Bacterial global gene regulatory networks. Medical search. Frequent questions

To further understand the consequences of targeting this global regulatory system, we perform RNA-Seq to investigate the transcriptional networks of bacterial cells under optimal growth as well as stress conditions. (pletzerlab.com)
This network is described to be mainly controlled by the master transcriptional regulators Spo0A, DegU, and ComA. (nature.com)
Furthermore, monitoring QS signaling gene expression revealed that AHL synthases LasI/RhlI and QS transcriptional regulators LasR/RhlR genes were inhibited and antagonized, respectively, by cerPAC. (nature.com)
Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. (frontiersin.org)
22 ]. The transcriptional regulator QstR, which might require a cofactor for its full activity (indicated by the triangle), positively regulates the comEA gene potentially by binding to a QstR-specific binding motif (indicated by the dashed box and so far unidentified). (biomedcentral.com)
We analyse transcriptional bursting within a stochastic non-equilibrium model which accounts for the coupling between the dynamics of DNA supercoiling and gene transcription. (arxiv-vanity.com)
Transcriptional and environmental control of bacterial denitrification and N2. (earlham.ac.uk)
Accepted August 23, 2012 ABSTRACT The catabolite control protein CcpA is a pleiotropic regulator that mediates the global transcriptional response to rapidly catabolizable carbohydrates, like glucose in Gram-positive bacteria. (studyres.com)
Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. (microbiologyresearch.org)

Series of lectures, selection of research papers on related topics and workshops will be given on understanding how global regulatory networks govern gene expression in bacteria. (universiteitleiden.nl)
ppGpp is an intracellular sensor that, in response to different types of stress, coordinates the rearrangement of the gene expression pattern of bacteria to promote adaptation and survival to new environmental conditions. (ibecbarcelona.eu)
Bacterial sphingomyelinases and phospholipases are a heterogeneous group of esterases which are usually surface associated or secreted by a wide variety of Gram-positive and Gram-negative bacteria. (inra.fr)
Analyzing bacteria in late exponential phase, we capture ~40% ( E. faecalis ) and 43% ( E. faecium ) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. (frontiersin.org)
These results highlight the potential impact of gene regulation in the adaptation of bacteria to the different habitats through the distribution of their regulatory potential among specific functions, and point to critical environmental factors that challenge the growth of any microbial community. (biomedcentral.com)
How bacteria talk to each other: regulation of gene expression by quorum sensing. (microbiologyresearch.org)
Furthermore, nucleotide sequences related to the cluster vanHAX are present in this DNA, suggesting that the prolonged use of avoparcin in agriculture led to the uptake of glycopeptide resistance genes by animal commensal bacteria, which were subsequently transferred to humans. (cdc.gov)

Two of these methods, signature-tagged mutagenesis and in vivo expression technology, do not directly measure gene expression and do not allow true genomic-scale analysis, but they have been devised to identify genes necessary for pathogens during real infections. (cdc.gov)
A second group of methods, which includes DNA microarrays and proteomics, have advantages that overcome the limitations implicit in signature-tagged mutagenesis and in vivo expression technology, namely, the ability to directly measure expression (gene or protein) levels on a true genome-wide scale, but their application to analysis of bacterial pathogens during real infections is still in its infancy. (cdc.gov)
Cancer immunotherapy targeting programmed cell death protein 1 (PD-1) enhances T-cell activity and is emerging for the treatment of certain viral infections, while its potential against bacterial infections remains elusive. (bvsalud.org)
As antibiotic resistance in microbial pathogens embodies a global threat to public health, it demands the development of novel strategies for managing microbial infections. (nature.com)
Over the last decade, research on antimicrobials has shifted towards an alternative approach to combat pathogens using anti-infective drugs that selectively interrupt virulence pathways to help prevent or cure bacterial infections. (nature.com)
These new antimicrobial and antibiofilm technologies will treat wound and medical device related infections, and will provide an alternative treatment to antibiotic classes in which bacterial resistance is high. (cdc.gov)
Effectiveness of antiviral treatment in human influenza A(H5N1) infections: analysis of a Global Patient Registry. (cdc.gov)

