Genomic Islands: Distinct units in some bacterial, bacteriophage or plasmid GENOMES that are types of MOBILE GENETIC ELEMENTS. Encoded in them are a variety of fitness conferring genes, such as VIRULENCE FACTORS (in "pathogenicity islands or islets"), ANTIBIOTIC RESISTANCE genes, or genes required for SYMBIOSIS (in "symbiosis islands or islets"). They range in size from 10 - 500 kilobases, and their GC CONTENT and CODON usage differ from the rest of the genome. They typically contain an INTEGRASE gene, although in some cases this gene has been deleted resulting in "anchored genomic islands".Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Islands: Tracts of land completely surrounded by water.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).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.CpG Islands: Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Genes, Bacterial: The functional hereditary units of BACTERIA.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Salmonella enterica: A subgenus of Salmonella containing several medically important serotypes. The habitat for the majority of strains is warm-blooded animals.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.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.Integrons: DNA elements that include the component genes and insertion site for a site-specific recombination system that enables them to capture mobile gene cassettes.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)Bacterial Proteins: Proteins found in any species of bacterium.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Cupriavidus: A genus of gram-negative, aerobic, rod-shaped bacteria, in the family BURKHOLDERIACEAE, that are mobile by means of peritrichous FLAGELLA. The genus was formerly called Wautersia and species in this genus were formerly in the genus RALSTONIA.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.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.Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.Vibrio vulnificus: A species of halophilic bacteria in the genus VIBRIO, which lives in warm SEAWATER. It can cause infections in those who eat raw contaminated seafood or have open wounds exposed to seawater.RNA, Transfer, Gly: A transfer RNA which is specific for carrying glycine to sites on the ribosomes in preparation for protein synthesis.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)Rhode IslandAmino 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.Indian Ocean Islands: Numerous islands in the Indian Ocean situated east of Madagascar, north to the Arabian Sea and east to Sri Lanka. Included are COMOROS (republic), MADAGASCAR (republic), Maldives (republic), MAURITIUS (parliamentary democracy), Pemba (administered by Tanzania), REUNION (a department of France), and SEYCHELLES (republic).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.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).Pacific Islands: The islands of the Pacific Ocean divided into MICRONESIA; MELANESIA; and POLYNESIA (including NEW ZEALAND). The collective name Oceania includes the aforenamed islands, adding AUSTRALIA; NEW ZEALAND; and the Malay Archipelago (INDONESIA). (Webster's New Geographical Dictionary, 1988, p910, 880)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.Prochlorococcus: A genus of marine planktonic CYANOBACTERIA in the order PROCHLOROPHYTES. They lack PHYCOBILISOMES and contain divinyl CHLOROPHYLL, a and b.Comparative Genomic Hybridization: A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.Genetic Variation: Genotypic differences observed among individuals in a population.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.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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.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).Gene Order: The sequential location of genes on a chromosome.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Haemophilus somnus: A species of gram-negative bacteria (currently incertae sedis) causing multisystem disease in CATTLE.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.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.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.Recombinases: A broad category of enzymes that are involved in the process of GENETIC RECOMBINATION.Salmonella Infections: Infections with bacteria of the genus SALMONELLA.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)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.Streptomyces lividans: An actinomycete used for production of commercial ANTIBIOTICS and as a host for gene cloning.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.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.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.Immunoglobulin Fab Fragments: Univalent antigen-binding fragments composed of one entire IMMUNOGLOBULIN LIGHT CHAIN and the amino terminal end of one of the IMMUNOGLOBULIN HEAVY CHAINS from the hinge region, linked to each other by disulfide bonds. Fab contains the IMMUNOGLOBULIN VARIABLE REGIONS, which are part of the antigen-binding site, and the first IMMUNOGLOBULIN CONSTANT REGIONS. This fragment can be obtained by digestion of immunoglobulins with the proteolytic enzyme PAPAIN.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).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.Salmonella typhimurium: A serotype of Salmonella enterica that is a frequent agent of Salmonella gastroenteritis in humans. It also causes PARATYPHOID FEVER.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.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.Genes, Archaeal: The functional genetic units of ARCHAEA.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.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.Proteus Infections: Infections with bacteria of the genus PROTEUS.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.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).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.Immunoglobulin Fragments: Partial immunoglobulin molecules resulting from selective cleavage by proteolytic enzymes or generated through PROTEIN ENGINEERING techniques.Prince Edward Island: An island in the Gulf of St. Lawrence constituting a province of Canada in the eastern part of the country. It is very irregular in shape with many deep inlets. Its capital is Charlottetown. Discovered by the French in 1534 and originally named Ile Saint-Jean, it was renamed in 1799 in honor of Prince Edward, fourth son of George III and future father of Queen Victoria. (From Webster's New Geographical Dictionary, 1988, p981 & Room, Brewer's Dictionary of Names, 1992, p433)DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Mediterranean Islands: Scattered islands in the Mediterranean Sea. The chief islands are the Balearic Islands (belong to Spain; Majorca and Minorca are among these), Corsica (belongs to France), Crete (belongs to Greece), CYPRUS (a republic), the Cyclades, Dodecanese and Ionian Islands (belong to Greece), MALTA (a republic), Sardinia and SICILY (belong to Italy). (From Webster's New Geographical Dictionary, 1988, p747)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.Alteromonas: A genus of gram-negative, straight or curved rods which are motile by means of a single, polar flagellum. Members of this genus are found in coastal waters and the open ocean. (From Bergey's Manual of Determinative Bacteriology, 9th ed)Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Salmonella paratyphi B: A serotype of SALMONELLA ENTERICA which is an agent of PARATYPHOID FEVER in humans.Bacterial Secretion Systems: In GRAM NEGATIVE BACTERIA, multiprotein complexes that function to translocate pathogen protein effector molecules across the bacterial cell envelope, often directly into the host. These effectors are involved in producing surface structures for adhesion, bacterial motility, manipulation of host functions, modulation of host defense responses, and other functions involved in facilitating survival of the pathogen. Several of the systems have homologous components functioning similarly in GRAM POSITIVE BACTERIA.