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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.R Factors: A class of plasmids that transfer antibiotic resistance from one bacterium to another by conjugation.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.Bacteriocin Plasmids: Plasmids encoding bacterial exotoxins (BACTERIOCINS).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 Size: The amount of DNA (or RNA) in one copy of a genome.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Genes, Bacterial: The functional hereditary units of BACTERIA.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.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.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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Genome, Protozoan: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.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.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.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.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).Extrachromosomal Inheritance: Vertical transmission of hereditary characters by DNA from cytoplasmic organelles such as MITOCHONDRIA; CHLOROPLASTS; and PLASTIDS, or from PLASMIDS or viral episomal DNA.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.Bacterial Proteins: Proteins found in any species of bacterium.DNA Replication: The process by which a DNA molecule is duplicated.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)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.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).Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.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.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.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.Replicon: Any DNA sequence capable of independent replication or a molecule that possesses a REPLICATION ORIGIN and which is therefore potentially capable of being replicated in a suitable cell. (Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Gene Order: The sequential location of genes on a chromosome.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.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.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.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).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.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.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 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.Genetic Variation: Genotypic differences observed among individuals in a population.F Factor: A plasmid whose presence in the cell, either extrachromosomal or integrated into the BACTERIAL CHROMOSOME, determines the "sex" of the bacterium, host chromosome mobilization, transfer via conjugation (CONJUGATION, GENETIC) of genetic material, and the formation of SEX PILI.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)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.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).Genome, Helminth: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.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.Genes, Viral: The functional hereditary units of VIRUSES.Genome, Plastid: The genetic complement of PLASTIDS as represented in their DNA.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.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.Replication Origin: A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)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)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.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).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.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Electrophoresis, Agar Gel: Electrophoresis in which agar or agarose gel is used as the diffusion medium.Viral Proteins: Proteins found in any species of virus.Cell Line: Established cell cultures that have the potential to propagate indefinitely.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.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.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.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.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.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.Plant Tumor-Inducing Plasmids: Plasmids coding for proteins which induce PLANT TUMORS. The most notable example of a plant tumor inducing plasmid is the Ti plasmid found associated with AGROBACTERIUM TUMEFACIENS.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Bacteriophages: Viruses whose hosts are bacterial cells.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.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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.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.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.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.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.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.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.Tetracycline: A naphthacene antibiotic that inhibits AMINO ACYL TRNA binding during protein synthesis.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Anti-Bacterial Agents: Substances that reduce the growth or reproduction of BACTERIA.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.beta-Lactamases: Enzymes found in many bacteria which catalyze the hydrolysis of the amide bond in the beta-lactam ring. Well known antibiotics destroyed by these enzymes are penicillins and cephalosporins.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 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.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.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.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)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.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.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.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Rhizobium: A genus of gram-negative, aerobic, rod-shaped bacteria that activate PLANT ROOT NODULATION in leguminous plants. Members of this genus are nitrogen-fixing and common soil inhabitants.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.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)Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.DNA, Superhelical: Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. This superhelical DNA is endowed with free energy. During transcription, the magnitude of RNA initiation is proportional to the DNA superhelicity.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.Interspersed Repetitive Sequences: Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.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.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.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.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.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.Deoxyribonucleases, Type II Site-Specific: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 3.1.21.4.Enterobacteriaceae: A family of gram-negative, facultatively anaerobic, rod-shaped bacteria that do not form endospores. Its organisms are distributed worldwide with some being saprophytes and others being plant and animal parasites. Many species are of considerable economic importance due to their pathogenic effects on agriculture and livestock.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.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.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).Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.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.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.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.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Electroporation: A technique in which electric pulses of intensity in kilovolts per centimeter and of microsecond-to-millisecond duration cause a temporary loss of the semipermeability of CELL MEMBRANES, thus leading to ion leakage, escape of metabolites, and increased uptake by cells of drugs, molecular probes, and DNA.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Plant Tumors: A localized proliferation of plant tissue forming a swelling or outgrowth, commonly with a characteristic shape and unlike any organ of the normal plant. Plant tumors or galls usually form in response to the action of a pathogen or a pest. (Holliday, P., A Dictionary of Plant Pathology, 1989, p330)Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.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.Polyploidy: The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Pseudomonas: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.Electrophoresis, Gel, Pulsed-Field: Gel electrophoresis in which the direction of the electric field is changed periodically. This technique is similar to other electrophoretic methods normally used to separate double-stranded DNA molecules ranging in size up to tens of thousands of base-pairs. However, by alternating the electric field direction one is able to separate DNA molecules up to several million base-pairs in length.