Further detailed analyses of these responses will increase understanding of the molecular mechanisms of pathogenesis, identify new bacterial virulence factors, and aid in the design of new vaccines. (cdc.gov)
Several bacterial sphingomyelinases and phospholipases are essential for virulence of extracellular, facultative, or obligate intracellular pathogens, as these enzymes contribute to phagosomal escape or phagosomal maturation avoidance, favoring tissue colonization, infection establishment and progression, or immune response evasion. (inra.fr)
Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum. (openwetware.org)

The developing complementary technologies of DNA microarrays and proteomics are allowing the response of bacterial pathogens to different environments to be probed at the whole genome level. (cdc.gov)
Some bacterial pathogens have been shown to substantially modify their surface components in response to the host immune system and modify their energy metabolism and transport pathways to allow efficient growth within the host. (cdc.gov)
Bacterial pathogens must be able to gain access to, persist in, and replicate in normally privileged sites within a host. (cdc.gov)
Because the environment encountered within a living host will be quite different from the external environment, pathogens must be able to regulate the necessary genes in coordination as they move from the environment to the host and from one host niche to another. (cdc.gov)
The primary aim of investigating bacterial pathogenesis is to understand the way that pathogens interact with the host to cause disease. (cdc.gov)
Anti-infective drugs that do not perturb survival or viability of bacterial pathogens should be less likely to promote resistance than conventional antibiotics 1 , 2 . (nature.com)
Antimicrobial resistance in bacterial pathogens is a major impediment to successful therapy, and in sever- al instances, bacterial strains have arisen that are refracto- ry to most available antimicrobial treatments (1). (cdc.gov)

La información en esta página debería ser considerada como ejemplos de información de antecedentes para la temporada de influenza 2021-2022 para la práctica médica respecto del uso de medicamentos antivirales contra la influenza. (cdc.gov)

A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell. (wikipedia.org)
Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in regulatory networks or cascades. (wikipedia.org)
Each time a cell divides, two cells result which, although they contain the same genome in full, can differ in which genes are turned on and making proteins. (wikipedia.org)
In parallel with this process of building structure, the gene cascade turns on genes that make structural proteins that give each cell the physical properties it needs. (wikipedia.org)
At one level, biological cells can be thought of as "partially mixed bags" of biological chemicals - in the discussion of gene regulatory networks, these chemicals are mostly the messenger RNAs (mRNAs) and proteins that arise from gene expression. (wikipedia.org)
A typical gene regulatory network looks something like this: The nodes of this network can represent genes, proteins, mRNAs, protein/protein complexes or cellular processes. (wikipedia.org)
Edges between nodes represent interactions between the nodes, that can correspond to individual molecular reactions between DNA, mRNA, miRNA, proteins or molecular processes through which the products of one gene affect those of another, though the lack of experimentally obtained information often implies that some reactions are not modeled at such a fine level of detail. (wikipedia.org)
The cytoplasmic Rap proteins exert their regulatory function by inhibiting the activity of their target regulator (Spo0F, DegU, or ComA) via dephosphorylation, or by directly blocking DNA binding. (nature.com)
The richness of gene expression programs-in a given cell across time, across distinct cell types, and in response to diverse stimuli-results from the combinatorial logic of spatially organized nucleic acid elements that bind transcription factors, RNA binding proteins, and microRNAs. (columbia.edu)
In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. (notulaebiologicae.ro)

Although analyses that give information on the expression of a few genes provide insight and have been responsible for a large proportion of the bacterial pathogenesis literature currently available, our ultimate goal is to understand expression changes across the whole genome. (cdc.gov)