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.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.Pseudomonas aeruginosa: A species of gram-negative, aerobic, rod-shaped bacteria commonly isolated from clinical specimens (wound, burn, and urinary tract infections). It is also found widely distributed in soil and water. P. aeruginosa is a major agent of nosocomial infection.Salmonella Infections, Animal: Infections in animals with bacteria of the genus SALMONELLA.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Attachment Sites, Microbiological: Specific loci on both the bacterial DNA (attB) and the phage DNA (attP) which delineate the sites where recombination takes place between them, as the phage DNA becomes integrated (inserted) into the BACTERIAL DNA during LYSOGENY.Adaptation, Biological: Changes in biological features that help an organism cope with its ENVIRONMENT. These changes include physiological (ADAPTATION, PHYSIOLOGICAL), phenotypic and genetic changes.Anthropology, Physical: The comparative science dealing with the physical characteristics of humans as related to their origin, evolution, and development in the total environment.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.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.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.DNA, Archaeal: Deoxyribonucleic acid that makes up the genetic material of archaea.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Synechococcus: A form-genus of spherical to rod-shaped CYANOBACTERIA in the order Chroococcales. They contain THYLAKOIDS and are found in a wide range of habitats.United States Virgin Islands: A group of islands in the Lesser Antilles in the West Indies, the three main islands being St. Croix, St. Thomas, and St. John. The capital is Charlotte Amalie. Before 1917 the U.S. Virgin Islands were held by the Danish and called the Danish West Indies but the name was changed when the United States acquired them by purchase.Anti-Bacterial Agents: Substances that reduce the growth or reproduction of BACTERIA.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.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.Proteus mirabilis: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria that is frequently isolated from clinical specimens. Its most common site of infection is the urinary tract.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.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.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.Pseudomonas syringae: A species of gram-negative, fluorescent, phytopathogenic bacteria in the genus PSEUDOMONAS. It is differentiated into approximately 50 pathovars with different plant pathogenicities and host specificities.Melanesia: The collective name for the islands of the Pacific Ocean northeast of Australia, including NEW CALEDONIA; VANUATU; New Hebrides, Solomon Islands, Admiralty Islands, Bismarck Archipelago, FIJI, etc. Melanesia (from the Greek melas, black + nesos, island) is so called from the black color of the natives who are generally considered to be descended originally from the Negroid Papuans and the Polynesians or Malays. (From Webster's New Geographical Dictionary, 1988, p748 & Room, Brewer's Dictionary of Names, 1992, p344)RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.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).Genetic Speciation: The splitting of an ancestral species into daughter species that coexist in time (King, Dictionary of Genetics, 6th ed). Causal factors may include geographic isolation, HABITAT geometry, migration, REPRODUCTIVE ISOLATION, random GENETIC DRIFT and MUTATION.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.Bacteriophages: Viruses whose hosts are bacterial cells.Corynebacterium: A genus of asporogenous bacteria that is widely distributed in nature. Its organisms appear as straight to slightly curved rods and are known to be human and animal parasites and pathogens.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Escherichia coli Infections: Infections with bacteria of the species ESCHERICHIA COLI.Integrases: Recombinases that insert exogenous DNA into the host genome. Examples include proteins encoded by the POL GENE of RETROVIRIDAE and also by temperate BACTERIOPHAGES, the best known being BACTERIOPHAGE LAMBDA.Geography: The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)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.Vibrio cholerae O1: Strains of VIBRIO CHOLERAE containing O ANTIGENS group 1. All are CHOLERA-causing strains (serotypes). There are two biovars (biotypes): cholerae and eltor (El Tor).Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.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.Environmental Microbiology: The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.Genomic Imprinting: The variable phenotypic expression of a GENE depending on whether it is of paternal or maternal origin, which is a function of the DNA METHYLATION pattern. Imprinted regions are observed to be more methylated and less transcriptionally active. (Segen, Dictionary of Modern Medicine, 1992)Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Burkholderia pseudomallei: A species of gram-negative, aerobic bacteria that causes MELIOIDOSIS. It has been isolated from soil and water in tropical regions, particularly Southeast Asia.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Pseudomonas Infections: Infections with bacteria of the genus PSEUDOMONAS.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.Haemophilus: A genus of PASTEURELLACEAE that consists of several species occurring in animals and humans. Its organisms are described as gram-negative, facultatively anaerobic, coccobacillus or rod-shaped, and nonmotile.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.Micronesia: The collective name for islands of the Pacific Ocean east of the Philippines, including the Mariana, PALAU, Caroline, Marshall, and Kiribati Islands. (From Webster's New Geographical Dictionary, 1988, p761 & Room, Brewer's Dictionary of Names, 1992, p350)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: 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.Burkholderia: A genus of gram-negative, aerobic, rod-shaped bacteria. Organisms in this genus had originally been classified as members of the PSEUDOMONAS genus but overwhelming biochemical and chemical findings indicated the need to separate them from other Pseudomonas species, and hence, this new genus was created.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.Channel Islands: A group of four British islands and several islets in the English Channel off the coast of France. They are known to have been occupied prehistorically. They were a part of Normandy in 933 but were united to the British crown at the time of the Norman Conquest in 1066. Guernsey and Jersey originated noted breeds of cattle. (From Webster's New Geographical Dictionary, 1988, p242)Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.
Many genomic islands are flanked by repeat structures and carry fragments of other mobile elements such as phages and plasmids ... many type 3 secretion systems and type 4 secretion systems are located on regions of DNA called genomic islands. These "islands ... A genomic island (GI) is part of a genome that has evidence of horizontal origins. The term is usually used in microbiology, ... Some genomic islands[which?] can excise themselves spontaneously from the chromosome and can be transferred to other suitable ...