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.Colicins: Bacteriocins elaborated by strains of Escherichia coli and related species. They are proteins or protein-lipopolysaccharide complexes lethal to other strains of the same species.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Molecular Weight: The sum of the weight of all the atoms in a molecule.Tetracycline Resistance: Nonsusceptibility of bacteria to the action of TETRACYCLINE which inhibits aminoacyl-tRNA binding to the 30S ribosomal subunit during protein synthesis.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.Salmonella: A genus of gram-negative, facultatively anaerobic, rod-shaped bacteria that utilizes citrate as a sole carbon source. It is pathogenic for humans, causing enteric fevers, gastroenteritis, and bacteremia. Food poisoning is the most common clinical manifestation. Organisms within this genus are separated on the basis of antigenic characteristics, sugar fermentation patterns, and bacteriophage susceptibility.Genes, Plant: The functional hereditary units of PLANTS.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.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.Genome, Microbial: The genetic complement of a microorganism as represented in its DNA or in some microorganisms its RNA.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Vaccines, DNA: Recombinant DNA vectors encoding antigens administered for the prevention or treatment of disease. The host cells take up the DNA, express the antigen, and present it to the immune system in a manner similar to that which would occur during natural infection. This induces humoral and cellular immune responses against the encoded antigens. The vector is called naked DNA because there is no need for complex formulations or delivery agents; the plasmid is injected in saline or other buffers.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.Symbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.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.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.Genes, Fungal: The functional hereditary units of FUNGI.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).Terminal Repeat Sequences: Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.Drug Resistance, Bacterial: The ability of 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).Deoxyribonuclease EcoRI: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequence G/AATTC at the slash. EcoRI is from E coliRY13. Several isoschizomers have been identified. EC 3.1.21.-.Klebsiella pneumoniae: Gram-negative, non-motile, capsulated, gas-producing rods found widely in nature and associated with urinary and respiratory infections in humans.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Streptomycin: An antibiotic produced by the soil actinomycete Streptomyces griseus. It acts by inhibiting the initiation and elongation processes during protein synthesis.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Kanamycin: Antibiotic complex produced by Streptomyces kanamyceticus from Japanese soil. Comprises 3 components: kanamycin A, the major component, and kanamycins B and C, the minor components.Genetic Techniques: Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.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.Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.INDEL Mutation: A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Salmonella typhimurium: A serotype of Salmonella enterica that is a frequent agent of Salmonella gastroenteritis in humans. It also causes PARATYPHOID FEVER.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.Drug Resistance, Multiple, Bacterial: The ability of bacteria to resist or to become tolerant to several structurally and functionally distinct drugs simultaneously. This resistance may be acquired through gene mutation or foreign DNA in transmissible plasmids (R FACTORS).Inverted Repeat Sequences: Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.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.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.DNA Helicases: Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.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)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.Transposases: Enzymes that recombine DNA segments by a process which involves the formation of a synapse between two DNA helices, the cleavage of single strands from each DNA helix and the ligation of a DNA strand from one DNA helix to the other. The resulting DNA structure is called a Holliday junction which can be resolved by DNA REPLICATION or by HOLLIDAY JUNCTION RESOLVASES.Streptomyces: A genus of bacteria that form a nonfragmented aerial mycelium. Many species have been identified with some being pathogenic. This genus is responsible for producing a majority of the ANTI-BACTERIAL AGENTS of practical value.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.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Genes, Archaeal: The functional genetic units of ARCHAEA.Penicillinase: A beta-lactamase preferentially cleaving penicillins. (Dorland, 28th ed) EC 3.5.2.-.Chloramphenicol: An antibiotic first isolated from cultures of Streptomyces venequelae in 1947 but now produced synthetically. It has a relatively simple structure and was the first broad-spectrum antibiotic to be discovered. It acts by interfering with bacterial protein synthesis and is mainly bacteriostatic. (From Martindale, The Extra Pharmacopoeia, 29th ed, p106)Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Chloramphenicol O-Acetyltransferase: An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.Kanamycin Resistance: Nonsusceptibility of bacteria to the antibiotic KANAMYCIN, which can bind to their 70S ribosomes and cause misreading of messenger RNA.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Agrobacterium tumefaciens: A species of gram-negative, aerobic bacteria isolated from soil and the stems, leafs, and roots of plants. Some biotypes are pathogenic and cause the formation of PLANT TUMORS in a wide variety of higher plants. The species is a major research tool in biotechnology.
In addition, actinomycete genomes contain extrachromosomal genetic elements such as rolling circle replication plasmids. These ... The chromosomal DNA of Streptomyces lividans 66 is linear. Mol Microbial. 14(5):1103. Redenbach M, Kieser HM, Denapaite D, ... Plasmid-borne streptothricin resistance in gram-negative bacteria. Plasmid. 12:3 189-196. Miyadoh S. 1993. Research on ... Gene: An International Journal on Genes and Genomes. 175:261-267. Sheldon PJ, Johnson DA, August PR, Liu HW, Sherman DH. 1996. ...
"The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis ... Bacillus cereus biovar anthracis is a variant of the Bacillus cereus bacterium that has acquired plasmids similar to those of ... "Bacillus cereus Biovar Anthracis Causing Anthrax in Sub-Saharan Africa-Chromosomal Monophyly and Broad Geographic Distribution ... virulence plasmids". PLoS One. 5 (7): e10986. doi:10.1371/journal.pone.0010986. ISSN 1932-6203. PMC 2901330 . PMID 20634886. ...
Transposable elements and other mobile genetic elements like plasmids and viruses could allow for chromosomal rearrangement and ... A phylogeny was constructed from 1689 identified genes and all homologs available from the rice genome (3177 gene families). ... Jain R, Rivera MC, Lake JA (March 1999). "Horizontal gene transfer among genomes: the complexity hypothesis". Proceedings of ... Bansal AK, Meyer TE (April 2002). "Evolutionary analysis by whole-genome comparisons". Journal of Bacteriology. 184 (8): 2260- ...
In bacteria, transposable elements can easily jump between the chromosomal genome and plasmids. In a study by Devaud et al. in ... Today, there are no active DNA Transposons in the human genome. Therefore, the elements found in the human genome are called " ... International Human Genome Sequencing Consortium (Feb 2001). "Initial sequencing and analysis of the human genome". Nature. 409 ... where the resistance genes were transposed in to the chromosomal genome. Class II transposable elements make up about 3% of the ...
The plasmid T-DNA is integrated semi-randomly into the genome of the host cell, and the tumor morphology genes on the T-DNA are ... Another discovery is that the diverse chromosomal structures in this group appear to be capable of supporting both symbiotic ... A modified Ti or Ri plasmid can be used. The plasmid is 'disarmed' by deletion of the tumor inducing genes; the only essential ... can harbour a Ti-plasmid. Non-Agrobacterium strains have been isolated from environmental samples which harbour a Ri-plasmid ...
An example of this is an antitoxin on the Erwinia chrysanthemi genome that counteracts the toxic activity of an F plasmid toxin ... It has also been proposed that chromosomal copies of plasmid toxin-antitoxin systems may serve as anti-addiction modules - a ... CcdB is found in recombinant bacterial genomes and an inactivated version of CcdA is inserted into a linearised plasmid vector ... Other theories propose the systems have evolved to increase the fitness of plasmids in competition with other plasmids. Thus, ...
