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.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.Genome Size: The amount of DNA (or RNA) in one copy of a genome.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Genome, Protozoan: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Genome, Helminth: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.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).Genome, Plastid: The genetic complement of PLASTIDS as represented in their DNA.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.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.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.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.Gene Order: The sequential location of genes on a chromosome.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.Genetic Variation: Genotypic differences observed among individuals in a population.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.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.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.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.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.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)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.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.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).RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Genes, Viral: The functional hereditary units of VIRUSES.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.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.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.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.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.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.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.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.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, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Viral Proteins: Proteins found in any species of virus.Gene Transfer, Horizontal: The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).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.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.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)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.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.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.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.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)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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.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.Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.Genes, Bacterial: The functional hereditary units of BACTERIA.Polyploidy: The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.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).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.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.Genes, Plant: The functional hereditary units of PLANTS.Genome, Microbial: The genetic complement of a microorganism as represented in its DNA or in some microorganisms its RNA.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.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.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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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.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.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)Bacterial Proteins: Proteins found in any species of bacterium.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.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.DNA Replication: The process by which a DNA molecule is duplicated.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.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.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.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.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.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.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).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.Bacteriophages: Viruses whose hosts are bacterial cells.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.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.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.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.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.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.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.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.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).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.Genes, Mitochondrial: Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.DNA, Chloroplast: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.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.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).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.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.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.Vertebrates: Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.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.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.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.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.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.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.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.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.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.RNA Viruses: Viruses whose genetic material is RNA.Plastids: Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.Virus Integration: Insertion of viral DNA into host-cell DNA. This includes integration of phage DNA into bacterial DNA; (LYSOGENY); to form a PROPHAGE or integration of retroviral DNA into cellular DNA to form a PROVIRUS.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.Genes, Archaeal: The functional genetic units of ARCHAEA.Sorghum: A plant genus of the family POACEAE. The grain is used for FOOD and for ANIMAL FEED. This should not be confused with KAFFIR LIME or with KEFIR milk product.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.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)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.Chromosomes, Human: Very long DNA molecules and associated proteins, HISTONES, and non-histone chromosomal proteins (CHROMOSOMAL PROTEINS, NON-HISTONE). Normally 46 chromosomes, including two sex chromosomes are found in the nucleus of human cells. They carry the hereditary information of the individual.Short Interspersed Nucleotide Elements: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).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 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.Segmental Duplications, Genomic: Low-copy (2-50) repetitive DNA elements that are highly homologous and range in size from 1000 to 400,000 base pairs.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.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.GC Rich Sequence: A nucleic acid sequence that contains an above average number of GUANINE and CYTOSINE bases.Mammals: Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.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)Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Hybridization, Genetic: The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Pan troglodytes: The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.Eukaryota: One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.Archaea: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.Genes, Duplicate: Two identical genes showing the same phenotypic action but localized in different regions of a chromosome or on different chromosomes. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Angiosperms: Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.Tetraodontiformes: A small order of primarily marine fish containing 340 species. Most have a rotund or box-like shape. TETRODOTOXIN is found in their liver and ovaries.DNA Copy Number Variations: Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.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.Diploidy: The chromosomal constitution of cells, in which each type of CHROMOSOME is represented twice. Symbol: 2N or 2X.Mutation Rate: The number of mutations that occur in a specific sequence, GENE, or GENOME over a specified period of time such as years, CELL DIVISIONS, or generations.Defective Viruses: Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.Chromosome Inversion: An aberration in which a chromosomal segment is deleted and reinserted in the same place but turned 180 degrees from its original orientation, so that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome.Untranslated Regions: The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.Crosses, Genetic: Deliberate breeding of two different individuals that results in offspring that carry part of the genetic material of each parent. The parent organisms must be genetically compatible and may be from different varieties or closely related species.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.Likelihood Functions: Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.Tandem Repeat Sequences: Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).Proteome: The protein complement of an organism coded for by its genome.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".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.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.Plant Diseases: Diseases of plants.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Zea mays: A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Genetic Techniques: Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.Alu Elements: The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.DNA, Algal: Deoxyribonucleic acid that makes up the genetic material of algae.Genes, Overlapping: Genes whose nucleotide sequences overlap to some degree. The overlapped sequences may involve structural or regulatory genes of eukaryotic or prokaryotic cells.Chromosomes, Mammalian: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of MAMMALS.Endogenous Retroviruses: Retroviruses that have integrated into the germline (PROVIRUSES) that have lost infectious capability but retained the capability to transpose.Genome-Wide Association Study: An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.Computer Graphics: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.Siphoviridae: A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by long, non-contractile tails.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.

*  The Nature and Dynamics of Bacterial Genomes | Science

... we estimate that this genome harbors hundreds of inactivated and otherwise functionless genes. Such regions will never yield a ... As a result, the coding potential of bacterial genomes can be substantially lower than originally predicted. Whereas only a ... Though generally small and gene rich, bacterial genomes are constantly subjected to both mutational and population-level ...
science.sciencemag.org/content/311/5768/1730

*  A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes - pdf download

A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes. . Download books free in ... genomic hybridisation CGH experiments have been used to study numerous biological problems including understanding genome ... Each stage of the process is described and we have compared a number of methods available for characterising bacterial genomic ... Although there are some programmes available for interpretation of bacterial transcriptomics data and CGH microarray data for ...
books.duhnnae.com/2017/jul5/150019232427-A-process-for-analysis-of-microarray-comparative-genomics-hybridisation-studies-for-bacterial-genomes.php

