PubMed: A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.Periodicals as Topic: A publication issued at stated, more or less regular, intervals.BooksPublishing: "The business or profession of the commercial production and issuance of literature" (Webster's 3d). It includes the publisher, publication processes, editing and editors. Production may be by conventional printing methods or by electronic publishing.MEDLINE: The premier bibliographic database of the NATIONAL LIBRARY OF MEDICINE. MEDLINE® (MEDLARS Online) is the primary subset of PUBMED and can be searched on NLM's Web site in PubMed or the NLM Gateway. MEDLINE references are indexed with MEDICAL SUBJECT HEADINGS (MeSH).Serial Publications: Publications in any medium issued in successive parts bearing numerical or chronological designations and intended to be continued indefinitely. (ALA Glossary of Library and Information Science, 1983, p203)Biological Science Disciplines: All of the divisions of the natural sciences dealing with the various aspects of the phenomena of life and vital processes. The concept includes anatomy and physiology, biochemistry and biophysics, and the biology of animals, plants, and microorganisms. It should be differentiated from BIOLOGY, one of its subdivisions, concerned specifically with the origin and life processes of living organisms.Pseudogenes: Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Peptidyl-Dipeptidase A: A peptidyl-dipeptidase that catalyzes the release of a C-terminal dipeptide, -Xaa-*-Xbb-Xcc, when neither Xaa nor Xbb is Pro. It is a Cl(-)-dependent, zinc glycoprotein that is generally membrane-bound and active at neutral pH. It may also have endopeptidase activity on some substrates. (From Enzyme Nomenclature, 1992) EC 3.4.15.1.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Thiamine: 3-((4-Amino-2-methyl-5-pyrimidinyl)methyl)-5-(2- hydroxyethyl)-4-methylthiazolium chloride.Fursultiamin: Compound used for therapy of thiamine deficiency. It has also been suggested for several non-deficiency disorders but has not yet proven useful.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Allosteric Regulation: The modification of the reactivity of ENZYMES by the binding of effectors to sites (ALLOSTERIC SITES) on the enzymes other than the substrate BINDING SITES.Metabolomics: The systematic identification and quantitation of all the metabolic products of a cell, tissue, organ, or organism under varying conditions. The METABOLOME of a cell or organism is a dynamic collection of metabolites which represent its net response to current conditions.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Thiamine Pyrophosphate: The coenzyme form of Vitamin B1 present in many animal tissues. It is a required intermediate in the PYRUVATE DEHYDROGENASE COMPLEX and the KETOGLUTARATE DEHYDROGENASE COMPLEX.Streptococcus pneumoniae: A gram-positive organism found in the upper respiratory tract, inflammatory exudates, and various body fluids of normal and/or diseased humans and, rarely, domestic animals.Bacterial Infections: Infections by bacteria, general or unspecified.Anti-Bacterial Agents: Substances that reduce the growth or reproduction of BACTERIA.Streptococcus: A genus of gram-positive, coccoid bacteria whose organisms occur in pairs or chains. No endospores are produced. Many species exist as commensals or parasites on man or animals with some being highly pathogenic. A few species are saprophytes and occur in the natural environment.Virulence: The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.Pneumococcal Infections: Infections with bacteria of the species STREPTOCOCCUS PNEUMONIAE.Polysaccharides, Bacterial: Polysaccharides found in bacteria and in capsules thereof.PolysaccharidesIgG Deficiency: A dysgammaglobulinemia characterized by a deficiency of IMMUNOGLOBULIN G.Bacterial Capsules: An envelope of loose gel surrounding a bacterial cell which is associated with the virulence of pathogenic bacteria. Some capsules have a well-defined border, whereas others form a slime layer that trails off into the medium. Most capsules consist of relatively simple polysaccharides but there are some bacteria whose capsules are made of polypeptides.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Antibodies, Bacterial: Immunoglobulins produced in a response to BACTERIAL ANTIGENS.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Wireless Technology: Techniques using energy such as radio frequency, infrared light, laser light, visible light, or acoustic energy to transfer information without the use of wires, over both short and long distances.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Gene Transfer, Horizontal: The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).AT Rich Sequence: A nucleic acid sequence that contains an above average number of ADENINE and THYMINE bases.Bacterial Proteins: Proteins found in any species of bacterium.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Buchnera: A genus of gram-negative bacteria which are obligately intracellular endosymbionts of APHIDS. The bacteria are found within specialized cells in the aphid body cavity.Aphids: A family (Aphididae) of small insects, in the suborder Sternorrhyncha, that suck the juices of plants. Important genera include Schizaphis and Myzus. The latter is known to carry more than 100 virus diseases between plants.Symbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Gene Transfer Techniques: The introduction of functional (usually cloned) GENES into cells. A variety of techniques and naturally occurring processes are used for the gene transfer such as cell hybridization, LIPOSOMES or microcell-mediated gene transfer, ELECTROPORATION, chromosome-mediated gene transfer, TRANSFECTION, and GENETIC TRANSDUCTION. Gene transfer may result in genetically transformed cells and individual organisms.

Chemokine mRNA expression in gastric mucosa is associated with Helicobacter pylori cagA positivity and severity of gastritis. (1/25659)

AIM: To investigate the association between the quantity of gastric chemokine mRNA expression, severity of gastritis, and cagA positivity in Helicobacter pylori associated gastritis. METHODS: In 83 dyspeptic patients, antral and corpus biopsies were taken for semiquantitative reverse transcription polymerase chain reaction (RT-PCR) and histological grading of gastritis. Gastritis was evaluated by visual analogue scales. Quantities of chemokine (IL-8, GRO alpha, ENA-78, RANTES, MCP-1) RT-PCR products were compared with G3PDH products. Each sample was also evaluated for the presence of cagA and ureA mRNA by RT-PCR. RESULTS: mRNA expression of all five chemokines was significantly greater in H pylori positive than in H pylori negative mucosa. In H pylori positive patients, in the antrum C-X-C chemokine mRNA expression was significantly greater in cagA positive patients than in cagA negative patients, but there were no significant differences in C-C chemokine mRNA expression. In H pylori positive patients, chemokine mRNA expression in the corpus was less than in the antrum. In contrast to the antrum, only GRO alpha mRNA expression was significantly greater in cagA positive infection. Polymorphonuclear cell infiltration was correlated with C-X-C chemokine mRNA expression. Significant correlations were also found between bacterial density and C-X-C chemokine mRNA expression. CONCLUSIONS: In H pylori infection, C-X-C chemokines may play a primary role in active gastritis. Infection with cagA positive H pylori induces greater gastric chemokine mRNA expression in the antral mucosa, which may be relevant to the increased mucosal damage associated with cagA positive H pylori infection.  (+info)

Evolutionary relationships of pathogenic clones of Vibrio cholerae by sequence analysis of four housekeeping genes. (2/25659)

Studies of the Vibrio cholerae population, using molecular typing techniques, have shown the existence of several pathogenic clones, mainly sixth-pandemic, seventh-pandemic, and U.S. Gulf Coast clones. However, the relationship of the pathogenic clones to environmental V. cholerae isolates remains unclear. A previous study to determine the phylogeny of V. cholerae by sequencing the asd (aspartate semialdehyde dehydrogenase) gene of V. cholerae showed that the sixth-pandemic, seventh-pandemic, and U.S. Gulf Coast clones had very different asd sequences which fell into separate lineages in the V. cholerae population. As gene trees drawn from a single gene may not reflect the true topology of the population, we sequenced the mdh (malate dehydrogenase) and hlyA (hemolysin A) genes from representatives of environmental and clinical isolates of V. cholerae and found that the mdh and hlyA sequences from the three pathogenic clones were identical, except for the previously reported 11-bp deletion in hlyA in the sixth-pandemic clone. Identical sequences were obtained, despite average nucleotide differences in the mdh and hlyA genes of 1.52 and 3.25%, respectively, among all the isolates, suggesting that the three pathogenic clones are closely related. To extend these observations, segments of the recA and dnaE genes were sequenced from a selection of the pathogenic isolates, where the sequences were either identical or substantially different between the clones. The results show that the three pathogenic clones are very closely related and that there has been a high level of recombination in their evolution.  (+info)