He led the team which first identified CpG islands-originally named "HpaII tiny fragments"-in vertebrate genomes. These are ... short genomic regions with a high density of CpG dinucleotides, and are commonly found in an unmethylated state within or ... His research focuses on understanding DNA methylation and CpG islands, and their role in diseases such as Rett syndrome. Bird ... Bird, A. P. (1986). "CpG-rich islands and the function of DNA methylation". Nature. 321 (6067): 209-13. doi:10.1038/321209a0. ...
HpaII Tiny Fragments) islands in mammalian genomes. She and her PhD student Margaret Gardiner-Garden were able to identify ... Frommer, M., McDonald, L.E., Millar, D.S., Collis, C.M., Watt, F., Grigg, G.W., Molloy, P.L. and Paul, C.L. (1992). A genomic ... "CpG islands. They showed that CpG islands are a distinct feature of vertebrate genomes and that CpG islands are associated with ... She is best known for developing a protocol to map DNA methylation by bisulphite genomic sequencing. Early in her career ...
Barrett, John C. (1994). Fragments from Antiquity: An Archaeology of Social Life in Britain, 2900-1200 BC. Oxford, U.K. and ... The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe (2017) Pearson 2005. p. 57. Pearson 2005. p. 17-19. ... The Neolithic British Isles refers to the period of British, Irish and Manx history that spanned from circa 4000 to circa 2,500 ... The final part of the Stone Age in the British Isles, it was a part of the greater Neolithic, or "New Stone Age", across Europe ...
... fragments of different sizes. Alternatively, gDNA fragments can be generated by sonication. Fragmented gDNA is incubated with ... First, genomic DNA (gDNA) is extracted from cells of interest by proteinase K treatment followed by phenol-chloroform ... Although this method is primarily used to localize specific CpG island promoters, it was used to detect R-loops at a minor ... Thus, the DNA-RNA containing fragments will bind to the beads by means of the antibody. The magnetic beads are washed to remove ...
... "mecCgene and genomic islands with suspected role in adaptation to extreme environment". Applied and Environmental Microbiology ... "Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements". Journal of Bacteriology. 193 ... The use of genomic data is now widespread and provides a valuable resource for researchers working with S. aureus. Whole genome ...
nov., isolated in Antarctica, harbours mecC gene and genomic islands with suspected role in adaptation to extreme environment. ... ISBN 1-904455-29-8. [1]. Chan CX, Beiko RG, Ragan MA (2011). "Lateral transfer of genes and gene fragments in Staphylococcus ... The use of genomic data is now widespread and provides a valuable resource for researchers working with S. aureus. Whole genome ...
With the advent of genomic sequences for model systems such as Drosophila melanogaster, Arabidopsis thaliana and C. elegans ... This process requires that DNA fragments from the closest known genetic marker are progressively cloned and sequenced, getting ... Tests used for this purpose include cross-species hybridization, identification of unmethylated CpG islands, exon trapping, ... Positional cloning typically involves the isolation of partially overlapping DNA segments from genomic libraries to progress ...
... is a major archaeological site 800 m (2,625 ft) from Teouma Bay on the island of Éfaté in Vanuatu. The site contains the ... 2016). "Genomic insights into the peopling of the Southwest Pacific". Nature. 538: 510-513. doi:10.1038/nature19844. PMID ... One common factor includes red pottery fragments bearing intricate designs. Many of the individuals were buried in different ... "The Teouma Lapita site and the early human settlement of the Pacific Islands"[1] Bedford, Stuart et al. 2007. "The excavation, ...
Reciprocally, around 60-70% of human genes have a CpG island in their promoter region.[21][22] The majority of CpG islands are ... Bacterial genomic DNA is not recognized by these restriction enzymes. The methylation of native DNA acts as a sort of primitive ... immunoprecipitation is used to isolate methylated DNA fragments for input into DNA detection methods such as DNA microarrays ( ... In mouse and human, around 60-70% of genes have a CpG island in their promoter region and most of these CpG islands remain ...
PCR allows isolation of DNA fragments from genomic DNA by selective amplification of a specific region of DNA. This use of PCR ... and is used to detect methylation of CpG islands in genomic DNA. DNA is first treated with sodium bisulfite, which converts ... If the genomic DNA sequence of a gene is known, RT-PCR can be used to map the location of exons and introns in the gene. The 5 ... Inverse PCR: is commonly used to identify the flanking sequences around genomic inserts. It involves a series of DNA digestions ...
Whole-genomic DNA amplification The bisulfite treated DNA is subjected to whole-genome amplification (WGA) via random hexamer ... For example, hypermethylation at the promoter CpG islands of a tumour suppressor gene, which in turn leads to its silencing, is ... Advantages No PCR is required, which means that there will be no selective bias towards shorter fragments. Ability to survey up ... The method looks at ~2 CpG sites per CpG island, providing genome-wide coverage of methylation patterns Disadvantages Not every ...
... and reducing fragment-length effects or biases. Also, the size of the fragment affects the binding of 5-methyl-cytidine (5mC) ... Genomic DNA is extracted (DNA extraction) from the cells and purified. The purified DNA is then subjected to sonication to ... There is a small fraction of CpG islands that can overlap or be in close proximity to promoter regions of transcription start ... The resulting fragments range from 300 to 1000 base pairs (bp) in length, although they are typically between 400 and 600 bp. ...
... fragments. The probability of covering a given location on the target with at least one fragment is therefore P = 1 − [ 1 − L G ... Each car is a sequenced clone, and the curb is the genomic target. Each clone sequenced is screened to ensure that subsequently ... They yield multitudes of small islands of sequenceable DNA products. Wendl and Barbazuk proposed an extension to Lander- ... One of the more frequently used results from this model is the expected number of contigs, given the number of fragments ...