... and since the numerous genes promoting DNA transfer are in the plasmid genome rather than in the bacterial genome, it has been ... some of the donor's chromosomal DNA may also be transferred with the plasmid DNA. The amount of chromosomal DNA that is ... If the F-plasmid that is transferred has previously been integrated into the donor's genome (producing an Hfr strain ["High ... The F-plasmid is an episome (a plasmid that can integrate itself into the bacterial chromosome by homologous recombination) ...
An Hfr cell can transfer a portion of the bacterial genome. Despite being integrated into the chromosomal DNA of the bacteria, ... A conjugative plasmid capable of chromosome integration is also called an episome (a segment of DNA that can exist as a plasmid ... integrated into its chromosomal DNA. The integration of the plasmid into the cell's chromosome is through homologous ... A high-frequency recombination cell (Hfr cell) (also called an Hfr strain) is a bacterium with a conjugative plasmid (for ...
The genome in a prokaryote is held within a DNA/protein complex in the cytosol called the nucleoid, which lacks a nuclear ... Plasmid mediated transfer of host bacterial DNA (conjugation) also appears to be an accidental process rather than a bacterial ... The complex contains a single, cyclic, double-stranded molecule of stable chromosomal DNA, in contrast to the multiple linear, ... Conjugation in the well-studied E. coli system is controlled by plasmid genes, and is an adaptation for distributing copies of ...
In addition to chromosomal DNA, Azotobacter can contain plasmids.[30] ... Genome[edit]. The nucleotide sequence of chromosomes of Azotobacter vinelandii, strain AvOP, is partially determined. This ... "Archived from the original (A project to study the genome of Azotobacter vinelandii) on 20 May 2013. Retrieved 13 September ... "Plasmids of Azotobacter vinelandii". Journal of Bacteriology. 170 (4): 1984-1985. doi:10.1128/jb.170.4.1984-1985.1988. PMC ...
Genomic deoxyribonucleic acid is chromosomal DNA, in contrast to extra-chromosomal DNAs like plasmids. It is also then ... The genome of an organism (encoded by the genomic DNA) is the (biological) information of heredity which is passed from one ... That genome is transcribed to produce various RNAs, which are necessary for the function of the organism. Precursor mRNA (pre- ...
... modification systems have been reported to move between prokaryotic genomes within mobile genetic elements such as plasmids, ... Still, they are more frequently a chromosomal-encoded barrier to MGEs than an MGE-encoded tool for cell infection. Natural ... "Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes". Genome Biol. 16 ... "Sputnik's genome reveals further insight into its biology. Although 13 of its genes show little similarity to any other known ...
Conjugation may mediate the transfer of chromosomal sequences by plasmids that integrate into the chromosome. Despite the ... The descendant small genome content depends on the content of chromosomal deletions that occur in the early stages of genome ... there is relatively little variation in genome size when compared with the genome sizes of other major groups of life. Genome ... Bacterial genomes are generally smaller and less variant in size among species when compared with genomes of animals and single ...
This makes targeted gene correction or genome editing a viable option in human cells. Since ZFN-encoding plasmids could be used ... Lee HJ, Kim E, Kim JS (December 2009). "Targeted chromosomal deletions in human cells using zinc finger nucleases". Genome Res ... Chimeric nuclease Genome editing Gene targeting Zinc finger protein Zinc finger chimera Protein engineering Genome engineering ... Kandavelou K, Chandrasegaran S (2008). "Plasmids for Gene Therapy". Plasmids: Current Research and Future Trends. Caister ...
June 2008). "The Chlamydia trachomatis Plasmid Is a Transcriptional Regulator of Chromosomal Genes and a Virulence Factor". ... April 2012). "Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by ... trachomatis strains have an extrachromosomal plasmid. Chlamydia species can exchange DNA between the different strains, thus ...
Lee HJ, Kim E, Kim JS (January 2010). "Targeted chromosomal deletions in human cells using zinc finger nucleases". Genome Res. ... Kandavelou K, Chandrasegaran S (2008). "Plasmids for Gene Therapy". In Lipps, Georg. Plasmids: Current Research and Future ... rAAV mediated genome-editing improves the efficiency of this technique to permit genome engineering in any pre-established and ... Recombinant adeno-associated virus (rAAV) based genome engineering is a genome editing platform centered on the use of rAAV ...
The genome consists of 2.79 Mega-bases on a circular chromosome with four circular plasmids. The genome includes 4,246 genes of ... The GC-content of the genome is 61%. In a 2008 study by Castillo, et al., chromosomal DNA was ioslated using the Marmur methods ... In 2014, the complete genome of H. larsenii was sequenced using Illumina dye sequencing HiSeq 2000 by Iain Anderson as part of ... The closest neighboring species Natrialba aegypitaca and Natrialba asiatica had a 94.5% and 93.3% genome similarity, ...
Additional plasmid mini-preps demonstrated that neither plasmid was retained in the cells, therefore indicating plasmid curing ... No-SCAR is able to manipulate the E. coli genome without the use of the chromosomal markers detailed in previous recombineering ... These components make up the pKDsg-XXX plasmid to facilitate λ-red mediated alterations of the E. coli genome, where -XXX ... Following successful recombination of the linear DNA to the target genome, plasmid origins and markers can be re-used as a ...
Plasmids are small extra-chromosomal DNAs that may contain genes for antibiotic resistance, enzymes that degrade unusual ... "Genomes Online Database". Genomes Online Database. Joint Genome Institute. Retrieved 14 Sep 2016. Nakabachi A, Yamashita A, Toh ... Plasmids that are maintained at a high copy number per cell typically lack partition systems because plasmids will randomly ... genome-genome hybridisation, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the ...