A 55-kilodalton immunodominant antigen of Porphyromonas gingivalis W50 has arisen via horizontal gene transfer. (3/25659)

A 55-kDa outer membrane protein of Porphyromonas gingivalis W50 is a significant target of the serum immunoglobulin G antibody response of periodontal disease patients and hence may play an important role in host-bacterium interactions in periodontal disease. The gene encoding the 55-kDa antigen (ragB, for receptor antigen B) was isolated on a 9.5-kb partial Sau3AI fragment of P. gingivalis W50 chromosomal DNA in pUC18 by immunoscreening with a monoclonal antibody to this antigen. The 1.6-kb open reading frame (ORF) encoding RagB was located via subcloning and nested-deletion analysis. Sequence analysis demonstrated the presence of an upstream 3.1-kb ORF (ragA) which is cotranscribed with ragB. A number of genetic characteristics suggest that the ragAB locus was acquired by a horizontal gene transfer event. These include a significantly reduced G+C content relative to that of the P. gingivalis chromosome (42 versus 48%) and the presence of mobility elements flanking this locus in P. gingivalis W50. Furthermore, Southern blotting and PCR analyses showed a restricted distribution of this locus in laboratory and clinical isolates of this bacterium. The association of ragAB+ P. gingivalis with clinical status was examined by PCR analysis of subgingival samples. ragAB+ was not detected in P. gingivalis-positive shallow pockets from periodontal disease patients but was present in 36% of the P. gingivalis-positive samples from deep pockets. These data suggest that the ragAB locus was acquired by certain P. gingivalis strains via horizontal gene transfer and that the acquisition of this locus may facilitate the survival of these strains at sites of periodontal destruction.  (+info)

Cloning and expression of the dnaK gene of Campylobacter jejuni and antigenicity of heat shock protein 70. (4/25659)

Campylobacter jejuni is a leading cause of infectious diarrhea throughout the world. In addition, there is growing evidence that Guillain-Barre syndrome, an inflammatory demyelinating disease of the peripheral nervous system, is frequently preceded by C. jejuni infection. In the present study, the hrcA-grpE-dnaK gene cluster of C. jejuni was cloned and sequenced. The dnaK gene consists of an open reading frame of 1,869 bp and encodes a protein with a high degree of homology to other bacterial 70-kDa heat shock proteins (HSPs). The overall percentages of identity to the HSP70 proteins of Helicobacter pylori, Borrelia burgdorferi, Chlamydia trachomatis, and Bacillus subtilis were calculated to be 78.1, 60.5, 57.2, and 53. 8%, respectively. Regions similar to the Escherichia coli sigma70 promoter consensus sequence and to a cis-acting regulatory element (CIRCE) are located upstream of the hrcA gene. Following heat shock, a rapid increase of dnaK mRNA was detectable, which reached its maximum after 20 to 30 min. A 6-His-tagged recombinant DnaK protein (rCjDnaK-His) was generated in E. coli, after cloning of the dnaK coding region into pET-22b(+), and purified by affinity and gel filtration chromatography. Antibody responses to rCjDnaK-His were significantly elevated, compared to those of healthy individuals, in about one-third of the serum specimens obtained from C. jejuni enteritis patients.  (+info)

Yops of Yersinia enterocolitica inhibit receptor-dependent superoxide anion production by human granulocytes. (5/25659)

The virulence plasmid-borne genes encoding Yersinia adhesin A (YadA) and several Yersinia secreted proteins (Yops) are involved in the inhibition of phagocytosis and killing of Yersinia enterocolitica by human granulocytes. One of these Yops, YopH, dephosphorylates multiple tyrosine-phosphorylated proteins in eukaryotic cells and is involved in the inhibition of phagocytosis of Y. enterocolitica by human granulocytes. We investigated whether antibody- and complement-opsonized plasmid-bearing (pYV+) Y. enterocolitica inhibits O2- production by human granulocytes in response to various stimuli and whether YopH is involved. Granulocytes were preincubated with mutant strains unable to express YadA or to secrete Yops or YopH. O2- production by granulocytes during stimulation was assessed by measuring the reduction of ferricytochrome c. PYV+ Y. enterocolitica inhibited O2- production by granulocytes incubated with opsonized Y. enterocolitica or N-formyl-Met-Leu-Phe (f-MLP). This inhibitory effect mediated by pYV did not affect receptor-independent O2- production by granulocytes in response to phorbol myristate acetate, indicating that NADPH activity remained unaffected after activation of protein kinase C. The inhibition of f-MLP-induced O2- production by granulocytes depends on the secretion of Yops and not on the expression of YadA. Insertional inactivation of the yopH gene abrogated the inhibition of phagocytosis of antibody- and complement-opsonized Y. enterocolitica by human granulocytes but not of the f-MLP-induced O2- production by granulocytes or tyrosine phosphorylation of granulocyte proteins. These findings suggest that the specific targets for YopH are not present in f-MLP receptor-linked signal transduction and that other Yop-mediated mechanisms are involved.  (+info)

Complete nucleotide sequence of the 27-kilobase virulence related locus (vrl) of Dichelobacter nodosus: evidence for extrachromosomal origin. (6/25659)

The vrl locus is preferentially associated with virulent isolates of the ovine footrot pathogen, Dichelobacter nodosus. The complete nucleotide sequence of this 27.1-kb region has now been determined. The data reveal that the locus has a G+C content much higher than the rest of the D. nodosus chromosome and contains 22 open reading frames (ORFs) encoding products including a putative adenine-specific methylase, two potential DEAH ATP-dependent helicases, and two products with sequence similarity to a bacteriophage resistance system. These ORFs are all in the same orientation, and most are either overlapping or separated by only a few nucleotides, suggesting that they comprise an operon and are translationally coupled. Expression vector studies have led to the identification of proteins that correspond to many of these ORFs. These data, in combination with evidence of insertion of vrl into the 3' end of an ssrA gene, are consistent with the hypothesis that the vrl locus was derived from the insertion of a bacteriophage or plasmid into the D. nodosus genome.  (+info)

Genetic characterization of a new type IV-A pilus gene cluster found in both classical and El Tor biotypes of Vibrio cholerae. (7/25659)

The Vibrio cholerae genome contains a 5.4-kb pil gene cluster that resembles the Aeromonas hydrophila tap gene cluster and other type IV-A pilus assembly operons. The region consists of five complete open reading frames designated pilABCD and yacE, based on the nomenclature of related genes from Pseudomonas aeruginosa and Escherichia coli K-12. This cluster is present in both classical and El Tor biotypes, and the pilA and pilD genes are 100% conserved. The pilA gene encodes a putative type IV pilus subunit. However, deletion of pilA had no effect on either colonization of infant mice or adherence to HEp-2 cells, demonstrating that pilA does not encode the primary subunit of a pilus essential for these processes. The pilD gene product is similar to other type IV prepilin peptidases, proteins that process type IV signal sequences. Mutational analysis of the pilD gene showed that pilD is essential for secretion of cholera toxin and hemagglutinin-protease, mannose-sensitive hemagglutination (MSHA), production of toxin-coregulated pili, and colonization of infant mice. Defects in these functions are likely due to the lack of processing of N termini of four Eps secretion proteins, four proteins of the MSHA cluster, and TcpB, all of which contain type IV-A leader sequences. Some pilD mutants also showed reduced adherence to HEp-2 cells, but this defect could not be complemented in trans, indicating that the defect may not be directly due to a loss of pilD. Taken together, these data demonstrate the effectiveness of the V. cholerae genome project for rapid identification and characterization of potential virulence factors.  (+info)

Characterization of Moraxella (Branhamella) catarrhalis lbpB, lbpA, and lactoferrin receptor orf3 isogenic mutants. (8/25659)

Pathogenic members of the family Neisseriaceae produce specific receptors to acquire iron from their host's lactoferrin and transferrin. Recently, putative Moraxella catarrhalis lactoferrin receptor genes and a third open reading frame (lbpB, lbpA, and orf3) were cloned and sequenced. We describe the preliminary characterization of isogenic mutants deficient in LbpB, LbpA, or Orf3 protein.  (+info)