MethyLight Pyrosequencing Restriction landmark genomic scanning Arbitrary primed PCR HELP assay (HpaII tiny fragment enrichment ... there are about 600 to 800 heavily methylated CpG islands in promoters of genes in the tumors while these CpG islands are not ... Recently, however, scientists have been moving toward a more genomic approach to determine an entire genomic profile for ... CpG island methylation is important in regulation of gene expression, yet cytosine methylation can lead directly to ...
Detects copy number variation using amplified restriction-digested genomic fragments that are hybridized to human ... One major source of epigenetic change is altered methylation of CpG islands at the promoter region of genes (see DNA ... It focuses on genomic, epigenomic and transcript alterations in cancer. Cancer is a genetic disease caused by accumulation of ... show that ME2 genomic deletion in pancreatic ductal adenocarcinoma cells results in high endogenous reactive oxygen species, ...
Exonic mutations can lead to deletion of an entire exon, or a fragment of an exon if the mutation creates a new splice site. ... The NF1 promoter lies within a CpG island that is 472-bp long, consisting of 43 CpG dinucleotides, and extends into the start ... NF1 spans over 350-kb of genomic DNA and contains 62 exons. 58 of these exons are constitutive and 4 exhibit alternative ... however some studies have found neurofibromin or fragments of it in the nucleus. Neurofibromin does contain a nuclear ...
Using MspI to digest genomic DNA results in fragments that always start with a C (if the cytosine is methylated) or a T (if a ... DNA fragments of 40-220 base pair are representative of the majority of promoter sequences and CpG islands Bisulfite conversion ... Fragment purification: The desired size of fragments is then selected to be purified. The different sizes of the fragments are ... When using this particular enzyme, each fragment will have a CpG at each end. This digestion results in DNA fragments of ...
There are no fragment biases in MeDIP experiment (approximate range of DNA fragment sizes is 400-700 bp). The errors on the ... Imagine two different genomic regions, A and B. Region A has six CpGs (DNA methylation in mammalian somatic cells generally ... Most CpG-poor regions are constitutively methylated while most CpG-rich regions (CpG islands) are constitutively unmethylated. ... The isolated fragments of DNA are either hybridized to a microarray chip (MeDIP-chip) or sequenced by next-generation ...
This protein fragment was used by Cambridge BioSciences (Later named Cambridge BioTech) to develop a rapid test for HIV ... The approval of Benlysta fulfilled the hopes that the new genomic method of drug discovery would lead to the treatment of ... "Gibbon Ape Leukemia Virus Hall's Island: New Strain of Gibbon Ape Leukemia Virus". Journal of Virology. 29 (1): 395-400. PMC ... The first application of this knowledge was to design a fragment of the virus envelope protein that could be used to accurately ...
... also called genomic signatures. If a fragment of the genome strongly deviates from the genomic signature, this is a sign of a ... The existence of genomic islands, short (typically 10-200kb long) regions of a genome which have been acquired horizontally, ... Langille, M. G. I.; Hsiao, W. W. L.; Brinkman, F. S. L. (2010). "Detecting genomic islands using bioinformatics approaches". ... Vernikos, G. S.; Parkhill, J (2008). "Resolving the structural features of genomic islands: A machine learning approach". ...
The genome of Bacillus safensis strain FO-036b shows a GC content of 41.0-41.4 mol%. The Bacillus safensis VK genomic DNA was ... Thirty-nine contigs, overlapping DNA fragments, greater in size than 200 base pairs were observed in strain VK. This strain ... Xiamen Island Bacillus safensis NP-4 - surface water - Arctic Ocean Bacillus safensis 15-BO4 10-15-3 - Sediment - Bering Sea ...
He reports works on linguistics by Forster and Toth which suggest that the Indo-European languages began to fragment some ... May 2017). "The Beaker Phenomenon and the Genomic Transformation of Northwest Europe". bioRxiv 135962 . "Excavating Past ... Western Scotland and the Western Isles including Skye in Scotland, Anglesey in Wales, the Isle of Man and the Wirral, Mid- ... In 2007 Bryan Sykes produced an analysis of 6,000 samples from the OGAP project in his book Blood of the Isles. Stephen ...
When genomic M. ulcerans DNA is digested with the restriction enzyme AluI, many 1109 base-pair fragments were obtained. These ... The recent outbreak of the disease on Philip Island, Victoria, was initially associated with the building of a roadway, ... The AFLP technique is based on the selective PCR amplification of restriction fragments from a total digest of genomic DNA. ... selective amplification of sets of restriction fragments; and gel analysis of the amplification fragments. Typically 50-100 ...
Doe, M. .; Relkovic, D. .; Garfield, S. .; Dalley, W. .; Theobald, E. .; Humby, T. .; Wilkinson, S. .; Isles, R. . (Jun 2009 ... Labialle S, Cavaillé J (2011). "Do repeated arrays of regulatory small-RNA genes elicit genomic imprinting?". BioEssays. 33 (8 ... Bioinformatical analyses have revealed that putatively snoRNA-derived, miRNA-like fragments occur in different organisms. ... The 14q32 domain has been shown to share common genomic features with the imprinted 15q11-q13 loci and a possible role for ...
A single 15 mm (0.6 in) fragment from a large lower bill (UCMP 143274), found in deposits from the Lance Creek Formation in ... Some Caribbean and Pacific islands are home to endemic species.[36] By far the greatest number of parrot species come from ... Genomic analysis provides strong evidence that parrots are the sister group of passerines, forming the clade Psittacopasserae, ... Many parrots occur only on islands and are vulnerable to introduced species such as rats and feral cat, as they lack the ...
