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GenomeGenome, BacterialGenome, ViralGenome, PlantGenome, HumanGenome, MitochondrialGenome, FungalGenome SizeSequence Analysis, DNAGenome, ArchaealPhylogenyBase SequenceGenome, InsectEvolution, MolecularGenome, ProtozoanGenomicsGenome, ChloroplastChromosome MappingGenome, HelminthOpen Reading FramesGenome, PlastidSequence AlignmentSyntenyHuman Genome ProjectDNA, ViralMolecular Sequence DataGene OrderComputational BiologyGenetic VariationModels, GeneticAmino Acid SequenceDatabases, GeneticRecombination, GeneticSpecies SpecificityMultigene FamilyChromosomes, Artificial, BacterialGene DuplicationRepetitive Sequences, Nucleic AcidRNA, ViralGenes, ViralSoftwareMolecular Sequence AnnotationDNA Transposable ElementsBase CompositionDNA, MitochondrialSequence Homology, Nucleic AcidMutationCloning, MolecularContig MappingDNA, BacterialConserved SequenceDNA, PlantViral ProteinsGene Transfer, HorizontalTranscription, GeneticRetroelementsNucleic Acid HybridizationDatabases, Nucleic AcidChromosomes, PlantExpressed Sequence TagsHigh-Throughput Nucleotide SequencingPseudogenesPhysical Chromosome MappingPolymerase Chain ReactionAlgorithmsBiological EvolutionVirus ReplicationGenomic InstabilityGenes, BacterialPolyploidyGenetic MarkersDNAGene Expression ProfilingSequence Homology, Amino AcidGenes, PlantGenome, MicrobialPlasmidsInternetGenome ComponentsCell LineSequence HomologyOryza sativaChromosomesBacterial ProteinsDNA, IntergenicGene RearrangementNucleic Acid ConformationPolymorphism, Single NucleotideChromosomes, BacterialOligonucleotide Array Sequence AnalysisDNA ReplicationMutagenesis, InsertionalDNA Restriction EnzymesCluster AnalysisGenetic LinkageGene LibraryGene DosageCodonDNA PrimersBacteriophagesPhenotypeRestriction MappingGenotypeSelection, GeneticGenesIntronsTerminal Repeat SequencesUser-Computer InterfaceProphagesBlotting, SouthernINDEL MutationMicrosatellite RepeatsEscherichia coliGenes, MitochondrialDNA, ChloroplastGene DeletionGenomic LibraryComparative Genomic HybridizationArabidopsisRNA, TransferVertebratesProkaryotic CellsSymbiosisSequence Analysis, RNAPromoter Regions, GeneticInterspersed Repetitive SequencesRNA, MessengerPlantsSaccharomyces cerevisiaeVirulenceInverted Repeat SequencesRNA VirusesPlastidsVirus IntegrationBacteriaGenes, ArchaealSorghumGene Expression Regulation, BacterialGene Expression Regulation, ViralDNA, CircularGenetic LociChromosomes, HumanShort Interspersed Nucleotide ElementsGenetic VectorsGenetic EngineeringSegmental Duplications, GenomicDNA, ComplementaryPolymorphism, GeneticDrosophila melanogasterEukaryotic CellsMetabolic Networks and PathwaysGC Rich SequenceMammalsCell NucleusLong Interspersed Nucleotide ElementsTranscriptomeHybridization, GeneticAllelesPan troglodytesEukaryotaArchaeaQuantitative Trait LociGenes, DuplicateAngiospermsSequence DeletionCapsidTetraodontiformesDNA Copy Number VariationsGene Expression RegulationDiploidyMutation RateDefective VirusesChromosome InversionUntranslated RegionsCrosses, GeneticDNA-Binding ProteinsLikelihood FunctionsTandem Repeat SequencesProteomeGenomic IslandsExonsDNA, FungalBinding SitesDNA RepairPlant DiseasesPlant ProteinsZea maysRNAGenetic Techniques5' Untranslated RegionsAlu ElementsChromatinDNA, AlgalGenes, OverlappingChromosomes, MammalianEndogenous RetrovirusesGenome-Wide Association StudyComputer GraphicsSiphoviridaeDNA MethylationGene Expression
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 prokaryotic beta-recombinase catalyzes site-specific recombination in mammalian cells. (1/7812)

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)

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

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)

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

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)

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

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)

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. (5/7812)

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)

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

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)

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

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)

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

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)