  • Bacterial genomes are known to harbor pseudogenes. (genetics.org)
  • For instance, in plant mitochondrial genomes, which have an α-proteobacterial ancestry, most, if not all, of the laterally transferred genes are pseudogenes ( R ichardson and P almer 2007 ). (genetics.org)
  • and most of them are transient in bacterial genomes ( L erat and O chman 2005 ). (genetics.org)
  • reported that genomes with truncated homologs might erroneously lead to false inferences of "gene gain" rather than multiple instances of "gene loss. (genetics.org)
  • The team set out to sequence the genomes of 112 B. dolosa isolates taken from 14 of the infected patients, mapping genetic changes over time to reveal both the route of the infection's spread and which genes faced the greatest selective pressure - in other words, how the bacteria evolved when challenged by human defenses and medical treatment. (innovations-report.com)
  • In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. (mdpi.com)
  • In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods. (mdpi.com)
  • Inadvertently incorporated into the genomes of their edited mouse cells they found DNA from the E.coli genome (a bacterium) and from the cow genome, along with goat DNA.The researchers traced this adventitious presence to contaminants of standard components of the gene-editing process, such as cell culture media. (biofuelsdigest.com)
  • The stx genes carried by STEC strains are, with one possible exception (stx2e), encoded on bacteriophage genomes integrated into the bacterial chromosome. (cdc.gov)
  • The location of stx genes (predominantly on λ-like bacteriophage genomes integrated into the chromosome of their host bacterium) has important implications because the induction of the SOS response, an extensively characterized genetic regulatory mechanism, induces high-level expression of previously silent bacteriophage genes ( 9 ). (cdc.gov)
  • The correct taxonomic assignment of bacterial genomes is a primary and challenging task. (biomedcentral.com)
  • In this study, we have proposed a comprehensive method which uses the taxon-specific genes for the correct taxonomic assignment of existing and new bacterial genomes. (biomedcentral.com)
  • The taxon-specific genes identified at each taxonomic rank have been successfully used for the taxonomic classification of 2,342 genomes present in the NCBI genomes, 36 newly sequenced genomes, and 17 genomes for which the complete taxonomy is not yet known. (biomedcentral.com)
  • This approach has been implemented for the development of a tool 'Microtaxi' which can be used for the taxonomic assignment of complete bacterial genomes. (biomedcentral.com)
  • The taxon-specific gene based approach provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes. (biomedcentral.com)
  • However, genomes harbor two very different categories of genes: those genes present in a majority of organisms - persistent genes - and those present in very few organisms - rare genes. (biomedcentral.com)
  • We show that two classes of genes are significantly clustered in bacterial genomes: the highly persistent and the rare genes. (biomedcentral.com)
  • Yet, genes persistently present in bacterial genomes are also clustered and we try to understand why. (biomedcentral.com)
  • We show that the strong selective pressure acting on the function of persistent genes, in a permanent state of flux of genes in bacterial genomes, maintaining their size fairly constant, that drives persistent genes clustering. (biomedcentral.com)
  • The availability of a rapidly increasing number of completely sequenced bacterial genomes makes it possible to explore gene order conservation in related and distant species. (biomedcentral.com)
  • Hypotheses accounting for the clustering of genes in genomes basically break into three main categories. (biomedcentral.com)
  • It mainly concerned developing a program that reads in the sequences of all genes present on a specified set of bacterial genomes and then creates clusters of related genes. (sharcnet.ca)
  • The broadened scope of sequenced bacterial genomes to include also free-living and environmental species provided a larger sample to analyze the bacterial SET domain genes. (unl.edu)
  • Trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. (asm.org)
  • The available data from several systematic experimental approaches to define all the essential genes in some completely sequenced bacterial genomes were also considered, and a reconstruction of a minimal metabolic machinery necessary to sustain life was carried out. (asm.org)
  • Comparative genomics shows that most bacterial proteins are highly conserved in evolution, allowing predictions to be made about the functions of most products of uncharacterized genomes based on model organisms, such as Escherichia coli and Bacillus subtilis (gram-positive and gram-negative bacteria, respectively), for which abundant high-quality genetic and biochemical information has been obtained in the past. (asm.org)
  • Although bacterial genomes differ vastly in their sizes and gene repertoires, no matter how small, they must contain all the information to allow the cell to perform many essential (housekeeping) functions that give the cell the ability to maintain metabolic homeostasis, reproduce, and evolve, the three main properties of living cells ( 53 ). (asm.org)
  • Reconstruction of the minimal gene set can take advantage of the increasing knowledge of completely characterized genomes. (asm.org)
  • We analyze hundreds of bacterial genomes and find that the coding sequences of highly expressed genes systematically contain fewer SD sequences than expected, yielding a robust correlation between the normalized occurrence of SD sites and protein abundances across a range of bacterial taxa. (g3journal.org)
  • Among the latter, virulence genes and genes encoding the bacterial cell wall elements have been prone to serial gene deletions, as evidenced in insect endosymbiont genomes sequenced so far ( 1 , 15 , 34 ). (pubmedcentralcanada.ca)
  • They speculated that bacterial effector proteins transferred to target cells via Type VI secretion systems might be especially effectively maintained in eukaryotic genomes. (evmedreview.com)
  • ARG-ANNOT (Antibiotic Resistance Gene-ANNOTation) is a new bioinformatic tool that was created to detect existing and putative new antibiotic resistance (AR) genes in bacterial genomes. (asm.org)
  • Finally, the analysis of 178 Acinetobacter baumannii and 20 Staphylococcus aureus genomes allowed the detection of a significantly higher number of AR genes than the Resfinder gene analyzer and 11 point mutations in target genes known to be associated with AR. (asm.org)
  • We have created a concise database for BLAST using a Bio-Edit interface that can detect AR genetic determinants in bacterial genomes and can rapidly and easily discover putative new AR genetic determinants. (asm.org)
  • Next-generation sequencing technologies have greatly reduced the cost for sequencing bacterial genomes and metagenomes and have increased the likelihood of rapid whole-bacterial-genome sequencing in clinical microbiology laboratories ( 1 ). (asm.org)
  • An exponential increase in genome releases has occurred as more and more bacterial genomes are sequenced in a short time span. (asm.org)
  • Moreover, because released sequences are not always complete sequences (for both bacterial genomes and metagenomes), sequence analysis and annotation should be performed on contigs or short sequences to detect putative functions, especially for AR genes. (asm.org)
  • Background: Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. (diva-portal.org)
  • Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. (biomedcentral.com)
  • It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies of prokaryotic genomes. (biomedcentral.com)
  • In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation. (biomedcentral.com)
  • By analyzing 21 Escherichia genomes, we confirm that genes coding for secreted proteins-the secretome-are very frequently lost and gained and are associated with mobile elements. (uzh.ch)
  • The Glimmer gene-finding software has been successfully used for finding genes in bacteria, archaea and viruses representing hundreds of species. (nih.gov)
  • The new methods dramatically reduce the rate of false-positive predictions, while maintaining Glimmer's 99% sensitivity rate at detecting genes in most species, and they find substantially more correct start sites, as measured by comparisons to known and well-curated genes. (nih.gov)
  • GSIII genes have been found in only a few bacterial species. (springer.com)
  • In order to study the evolution of GS, we cloned and sequenced GSI genes from two divergent archaeal species: the extreme thermophile Pyrococcus furiosus and the extreme halophile Haloferax volcanii . (springer.com)
  • We suspect that the similarity of GSI-α genes from Euryarchaeota and several bacterial species does not reflect a common phylogeny but rather lateral transmission between archaea and bacteria. (springer.com)
  • There's a large pool of bacterial species whose sodium channels might have slightly different electrical characteristics to draw from," said Nguyen. (eurekalert.org)
  • This method is of general use since there are a number of suitable vectors and polA strains are available in both Escherichia coli and Salmonella typhimurium, the two most widely studied bacterial species. (pnas.org)