In the case of the mlp, neither the direct comparison of the concentrations of the fragments (Fig. 5A; wet/dry ratio=0.94) nor ... which incorporates a genomic DNA removal process. Two forward (F1 and F2) and two backward (R1 and R2) primers were constructed ... 1994a). Exercise in the terrestrial Christmas Island red crab Gecarcoidea natalis I. Blood gas transport J. Exp. Biol. 188, 235 ... 1993). The role of Red Land Crabs in restructuring rain forest on Christmas Island, Indian Ocean. Ph.D. thesis, Monash ...
Differential genomic DNA hybridization array. A library of DNA fragments from P. aeruginosa X24509 in M13 was spotted, in ... Identification of a Genomic Island Present in the Majority of Pathogenic Isolates of Pseudomonas aeruginosa Xiaoyou Liang, Xuan ... However, the locus containing the 6,729 bp is a "hot spot" for integration of genomic islands, since we identified at least one ... The X24509-specific region designated PAGI-1 (for "P. aeruginosa genomic island 1", which is absent from PAO1, starts at 925 bp ...
In preferred embodiments, a segment of genomic DNA is inserted between 5′ and 3′ viral long terminal repeats (LTRs) in a vector ... or library of vectors containing a plurality of independent genomic sequences) is then introduced into a retroviral packaging ... provides systems utilizing unique features of retroviral replication to analyze uncharacterized genes derived from genomic DNA ... The present invention relates to the expression and screening of genomic DNA sequences encoding uncharacterized genes and ...
... the overall synteny is well preserved and the flexible genomic islands seem to code for equivalent functions and be located at ... Strain specific genomic islands. In addition, there are genomic islands that are found only in one of the strains. Five unique ... To allow the interactive visualization of genomic fragment comparisons Artemis v.12 [72], Artemis Comparison Tool ACTv.9 [73] ... The fact that flexible genomic islands are found at equivalent genomic context, even when considering different species of the ...
Doublet B, Lailler R, Meunier D, Brisabois A, Boyd D, Mulvey M, Variant Salmonella genomic island 1 antibiotic resistance gene ... When tested by long PCR, all 20 S. Java isolates produced a 10,041-bp fragment identical to that produced by P3170700. ... PCR was used to determine whether the pentaresistant phenotype was due to the presence of the Salmonella genomic island 1 (SGI1 ... Partial characterisation of a genomic island associated with the multidrug resistance region of Salmonella enterica Typhimurium ...
The present invention relates to the chemically modified genomic sequences of genes associated with DNA repair, to ... DATABASE EBI [Online] H. sapiens CpG island DNA genomic Mse1 fragment, 23 October 1995 (1995-10-23) MACDONALD M.: Database ... b) fragments of the chemically pretreated genomic DNA are amplified using sets of primer oligonucleotides according to Claim 8 ... The genomic DNA to be analyzed is preferably obtained form usual sources of DNA such as cells or cell components, for example, ...
Many genomic islands are flanked by repeat structures and carry fragments of other mobile elements such as phages and plasmids ... many type 3 secretion systems and type 4 secretion systems are located on regions of DNA called genomic islands. These "islands ... A genomic island (GI) is part of a genome that has evidence of horizontal origins. The term is usually used in microbiology, ... Some genomic islands[which?] can excise themselves spontaneously from the chromosome and can be transferred to other suitable ...
In the case of GI 7, fragments of this island were found in the B. mallei genome, suggesting that a similar island may have ... A striking feature of the genome was the presence of 16 genomic islands (GIs) that together made up 6.1% of the genome. Further ... Abbreviations: GI, genomic island; CDS, coding sequence; Mb, megabase pair; IS, insertion sequence. ... Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Matthew T. G. Holden, Richard W. Titball, ...
Therefore, this E. coliK-12-specific DNA fragment could represent a genomic island. Our study presents for the first time in ... identification of different types of genomic islands. The structure of PAI III536 ofE. coli strain 536 and that of the genomic ... Analysis of thrW downstream region in differentE. coli strains: identification of E. coliK-12-specific genomic island.The PCR- ... Mobile genetic elements such as plasmids, bacteriophages, and pathogenicity islands belong to a group of genomic additions that ...
... capB and genomic island IV and primers for conventional PCRs targeting gene fragments of genomic islands I to VI and plasmid ... Isolates from RCA and DRC harboured genomic islands I to V, but like the CAM strain lacked genomic island VI and plasmid pCI-14 ... cereus ISP3191 [35], whereas the genomic islands (except the relatively wide distributed Island III) are absent. ... Whole genome sequencing of one isolate from Côte dIvoire revealed the presence of six genomic islands (12-22 kb in size) and a ...
Genomic islands carrying virulence-associated genes are well-known in P. aeruginosa. Kiewitz et al., Microbiology 146: 2365- ... A kinetic study of the release of azurin and the 15 kb DNA fragment in absence of any other chromosomal DNA fragment on ... and SEQ ID NOS: 26-62, suggesting that the released DNA came from a genomic island in strain 8822. No plasmid DNA isolated by ... 175:79-85 (2001). A single genomic island, PAGI-1, having at least two different DNA segments of G+C content 63.7% and 54.9% ...
... of left and right junctions of Salmonella genomic island 1. PFGE, pulsed-field gel electrophoresis; MLST, multilocus sequence ... Dendrograms of macrorestriction fragments of all (A) and ciprofloxacin-resistant (B) Salmonella enterica serovar Kentucky ... Prince Edward Island, Canada (L. Ang); Institut National de Santé Publique du Quebec, Montreal, Quebec, Canada (S. Bekal); ... Prince Edward Island. Letters in parentheses indicate drugs that had intermediate MICs. ...
2008) Socotra Island the forgotten fragment of Gondwana: Unmasking chameleon lizard history with complete mitochondrial genomic ... 2008) Genomic sequencing of single microbial cells from environmental samples. Current Opinion in Microbiology 11(3), 198-204. ... 2008) Toward a standards-compliant genomic and metagenomic publication record. OMICS 12(2), 157-60. 10.1089/omi.2008.A2B2. More ... 2008) Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS 12(2), 137-41. ...