Using whole genome comparison to detect sequence similarities between plants and microbesUsing whole genome comparison to detect sequence similarities between plants and microbes
With an increasing amount of whole genome sequence data becoming available on a daily basis we have an opportunity to study the interactions and dynamics of different organisms on a whole genome level. In the past, reports of horizontal gene transfer have focused mainly on the identification of single genes that show distorted phylogenetic profiles to that of the organism it was isolated from. This study firstly did whole genome comparisons between the rice nuclear and plastid genomes to determine the level and dynamics gene transfer and insertion of the chloroplast ad mitochondrial genomes into that of the nuclear genome of rice. Secondly, it looked to identify sequence similarities between the rice genome and microbial genomes by performing whole genome comparisons between the rice genome and that of several microbial genomes. These sequences were analyzed further to identify possible instances of horizontal transfer of DNA from microbes to the rice genome. Using this approach, this study ...
Pan-Tetris: an interactive visualisation for Pan-genomes | BMC Bioinformatics | Full TextPan-Tetris: an interactive visualisation for Pan-genomes | BMC Bioinformatics | Full Text
Large-scale genome projects have paved the way to microbial pan-genome analyses. Pan-genomes describe the union of all genes shared by all members of the species or taxon under investigation. They offer a framework to assess the genomic diversity of a given collection of individual genomes and moreover they help to consolidate gene predictions and annotations. The computation of pan-genomes is often a challenge, and many techniques that use a global alignment-independent approach run the risk of not separating paralogs from orthologs. Also alignment-based approaches which take the gene neighbourhood into account often need additional manual curation of the results. This is quite time consuming and so far there is no visualisation tool available that offers an interactive GUI for the pan-genome to support curating pan-genomic computations or annotations of orthologous genes. We introduce Pan-Tetris, a Java based interactive software tool that provides a clearly structured and suitable way for the visual
Twenty years of bacterial genome sequences - ACGTTwenty years of bacterial genome sequences - ACGT
Take-Home Message comic #5 celebrates an amazing milestone. During my PhD, I kept a little list pinned to the filing cabinet next to my desk, a list which contained details of every sequenced genome. This was something that was much easier when the number of published genomes was still in the single digits!. This is my favorite Take-Home Message comic to date. I feel that we are slowly settling in on a style that works well for this medium, and Abbys drawings just seem to get better and better. ...
Draft genome sequences of Escherichia coli strains isolated from septic patients<...Draft genome sequences of Escherichia coli strains isolated from septic patients<...
TY - JOUR. T1 - Draft genome sequences of Escherichia coli strains isolated from septic patients. AU - Dunitz, Madison I.. AU - Coil, David A.. AU - Jospin, Guillaume. AU - Eisen, Jonathan A. AU - Adams, Jason Yeates. PY - 2014. Y1 - 2014. N2 - We present the draft genome sequences of six strains of Escherichia coli isolated from blood cultures collected from patients with sepsis. The strains were collected from two patient sets, those with a high severity of illness, and those with a low severity of illness. Each genome was sequenced by both Illumina and PacBio for comparison.. AB - We present the draft genome sequences of six strains of Escherichia coli isolated from blood cultures collected from patients with sepsis. The strains were collected from two patient sets, those with a high severity of illness, and those with a low severity of illness. Each genome was sequenced by both Illumina and PacBio for comparison.. UR - ...
Community-wide analysis of microbial genome sequence signatures | Genome Biology | Full TextCommunity-wide analysis of microbial genome sequence signatures | Genome Biology | Full Text
It has been suggested that environmental constraints strongly shape nucleotide composition [26, 49-51]. If this were the case, two effects should be apparent in genome signatures of AMD populations. First, shared pressures deriving from the extreme AMD environment would drive genome signatures together, potentially obscuring differences between populations. Second, since each genome encodes proteins destined for diverse environments (that is, intracellular and extracellular), there should be prominent intra-genome variation of genome signature and scattering of fragments from the same genome into disparate regions of the SOM. Neither of these expectations is met in the AMD dataset. There are vast differences in nucleotide composition between populations, with genomic %GC ranging from 35% (ARMAN-4 and ARMAN-5) to 69% (low-abundance Actinobacteria) and genome signatures forming discrete clusters. Amino acid compositional constraints required for stability of proteins exposed to acidic solutions do ...
ASMscience | Gene Transfer in Gram-NeASMscience | Gene Transfer in Gram-Ne
