• genetics
  • In honoring Campbell, ASM officials cited his "exceptional insights and achievements in the field of molecular genetics - a career of groundbreaking research that has had a profound influence on several fields, including molecular cloning and gene therapy. (wikipedia.org)
  • metabolism
  • In the presence of toluene, menadione reduced TodS activity whereas toluene did not stimulate activity in the presence of menadione.The opposing effects of menadione on glucose and toluene metabolism may be partially responsible for the interwoven regulation of both catabolic pathways.This work provides mechanistic detail on how complex sensor kinases integrate different types of signal molecules. (nih.gov)
  • Although initially discovered by regulating carbohydrate metabolism, the CRP-cAMP complex controls a major regulatory network in Gram-negative bacteria, including a broad subset of genes spread into different functional categories of the cell. (nih.gov)
  • The novel antiterminator structure consists of two small hairpins with highly conserved terminal loop residues, both features being essential for successful antitermination.Despite the unrelatedness of the species in which they are found, the majority of the ANTAR-associated genes are thematically related to nitrogen management.These data suggest that the central tenets for gene regulation by ANTAR antitermination occur widely in nature to specifically control nitrogen metabolism. (nih.gov)
  • These data suggest that the central tenets for gene regulation by ANTAR antitermination occur widely in nature to specifically control nitrogen metabolism. (nih.gov)
  • This regulation controls parts of the sulfur metabolism of marine bacteria. (wikipedia.org)
  • Genome
  • Epigenetics most often denotes changes in a chromosome that affect gene activity and expression, but can also be used to describe any heritable phenotypic change that does not derive from a modification of the genome, such as prions. (wikipedia.org)
  • However, riboswitch transcripts subsequently modulate the expression of a gene located elsewhere in the genome. (wikipedia.org)
  • Shortly thereafter, a series of papers were published by Youssef Idaghdour and his colleagues looking at the role of environmental factors on gene expression throughout the genome where they found that only 5% of the variation in genomic expression was attributable to genetic factors (i.e. sequence variation in the genome) whereas, as much as half was due to the living environment of the individual, either urban or rural. (wikipedia.org)
  • The dormant form of the lambda genome was called the 'prophage' Study of phage lambda over the next 50 years provided valuable insights into virus life cycles, the regulation and expression of genetic material, and the mechanism of integration and excision of genetic material into chromosomal locations. (wikipedia.org)
  • These methods can also quickly uncover single-nucleotide polymorphisms, insertions and deletions by mapping unassembled reads against a well annotated reference genome, and thus provide a list of possible gene differences that may be the basis for any functional variation among strains. (wikipedia.org)
  • The genome of an organism contains anywhere from a few hundred to thousands of different genes, all encoding a singular product or more. (wikipedia.org)
  • encode
  • Although MG1655 does not encode a T7 RNA polymerase gene, the pde genes were expressed from a fortuitous promoter at sufficiently high levels to partially restore the swimming defect of MG1655 ΔyhjH in semi-solid agar. (nih.gov)
  • Literature suggests that nearly 8% of human genes encode transcription factors and the functions and specificities of their interactions remain largely unexplored. (wikipedia.org)
  • bacteria
  • How many genes do bacteria and animals have? (brainscape.com)
  • Moreover, the underlying studies revealed that CRP-cAMP controls the expression of another global regulator in Gram-negative bacteria, the leucine-responsive protein Lrp. (nih.gov)
  • lpxC and yafS are the most suitable internal controls to normalize real time RT-qPCR expression in the phytopathogenic bacteria Dickeya dadantii. (nih.gov)
  • Here, we propose a set of reference genes, of the phytopathogenic bacteria Dickeya dadantii and Pectobacterium atrosepticum, which are stable in a wide range of growth conditions. (nih.gov)
  • We measured the expression of these reference gene candidates using quantitative RT-PCR in 50 different experimental conditions, mimicking the environment encountered by the bacteria in their host and directly during the infection process in planta. (nih.gov)
  • Thus, these genes are considered suitable for use as reference genes for the normalization of real-time RT-qPCR data of the two main pectinolytic phytopathogenic bacteria D. dadantii and P. atrosepticum and, probably, of other Enterobacteriaceae. (nih.gov)
  • Moreover, we defined general criteria to select good reference genes in bacteria. (nih.gov)
