Functional categories gene expression regulation bacterial. Medical search. Frequent questions

Co-immunoprecipitation, bacterial two-hybrid and pull-down analyses showed that PilH and PilG were able to interact with district subsets of proteins that potentially account for their regulatory impact. (biomedcentral.com)
Taken together, we demonstrate that for the conditions tested PilG and PilH have inverse regulatory effects on flagellum-dependent and pili-dependent motility in Xcc and that this regulatory impact depends on these proteins influences on genes/proteins involved in flagellar biosynthesis and pilus assembly. (biomedcentral.com)
To begin to better understand the regulation of immune effector proteins by the IMD pathway, we used oligonucleotide microarrays and iTRAQ to analyze differences in mRNA and protein expression, respectively, between transgenic Anopheles stephensi mosquitoes exhibiting blood meal-inducible overexpression of an active recombinant Rel2 and their wild-type conspecifics. (johnshopkins.edu)
We sought to determine if there was antibody deposition in SAH livers and whether antibodies extracted from SAH livers were cross-reactive against both bacterial antigens and human proteins. (elifesciences.org)
Protein-protein interaction (PPI) networks and modules were constructed to identify hub genes with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape. (researchsquare.com)
Downstream genes involved in type VII secretion systems, cell wall synthesis (polyketide biosynthesis proteins), and iron uptake were changed in response to the intracellular environment of macrophages. (biomedcentral.com)
The obvious next step is to integrate this information and learn how genes, proteins, and/or epigenetic factors influence the phenotype of a disease in context of the system. (rsc.org)
In addition to the host regulatory mechanisms response to disease, the microbiome can make changes to the expression of the host features such as their genes, proteins, and/or PTMs. (rsc.org)
PTMCode is a resource of known and predicted functional associations between protein post-translational modifications (PTMs) within and between interacting proteins. (biokeanos.com)
Our project offers a unique opportunity for Master's student to gain hands-on experience focused on transcriptional regulators with importance in expression of genes of outer membrane proteins that are essential in host-pathogen interaction. (lu.se)
A couple of key findings were that gene sequences did not predict successful protein expression, solubility and activity, and that the successful strategy involved expressing genes from the extreme thermophile Methanothermobacter thermautotrophicus , which might account for the proteins' greater stability in a heterologous system. (plantae.org)
However, little is known about the expression of HBD-1 or HBD-2 in tissues of the oral cavity and whether these proteins are secreted. (lookformedical.com)

We demonstrated that only 39 differentially expressed genes (DEGs) were present in all species. (frontiersin.org)
While multiple immune genes were up-regulated, a majority of the differentially expressed genes have no known immune function in mosquitoes. (johnshopkins.edu)
By integrating two datasets (GSE77459 and GSE92681) in the GEO database using the sva and limma packages of R, differentially expressed genes (DEGs) of pulpitis were identified. (researchsquare.com)

Then, the DEGs were analysed to identify biological pathways of dental pulp inflammation with Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Set Enrichment Analysis (GSEA). (researchsquare.com)

The FMO family of genes is conserved across all phyla that have been studied so far, therefore some form of the FMO gene family can be found in all studied eukaryotes. (wikipedia.org)
Small regulatory RNAs (sRNAs) play key roles in modulating gene expression in both prokaryotes and eukaryotes. (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)

Here, we characterize the role of this alarmone in the regulation of the hlyCABD(II) operon of the UPEC isolate J96, encoding the toxin alpha-hemolysin that induces cytotoxicity during infection of bladder epithelial cells. (ibecbarcelona.eu)
Prototrophy suppressor mutations in a ppGpp-deficient strain restore the alpha-hemolysin expression from this operon to wild-type levels, confirming the requirement of ppGpp for its expression. (ibecbarcelona.eu)
Our analysis showed that mRNA abundances, gene organization (operon) and gene essentiality are correlated in Buchnera (i.e., the most expressed genes are essential genes organized in operons) whereas no link between mRNA abundances and gene strand bias was found. (biomedcentral.com)
It has also been shown that neighbouring genes in a bacterial chromosome tend to be co-expressed, even if they are not in the same operon [ 10 ], suggesting the existence of a "supra-operonic" organization [ 11 ]. (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)