One realization that has come from comparing multiple bacterial genome sequences, including multiple isolates from the same species, is that gene transfer is an important force in bacterial genome evolution. In the laboratory gene transfer is essential for the study of bacteria and for learning more about all living organisms. Three processes in bacteria can broadly define the transfer of DNA: transformation, transduction, and conjugation. This chapter focuses on the many genetic tools available to manipulate the genetic content of Escherichia coli. A DNA molecule that does not have its own origin of replication must integrate into either the host chromosome or another autonomously replicating element such as an endogenous plasmid. In E. coli a modified derivative of the bacteriophage T4 offers some advantages for transduction in that it packages twice as much DNA as P1 and also is less sensitive to capsules found on many pathogenic strains of E. coli. Transformation of bacteria by use of either
Analysis of plant pan-genomes and transcriptomes with GET HOMOLOGUES-EST, a clustering solution for sequences of the same...Analysis of plant pan-genomes and transcriptomes with GET HOMOLOGUES-EST, a clustering solution for sequences of the same...
The pan-genome of a species is defined as the union of all the genes and non-coding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19 Arabidopsis thaliana ecotypes and then applied to the analysis of transcripts from 16 Hordeum vulgare genotypes. The goal was to sample their pan-genomes and classify sequences as core, if detected in all accessions, or accessory, when absent in some of them. The resulting sequence clusters were used to simulate pan-genome growth, and to compile Average Nucleotide Identity matrices that summarize intra-species variation. Although transcripts were found to under-estimate pan-genome size by at least 10%, we concluded that clusters of ...
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of...Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of...
Functional annotation of genomes is a critical aspect of the genomics enterprise. Without reliable assignment of gene function at the appropriate level of specificity, new genome sequences are plainly useless. The primary methodology used for genome annotation is the sequence database search, the results of which allow transfer of functional information from experimentally characterized genes (proteins) to their uncharacterized homologs in newly sequenced genomes [1,2,3]. However, general-purpose, archival sequence databases are not particularly suited for the purpose of genome annotation. The quality of the annotation of a new genome produced using a particular database critically depends on the reliability and completeness of the annotations in the database itself. As far as annotation is concerned, the purpose of primary sequence databases is to faithfully preserve the description attached to each sequence by its submitter. In their capacity as sequence archives, such databases include no ...
BacMap - WikipediaBacMap - Wikipedia
BacMap is a freely available web-accessible database containing fully annotated, fully zoomable and fully searchable chromosome maps from more than 2500 prokaryotic (archaebacterial and eubacterial) species.[1] BacMap was originally developed in 2005 to address the challenges of viewing and navigating through the growing numbers of bacterial genomes that were being generated through large-scale sequencing efforts. Since it was first introduced, the number of bacterial genomes in BacMap has grown by more than 15X. Essentially BacMap functions as an on-line visual atlas of microbial genomes. All of the genome annotations in BacMap were generated through the BASys genome annotation system.[3] BASys is a widely used microbial annotation infrastructure that performs comprehensive bionformatic analyses on raw (or labeled) bacterial genome sequence data. All of the genome (chromosome) maps in BacMap were constructed using the program known as CGView.[4] CGView is a popular visualization program for ...
The Y.O.R.F.: Investigating the Smallest Bacterial GenomeThe Y.O.R.F.: Investigating the Smallest Bacterial Genome
Where did this copy of AS originate from? It aligned well with the version of AS from P. aeruginosa and appeared to have a bacterial origin but was not found on the C. ruddii genome or the psyllid mitochondrial genome, both of which have been sequenced. Several lines of evidence ruled out the presence of a second bacterial endosymbiont in this symbiosis and since no plasmids had been reported during DNA sequencing of C. ruddii the source of this sequence appeared to be the nuclear genome of P. venusta itself. The presence of this bacterial sequence in the eukaryotic genome suggests that LGT may have taken place between a bacterial genome and the insect nuclear genome. This would be one explanation for the fact that C. ruddii has only 182 ORFs, which is significantly lower than the predicted minimal bacterial genome. However, it is also possible that C. ruddii uses mitochondrial proteins to survive and so LGT is not the only explanation for the low ORF count. ...
Genes | Free Full-Text | Ecological and Temporal Constraints in the Evolution of Bacterial Genomes | HTMLGenes | Free Full-Text | Ecological and Temporal Constraints in the Evolution of Bacterial Genomes | HTML
Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation. In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods.
GenomeGenome
In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome (Bacteriophage MS2). The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs.[7] The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research.. The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of ...