We found that WalKR is a master regulator of cell growth, coordinating the expression of genes from multiple, fundamental S. aureus cellular processes, including those involved in maintaining cell wall metabolism, protein biosynthesis, nucleotide metabolism, and the initiation of DNA replication. (bvsalud.org)
The population-heterogeneity regulatory network of B. subtilis is further controlled by a family of response regulator aspartyl-phosphate (Rap) phosphatases and their cognate phosphatase-regulator (Phr) peptides. (nature.com)
Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. (liverpool.ac.uk)
Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. (liverpool.ac.uk)
RsmQ acts as a global regulator, controlling the host proteome through direct interaction with host mRNAs and interference with the host's translational regulatory network. (liverpool.ac.uk)
RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle. (liverpool.ac.uk)
The cyclic adenosine monophosphate (cAMP) receptor protein CRP, which is the global regulator of CCR, binds to regulatory DNA elements called CRP sites when in complex with cAMP. (biomedcentral.com)
This gene encodes a protein that is the master regulator of transformation and a homolog of Sxy, which was first described in Haemophilus influenzae [ 7 ],[ 8 ]. (biomedcentral.com)

In this chapter we briefly describe some of the most recent findings on regulatory network evolution from the perspective of DNA-binding transcription factors. (caister.com)
The chapter is divided into sections covering the evolution of transcription factors and their domains, their evolution, and a global analysis. (caister.com)
Global Screening of Potential C. Albican Biofilm-Related Transcription Factors (TFs) by Network Comparison via Big Database Mining and Microarray Data7. (elsevier.com)
2023. Editorial: Role of Transcription Factors and Sigma Factors in Bacterial Stress. (openwetware.org)
Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms. (openwetware.org)
We are testing the hypothesis that specific transcription factors form regulatory networks to execute gene expression programs important for SSC fate decisions (self-renewal and differentiation), and ultimately, spermatogenesis. (utsa.edu)
For this, we have developed a computational protocol to extract regulatory regions and their corresponding transcription factors binding sites directly from metagenomic reads and applied it to three well known environments: Acid Mine, Whale Fall, and Waseca Farm. (biomedcentral.com)
Networks of WRKY transcription factors in defense signaling. (notulaebiologicae.ro)

These studies have revealed fundamental new insights into the genetic and regulatory underpinnings of a variety of phenomena including complex bacterial behaviors, antibiotic resistance & persistence, metazoan development, oncogenesis, metastatic progression, and cellular adaptation to extreme environments. (columbia.edu)
A better understanding of how these species cause disease and spread antibiotic resistance requires a knowledge of how its genes are controlled, on both the DNA and the RNA level. (frontiersin.org)
Abt Associates-a global company that conducts research, consulting, and technical services in health, environmental and social policy, technology, and international development-commits to pursuing opportunities within new and existing global projects to conduct antibiotic resistance mapping, landscaping, and trend analysis. (cdc.gov)

Post-genomic analysis techniques such as next-generation sequencing have produced vast amounts of data about micro organisms including genetic sequences, their functional annotations and gene regulatory interactions. (uni-bielefeld.de)
Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions. (uni-bielefeld.de)
Chapters discuss systems immunology, systems infection microbiology, systematic inflammation and immune responses in restoration and regeneration process, systems' innate and adaptive immunity in infection process, systematic genetic and epigenetic pathogenic/defensive mechanism during bacterial infection on human cells is introduced, and the systematic genetic and epigenetic pathogenic/defensive mechanisms during viral infection on human cells. (elsevier.com)
Part V: Systematic Genetic and Epigenetic pathogenic/ Defensive Mechanism During Bacterial Infection on Human cells 15. (elsevier.com)
Genetic-and-epigenetic Interspecies Networks for Cross-talk Mechanisms in Human Macrophages and Dendritic Cells during MTB Infection16. (elsevier.com)
Investigating the Progression of Cross-talk Mechanism in Caco-2 Cells during Clostridium difficile Infection by Constructing Genetic and Epigenetic Interspecies Networks: Big Data Mining and Genome-wide Identification17. (elsevier.com)
Expansion of gene families facilitates robustness and evolvability of biological processes but impedes functional genetic dissection of signalling pathways. (earlham.ac.uk)
The evolving concept of the gene, of genetic interactions and gene networks, as well as chromosome mechanics will be the focus of the course. (princeton.edu)

