Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Genes, Bacterial: The functional hereditary units of BACTERIA.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Escherichia coli K12: A species of gram-negative, rod-shaped bacteria belonging to the K serogroup of ESCHERICHIA COLI. It lives as a harmless inhabitant of the human LARGE INTESTINE and is widely used in medical and GENETIC RESEARCH.Escherichia coli Infections: Infections with bacteria of the species ESCHERICHIA COLI.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.Bacterial Proteins: Proteins found in any species of bacterium.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Escherichia coli O157: A verocytotoxin-producing serogroup belonging to the O subfamily of Escherichia coli which has been shown to cause severe food-borne disease. A strain from this serogroup, serotype H7, which produces SHIGA TOXINS, has been linked to human disease outbreaks resulting from contamination of foods by E. coli O157 from bovine origin.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.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.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Genome Size: The amount of DNA (or RNA) in one copy of a genome.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Bacteriophage lambda: A temperate inducible phage and type species of the genus lambda-like viruses, in the family SIPHOVIRIDAE. Its natural host is E. coli K12. Its VIRION contains linear double-stranded DNA with single-stranded 12-base 5' sticky ends. The DNA circularizes on infection.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Lysogeny: The phenomenon by which a temperate phage incorporates itself into the DNA of a bacterial host, establishing a kind of symbiotic relation between PROPHAGE and bacterium which results in the perpetuation of the prophage in all the descendants of the bacterium. Upon induction (VIRUS ACTIVATION) by various agents, such as ultraviolet radiation, the phage is released, which then becomes virulent and lyses the bacterium.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Genome, Protozoan: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.Genetic Techniques: Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Genetic Complementation Test: A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Transduction, Genetic: The transfer of bacterial DNA by phages from an infected bacterium to another bacterium. This also refers to the transfer of genes into eukaryotic cells by viruses. This naturally occurring process is routinely employed as a GENE TRANSFER TECHNIQUE.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.DNA-Directed RNA Polymerases: Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).Adhesins, Escherichia coli: Thin, filamentous protein structures, including proteinaceous capsular antigens (fimbrial antigens), that mediate adhesion of E. coli to surfaces and play a role in pathogenesis. They have a high affinity for various epithelial cells.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Genome, Helminth: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.Genome, Plastid: The genetic complement of PLASTIDS as represented in their DNA.Synteny: The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.Genetic Variation: Genotypic differences observed among individuals in a population.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.Gene Order: The sequential location of genes on a chromosome.Campylobacter coli: A species of gram-negative, rod-shaped bacteria isolated from the intestinal tract of swine, poultry, and man. It may be pathogenic.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Genes, Viral: The functional hereditary units of VIRUSES.Kinetics: The rate dynamics in chemical or physical systems.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.Recombinant Proteins: Proteins prepared by recombinant DNA technology.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Viral Proteins: Proteins found in any species of virus.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).DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Coliphages: Viruses whose host is Escherichia coli.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the 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.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Bacterial Outer Membrane Proteins: Proteins isolated from the outer membrane of Gram-negative bacteria.RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Enteropathogenic Escherichia coli: Strains of ESCHERICHIA COLI characterized by attaching-and-effacing histopathology. These strains of bacteria intimately adhere to the epithelial cell membrane and show effacement of microvilli. In developed countries they are associated with INFANTILE DIARRHEA and infantile GASTROENTERITIS and, in contrast to ETEC strains, do not produce ENDOTOXINS.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Shiga-Toxigenic Escherichia coli: Strains of ESCHERICHIA COLI with the ability to produce at least one or more of at least two antigenically distinct, usually bacteriophage-mediated cytotoxins: SHIGA TOXIN 1 and SHIGA TOXIN 2. These bacteria can cause severe disease in humans including bloody DIARRHEA and HEMOLYTIC UREMIC SYNDROME.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Enterotoxigenic Escherichia coli: Strains of ESCHERICHIA COLI that produce or contain at least one member of either heat-labile or heat-stable ENTEROTOXINS. The organisms colonize the mucosal surface of the small intestine and elaborate their enterotoxins causing DIARRHEA. They are mainly associated with tropical and developing countries and affect susceptible travelers to those places.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Anti-Bacterial Agents: Substances that reduce the growth or reproduction of BACTERIA.Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.Feces: Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.Bacteriophages: Viruses whose hosts are bacterial cells.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Uropathogenic Escherichia coli: Strains of Escherichia coli that preferentially grow and persist within the urinary tract. They exhibit certain virulence factors and strategies that cause urinary tract infections.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.Bacterial Adhesion: Physicochemical property of fimbriated (FIMBRIAE, BACTERIAL) and non-fimbriated bacteria of attaching to cells, tissue, and nonbiological surfaces. It is a factor in bacterial colonization and pathogenicity.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Culture Media: Any liquid or solid preparation made specifically for the growth, storage, or transport of microorganisms or other types of cells. The variety of media that exist allow for the culturing of specific microorganisms and cell types, such as differential media, selective media, test media, and defined media. Solid media consist of liquid media that have been solidified with an agent such as AGAR or GELATIN.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.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.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.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.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Enterohemorrhagic Escherichia coli: Strains of ESCHERICHIA COLI that are a subgroup of SHIGA-TOXIGENIC ESCHERICHIA COLI. They cause non-bloody and bloody DIARRHEA; HEMOLYTIC UREMIC SYNDROME; and hemorrhagic COLITIS. An important member of this subgroup is ESCHERICHIA COLI O157-H7.Molecular Weight: The sum of the weight of all the atoms in a molecule.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Genetic Engineering: Directed modification of the gene complement of a living organism by such techniques as altering the DNA, substituting genetic material by means of a virus, transplanting whole nuclei, transplanting cell hybrids, etc.