  • Jennifer Tsang and Timothy R. Hoover, "Themes and Variations: Regulation of RpoN-Dependent Flagellar Genes across Diverse Bacterial Species," Scientifica , vol. 2014, Article ID 681754, 14 pages, 2014. (hindawi.com)
  • Methods of allele frequency analysis developed for use in studies of animal and plant populations are, in principle, applicable to bacterial species as well. (genetics.org)
  • Using molecular typing methods it is now also possible to survey the genetic variation of a bacterial species in its natural environment. (genetics.org)
  • The results indicate that the method should be applicable to any non-essential gene in numerous bacterial species. (nih.gov)
  • The discovery suggests not only that edited organisms may acquire random foreign DNA, but that present methods of gene-editing can transmit genetic elements, viruses, and other pathogenic agents between species. (biofuelsdigest.com)
  • More than 700 types of bacterial species have been detected in the oral cavity, and some have been identified to play a significant role in the development of oral disease. (clinicaltrials.gov)
  • To demonstrate the effectiveness of RNA later at preserving RNA in intact bacteria, samples from five bacterial species, Escherichia coli, Pseudomonas aeruginosa, Campylobacter fetus, Bacillus subtilis and Staphylococcus aureus, were suspended in RNAlater and incubated at 25°C or 4°C for up to one week. (thermofisher.com)
  • However, studies examining the effect of macrolactin on both the soil bacterial community and the intrinsic bacterial species that harbor genes responsible for the production of this antibiotic have not been conducted so far. (frontiersin.org)
  • Moreover, the populations of the intrinsic bacterial species which harbor genes responsible for macrolactin production were inhibited when the external source antibiotic was applied. (frontiersin.org)
  • Agrobacterium tumefaciens , which causes tumorigenic diseases in many plant species, requires a Ca 2+ -dependent adhesin ( 35 ), a repertoire of proteins encoded by att genes ( 22 , 23 ), exo- and capsular polysaccharides ( 30 ), and cellulose fibrils ( 21 , 22 ) to attach to roots. (asm.org)
  • Several computational approaches have been proposed for the taxonomic assignment of bacterial species. (biomedcentral.com)
  • Mapping Heat Resistance in Yeasts In a proof-of-concept study, researchers demonstrated that a new genetic mapping strategy called RH-Seq can identify genes that promote heat resistance in the yeast Saccharomyces cerevisiae, allowing this species to grow better than its closest relative S. paradoxus at high temperatures. (doe.gov)
  • First Monoploid Reference Sequence of Sugarcane For the highly polyploid sugarcane, an international team of researchers has successfully assembled a first monoploid reference sequence using a targeted approach that focused on the gene rich part of the genome by harnessing information from a sequenced related species - sorghum. (doe.gov)
  • Complete genome sequences are becoming available for a large number of diverse bacterial species. (asm.org)
  • Of the four tae genes found in bacterial species, three have been transferred to one or another eukaryotic genome. (evmedreview.com)
  • Third, the authors acquired evidence for expression of the dae genes in a species of ameba. (evmedreview.com)
  • They also found previously published evidence for dae gene expression in a species of lancelet, a small marine organism. (evmedreview.com)
  • Fourth, several examples of eukaryotic Dae proteins from tick, ameba, and lancelet species were tested for the ability to enzymatically degrade peptidoglycan, a major component in bacterial cell walls. (evmedreview.com)
  • did not find any evidence for transfer of bacterial housekeeping amidases to eukaryotic species. (evmedreview.com)
  • The 16S rDNA sequencing was carried out to correlate the phylogenetic relationship of P. fluorescens with other bacterial species after treatment. (vixra.org)
  • Based on nucleotides homology and phylogenetic analysis using 16S rDNA gene sequencing, treated sample was detected to be Pseudomonas entomophila (GenBank Accession Number: AY907566) with 96% identity of gene sequencing data, which was nearest homolog species to P. fluorescens (Accession No. EF672049). (vixra.org)
  • Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including Escherichia coli, the model pathogen Salmonella, the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis (the causative agent of tularaemia), Streptococcus pyogenes, the pathogen Staphylococcus aureus, and the plant pathogen Xanthomonas oryzae pathovar oryzae. (wikipedia.org)
  • The Staphylococcus enterotoxin A ( sea ) gene carried by virulent strains of S. aureus is encoded by multiple phages, including ϕ 11, ϕ 12, ϕ 13, 80 α , and 42D [ 18 - 21 ]. (hindawi.com)
  • Bacterial Strains and Culture. (pnas.org)
  • A general system is described that facilitates gene replacements such that the recombinant strains are not labelled with antibiotic resistance genes. (nih.gov)
  • To better understand UTIs and potentially offer new therapeutic strategies, a team of researchers analyzed 43 strains of E . coli sampled from 14 women with recurrent UTIs, and found that infection depends on both individual host susceptibility and how the bacteria express their genes. (broadinstitute.org)
  • Among the characterized genes were strains with insertions in the intergenic region between agfB , the surface-exposed aggregative fimbria (curli) nucleator, and agfD , a transcriptional regulator of the LuxR superfamily, and rpoS , the stationary-phase sigma factor. (asm.org)
  • Our hypothesis is that acquisition of copper hyper-resistance via horizontal gene transfer plays a crucial role in the emergence of S. aureus strains, and potentially other pathogenic bacteria, with increased infectivity conferred through their improved resistance to the copper-dependent killing mechanisms of the host's immune cells. (findaphd.com)
  • Many exotoxin genes are carried on mobile genetic elements, including bacterial viruses (bacteriophage or phage). (hindawi.com)
  • As highly mobile genetic elements, phage can readily move between different environments, and are generally more resistant to environmental stress than their bacterial counterparts [ 4 - 11 ]. (hindawi.com)
  • A team led by a plant pathologist at the University of California, Riverside, has identified a regulatory, genetic mechanism in plants that could help fight bacterial infection. (phys.org)
  • Recent breakthroughs in molecular technology, most significantly the polymerase chain reaction (PCR) and in situ hybridization, have allowed the detection of genetic variation in bacterial communities without prior cultivation. (genetics.org)
  • A genetic system was devised that positively selects for bacterial genes that are specifically induced when bacteria infect their host. (sciencemag.org)
  • This genetic system was designed to be of general use in a wide variety of bacterial-host systems and has several applications in both vaccine and antimicrobial drug development. (sciencemag.org)
  • He used a genetic reporter that fluoresces or generates a color when the gene cluster is activated to easily identify positive hits. (phys.org)
  • A new discovery by researchers at Columbia University Vagelos College of Physicians and Surgeons could fix one of the major shortcomings of current gene-editing tools, including CRISPR, and offer a powerful new approach for genetic engineering and gene therapy. (biotechnews.com.au)
  • This makes gene editing difficult or impossible in some cell types, and severely constrains researchers' ability to introduce precise genetic modifications in a safe manner. (biotechnews.com.au)
  • This transposon has co-opted the bacterium's CRISPR-Cas system, normally used to thwart mobile genetic elements, to insert itself into different regions of the bacterial genome. (biotechnews.com.au)
  • Insights into Functional Diversity in Neurospora This proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi. (doe.gov)
  • The proposed minimal genome contains 206 protein-coding genes with all the genetic information necessary for self-maintenance and reproduction in the presence of a full complement of essential nutrients and in the absence of environmental stress. (asm.org)
  • Horizontal gene transfer rapidly changes bacterial genetic repertoire and contributes to bacterial evolution. (illinois.edu)
  • CONCLUSION: Our analysis matches the predictions of our model suggesting that horizontal transfer promotes cooperation, as transmission increases local genetic relatedness at mobile loci and enforces cooperation on the resident genes. (uzh.ch)
  • Cis-acting sRNAs interact with genes encoded on the same genetic locus as the sRNA. (wikipedia.org)
  • Bacterial transcription is the process in which messenger RNA transcripts of genetic material in bacteria are produced, to be translated for the production of proteins. (wikipedia.org)
  • Behrmann I, Hillemann D, Pühler A, Strauch E, Wohlleben W (1990) Overexpression of a Streptomyces viridochromogenes gene ( glnII ) encoding a glutamine synthetase similar to those of eucaryotes confers resistance against the antibiotic phosphinothricyl-alanylalanine. (springer.com)
  • Known as 'horizontal gene transfer', this phenomenon is understood to have played a role in developing the global antimicrobial resistance (AMR) crisis. (eurekalert.org)