ppGpp is required for the expression of the alpha-hemolysin encoded in hlyCABD(II) by stimulating its transcriptional expression. (ibecbarcelona.eu)
Phenotypic transcriptional and functional examination of the peripheral mononuclear cells revealed age-, time, and disease severity-specific adaptations. (medrxiv.org)
The up-regulation of photosynthesis by ethanol was also further confirmed at transcriptional level. (biomedcentral.com)
The major events in the regulation of the host response on a transcriptional level occur within the first 3 days after infection. (biomedcentral.com)

However, a group of researchers found a sixth FMO gene located on human chromosome 1. (wikipedia.org)
In addition to the sixth FMO discovered as of 2002, the laboratories of Dr. Ian Philips and Elizabeth Sheppard discovered a second gene cluster in humans that consists of 5 additional pseudogenes for FMO on human chromosome 1. (wikipedia.org)
Past genomic studies have comprehensively described the organization of the bacterial chromosome, for example in terms of gene localization, order and orientation. (biomedcentral.com)
This organization of the chromosome can be described as being an adaptive and functional tool, essential for the survival of the bacterial cell. (biomedcentral.com)
Gene organization in the bacterial chromosome has very well known effects on transcription and a standard example is the organization of genes into operons, which allows for a sophisticated regulation of gene expression [ 9 ]. (biomedcentral.com)
Tumor suppressor genes located in the 5q21 region on the long arm of human chromosome 5. (edu.au)
A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human CHROMOSOME 17 at locus 17q21. (edu.au)
A tumor suppressor gene (GENES, TUMOR SUPPRESSOR) located on human chromosome 13 at locus 13q12.3. (edu.au)
The beta-defensin genes mapped closely on rat chromosome 16 and were closely linked to the alpha-defensins genes, suggesting that they are part of a gene cluster, similar to the organization reported for humans. (lookformedical.com)
Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. (cdc.gov)

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)
PRODORIC is a comprehensive database about gene regulation and gene expression in prokaryotes. (biokeanos.com)

Analyses of FMO genes across several species have shown extensive silent DNA mutations, which indicate that the current FMO gene family exists because of selective pressure at the protein level rather than the nucleotide level. (wikipedia.org)
By transcriptome analyses (RNA-seq and RT-PCR) we confirm these observations as PilG is shown to upregulate many genes involved chemotaxis and flagellar biosynthesis but these similar genes were downregulated by PilH. (biomedcentral.com)
Moreover, transcriptomic analyses have demonstrated that, in free-living bacteria, gene transcription levels and chromosomal organization are mutually influenced. (biomedcentral.com)

Using an oligonucleotide-based microarray, we normalized the transcriptomic data by genomic DNA signals in order to have access to inter-gene comparison data. (biomedcentral.com)
In addition to low-throughput methods, transcript levels for many genes at once can be measured with DNA microarray technology or "tag based" technologies like Serial analysis of gene expression (SAGE) or the more advanced version SuperSAGE, which can provide a relative measure of the cellular concentration of different messenger RNAs . (wikidoc.org)
Recent advances in microarray technology allow for the quantification, on a single array, of transcript levels for every known gene in the human genome. (wikidoc.org)
Of 54 detectable E. coli sRNAs in our microarray analysis, 30 sRNAs showed a differential expression upon HU stress, of which 28 sRNAs displayed a YbeY-dependent change in expression. (biomedcentral.com)
In this study, we performed a new bioinformatics analysis on microarray-based gene expression data obtained from the public domain to explore genes that were differentially induced by drugs between the group of capreomycin and PA-824 and the group of mainly the first-line TB drugs. (hindawi.com)
Beyond this time, no differences in global gene expression in infected and control animals were detectable by microarray analysis. (biomedcentral.com)
Furthermore, microarray profiling identified 226 genes with differential expression in the liver of animals treated with MSC, with cellular signaling, and actin cytoskeleton regulation as key upregulated processes. (frontiersin.org)