To deal with environmental stress conditions, microbes have evolved complex hierarchical regulatory networks to trigger molecular responses that alter gene expression and protein activity. (pletzerlab.com)
Thus, to fully exploit microbes in synthetic biology applications, complex gene regulatory systems and their behaviors in diverse conditions need to be better understood. (confex.com)
The actual origins of acquired resistance genes are unknown, but environmental microbes, including the strains producing antimicrobial agents, are believed to be important sources (4,5). (cdc.gov)

This mRNA interference leads to large-scale proteomic changes in metabolic genes, key regulators, and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. (liverpool.ac.uk)
The expression of a gene is shaped by the convergence of upstream inputs that impinge upon DNA and RNA sequence elements in the vicinity of genes, leading to precise modulation of global mRNA and protein abundances. (columbia.edu)
We have applied a multipronged approach of loss-of-function studies, genome-wide mRNA and sRNA expression profiling, pathway analysis, target prediction, literature mining and network analysis to unravel YbeY-dependent molecular responses of E. coli exposed to hydroxyurea (HU). (biomedcentral.com)
Further applying a 'context likelihood of relatedness' algorithm, we reverse engineered the YbeY-dependent Hfq-dependent sRNA-mRNA network as well as YbeY-dependent Hfq-independent sRNA-mRNA network. (biomedcentral.com)
The most extensively characterized class of bacterial sRNAs are the trans -encoded sRNAs that are encoded distant from the genes for their mRNA targets and that typically have only limited complementarity (10-30 nt) [ 2 ]. (biomedcentral.com)

Our work demonstrated that, indeed, this strategy can systematically reveal the regulatory vocabulary and grammar in DNA, enabling prediction of global gene expression dynamics from DNA sequence alone. (columbia.edu)
Prediction of Infection-Associated Genes via a Cellular Network Approach: A C. Albican Infection Case Study6. (elsevier.com)
Nonlinear Prediction of Network Traffic Measurements Data. (vldb.org)
Small-Time Scale Network Traffic Prediction Using Complex Network Models. (vldb.org)
Expression profiles analysis identifies the values of carcinogenesis and the prognostic prediction of three genes in adrenocortical carcinoma. (cancerindex.org)

Conceptual parallels exist between bacterial and eukaryotic small-RNA (sRNA) pathways, yet relatively little is known about which protein may recognize and recruit bacterial sRNAs to interact with targets. (biomedcentral.com)
Other bacterial sRNAs, referred to as cis -encoded sRNAs, are present in close proximity to their targets, such as upstream, opposite of the 5′ UTR of the target, or between two genes in an operon [ 2 ]. (biomedcentral.com)
Like microRNAs (miRNAs) in eukaryotes, trans -acting bacterial sRNAs appear to recognize their targets by a seed-pairing mechanism using seeds as small as 6-7 nucleotides. (biomedcentral.com)

By binding to the promoter region at the start of other genes they turn them on, initiating the production of another protein, and so on. (wikipedia.org)
This mechanism requires that the gene in question is highly expressed, so that multiple polymerases can be recruited to its promoter within minutes. (arxiv-vanity.com)
In silico promoter analysis of 1.5 kb promoter regions of NPR1 gene revealed that NPR1 contains 23 MYB and 20 WRKY transcription factor binding sites. (notulaebiologicae.ro)

First described to modulate metabolic adaptive responses, ppGpp modulates the expression of genes belonging to very diverse functional categories. (ibecbarcelona.eu)

However, this work also revealed that WalR directly regulates at least five essential genes involved in lipoteichoic acid synthesis (ltaS): translation (rplK), DNA compaction (hup), initiation of DNA replication (dnaA, hup) and purine nucleotide metabolism (prs). (bvsalud.org)
We will look at how environmental signals (e.g. nutrients, stress) are translated to switch sets of genes on and off, and how this affects metabolism, development and antibiotic production. (universiteitleiden.nl)
The CcpA regulon comprises genes involved in sugar uptake, fermentation and amino acids metabolism, confirming the role of CcpA as a link between carbon and nitrogen pathways. (studyres.com)