  • H-NS is about 15.6 kDa and assists in the regulation of bacterial transcription in bacteria by repressing and activating certain genes. (wikipedia.org)
  • As one example, quorum sensing (QS) enables bacteria to restrict the expression of specific genes to the high cell densities at which the resulting phenotypes will be most beneficial. (wikipedia.org)
  • Many species of bacteria use quorum sensing to coordinate gene expression according to the density of their local population. (wikipedia.org)
  • In order for the bacteria to use quorum sensing constitutively, they must possess three characteristics: to secrete a signaling molecule, an autoinducer, to detect the change in concentration of signaling molecules, and to regulate gene transcription as a response. (wikipedia.org)
  • However, they have a receptor that detects AHLs from other bacteria and change their gene expression in accordance with the presence of other "quorate" populations of Gram-negative bacteria. (wikipedia.org)
  • Toxin-antitoxin genes are often transferred through horizontal gene transfer and are associated with pathogenic bacteria, having been found on plasmids conferring antibiotic resistance and virulence. (wikipedia.org)
  • Early studies on bacterial viruses began after the discovery by Twort and d'Herelle of 'filterable agents' which were able to destroy bacteria. (wikipedia.org)
  • Self-activating prey, where the randomized region facilitate reporter expression in the absence of TF binding, are removed by transforming the reporter vector library into bacteria in the absence of bait and assaying for growth on plates containing 5-fluoro-orotic acid (5-FOA). (wikipedia.org)
  • Humans
  • Research has shown that the activity of gene profiles or gene programs can be affected by the physical and social environments that humans inhabit. (wikipedia.org)
  • RNAs
  • Small regulatory RNAs (sRNAs) from bacterial chromosomes became the focus of research over the past five years. (nih.gov)
  • Furthermore, bioinformatic searches using this conserved antiterminator motif identified many new ANTAR target RNAs in phylogenetically diverse bacterial species, some comprising complex regulons. (nih.gov)
  • Post-genomic research has rendered bacterial small non-coding RNAs (sRNAs) as major players in post-transcriptional regulation of gene expression in response to environmental stimuli. (wikipedia.org)
  • These data included conserved RNA secondary structures often found in the untranslated regions (UTRs) of the relevant genes and the success of procedures to create artificial small molecule-binding RNAs called aptamers. (wikipedia.org)
  • Clusters
  • The genomes of G. sulfurreducens, G. metallireducens, and G. uraniireducens contain multiple (approximately 70) homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively). (nih.gov)
  • Unlike the single gene cluster of E. coli, the Geobacter clusters are not all located near the flagellar genes. (nih.gov)
  • The numerous chemoreceptors and chemotaxis-like gene clusters of Geobacter appear to be responsible for a diverse set of signaling functions in addition to chemotaxis, including gene regulation and biofilm formation, through functionally and spatially distinct signaling pathways. (nih.gov)
  • Gene positioning provides further evidence that the group A and B homologs bind to MCPs containing the C-terminal pentapeptide: these homologs are located in che clusters with pentapeptide-containing MCPs (Figure 1). (nih.gov)
  • Streptococcus
  • Biochemical studies reveal that the domain is a glucosyltransferase, and it catalyses the transfer of glucose to the branch point of the hexasaccharide O-linked to the serine-rich repeat of the bacterial adhesin, Fap1 of Streptococcus parasanguinis. (nih.gov)
  • Adherence to host cells is important in microbial colonization of a mucosal surface, and Streptococcus pneumoniae adherence was significantly enhanced by expression of an extracellular pilus composed of three subunits, RrgA, RrgB and RrgC. (nih.gov)
  • Protein
  • The last gene of the cluster encodes the fourth listerial GGDEF domain protein, PssE, that functions as an I-site c-di-GMP receptor essential for exopolysaccharide synthesis. (nih.gov)
  • An ANTAR protein, EutV, regulates the ethanolamine-utilization genes (eut) in Enterococcus faecalis. (nih.gov)
  • The aidB gene encodes a protein of ca. 60 kDa that is homologous to several mammalian acyl coenzyme A dehydrogenases. (umassmed.edu)
  • In order to examine the role of BlaA in regulation, we here report on over-expression of a GST-BlaA fusion protein in Escherichia coli and its use for antibody preparation. (uliege.be)
  • In 2002, the first comprehensive proofs of multiple classes of riboswitches were published, including protein-free binding assays, and metabolite-binding riboswitches were established as a new mechanism of gene regulation. (wikipedia.org)
  • HIS3 encodes a protein required for histidine biosynthesis and thus only those cells containing bait-prey combinations that activate the reporter genes will be able to grow. (wikipedia.org)