Biofilm formation is an important process in bacterial pathogens and several lines of evidence suggest that in X. a. pv. (hdac-inhibitors.com)
2022 ) Gene Expression Regulation in Airway Pathogens: Importance for Otitis Media. (lu.se)
Those immune defects lead to infections with bacterial, viral, and fungal pathogens that begin during infancy and, if untreated, result in a fatal outcome in the first few years of life. (medscape.com)

Molecular characterization of an elicitor-responsive lectin receptor-like kinase gene (GhLec-RK2 ) from cotton, Gossypium hirsutum. (uj.ac.za)
Molecular characterization and regulation of a Nicotiana tabacum S-domain receptor-like kinase gene induced during an early rapid response to lipopolysaccharides. (uj.ac.za)
Molecular characterization of an elicitor-responsive Armadillo repeat gene (GhARM) from cotton (Gossypium hirsutum). (uj.ac.za)
Molecular cloning and characterization of rat genes encoding homologues of human beta-defensins. (lookformedical.com)
RNA sequencing has been used for the genome-wide quantification of absolute transcript levels, the identification of novel genes, the characterization of transcript structure (including 50 and 30 ends, introns, and exons), and the mining of molecular markers. (springeropen.com)

The results showed that ethanol exposure induced genes involved in common stress responses, transporting and cell envelope modification. (biomedcentral.com)

Numerous genes were differentially regulated at both the mRNA and protein levels following induction of Rel2. (johnshopkins.edu)
The expression of many genes is regulated after transcription (i.e., by microRNAs or ubiquitin ligases ), so an increase in mRNA concentration need not always increase expression. (wikidoc.org)
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)
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)
Defensin mRNA expression was quantitated by RNase protection assays. (lookformedical.com)
HBD-1 mRNA expression was detected in the gingiva, parotid gland, buccal mucosa, and tongue. (lookformedical.com)
Expression of HBD-2 mRNA was detected only in the gingival mucosa and was most abundant in tissues with associated inflammation. (lookformedical.com)

Using a solid methodology that includes state-of-the-art microscopy, proteome arrays, and gene ontology assays, it provides strong evidence that liver-derived IgG and IgA with cytotoxic properties and reactivity to both gut-derived E.coli and autoantigens accumulated in hepatocytes of SAH patients but not of healthy controls. (elifesciences.org)
Here we hypothesize that the reported unfavorable classification results in the set-level framework were due to the adoption of unsuitable gene sets defined typically on the basis of the Gene ontology and the KEGG database of metabolic networks. (biomedcentral.com)
In the former case, a gene set corresponds to an ontology term (representing a function, process, or a cellular component) and collects all genes annotated by that term. (biomedcentral.com)
In garlic, the next-generation sequencing analysis based on RNA from renewal buds resulted in de novo assembly of 128,000 unigenes that were annotated and analyzed with respect to Gene Ontology (GO) and metabolic pathways [ 28 ]. (springeropen.com)

Developmental and tissue specific expression has been studied in several mammalian species, including humans, mice, rats, and rabbits. (wikipedia.org)
However, because FMO expression is unique to each animal species, it is difficult to make conclusions about human FMO regulation and activity based on other mammalian studies. (wikipedia.org)
It is likely that species-specific expression of FMO's contributes to differences in susceptibility to toxins and xenobiotics as well as the efficiency with excreting among different mammals. (wikipedia.org)
Taken together, our results add to our holistic understanding of alarmone metabolism across diverse bacterial species. (bvsalud.org)
The operation of the stringent response, a highly conserved survival mechanism, is known to help many bacterial species cause persistent or virulent infections. (bvsalud.org)
Our group is interested in the research of clinically relevant bacterial species that mainly cause upper and lower airway infections and their interactions with the host. (lu.se)
The position of the endospore differs among bacterial species and is useful in identification. (bionity.com)
There are many microorganisms colonized in the human intestine, and more than 1000 bacterial species in the intestinal ecosystem of a single individual. (frontiersin.org)