Both methods utilize plasmids, which carry DNA inside a cell that can replicate independently of chromosomal DNA. This is the ... Genome analysis of Acanthamoeba castellanii, an amoebozoan, revealed that a significant portion of the genome that is expressed ... When analyzed, the genome of Acanthamoeba castellanii shows genes with orthologs currently found in a diverse range of bacteria ... For gene delivery to be successful, foreign DNA must survive long enough in the host cell to integrate into its genome. This ...
have used pTBN12, a well-defined plasmid, as a probe with AluI restriction fragments. The probe was able to distinguish 11 RFLP ... In this case, the primers are directed towards repetitive chromosomal elements such as IS6110 in M. tuberculosis and the ERIC ... Using this technique, the M. ulcerans genome has been found to produce three different restriction profiles related to the ... In this method, restriction enzymes that cut DNA infrequently are used to generate large fragments of chromosomal DNA, which ...
This repair mechanism induces errors in the genome via indels (insertion or deletion), or chromosomal rearrangement; any such ... Once the TALEN constructs have been assembled, they are inserted into plasmids; the target cells are then transfected with the ... Genome editing with engineered nucleases Zinc finger nuclease Meganuclease CRISPR Boch J (February 2011). "TALEs of genome ... plasmids, and the gene products are expressed and enter the nucleus to access the genome. Alternatively, TALEN constructs can ...
... with a covalently attached protein may assist with bacterial conjugation and integration of the plasmids into the genome. These ... Certain organisms, such as yeast, rely on chromosomal DNA replication to produce eccDNA whereas eccDNA formation can occur in ... Fertility plasmids, or f plasmids, allow for conjugation to occur whereas resistance plasmids, or r plasmids, contain genes ... Circular bacterial plasmids are classified according to the special functions that the genes encoded on the plasmid provide. ...
Wang H.H., Isaacs F. J., Carr P.A., Sun Z.Z., Xu G., Forest C.R., Church G.M. (2009). "Programming cells by multiplex genome ... Ellis H. M., Yu D., DiTizio T., Court D. L. (2001). "High efficiency mutagenesis, repair, and engineering of chromosomal DNA ... 1983) Genetic applications of yeast transformation with linear and gapped plasmids. Methods. Enzymol. 101: 228-245. Moerschell ... Multiplex Automated Genome Engineering, in the Church lab. With the development of CRISPR technologies, construction of CRISPR ...
... s alter the genome by blocking the function of a host gene; they can either replace the host gene with one that codes ... The transposase plasmid portion drives the transposition of the P transposon backbone, containing the transgene of interest and ... These sites, unlike P elements, can be specifically inserted to flank a chromosomal segment of interest, aiding in targeted ... Additionally, P elements often consist of two plasmid components, one known as the P element transposase and the other, the P ...
... though those of dinophyte algae are a notable exception-their genome is broken up into about forty small plasmids, each 2,000- ... Arabidopsis thaliana has multiple isoforms of Toc75 that are named by the chromosomal positions of the genes that code for them ... Over time, many parts of the chloroplast genome were transferred to the nuclear genome of the host,[4][7][26] a process called ... Many of the chloroplast's protein complexes consist of subunits from both the chloroplast genome and the host's nuclear genome ...
... for the plasmid ORFs is 2-fold weaker than that for the chromosomal ORFs (Tables 1 and 2). However, plasmid sequences are not ... Plasmids that are not in our study are largely those that are homologous to the cp32 plasmids in B31. Had these plasmids been ... JD1/N40 scaffolds that uniquely (1:1) match the B31 genome were identified as orthologous genome segments. JD1/N40 plasmids ... of chromosomal ORFs and approximately one half of the plasmids in B31 (Tables 1 and 2). Plasmid profiles differ among the ...
In addition to chromosomal DNA, Azotobacter can contain plasmids.[30] ... Genome[edit]. The nucleotide sequence of chromosomes of Azotobacter vinelandii, strain AvOP, is partially determined. This ... "Archived from the original (A project to study the genome of Azotobacter vinelandii) on 20 May 2013. Retrieved 13 September ... "Plasmids of Azotobacter vinelandii". Journal of Bacteriology. 170 (4): 1984-1985. doi:10.1128/jb.170.4.1984-1985.1988. PMC ...
A) Chromosomal comparison: blue, B.anthracis Ames; green, B.cereus ATCC 10987; red, B.cereus ATCC 14579. (B) Plasmid comparison ... The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus ... The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus ... The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus ...
... homologous to mitochondrial plasmid-like DNAs are located within limited chromosomal regions on the rice nuclear genome. In: ... N2 - The chromosomal locations of restriction fragments of nuclear DNA that were homologous to four mitochondrial plasmid-like ... AB - The chromosomal locations of restriction fragments of nuclear DNA that were homologous to four mitochondrial plasmid-like ... The chromosomal locations of restriction fragments of nuclear DNA that were homologous to four mitochondrial plasmid-like DNAs ...
All isolates contained a closely related plasmid (pKPC2) harboring blaKPC-2, a K. pneumoniae carbapenemase gene, and had a ... A) Analysis generated using 63,297 single-nucleotide polymorphism sites in the core genome. The chromosomal sequence of SGH10 ( ... Acquisition of Plasmid with Carbapenem-Resistance Gene blaKPC2 in Hypervirulent Klebsiella pneumoniae, Singapore Yahua Chen, ... B) Analysis generated from the alignment of K. pneumoniae virulence plasmids from the first isolates collected from different ...
The genetic material of bacteria and plasmids is DNA. Bacterial viruses (bacteriophages or phages) have DNA or RNA as genetic ... F plasmid and chromosomal DNA are indicated by heavy and fine lines, respectively. For additional data concerning the genomes ... Other bacterial strains have additional replicons, such as plasmids and bacteriophages.. Chromosomal DNA. Bacterial genomes ... Phage genomes, like plasmids, encode functions required for replication in bacteria, but unlike plasmids they also encode ...