Element: ItalicElement: Italic
sec id="bid.36", ,title,Microbial Genomes,/title, ,p,... A CON entry, containing instructions on how to put the pieces back together, is also made. The CON entry contains descriptor information, such as source organism and references, as well as a join statement providing explicit instructions on how to generate the complete genome from the pieces. The Accession number assigned to the CON record is also added as a secondary Accession number on each of the pieces that make up the complete genome (see ,xref ref-type="fig" rid="bid.37",Figure 2,/xref,). ,fig id="bid.37", ,label,2,/label, ,caption,,title,A GenBank CON entry for a complete bacterial genome.,/title, ,p,The information toward the ,italic,bottom,/italic, of the record describes how to generate the complete genome from the pieces.,/p, ,/caption, ,graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="ch1f2" mime-subtype="gif"/, ,/fig, ,/p, ... ,/sec ...
Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in...Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in...
In 1995, the release of the first fully sequenced bacterial genome heralded a new era of bacterial genomic research (21). Over the past 20 years, the number of sequenced bacterial genomes has risen exponentially, and new research strategies, techniques, and applications have emerged to exploit the opportunities that these resources provide. While raw genomic sequence data are valuable, the availability of fully annotated genome sequences, outlining the positions of known genes and genomic features, dramatically increases their utility. Global expression analysis techniques such as microarrays and RNA-seq depend heavily on annotated genome sequences as a reference source for genes in the bacterial cell. These techniques have proved extremely useful; however, recently, certain limitations to their application are becoming apparent. A major concern in this regard is that they do not provide expression data for genes that are not included in genome annotation files. Bacterial sRNAs represent a class ...
Microbiology Society Journals | Using comparative genome analysis to identify problems in annotated microbial genomesMicrobiology Society Journals | Using comparative genome analysis to identify problems in annotated microbial genomes
Genome annotation is a tedious task that is mostly done by automated methods; however, the accuracy of these approaches has been questioned since the beginning of the sequencing era. Genome annotation is a multilevel process, and errors can emerge at different stages: during sequencing, as a result of gene-calling procedures, and in the process of assigning gene functions. Missed or wrongly annotated genes differentially impact different types of analyses. Here we discuss and demonstrate how the methods of comparative genome analysis can refine annotations by locating missing orthologues. We also discuss possible reasons for errors and show that the second-generation annotation systems, which combine multiple gene-calling programs with similarity-based methods, perform much better than the first annotation tools. Since old errors may propagate to the newly sequenced genomes, we emphasize that the problem of continuously updating popular public databases is an urgent and unresolved one. Due to the
Human contamination in bacterial genomes has created thousands of spurious proteins<...Human contamination in bacterial genomes has created thousands of spurious proteins<...
TY - JOUR. T1 - Human contamination in bacterial genomes has created thousands of spurious proteins. AU - Breitwieser, Florian P.. AU - Pertea, Mihaela. AU - Zimin, Aleksey V.. AU - Salzberg, Steven L.. PY - 2019. Y1 - 2019. N2 - Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of complete and draft bacterial and archaeal genomes in the NCBI RefSeq database reveals that 2250 genomes are contaminated by human sequence. The contaminant sequences derive primarily from high-copy human repeat regions, which themselves are not adequately represented in the current human reference genome, GRCh38. The absence of the sequences from the human assembly offers a likely explanation for their presence in bacterial assemblies. In some cases, the contaminating contigs have been erroneously annotated as containing protein-coding sequences, which over time have ...
Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes | BMC...Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes | BMC...
Escherichia coli exists in commensal and pathogenic forms. By measuring the variation of individual genes across more than a hundred sequenced genomes, gene variation can be studied in detail, including the number of mutations found for any given gene. This knowledge will be useful for creating better phylogenies, for determination of molecular clocks and for improved typing techniques. We find 3,051 gene clusters/families present in at least 95% of the genomes and 1,702 gene clusters present in 100% of the genomes. The former soft core of about 3,000 gene families is perhaps more biologically relevant, especially considering that many of these genome sequences are draft quality. The E. coli pan-genome for this set of isolates contains 16,373 gene clusters. A core-gene tree, based on alignment and a pan-genome tree based on gene presence/absence, maps the relatedness of the 186 sequenced E. coli genomes. The core-gene tree displays high confidence and divides the E. coli strains into the observed MLST