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Prophages: Genomes of temperate BACTERIOPHAGES integrated into the DNA of their bacterial host cell. The prophages can be duplicated for many cell generations until some stimulus induces its activation and virulence.Fimbriae, Bacterial: Thin, hairlike appendages, 1 to 20 microns in length and often occurring in large numbers, present on the cells of gram-negative bacteria, particularly Enterobacteriaceae and Neisseria. Unlike flagella, they do not possess motility, but being protein (pilin) in nature, they possess antigenic and hemagglutinating properties. They are of medical importance because some fimbriae mediate the attachment of bacteria to cells via adhesins (ADHESINS, BACTERIAL). Bacterial fimbriae refer to common pili, to be distinguished from the preferred use of "pili", which is confined to sex pili (PILI, SEX).Bacterial Toxins: Toxic substances formed in or elaborated by bacteria; they are usually proteins with high molecular weight and antigenicity; some are used as antibiotics and some to skin test for the presence of or susceptibility to certain diseases.Conjugation, Genetic: A parasexual process in BACTERIA; ALGAE; FUNGI; and ciliate EUKARYOTA for achieving exchange of chromosome material during fusion of two cells. In bacteria, this is a uni-directional transfer of genetic material; in protozoa it is a bi-directional exchange. In algae and fungi, it is a form of sexual reproduction, with the union of male and female gametes.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.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.Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.Virulence Factors: Those components of an organism that determine its capacity to cause disease but are not required for its viability per se. Two classes have been characterized: TOXINS, BIOLOGICAL and surface adhesion molecules that effect the ability of the microorganism to invade and colonize a host. (From Davis et al., Microbiology, 4th ed. p486)Genes, Plant: The functional hereditary units of PLANTS.DNA, Recombinant: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Polyploidy: The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Chromosomes: In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Oryza sativa: Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.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.Diarrhea: An increased liquidity or decreased consistency of FECES, such as running stool. Fecal consistency is related to the ratio of water-holding capacity of insoluble solids to total water, rather than the amount of water present. Diarrhea is not hyperdefecation or increased fecal weight.Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.DNA Repair: The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.Escherichia coli Vaccines: Vaccines or candidate vaccines used to prevent or treat both enterotoxigenic and enteropathogenic Escherichia coli infections.Genome, Microbial: The genetic complement of a microorganism as represented in its DNA or in some microorganisms its RNA.Genome Components: The parts of a GENOME sequence that are involved with the different functions or properties of genomes as a whole as opposed to those of individual GENES.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Gene Dosage: The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Drug Resistance, Microbial: The ability of microorganisms, especially bacteria, to resist or to become tolerant to chemotherapeutic agents, antimicrobial agents, or antibiotics. This resistance may be acquired through gene mutation or foreign DNA in transmissible plasmids (R FACTORS).Transformation, Bacterial: The heritable modification of the properties of a competent bacterium by naked DNA from another source. The uptake of naked DNA is a naturally occuring phenomenon in some bacteria. It is often used as a GENE TRANSFER TECHNIQUE.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Meningitis, Escherichia coli: A form of gram-negative meningitis that tends to occur in neonates, in association with anatomical abnormalities (which feature communication between the meninges and cutaneous structures) or as OPPORTUNISTIC INFECTIONS in association with IMMUNOLOGIC DEFICIENCY SYNDROMES. In premature neonates the clinical presentation may be limited to ANOREXIA; VOMITING; lethargy; or respiratory distress. Full-term infants may have as additional features FEVER; SEIZURES; and bulging of the anterior fontanelle. (From Menkes, Textbook of Child Neurology, 5th ed, pp398-400)Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.beta-Galactosidase: A group of enzymes that catalyzes the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-galactosides. Deficiency of beta-Galactosidase A1 may cause GANGLIOSIDOSIS, GM1.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.DNA Replication: The process by which a DNA molecule is duplicated.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.Membrane Transport Proteins: Membrane proteins whose primary function is to facilitate the transport of molecules across a biological membrane. Included in this broad category are proteins involved in active transport (BIOLOGICAL TRANSPORT, ACTIVE), facilitated transport and ION CHANNELS.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)DNA, Circular: Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Serotyping: Process of determining and distinguishing species of bacteria or viruses based on antigens they share.Genetics, Microbial: A subdiscipline of genetics which deals with the genetic mechanisms and processes of microorganisms.Transformation, Genetic: Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Urinary Tract Infections: Inflammatory responses of the epithelium of the URINARY TRACT to microbial invasions. They are often bacterial infections with associated BACTERIURIA and PYURIA.Fimbriae Proteins: Proteins that are structural components of bacterial fimbriae (FIMBRIAE, BACTERIAL) or sex pili (PILI, SEX).Shiga Toxin: A toxin produced by SHIGELLA DYSENTERIAE. It is the prototype of class of toxins that inhibit protein synthesis by blocking the interaction of ribosomal RNA; (RNA, RIBOSOMAL) with PEPTIDE ELONGATION FACTORS.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.
"Genome and genetics timeline - 1973". Genome news network.. *^ Morrow, J. F.; Cohen, S. N.; Chang, A. C.; Boyer, H. W.; Goodman ... in E.coli. Genentech announced the production of genetically engineered human insulin in 1978. The insulin produced by ... "Any idiot can do it.' Genome editor CRISPR could put mutant mice in everyone's reach". Science , AAAS. 2016-11-02. Retrieved ... In 2010, scientists at the J. Craig Venter Institute, announced that they had created the first synthetic bacterial genome. ...
"Entrez Gene: ELAC1 elaC homolog 1 (E. coli)". Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and ... expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121-7. doi:10.1101/ ...
"An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biology. 4 (9): R54. doi:10.1186/gb-2003-4-9- ... "A functional update of the Escherichia coli K-12 genome". Genome Biology. 2 (9): RESEARCH0035. doi:10.1186/gb-2001-2-9- ... Bacteria genomes usually encode a few hundred to a few thousand genes. The genes in bacterial genomes are usually a single ... genome-genome hybridisation, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the ...
Moxon, E. R.; Higgins, C. F. (1997). "E. Coli genome sequence. A blueprint for life". Nature. 389 (6647): 120-121. doi:10.1038/ ... Py, B. A.; Higgins, C. F.; Krisch, H. M.; Carpousis, A. J. (1996). "A DEAD-box RNA helicase in the Escherichia coli RNA ... Manson, M. D.; Blank, V.; Brade, G.; Higgins, C. F. (1986). "Peptide chemotaxis in E. Coli involves the Tap signal transducer ... Coli". Cell. 52 (4): 569-584. doi:10.1016/0092-8674(88)90470-9. PMID 2830029. Newbury, S. F.; Smith, N. H.; Higgins, C. F. ( ...
SGA utilizes the entire genome yeast knock-out set created by the yeast genome deletion project. Synthetic genetic array ... Methodology has since been developed to allow SGA analysis in S.pombe and E. coli. Synthetic genetic array analysis was ... Using SGA methodology a query gene deletion mutant can be crossed to an entire genome deletion set to identify any SSL ... "Saccharomyces Genome Deletion Project". "Yeast Knockout Strains". Open Biosystems. Archived from the original on November 19, ...
... coli K12 genome used DeCypher Smith-Waterman to determine the function of new translated sequences. In 2002, the rice genome, ... "The Complete Genome Sequence of Escherichia coli K-12". Science. 277 (5331): 1453-1462. doi:10.1126/science.277.5331.1453. PMID ... Venter, J. Craig (October 18, 2007). A Life Decoded: My Genome: My Life. New York, New York: Viking Adult. ISBN 0-670-06358-4. ... Gillis, Justing (August 11, 2005). "Rice Genome Fully Mapped". washingtonpost.com. Goff, S. A.; Ricke, D.; Lan, T. H.; Presting ...
"Escherichia coli 16S ribosomal RNA". "Halobacterium salinarum 18S ribosomal RNA". "Homo sapiens 18S ribosomal RNA (nuclear)". ... "Sequence and organization of the human mitochondrial genome". Nature. 290 (5806): 457-465. doi:10.1038/290457a0. "Arabidopsis ... Homo sapiens mitochondrion, complete genome. "Revised Cambridge Reference Sequence (rCRS): accession NC_012920", National ...