  • The HMS professor of systems biology studies bacterial evolution, exploring such questions as how antibiotic resistance arises. (innovations-report.com)
  • The finding provides a novel target for drugs that could minimize the incidence of bacterial resistance. (medindia.net)
  • Detailed antibiotic resistance gene (ARG) surveillance at regional, national, and global scale is required for the development of strategies aiming to mitigate this health threat. (nature.com)
  • In this study, we compared the structure of the fecal microbiota between feral and domestic goats using the G2 PhyloChip and assessed the presence of five tetracycline resistance genes [ tet (M), tet (S), tet (O), tet (Q) and tet (W)] by PCR. (mdpi.com)
  • Both feral and domestic goats carried antibiotic resistance genes tet (O) and tet (W), but domestic goats additionally carried tet (Q). Diet, host genetics and antibiotic exposure are likely determinant factors in shaping the intestinal microbiota and may explain the differences observed between feral and domestic goats fecal microbiota. (mdpi.com)
  • The problem is i am using a suicide vector pFS100 a derivative of pGP704 carrying a 'pir' dependent origin of replication from plasmid R6K and gene encoding resistance to ampicillin and kanamycin but no sacB gene marker in it. (protocol-online.org)
  • The rice xa5 gene for disease resistance to Xanthomonas oryzae pv. (apsnet.org)
  • xa5 is unusual in that it is recessive and does not conform to one of the typical resistance gene structural classes. (apsnet.org)
  • However, the discovery in the 1970s of spiroplasmas, very small, thermostable, wall-less, helical-fibrillar bacteria that pass through 0.2-μm bacterial filters and show remarkable resistance to many common biocides including heat ( 47 ), provided a possible bacterial candidate for the infectious agent of TSEs. (asm.org)
  • Prevalence of sulfonamide resistance genes in bacterial isolates from manured agricultural soils and pig slurry in the United Kingdom. (sigmaaldrich.com)
  • The prevalences of three sulfonamide resistance genes, sul1, sul2, and sul3 and sulfachloropyridazine (SCP) resistance were determined in bacteria isolated from manured agricultural clay soils and slurry samples in the United Kingdom over a 2-year period. (sigmaaldrich.com)
  • Our data show that this novel, horizontally gene transferred copper resistance locus is associated with the SCCmec elements of USA300. (findaphd.com)
  • These genes are additional to existing core genome copper resistance mechanisms, and are not found in typical S. aureus lineages, but are increasingly identified in emerging pathogenic isolates. (findaphd.com)
  • Multiple genes for heavy metal resistance have been identified in L. monocytogenes. (findaphd.com)
  • 2018 A horizontally gene transferred copper resistance locus confers hyper-resistance to antibacterial copper toxicity and enables survival of community acquired methicillin resistant Staphylococcus aureus USA300 in macrophages. (findaphd.com)
  • Bacterial superintegrons, a source of new genes with adaptive functions Ilyina, T. 2006-11-07 00:00:00 Data on the structural organization of the platform of integrons, gene cassettes, and integrons with integrated cassettes of genes encoding drug resistance are briefly summarized. (deepdyve.com)
  • Data obtained during recent years about superintegrons or chromosomal integrons, characteristics of their organization, the presence of genes with known adaptive and unidentified functions in them, as well as data on the differences between superintegrons and previously described multiple resistance integrons, are considered in more detail. (deepdyve.com)
  • Data on the structural organization of the platform of integrons, gene cassettes, and integrons with integrated cassettes of genes encoding drug resistance are briefly summarized. (deepdyve.com)
  • CRISPR-Cas9 gene drives to eradicate antimicrobial resistance from bacterial communities. (findaphd.com)
  • The most important resistance mechanisms are carried on plasmids, which are mobile DNA elements that can spread by horizontal gene transfer within bacterial populations. (findaphd.com)
  • This project "CRISPR-Cas9 gene drives to eradicate antimicrobial resistance from bacterial communities" will develop a recently discovered bacterial immune system called CRISPR-Cas to target and destroy mobile bacterial resistance plasmids. (findaphd.com)
  • After building a database that includes 1,689 antibiotic resistance genes, the software was tested in a blind manner using 100 random sequences selected from the database to verify that the sensitivity and specificity were at 100% even when partial sequences were queried. (asm.org)
  • RAST also provides little information about antibiotic resistance (AR) genes. (asm.org)
  • A set of resistance-gene analog (RGA) sequences identified 121 RGA-containing BAC clones representing 20 different regions of the genome with an average of 6.1 clones per locus. (arizona.edu)
  • Researchers at Harvard Medical School and Children's Hospital Boston have retraced the evolution of an unusual bacterial infection as it spread among cystic fibrosis patients by sequencing scores of samples collected during the outbreak, since contained. (innovations-report.com)
  • Cystic fibrosis (CF) is a hereditary disease that renders the lungs susceptible to bacterial infection. (innovations-report.com)
  • An important gene in bacterial infection has been discovered by researchers at Osaka University use molecular-level analyses of evolution. (medindia.net)
  • Over the course of evolution, hosts--such as humans--develop increasingly sophisticated defenses against bacterial infection, while bacteria in turn develop new strategies to overcome these defenses in a biological arms race. (medindia.net)
  • The team used molecular evolutionary analysis of gene sequences to identify a gene that has been largely prevented from mutating into other variant forms, suggesting that it is essential for the infection and/or reproduction of this bacterium. (medindia.net)
  • Impetigo is a contagious bacterial skin infection mostly affecting children and is characterized by blister-like sores that could form pus and later scabs. (medindia.net)
  • A new study reveals that the multipotent stromal cells (MSCs) of persons with diabetes have diminished capacity to fight off bacterial infection, providing new understanding into the basis of diabetes-associated immune dysfunction. (phys.org)
  • Discovery of a gene that helps plants control their response to disease could aid efforts to develop crops that are resistant to infection, research suggests. (phys.org)
  • In this study, a maximum-likelihood estimator (MLE) of bacterial allele frequencies designed for use with presence-absence data is derived using an explicit stochastic model of the host infection (or bacterial sampling) process. (genetics.org)
  • The group where the gene for Toll2 was switched off, survived the bacterial infection," says Wiersinga. (infectioncontroltoday.com)
  • Because the concentration of scrapie infectivity was at a known high level, it is very unlikely that a bacterial infection at the same concentration could have escaped detection. (asm.org)
  • Further comparative genomic and transcriptomic analyses showed infection severity correlated with the expression levels of certain genes shared by nearly all E . coli , including genes involved in motility and nutrient utilization. (broadinstitute.org)
  • That's really important for clinicians because if they see a pattern of gene expression that indicates a viral infection, they could feel comfortable not prescribing antibiotics," Storch added. (healthcanal.com)
  • The very active genes tell us that an infection is making a patient sick, while quiet genes tell us either there's no infection or maybe a bacterium or virus is there, but it's not causing fever or illness. (healthcanal.com)
  • Whole genome sequencing projects, together with more targeted studies, have identified hundreds of DNA-binding proteins that contribute to the patterns of gene expression observed during infection as well as providing important insights into the nature of the gene products whose expression is being controlled by these proteins. (clinsci.org)
  • The researchers are continuing to analyze the effects of bacterial infection on immune system cells known as macrophages to determine how the bacteria could breach the blood-brain barrier. (ufl.edu)
  • I check for the gene knockout in 'centrimide+kan+amp' plate with PAO1 using the gene inserted suicide vector pFS100 and get no growth (showing the gene is essential) whereas the control plate without antibiotic markers show growth. (protocol-online.org)
  • Gene clustering plays an important role in the organization of the bacterial chromosome and several mechanisms have been proposed to explain its extent. (biomedcentral.com)
  • During this process, genes within batches coding for coupled functions will have a higher chance of increasing the organism fitness, and thus their own, than uncoupled genes, which would require pre-existence of the interacting partners in the chromosome. (biomedcentral.com)
  • Examples : Integration of bacteriophage DNA into host bacterial chromosome Immunoglobulin and T Cell Receptor genes DNA rearrangements via Transposition involves the movement of sequences throughout the genome and has no requirement for sequence homology. (coursehero.com)