Identification of Unannotated Small Genes in Salmonella | G3: Genes | Genomes | GeneticsIdentification of Unannotated Small Genes in Salmonella | G3: Genes | Genomes | Genetics
Bacterial genomes serve as a blueprint in all aspects of biological research, and therefore accurate genome annotation is of paramount importance. However, increasing evidence indicates that currently annotated bacterial genomes have missed many genes encoding small proteins ≤60 aa (Wood et al. 2012; Warren et al. 2010). A small gene, or a small open reading frame (sORF), has previously been defined as one encoding proteins of ≤60 aa (Hemm et al. 2010); or alternatively, it accommodates those up to 100 aa (Andrews and Rothnagel 2014). While small proteins have been increasingly reported for their important cellular roles in bacteria (Alix and Blanc-Potard 2008; Martin et al. 2015; Hobbs et al. 2012), studies on small proteins are limited, partly because many small genes are unannotated in sequenced bacterial genomes (Alix and Blanc-Potard 2009; Storz et al. 2014). Despite much effort made to improve gene annotation, the accurate identification of small genes has been a persistent challenge ...
Microbiology Society Journals | Genome Update: rRNAs in sequenced microbial genomesMicrobiology Society Journals | Genome Update: rRNAs in sequenced microbial genomes
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Frontiers | Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic...Frontiers | Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic...
Elucidating the adaptive strategies and plasticity of bacterial genomes in situ is crucial for understanding the epidemiology and evolution of pathogens threatening human health. While much is known about the evolution of E. coli in controlled laboratory environments, less effort has been made to elucidate the genome dynamics of E. coli in its native settings. Here, we follow the genome dynamics of co-existing E. coli lineages in situ of the infant gut during the first year of life. One E. coli lineage causes a urinary tract infection (UTI) and experiences several alterations of its genomic content during subsequent antibiotic treatment. Interestingly, all isolates of this uropathogenic E. coli strain carried a highly stable plasmid implicated in virulence of diverse pathogenic strains from all over the world. While virulence elements are certainly beneficial during infection scenarios, their role in gut colonization and pathogen persistence is poorly understood. We performed in vivo competitive
How to Download Bacterial Genomes Using the Entrez API | NCBI InsightsHow to Download Bacterial Genomes Using the Entrez API | NCBI Insights
Given the size of modern sequence databases, finding the complete genome sequence for a bacterium among the many other partial sequences can be a challenge. In addition, if you want to download sequences for many bacterial species, an automated solution might be preferable. In this post well discuss how to download bacterial genomes programmatically for…
Journal Announcements: January 2013 | ASM JournalsJournal Announcements: January 2013 | ASM Journals
WASHINGTON, DC - January 28, 2013 - The American Society for Microbiology has published the first issue of its new online-only, open access journal, Genome AnnouncementsTM, focusing exclusively on reports of microbial genome sequences.. Genome Announcements features short manuscripts announcing the availability of recently sequenced genomes of prokaryotic and eukaryotic microbes and viruses in public databases. These announcements inform readers of the availability of new genome sequences and provide the rationale for sequencing a particular organism, as well as details of the methodologies and protocols used in assembly of the genome sequence.. Although genome sequence data typically are deposited in GenBank or other shared databases, the rationale for sequencing a particular organism and the detailed methodologies and protocols used often are not readily available. In the past, several ASM journals published Genome Announcement article types, brief reports stating that the genome of a ...
How to sequence a bacterial genome at the end of 2012 | In between lines of codeHow to sequence a bacterial genome at the end of 2012 | In between lines of code
A potential user (customer) of our sequencing platform asked how to generate reference genomes for his 4 bacterial strains. His question inspired me to write this post. The suggestions below are not absolute, just my thoughts on how one these days could go about sequencing a bacterial genome using one or more of the sequencing…
DNA & RNA Purification Bacterial Genomic Miniprep Kit | China-Mainland | Sigma-AldrichDNA & RNA Purification Bacterial Genomic Miniprep Kit | China-Mainland | Sigma-Aldrich
The GenElute Bacterial Genomic Kit provides a simple and convenient technique to isolate high quality DNA from both Gram(-) and Gram(+) bacteria. This kit combines the advantages of a silica-based system with a microspin format, eliminating the need for expensive resins and hazardous organic compounds.
Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes « Research Papers «...Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes « Research Papers «...
The sensitivity of this procedure to resolve variation within a bacterial species is demonstrated: genome sizes and repeat structure of five environmental strains of E. coli from short Illumina reads were estimated by this method, and total genome sizes corresponded well with those obtained for the same strains by pulsed-field gel electrophoresis. In addition, this approach was applied to read-sets for completed genomes and shown to be accurate over a wide range of microbial genome sizes. ...