*  The Genome Factory: Bacterial genome annotation systems

What is genome annotation?. Genome annotation is the process of identifying features of interest on a genome sequence. Some of ... Below I list the tools I am aware of for performing and curating bacterial genome annotation. If I've missed any please let me ... You get a bacterial isolate. You sequence it. You manage to get some contigs after mucking around with some de novo assembly ... The Genome Factory Bioinformatics tips, tricks, tools and commentary with a microbial genomics bent. Written by Torsten Seemann ...
thegenomefactory.blogspot.com/2013/03/bacterial-genome-annotation-systems.html?showComment=1475163424355

*  The Microbe Project Report: Background

NSF in genome-enabled microbiological science in light of the overall federal investment in this area. Escherichia coli. Photo ... This bacterial species represents a new and important type of phototroph in the ocean and the potential exists for the ... The first goal is to develop a set of tools for accurate, automated genome analysis to support genome assembly and gene finding ... There are already too many examples of improper genome annotation in existing databases, and as each new genome project is ...
https://nsf.gov/pubs/2002/nsf01208/background.htm

*  PNNL: Sequenced Genomes Make Good Neighbors

PNNL scientists demonstrated a trans-organism search strategy for determining effectiveness of neighboring genome sequences for ... Stephen Callister, selected multiple genome sequences for Shewanellae to test the concept, not only because of the large number ... An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences.' PLoS ONE 5(11 ... They demonstrated a trans-organism search strategy for determining the extent to which near-neighbor genome sequences can be ...
https://pnnl.gov/science/highlights/highlight.asp?id=882

*  Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of...

APE1618 belongs to a distinct family of (otherwise) bacterial aconitases (e.g E. coli AcnA and B. subtilis CitB). APE1816 also ... Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of ... Genome Res. 1999, 9: 689-710.PubMedGoogle Scholar. *. Aravind L, Koonin EV: Novel predicted RNA-binding domains associated with ... Genome Res. 1998, 8: 1038-1047.PubMedGoogle Scholar. *. Koonin EV, Mushegian AR, Bork P: Non-orthologous gene displacement. ...
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2000-1-5-research0009

*  AliTV-interactive visualization of whole genome comparisons [PeerJ]

... which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or ... Whole genome alignments and comparative analysis are key methods in the quest of unraveling the dynamics of genome evolution. ... Efficient inference of recombination hot regions in bacterial genomes.. Molecular Biology and Evolution 31(6):1593-1605 ... The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology.. Molecular BioSystems 4(5):363-371 ...
https://peerj.com/articles/cs-116/

*  Bacterial Genome Sequencing Strains Page 1

ATCC provides all the cultures you need to perform complex analysis of bacterial sequenced genomes. ... Bacterial Genome Sequencing Strains * Clostridium phytofermentans Warnick et al. (ATCC® 700394™) ATCC® Number: 700394™ Strain ...
https://atcc.org/Products/Cells_and_Microorganisms/Bacteria/Bacterial_Genome_Sequencing_Strains.aspx?dsNav=Ro:200,Ns:Organism_Accepted_Name|101|1|

*  Bacterial Genome Sequencing Strains Page 1

ATCC provides all the cultures you need to perform complex analysis of bacterial sequenced genomes. ... Bacterial Genome Sequencing Strains Fast STR Profiling Service Authentication of cell lines via STR profile analysis is ...
https://atcc.org/en/Products/Cells_and_Microorganisms/Bacteria/Bacterial_Genome_Sequencing_Strains.aspx?dsNav=Ns:Organism_Accepted_Name|101|1|,Up:Page_By_Accepted_Name,Nrc:id-1000563,N:4294926051

*  Bacterial Genome Sequencing Strains Page 1

ATCC provides all the cultures you need to perform complex analysis of bacterial sequenced genomes. ... Bacterial Genome Sequencing Strains * Gardnerella vaginalis (Gardner and Dukes) Greenwood and Pickett (ATCC® 14019™) ATCC® ...
https://atcc.org/en/Products/Cells_and_Microorganisms/Bacteria/Bacterial_Genome_Sequencing_Strains.aspx?dsNav=Ns:Organism_Accepted_Name|101|1|,N:4294966204

*  Bacterial Genome Sequencing Strains Page 30

ATCC provides all the cultures you need to perform complex analysis of bacterial sequenced genomes. ... Bacterial Genome Sequencing Strains * Abiotrophia defectiva (Bouvet et al.) Kawamura et al. (ATCC® 49176™) ATCC® Number: 49176™ ...
https://atcc.org/en/Products/Cells_and_Microorganisms/Bacteria/Bacterial_Genome_Sequencing_Strains.aspx

*  One Bacterial Cell, One Complete Genome

No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an ... Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude ... For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement ... Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms ( ...
journals.plos.org/plosone/article?id=10.1371/journal.pone.0010314

*  Altmetric - Design and synthesis of a minimal bacterial genome

Design and synthesis of a minimal bacterial genome. User burtzev, in the Genetics, genes and genomes subreddit, 24 Mar 2016. ... Design and synthesis of a minimal bacterial genome. User burtzev, in the Microbiology subreddit, 24 Mar 2016. ... Design and synthesis of a minimal bacterial genome. User burtzev, in the genomics subreddit, 24 Mar 2016. ... Design and synthesis of a minimal bacterial genome. Overview of attention for article published in Science, March 2016 ...
https://altmetric.com/details/6316462/reddit