Dysfunction of the regulatory mechanisms maintaining this balance between active immunity and tolerance in the gut may lead to mucosal inflammation and damage and GI diseases. (medscape.com)

A limited study had indicated that in Sinorhizobium meliloti the YbeY ortholog regulates the accumulation of sRNAs as well as the target mRNAs, raising the possibility that YbeY may play a previously unrecognized role in bacterial sRNA regulation. (biomedcentral.com)
We identified previously unrecognized putative CRP-S sites upstream of both genes. (biomedcentral.com)

Differential expressed genes between a Pseudomonas aeruginosa stringent response mutant and wilt-type strain under optimum growth conditions. (pletzerlab.com)
Global Regulatory Pathways Converge To Control Expression of Pseudomonas aeruginosa Type IV Pili. (wolfganglab.com)
RsmV, a Small Noncoding Regulatory RNA in Pseudomonas aeruginosa That Sequesters RsmA and RsmF from Target mRNAs. (wolfganglab.com)
Functional Analyses of the RsmY and RsmZ Small Noncoding Regulatory RNAs in Pseudomonas aeruginosa . (wolfganglab.com)

B. subtilis possesses a complex regulatory network that leads the cells within the biofilm to generate a phenotypically heterogeneous population. (nature.com)
2023. The gene regulatory network of Staphylococcus aureus ST239-SCCmecIII strain Bmb9393 and assessment of genes associated with the biofilm in diverse backgrounds. (openwetware.org)

will have knowledge of technologies to analyse global gene expression profiles, such as microarrays, proteomics, RNAseq and ChipSeq. (universiteitleiden.nl)

This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. (cancerindex.org)
The udhA gene of Escherichia coli encodes a soluble pyridine nucleotide transhydrogenase. (microbiologyresearch.org)
The third gene, vanA , Francisco, CA). encodes an ATP-dependent D-Ala-D-Lac ligase. (cdc.gov)

Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes. (openwetware.org)
Following this, the differentially expressed genes (DEGs) were included in Gene Ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, protein‑protein interaction network and survival analyses. (cancerindex.org)

We use RNA-Seq and Tn-Seq (transposon insertion sequencing) to investigate the transcriptome and essential genes that contribute to inter- and host-pathogen interactions. (pletzerlab.com)
More recently, metagenomic studies have gone beyond the sequencing of DNA and the counting of genes, and have incorporated techniques and protocols to detect, measure and analyze their transcriptome. (biomedcentral.com)
By whole transcriptome analyses, we characterized glucosedependent and CcpA-dependent gene regulation in Clostridium difficile. (studyres.com)

The nucleotide sequences of rbsD , rbsA , and rbsC genes of Escherichia coli K 12. (microbiologyresearch.org)
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. (microbiologyresearch.org)
Lysine represses transcription of the Escherichia coli dapB gene by preventing its activation by the ArgP activator. (microbiologyresearch.org)

This altered gene expression also correlated directly with protein levels, bacterial capacity for DNA uptake, and natural transformability. (biomedcentral.com)

Gates can be modularly composed into multi-component systems to approximate the behavior of formal chemical reaction networks (CRN), demonstrating a new use for CRNs as a molecular programming language. (jove.com)
Within the research in Molecular Biology, one important field along the years has been the analyses on how prokaryotes regulate the expression of their genes and what the consequences of these activities are. (ibecbarcelona.eu)
Alignments and comparison of molecular networks across species will help detect orthologs and conserved functional modules and provide insights on the evolutionary relationships of the compared species. (biomedcentral.com)
Network Biology Approaches to Identify Molecular and Systems-Level Difference. (earlham.ac.uk)
Evaluation of gene expression of different molecular biomarkers of stress res. (earlham.ac.uk)

Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. (liverpool.ac.uk)
MiRNAs are crucial regulators of gene expression found across both the plant and animal kingdoms. (earlham.ac.uk)
Finally, CcpA controls a complex and extended regulatory network through the modulation of a large set of regulators. (studyres.com)

Central to this investigation is an understanding of what gene products are required and expressed during a natural infection and how this expression changes over time (from initial colonization to causation of disease and spread of the pathogen to new hosts) and space (in different cells or tissues within the host). (cdc.gov)
Staphylococcus aureus (S. aureus) is the most common bacterial infection, and it poses a challenge to the healthcare system due to its significant ability to develop resistance toward current available therapies. (bvsalud.org)
Our data further support the role of ppGpp participating in the coordinated regulation of the expression of bacterial factors required during infection. (ibecbarcelona.eu)
Chlamydia trachomatis is the leading cause of both bacterial sexually transmitted infection and infection-derived blindness world-wide. (plos.org)
Identification of Infection-Related and Defense-Related Genes through A Dynamic Host-Pathogen Interaction Network via A C. Albicans-Zebrafish Infection Model8. (elsevier.com)
One-hit wonder: Late after burn injury, granulocytes can clear one bacterial infection but cannot control a subsequent infection. (wolfganglab.com)
Systemic acquired resistance: turning local infection into global defense. (notulaebiologicae.ro)

Context-dependent regulation of gene expression is fundamental to all cellular behaviors. (columbia.edu)
But it is not known whether and how the regulation of gene expression also contributes to adaptation. (biomedcentral.com)

In contrast, local network alignment only identifies highly similar subnetworks, which are more likely to be functional components such as pathways. (biomedcentral.com)
Resistance arises by mutation (influencing the target or efflux of the antimicrobial agent) or by the acquisition of resistance genes (encoding antimicrobial or target alter- ation, or alternate pathways) (2,3). (cdc.gov)

PRODORIC2: the bacterial gene regulation database in 2018. (uni-bielefeld.de)

The additional information generated by whole genome studies goes far beyond that derived by characterizing in isolation more genes and gene products, because analysis of the whole genome allows complete regulatory networks to be identified and characterized. (cdc.gov)
Natural competence is a mode of horizontal gene transfer, which is based on the ability of a bacterium to take up free DNA from the environment and recombine it with the bacterial genome resulting in natural transformation. (biomedcentral.com)
Using combination of chromatin immunoprecipitation and genome sequence analysis, we detected 55 CcpA binding sites corresponding to 140 genes directly controlled by CcpA. (studyres.com)
The analyzed gene datasets were downloaded from the Gene Expression Omnibus and The Cancer Genome Atlas (TCGA) database. (cancerindex.org)

Small regulatory RNAs (sRNAs) play key roles in modulating gene expression in both prokaryotes and eukaryotes. (biomedcentral.com)

The capabilities of organisms to contend with environmental changes depend on their repertoire of genes and their ability to regulate their expression. (caister.com)

Consistent with prior findings, the direct regulon includes multiple autolysin genes. (bvsalud.org)

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. (ibecbarcelona.eu)

This gene is localized to chromosome 20 and has pseudogenes which reside on chromosomes 1 and 22. (cancerindex.org)

Even when grown in liquid mixed cultures, where environmental conditions are assumed to be homogeneous, B. subtilis cells can be found as single flagellated cells or as non-flagellated chained cells due to stochastic variation in the expression of motility-related genes 3 . (nature.com)
This multi-stability can be explained by stochastic transitioning among multiple stable states of gene expression which are often the results of positive feedback loops in gene regulatory networks. (confex.com)
Although such a "bet-hedging" strategy can increase bacterial fitness in unpredictable environments, such stochastic processes can prevent synthetic biologists from predictably engineering microbial cells that need to face uncontrolled environments. (confex.com)
Aleksandra Walczak received her PhD in physics at UCSD working on models of stochastic gene expression. (elifesciences.org)