Species identification by sequencing the bacterial genome at seven key loci acheter cialis.Species identification by sequencing the bacterial genome at seven key loci acheter cialis.
Species identification by sequencing the bacterial genome at seven key loci, uncovering achieved similar combinations of sequences with certain bacterial
Harvard Scientists Dive Into Structure of Bacterial Genomes | News | The Harvard CrimsonHarvard Scientists Dive Into Structure of Bacterial Genomes | News | The Harvard Crimson
Harvard scientists have unraveled the inner architecture of bacterial genomes in a breakthrough discovery that may shed light on how chromosomes organize within a cell.. The findings came after researchers applied a new visualization technique that generated the first fluorescence super-resolution images of chromosomes within a single bacterial cell.. The work demonstrates "the massive potential provided by the combination of emerging super-resolution microscopy and clever biochemistry," wrote Stefan W. Hell, director at the Max Planck Institute for Biophysical Chemistry, in an emailed statement. He added that the findings "open a new chapter in the study of bacteria molecular organization.". The findings provide the first detailed picture of a class of DNA-interacting proteins called nucleoid-associated proteins (NAPs). This close-up look helped scientists determine their role in organizing chromosomes in bacteria, according to Xiaoliang Sunney Xie, a Harvard professor of chemistry and chemical ...
Looping and clustering model for the organization of partitioning proteins on the bacterial genomeLooping and clustering model for the organization of partitioning proteins on the bacterial genome
The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe
Using CRISPR Proteins To Record A Video Clip Into Bacterial GenomesUsing CRISPR Proteins To Record A Video Clip Into Bacterial Genomes
Scientists at Harvard have used a modified CRISPR gene editing tool to insert coded sequences into bacterial genomes matching a video clip.
Pan-Genomic Approaches for Comprehensive Blood Screening of Novel or Emerging Infectious Agents - Charles ChiuPan-Genomic Approaches for Comprehensive Blood Screening of Novel or Emerging Infectious Agents - Charles Chiu
Pan-Genomic Approaches for Comprehensive Screening of Novel or Emerging Infectious Agents in Blood Emerging infectious agents, the latest of which is Zika virus...
MedVetNet Microarray Data Analysis WorkshopMedVetNet Microarray Data Analysis Workshop
The workshop will focus on the design and analysis of pan-genomic microarrays. Due to the massive availability of sequences of genomes of microbes and other organisms, the degree of sequence variation is becomming measurable both across bacterial species, but also within different isolates of the same species. Indeed, the pan-genome, defined as the total number of unique genes observed in any isolates of a given species, can be much larger than the individual genome of any single isolate. For the microarray analyst, genetic variation between isolates of the same species presents new challenges since a traditional microarray designed to target one specific genome is likely to perform very poorly if used with another, different isolate. As the number of fully sequenced genomes of indepentent isolates for each bacterial species increases, it becommes possible to design pan-genomic microarrays capable of targeting any and all unique genes ever observed in that species. The advantages of this ...
Biological Blueprints: How Genes are Studied - Infective | PerspectiveBiological Blueprints: How Genes are Studied - Infective | Perspective
The first step of bacterial cloning is to get the gene of interest into the bacterial genome. Bacteria are one-celled, prokaryotic organisms and have simpler cellular structures than humans, who are complex and multi-cellular eukaryotes. The genomes of each are stored slightly differently: both rely on large, long structures of DNA called chromosomes, but while you can think of a bacterial genome as one large, single circle of DNA twisted up like a convoluted rubber band and free-floating in the bacterial cell, the human chromosome structure (26 chromosomes in total) is a long linear string of DNA twisted up and tucked away neatly into a sub-packet of the cell called the nucleus-think what happens to your headphones when you put them in your pocket. In addition to their larger, circular chromosome, bacteria have other small, circular, free-floating pieces of DNA called plasmids. These plasmids are maintained and copied separately from the larger circular chromosome. Because bacteria can pick up ...
Draft Genome Sequence of a New Oscillospiraceae Bacterium Isolated from Anaerobic Digestion of Biomass | Microbiology Resource...Draft Genome Sequence of a New Oscillospiraceae Bacterium Isolated from Anaerobic Digestion of Biomass | Microbiology Resource...
Here, we present the genome sequence and annotation of the novel bacterial strain HV4-5-C5C, which may represent a new genus within the family Oscillospiraceae (order Eubacteriales). This strain is a potential keystone species in the hydrolysis of complex polymers during anaerobic digestion of biomass. ...
Chinese Lab Speeds Through Genome Processing With GPUs - SlashdotChinese Lab Speeds Through Genome Processing With GPUs - Slashdot