By expressing a bacterial pyruvate decarboxylase ( pdc ) and alcohol dehydrogenase ( adh ) from the bacterium Z. mobilis in the cyanobacterium Synechococcus sp. (biomedcentral.com)
In our proposed project, you would investigate expression regulation in clinically significant bacterium non-typeable Haemophilus influenzae (NTHi). (lu.se)
In a new discovery that increases our understanding of gene transfer, a research team centered at University of Tsukuba has studied a gene in marine invertebrates called ascidians originally came from a common bacterium. (phys.org)

Functional enrichment analysis showed that the DEPRGs had a close relationship with inflammation. (hindawi.com)

The highly conserved bacterial YbeY RNase has structural similarities to the MID domain of AGOs. (biomedcentral.com)

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)
Non-motile bacteria are more immunogenic due to a lower expression of arnT upon host-cell contact, but do not produce spermidine and are phagocytosed less. (elifesciences.org)
However, despite the numerous studies on bacterial motility in other Gram-negative bacteria, only limited work has been carried out examining the motility regulation in Xcc . (biomedcentral.com)
Genomic studies on bacteria have clearly shown the existence of chromosomal organization as regards, for example, to gene localization, order and orientation. (biomedcentral.com)
This is a perfect illustration of the mutual influence between gene expression levels and chromosomal organization in bacteria. (biomedcentral.com)
Previous studies have suggested that the bacteria-derived mitochondria would be the optimal place for nitrogenase production, and many of the genes encoding nitrogenase subunits have been successfully expressed in yeast mitochondria, but the resulting complex lacked the essential metal cofactor. (plantae.org)
Cystic fibrosis mice have been generated by gene targeting but show little lung disease without repeated exposure to bacteria. (lookformedical.com)

Selected up-regulated genes from multiple functional categories were tested for both anti- Plasmodium and anti-bacterial action using RNA interference (RNAi). (johnshopkins.edu)
The presence of cross-reacting anti-bacterial IgG and IgA autoantibodies in the liver may participate in the pathogenesis of SAH. (elifesciences.org)

This results in the expression of spermidine on the surface, which specifically activates the PIP 3 -pathway to induce phagocytic uptake into primary or immortalized murine cells. (elifesciences.org)
Diarrhea-predominant IBS (IBS-D) demonstrated shifts in the metatranscriptome and metabolome including increased bile acids, polyamines, succinate pathway intermediates (malate, fumarate), and transcripts involved in fructose, mannose, and polyol metabolism compared to constipation-predominant IBS (IBS-C). A classifier incorporating metabolites and gene-normalized transcripts differentiated IBS-D from IBS-C with high accuracy (AUC 0.86). (biomedcentral.com)
Based on our experimental findings, we conclude that increased expression of the IMD immune pathway-controlled transcription factor Rel2 affects the expression of numerous genes with diverse functions, suggesting a broader physiological impact of immune activation and possible functional versatility of Rel2. (johnshopkins.edu)
The GSEA results provided further functional annotations, including complement system, IL6/JAK/STAT3 signalling pathway and inflammatory response pathways. (researchsquare.com)
a single set may e.g. collect all genes acting in a specific metabolic pathway. (biomedcentral.com)
In the latter, a gene set contains genes whose product acts in a specific cellular pathway. (biomedcentral.com)