Genome Project-Write. *Genome sequencing of endangered species. *Genome Valley. *Genotyping by sequencing ...
This was done in a 4.7 million basepair genome of an industrially useful microbe (E. coli) with the goal of making a safer and ... "Personal Genome Project". Retrieved 25 May 2013.. *^ "Okay, You've Sequenced My Genome: Are You Sure You Got it Right?". NGS ... Synthetic biology and genome engineering. He has co-developed "genome engineering" technologies since 1997 via either ... To aid in the interpretation and sharing of genomes, Church, in 2005, initiated the Personal Genome Project (PGP), which ...
The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged ... Meselson M, Stahl FW (July 1958). "THE REPLICATION OF DNA IN ESCHERICHIA COLI". Proceedings of the National Academy of Sciences ... The reasons for the presence of so much noncoding DNA in eukaryotic genomes and the extraordinary differences in genome size, ... Data sets representing entire genomes' worth of DNA sequences, such as those produced by the Human Genome Project, are ...
Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 1993 Nov ... This process has contributed to the mass of genomes of modern multicellular organisms, at the same time keeping genomes in flux ... in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol. 2013;5(3):578-90. doi: 10.1093/gbe/ ... Brosius J. Echoes from the past--are we still in an RNP world? Cytogenet Genome Res. 2005;110(1-4):8-24. Brosius J. RNAs from ...
Human AOX1 genome location and AOX1 gene details page in the UCSC Genome Browser. Wang AG, Yoon SY, Oh JH, et al. (2006). " ... 2009). "Purification and mechanism of human aldehyde oxidase expressed in Escherichia coli". Drug Metab. Dispos. 37 (12): 2393- ... Bonaldo MF, Lennon G, Soares MB (1996). "Normalization and subtraction: two approaches to facilitate gene discovery". Genome ...
The largest mRNA, (which is longer than the viral genome), is used to make the new copies of the genome and to make the capsid ... coli". Nature. 281 (5733): 646-50. Bibcode:1979Natur.281..646G. doi:10.1038/281646a0. PMID 399327.. ... The genome of HBV is made of circular DNA, but it is unusual because the DNA is not fully double-stranded. One end of the full ... There are four known genes encoded by the genome, called C, X, P, and S. The core protein is coded for by gene C (HBcAg), and ...
"Escherichia coli str. K-12 substr. MG1655, complete genome [Genbank Accession Number: U00096]". GenBank. NCBI. Retrieved 2013- ... For example, the E. coli K-12 genome contains 2705 TAA (63%), 1257 TGA (29%), and 326 TAG (8%) stop codons (GC content 50.8%). ... Researchers at University of Memphis found that the ratios of the stop-signals on the three reading frames of a genome ( ... Codons that can form hidden stops are used in genomes more frequently compared to synonymous codons that would otherwise code ...
BLAST and exclude E. coli genome sequences. Using MEGABLAST, Hi-Fi reads are then matched to sequences in annotated databases ... Bacteria, usually E. coli, are then transformed using the cDNA vectors and selected using a marker, the collection of ... As pathogen genomes mutates quickly, nucleotide-nucleotide alignments, or blastn, is usually uninformative as it is possible to ... Reference human genome - eliminates genes that have been missed by the annotation process and any contaminating genomic ...
"Entrez Gene: MLH3 mutL homolog 3 (E. coli)". Sonntag Brown M, Lim E, Chen C, Nishant KT, Alani E (2013). "Genetic analysis of ... Genome Research. 16 (1): 55-65. doi:10.1101/gr.4039406. PMC 1356129 . PMID 16344560. Taylor NP, Powell MA, Gibb RK, Rader JS, ... mlh3 mutations reveals interactions between crossover promoting factors during meiosis in baker's yeast". G3: Genes, Genomes, ...
"An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54. doi:10.1186/gb-2003-4-9-r54 ... Stone SR, Morrison JF (July 1988). "Dihydrofolate reductase from Escherichia coli: the kinetic mechanism with NADPH and reduced ... Helmstaedt K, Krappmann S, Braus GH (September 2001). "Allosteric Regulation of Catalytic Activity: Escherichia coli Aspartate ... "Global organization of metabolic fluxes in the bacterium Escherichia coli". Nature. 427 (6977): 839-43. Bibcode:2004Natur.427.. ...
1997). "The Complete Genome Sequence of Escherichia coli K-12". Science. 277 (5331): 1453-1462. doi:10.1126/science.277.5331. ... Mass calculated from volume assuming density of 1 g/mL "E. coli Statistics". The CyberCell Database. Retrieved 2011-09-11. " ... "Prochlorococcus marinus MIT 9313 - Home". Joint Genome Institute. Retrieved 2011-11-01. "Size (diameter) of most abundant ...
"An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54. doi:10.1186/gb-2003-4-9-r54 ... In eukaryotes the genome is held within the cell nucleus, which is separated from the cytosol by nuclear pores that block the ... Estimates of the number of metabolites in single cells such as E. coli and baker's yeast predict that under 1,000 are made. ... In prokaryotes the cytosol contains the cell's genome, within a structure known as a nucleoid. This is an irregular mass of DNA ...
"An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biology. 4 (9): R54. doi:10.1186/gb-2003-4-9- ... Edwards, J. S.; Ibarra, R. U.; Palsson, B. O. (2001). "In silico predictions of Escherichia coli metabolic capabilities are ... Forster, J.; Famili, I.; Fu, P.; Palsson, B. Ø.; Nielsen, J. (2003). "Genome-Scale Reconstruction of the Saccharomyces ... the development of analysis procedures for genome-scale models, and the experimental verification of these models in ...
The Complete Genome Sequence of Escherichia coli K-12». Science. ۲۷۷ (۵۳۳۱): ۱۴۵۳-۱۴۶۲. . doi:10.1126/science.277.5331.1453. ... E. coli Statistics». The CyberCell Database. دریافتشده در ۲۰۱۱-۰۹-۱۱. .. *↑ «Surface area and volume of spermatozoa - Human ... Joint Genome Institute. دریافتشده در ۲۰۱۱-۱۱-۰۱. .. *↑ «Size (diameter) of most abundant cyanobacteri - Prochlorococcus - BNID ... دیانای sequence of length 4.6 Mbp, the length of the اشریشیا کلی genome ...
"Genome sequence of enterohaemorrhagic Escherichia coli O157:H7". Nature. 409 (6819): 529-533. doi:10.1038/35054089. PMID ...
Genome sequence of Neisseria lactamica (an ST640 strain). Published on the Wellcome Trust Sanger Institute ftp server. Sequence ... Todar, K. "Pathogenic E. coli". Online Textbook of Bacteriology. University of Wisconsin-Madison Department of Bacteriology. ... Sequence data from the Neisseria lactamica ATCC 23970 genome sequencing project.. ... data from the Neisseria lactamica Y92-1009 genome sequencing project. ...