Eric Smalley writes The worlds largest genome sequencing center once needed four days to analyze data describing a human genome. Now it needs just six hours. The trick is servers built with graphics chips — the sort of processors that were originally designed to draw images on your personal ...
Rapid Editing and Evolution of Bacterial Genomes Using Libraries of Synthetic DNA - PubMedRapid Editing and Evolution of Bacterial Genomes Using Libraries of Synthetic DNA - PubMed
Multiplex automated genome engineering (MAGE) is a powerful technology for in vivo genome editing that uses synthetic single-stranded DNA (ssDNA) to introduce targeted modifications directly into the Escherichia coli chromosome. MAGE is a cyclical process that involves transformation of ssDNA (by el …
Hacking the genome with a MAGE and a CAGE - PhenomenaHacking the genome with a MAGE and a CAGE - Phenomena
MAGE, the older of the two techniques, made its debut two years ago. It stands for "multiplex automated genome engineering", a fancy way of saying that it can easily change a genome many times over. It was originally used to create millions of small variants of bacterial genomes, producing a multitude of strains that can be tested for new abilities. As Jo Marchant puts it in her excellent feature, its an "evolution machine". In its debut, within a matter of days, it had evolved a strain of E.coli that would produce large amounts of lycopene, a pigment that makes tomatoes red.. MAGE is a versatile editor. Not only can it create many diverse changes in a group of cells, it can also create many specific changes in a single cell. Thats what Isaacs, Carr and Wang have now done. TAG appears in 314 places throughout the E.coli genome as a stop codon. For each one, the team created a small stretch of DNA that had TAA instead of TAG, surrounded by exactly the same letters. They fed these edited ...
Most recent papers with the keyword Pangenome | Read by QxMDMost recent papers with the keyword Pangenome | Read by QxMD
Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome ...
Fischbach joins project to generate drugs from bacterial genomes | School of Pharmacy | UCSFFischbach joins project to generate drugs from bacterial genomes | School of Pharmacy | UCSF
Bacteria generate small molecules to fend off their fellow microbes. They also produce molecules that affect the response of host organisms-including humans-to their presence. Such molecules have been a major source of antibiotics, immunosuppressants, anti-cancer agents, and other drugs. But their discovery has not been systematic and the products of bacteria living in our bodies have only recently drawn scientific notice.. However, thanks to genome sequencing, there are now databases containing the blueprints (sequences) of 160 million genes from nearly a quarter-million organisms, including the genes of bacteria species that live in and interact with us-the human microbiome. These bacterial genes encode molecules that could yield narrow-spectrum antibiotics, immune system regulators, and neuroactive drugs. But first scientists must find the potentially therapeutic needles in this genomic haystack.. Research in the laboratory of Michael Fischbach, PhD, a faculty member of the UCSF School of ...
Pharmaceutical Microbiology: Are bacteria as individual as people?Pharmaceutical Microbiology: Are bacteria as individual as people?
We can think of the bacterial genome as having two parts," says Professor Young. "The core genome does the basic housekeeping and is much the same in all members of the species, while the accessory genome has packages of genes that are not essential to the operation of the cell, but can be very useful in coping with aspects of the real world ...
Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2.Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2.
The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format. By default, clicking on the export buttons will result in a download of the allowed maximum amount of items. To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export. After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format. ...
Bacterial Genomes: From DNA to Protein Function Using Bioinformatics - Wellcome Genome Campus Advanced Courses and Scientific...Bacterial Genomes: From DNA to Protein Function Using Bioinformatics - Wellcome Genome Campus Advanced Courses and Scientific...
Use bioinformatics to explore DNA sequences and protein functions, to find the determinants of virulence in microbes with this free online course.
Draft Genome Sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10Draft Genome Sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10
Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisrame A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wesolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL., Nature 430(6995), 2004 ...
Angry by Choice: December 2007Angry by Choice: December 2007
Back to the clever bit, the authors realized that putting these plasmids into E.coli represents HGT. These vectors are in fact derived from natural E.coli strains and are transferred naturally between strains. So, through the process of obtaining genome sequence for a variety of bacterial species, Sorek et al realized that the scientific community had inadvertantly set up an experiment to determine the limits of HGT. They simply (and by "simply" I mean anyone with a computer and knowledge of these systems could have done it, it is not meant to diminish the work or insights of the authors) took available genome sequence information from 79 distinct species and looked to see what was not sequenced using the process described above. Again, the idea being if a region was not sequenced, it must not have been propagated in E.coli (the gaps in a genome sequence are obtained using other more labor intensive methods). Indeed, the authors found regions from these species that were not able to be ...