cAMP is associated with kinases function in several biochemical processes, including the regulation of glycogen , sugar , and lipid metabolism . (wikipedia.org)
Brain and muscle Arnt-like protein-1 ( BMAL1 ) knockout mice exhibit accelerated aging, abnormal glucose metabolism, and impaired adipocyte differentiation, among other phenotypes, which are effects associated with the BMAL1 gene. (go.jp)
Most of us learned intermediary metabolism via the general model of bacterial or perhaps hepatocyte biolochemistry. (marclab.org)
When differentiated human THP-1 cells were infected with MAP, the expression of various genes associated with stress responses and metabolism was altered in both host and MAP at 3 h post-infection. (biomedcentral.com)
Notably, alterations in gene sets involved in arginine metabolism were observed in both the host and MAP, along with significant downregulation of NOS2 expression. (biomedcentral.com)

Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation , morphogenesis and the versatility and adaptability of any organism . (wikidoc.org)
Gene regulation may also serve as a substrate for evolutionary change, since control of the timing, location, and amount of gene expression can have a profound effect on the functions (actions) the gene in the organism. (wikidoc.org)
The number of copies of a given gene present in the cell of an organism. (edu.au)
The ability of genes or alleles to affect the representation of the host organism in a biome is an operational definition for the "function" of the gene (in that context). (genomicglossaries.com)
The transfer of genes from one organism to another is potentially a rapid way for evolution to occur and for complicated novel functions to emerge. (phys.org)

Pulpitis is an inflammatory disease of the dental pulp, and bacterial infection is considered to be the most important trigger of pulpitis[3]. (researchsquare.com)
On the host side, upregulation of inflammatory cytokine genes was observed along with pattern recognition receptor genes. (biomedcentral.com)
Naive DeltaF508 -/- and +/- mice showed no pulmonary inflammation and after inhaled Pseudomonas aeruginosa had similar inflammatory responses and bacterial clearance rates. (lookformedical.com)
Macrophages, which are functional plasticity cells, have the ability to phagocytize and digest foreign substances and acquire pro-(M1-like) or anti-inflammatory (M2-like) phenotypes according to their microenvironment. (frontiersin.org)

The pattern of detection of a gene or gene product may be described using terms such as facultative , constitutive , circadian , cyclic , housekeeping , or inducible [1] . (wikidoc.org)
HBD-1 expression was constitutive, while HBD-2 expression was induced by IL-1beta and LPS. (lookformedical.com)

One gene was highly similar to the human beta-defensin-1 (HBD-1) gene and mouse beta-defensin-1 gene at both the nucleic acid and amino acid levels and was termed rat beta-defensin-1 (RBD-1). (lookformedical.com)

Gene - An International Journal of Functional and Evolutionary Genomics. (uj.ac.za)
Six among the 42 genes identified in this study are on the list of the top 100 persistence targets selected by the TB Structural Genomics Consortium. (hindawi.com)
Garlic contains various bioactive compounds whose metabolic pathways, plant-pathogen interactions, defensive genes, identify interaction networks, and functional genomics were not previously predicted in the garlic at the genomic level. (springeropen.com)

First described to modulate metabolic adaptive responses, ppGpp modulates the expression of genes belonging to very diverse functional categories. (ibecbarcelona.eu)
We demonstrate that not only the presence of pathogen inherent molecular patterns induces immune responses, but that bacterial motility is linked to a host-cell-induced expression of additional immune modulators. (elifesciences.org)
Gene expression signatures within memory B cells suggest qualitative differences in the antibody responses in aged patients with severe disease. (medrxiv.org)
Many of these genes are related to stress responses. (hindawi.com)

In this setting, high-dimensional vectors of features corresponding to genes are converted into lower-dimensional vectors of features corresponding to biologically interpretable gene sets. (biomedcentral.com)

For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. (ind.in)