*  The Genome Factory: What bacterial genome assemblers are people using?

files available at NCBI FTP to see what genome assembly software is being used for bacterial genomes. Now, like any user ... As of April 2016, there are about 70,000 genome assemblies in Genbank (draft and complete), with the majority being bacterial ... Genome-Assembly-Data-END## Method. I decided to parse this header for all the bacterial .gbff.gz. (GenBank File Format, aka . ... The Genome Factory Bioinformatics tips, tricks, tools and commentary with a microbial genomics bent. Written by Torsten Seemann ...
thegenomefactory.blogspot.com/2016/04/what-bacterial-genome-assemblers-are.html

*  Question about next step in a de novo bacterial genome assembly - SEQanswers

Question about next step in a de novo bacterial genome assembly General ... Question about next step in a de novo bacterial genome assembly I am trying to de novo assemble a large bacterial genome (~9.2 ... bacterial genome MuG. General. 2. 03-28-2017 04:13 PM. Automated pipeline for de novo Bacterial genome assembly Morgane_AUS. ... Genome Res De novo bacterial genome sequencing: millions of very short reads assembly b_seite. Literature Watch. 0. 03-12-2008 ...
seqanswers.com/forums/showthread.php?t=77297

*  Bacterial Genes in the Aphid Genome: Absence of Functional Gene Transfer from Buchnera to Its Host

However, the aphid genome does contain eight transcribed genes of apparent bacterial origin, some of which have been duplicated ... used the newly available sequence of the pea aphid genome to conduct an exhaustive computational search for genes of bacterial ... We found that no functional genes have been transferred from Buchnera, ruling out such transfer as a driving force in genome ... In organelles, part of the answer involves gene transfer to the host genome, allowing maintenance of essential functions. So ...
journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000827&imageURI=info:doi/10.1371/journal.pgen.1000827.g003

*  Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome | Science

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. By Daniel G. Gibson, John I. Glass, Carole Lartigue ... Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. By Daniel G. Gibson, John I. Glass, Carole Lartigue ... Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome Message Subject. (Your Name) has forwarded a page to ... and assembly of the 1.08-mega-base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence ...
science.sciencemag.org/content/329/5987/52.long

*  bacterial flagellum | The Genome's Tale

Posts tagged 'bacterial flagellum'. *3May 22, 2012Molecular Machines and Evolution, Part 1 ...
https://thegenomestale.wordpress.com/tag/bacterial-flagellum/

*  The Tree of Life: The story behind "Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems"

The story behind "Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems" ...
https://phylogenomics.blogspot.com/2014/02/the-story-behind-programmable-removal.html

*  Genome trees constructed using five different approaches suggest new major bacterial clades

Genome alignment, evolution of prokaryotic genome organization and prediction of gene function using genomic context. Genome ... Genome trees constructed using five different approaches suggest new major bacterial clades. Yuri I Wolf,#1 Igor B Rogozin,#1 ... Nevertheless, all genome-to-genome comparisons included at least 100 (for the smallest genomes such as the mycoplasmas), and ... Genome trees constructed with three different approaches. Genome trees were generated using the approaches described under ...
pubmedcentralcanada.ca/pmcc/articles/PMC60490/?lang=en-ca

*  9780077774509 - Prescott's Microbiology with Connect | eCampus.com

Bacterial Genome Replication and Expression. 14. Regulation of Bacterial Cellular Processes 15. Eukaryotic and Archaeal Genome ... 3. Bacterial Cell Structure 4. Archaeal Cell Structure 5. Eukaryotic Cell Structure 6. Viruses and Other Acellular Infectious ...
ecampus.com/prescotts-microbiology-connect-plus-access/bk/9780077774509

*  Sabinet | Diagnosis of bacterial endophthalmitis by polymerase chain reaction using universal primers for eubacterial genome

Eubacterial genome, was detected in 9 (18%) of 28 bacteriologically negative specimens. Among the 19 eubacterial PCR negative ... Nested PCR directed at the 16S rDNA using universal primers for eubacterial genome was done. Of the 20 controls 2 (10%) were ... We evaluated polymerase chain reaction (PCR) in the diagnosis of bacterial endophthalmitis using vitreous fluid (VF) and ... On the other hand PCR for eubacterial genome showed 100% correlation with the 22 (44%) bacteriologically positive specimens. ...
journals.co.za/content/mdv/4/1/AJA16872010_37

*  Altmetric's High Five - Fantastic Monsters (March 2016) - The Science Council : The Science Council

1. Minimal bacterial genome. Image credit: Wellcome Images. Our top paper this month is "Design and synthesis of a minimal ... 1. Design and synthesis of a minimal bacterial genome. 2. A bacterium that degrades and assimilates poly(ethylene terephthalate ... In the study, researchers from the Craig Venter Institute built a minimal genome (a genome including only the genes essential ... The minimal genome these researchers built was based on the relatively simple genome of the bacteria Mycoplasma mycoides, a ...
sciencecouncil.org/altmetrics-high-five-fantastic-monsters-march-2016/

*  News Bureau | ILLINOIS

CRISPR mines bacterial genome for hidden pharmaceutical treasure. Apr 10, 2017 10:00 am1093 views ... Antibiotic breakthrough: Team discovers how to overcome gram-negative bacterial defenses. May 10, 2017 12:00 pm2193 views ...
https://news.illinois.edu/blog/viewCategory/6367?ACTION=POST_LIST&queryCategory=370