  • polymerase
  • Only once this region has been bound with the appropriate set of TFs, and in the proper order, can RNA polymerase bind and begin transcribing the gene. (wikipedia.org)
  • functional categories
  • Most (83%) of the significantly altered transcripts were down-regulated after 30 minutes of incubation in blood, and all functional categories of genes were abundantly represented. (nih.gov)
  • Out of these, we retained 10 genes representing different functional categories, different levels of expression (low, medium, and high) and with no systematic variation in expression correlating with growth conditions. (nih.gov)
  • swarming motility
  • After 20 minutes of exposure to 0.82 mM OPP, genes involved in the exhibition of swarming motility and anaerobic respiration were upregulated. (nih.gov)
  • Results from this study indicate that after 20 minutes of exposure to OPP, genes that have been linked to the exhibition of anaerobic respiration and swarming motility were upregulated. (nih.gov)
  • chromosomes
  • The 23 pairs of DNA molecules called chromosomes contain the approximately 21,000 genes comprising the "human blueprint. (wikipedia.org)
  • Reporter
  • The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. (wikipedia.org)
  • The other plasmid contains a region of randomized sequence representing potential binding sites (prey) which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes. (wikipedia.org)
  • In other words, if cells can grow despite a high concentration of 3-AT, bait-prey binding must be of high enough stringency to drive reporter gene expression (HIS3) at a sufficient level to overcome the resulting competitive inhibition. (wikipedia.org)
  • disinfectants
  • The exopolysaccharide also greatly enhances bacterial tolerance to commonly used disinfectants as well as desiccation, which may contribute to survival of L. monocytogenes on contaminated food products and in food-processing facilities. (nih.gov)
  • mutation
  • The architecture of a prototypical bacterial signaling circuit enables a single point mutation to confer novel network properties. (nih.gov)
  • Binding Sites
  • In this way, researches can gauge how strongly bait binds its prey (correlated with the level of expression of HIS3) and thus determines which nucleotide binding-sites have strong or weak preferences for a given base. (wikipedia.org)
  • coli
  • Finally, the regulation of gene expression in Geobacter differs from E. coli. (nih.gov)
  • This assay is used for measuring the expression of Escherichia coli lacZ, the antisense target for experimental testing and validation. (nih.gov)
  • Expression of the Escherichia coli aidB gene is induced in vivo by alkylation damage in an ada-dependent pathway and by anaerobiosis or by acetate at pH 6.5 in an ada-independent fashion. (umassmed.edu)
  • Dr. Campbell's research was focused on a specific bacterial virus, phage lambda, and its host bacterium E. coli, but the model provided insights into how extrachromosomal DNA can be inserted and excised in other organisms. (wikipedia.org)
  • While study of the regulation of integration and excision of phage lambda in E coli has been a primary focus of his research, Dr. Campbell and research associates also studied regulation and expression of E coli genes linked to the lambda insertion location, including the biotin (bio) and galactose (gal) genes. (wikipedia.org)
  • riboswitches
  • Prior to the discovery of riboswitches, the mechanism by which some genes involved in multiple metabolic pathways were regulated remained mysterious. (wikipedia.org)
  • Riboswitches are often conceptually divided into two parts: an aptamer and an expression platform. (wikipedia.org)
  • regulates
  • The expression platform is what regulates gene expression. (wikipedia.org)
  • A TPP riboswitch in Neurospora crassa (a fungus) controls alternative splicing to conditionally produce an Upstream Open Reading Frame (uORF), thereby affecting the expression of downstream genes A TPP riboswitch in plants modifies splicing and alternative 3'-end processing A riboswitch in Clostridium acetobutylicum regulates an adjacent gene that is not part of the same mRNA transcript. (wikipedia.org)
  • For example, a transcription factor that regulates a gene on chromosome 6 might itself have been transcribed from a gene on chromosome 11. (wikipedia.org)
  • binds
  • The aptamer directly binds the small molecule, and the expression platform undergoes structural changes in response to the changes in the aptamer. (wikipedia.org)
  • sRNAs
  • Rhizobial adaptations to soil and plant cell environments require the coordinate expression of complex gene networks in which sRNAs are expected to participate. (wikipedia.org)
  • upstream
  • Consequently, the new KS based method proposed here, which assigns P -values to fixed length upstream regions, provides a fast and accurate approach for predicting bacterial transcription targets. (frontiersin.org)