A presentation by Tara Kirk Sell of the Johns Hopkins Center for Health Security on Technologies to Address Global Catastrophic Biological Risks. (slideshare.net)
Biological Network Modeling and System Identification in Systems Immunology3. (elsevier.com)
In the context of system biology, the concept of network is widely used in representing the interactions between various biological macromolecules. (biomedcentral.com)
Comparative analyses of these networks can facilitate the identification of conserved components across biological systems and further inference of the biological functions of these components. (biomedcentral.com)
A biological network is commonly represented as an undirected graph, in which each vertex corresponds to a biomolecule, e.g. protein, and each edge denotes an interaction between two biomolecules. (biomedcentral.com)
In recent years, with the development of high-throughput experimental techniques such as the yeast two-hybrid system [ 5 ] and co-immunoprecipitation [ 6 ], the amount of biological networks has been increasing rapidly, leading to a huge demand for efficient network alignment methods and tools. (biomedcentral.com)
Biological networks are graphs used to represent the inner workings of a biological system. (earlham.ac.uk)
Networks describe the relationships of the elements of biological systems using edges. (earlham.ac.uk)

It is a highly active phospholipase exposed at the bacterial surface and shows an extraordinary activation mechanism by tetramer deoligomerization. (inra.fr)

ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana. (notulaebiologicae.ro)

IMPORTANCE The opportunistic human pathogen Staphylococcus aureus uses an array of protein sensing systems called two-component systems (TCS) to sense environmental signals and adapt its physiology in response by regulating different genes. (bvsalud.org)

Taking the density of regulatory sites in promoters as a measure of the potential and complexity of gene regulation, we found it to be quantitatively the same in all three environments, despite their different physico-chemical conditions and species composition. (biomedcentral.com)

Moreover, comparative analyses found RsmQ to be encoded on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. (liverpool.ac.uk)
However, such analyses are not trivial due to the complexity of network and high computational cost. (biomedcentral.com)

These molecules and their interactions comprise a gene regulatory network. (wikipedia.org)
We explore diverse elements associated with the evolution of regulatory networks, such as gene duplication, where new interactions can emerge together with their upstream and downstream binding sites. (caister.com)
In this article we introduce the updated version 6.0 of CoryneRegNet and describe the updated database content which includes, 6352 corynebacterial regulatory interactions compared with 4928 interactions in release 5.0 and 3235 regulations in release 4.0, respectively. (uni-bielefeld.de)
We also demonstrate how we support the community by integrating analysis and visualization features for transiently imported custom data, such as gene regulatory interactions. (uni-bielefeld.de)

Global regulatory systems enable the coordination of downstream effectors that help recognize and appropriately respond to new environments. (pletzerlab.com)
While the sequencing of metagenomes provides an overview of the genes present in specific environments that can potentially play a role in adaptation, the analysis of expression provides a more precise picture of what functions are expressed and active in a particular moment of the environment. (biomedcentral.com)

sequence and function of genes encoding a second sensory pathway. (microbiologyresearch.org)

The proposed algorithm was applied and validated in aligning the protein-protein interaction network of Kaposi's sarcoma associated herpesvirus (KSHV) and that of varicella zoster virus (VZV). (biomedcentral.com)

Our vision of systems biology originated when the very first microarray gene expression datasets appeared in the late 1990's. (columbia.edu)
The ability to rapidly rediscover gene regulatory programs that had taken decades to uncover demonstrated the power of this 'reverse engineering' paradigm for rapidly advancing biology. (columbia.edu)
The identification of these regulatory elements and elucidation of the rules by which they operate remains a central challenge for modern biology. (columbia.edu)
This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. (frontiersin.org)
Systems Biology Approach to Construct the Gene Regulatory Network of Systemic Inflammation via Microarray and Database Mining4. (elsevier.com)

In single-celled organisms, regulatory networks respond to the external environment, optimising the cell at a given time for survival in this environment. (wikipedia.org)
However, we now have a number of methods that allow identification of genes critical for survival in a host as well as methods that allow direct measurement of gene expression during interaction with a host. (cdc.gov)
Here, we reveal for the first time the full extent of the regulatory network of WalKR, the only staphylococcal TCS that is indispensable for survival under laboratory conditions. (bvsalud.org)