  • To develop the resources for positional cloning and structural genomic analyses in barley, we constructed a bacterial artificial chromosome (BAC) library for the cultivar Morex using the cloning enzyme HindIII. (arizona.edu)
  • Addgene: Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes. (addgene.org)
  • A wide variety of mechanisms that control gene expression in bacteria are based on conditional transcription termination. (asm.org)
  • Generally, in these mechanisms, a transcription terminator is located between a promoter and a downstream gene(s), and the efficiency of the terminator is controlled by a regulatory effector that can be a metabolite, protein, or RNA. (asm.org)
  • The changes in gene expression correlate positively with both epigenetic changes and chromatin accessibility of promoters at transcription start sites of genes induced by both types of membrane vesicles. (uio.no)
  • An experimental‐computational approach is applied to dissect the contribution of specific transcription factor‐mediated versus global growth‐dependent regulation to bacterial gene expression, and obtain a quantitative understanding of dynamic adaptations in arginine biosynthesis of E. coli . (embopress.org)
  • We present a model‐based approach to quantitatively dissect simultaneous contributions from specific transcription factors and the global growth status to bacterial gene expression, based on parameter inference from GFP‐based promoter activity measurements. (embopress.org)
  • Real-time reverse transcription-PCR quantification of the wPGRP gene transcript performed at different points in insect development has shown a high steady-state level in the bacteria-bearing organ (the bacteriome) of larvae and a high level of wPGRP up-regulation in the symbiotic nymphal phase. (pubmedcentralcanada.ca)
  • In addition to the receiver domain, Skn7 also contains a DNA binding and transcription activation domain, which is analogous to that found in most bacterial response regulators. (plantcell.org)
  • The direction of transcription is represented by arrows, and gene names are indicated. (asm.org)
  • The active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25D), plays an important immunomodulatory role, regulating transcription of genes in the innate and adaptive immune system. (g3journal.org)
  • Therefore, the present study aimed to evaluate the effects of copper and bacterial lipopolysaccharide (LPS), alone and in combination, on the transcription of target genes related with immune system, respiratory burst activity and cell death, using rainbow trout macrophages as in vitro model. (stir.ac.uk)
  • This unit provides a chronological in‐depth description of all protocols needed for quantitative reverse transcription-PCR (Q‐RT‐PCR) analysis of Borrelia burgdorferi gene expression within infected mouse tissues. (currentprotocols.com)
  • Alternately, sRNAs may interact with mRNA targets and regulate gene expression by binding to complementary mRNA and blocking transcription, or by unmasking or blocking the ribosome-binding site. (wikipedia.org)
  • Bozouklian H, Elmerich C (1986) Nucleotide sequence of the AzospirMum brasilense Sp7 glutamine synthetase structural gene. (springer.com)
  • One isolate was confirmed positive for the sea gene, and the sequence of the sea gene was determined. (hindawi.com)
  • In dMLA, two target specific half-probes (20 bp) are designed to anneal to adjacent regions on a target gene sequence within the extracted DNA of a bacterial isolate (Fig. 1a ). (nature.com)
  • p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence. (uniprot.org)
  • section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. (uniprot.org)
  • According to the researchers, sequence variations that affect gene expression, rather than protein-coding potential, appear to be key drivers of urovirulence. (broadinstitute.org)
  • Once the 16S rRNA gene sequence is determined it can be used as definitive comparative feature. (biomedcentral.com)
  • Their new technology, called INTEGRATE, harnesses bacterial jumping genes to reliably insert any DNA sequence into the genome without cutting DNA. (biotechnews.com.au)
  • The best current tool, built with components from one kind of bacterial CRISPR-Cas system, cuts both strands of the DNA molecule at a specific sequence, like adding a paragraph break to a block of text. (biotechnews.com.au)
  • The researchers harnessed this discovery to create a gene-editing tool that can be programed to insert any DNA sequence into any site in a bacterial genome. (biotechnews.com.au)
  • And by replacing the transposon sequence with other DNA payloads, they could insert sequences up to 10,000 bases long into a bacterial genome. (biotechnews.com.au)
  • Previous research identified the Shine-Dalgarno (SD) sequence as a modulator of translation initiation in bacterial genes, while codon usage biases are frequently implicated as a primary determinant of elongation rate variation. (g3journal.org)
  • Among these architectural elements is the structure of DNA itself, its variable nature at a topological rather than just at a base-sequence level and its ability to play an active (as well as a passive) part in the gene regulation process. (clinsci.org)
  • Notably, BLAST analysis results obtained using the rmtF gene sequence (a new aminoglycoside-modifying enzyme gene sequence that is not included in the database) as a query revealed that the tool was able to link this sequence to short sequences (17 to 40 bp) found in other genes of the rmt family with significant E values. (asm.org)
  • A second Arabidopsis gene with a sequence highly similar to IBC6 was identified. (plantcell.org)
  • Sequence analysis revealed that IBC6 and IBC7 are similar to the receiver domain of bacterial two-component response regulators. (plantcell.org)
  • The first two algorithms employ an inhomogeneous Markov model for short DNA segments ( i.e. k -tuples), from which an estimate of the likelihood for the segment to belong to a protein coding sequence is derived after a training with existing gene data. (biomedcentral.com)
  • Implementation of advanced gene regulatory circuits will require orthogonal transcriptional systems that can be simultaneously controlled and that can produce several different control states. (diva-portal.org)
  • Herein, we review engineered light-sensor systems with potential for in vivo regulation of gene expression in bacteria, and highlight different means of extending the range of available light input and transcriptional output signals. (diva-portal.org)
  • its expression reflects the transcriptional activity of the stx2 gene and can be visualized in simple agar plate assays and quantified in biochemical assays. (cdc.gov)
  • Gene expression is regulated by specific transcriptional circuits but also by the global expression machinery as a function of growth. (embopress.org)
  • We thereby uncover two principles of joint regulation: (i) specific regulation by repression dominates the transcriptional response during metabolic steady states, largely repressing the biosynthesis genes even when biosynthesis is required and (ii) global regulation sets the maximum promoter activity that is exploited during the transition between steady states. (embopress.org)
  • A joint Bayesian analysis enabled clustering of genes into patterns of shared transcriptional response across treatments. (g3journal.org)
  • Pathways such as mTOR signaling, EIF2 signaling, IL-8 signaling, and Tec Kinase signaling were enriched among genes with opposite transcriptional responses to 1,25D and LPS, respectively, highlighting the important roles of these pathways in mediating the immunomodulatory activity of 1,25D. (g3journal.org)
  • Furthermore, a subset of genes with evidence of interethnic differences in transcriptional response was also identified, suggesting that in addition to the well-established interethnic variation in circulating levels of vitamin D, the intensity of transcriptional response to 1,25D and LPS also varies between ethnic groups. (g3journal.org)
  • In this study, we focused on characterizing the transcriptional response to 1,25D in primary monocytes in the presence or absence of a proinflammatory stimulus, bacterial lipopolysaccharide (LPS). (g3journal.org)
  • Transcriptional regulatory networks are fundamental to how microbes alter gene expression in response to environmental stimuli, thereby playing a critical role in bacterial pathogenesis. (prolekare.cz)
  • However, understanding how bacterial transcriptional regulatory networks function during host-pathogen interaction is limited. (prolekare.cz)
  • The RpoS gene in E. coli encodes sigma 38, a sigma factor which regulates stress response and acts as a transcriptional regulator for many genes involved in cell adaptation. (wikipedia.org)
  • The intent of the present study was to identify genes required for attachment of S. enterica serovar Newport to plant tissue. (asm.org)
  • Gene expression of the triggering receptor on myeloid cells ( TREM)-1 and G-coupled-protein receptor kinase ( GRK )-2 in PMNs isolated from patients was analysed to identify genes correlated with the severity of pathophysiological conditions. (medsci.org)
  • The coded panel was searched for bacterial 16S rRNA gene sequences, using primers selective for spiroplasma sequences, primers selective for mollicutes in general, and universal bacterial primers. (asm.org)