*  DNA Clean-Up Buffers

Genome Editing * CRISPR Cas9 * Resources * About CRISPR/Cas9 * About Guide-it Kits ... Bacterial Expression Systems * His-Tagged * HAT-Tagged * High Yield Expression * B. subtilis Secretory Protein ...
clontech.com/US/Products/Nucleic_Acid_Purification/Accessories/Buffers_and_Enzymes/DNA_Clean-Up?sitex=10020:22372:US&PROD=sqFQ121JCqKKoivj5WBi_nix:S&PROD_pses=ZGC487EBFB2F906FB7E118CE951380B235928F9D77FFAEFABAD84A1AEF8951C90B3A96A406F1954B59496D028746E62EB1DFC11F2ECC9EA160

List of sequenced eukaryotic genomesGlobal microbial identifier: The genomic epidemiological database for global identification of microorganisms or global microbial identifier (GMI) is a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect and track-and-trace infectious disease outbreaks and emerging pathogens. The database holds two types of information: 1) genomic information of microorganisms, linked to, 2) metadata of those microorganism such as epidemiological details.NADH-QDNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Molecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.PlasmoDB: PlasmoDB is a biological database for the genus Plasmodium. The database is a member of the EuPathDB project.Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.Chromosome regionsOpen reading frame: In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of codons that do not contain a stop codon (usually UAA, UAG or UGA).CS-BLASTCancer Genome Project: The Cancer Genome Project, based at the Wellcome Trust Sanger Institute, aims to identify sequence variants/mutations critical in the development of human cancers. Like The Cancer Genome Atlas project within the United States, the Cancer Genome Project represents an effort in the War on Cancer to improve cancer diagnosis, treatment, and prevention through a better understanding of the molecular basis of this disease.Coles PhillipsPSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.Genetic variation: right|thumbProtein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Extracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.Recombination (cosmology): In cosmology, recombination refers to the epoch at which charged electrons and protons first became bound to form electrically neutral hydrogen atoms.Note that the term recombination is a misnomer, considering that it represents the first time that electrically neutral hydrogen formed.ParaHox: The ParaHox gene cluster is an array of homeobox genes (involved in morphogenesis, the regulation of patterns of anatomical development) from the Gsx, Xlox (Pdx) and Cdx gene families.Gene duplication: Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene.Direct repeat: Direct repeats are a type of genetic sequence that consists of two or more repeats of a specific sequence.Mac OS X Server 1.0Composite transposon: A composite transposon is similar in function to simple transposons and Insertion Sequence (IS) elements in that it has protein coding DNA segments flanked by inverted, repeated sequences that can be recognized by transposase enzymes. A composite transposon, however, is flanked by two separate IS elements which may or may not be exact replicas.Haplogroup L0 (mtDNA)Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Ligation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.Horizontal gene transfer in evolutionEukaryotic transcription: Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells.Ty5 retrotransposon: The Ty5 is a type of retrotransposon native to the Saccharomyces cerevisiae organism.Sequence clustering: In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" (ESTs) or protein origin.Massive parallel sequencing: Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged in 1994-1998 and became commercially available since 2005.Thermal cyclerClonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.PaleopolyploidyDNA condensation: DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems.Gene signature: A gene signature is a group of genes in a cell whose combined expression patternItadani H, Mizuarai S, Kotani H. Can systems biology understand pathway activation?Adjustable spannerTriparental mating: Triparental mating is a form of Bacterial conjugation where a conjugative plasmid present in one bacterial strain assists the transfer of a mobilizable plasmid present in a second bacterial strain into a third bacterial strain. Plasmids are introduced into bacteria for such purposes as transformation, cloning, or transposon mutagenesis.Internet organizations: This is a list of Internet organizations, or organizations that play or played a key role in the evolution of the Internet by developing recommendations, standards, and technology; deploying infrastructure and services; and addressing other major issues.Weedy rice: Weedy rice, also known as red rice, is a variety of rice (Oryza) that produces far fewer grains per plant than cultivated rice and is therefore considered a pest. The name "weedy rice" is used for all types and variations of rice which show some characteristic features of cultivated rice and grow as weeds in commercial rice fields.Premature chromosome condensation: Premature chromosome condensation (PCC) occurs in eukaryotic organisms when mitotic cells fuse with interphase cells. Chromatin, a substance that contains genetic material such as DNA, is normally found in a loose bundle inside a cell's nucleus.Ferric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Intergenic region: An Intergenic region (IGR) is a stretch of DNA sequences located between genes. Intergenic regions are a subset of Noncoding DNA.Chromothripsis: Chromothripsis is the phenomenon by which up to thousands of clustered chromosomal rearrangements occur in a single event in localised and confined genomic regions in one or a few chromosomes, and is known to be involved in both cancer and congenital diseases. It occurs through one massive genomic rearrangement during a single catastrophic event in the cell's history.Nucleic acid structure: Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar.WGAViewer: WGAViewer is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a genome wide association study (GWAS). Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium (LD) with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP.Circular bacterial chromosome: A circular bacterial chromosome is a bacterial chromosome in the form of a molecule of circular DNA. Unlike the linear DNA of most eukaryotes, typical bacterial chromosomes are circular.Cellular microarray: A cellular microarray is a laboratory tool that allows for the multiplex interrogation of living cells on the surface of a solid support. The support, sometimes called a "chip", is spotted with varying materials, such as antibodies, proteins, or lipids, which can interact with the cells, leading to their capture on specific spots.DNA re-replication: DNA re-replication (or simply rereplication) is an undesirable and possibly fatal occurrence in eukaryotic cells in which the genome is replicated more than once per cell cycle. Rereplication is believed to lead to genomic instability and has been implicated in the pathologies of a variety of human cancers.Signature-tagged mutagenesis: Signature-tagged mutagenesis (STM) is a genetic technique used to study gene function. Recent advances in genome sequencing have allowed us to catalogue a large variety of organisms' genomes, but the function of the genes they contain is still largely unknown.Restriction fragment: A restriction fragment is a DNA fragment resulting from the cutting of a DNA strand by a restriction enzyme (restriction endonucleases), a process called restriction. Each restriction enzyme is highly specific, recognising a particular short DNA sequence, or restriction site, and cutting both DNA strands at specific points within this site.Genetic linkage: Genetic linkage is the tendency of alleles that are located close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be genetically linked.Library (biology): In molecular biology, a library is a collection of DNA fragments that is stored and propagated in a population of micro-organisms through the process of molecular cloning. There are different types of DNA libraries, including cDNA libraries (formed from reverse-transcribed RNA), genomic libraries (formed from genomic DNA) and randomized mutant libraries (formed by de novo gene synthesis where alternative nucleotides or codons are incorporated).Copy number analysis: Copy number analysis usually refers to the process of analyzing data produced by a test for DNA copy number variation in patient's sample. Such analysis helps detect chromosomal copy number variation that may cause or may increase risks of various critical disorders.Codon Adaptation Index: The Codon Adaptation Index (CAI) is the most widespread technique for analyzing Codon usage bias. As opposed to other measures of codon usage bias, such as the 'effective number of codons' (Nc), which measure deviation from a uniform bias (null hypothesis), CAI measures the deviation of a given protein coding gene sequence with respect to a reference set of genes.CTXφ Bacteriophage: The CTXφ bacteriophage is a filamentous bacteriophage that contains the genetic material needed by the Vibrio cholerae bacterium for the production of cholera toxin, or CT. CTXφ is a positive virus with single-stranded DNA (ssDNA).