"The Complete Genome Sequence of Escherichia coli K-12". Science 277 (5331): 1453-1462. doi:10.1126/science.277.5331.1453. CS1 ... The Arabidopsis Genome Initiative (2000). "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana". Nature ... 2006). "The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)". Science 313 (5793): 1596-604. doi:10.1126/science. ... 2002). "A draft sequence of the rice genome (Oryza sativa L. ssp. indica)". Science 296 (5565): 79-92. doi:10.1126/science. ...
Richmond, CS; Glasner, JD; Mau, R; Jin, H; Blattner, FR (Oct 1, 1999). "Genome-wide expression profiling in Escherichia coli K- ... Waldminghaus, T; Gaubig, LC; Klinkert, B; Narberhaus, F (Sep-Oct 2009). "The Escherichia coli ibpA thermometer is comprised of ... Gaubig, LC; Waldminghaus, T; Narberhaus, F (Jan 2011). "Multiple layers of control govern expression of the Escherichia coli ... and is the most drastically upregulated operon under heat-shock in Escherichia coli. IbpA is regulated by a ROSE element found ...
International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome.. Nature. 2001, 409 (6822 ... Escherichia coli. 大腸桿菌 4,600,000 4,400 Saccharomyces cerevisiae. 釀酒酵母 12,000,000 5,538 ... Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome.. Nature. 2002, 420 (6915 ... Large-scale sequencing of the chimpanzee genome is now imminent.. ". Olson M, Varki A. Sequencing the chimpanzee genome: ...
Laboratory DNA Science: An Introduction to Recombinant DNA Techniques and Methods of Genome Analysis. Menlo Park, CA: Addison- ... One of the enzymes most widely used in recombinant DNA work is Eco R1, which is isolated from Escherichia coli RY13. Other ... Thus, the fifth restriction enzyme from E. coli is called EcoRV (pronounced e, ko, r five). Besides cloning , restriction ... Mapping means determining the order of the restriction enzyme sites in the genome. These maps form a foundation for much other ...
Using Nanopore sequencing, we describe here the circular genome of an Escherichia coli sequence type 410 (ST410) strain with ... N2 - Using Nanopore sequencing, we describe here the circular genome of an Escherichia coli sequence type 410 (ST410) strain ... AB - Using Nanopore sequencing, we describe here the circular genome of an Escherichia coli sequence type 410 (ST410) strain ... abstract = "Using Nanopore sequencing, we describe here the circular genome of an Escherichia coli sequence type 410 (ST410) ...
"Escherichia coli K12" . (That genome is currently indexed as "Escherichia coli str. K-12 substr. MG1655", since there are ... The complete genome sequence of Escherichia coli K-12. Science. 1997; 277:1453-1462 View ArticlePubMed. ... In an era when microbial genome sequencing was not as commonplace as it is now, using a taxid as a key to retrieve the genome ... followed within a year by Escherichia coli. In those days each new genome sequence was of significant scientific interest and ...
Escherichia coli CFT073, complete genome Escherichia coli CFT073, complete genome. gi,26245917,ref,NC_004431.1, ...
Escherichia coli BL21(DE3), complete genome Escherichia coli BL21(DE3), complete genome. gi,387823261,ref,NC_012892.2, ...
Although chromosome size in natural isolates of E. coli can vary by as much as 1,000 kb (41-44), the E. coli genome has not ... Rate of Horizontal Transfer in E. coli.. To determine the age of acquired genes in the E. coli MG1655 genome, the 755 genes ... coli genome were acquired nearly 100 Myr ago, just after the estimated time of divergence of E. coli and S. enterica; however, ... coli. These 755 horizontally transferred genes constitute 547.8 kb of DNA and were introduced into the E. coli genome in at ...
Second Announcement: Third International E. coli Genome Meeting The Third International E. coli Genome Meeting will be held ... E. coli Genome meeting. Monica Riley mriley at HOH.MBL.EDU Mon Sep 5 19:15:11 EST 1994 *Next message: food web ... This Meeting will include invited talks, poster sessions, and workshops analyzing the E. coli genome at the genetic, sequence, ... Specific topics will include: status reports on large-scale sequence efforts; genome mapping technologies; applications of ...
... Mark Pallen School of Medicine, University of Birmingham, Birmingham, ... Professor Pallens lecture, entitled Escherichia coli: From genome sequences to consequences, provides a summary of the ...
Ontology (42) KEGG BRITE (42) Pathway (321) KEGG PATHWAY (120) KEGG MODULE (201) Disease (1) KEGG DISEASE (1) Genome (1) ... Uropathogenic Escherichia coli (UPEC) strain with a multidrug resistance phenotype and the capacity to produce extended- ...
A transcriptional regulatory system (TRS) connects a cells environmental cues to its genome and in turn determines which genes ...
UW E. coli Genome Project Overview. We sequenced the E. coli K-12 genome, and continue to maintain and update its annotation. ... We also sequenced six additional enterobacterial strains which are pathogens related to E. coli K-12, and many plasmids. The ...
... sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. ...
We present the complete genome sequence of uropathogenic Escherichia coli, strain CFT073. A three-way genome comparison of the ... CFT073 Genome Organization Relative to Other E. coli.. The assembly of DNA sequences from a shotgun library of CFT073 DNA ... The net result is a mosaic genome structure in which newly acquired genes in each of the E. coli types are placed into a ... Two copies are associated with the type I fimbrial locus present in the same place as other E. coli genomes. There are two ...
Homology between E. coli proteins and the other sequenced genomes. Figure 3 also presents comparisons of the 4288E. coli ... Since the inception of the E. coliproject, six other complete genomes have become publicly available (3). Genome sequences, ... coli genome (53). The number and distribution of these sequences in the whole genome are summarized in Fig. 2. The largest ... coli genome; the similarity is plotted as described in Fig. 3 for the complete genome comparisons. ...
59 BASIC BIOLOGICAL SCIENCES; E. coli evolution; basic genome; core genome; recombinant transfer; generalized transduction. ... An approximation to the ~4-Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been ... Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and ... Moderately diverged genome pairs (0.4-1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying ...
CRISPR interference or inhibition gRNA library for functional genomics screening in bacteria like Escherichia coli (E. coli) ... Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. Rousset F, Cui L, Siouve E, ... This library contains ~93,000 unique guide RNAs targeting random positions along the genome of E. coli MG1655 with a NGG PAM ... E. coli Genome-wide Inhibition library was a gift from David Bikard (Addgene #115927) ...
... we have developed a genome-engineering tool for determining essential genes and minimizing bacterial genomes. We made two large ... An increasing number of microbial genomes have been completely sequenced, and functional analyses of these genomic sequences ... Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system Nat Biotechnol. 2002 Oct;20(10):1018- ... we have developed a genome-engineering tool for determining essential genes and minimizing bacterial genomes. We made two large ...