  • After 70 PCR cycles, nearly all samples yielded amplified products which were homologous to various bacterial 16S rRNA gene sequences, including those of frequent environmental contaminants. (asm.org)
  • Heterotrophic plate count using ISO 6222 agar (HPC) vs. in situ bacterial (DF) community structure from corresponding samples of a drinking water distribution system were investigated by 16S rRNA gene-based polymerase chain reaction denaturing gradient gel electrophoresis (PCR DGGE) profiling. (scielo.org.za)
  • In order to ensure accurate and reproducible 16S rRNA gene profile analysis, rigorous methodical evaluation and standardisation procedures were undertaken (DGGE optimisation, replication of PCR, multiple-lane standardisation, representative sampling volume determination, application of multiple similarity coefficients). (scielo.org.za)
  • Spatial- and temporal-based 16S rRNA gene amplicon profile analysis from recovered communities further revealed contrasting results. (scielo.org.za)
  • Previous studies of UPEC have identified genes believed to give E . coli a potent ability to colonize the bladder. (broadinstitute.org)
  • The culture of the recombinant (pCom8-GPo1 alkB/E. coli DH5α) with the oil biodegradation bacterial consortium increased the degradation ratio of diesel oil at 24 h from 31% to 50%, and the facilitation rates were increased as the proportion of pCom8-GPo1 alkB / E. coli DH5α to the consortium increased. (scielo.br)
  • The results suggested that the expression of the GPo1 gene in E. coli DH5α could enhance the function of diesel oil degradation by the bacterial consortium. (scielo.br)
  • Since a Dae2 mutant without amidase activity was not lytic against permeabilized E. coli and Bacillus subtilis (for which peptidoglycan is accessible on the cell surface even without permeabilization), the authors concluded that Dae2 is effective as an anti-bacterial agent by virtue of amidase activity. (evmedreview.com)
  • MicF in E. coli was found to regulate the expression of a key structural gene that makes up the outer membrane of the E. coli cell. (wikipedia.org)
  • Reports of microtubule-like structures in bacterial ectosymbionts ("epixenosomes") of ciliates in the genus Euplotidium present the most compelling structural evidence yet for the existence of tubulin-containing elements in bacteria. (pnas.org)
  • Sugino H, Sasaki M, Azakami H, Yamashita M, Murooka Y. A monoamine-regulated Klebsiella aerogenes operon containing the monoamine oxidase structural gene (maoA) and the maoC gene. (labome.org)
  • Arai H, Igarashi Y, Kodama T. The structural genes for nitric oxide reductase from Pseudomonas aeruginosa. (labome.org)
  • Flagellin, the structural component of bacterial flagella, is secreted by pathogenic and commensal bacteria. (jimmunol.org)
  • Structural genes encode proteins needed for cellular processes such as metabolism, biosynthesis, structure, hormone, etc. (coursehero.com)
  • One possibility is that the phage can replicate itself using phage and host factors, resulting in lysis of the bacterial host and release of new phage (the lytic lifestyle). (hindawi.com)
  • Alternatively, the phage can integrate into the bacterial genome and the bacterial host can utilize certain genes the phage carries in its genome for its own benefit (the lysogenic lifestyle) [ 13 ]. (hindawi.com)
  • To explore this hypothesis, we cultured environmental bacteria and screened them for a phage-encoded exotoxin gene. (hindawi.com)
  • In this study, we describe the isolation of bacteria from environmental ambient air and the screening of the isolates for the phage-encoded sea gene using an exotoxin-specific colony PCR assay. (hindawi.com)
  • This is the first report of an alternative bacterial host from the environment that carries a phage-encoded exotoxin gene that is commonly associated with a different bacterial host. (hindawi.com)
  • Phage production is linked to induction of the bacterial SOS response, a ubiquitous response to DNA damage. (cdc.gov)
  • In this work, reported in the journal Communications Biology, the team focused on genes encoding proteins called choline-binding proteins (CBPs), which are present on the bacterial cell surface and interact with the host's immune system. (medindia.net)
  • These findings suggest that the signals for the actions of HU proteins are located in the DNA regions upstream from the sites near the 5' extremities of the coding regions of the hupB and hupA genes. (labome.org)
  • Because a major function of SET domain proteins is the chemical modification of chromatin and bacteria do not have chromatin, there is no apparent functional requirement for the existence of bacterial SET domain genes. (unl.edu)
  • If the proteins Dae lacked such secretion signals, it might be more plausible to argue that the genes may have bacterial origins but were not functional in their new eukaryotic hosts. (evmedreview.com)
  • Recombinant CcpA and CovR bound with high-affinity to the promoter regions of several co-regulated genes, including those encoding proteins involved in carbohydrate and amino acid metabolism. (prolekare.cz)
  • These proteins are costly, rendering populations of cooperators vulnerable to exploitation by nonproducing cheaters arising by gene loss or migration. (uzh.ch)
  • However, the dynamics of AMR transfer through bacterial populations and its direct impact on human disease is poorly understood. (eurekalert.org)
  • Studies that provide evidence for translocations of gene cassettes from stationary chromosomal integrons into integrons associated with mobile elements resulting in gene flows in natural bacterial populations, which favors their survival and adaptation to changing environment, are also reviewed. (deepdyve.com)
  • First, the student will use mathematical modelling to generate predictions when mobile CRISPR-Cas9 can remove AMR genes from bacterial populations. (findaphd.com)
  • Benachenhou-Lahfa N, Forterre P, Labedan B (1993) Evolution of glutamate dehydrogenase genes: evidence for paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life. (springer.com)
  • The researchers then delivered three genes to the electrically inactive cells: one bacterial gene for a sodium ion channel and two supporting genes encoding a potassium channel and connexin-43, a protein that helps shuttle electrical signals between cells. (eurekalert.org)
  • In this study, we investigated the organization and expression of these genes and conducted a comparative analysis of the bacterial and eukaryotic protein sequences, focusing on their phylogeny and 3D structures. (pnas.org)
  • At present, the leading candidate for an evolutionary precursor of tubulin in the bacterial/archaeal domains is the cell division protein, FtsZ. (pnas.org)
  • The method is based on the conditional replication of derivatives of the lactococcal plasmid pWV01, which lacks the repA gene encoding the replication initiation protein. (nih.gov)
  • Wiersinga and the Laboratory for Experimental Internal Medicine discovered which gene-protein combination renders the lethal bacteria B. pseudomallei harmless. (infectioncontroltoday.com)
  • reported that overexpression of SlNRC4a in N. benthamiana enhances ROS production elicited by the bacterial flagellin peptide flg22 and the fungal protein ethylene-inducing xylanase (EIX). (plantphysiol.org)
  • In recent years, several research groups have tried to define the essential set of survival protein-encoding genes in bacteria by different experimental and computational methods (reviewed in references 22 , 24 , 38 , and 79 ). (asm.org)
  • We further show that depletion of SD sequences within ribosomal protein genes is correlated with organismal growth rates, supporting the hypothesis of strong selection against the presence of these sequences in coding regions and suggesting their association with translation efficiency in bacteria. (g3journal.org)
  • Of key importance, the authors show that decreasing expression of the dae2 gene in I. scapularis ticks is associated with higher loads of B. burgdorferi , suggesting, in conjunction with other evidence, that the Dae2 protein is used by the tick to control the load of spirochetes. (evmedreview.com)
  • With the pathogen Salmonella typhimurium, the genes identified by this selection show a marked induction in bacteria recovered from mouse spleen. (sciencemag.org)
  • I am trying to knockout a gene which is essential for growth of the pathogen Pseudomonas aeruginosa PAO1 (has no sacB gene in it). (protocol-online.org)
  • In contrast, the more recently recognized proinflammatory bacterial product (or pathogen-associated molecular pattern) flagellin is a potent activator of intestinal epithelial proinflammatory gene expression ( 3 , 5 , 6 ). (jimmunol.org)
  • The fact that the cbpJ gene is under strict negative selective pressure makes it a particularly attractive target for drugs, as this pressure would limit the likelihood of drug-resistant mutants emerging. (medindia.net)
  • The tags from a mixed population of bacterial mutants representing the inoculum and bacteria recovered from infected hosts were detected by amplification, radiolabeling, and hybridization analysis. (sciencemag.org)
  • I know that counterselectable markers are often instrumental for the construction of mutants when under appropriate growth conditions, a counterselectable gene promotes the death of the microorganisms harboring it. (protocol-online.org)