Chromosomal stasis versus plasmid plasticity in aphid endosymbiont Buchnera aphidicola. A Latorre, R Gil, F J Silva, A Moya ... Chromosomal localization of Wolbachia inserts in the genomes of two subspecies of Chorthippus parallelus forming a Pyrenean ... Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect. Natsuko Kondo, Naruo Nikoh, Nobuyuki ... Plasmids and Rickettsial Evolution: Insight from Rickettsia felis. Joseph J. Gillespie, Magda S. Beier, M. Sayeedur Rahman, ...
Lee HJ, Kim E, Kim JS (January 2010). "Targeted chromosomal deletions in human cells using zinc finger nucleases". Genome Res. ... Kandavelou K, Chandrasegaran S (2008). "Plasmids for Gene Therapy". In Lipps, Georg. Plasmids: Current Research and Future ... rAAV mediated genome-editing improves the efficiency of this technique to permit genome engineering in any pre-established and ... Recombinant adeno-associated virus (rAAV) based genome engineering is a genome editing platform centered on the use of rAAV ...
Genome annotation databases. Ensembl eukaryotic genome annotation project. More...Ensembli. ENST00000276127; ENSP00000276127 ... The DNASU plasmid repository. More...DNASUi. 53336. Structural Biology Knowledgebase. Search.... ... Genome annotation databases. Ensembl eukaryotic genome annotation project. More...Ensembli. ENST00000276127; ENSP00000276127 ... They may also represent different stages in a genome project and include components such as contigs, scaffolds or Whole Genome ...
Yersinia pestis DNA is needed for genome sequencing, molecular cloning, protein expression, PCR detection, and other ... Yersinia pestis DNA is needed for genome sequencing, molecular cloning, protein expression, PCR detection, and other ... Yersinia pestis Chromosomal DNA Plasmid Extraction Quality and quantity determination This is a preview of subscription content ... After chromosomal and plasmid DNA extraction, the quality and quantity of extracted DNA should be evaluated. ...
The plasmids may provide a reservoir of mobile elements that promote adaptive chromosomal rearrangements under particular ... The genome of B. pseudofirmus OF4 includes two plasmids that are lost from some mutants without viability loss. ... Draft Genome Sequence of Bacillus alcalophilus AV1934, a Classic Alkaliphile Isolated from Human Feces in 1934, Genome ... Nan Jia, Jin Du, Ming-Zhu Ding, Feng Gao, Ying-Jin Yuan, Yu Xue, Genome Sequence of Bacillus endophyticus and Analysis of Its ...
The fully annotated chromosomal genome is available in the EMBL/GenBank databases with accession number AL645882. Two plasmids ... Published Genome Data. The chromosome is 8,667,507 bp long with a G+C content of 72.1% and is predicted to contain 7825 protein ... Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).. Bentley SD, Chater KF, Cerdeño-Tárraga AM, ... Wellcome Sanger Institute, Genome Research Limited (reg no. 2742969) is a charity registered in England with number 1021457 , ...
The chromosomal DNA mobilization mediated by pLS20catΔoriT will allow us to develop a novel genetic tool for the rapid, easy, ... This resulted in the complete loss of the conjugative transfer of the plasmid but still allowed it to mobilize a co-resident ... mobilizable plasmid. Moreover, pLS20catΔoriT was able to mobilize longer DNA segments, up to 113 kb of chromosomal DNA ... In addition, it can function as a helper plasmid, mediating the mobilization of an independently replicating co-resident ...
In addition, actinomycete genomes contain extrachromosomal genetic elements such as rolling circle replication plasmids. These ... The chromosomal DNA of Streptomyces lividans 66 is linear. Mol Microbial. 14(5):1103. Redenbach M, Kieser HM, Denapaite D, ... Plasmid-borne streptothricin resistance in gram-negative bacteria. Plasmid. 12:3 189-196. Miyadoh S. 1993. Research on ... Gene: An International Journal on Genes and Genomes. 175:261-267. Sheldon PJ, Johnson DA, August PR, Liu HW, Sherman DH. 1996. ...
Some DNA gain was chromosomal but most was in plasmids. One isolate had a large region (8,644 bp) missing, which was probably ... Genome innovation by the presence of unique DNA, attributable to HGT from related bacteria, varied greatly among the isolates, ... Whole genome sequence comparison of eight independent isolates of this population from mussels or clinical cases (from ... Differences of 1366 to 217,729 bp genome length and 13 to 164 bp single nucleotide variants (SNVs) were found. Most genomic ...
... essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. To ... Comparisons between this plasmid and complete rhizobial genomes and symbiotic compartments already sequenced show a general ... The symbiotic plasmid is a circular molecule of 371,255 base-pairs containing 359 coding sequences. Nodulation and nitrogen- ... We report the complete sequence of the symbiotic plasmid of Rhizobium etli CFN42, a microsymbiont of beans, and a comparison ...
whose genomes have been sequenced to date and is derived from an ancestral plasmid. LPP-1 encodes a large array of proteins ... Phylogenetic analysis reveals that these plasmids have arisen from an ancestral plasmid, which has undergone extensive ... of the total pan-plasmid (2,095 CDS), conserved among all LPP-1 plasmid sequences, includes those required for thiamine and ... The LPP-1 plasmid sequences range in size from ~281 to 794 kb and carry between 238 and 750 protein coding sequences (CDS). A ...
We thank Feng Zhang for plasmid pX330, Marc Ouellette and Barbara Papadopoulou for plasmids pSPneo and pSPhyg, and Dan ... Optimized CRISPR-Cas9 Genome Editing for Leishmania and Its Use To Target a Multigene Family, Induce Chromosomal Translocation ... Optimized CRISPR-Cas9 genome editing for Leishmania and its use to target a multigene family, induce chromosomal translocation ... Optimized CRISPR-Cas9 Genome Editing for Leishmania and Its Use To Target a Multigene Family, Induce Chromosomal Translocation ...