Non-protein coding genes (e.g. rRNA genes, tRNA genes) are not translated into protein. (wikidoc.org)
Fig. 5: Metabolic and pathological regulation tRNA modifications in human mitochondria. (nature.com)

the cell may regulate the transcription of individual genes through regulatory molecules (ex. (powershow.com)
Because it is very difficult to clone a GFP-fused protein into its native location in the genome, however, this method often cannot be used to measure endogenous regulatory mechanisms (GFP-fusions are therefore most often expressed on extra-genomic DNA such as an expression vector ). (wikidoc.org)
We explore an alternative approach to defining gene sets, based on regulatory interactions, which we expect to collect genes with more correlated expression. (biomedcentral.com)
We define two families of gene sets using information on regulatory interactions, and evaluate them on phenotype-classification tasks using public prokaryotic gene expression data sets. (biomedcentral.com)
Under the Clinical Laboratory Improvement Amendments of 1988 (CLIA) regulations, laboratory testing is categorized on the basis of the level of testing complexity as either waived (i.e., from routine regulatory oversight) or nonwaived testing (which includes tests of moderate and high complexity). (cdc.gov)

The effect of Buchnera genome evolution on gene expression levels has also been analysed in order to assess the constraints imposed by the obligate symbiosis with aphids, underlining the importance of some gene sets for the survival of the two partners. (biomedcentral.com)
In terms of the distribution of identified genes in a specific category relative to the whole genome, only the categories of PE/PPE and conserved hypotheticals have statistical significance. (hindawi.com)
However, even when the two organisms in question are in close proximity to each other, such as in a symbiotic or parasitic relationship, the transfer of genetic material and its introduction into a new genome only marks the initial step for successful horizontal gene transfer. (phys.org)
AP-2 inherently binds to GC-rich regions, so it was already primed to start interacting with the bacterial GC-rich DNA once it had integrated into the ascidian genome," first author Yasunori Sasakura says. (phys.org)

Fecal samples were collected from a racially/ethnically diverse cohort of 495 subjects, including 318 IBS patients and 177 healthy controls, for analysis by 16S rRNA gene sequencing ( n = 486), metatranscriptomics ( n = 327), and untargeted metabolomics ( n = 368). (biomedcentral.com)

Bacterial persistence in vivo is analogous to the stationary phase culture in vitro [ 2 ]. (hindawi.com)
You will also employ functional assays investigating host-pathogen interactions in vitro, such as serum bactericidal assay or adherence to eukaryotic cells. (lu.se)

Metabolic modular composition of tissues is visualized by CMP, even when gene or protein expression patterns cannot be invoked to detect them. (marclab.org)
In this review, we discuss considerations of the study design for each data feature, the limitations in gene and protein abundance and their rate of expression, the current data integration methods, and microbiome influences on gene and protein expression. (rsc.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)
Rapid developments in these techniques have not only accelerated investigations into the process of pathogenic infection and defense strategies in fish, but also used to identify immunity-related genes in fish. (frontiersin.org)
Whereas in the acute phase of the disease immunoregulatory processes prevail in the hippocampus and the cortex, we observed a strong activation of neurogenic processes in the hippocampal dentate gyrus, both by gene expression and immunohistology starting as early as 3 days after infection. (biomedcentral.com)

A total of 470 DEGs comprising 394 upregulated and 76 downregulated genes were found in pulpitis tissue. (researchsquare.com)

Some chemical compounds can inhibit the functional roles of topoisomerases in organisms. (excedr.com)
This gene encodes a protein that helps form an external protective coating, the loss of which leads to a lack of cellulose production and has adverse effects on these organisms. (phys.org)

Mutations of this gene are associated with the formation of HEREDITARY BREAST AND OVARIAN CANCER SYNDROME. (edu.au)
Mutations in this gene predispose humans to breast and ovarian cancer. (edu.au)
Sequence analysis revealed that this region contains a binding site of a transcription factor called AP-2 and, when we induced mutations in this binding site, the expression of cellulose synthase in the ascidian epidermis disappeared. (phys.org)

