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During their life cycle plants undergo a wide variety of morphological and developmental changes. Impinging these developmental processes there is a layer of gene, protein and metabolic networks that are responsible for the initiation of the correct developmental transitions at the right time of the year to ensure plant life success. New omic technologies are allowing the acquisition of massive amount of data to develop holistic and integrative analysis to understand complex processes. Among them, Microarray, Next-generation Sequencing (NGS) and Proteomics are providing enormous amount of data from different plant species and developmental stages, thus allowing the analysis of gene networks globally. Besides, the comparison of molecular networks from different species is providing information on their evolutionary history, shedding light on the origin of many key genes/proteins. Moreover, developmental processes are not only genetically programed but are also affected by internal and external signals. Metabolism, light, hormone action, temperature, biotic and abiotic stresses, etc. have a deep effect on developmental programs. The interface and interplay between these internal and external circuits with developmental programs can be unraveled through the integration of systematic experimentation with the computational analysis of the generated omics data (Molecular Systems Biology). This Research Topic intends to deepen in the different plant developmental pathways and how the corresponding gene networks evolved from a Molecular Systems Biology perspective. Global approaches for photoperiod, circadian clock and hormone regulated processes; pattern formation, phase-transitions, organ development, etc. will provide new insights on how plant complexity was built during evolution. Understanding the interface and interplay between different regulatory networks will also provide fundamental information on plant biology and focus on those traits that may be important for next-generation agriculture.

Plant Development --- Omics --- Molecular Systems Biology --- Evolution --- Gene Regulatory Networks

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Cancer --- Systems biology. --- Neoplasms --- Gene Expression Regulation, Neoplastic --- Gene Regulatory Networks --- Genes, Neoplasm --- Systems Biology --- Gene regulatory networks. --- Research --- Methodology. --- genetics. --- physiology. --- methods.

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The members of the Streptomyces genus are mainly known for their high potential to produce secondary metabolites such as antibiotics, anti-cancer drugs, volatile organic compounds, herbicides. Mostly saprophytic, few exceptions have a phytopathogenic lifestyle, with S. scabies as a model species. Research on the pathogenicity of this bacteria - the predominant causal agent of the common scab (CS) disease – has begun more than 20 years ago. The phytotoxin thaxtomin A is the main virulence factor directly related to its pathogenic lifestyle, however many molecular mechanisms still remain misunderstood and ignored. Based on computational regulon prediction and proteomics, novel gene/protein candidates involved in the development of the virulent behaviour of S. scabies have been identified. In particular, a new hypothetical signalling pathway suggesting a tight link between the cello-oligosaccharides transport and the access to the host reservoir of starch has been proposed.
The principal aim of this Master thesis was to investigate the role of two actors supposed to be involved in this pathway - the MalR regulator and the cytoplasmic component of the AfsQ1-AfsQ2 TCS -, evaluating the effects of their deletion through the PCR-targeting strategy. During this Master thesis we showed that these two important regulators certainly participate in the pathogenic lifestyle of S. scabies. The absence of MalR prevents S. scabies from perceiving the cellobiose as a signal to trigger virulence, while afsQ1 deletion resulted in increased toxin production rates, in a significant impairment of A. thaliana growth and in more severe pitting and necrosis of potato tuber slices.
A further objective of this work aimed to generate new strains of S. scabies with improved thaxtomin production yields. Indeed, the properties of this phytotoxin made it a prime candidate as bioherbicide, however, nowadays the production costs are still too high for a large-scale application. Earlier works have shown that the mutation of either cebR or bglC genes resulted in an overproduction of thaxtomin A, therefore we have investigated the possibility that combining the deletion of both genes would turn in even higher production rates. The new generated strains are capable of producing significant toxin rates, however, although significant, did not exceed those of the single mutants.

common scab disease --- plan pathogen --- regulatory networks --- plant-microbe interactions --- herbicide --- Sciences du vivant > Microbiologie