This study demonstrated the genomic differences between PA and nPA B. amyloliquefaciens and B. subtilis from different niches ... cotton)] to perform comparative analysis and investigate the genomic characteristics and evolution traits of both species in ... cotton)] to perform comparative analysis and investigate the genomic characteristics and evolution traits of both species in ... Itakura et al., demonstrated that the Bradyrhizobium japonicum strains acquired additional DNA fragments (e.g., genomic islands ...
BLAST searches identified relevant DNA fragments in a draft genome sequence. PCR was used to assemble fragments and map ... formed a 19.5 kb genomic resistance island (GRI), designated AbGRI2-1, containing five copies of IS26. Part of this island was ... A novel family of genomic resistance islands, AbGRI2, contributing to aminoglycoside resistance in Acinetobacter baumannii ... AbGRI2-1 is the largest so far of a new type of GRI designated AbGRI2 to distinguish them from the islands in comM in GC1 ...
The first CpG island (indicated as fragment F1) was located within 5′ upstream region of HOXA10 exon1 gene (accession number: ... Genomic organization of HOXA10 locus used for methylation analysis. CpG island (blue region) identified by MethPrimer program ( ... 1 upper panel). The second and the third CpG islands (indicated as fragments F2 and F3 respectively) were located in the intron ... from 1 to 21 for fragment F2 (gray box) and from 1 to 10 for fragment F3 (gray box). Exon sequences are indicated as white box ...
Socotra Island the forgotten fragment of Gondwana: Unmasking chameleon lizard history with complete mitochondrial genomic data ...
Socotra Island the forgotten fragment of Gondwana: Unmasking chameleon lizard history with complete mitochondrial genomic data ... S Greece (Aegean Islands, Crete, Chios, Samos), Malta, S Portugal, S Spain, S/E Turkey, Cyprus, Italy (Apulia, Calabria),. N ... Chamaeleo chamaeleon has been reported from the Canary Islands but these are most likely escaped pets that do not form viable ... The presence of Chamaeleo chamaeleon (Reptilia) on the Maltese islands, in a note on the occurrence on this species of ...
MethylCollector Ultra is a fast magnetic assay to enrich for CpG-methylated DNA from cell or tissue samples fragmented by ... Ultra offers a fast magnetic assay capable of efficiently isolating methylated CpG islands from fragmented genomic DNA*. ... Methylated CpG Island Recovery Assay (MIRA). MethylCollector™ Ultra is based on the Methylated CpG Island Recovery Assay (MIRA ... that specifically binds methylated CpGs of genomic DNA fragments that have been prepared by sonication or enzymatic digestion. ...
Missing fragments are randomly distributed over the genome. A selected subset of genomic fragments was amplified by PCR from ... The genomic islands that have been described before also generally have a much smaller size than the lifestyle adaptation ... To assess if this versatility is linked to a variable gene pool, microarrays containing a subset of small genomic fragments of ... Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2:414-424. ...
Genomic islands (GIs) comprise important and interesting horizontally transferred sequences, but information about acquisition ... Similarly, GIs VvI-3 and VvI-4 of chromosome I together with the region between these two islands are compositionally similar, ... 2). As a reference clade of compositionally similar fragments, three 15 kbp fragments of regions outside the genomic islands of ... are non-anomalous genomic fragments used as a reference clade. Ct1 and Ct2 represent Chlamydia trachomatis genomic fragments ...
Skeletal fragments from t... In 1994, human skeletal remains were found at Hummervikholmen, a small island in the Søgne ... Genomic data suggest two main migrations into Scandinavia after the last ice age. Press Release • Jan 09, 2018 19:00 GMT ... Skeletal fragments from the Hummervikholmen site. Photo: Beate Kjørslevik. In a new study published in PLOS Biology, an ... The cave of Stora Förvar, situated on the small island of Stora Karlsö, off the west coast of Gotland in the Baltic Sea, was ...
... in the susceptible-resistant clusters contained small fragments or partial sequences of the 43-kb Salmonella genomic island 1 ( ... The Salmonella genomic island 1 is an integrative mobilizable element. Mol Microbiol 55:1911-1924. doi:10.1111/j.1365-2958.2005 ... Salmonella genomic islands and antibiotic resistance in Salmonella enterica. Future Microbiol 5:1525-1538. doi:10.2217/fmb. ... The genetics of Salmonella genomic island 1. Microbes Infect 8:1915-1922. doi:10.1016/j.micinf.2005.12.028. ...
... namely Tn10 and two antibiotic resistance islands designated ARI-A and ARI-B. These two islands, inserted at two different ... The ARI-A or ARI-B islands from different IncHI5 plasmids carried distinct profiles of antimicrobial resistance markers and ... The ARI-A or ARI-B islands from different IncHI5 plasmids carried distinct profiles of antimicrobial resistance markers and ... These two islands, inserted at two different fixed sites of IncHI5 backbones, were derived from the prototype Tn3-family ...
... with the fragments in between if applicable). The occupancy at the known insertion sites comM and pho were examined. ... AbaR-type genomic islands in non-baumannii Acinetobacter species isolates from South Korea. Antimicrob Agents Chemother 59:5824 ... AbaR-type genomic islands (AbaRs) are a class of important mobile genetic elements (MGEs) known to be involved in multiple ... Thus, the term AbaR (AbaR-type genomic island) used in this study broadly refers to a class of mobile genetic elements whose ...