GENOME ANNOUNCEMENTS. Genome of Multidrug-Resistant Uropathogenic Escherichia coli Strain NA114 from India Tiruvayipati Suma ... Genome of Multidrug-Resistant Uropathogenic Escherichia coli Strain NA114 from India Tiruvayipati Suma Avasthi, Narender Kumar ... Genome of Multidrug-Resistant Uropathogenic Escherichia coli Strain NA114 from India Tiruvayipati Suma Avasthi, Narender Kumar ... Genome of Multidrug-Resistant Uropathogenic Escherichia coli Strain NA114 from India Message Subject (Your Name) has forwarded ...
... caused by avian pathogenic Escherichia coli (APEC), is a significant disease, causing extensive animal and financial losses ... Complete Genome Sequence of the Avian Pathogenic Escherichia Coli Strain APEC O78 Genome Announc. 2013 Mar 21;1(2):e0002613. ... Here, we present the fully closed genome sequence of a typical avian pathogenic E. coli strain belonging to the serogroup O78. ... Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is a significant disease, causing extensive animal and ...
Probabilistic Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks in Escherichia Coli and Mycobacterium ... Towards Genome Engineering in Chinese Hamster Ovary Cells. Worth over $30 billion, therapeutic proteins, produced by ... After validating the approach, we then applied the method to build the first genome-scale integrated metabolic-regulatory model ... Using PROM, we construct an integrated regulatory-metabolic network for the model organism, Escherichia coli, and demonstrate ...
Here, we performed high-throughput tests on the E. coli a complete set of E. coli K-12 ORF archive (ASKA) collection to ... Escherichia coli is one of the most favorable hosts for this purpose. Although a number of strategies for optimizing protein ... quantify the effects of overexpressing individual E. coli genes on its growth. The results indicated that overexpressing ... Genome-Wide Quantification of the Effect of Gene Overexpression on Escherichia coli Growth. Hao Chen 1. ...
Maintained by the Department of Genetics at the University of Wisconsin-Madison, the E. coli Genome Project site is divided ... Also available are instructions for retrieving the complete E. coli K-12 genome sequence. ...
Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple ...
IsolatesSequenceAnnotationGenomicBacteriaO157VirulenceMG1655GeneBacteriumPathogenBacterial genomeSequence typeNucleotideCFT073ReconstructionReport the complete genomePlasticityPathogensWhole-genome transcriptionalGeneticsUropathogenic EscherichiaHemolytic Uremic SOrganismPresent the draft genomeEnterohemorrhagicMetabolismShiga Toxin-producing EEvolutionaryClosely relatedInstitute for Genome SciencesTranscriptionalMultidrug-resistantPhage genomesCalled Shiga toxinsMicrobial genomesDraftCompleteReference genomeComparativeLineagesMolecular biologyAnalysis
- We sequenced the E. coli K-12 genome, and continue to maintain and update its annotation. (wisc.edu)
- The genome sequence was annotated in the multiuser, web-based annotation environment called magpie ( 7 ). (pnas.org)
- Motivated by these facts, we performed complete in-depth sequencing, annotation, and analysis of the genome of UPEC strain NA114, which was originally obtained from the urine of a 70-year-old male patient with prostatitis from Pune. (asm.org)
- Becker SA, Palsson BO (2005) Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. (springer.com)
- Here we describe the isolation of few E. coli phages specifically ADB-2 and S. typhimurium bacteriophages from poultry fecal sample, its molecular characterization, genome sequencing and functional annotation. (omicsonline.org)
- Several inconsistencies in genome annotation were verified experimentally, and up to 55 candidates await further investigation. (uzh.ch)
- Our findings demonstrate how an up-to-date 2-D gel-based proteomics approach can be used for improving the annotation of prokaryotic genomes. (uzh.ch)
- This updated metabolic reconstruction includes: (1) an alignment with the latest genome annotation and the metabolic content of EcoCyc leading to the inclusion of the activities of 1260 ORFs, (2) characterization and quantification of the biomass components and maintenance requirements associated with growth of E. coli and (3) thermodynamic information for the included chemical reactions. (embopress.org)
- Genome sequencing and annotation, along with biochemical characterization of cellular machinery, has enabled reconstruction of cellular processes on the genomic scale since the turn of the millennium. (embopress.org)
- Building on the rich history of E. coli metabolic reconstruction ( Figure 1 ), we generated an updated genome‐scale metabolic reconstruction for E. coli containing 1260 ORFs from the latest genome annotation ( Riley et al , 2006 ). (embopress.org)
- Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. (genome.jp)
- Whole-genome libraries in M13Janus and pBluescript were prepared from genomic DNA as described ( 4 , 5 ). (pnas.org)
- This study revealed the organization features of Escherichia coli genomic functional units in the 3D space and furthered our understanding of the link between the three-dimensional structure of chromosomes and biological function. (biomedcentral.com)
- A team led by University of Maryland School of Medicine Institute for Genome Sciences researchers has unraveled the genomic code of the E. coli bacterium that caused the ongoing deadly outbreak in Germany that began in May 2011. (infectioncontroltoday.com)
- Rasko and colleagues at the Institute for Genome Sciences analyzed the genomic data using computational tools, some of which were developed at the Institute. (infectioncontroltoday.com)
- Raskos expertise is in the molecular pathogenesis and evolution of E. coli, which helped his team to interpret the massive amount of genomic data involved and learn more about the microbe and how it fits into the overall picture of E. coli. (infectioncontroltoday.com)
- One E. coli lineage causes a urinary tract infection (UTI) and experiences several alterations of its genomic content during subsequent antibiotic treatment. (frontiersin.org)
- Comparative genomic analysis of AR1 and four other completely sequenced T4-like genomes (RB32, RB69, T4, and JS98) indicated that they share a well-organized and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. (asm.org)
- i JR904 will help to outline the genotype-phenotype relationship for E. coli K-12, as it can account for genomic, transcriptomic, proteomic and fluxomic data simultaneously. (biomedcentral.com)
- The complete genomic analysis of phage ADB-2 provides new insights into its characteristics and interactions with the host bacterium Escherichia coli. (omicsonline.org)
- The LA PCR Genome Set includes highly purified, high molecular weight human genomic DNA PCR controls, E.coli genomic DNA PCR controls and appropriate primers. (clontech.com)
- To identify traits specific for E. coli A0 34/86, we used a minimal tiling set of 148 BAC clones of A0 34/86 genomic DNA, to construct restriction-digested BAC arrays. (pasteur.fr)
- Whole-genomic DNA of E. coli CR694 was prepared using the Nextera XT DNA sample preparation kit (Illumina, USA) and sequenced using the Illumina HiSeq 2000 (Illumina) at the Australian Genome Research Facility. (asm.org)
- cDNA library was prepared and sequenced in Mouse Genome Encyclopedia Project of Genome Exploration Research Group in Riken Genomic Sciences Center and Genome Science laboratory in RIKEN. (antibody-antibodies.com)
- We have constructed Nhel and Xhol optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. (elsevier.com)
- Here, we investigate global genomic differences between representative members of E. coli phylogenetic group A and discuss their functional consequences on cellulose production. (biomedcentral.com)