(1/7812) The prokaryotic beta-recombinase catalyzes site-specific recombination in mammalian cells.

The development of new strategies for the in vivo modification of eukaryotic genomes has become an important objective of current research. Site-specific recombination has proven useful, as it allows controlled manipulation of murine, plant, and yeast genomes. Here we provide the first evidence that the prokaryotic site-specific recombinase (beta-recombinase), which catalyzes only intramolecular recombination, is active in eukaryotic environments. beta-Recombinase, encoded by the beta gene of the Gram-positive broad host range plasmid pSM19035, has been functionally expressed in eukaryotic cell lines, demonstrating high avidity for the nuclear compartment and forming a clear speckled pattern when assayed by indirect immunofluorescence. In simian COS-1 cells, transient beta-recombinase expression promoted deletion of a DNA fragment lying between two directly oriented specific recognition/crossing over sequences (six sites) located as an extrachromosomal DNA substrate. The same result was obtained in a recombination-dependent lacZ activation system tested in a cell line that stably expresses the beta-recombinase protein. In stable NIH/3T3 clones bearing different number of copies of the target sequences integrated at distinct chromosomal locations, transient beta-recombinase expression also promoted deletion of the intervening DNA, independently of the insertion position of the target sequences. The utility of this new recombination tool for the manipulation of eukaryotic genomes, used either alone or in combination with the other recombination systems currently in use, is discussed.  (+info)

(2/7812) Comparison of synonymous codon distribution patterns of bacteriophage and host genomes.

Synonymous codon usage patterns of bacteriophage and host genomes were compared. Two indexes, G + C base composition of a gene (fgc) and fraction of translationally optimal codons of the gene (fop), were used in the comparison. Synonymous codon usage data of all the coding sequences on a genome are represented as a cloud of points in the plane of fop vs. fgc. The Escherichia coli coding sequences appear to exhibit two phases, "rising" and "flat" phases. Genes that are essential for survival and are thought to be native are located in the flat phase, while foreign-type genes from prophages and transposons are found in the rising phase with a slope of nearly unity in the fgc vs. fop plot. Synonymous codon distribution patterns of genes from temperate phages P4, P2, N15 and lambda are similar to the pattern of E. coli rising phase genes. In contrast, genes from the virulent phage T7 or T4, for which a phage-encoded DNA polymerase is identified, fall in a linear curve with a slope of nearly zero in the fop vs. fgc plane. These results may suggest that the G + C contents for T7, T4 and E. coli flat phase genes are subject to the directional mutation pressure and are determined by the DNA polymerase used in the replication. There is significant variation in the fop values of the phage genes, suggesting an adjustment to gene expression level. Similar analyses of codon distribution patterns were carried out for Haemophilus influenzae, Bacillus subtilis, Mycobacterium tuberculosis and their phages with complete genomic sequences available.  (+info)

(3/7812) Genomic complexity among strains of the facultative photoheterotrophic bacterium Rhodobacter sphaeroides.

Pulsed-field gel electrophoresis following the use of rare cutting restriction endonucleases together with Southern hybridization, using markers distributed on chromosomes I and II of Rhodobacter sphaeroides 2.4.1, has been used to examine approximately 25 strains of R. sphaeroides in an effort to assess the occurrence of genome complexity in these strains. The results suggest that genome complexity is widespread and is accompanied by substantial genomic heterogeneity.  (+info)

(4/7812) Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage.