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This book offers an essential introduction to the latest advances in delayed genetic regulatory networks (GRNs) and presents cutting-edge work on the analysis and design of delayed GRNs in which the system parameters are subject to uncertain, stochastic and/or parameter-varying changes. Specifically, the types examined include delayed switching GRNs, delayed stochastic GRNs, delayed reaction–diffusion GRNs, delayed discrete-time GRNs, etc. In addition, the solvability of stability analysis, control and estimation problems involving delayed GRNs are addressed in terms of linear matrix inequality or M-matrix tests. The book offers a comprehensive reference guide for researchers and practitioners working in system sciences and applied mathematics, and a valuable source of information for senior undergraduates and graduates in these areas. Further, it addresses a gap in the literature by providing a unified and concise framework for the analysis and design of delayed GRNs.

Gene regulatory networks. --- Circuits, Gene --- Gene circuits --- Gene modules --- Gene networks --- Genetic regulatory networks --- GRNs (Gene regulatory networks) --- Modules, Gene --- Networks, Gene regulatory --- Networks, Transcriptional --- Regulatory networks, Gene --- Transcriptional networks --- Genetic regulation --- Nucleotide sequence --- Vibration. --- Engineering. --- Vibration, Dynamical Systems, Control. --- Computational Intelligence. --- Construction --- Industrial arts --- Technology --- Cycles --- Mechanics --- Sound --- Dynamical systems. --- Dynamics. --- Computational intelligence. --- Dynamical systems --- Kinetics --- Mathematics --- Mechanics, Analytic --- Force and energy --- Physics --- Statics --- Intelligence, Computational --- Artificial intelligence --- Soft computing

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The Overview of the Topic was the following: “One of the most active areas of research in molecular microbiology has been the study of how bacteria modulate their genetic activity and its consequences. The prokaryotic world has received much interest not only because the resulting phenomena are important to cells, but also because many of the effects often can be readily measured. Contributing to the interest of the present topic is the fact that modulation of gene activity involves the sensing of intra- and inter-cellular conditions, DNA binding and DNA dynamics, and interaction with the replication/transcription machinery of the cell. All of these processes are fundamental to the operation of a genetic entity and condition their lifestyle. Further, the discoveries achieved in the bacterial world have been of ample use in eukaryotes. In addition to the fundamental interest of understanding modulation of prokaryotic lifestyle by DNA-binding proteins, there is an added interest from the healthcare point of view. As it is well known the antibiotic-resistance strains of pathogenic bacteria are a major world problem, so that there is an urgent need of innovative technologies to tackle it. Most of the acquired resistances are spread by processes of horizontal gene transfer mediated by mobile elements in which DNA replication and gene expression are of basic interest. There is an imperative of finding new alternatives to the ‘classical’ way of treatment of bacterial infections and these new alternatives include the discovery of new drugs and of new bacterial targets. Nevertheless, these new alternatives will find a dead-end if we are unable to obtain a better understanding of the basic processes modulating bacterial gene expression. Our goal to achieve with this Topic of Frontiers is to accelerate our understanding of protein-DNA interactions. First, the topic will bring together several very active researchers in the study of gene replication, gene regulation, the strategies applied by the different proteins that participate in these processes, and their consequences. We will also acquire an in-depth knowledge of some of the mechanisms of gene regulation, gene transfer and gene replication. Further, the readers of the papers will realize the importance of the topic and will learn the most recent thinking, results, and approaches in the area”. We are fully confident that we have exceeded our expectations. Now we are proud to present the final output of the Topic, which is the eBook. It includes 24 articles contributed by 118 authors. As of today, Monday, 16th, January 2017, the total number of readings has reached 19,284, 14,921 article views, and 2,944 article downloads.

control of gene expression --- Global Regulatory Networks --- prokaryotes --- DNA replication and DNA segregation --- bacterial pathogens --- horizontal gene transfer