospore development in S. scitamineum.

scholarly journals Genetic analysis of blood molecular phenotypes reveals regulatory networks affecting complex traits: a DIRECT study.

2021 ◽  
Author(s):  
Ana Viñuela ◽  
Andrew A Brown ◽  
Juan Fernandez ◽  
Mun-gwan Hong ◽  
Caroline A Brorsson ◽  
...  
Keyword(s):  
Complex Traits ◽  
Regulatory Networks ◽  
Disease Risk ◽  
Association Studies ◽  
Genetic Regulation ◽  
Underlying Mechanism ◽  
Molecular Networks ◽  
Genome Wide Association Studies ◽  
Molecular Phenotypes ◽  
Shared Genetic

Genetic variants identified by genome-wide association studies can contribute to disease risk by altering the production and abundance of mRNA, proteins and other molecules. However, the interplay between molecular intermediaries that define the pathway from genetic variation to disease is not well understood. Here, we evaluated the shared genetic regulation of mRNA molecules, proteins and metabolites derived from whole blood from 3,029 human donors. We find abundant allelic heterogeneity, where multiple variants regulate a particular molecular phenotype, and pleiotropy, where a single variant was associated with multiple molecular phenotypes over multiple genomic regions. We find varying proportions of shared genetic regulation across phenotypes, highest between expression and proteins (66.6%). We were able to recapitulate a substantial proportion of gene expression genetic regulation in a diverse set of 44 tissues, with a median of 88% shared associations for blood expression and 22.3% for plasma proteins. Finally, the genetic and molecular associations were represented in networks including 2,828 known GWAS variants. One sub-network shows the trans relationship between rs149007767 and RTEN, and identifies GRB10 and IKZF1 as candidates mediating genes. Our work provides a roadmap to understanding molecular networks and deriving the underlying mechanism of action of GWAS variants across different molecular phenotypes.

scholarly journals Genetic architecture and regulatory impact on hepatic microRNA expression linked to immune and metabolic traits

Open Biology ◽  
2017 ◽  
Vol 7 (11) ◽  
pp. 170101 ◽  
Author(s):  
Siriluck Ponsuksili ◽  
Nares Trakooljul ◽  
Frieder Hadlich ◽  
Fiete Haack ◽  
Eduard Murani ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Regulatory Networks ◽  
Genetic Regulation ◽  
Haemoglobin Concentration ◽  
Plasma Parameters ◽  
Association Analyses ◽  
Expression Levels ◽  
Metabolic Traits ◽  
Clinical Biomarkers ◽  
Wide Range

Regulation of microRNA (miRNA) expression contributes to a wide range of target gene expression and phenotypes. The miRNA expression in the liver, the central metabolic organ, was examined in 209 pigs, and integrated with haematological and clinical biomarkers of metabolic and overall health, mRNA-target expression levels and single-nucleotide polymorphism (SNP) genotypes. The expression levels of 426 miRNA species correlated with plasma haematological or biochemical traits ( r ² = |0.19–0.45|, false discovery rate < 5%). Pairs of these miRNAs and their predicted target mRNAs showing expressing levels associated with the identical traits were examined to understand how immune and metabolic traits are affected by miRNA-mediated regulatory networks derived by mapping miRNA abundance as an expression quantitative trait. In total, 221 miRNA-expression-QTL correspond to 164 SNPs and 108 miRNAs, including miR-34a, miR-30e, miR-148-3p, miR-204, miR-181-5p, miR-143-5p and let-7 g that also correlate with the biomarkers. Sixty-one SNPs were simultaneously associated with 29 miRNA and 41 mRNA species. The expression levels of 13 out of 29 miRNA were correlated with one of the biochemical or haematological traits. For example, the expression levels of miR-34a were correlated with serum phosphorus and cholesterin levels; miR-204, miR-15a and miR-16b were correlated with triglyceride. For haematological traits, the expression levels of miR-652 and miR-204 were correlated with the mean corpuscular haemoglobin concentration, and the expression of miR-143 was correlated with plateletcrit. Pleiotropic association analyses revealed genetic links between mRNA and miRNA on SSC6 for miR-34a, SSC9 for miR-708 and SSC14 for miR-652. Our analysis of miRNA and mRNA transcript profiles, their correlation with clinically important plasma parameters of hepatic functions as well as information on their genetic regulation provide novel regulatory networks and potential new biomarkers for immune and metabolic traits.

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