  • Sixty-five percentage of these mutants had insertions in uncharacterized genes. (asm.org)
  • Although not a primary purpose, the model incorporating truncated genes could be potentially used for phylogeny reconstruction using gene family content. (genetics.org)
  • Moreover, we have demonstrated that membrane vesicles obtained only from V. cholerae induced the expression of genes associated with epithelial cell differentiation. (uio.no)
  • In insects, endosymbionts are maternally inherited, and early insect embryogenesis is marked by bacterial invasion and the subsequent differentiation of specialized host cells, called bacteriocytes, that often form an organ called the bacteriome ( 4 , 18 ). (pubmedcentralcanada.ca)
  • Here we describe oligonucleotide fingerprinting of rRNA genes (OFRG), a method that permits identification of arrayed rRNA genes (rDNA) through a series of hybridization experiments using small DNA probes. (asm.org)
  • The subsequent development of strategies to analyze rRNA molecules and rRNA genes (rDNA) obtained from the environment provided a culture-independent means to examine the immense diversity of microorganisms inhabiting the natural world ( 3 , 14 , 21 , 29 ). (asm.org)
  • A broad-range bacterial PCR targeting rRNA genes (rDNAs) was used to directly analyze 536 clinical samples obtained from 459 hospitalized patients during a 4-year study period. (asm.org)
  • Due to evolutionary constraints associated with a strictly intracellular life style and maternal inheritance of the symbionts, selection pressure favors, during the host-symbiont coevolution, deletions of bacterial genes encoding redundant metabolic pathways with the host ( 34 ), DNA recombinational repair genes ( 11 ), and genes becoming "unnecessary" to the new association. (pubmedcentralcanada.ca)
  • Stx genes are coexpressed with genes of the bacteriophage ( 10 , 11 ), and certain quinolones (known to be potent SOS inducers) induce increases in toxin ( 12 , 13 ) and bacteriophage production ( 13 ) of two to three orders of magnitude within 2 to 4 hours. (cdc.gov)
  • Similar results were obtained when arrays were probed with RNA prepared from B. subtilis cells that were stored in RNA later for one week at 4°C. RNA later is thus an ideal solution for maintaining the expression profile of bacterial mRNA when immediate RNA isolation is not possible or practical. (thermofisher.com)
  • Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. (jcvi.org)
  • 16S rRNA Illumina MiSeq sequencing showed that continuous application of macrolactin reduced the α-diversity of the soil bacterial community and thereby changed the relative abundance of microbes at both the phylum and genus level. (frontiersin.org)
  • The results of this study suggested that a bactericide from a microbial source could decrease the diversity of the soil bacterial community and change the bacterial community structure. (frontiersin.org)
  • The pores in bacterial cell walls are too small for the charged luciferin molecules to fit through. (photonics.com)
  • Yong Wang, assistant professor of physics, and graduate student Asmaa Sadoon have been studying how molecules travel through bacterial cytoplasm in order to understand more about how these tiny organisms function. (phys.org)
  • Noise is hence a genome-wide phenomenon that arises from the stochastic nature of the biochemical reactions that take place during gene expression and the relatively low abundance of the molecules involved. (biochemsoctrans.org)
  • In an article published last week in the journal Proceedings of the National Academy of Sciences , Seyedsayamdost reported a strategy to quickly screen whole libraries of compounds to find elicitors, small molecules that can turn on a specific gene cluster. (phys.org)
  • Many of these microbes release molecules such as LPS, which has the potential of inducing proinflammatory gene expression if internal access to the host is gained. (jimmunol.org)
  • Toll-like receptors (TLR) 4 are an evolutionarily conserved family of receptors that function in innate immunity via recognition of conserved patterns in bacterial molecules (for review, see Ref. 7 ). (jimmunol.org)
  • Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. (jcvi.org)
  • Type VI secretion amidase effector (Tae) molecules (encoded by tae genes) can kill rival bacteria by degrading their cells walls when delivered into those competing cells. (evmedreview.com)
  • also argue that in order to be effective in killing most bacteria in vivo , secretion of Dae2 would need to be accompanied by secretion of molecules that can cause breaches in the bacterial outer membrane thereby allowing the Dae2 molecules access to the peptidoglycan in the cell wall. (evmedreview.com)
  • The mRNA-effector complex adopts a distinct structure that sequesters the ribosome-binding site and leads to a reduction in gene expression. (nature.com)
  • PCR amplification of 16S rRNA genes, or "ribotyping," is a powerful method for detecting and identifying microbial agents in environmental and clinical specimens. (asm.org)
  • We demonstrate here digital multiplex ligation assay (dMLA) as a low-cost targeted genomic detection workflow capable of highly-parallel screening of bacterial isolates for multiple target gene regions simultaneously. (nature.com)
  • Here, dMLA is used for simultaneous detection of 1187 β-lactamase-encoding genes, including extended spectrum β-lactamase (ESBL) genes, in 74 bacterial isolates. (nature.com)
  • Here, we present a digital multiplex ligation assay (dMLA) for simultaneous detection of 1187 β-lactamase-encoding genes within 74 bacterial isolates. (nature.com)
  • The researchers are seeking to develop a system for monitoring bacterial gene expression in response to signals from the natural environment using a blend of membrane diffusion cell, genomics and optical detection technologies. (stanford.edu)
  • Researchers have developed a way to use firefly luciferase - which is much brighter than bacterial luciferase - as a chemiluminescent reporter in bacteria. (photonics.com)
  • In Japan, Jonathan Latham reports that researchers have discovered that standard methods of animal and plant gene-editing introduce DNA from unexpected sources . (biofuelsdigest.com)
  • KNOXVILLE--Researchers at the University of Tennessee, Knoxville, have identified a set of bacterial genes that may help them find ways to lessen the severity of the disease malaria. (brightsurf.com)
  • HHMI researchers have identified a gene. (bio-medicine.org)
  • HHMI researchers have identified a gene that enables mycobacteria--the cause of tuberculosis and leprosy--to form biofilms. (bio-medicine.org)
  • GAINESVILLE, Fla. - By analyzing the genes of bacteria, University of Florida researchers have moved a step closer to pinpointing how two brain disorders common in small-breed dogs occur. (ufl.edu)
  • After 35 PCR cycles, no samples were positive for spiroplasma or any other bacterial DNA, while control Spiroplasma mirum genomic DNA, spiked at 1% of the concentration required to account for the scrapie infectivity present, was readily detected. (asm.org)
  • One important question raised by the availability of complete genomic sequences is how many genes are essential for cellular life. (asm.org)
  • Hence, association features may rely not only on the host functions but also on the level of bacterial genomic alteration and, thereby, on the age of the association. (pubmedcentralcanada.ca)
  • More recent associations have fewer bacterial genomic alterations than their free-living relatives. (pubmedcentralcanada.ca)
  • Maximum-likelihood estimates (MLEs) of the new model reveal fast rates of gene insertions/deletions on recent branches, suggesting a fast turnover of many recently transferred genes. (genetics.org)
  • Using the method, we have constructed two chromosomal deletions in the chemotaxis gene region of S. typhimurium. (pnas.org)
  • One exception is ERS (for e thylene r esponse s ensor), a member of the Arabidopsis ETR gene family, which is comprised solely of a histidine kinase and a putative ethylene binding domain. (plantcell.org)
  • The present study examines patterns of transcriptome-wide response to 1,25D, and the bacterial lipopolysaccharide (LPS) in primary human monocytes, to elucidate pathways underlying the effects of 1,25D on the immune system. (g3journal.org)
  • Organization of the chromosomal region containing the genes responsible for the synthesis and export of type I O-PS in B. pseudomallei . (asm.org)
  • Finally, we demonstrate that mobile elements are in conflict with their chromosomal hosts over the chimeric ensemble's social strategy, with mobile elements enforcing cooperation on their otherwise selfish hosts via the cotransfer of secretome genes with "mafia strategy" addictive systems (toxin-antitoxin and restriction-modification). (uzh.ch)
  • To find new gene-editing tools, Sternberg and three graduate students looked to bacteria to find variations of well-studied CRISPR-Cas systems with unusual properties that would reveal new tool capabilities. (biotechnews.com.au)
  • The addition of 1,25D during stimulation with LPS induced significant upregulation of genes in the antimicrobial and autophagy pathways, and downregulation of proinflammatory response genes compared to LPS treatment alone. (g3journal.org)