We report DNA and predicted protein sequence similarities, implying homology, among genes of double-stranded DNA (dsDNA) bacteriophages and prophages spanning a broad phylogenetic range of host bacteria. The sequence matches reported here establish genetic connections, not always direct, among the lambdoid phages of Escherichia coli, phage phiC31 of Streptomyces, phages of Mycobacterium, a previously unrecognized cryptic prophage, phiflu, in the Haemophilus influenzae genome, and two small prophage-like elements, phiRv1 and phiRv2, in the genome of Mycobacterium tuberculosis. The results imply that these phage genes, and very possibly all of the dsDNA tailed phages, share common ancestry. We propose a model for the genetic structure and dynamics of the global phage population in which all dsDNA phage genomes are mosaics with access, by horizontal exchange, to a large common genetic pool but in which access to the gene pool is not uniform for all phage.  (+info)

(5/7812) Identification of a ribonuclease H gene in both Mycoplasma genitalium and Mycoplasma pneumoniae by a new method for exhaustive identification of ORFs in the complete genome sequences.

Exhaustive identification of open reading frames in complete genome sequences is a difficult task. It is possible that important genes are missed. In our efforts to reanalyze the intergenic regions of Mycoplasma genitalium and Mycoplasma pneumoniae, we have newly identified a number of new open reading frames (ORFs) in both M. genitalium and M. pneumoniae. The most significant identification was that of a ribonuclease H enzyme in both species which until now has not been identified or assumed absent and interpreted as such. In this paper we discuss the biological importance of RNase H and its evolutionary implication. We also stress the usefulness of our method for identifying new ORFs by reanalyzing intergenic regions of existing ORFs in complete genome sequences.  (+info)

(6/7812) The use of gene clusters to infer functional coupling.

Previously, we presented evidence that it is possible to predict functional coupling between genes based on conservation of gene clusters between genomes. With the rapid increase in the availability of prokaryotic sequence data, it has become possible to verify and apply the technique. In this paper, we extend our characterization of the parameters that determine the utility of the approach, and we generalize the approach in a way that supports detection of common classes of functionally coupled genes (e.g., transport and signal transduction clusters). Now that the analysis includes over 30 complete or nearly complete genomes, it has become clear that this approach will play a significant role in supporting efforts to assign functionality to the remaining uncharacterized genes in sequenced genomes.  (+info)

(7/7812) The tricarboxylic acid cycle of Helicobacter pylori.

The composition and properties of the tricarboxylic acid cycle of the microaerophilic human pathogen Helicobacter pylori were investigated in situ and in cell extracts using [1H]- and [13C]-NMR spectroscopy and spectrophotometry. NMR spectroscopy assays enabled highly specific measurements of some enzyme activities, previously not possible using spectrophotometry, in in situ studies with H. pylori, thus providing the first accurate picture of the complete tricarboxylic acid cycle of the bacterium. The presence, cellular location and kinetic parameters of citrate synthase, aconitase, isocitrate dehydrogenase, alpha-ketoglutarate oxidase, fumarate reductase, fumarase, malate dehydrogenase, and malate synthase activities in H. pylori are described. The absence of other enzyme activities of the cycle, including alpha-ketoglutarate dehydrogenase, succinyl-CoA synthetase, and succinate dehydrogenase also are shown. The H. pylori tricarboxylic acid cycle appears to be a noncyclic, branched pathway, characteristic of anaerobic metabolism, directed towards the production of succinate in the reductive dicarboxylic acid branch and alpha-ketoglutarate in the oxidative tricarboxylic acid branch. Both branches were metabolically linked by the presence of alpha-ketoglutarate oxidase activity. Under the growth conditions employed, H. pylori did not possess an operational glyoxylate bypass, owing to the absence of isocitrate lyase activity; nor a gamma-aminobutyrate shunt, owing to the absence of both gamma-aminobutyrate transaminase and succinic semialdehyde dehydrogenase activities. The catalytic and regulatory properties of the H. pylori tricarboxylic acid cycle enzymes are discussed by comparing their amino acid sequences with those of other, more extensively studied enzymes.  (+info)

(8/7812) Functional insights from structural predictions: analysis of the Escherichia coli genome.

Fold assignments for proteins from the Escherichia coli genome are carried out using BASIC, a profile-profile alignment algorithm, recently tested on fold recognition benchmarks and on the Mycoplasma genitalium genome and PSI BLAST, the newest generation of the de facto standard in homology search algorithms. The fold assignments are followed by automated modeling and the resulting three-dimensional models are analyzed for possible function prediction. Close to 30% of the proteins encoded in the E. coli genome can be recognized as homologous to a protein family with known structure. Most of these homologies (23% of the entire genome) can be recognized both by PSI BLAST and BASIC algorithms, but the latter recognizes an additional 260 homologies. Previous estimates suggested that only 10-15% of E. coli proteins can be characterized this way. This dramatic increase in the number of recognized homologies between E. coli proteins and structurally characterized protein families is partly due to the rapid increase of the database of known protein structures, but mostly it is due to the significant improvement in prediction algorithms. Knowing protein structure adds a new dimension to our understanding of its function and the predictions presented here can be used to predict function for uncharacterized proteins. Several examples, analyzed in more detail in this paper, include the DPS protein protecting DNA from oxidative damage (predicted to be homologous to ferritin with iron ion acting as a reducing agent) and the ahpC/tsa family of proteins, which provides resistance to various oxidating agents (predicted to be homologous to glutathione peroxidase).  (+info)