There will be involved gene engineering and molecular biology methods such as PCR, SDS-PAGE, qPCR, western blot, DNA-protein interaction assays, flow cytometry etc. (lu.se)

So, if you are a Master's student looking for a challenging but also rewarding research project, who is interested in bacterial genetics, we encourage you to apply to our project. (lu.se)
Our study contains an extensive sequencing and functional gene-annotation analysis of A. sativum L. The findings provide insights into the molecular basis of TFs, defensive genes, and a reference for future studies on the genetics and breeding of A. sativum L. (springeropen.com)

Truncation of the first exon, which appears to regulate c-myc expression, is crucial for tumorigenicity. (edu.au)

The NAC transcription factor gene ANAC072 is differentially expressed in Arabidopsis thaliana in response to microbe-associated molecular pattern (MAMP) molecules. (uj.ac.za)
Distinct carbohydrate and lipid-based molecular patterns within lipopolysaccharides from Burkholderia cepacia contribute to defense-associated differential gene expression in Arabidopsis thaliana. (uj.ac.za)

In Escherichia coli, ppGpp regulates the expression of cellular factors that are important during urinary tract infections. (ibecbarcelona.eu)
This bias is even more important when the essentiality of genes is taken into account, and essential genes distribution bias reaches 76% and 94% in Escherichia coli and Bacillus subtilis respectively [ 4 ]. (biomedcentral.com)

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)
By integrating different datasets from the Gene Expression Omnibus (GEO) database, we analysed a merged expression matrix of pulpitis, aiming to identify biological pathways and diagnostic biomarkers of pulpitis. (researchsquare.com)
We compared the ortholog gene family of the A. sativum transcriptome to A. thaliana , O. sativa , and Z. mays and found that 12,077 orthologous gene families are specific to A. sativum L. Furthermore, we identified genes involved in plant defense mechanisms, their protein-protein interaction network, and plant-pathogen interaction pathways. (springeropen.com)

Its examples are bacterial toxins MccB17, ParE, and YacG. (excedr.com)

The analysis of physiological interactions such as nutrition, signaling, growth regulation, and defense mechanisms in complex heterocellular tissues requires a clear understanding of the metabolomes of each system compartment. (marclab.org)
The interactions include direct (physical) and indirect (functional) associations. (biokeanos.com)
DroID, the Drosophila Interactions Database, assembles gene and protein interaction data from a variety of sources into one easily accessible, comprehensive database. (biokeanos.com)

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)

Collectively, our data indicate that MSC therapy rescues impaired mitochondrial morphology, enhances host metabolic capacity, and induces widespread host gene shifting. (frontiersin.org)

Finally, we used gene knockout strains to validate the potential target genes related to ethanol tolerance. (biomedcentral.com)
Over time, OspC genes were transferred between strains through recombinations involving the whole or parts of the gene and one or both flanks. (cdc.gov)

Activation of camalexin biosynthesis in Arabidopsis thaliana in response to perception of bacterial lipopolysaccharides: a gene-to-metabolite study. (uj.ac.za)

We demonstrate that upon hitting a host cell, motile Pseudomonas aeruginosa induce a specific gene expression program. (elifesciences.org)
Another commonly used method for assaying the amount of a particular protein in a cell is to fuse a copy of the protein to a reporter gene such as Green fluorescent protein , which can be directly imaged using a fluorescent microscope. (wikidoc.org)
Foxo3a was expressed in 82.1%, 78.3%, and 77.5% of neutrophils, T lymphocytes, and B lymphocytes, respectively, and statistical analysis using the Kruskal-Wallis test followed by the Steel-Dwass test showed no significant difference of Foxo3a expression among the three cell types. (go.jp)
MAP upregulates stress-responsive global gene regulators, such as two-component systems and sigma factors, in response to oxidative and cell wall stress. (biomedcentral.com)
While the rest of a bacterial cell may stain, the endospore is left colourless. (bionity.com)
To test whether beta-defensin expression was inducible, gingival keratinocyte cell cultures were treated with interleukin-1beta (IL-1beta) or bacterial lipopolysaccharide (LPS) for 24 h. (lookformedical.com)