- Comparative genomics holds significant promise in understanding the genome organization of such bacteria and thereby identifying coordinates highly relevant in the development of intervention strategies ( 1 ). (asm.org)
- Scientists found that the genome of the German outbreak E. coli strain was mostly enteroaggregative E. coli, a subtype of the bacteria. (infectioncontroltoday.com)
- The reason is that certain antibiotics used against "E. coli" can actually stimulate virally infected bacteria to produce more viruses and viral toxins. (vidyya.com)
- The antibiotics kill the "E. coli", but in their death throes the bacteria release more of these toxins," Dr. Plunkett explains. (vidyya.com)
- With systems biology and genome-scale science emerging and describing the phenotypic functions of bacteria, it is now possible to comprehensively elucidate the structure of the σ-factor network. (biomedcentral.com)
- This method builds upon heterologous gene replacement in bacteria, whereby the bacterial genome is introduced with a synthetic ancient gene. (springer.com)
- Scientists study the unusual genome evolution of the bacteria that live within a genus of cicadas. (the-scientist.com)
- Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). (cdc.gov)
- If you put bacteria in a stressful environment, they will begin to mutate, because their genome seems designed to do that . (drwile.com)
- Since many pathways in mixed-acid fermentation produce hydrogen gas, these pathways require the levels of hydrogen to be low, as is the case when E. coli lives together with hydrogen-consuming organisms, such as methanogens or sulphate-reducing bacteria. (wikipedia.org)
- Reiland, H. , Omolo, M. , Johnson, T. and Baumler, D. (2014) A Survey of Escherichia coli O157:H7 Virulence Factors: The First 25 Years and 13 Genomes. (scirp.org)
- We report the genome organization and analysis of the first completely sequenced T4-like phage, AR1, of Escherichia coli O157:H7. (asm.org)
- The 167,435-bp AR1 genome is currently the largest among all the sequenced E. coli O157:H7 phages. (asm.org)
- For instance, a number of phages have been isolated from the notorious E. coli strain O157:H7, which is an important and well-known human pathogen in uncooked and contaminated food ( 20 ) that may cause serious complications of bloody diarrhea, thrombotic thrombocytopenic purpura (TTP), and hemolytic-uremic syndrome (HUS) ( 58 ). (asm.org)
- The genomes of 12 E. coli O157:H7 phages have been sequenced completely and published in the NCBI genome database. (asm.org)
- Two other sequenced lytic phages, Rv5 and WV8, are the only two known E. coli O157:H7 lytic phages which belong to the Myoviridae phage family ( 53 , 54 ). (asm.org)
- AR1, a lytic phage that can efficiently infect the E. coli O157:H7 strain, was identified from the stool of cows by Ronner and Cliver in 1990 ( 70 ). (asm.org)
- The type of foodborne "E. coli" that was sequenced, designated O157:H7, is a worldwide threat to public health and has triggered scores of recent outbreaks of hemorrhagic colitis (painful, bloody diarrhea) and many fatalities from kidney failure, according to project leaders at the Genome Center of the University of Wisconsin-Madison (UW-Madison). (vidyya.com)
- E. coli' O157:H7 is one of the most dangerous pathogens threatening our food and water supplies," says Anthony S. Fauci, M.D., director of NIAID. (vidyya.com)
- Better ways to diagnose, treat and prevent "E. coli" O157:H7 infections are badly needed. (vidyya.com)
- Thymol, carvacrol, and trans -cinnamaldehyde are essential oil (EO) compounds with broad-spectrum antimicrobial activities against foodborne pathogens, including Escherichia coli O157:H7. (asm.org)
- However, little is known regarding direct resistance and cross-resistance development in E. coli O157:H7 after adaptation to sublethal levels of these compounds, and information is scarce on microbial adaptive responses at a molecular level. (asm.org)
- The present study demonstrated that E. coli O157:H7 was able to grow in the presence of sublethal thymol (1/2T), carvacrol (1/2C), or trans -cinnamaldehyde (1/2TC), displaying an extended lag phase duration and a lower maximum growth rate. (asm.org)
- This study demonstrated the development of direct resistance and cross-resistance and characterized whole-genome transcriptional responses in E. coli O157:H7 adapted to sublethal thymol, carvacrol, or trans -cinnamaldehyde. (asm.org)
- The data suggested that caution should be exercised when using EO compounds as food antimicrobials, due to the potential stress resistance development in E. coli O157:H7. (asm.org)
- IMPORTANCE The present study was designed to understand transcriptomic changes and the potential development of direct and cross-resistance in essential oil (EO)-adapted Escherichia coli O157:H7. (asm.org)
- The results demonstrated altered growth behaviors of E. coli O157:H7 during adaptation in sublethal thymol, carvacrol, and trans -cinnamaldehyde. (asm.org)
- A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933. (ucsd.edu)
- Escherichia coli EDL933 is the prototypic strain for enterohemorrhagic E. coli serotype O157:H7, associated with deadly food-borne outbreaks. (ucsd.edu)
- This entry was posted in E. coli and tagged e. coli O157 , food safety , virulence by Doug Powell . (barfblog.com)
- The bacteriophage phiJLA23 was isolated from an animal feces sample and lytic activity was demonstrated against the Escherichia coli O157:H7 strain. (asm.org)
- Escherichia coli O157:H7 is an important human pathogen of worldwide importance that has been implicated in several outbreaks, and its antibiotic resistance is increasing ( 1 , 2 ). (asm.org)
- We report the characterization of the complete genome sequence of the E. coli O157:H7 phage phiJLA23. (asm.org)
- E. coli O157:H7 is a common pathogen found in contaminated food and water. (elsevier.com)
- Multidrug-resistant E. coli EC302/04 was isolated from a tracheal aspirate, and its genome sequence is expected to provide insights into antimicrobial resistance as well as adaptive and virulence mechanisms of E. coli involved in LRTI. (biomedsearch.com)
- We determined how the host inflammatory response during UTI drives Upec genome instability and evaluated the role of multiple factors of genome replication and repair for their roles in the maintenance of genome integrity and thus virulence during UTI. (northwestern.edu)
- The availability of the complete sequence of Escherichia coli strain MG1655 provides the first opportunity to assess the overall impact of horizontal genetic transfer on the evolution of bacterial genomes. (pnas.org)
- This library contains ~93,000 unique guide RNAs targeting random positions along the genome of E. coli MG1655 with a NGG PAM motif. (addgene.org)
- Screens can be performed using strain LC-E75 ( #115925 ), E. coli strain MG1655 expressing dCas9 under the control of a Tet promoter integrated at the 186 attB site, or strain FR-E01 ( #118727 ), E. coli strain MG1655 expressing dCas9 under the control of a Tet promoter integrated at the HK022 attB site. (addgene.org)
- Constraint-based models of Escherichia coli K-12 MG1655 have been developed and used to study the bacterium's metabolism and phenotypic behavior. (biomedcentral.com)
- We applied this approach to whole genome sequencing data [ 4 ] (~100x per sample using 90bp x 2 paired end Illumina sequencing) obtained from 38 lines of Escherichia coli PFM2, a derivative strain of E. coli K-12 MG1655, and 34 lines of a mismatch repair deficient (deletion of mutL ) derivative that were propagated for ~3,080 and ~375 generations respectively via a mutation accumulation (MA) strategy. (biomedcentral.com)
- Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655. (ucsd.edu)
- Here, we perform a genome-scale reconstruction of the OxyR, SoxR, and SoxS regulons in Escherichia coli K-12 MG1655. (ucsd.edu)
- An updated genome‐scale reconstruction of the metabolic network in Escherichia coli K‐12 MG1655 is presented. (embopress.org)
- The DNA sequence of the gene itself also can provide clues to its origin and ancestry within a genome. (pnas.org)
- The six least-diverged genome-pairs have one or two recombinant transfers of length ~40-115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. (osti.gov)
- Chen H, Venkat S, Wilson J, McGuire P, Chang AL, Gan Q, Fan C. Genome-Wide Quantification of the Effect of Gene Overexpression on Escherichia coli Growth. (mdpi.com)
- Both show that an important factor in determining transcription profiles - when and to what extent a gene is expressed - is the location of the gene within the context of the E. coli K-12 chromosome. (biomedcentral.com)
- 2005a) Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli . (springer.com)
- 2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. (springer.com)
- We describe a targeted, continual multigene editing strategy that was applied to the Escherichia coli genome by using the Streptococcus pyogenes type II CRISPR-Cas9 system to realize a variety of precise genome modifications, including gene deletion and insertion, with a highest efficiency of 100%, which was able to achieve simultaneous multigene editing of up to three targets. (asm.org)
- In our previously published study, we provided high‐resolution measurements of RNA synthesis and degradation lifetimes and proposed a model to explain the coordination of gene expression in Escherichia coli given the measured constraints. (embopress.org)
- A gene which specifies the activity of phosphopyruvate synthase has been located on the genome of Escherichia coli . (royalsocietypublishing.org)
- The observed variation in the ltfA gene of these phages, resulting from a recent recombination event, may explain the observed host-range differences, suggesting that a modular mechanism makes a significant contribution to the short-term evolution (or adaptation) of T5-like phage genomes in the intestinal ecosystem. (epfl.ch)
- The dnaQ gene of Escherichia coli encodes the ε subunit of DNA polymerase III, which provides the 3′ → 5′ exonuclease proofreading activity of the replicative polymerase. (g3journal.org)
- Two novel E. coli phages, the T1-like siphophage LL5 and the rV5-like myophage LL12, were subjected to forward genetic screens against the Keio collection, a library of single non-essential gene deletions in E.coli str. (preprints.org)
- Furthermore, a putative endolysin gene was identified in the genome of the bacteriophage phiJLA23. (asm.org)
- Here, we present the results from a systems approach that integrates multiple genome-scale measurements to reconstruct the regulatory network of σ-factor-gene interactions in E. coli . (biomedcentral.com)
- Specifically, we engineered an approximately 700-million-year-old inferred ancestral variant of tufB , an essential gene encoding elongation factor Tu, and inserted it in a modern Escherichia coli genome in place of the native tufB gene. (springer.com)
- Applications demonstrating the capabilities of the genome‐scale metabolic model to predict high‐throughput experimental growth and gene deletion phenotypic screens are presented. (embopress.org)
- The bacterium Escherichia coli is one of the best and most thoroughly studied free-living organisms. (pnas.org)
- 2004) Global organization of metabolic fluxes in the bacterium Escherichia coli . (springer.com)
- Escherichia coli is perhaps the best characterized and studied bacterium and is of interest industrially, genetically and pathologically. (biomedcentral.com)
- Similarly, the metabolic reconstruction of the bacterium E. coli is arguably the most advanced because it possesses the most complete body of data available for its metabolism and growth behavior. (embopress.org)
- also known as E. coli) is a Gram-negative, facultatively anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms). (wikipedia.org)
- E. coli is a Gram-negative, facultative anaerobic (that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation or anaerobic respiration if oxygen is absent) and nonsporulating bacterium. (wikipedia.org)
- The pathogen genomes are as different from each other as each pathogen is from the benign strain. (pnas.org)
- After validating the approach, we then applied the method to build the first genome-scale integrated metabolic-regulatory model for Mycobacterium tuberculosis, a critically important human pathogen. (aiche.org)
- The research may be the first time that such a comprehensive scientific analysis of an emerging pathogen took place in the first days and weeks of an outbreak, according to the studys lead author, David A. Rasko, PhD, assistant professor of microbiology and immunology at the University of Maryland School of Medicine, and a research scientist at the Institute for Genome Sciences. (infectioncontroltoday.com)
- Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen capable of causing severe disease in humans. (cdc.gov)
- At this point, biologists knew that they were facing a previously unknown pathogen and that traditional methods would not suffice - computational biologists would be needed to assemble and analyze the genome of the newly emerged pathogen. (coursera.org)
- The presence of E. coli triggered investigation of both host and pathogen. (infectoforum.net)
- By analyzing the complete nucleotide sequence of the E. coli genome, the present study provides the first accurate appraisal of the rate of horizontal transfer on an evolutionary timescale, its effects on the organization of a bacterial genome, and its role in bacterial diversification and speciation. (pnas.org)
- The DNA interaction data of Escherichia coli , measured by the genome conformation capture (GCC) technique, have recently become available, which allowed us to investigate the spatial features of bacterial genome organization. (biomedcentral.com)
- In this study, we attempted to use these valuable datasets to investigate the spatial features of bacterial genome organization. (biomedcentral.com)
- Complete Genome Sequence of a CTX-M-15-Producing Escherichia coli Strain from the H30Rx Subclone of Sequence Type 131 from a Patient with Recurrent Urinary Tract Infections, Closely Related to a Lethal Urosepsis Isolate from the Patient's Sister. (gwu.edu)
- We report here the draft genome sequence of uropathogenic Escherichia coli sequence type 648 (ST648) possessing bla NDM-5 from a 55-year-old female in Australia with a history of travel to India. (asm.org)
- Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 Escherichia coli Strain Sanji with Novel In Silico Serotype O89b:H9. (pacb.com)
- Although C. jejuni and C. coli differ by ∼15% at the nucleotide sequence level across the genome ( 4 ), a single multilocus sequence typing (MLST) scheme has been widely adopted for the epidemiological and population analysis of both organisms ( 5 , 6 ). (asm.org)
- The complete nucleotide sequence of hepatitis B virus genome (subtype ayw) cloned in Escherichia coli has been determined using the Maxam and Gilbert method and the dideoxynucleotide method. (harvard.edu)
- Its genome sequence - the series of nucleotide bases (labeled A, T, G, and C) that make up the source code for running the machinery of the cell - has been known since 1997. (bestinscience.com)
- Like K-12, the two B genomes each contain about 4.6 million nucleotide base pairs (Ts linked with As or Gs linked with Cs). (bestinscience.com)