  • Here we present a summary of S. enterica serovar Typhi P-stx-12 and its unique features, together with the description of the complete genomic sequencing and annotation. (standardsingenomics.org)
  • In order to understand the genetic makeup of pathogenic P. aeruginosa strains, a method of differential hybridization of arrayed libraries of cloned DNA fragments was developed. (asm.org)
  • Survey of the incidence of PAGI-1 revealed that this island is present in 85% of the strains from clinical sources. (asm.org)
  • Alternatively, one or both of the transcriptional regulators encoded in PAGI-1 may control the expression of genes in the P. aeruginosa chromosome, which provides a selective advantage for strains that have acquired this genomic island. (asm.org)
  • Although these two strains belong to a clearly different species from A. macleodii , the overall synteny is well preserved and the flexible genomic islands seem to code for equivalent functions and be located at similar positions. (biomedcentral.com)
  • They tend to be found at the same genomic location and context but they are often completely absent from some strains. (biomedcentral.com)
  • The sfa I determinant encoding the S-fimbrial adhesin of uropathogenic Escherichia coli strains was found to be located on a pathogenicity island of uropathogenic E. coli strain 536. (asm.org)
  • This study demonstrated the genomic differences between PA and nPA B. amyloliquefaciens and B. subtilis from different niches and the involved evolutional traits, and has implications for screening of PGPR strains in agricultural production. (frontiersin.org)
  • To further investigate the genomic diversity of Campylobacter , we conducted a comparative genomic analysis from a collection of 67 C. jejuni and 12 Campylobacter coli strains isolated from various geographical locations and clinical and veterinary sources. (asm.org)
  • Utilizing PCR, we demonstrated that 55% of the C. jejuni strains examined were positive for at least one RM1221-like genomic element and 27% were positive for two or more of these CJIEs. (asm.org)
  • Furthermore, many C. coli strains were positive for either genomic element CJIE1 or CJIE3. (asm.org)
  • A comparative genomic hybridization (CGH) analysis of 35 of the 67 C. jejuni strains confirmed the presence of genomic elements similar to those in strain RM1221. (asm.org)
  • Interestingly, the DNA microarray analysis demonstrated that these genomic elements in the other C. jejuni strains often exhibited modular patterns with some regions of the CJIEs present and other regions either absent or highly divergent compared to strain RM1221. (asm.org)
  • The classification of strains by mucABD genotype was generally concordant with that by genome-wide SpeI fragment pattern or multilocus SNP genotypes. (microbiologyresearch.org)
  • With an array-based methylation sensitive amplified fragment length polymorphism (MS-AFLP) method we analyzed 8 tubular (TA) and 19 serrated (SSA) adenomas, and 14 carcinomas with (MSI) and 12 without (MSS) microsatellite instability. (biomedcentral.com)
  • Further analysis revealed these islands to be variably present in a collection of invasive and soil isolates but entirely absent from the clonally related organism B. mallei . (pnas.org)
  • A novel family of genomic resistance islands, AbGRI2, contributing to aminoglycoside resistance in Acinetobacter baumannii isolates belonging to gl. (nih.gov)
  • AbGRI2-1 is the largest so far of a new type of GRI designated AbGRI2 to distinguish them from the islands in comM in GC1 isolates (AbaR type) and in GC2 isolates (AbGRI1 type). (nih.gov)
  • Clear similarities between antibiotic resistance islands in the chromosomes of extensively antibiotic-resistant isolates from the two dominant, globally distributed Acinetobacter baumannii clones, GC1 and GC2, suggest a common origin. (asm.org)
  • After minor rearrangements, this R1215 resistance island can generate AbGRI2-0*, the predicted earliest form of the IS 26 -bounded AbGRI2-type resistance island of GC2 isolates, and to the multiple antibiotic resistance region (MARR) of AbaR0, the precursor of this region in AbaR-type resistance islands in the GC1 group. (asm.org)
  • In fact, the Science list of six Areas to Watch in 2012 puts genomic epidemiology fourth-right after the Higgs boson, faster-than-light neutrinos, and stem-cell metabolism. (cdc.gov)
  • These islands represent highly distinctive evolutionary settings for terrestrial biotas: they have never been connected to continental landmasses and trans-oceanic founder speciation, followed by varying degrees of in situ cladogenesis, is the primary diversification process [ 3 ]-[ 6 ]. (biomedcentral.com)
  • 6 Center for Conservation and Evolutionary Genetics, National Zoological Park/National Museum of Natural History and Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Santo Tomás, 11340. (scielo.org.mx)
  • Many genomic islands are flanked by repeat structures and carry fragments of other mobile elements such as phages and plasmids. (wikipedia.org)
  • Bacillus anthracis has been classically defined as a clade with low genomic diversity within the B . cereus sensu lato group, whose members carry two virulence plasmids, pXO1 and pXO2, and exhibit a set of known phenotypic characteristics [ 1 - 3 ]. (plos.org)
  • The ARI-A or ARI-B islands from different IncHI5 plasmids carried distinct profiles of antimicrobial resistance markers and associated mobile elements, and complex events of transposition and homologous recombination accounted for assembly of these islands. (frontiersin.org)
  • MethylCollector™ Ultra is based on the Methylated CpG Island Recovery Assay (MIRA) which utilize a His-tagged recombinant methyl-binding protein complex, comprised of MBD2b/MBD3L1, that specifically binds methylated CpGs of genomic DNA fragments that have been prepared by sonication or enzymatic digestion. (activemotif.com)
  • CpG islands represent 1% of the genome and have a high density of nonmethylated CpGs. (els.net)
  • Although this plasticity may, in many cases, depend on the simple transfer of mobile genetic elements, it often appears to result in very complex mosaic-structured genomic rearrangements. (asm.org)
  • The team compared the genomic data to the genetic variation of Mesolithic hunter-gathers from other parts of Europe. (mynewsdesk.com)
  • AbaR-type genomic islands (AbaRs) are a class of important mobile genetic elements (MGEs) known to be involved in multiple antimicrobial resistance in A. baumannii ( 1 - 7 ). (asm.org)