genomes


  • Some of the features relevant to bacterial genomes are protein coding genes, non-coding RNAs, and operons. (blogspot.com)
  • As of April 2016, there are about 70,000 genome assemblies in Genbank (draft and complete), with the majority being bacterial genomes. (blogspot.com)
  • files available at NCBI FTP to see what genome assembly software is being used for bacterial genomes. (blogspot.com)
  • The determination of multiple, complete genome sequences of bacteria, archaea and eukaryotes has created the opportunity for a new level of phylogenetic analysis that is based not on a phylogenetic tree for selected molecules, for example, rRNAs, as in traditional molecular phylogenetic studies [ 1 , 2 ], but (ideally) on the entire body of information contained in the genomes. (pubmedcentralcanada.ca)
  • The most straightforward version of this type of analysis, to which we hereinafter refer to as 'genome-tree' building, involves scaling-up the traditional tree-building approach and analyzing the phylogenetic trees for multiple gene families (in principle, all families represented in many genomes), in an attempt to derive a consensus, 'organismal' phylogeny [ 3 - 5 ]. (pubmedcentralcanada.ca)
  • We demonstrate the utility of whole genome mapping (WGM) as a tool to identify mis-assemblies and to guide k-mer selection and higher quality de novo genome assembly of bacterial genomes. (biomedcentral.com)
  • Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis. (nih.gov)
  • Miniature inverted-repeat transposable elements (MITEs) are non-autonomous transposons (devoid a transposase gene, tps) involving insertion/deletion of genomic DNA in bacterial genomes influencing gene functions. (usda.gov)

bacteria


  • All constructed trees support the separation of the two primary prokaryotic domains, bacteria and archaea, as well as some terminal bifurcations within the bacterial and archaeal domains. (pubmedcentralcanada.ca)
  • The minimal genome these researchers built was based on the relatively simple genome of the bacteria Mycoplasma mycoides , a parasite that infects cattle, but the study presented a twist. (sciencecouncil.org)
  • Recent work by the group on the genitourinary microbiome (GUM) has shown that female urine, even in the absence of culture evidence of bacteria does have evidence of bacterial DNA. (clinicaltrials.gov)
  • From this the investigators can hypothesize that urinary bacteria contribute to urinary symptoms and that there is a difference in the bacterial communities in the urine of women who respond to Solifenacin, a drug used to treat OAB, versus those that do not. (clinicaltrials.gov)
  • Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools. (nih.gov)
  • The aim of this study was to establish a link between periodontal disease and Alzheimer's disease (AD) with a view to identifying the major periodontal disease bacteria (Treponema denticola, Tannerella forsythia, and Porphyromonas gingivalis) and/or bacterial components in brain tissue from 12 h postmortem delay. (blogspot.com)

regions of the genome


  • Obviously, we have gaps and are very likely missing some regions of the genome as our contigs span ~8.8MB. (seqanswers.com)

digitized genome sequence


  • We report the design, synthesis, and assembly of the 1.08-mega-base pair Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a M. capricolum recipient cell to create new M. mycoides cells that are controlled only by the synthetic chromosome. (sciencemag.org)

complete genome sequences


  • The availability of multiple complete genome sequences from diverse taxa prompts the development of new phylogenetic approaches, which attempt to incorporate information derived from comparative analysis of complete gene sets or large subsets thereof. (pubmedcentralcanada.ca)
  • Three Complete Genome Sequences of Genotype G Mumps Virus from the 2016 Outbreak in Arkansas, USA. (nih.gov)

2016


  • A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features " was published in Nature Communications in March 2016. (sciencecouncil.org)

Genetics


  • Presentation Abstracts Telomere dysfunction induced mitochondrial compromise and ageing Telomeres in cancer and stem cell failure Sequencing and the genetics of disease The molecular back-and-forth of co-adapted plant/bacterial pathogen interactions Will extending amphibian limbs lead to extending mammalian life? (ufl.edu)
  • The molecular basis of alpha-1-antitrypsin deficiency Pharmacogenomic biomarkers and personalized medicine: focus on cytochrome P450 enzymes Translating genetics research to improve patient care Plant-pathogen coevolution gone awry: pathogen emergence in the age of globalization A possible strategy for citrus canker control using a bacterial-derived transgene that triggers programmed cell death Poster sessions 1. (ufl.edu)

sequences


  • Often users are not bio-informaticians and, in a black box approach, utilise assembly parameters such as contig length and N50 to generate whole genome sequences, potentially resulting in mis-assemblies. (biomedcentral.com)
  • Draft genome sequences of Actinomyces timonensis strain 7400942T and its prophage. (biomedsearch.com)

genes


  • In the study, researchers from the Craig Venter Institute built a minimal genome (a genome including only the genes essential for life). (sciencecouncil.org)
  • First, we base our simplified bacterial gene set (SBGS) on experimentally determined essential genes to ensure that the genes included in the SBGS are critical. (nature.com)

Microbial


  • Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. (sanger.ac.uk)
  • Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. (nih.gov)
  • The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. (nih.gov)

minimal


  • Our top paper this month is " Design and synthesis of a minimal bacterial genome ," published in Science magazine. (sciencecouncil.org)

genomics


  • Is the Subject Area "Bacterial genomics" applicable to this article? (plos.org)
  • The Pathogen genomics group is collaborating with a number of external groups to explore and enable whole genome sequencing in clinical microbiology. (sanger.ac.uk)