Helicobacter pylori interstrain restriction-modification diversity prevents genome subversion by chromosomal DNA from competing ... The presence of multiple plasmid-borne R-M systems in the segmented genome of B. burgdorferi, the heterogeneity in plasmid ... In brief, 20 μg of E. coli pNP or pBBE02 plasmid DNA, 1 to 20 μg of E. coli shuttle vector DNA, or 10 μg of total plasmid DNA ... However, plasmid DNA purified from B. burgdorferi transformed naïve B. burgdorferi much more efficiently than plasmid DNA from ...
Four pUC18-derived plasmids and five pBR322-derived plasmids contained a region of the genome that mapped to min 19 (Fig.1A). ... One chromosomal region, defined by a single plasmid, contained rob and creBC. Since rob is involved in drug resistance (45), ... "L" and "H" are plasmid names (e.g., L13 and H7), with "L" referring to pBR322-based plasmids and "H" referring to pUC18-based ... Another cluster of 7 pUC18-derived plasmids and 11 pBR322-derived plasmids shared a single common gene, sdiA from min 43 (Fig.1 ...
The genome sequences were produced as full genomes, chromosomes only and with plasmid sequences pulled out themselves too. ... 19 genes were shown to be core on the plasmid, and 2464 chromosomal genes were conserved across the clade. Nucleotide identity ... The core genomes of the plasmid and chromosome will be analysed to elucidate orthologous and paralogous sequences, and to ... This was a successful project where it was revealed that plasmids were co-speciating with the genomes of the strains within the ...
Whole-genome sequencing and bioinformatics.Complete genomic DNA (chromosomal DNA and plasmids) was isolated using the Qiagen ... The NCBI Prokaryotic Genome Annotation Pipeline was used for complete genome annotation. Detection of resistance genes, plasmid ... Plasmids are large, circular DNA molecules that are not part of the chromosomal DNA of the bacteria, and in the case of ... In addition to the two large plasmids, two small cryptic plasmids of 4,572 bp and 4,163 bp were present. These plasmids did not ...
Chromosomal localization of H60b and H60c was deduced based on the mouse genome assembly (NCBI Build 37.1). We deduced the exon ... The coding regions of mouse H60 molecules excluding the signal peptide were obtained by PCR using the plasmid cDNA isolated ... BLAST searches of the mouse genome sequence were conducted using H60a, H60b, or H60c cDNA sequences as queries. ... DNA for transfection was isolated with the EndoFree plasmid purification kit purchased from Qiagen. ...
Some bacteria have extra chromosomal DNA-a mini-chromosome called a plasmid. Plasmids contain only a few genes but are rapidly ... The entire complement of chromosomes in a given cell or for a given species is referred to as the genome. Plant genomes vary in ... duplication of a chromosomal segment occurs, g) inversion of a chromosomal segment occurs. Down syndrome , for instance, is ... duplication of a chromosomal segment occurs, g) inversion of a chromosomal segment occurs. Down syndrome , for instance, is ...
An E. coli/Shigella pan-genome microarray, containing the chromosomal content of E24377A, was used to examine the ... and the chromosomal content is printed on the microarray utilized in this study (10); the six plasmids present in the isolate, ... Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J. ... Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25. ...
  • Crossspecies gene transfer has been suggested at other loci as well ( 21 ), and Stevenson and Miller ( 22 ) concluded that intracellular transfers of cp32 plasmids have occurred. (pnas.org)
  • Another emerging application of rAAV based genome editing is for gene therapy in patients, due to the accuracy and lack of off-target recombination events afforded by the approach. (wikipedia.org)
  • Our findings have basic implications for horizontal gene transfer among B. burgdorferi strains with distinct plasmid contents. (asm.org)
  • The loss of two linear plasmids, lp25 and lp56, was shown to correlate with enhanced shuttle vector transformation, suggesting that specific lp25 and lp56 gene products present a barrier to stable introduction of foreign DNA ( 34 ). (asm.org)
  • Finally, we analyzed the type of modification present on DNA isolated from B. burgdorferi with different plasmid or gene contents. (asm.org)
  • Horizontal gene transfer of resistance plasmids can complicate hospital outbreaks and cause problems in epidemiological tracing, since tracing is usually based on bacterial clonality. (asm.org)
  • We demonstrate that all ESBL-KP isolates contained two plasmids with the bla CTX-M-15 gene located on the smaller one (~80 kbp). (asm.org)
  • The same ESBL-KP clone was present in follow-up samples for up to 2 years in some patients, and the plasmid carrying the bla CTX-M-15 gene was stable throughout this time period. (asm.org)
  • This CRISPR system could also be used to generate specific chromosomal translocations, which will help in the study of Leishmania gene expression and transcription control. (asm.org)
  • Linearized plasmids carrying a Saccharomyces cerevisiae URA3 gene efficiently transformed the ura3 auxotroph to prototrophy. (genetics.org)
  • Sequence analysis suggested that illegitimate recombination is nonrandom at the single-gene level and that the integrating plasmid has a preference for inserting into noncoding regions of the genome. (genetics.org)
  • This plasmid, dubbed "Superloser," was designed with reduced sequence similarity to commonly used yeast plasmids ( i.e. , pRS400 series) to limit recombination, a process that in our experience leads to retention of the yeast gene(s) instead of the desired gene(s). (g3journal.org)
  • This method works by having a null allele of a gene on the chromosome, kept alive by a wild-type copy on a counter-selectable plasmid - typically employing the URA3 marker. (g3journal.org)
  • These background colonies consist of two major types: 1) spontaneous inactivation of the URA3 marker or 2) formation of plasmid recombinants in which the incoming plasmid lacking URA3 acquires the essential gene ( e.g. , yeast histones), or the resident plasmid acquires the incoming selectable marker. (g3journal.org)