  • Increasing the resolution of genetic and genomic methods is however only one factor in improving the ability to make inferences from molecular epidemiologic studies. (cdc.gov)
  • Information on genetic variability is needed, as the species is restricted to sky islands, which are small and often locally fragmented habitats. (scielo.org.mx)
  • Given the inherent vulnerability of these naturally isolated populations with their locally fragmented distributions, the genetic data support a need for conservation focused on protection of suitable habitats. (scielo.org.mx)
  • A metabolic island was identified that contained citrate fermentation, l -rhamnose and OGA metabolism clusters as well as a CRISPR-Cas system. (biomedcentral.com)
  • 10. The method of claim 1 , wherein said analyzing of said genomic clone comprises amplification of said genomic clone with PCR primers. (google.com)
  • Amplification of the HN coding region was done using oligonucleotides 5′-AAA GGATCC GCTAGCACACCTAGCGAT-3′ and 5′-AGGC TCTAGA TTGCCAGACCTGGC-3′, which amplify a 1,585-bp fragment, excluding the first 150 bp coding for 50 amino acids of the protein predicted as the signal peptide and the transmembrane domain ( 6 ). (asm.org)
  • A causal association between Y. pestis and historical plague is suggested by the PCR amplification of ancient Y. pestis DNA fragments from skeletons dating between the 13th century and 1722 ( 16 , 17 ), but independent confirmation of these results has not been possible ( 18 ). (pnas.org)
  • Identification of the subset of GEIs that encode for virulence factors, referred to as pathogenicity islands (PAIs), can lead to the understanding of the organism's pathogenicity within the host. (beds.ac.uk)
  • The 3.5-kb upstream genomic region containing part of the first exon showed strong promoter activity in NG108-15 neuroblastoma cells but much less in 293T cells, suggesting that this fragment is sufficient for neural cell-directed promoter activity. (ebscohost.com)
  • By deleting the genomic region containing the five GC boxes, it was shown that the minimal promoter region is primarily comprised of five copies of the Sp1-binding site located upstream from the transcription initiation site. (ebscohost.com)
  • Transgenes encompassing dual-promoter CpG islands from the human TBP and HNRPA2B1 loci are resistant to heterochromatin-mediated silencing. (merckmillipore.com)
  • In this respect, experimental research suggested that DNMT3b depletion can reduce aberrant promoter CpG island hypermethylation in cancer cells ( 15 - 17 ), whereas DNMT3b overexpression initiated promoter hypermethylation of tumor suppressor genes and the formation of colonic miroadenomas ( 18 ). (aacrjournals.org)
  • The presence of four pathogenicity islands (PAIs I 536 to IV 536 ) has been described for E. coli strain 536 so far. (asm.org)
  • Earlier findings implied that the sfa I determinant is part of a pathogenicity island of strain 536 designated PAI III 536 ( 23 ). (asm.org)
  • The HN coding region was amplified from cDNA synthesized from genomic NDV RNA (La Sota strain, provided by the National Service for Animal Health [SENASA]) isolated using TRIzol (Life Technologies, Grand Island, NY), following the manufacturer's instructions. (asm.org)
  • Given the profound impact that DNA methylation exerts on the transcriptional profile and genomic stability of cancer cells, its characterization is essential to fully understand the complexity of cancer biology, improve tumor classification, and ultimately advance cancer patient management and treatment. (springer.com)
  • DNA CpG island hypermethylation was detected at promoters of genes involved in cell growth control and genomic stability. (diabetesjournals.org)
  • Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated. (asm.org)
  • The utility of such genomic approaches and their applicability to diverse questions in microbial ecology have only begun to be explored and exploited. (asm.org)
  • Although they collectively range across a 10,000 km swath of Oceania, half of the family's total species diversity is endemic to a single Eastern Pacific hot spot archipelago (the Society Islands) and all three partulid genera display highly distinctive distributions. (biomedcentral.com)
  • The pronounced east-west geographic disjunction exhibited by the genus Partula stems from a much older long-distance dispersal event and its high taxonomic diversity in the Society Islands is a product of a long history of within-archipelago diversification. (biomedcentral.com)
  • For England, Wales, and the Channel Islands, drug-resistant S. Java was found in humans: 25 in 2000, 36 in 2001, 49 in 2002, and 4 in 2003 (January 1-March 31). (cdc.gov)
  • Enzymatic unlinking of circular BAC, long bacterial genomic templates and eucaryotic DNA samples with GC- and CT-rich islands with newly developed TF II allows to reduce the duration of the denaturation step during cycle sequencing and results in high yield and quality of Sanger fragments. (imgs.org)
  • Recent genomic advances ( 10 , 12 , 27 ) have provided the opportunity to undertake comparative studies of pathogenic and nonpathogenic aspergilli. (asm.org)
  • As a test of the island refugia hypothesis in Pleistocene Florida, we use a coalescent approach to estimate the divergence times of modern green anole lineages. (springer.com)
  • We find that all demographic events occurred during or after the Upper Pliocene and suggest that green anole diversification was driven by population divergence on interglacial island refugia in Florida during the Lower Pleistocene, while the region was often separated from continental North America. (springer.com)
  • In preferred embodiments, a segment of genomic DNA is inserted between 5′ and 3′ viral long terminal repeats (LTRs) in a vector (e.g., a plasmid, cosmid, or artificial chromosome vector). (google.com)
  • We describe previously uncharacterized metabolism islands that were hotspots for the gain and loss of functional modules likely mediated by transposons. (biomedcentral.com)
  • However, due to previous technical limitations associated with sequencing ancient DNA, no functional genomic study or population study on Haast's Eagle has so far been conducted. (apscience.org.au)
  • The analyses will help identifying potential causes for Haast's Eagle extinction as well as the functional genomic basis for island gigantism in this iconic New Zealand bird species. (apscience.org.au)
  • The availability of AscI as a restriction landmark for RLGS allows for scanning almost twice as many CpG islands in the human genome compared with using NotI only. (northwestern.edu)