Illumina


  • With the advent of next-generation sequencer (NGS) platforms, such as 454 Roche, SOLiD and Illumina, there has been an increase in the number of projects for whole-genome sequencing (WGS) mainly due to cost reduction and the increased speed of sequencing and data generation. (biomedsearch.com)

Isolates


  • In this study, a total of 326 bacterial isolates collected in China and Florida were examined. (usda.gov)
  • MITE mobility was evidenced by the presence of "full" (with MITE) / "empty" (without MITE) isolates in the bacterial pan-genome. (usda.gov)

mycoides


  • A synthetic Mycoplasma mycoides genome transplanted into M. capricolum was able to control the host cell. (sciencemag.org)

whole genome s


  • To the best of our knowledge, this is the first documentation that reports the whole genome sequence and quorum-quenching activity of Staphylococcus sp. (biomedsearch.com)

sequencer


  • Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer. (biomedsearch.com)

Gardnerella


  • Participants were classified into Low Biomass, Lactobacillus, Gardnerella, Diverse, and Other urotypes based on the bacterial DNA at baseline. (clinicaltrials.gov)

Mycoplasma


  • Mycoplasma genitalium , a free-living bacterium with the smallest gene repertoire among the organisms sequenced to date, is an ideal species for MGS research and synthetic biology 11 and has become the first genome to be subjected to genome-scale gene essentiality screening 12 . (nature.com)

short reads


  • De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. (nih.gov)

annotation


  • What is genome annotation? (blogspot.com)
  • Genome annotation is the process of identifying features of interest on a genome sequence. (blogspot.com)
  • The accuracy and richness of a genome annotation is important, and sometimes critical, to downstream biological interpretation. (blogspot.com)
  • Below I list the tools I am aware of for performing and curating bacterial genome annotation. (blogspot.com)

contigs


  • This will help join contigs into scaffolds and hopefully a full genome, but we will likely have very low coverage/inaccuracies for those areas of the genome that the miSeq missed. (seqanswers.com)

assemblies


  • We demonstrate that whole genome mapping can be used to identify these mis-assemblies and can guide the selection of the best k-mer size which yields the highest N50 without mis-assemblies. (biomedcentral.com)

prokaryotic


  • We conclude that, the extensive horizontal gene flow and lineage-specific gene loss notwithstanding, extension of phylogenetic analysis to the genome scale has the potential of uncovering deep evolutionary relationships between prokaryotic lineages. (pubmedcentralcanada.ca)
  • The present study presents a modus operandi that enables a greater and better use of data obtained from semiconductor sequencing for obtaining the complete genome from a prokaryotic microorganism, C. pseudotuberculosis, which is not a traditional biological model such as Escherichia coli. (biomedsearch.com)

Factory


  • The Genome Factory: What bacterial genome assemblers are people using? (blogspot.com)

Coverage


  • It's unlikely that you are completely missing coverage of 400kbp of your genome. (seqanswers.com)
  • The Ion Torrent platform is an example of these technologies, characterized by lower coverage, generating challenges for the genome assembly. (biomedsearch.com)

Scientists


  • Scientists design a bacterial genome with only 57 codons. (the-scientist.com)
  • Access to data from thousands of genotyping customers helped scientists detect novel associations with the disorder across the genome. (the-scientist.com)

Microbiology


  • Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. (sanger.ac.uk)

diagnosis


  • Confirmation of the diagnosis of bacterial endophthalmitis is dependent onmicrobiological isolation of organisms. (journals.co.za)
  • We evaluated polymerase chain reaction (PCR) in the diagnosis of bacterial endophthalmitis using vitreous fluid (VF) and aqueous humour (AH) specimens. (journals.co.za)
  • It is concluded that PCR is a reliable tool for the diagnosis of bacterial endophthalmitis. (journals.co.za)

draft


analysis


  • Genome-wide genetic diversity analysis of two Pinus species 2. (ufl.edu)

Rapid


  • Rapid single-colony whole-genome sequencing of bacterial pathogens. (sanger.ac.uk)
  • Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. (sanger.ac.uk)
  • Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak. (sanger.ac.uk)

assembly


  • Any recommendations on if A or B should be sufficient for a genome assembly given where we are at or will both be necessary? (seqanswers.com)
  • De novo genome assembly can be challenging due to inherent properties of the reads, even when using current state-of-the-art assembly tools based on de Bruijn graphs. (biomedcentral.com)
  • In this paper, we evaluated the utility of WGM for proper k-mer size selection and for optimization of parameters for de novo genome assembly. (biomedcentral.com)
  • Ensuing, using WGM, a whole genome map of S. aureus EMRSA-15 was generated which, using MapSolver, was aligned with the assembly files corresponding to different k-mer sizes. (biomedcentral.com)

species


  • Bacterial 16S rRNA can be isolated from urine and sequenced to identify bacterial species present in urine. (clinicaltrials.gov)

provides


  • Bacterial whole genome sequencing provides the ultimate level of resolution for transmission tracking, and can be used to predict drug resistance. (sanger.ac.uk)

human


  • Host and bacterial ligands that interact with the same cell-surface receptor induce different activities in human macrophages. (the-scientist.com)

study


  • Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. (sanger.ac.uk)
  • Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. (sanger.ac.uk)

high


  • The latter tree supported three potential high-level bacterial clades,: i) Chlamydia-Spirochetes, ii) Thermotogales-Aquificales (bacterial hyperthermophiles), and ii) Actinomycetes-Deinococcales-Cyanobacteria. (pubmedcentralcanada.ca)
  • Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting. (sanger.ac.uk)

Present