- Data deposition: The annotated genome sequence has been deposited at the European Nucleotide Archive under the accession number PRJEB21000. (biomedcentral.com)
- Since the release of the first genome-scale metabolic reconstruction of the E. coli metabolic network in 2000, there has been a growing number of researchers around the world adapting it for a broad range of studies (Feist 2008). (springer.com)
- In this chapter, we will describe foundational concepts central to the reconstruction process and model formulation, the history of reconstruction of the E. coli metabolic network, the development of reconstruction technology, genome-scale constraint based modeling with key exemplary case studies of uses of the E. coli metabolic reconstruction, and insights into the future of the field. (springer.com)
- As such, this chapter should serve as a guide to those interested in either expanding the application of the E. coli reconstruction or adapting established applications to other organisms. (springer.com)
- DAS Tool for Genome Reconstruction from Metagenomes Through the JGI's Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. (doe.gov)
- The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism. (embopress.org)
- We report the complete genome sequence of E. coli strain NA114 from India, a UPEC strain with a multidrug resistance phenotype and the capacity to produce extended-spectrum beta-lactamase. (asm.org)
- Here we report the complete genome sequence of E. coli 1094, a biofilm forming and cellulose-producing strain isolated from the feces of a healthy human male. (biomedcentral.com)
- The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer. (sciencemag.org)
- Elucidating the adaptive strategies and plasticity of bacterial genomes in situ is crucial for understanding the epidemiology and evolution of pathogens threatening human health. (frontiersin.org)
- Vijayendran C, Polen T, Wendisch V, Friehs K, Niehaus K, Flaschel E. The plasticity of global proteome and genome expression analysis in a well studied closely related model organism, Escherichia coli. (uni-bielefeld.de)
- The plasticity of global proteome and genome expression analysis in a well studied closely related model organism, Escherichia coli", Molecular & Cellular Proteomics , vol. 4, 2005, pp. (uni-bielefeld.de)
- Extraintestinal E. coli are another varied group of life-threatening pathogens of this manifestly versatile species. (pnas.org)
- The extraintestinal E. coli differ from the diarrheal pathogens because they can behave as either harmless human intestinal inhabitants or serious pathogens when they enter the urinary tract, bloodstream, or cerebrospinal fluid. (pnas.org)
- Infections with Gram-negative multidrug-resistant (MDR) pathogens, particularly those caused by β-lactamase-producing Escherichia coli , constitute a major reason for the "global SOS" in public health ( 1 ). (asm.org)
- In order to probe the extent of these regulatory networks, we have measured whole-genome transcriptional profiles of the E. coli response to the superoxide-generating agent paraquat (PQ), an inducer of the soxRS system, and to the weak acid salt sodium salicylate (NaSal), an inducer of the marRA system. (asm.org)
- Uropathogenic Escherichia coli (UPEC) strain with a multidrug resistance phenotype and the capacity to produce extended-spectrum beta-lactamase. (genome.jp)
- Genome of multidrug-resistant uropathogenic Escherichia coli strain NA114 from India. (genome.jp)
- Uropathogenic Escherichia coli (UPEC) causes serious infections in people at risk and has a significant environmental prevalence due to contamination by human and animal excreta. (asm.org)
- Uropathogenic Escherichia coli (Upec) produces ~80% of community-acquired UTI, the second most common infection in humans. (northwestern.edu)
- The availability of the complete sequence of E. coli should stimulate further research toward a more complete understanding of this important experimental, medical, and industrial organism. (sciencemag.org)
- Using PROM, we construct an integrated regulatory-metabolic network for the model organism, Escherichia coli, and demonstrate PROM's ability to model the effect of perturbations to transcriptional regulators and predict microbial growth. (aiche.org)
- E. coli is the most widely studied prokaryotic model organism, and an important species in the fields of biotechnology and microbiology, where it has served as the host organism for the majority of work with recombinant DNA. (wikipedia.org)
- 2007) Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes. (springer.com)
- 2007) GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. (springer.com)
- Borodina I, Krabben P, Nielsen J (2005) Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. (springer.com)
- i JR904 is a more complete and chemically accurate description of E. coli metabolism than i JE660a. (biomedcentral.com)
- A constraint-based model of E. coli metabolism can accomplish this and serve as a model centric database. (biomedcentral.com)
- WEbcoli is a WEb application for in silico designing, analyzing and engineering Escherichia coli metabolism. (oup.com)
- Of the available genome‐scale reconstructions, those for metabolism are most prevalent due to the large body of work characterizing and cataloging metabolic processes. (embopress.org)
- We propose an integrated metabolic model wherein E. coli glycogen metabolism is highly interconnected with a wide variety of cellular processes and is tightly adjusted to the nutritional and energetic status of the cell. (unavarra.es)
- for example, no phenotype distinguishing the closely related taxa Escherichia coli and Salmonella enterica can be attributed to point mutational processes. (pnas.org)
- are genetically closely related to Escherichia coli to the extent that they should be classified as one species [ 2 , 3 ]. (springer.com)
- Genome sequence of multidrug-resistant Escherichia coli EC302/04, isolated from a human tracheal aspirate. (biomedsearch.com)
- Since the inception of the E. coli project, six other complete genomes have become publicly available ( 3 ). (sciencemag.org)
- Also available are instructions for retrieving the complete E. coli K-12 genome sequence. (wisc.edu)
- BGI Releases a Complete De Novo E. Coli O104 Genome Assembly and is Making Its Detection Kit Protocols and Synthesized Primers Freely Available to Worldwide Disease Control an. (mdtmag.com)
- The new assembly includes more than 200x single-end reads from the Illumina HighSeq Platform, which allowed BGI to provide a more complete genome map and to correct any assembly errors from the previous version. (mdtmag.com)
- The complete genome sequence of the Escherichia phage ADB-2 genome can be accessed under the Gen Bank accession number JX912252.1. (omicsonline.org)
- Complete Genome Sequence of a CTX-M-15-Producing Escherichia coli Stra" by Timothy J. Johnson, Maliha Aziz et al. (gwu.edu)
- Here, we follow the genome dynamics of co-existing E. coli lineages in situ of the infant gut during the first year of life. (frontiersin.org)
- Waiting to Respire UC Berkeley and JGI researchers joined forces and data sets to describe bacterial genomes for related ("sibling") lineages that diverged from the bacterial tree before Cyanobacteria and its contemporaries. (doe.gov)
- Linda Pilarski, a researcher in the Department of Oncology, the Department of Medical Microbiology and Immunology, and Laboratory Medicine Pathology provides expertise in molecular biology and device development, McMullen and Yang are authorities on issues that arise during meat processing, G-nzle is an E. coli expert, and Patrick Pilarski contributes computer science expertise. (news-medical.net)