  • Another T-N11-A motif upstream of the blaU gene was also shown to bind BlaA. (uliege.be)
  • For example, comparative analysis of upstream regions of several genes expected to be co-regulated led to the description of the S-box (now the SAM-I riboswitch), the THI-box (a region within the TPP riboswitch), the RFN element (now the FMN riboswitch) and the B12-box (a part of the cobalamin riboswitch), and in some cases experimental demonstrations that they were involved in gene regulation via an unknown mechanism. (wikipedia.org)
  • Infection
  • A reliable normalization of the data, using several reference genes, is critical for an accurate quantification of gene expression.The two most stable genes (ABF-0017965 (lpxC) and ABF-0020529 (yafS) were successfully used for normalization of RT-qPCR data.We have identified at least two genes, lpxC (ABF-0017965) and yafS (ABF-0020509), whose expressions are stable in a wide range of growth conditions and during infection. (nih.gov)
  • We have identified at least two genes, lpxC (ABF-0017965) and yafS (ABF-0020509), whose expressions are stable in a wide range of growth conditions and during infection. (nih.gov)
  • In conditions of social stress however, the up-regulation of pro-inflammatory gene expression prepares the body to better deal with bodily injury and bacterial infection which is more likely under conditions of social stress either through hostile human contact, or increased predatory vulnerability due to separation from the social group. (wikipedia.org)
  • Concurrently, the down-regulation of anti-viral gene expression leaves the individual more vulnerable to viral infection such as the flu and the common cold. (wikipedia.org)
  • The 1940s produced the first pictures of bacterial viruses using electron microscopy produced the first photos of bacterial viruses, and research on the mechanism of infection and reproduction dramatically increased. (wikipedia.org)
  • chromosome
  • His most prominent discovery was the proposal of the "Campbell model" of virus insertion, where viral DNA is inserted into the host chromosome, becoming covalently bonded to the bacterial DNA, and then remains dormant until activation. (wikipedia.org)
  • organisms
  • Non-adherent RrgA-negative, RrgB- and RrgC-positive organisms produce pili, suggesting that pilus-mediated adherence is due to expression of RrgA, rather than the pilus backbone itself. (nih.gov)
  • This is an example of altruism and how bacterial colonies resemble multicellular organisms. (wikipedia.org)
  • mechanism
  • This study also suggests that the downregulation of the rmf and rpoS genes may be indicative of the mechanism by which OPP causes decreases in cell viability in P. aeruginosa. (nih.gov)
  • mRNA
  • Here, we present a detailed in vitro analysis of SR1, a sRNA of Bacillus subtilis that is involved in regulation of arginine catabolism by basepairing with its target, ahrC mRNA. (nih.gov)
  • Later on, this transcript, denoted micF, was found to be an asRNA of ompF and capable of downregulating the expression of ompF under stress by forming a duplex with the ompF mRNA. (wikipedia.org)
  • metabolic
  • Our work suggests that the metabolic sensor CRP-cAMP plays a role in coupling the expression of type 1 fimbriae to environmental conditions, thereby also affecting subsequent attachment and colonization of host tissues. (nih.gov)
  • Comparative
  • In 1986, the first comparative genomic study at a larger scale was published, comparing the genomes of varicella-zoster virus and Epstein-Barr virus that contained more than 100 genes each. (wikipedia.org)
  • sequences
  • The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. (wikipedia.org)
  • In parallel, a library of randomized oligonucleotides representing potential TF target sequences are cloned into a separate vector containing the selectable genes HIS3 and URA3. (wikipedia.org)
  • sequence
  • Examples of mechanisms that produce such changes are DNA methylation and histone modification, each of which alters how genes are expressed without altering the underlying DNA sequence. (wikipedia.org)
  • For example, small RNA viruses infecting animals (picornaviruses) and those infecting plants (cowpea mosaic virus) were compared and turned out to share significant sequence similarity and, in part, the order of their genes. (wikipedia.org)
  • The bacterial one-hybrid (B1H) system is a method for identifying the sequence-specific target site of a DNA-binding domain. (wikipedia.org)
  • structural
  • A plasmid bearing the blaU structural gene and the blaA-blaB regulatory region was constructed and shown to confer on an S. lividans host the capacity to produce inducible beta-lactamase. (uliege.be)
  • plasmid
  • For complementation purposes, plasmid pCBP68 (crp+) carrying the crp gene in the vector pLG338 (v.c.) was used. (nih.gov)
  • Plasmid stabilising toxin-antitoxin systems have been used as examples of selfish DNA as part of the gene centered view of evolution. (wikipedia.org)