  • We demonstrate the ability of this system to efficiently and precisely engineer point mutations and large single-gene deletions in the S. aureus genome and to yield highly enriched populations of engineered recombinants even in the absence of an externally selectable phenotype. (asm.org)
  • By virtue of utilizing inexpensive, commercially synthesized synthetic DNA oligonucleotides as substrates for recombineering and counterselection, this system provides a scalable, versatile, precise, inexpensive, and generally useful tool for producing isogenic strains in S. aureus which will enable the high-throughput functional assessment of genome variation and gene function across multiple strain backgrounds. (asm.org)
  • Stably transfected cells can be selected by co-transfection of a second plasmid carrying an antibiotic-resistance gene or by providing a resistance gene on the same vector as the gene of interest. (qiagen.com)
  • We constructed a pVPGX1- Cm r plasmid (a pVA1-type plasmid) by adding a chloramphenicol resistance gene as a marker in a donor AHPND-causing V. parahaemolyticus 20130629002S01 ( Vp 2S01). (frontiersin.org)
  • The S. acidocaldarius genome contains an integrated, and probably encaptured, pARN-type conjugative plasmid which may facilitate intercellular chromosomal gene exchange in S. acidocaldarius. (psu.edu)
  • A conjugative mechanism, rather than transformation or transduction, was invoked to account for gene exchange because no recombinants were detected without prolonged physical contact of the parental strains (indeed, a period of mixed growth was needed) and because the pattern of inheritance of groups of markers was consistent only with recombination of large segments of the parental genomes (25). (springer.com)
  • Previously, multiple attempts have failed to produce a mutant when either the -suicide plasmid system or the Red Disruption system was used to knock-out the asd gene [ 8 ] of SP . (hindawi.com)
  • After selection with the appropriate antibiotic, the Cm resistance gene can be eliminated using the helper plasmid pCP20. (hindawi.com)
  • NA (solid LB medium without NaCl) and NB (liquid LB medium without NaCl) with 10% sucrose were used during the gene allelic exchange experiments to select plasmids that had been excised from the chromosome. (hindawi.com)
  • He is remembered for coining the term 'genome' in 1920, by making a portmanteau of the words gene and chromosome. (absoluteastronomy.com)
  • A chromosomal ampC gene is also lacking in Klebsiella spp. (asm.org)
  • Conclusion: We have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. (ufl.edu)
  • An alternative method was, therefore, established by assembling Cas9 and gRNA in vitro, followed by transformation of the ribonucleoprotein complex with a plasmid containing the pyr4 marker gene into T. reesei TU-6. (springer.com)
  • A chromosomal region downstream of lba0889 carrying a highly expressed enolase gene was selected for insertion of the vaccine cassettes. (asm.org)
  • The staphylococcal chromosome cassette mec (SCC mec ) ( 15 , 16 , 21 ), the genetic element that carries the methicillin resistance gene, mecA , integrates into the orfX gene in the S. aureus genome in a site specific manner. (asm.org)
  • Plasmids can be considered to be part of the mobilome , since they are often associated with conjugation , a mechanism of horizontal gene transfer . (thefullwiki.org)
  • Rather, plasmids provide a mechanism for horizontal gene transfer within a population of microbes and typically provide a selective advantage under a given environmental state. (thefullwiki.org)
  • In this case, researchers grow bacteria containing a plasmid harboring the gene of interest. (thefullwiki.org)
  • The whole-genome sequence of an epidemic, multidrug-resistant Acinetobacter baumannii strain (strain ACICU) belonging to the European clone II group and carrying the plasmid-mediated bla OXA - 58 carbapenem resistance gene was determined. (asm.org)
  • In addition, gene sequence modifications, plasmid copy number, chaperonin co-expression, post-translational enzymatic modification, and process temperature were also required to allow final erythromycin A formation. (jove.com)
  • a) Escherichia coli cells observed after loss of EcoRI restriction‐modification gene complex (r+m+) placed on a ts plasmid by a temperature shift. (els.net)
  • b) Control E. coli cells losing restriction‐negative EcoRI gene complex (r−m+) placed on a ts plasmid by a temperature shift. (els.net)
  • 7 ). To ensure the accurate mapping of targeted gene deletions using K. pneumoniae Ecl8, whole-genome sequencing was undertaken. (asm.org)
  • Plasmids can be deliberately introduced into desired cells and utilized to overexpress a gene of interest in a specific cell line. (polyplus-transfection.com)
  • IL2RG, RAG1 and/or RAG2 gene) into the genome of a cell for provision of proteins lacking or deficient in SCID. (patents.com)
  • The recent demonstration by Chen and colleagues of enhanced transformation of B. burgdorferi following in vitro methylation of DNA ( 13 ) further supports the hypothesis that these B. burgdorferi plasmids encode R-M enzymes that degrade foreign DNA lacking the appropriate modification. (asm.org)
  • In this chapter we will review our knowledge of these plasmids, the virulence factors that they encode, and their role in disease. (asmscience.org)
  • As shown in a magnified reticulate body, the chlamydial plasmid has eight ORFs, which encode plasmid maintenance and chlamydia-specific functions. (rupress.org)
  • This project will analyse a bank of existing Illumina data to assemble high quality genomes and try to define the core genome of the Photorhabdus genus (both chromosomally and plasmidborne). (warwick.ac.uk)
  • Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium . (frontiersin.org)
  • Extrachromosomal genetic elements such as plasmids and bacteriophages are nonessential replicons which often determine resistance to antimicrobial agents, production of virulence factors, or other functions. (nih.gov)
  • Analysis of the proteins encoded on LPP-1 also showed that these plasmids contribute to a wide range of Pantoea phenotypes, including the transport and catabolism of various substrates, inorganic ion assimilation, resistance to antibiotics and heavy metals, colonization and persistence in the host and environment, pathogenesis and antibiosis. (biomedcentral.com)