This sensory network is key to S. aureus versatility and success as a pathogen. (bvsalud.org)

Insertional transposon mutagenesis is a frequently used technique with the enormous advantage not only of the generation of new phenotypes, but the identification of the mutated gene directly. (proteasomesignaling.com)
Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral. (earlham.ac.uk)

Host-Pathogen Interaction Network through Dynamic Interspecies Interaction Model and Big Database Mining9. (elsevier.com)

This set comprises six problems including medium and large-scale kinetic models of the bacterium E. coli , baker's yeast S. cerevisiae , the vinegar fly D. melanogaster , Chinese Hamster Ovary cells, and a generic signal transduction network. (biomedcentral.com)

Cross-Talk Network Biomarkers of Pathogen-Host Interaction Network from Innate to Adaptive Immunity13. (elsevier.com)
In addition we will address important areas of modern epidemiology such as the influence of early life factors on adult health and disease, but also the importance of the gene-diet-microbiota interaction for body function and health. (lu.se)

Among the functions with highest regulatory potential in each niche, we found significant enrichment of processes related to sensing and buffering external variable factors specific to each environment, like for example, the availability of co-factors in deep sea, of oligosaccharides in soil and the regulation of pH in the acid mine. (biomedcentral.com)

It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse. (frontiersin.org)
Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)

The top 14 hub genes were subsequently confirmed by reverse transcription‑quantitative polymerase chain reaction in ACC and adrenocortical adenoma samples. (cancerindex.org)

Global network alignment is to force the alignment to span the entire set of vertices, which can provide insightful views of similarities and differences cross species at the systemic level and help identify functional orthologs. (biomedcentral.com)
However, we found that each environment distributes their regulatory potential differently across their functional space. (biomedcentral.com)
Based on gene network analysis, NPR1, TGA2 and TGA3 were predicted to have functional cooperation with each other. (notulaebiologicae.ro)

With the arrival of the very first microarray expression experiments, we reasoned that the massive scale of the data may enable an entirely agnostic approach to discovering the underlying regulatory logic of gene expression. (columbia.edu)
Affymetrix microarray data analysis of A. thaliana under SA treatment demonstrated that most genes involved in NPR1 network are up-regulated under SA treatment. (notulaebiologicae.ro)

Plasmids manipulate bacterial behaviour through translational regulatory crosstalk. (liverpool.ac.uk)
the type of behaviour can be selected for by controlling gene activity and orientation. (arxiv-vanity.com)

Anatomy17

Organisms23

Diseases1

Chemicals and Drugs29

Analytical, Diagnostic and Therapeutic Techniques and Equipment31

Psychiatry and Psychology2

Phenomena and Processes71

Disciplines and Occupations5

Anthropology, Education, Sociology and Social Phenomena1

Information Science23

Health Care11

Transcriptional9

Bacteria7

Infections7

Virulence3

Pathogens7

20221

Proteins10

Pathogenesis1

Regulator8

Transcription factors8

Antibiotic resistance3

Genetic8

Microbes3

MRNA5

Prediction5

Targets3

Promoter3

Expression of ge1

Metabolism3

Mechanisms1

Previously unrecognized2

Pseudomonas4

Biofilm2

Proteomics1

Encodes3

Genomes2

Transcriptome3

Escherichia3

Uptake1

Molecular5

Regulators3

Infection7

Regulation of gene ex2

Pathways2

20181

Genome4

RNAs1

Regulate1

Regulon1

Modulation1

Chromosomes1

Stochastic4

Biological8

Mechanism1

Directly regulates1

Staphylococcus1

Promoters1

Analyses2

Interactions4

Environments2

Pathway1

Protein-protein int1

Biology5

Survival3

Sensory1

Identification2

Host-pathogen1

Signal transduction1

Interaction2

Enrichment1

Datasets2

Subsequently1

Functional3

Microarray2

Behaviour2