FMO genes are characterized by specific structural and functional constraints, which led to the evolution of different types of FMO's in order to perform a variety of functions. (wikipedia.org)

These findings will contribute to fish immunotherapy for the prevention and treatment of bacterial infections through the design of more specific and effective immune stimulants, adjuvants, and vaccines. (frontiersin.org)
These findings provide interesting insight into one way in which the conditions in the new host can facilitate expression of a newly transferred gene and its integration into the host's functions, reducing the improbability that a randomly inserted foreign gene could actually be beneficial. (phys.org)

We hypothesise that the hyperphosphorylated nucleotide alarmone ppGpp (guanosine tetraphosphate), acts as a pivotal regulator of these processes, given its established roles in nutrient management, degreening, and ROS regulation in leaves. (bvsalud.org)

. campestris ( Xcc ) involves the coordinate expression of many virulence factors, including surface appendages flagellum and type IV pili, which are required for pathogenesis and the colonization of host tissues. (biomedcentral.com)

The microenvironments of the low- and high-risk groups were assessed using xCell, the expression of immune checkpoints was determined, and gene set variation analysis (GSVA) was performed. (hindawi.com)
The analysis provided a list of gene targets for engineering ethanol tolerance in cyanobacterium Synechocystis . (biomedcentral.com)
Unlike in more conventional gene expression analysis, the set-level approach assumes that high-dimensional vectors of gene expressions are represented by lower-dimensional vectors of aggregated expressions. (biomedcentral.com)
Besides obvious benefits in the interpretability of the learned classifiers, the set-level approach is mainly motivated by the problem of high feature dimension contrasting with the low number of available samples, which has been characteristic of gene expression data analysis. (biomedcentral.com)

Conversely, KDM1A+2a(-/-) hESCs give rise to functional cardiac cells, displaying increased beating amplitude and frequency and enhanced expression of critical cardiogenic markers. (ibecbarcelona.eu)

Individual oscillating cells are synchronized with their neighbors, forming a coherent wave pattern of gene expression. (ens-lyon.fr)

Fusing a target protein to a reporter can also change the protein's behavior, including its cellular localization and expression level. (wikidoc.org)
with this, it is possible to use light to modulate DNA-binding activity, gene expression, or protein localization. (plantae.org)

Set-level classification of gene expression data has received significant attention recently. (biomedcentral.com)

Anatomy20

Organisms18

Diseases5

Chemicals and Drugs59

Analytical, Diagnostic and Therapeutic Techniques and Equipment44

Psychiatry and Psychology2

Phenomena and Processes102

Disciplines and Occupations4

Technology, Industry, Agriculture2

Information Science15

Health Care8

Proteins12

Differentially expressed genes3

Kyoto Encyclo1

Eukaryotes3

Operon5

Transcriptional4

Chromosome10

Prokaryotes2

Analyses3

Microarray7

Pathogens3

Characterization5

Induced genes involved1

MRNA7

Ontology4

Species8

Bacterium3

Enrichment analysis1

Highly conserved1

Bacteria7

Anti-bacterial2

Pathway6

Metabolism5

Organism5

Inflammatory4

Constitutive2

Nucleic acid1

Genomics3

Responses4

Biologically1

Sequences1

TRNA2

Regulatory5

Genome4

RRNA1

Vitro2

Protein expression2

Infection3

DEGs1

Organisms2

Mutations3

Assays1

Genetics2

Regulate1

Molecular2

Escherichia2

Pathways3

Toxins1

Interactions3

Interaction1

Induces1

Strains2

Biosynthesis1

Cell6

Structural1

Findings2

Processes1

Virulence factors1

Analysis4

Markers1

Pattern1

Localization2

Classification1