  • Plasmids are a central reason for the rapid global spread of bacterial resistance to antibiotics. (asm.org)
  • Resistance appeared initially in organisms such as Enterobacter cloacae , Citrobacter freundii , Serratia marcescens , and Pseudomonas aeruginosa that could, by mutation, overproduce their chromosomal AmpC (also termed class C or group 1) β-lactamase, thus providing resistance to both oxyimino- and 7-α-methoxy-cephalosporins and monobactams ( 74 ). (asm.org)
  • and Proteus mirabilis , and this resistance was found to be mediated by plasmids encoding extended-spectrum β-lactamases (ESBLs), which are enzymes that arose by mutations in TEM or SHV β-lactamases of more limited hydrolytic capacity ( 39 , 40 , 68 ). (asm.org)
  • Whole-genome sequencing (WGS) is a newer alternative for tuberculosis (TB) diagnostics and is capable of providing rapid drug resistance profiles while performing species identification and capturing the data necessary for genotyping. (asm.org)
  • Transmissible mobile genetic elements, such as plasmids and transposons, do not play a significant role in M. tuberculosis drug resistance ( 15 , 16 ). (asm.org)
  • Their high-level resistance is associated with multiple chromosomal substitutions in gyrA and parC. (jove.com)
  • The consequence of the ability of E. faecium to acquire broad host-range plasmids is that drug resistance can be widely and more easily spread. (kenyon.edu)
  • Yeh, Ting 2016-10-14 00:00:00 Unlike Ff-like coliphages, certain filamentous Inoviridae phages integrate their genomes into the host chromosome and enter a prophage state in their infectious cycle. (deepdyve.com)
  • Multipartite genomes like that of R. etli might enhance the adaptive potential of the bacterium, allowing the reassortment of essential, nonessential, and redundant functions to contend with challenging environments. (pnas.org)
  • Yet, of more than 166 sequenced and published bacterial genomes (National Center for Biotechnology Information/NCBI 2004) not including Archaea, at this time only eight are plant pathogens. (apsnet.org)
  • This resulted in the complete loss of the conjugative transfer of the plasmid but still allowed it to mobilize a co-resident mobilizable plasmid. (biomedcentral.com)
  • The sticky or aggregation substance facilitates the transfer of the plasmid to the recipient cell by helping them to stick together. (kenyon.edu)
  • CRISPR-Cas9-mediated genome editing has recently been adapted for Leishmania spp. (asm.org)
  • The CRISPR/Cas9 technology has been widely used for genome editing in mammalian cells, plants, and microbes. (springer.com)
  • Genome disruption using CRISPR/Cas9 has been reported for a variety of filamentous fungi [ 7 ], which commonly requires expression of cas9 in vivo. (springer.com)
  • Although linear DNA results in lower DNA uptake by the cells relative to supercoiled DNA, it yields optimal integration of DNA into the host genome. (qiagen.com)
  • Repair of DNA double‐strand breakage provides accurate products and innacurate products for host genome. (els.net)
  • Here, we report the identification of highly polymorphic loci identified by means of a comparison of three closely related genomes and their use in the study of population structure of B. burgdorferi . (pnas.org)
  • Large staphylococcal plasmids commonly carry antibiotic resistances and virulence loci, but relatively few have been completely sequenced. (g3journal.org)
  • The fully annotated chromosomal genome is available in the EMBL/GenBank databases with accession number AL645882 . (sanger.ac.uk)
  • We have sequenced the large virulence plasmid pWR501 from Shigella flexneri serotype 5a, and it is available from Genbank with accession number AF348706 . (wisc.edu)
  • note that the four plasmids present in strain 2457T have not been published, and are not represented in GenBank at this time. (wisc.edu)
  • Several pieces of evidence suggest an exogenous origin for the symbiotic plasmid (p42d) and p42a. (pnas.org)
  • Horizontal transfer of this plasmid was successfully performed from the AHPND- Vp 2S01 to a non-pathogenic strain of V. campbellii at the transfer efficiency of 2.6×10 −8 transconjugant/recipient, and DNase I treatment did not eliminate the transfer. (frontiersin.org)
  • We have sequenced the genome of R. leguminosarum biovar viciae strain 3841. (biomedcentral.com)
  • These experiments led to the genetic definition of two conjugative plasmids-SCP1 and SCP2-that were deduced to be present in an autonomous state in the wild-type A3(2) strain and to be lost, or in the case of SCP1 sometimes chromosomally integrated, in various of its derivatives. (springer.com)
  • I had a C. elegans strain with a construct integrated in the genome. (biostars.org)
  • The 2457T genome was compared with other Enterobacterial pathogens, including another recently sequenced S. flexneri 2a strain, 301. (wisc.edu)
  • Whole-genome shotgun libraries of strain 2457T were constructed in M13Janus (insert size ~2.0 kbp) and pBlueScript KS- (insert size ~5 kbp). (wisc.edu)
  • Clones were sequenced using dye terminator chemistry, collecting 66,219 reads on ABI377 and 3700 instruments (final coverage 7.2X). A whole-genome optical map of Xho I sites was prepared to aid the ordering of contigs during assembly and to confirm the endpoints and lengths of inversions in the strain comparsions. (wisc.edu)
  • Strain 2457T harbors four plasmids, which remain to be completed. (wisc.edu)
  • Overexpression of plasmid-encoded aroA and aroD doubled SA production than its parent strain. (biomedcentral.com)
  • Here we report a new plasmid shuffle vector for forcing budding yeast ( Saccharomyces cerevisiae ) to incorporate a new genetic pathway in place of a native pathway - even an essential one - while maintaining low false positive rates (less than 1 in 10 8 per cell). (g3journal.org)
  • Since the original publication, mcr-1 with or without the insertion element IS Apl1 has been detected on plasmids of different incompatibility groups, including IncI2, IncHI2, and IncX4, and in many different countries ( 1 - 3 ). (cdc.gov)