Scientists Achieve First Bacterial Genome Transplantation; Promise to Develop First Synthetic Organism | MedgadgetScientists Achieve First Bacterial Genome Transplantation; Promise to Develop First Synthetic Organism | Medgadget
Scientists at the J. Craig Venter Institute (JCVI), a genomics research facility, transplanted a bacterial chromosome from one type of bacteria into anothe
Blueprints for Anti-cancer Drugs Identified in Bacterial GenomesBlueprints for Anti-cancer Drugs Identified in Bacterial Genomes
Technology Networks is an internationally recognised publisher that provides access to the latest scientific news, products, research, videos and posters.
Oldest reconstructed bacterial genomes link farming, herding with emergence of new diseaseOldest reconstructed bacterial genomes link farming, herding with emergence of new disease
The Neolithic revolution, and the corresponding transition to agricultural and pastoralist lifestyles, represents one of the greatest cultural shifts in human history, and it has long been hypothesized that this might have ...
Welcome lecture - Module 1 | CourseraWelcome lecture - Module 1 | Coursera
Video created by Technical University of Denmark (DTU) for the course Whole genome sequencing of bacterial genomes - tools and applications. Welcome and introduction to typing of bacteria and use of Whole genome sequencing applied to ...
Fifty genome sequences reveal breast cancers complexity - Scientific AmericanFifty genome sequences reveal breast cancer's complexity - Scientific American
Scientific American is the essential guide to the most awe-inspiring advances in science and technology, explaining how they change our understanding of the world and shape our lives.
Study uncovers range of molecular alterations in head and neck cancers, new potential drug targets - TCGAStudy uncovers range of molecular alterations in head and neck cancers, new potential drug targets - TCGA
TCGA tumor genome sequencing analyses offer new insights into the effects of HPV and smoking, and find genomic similarities with other cancers.
AgroPages.com-New genome sequence highlights corns adaptability-Agricultural news-Agropages.comAgroPages.com-New genome sequence highlights corn's adaptability-Agricultural news-Agropages.com
New genome sequence highlights corns adaptability,University of Hawaiʻi at Mānoa researchers contributed to an historic release of a new, high-quality
Chlamydia (genus)Chlamydia (genus)
HeLaHeLa
Multicopy single-stranded DNAMulticopy single-stranded DNA
GLIMMERGLIMMER
Helicobacter pametensisHelicobacter pametensis
DNA adenine methyltransferase identificationDNA adenine methyltransferase identification
Helicobacter trogontumHelicobacter trogontum
Helicobacter canadensisHelicobacter canadensis
Helicobacter acinonychisHelicobacter acinonychis
Helicobacter brantaeHelicobacter brantae
Proline-Rich Coiled Coil 1Proline-Rich Coiled Coil 1
Helicobacter cholecystusHelicobacter cholecystus
List of rice diseasesList of rice diseases
Human microbiotaHuman microbiota
Global microbial identifierGlobal microbial identifier
Nancy A. MoranNancy A. Moran
Achromobacter xylosoxidansAchromobacter xylosoxidans
Corynebacterium glutamicumCorynebacterium glutamicum
DNADNA
Evolution of cellsEvolution of cells
EndosymbiontEndosymbiont
Jumping libraryJumping library
Horizontal gene transfer in evolutionHorizontal gene transfer in evolution
SymbiosisSymbiosis
CRISPRCRISPR
Rickettsia rickettsiiRickettsia rickettsii
RetronRetron
GlnA RNA motifGlnA RNA motif
Xanthomonas campestris pv. VesicatoriaXanthomonas campestris pv. Vesicatoria
Dictyoglomi-1 RNA motifDictyoglomi-1 RNA motif
Streptococcus pneumoniaeStreptococcus pneumoniae
EbolaEbola
Chloroplast DNAChloroplast DNA
AcneAcne
Caulobacter crescentusCaulobacter crescentus
SakeSake
Genetically modified tomatoGenetically modified tomato
Evolution of biological complexityEvolution of biological complexity
Fluorescence in situ hybridizationFluorescence in situ hybridization
EndosporeEndospore
David W. DeamerDavid W. Deamer
Mycobacterium avium subspecies paratuberculosisMycobacterium avium subspecies paratuberculosis
RAD51RAD51
Integral membrane proteinIntegral membrane protein
Cav1.2Cav1.2
ArchaeaArchaea
TATA boxTATA box
Haloarchaea bahasa Indonesia, ensiklopedia bebasHaloarchaea bahasa Indonesia, ensiklopedia bebas
FZD5FZD5
CitrusCitrus
ARNr 16S, a enciclopedia libreARNr 16S, a enciclopedia libre
Acid alpha-glucosidaseAcid alpha-glucosidase
ವಂಶವಾಹಿ - ವಿಕಿಪೀಡಿಯವಂಶವಾಹಿ - ವಿಕಿಪೀಡಿಯ
肺炎支原體 - 维基百科，自由的百科全肺炎支原體 - 维基百科，自由的百科全
ஏபிஓ குருதி குழு முறைமை - தமிழ் விக்கிப்பீடியாஏபிஓ குருதி குழு முறைமை - தமிழ் விக்கிப்பீடியா
RNA worldRNA world
효소 - 위키백과, 우리 모두의 백과사전효소 - 위키백과, 우리 모두의 백과사전
BleomycinBleomycin
AntigenAntigen
Rekayasa genetika bahasa Indonesia, ensiklopedia bebasRekayasa genetika bahasa Indonesia, ensiklopedia bebas
AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsTechnology, Industry, AgricultureInformation ScienceHealth Care
GenomeGenome, BacterialGenome, ViralGenome, PlantGenome, HumanGenome, MitochondrialGenome, FungalGenome SizeSequence Analysis, DNAGenome, ArchaealPhylogenyBase SequenceGenome, InsectEvolution, MolecularGenome, ProtozoanGenomicsGenome, ChloroplastChromosome MappingGenome, HelminthOpen Reading FramesGenome, PlastidSequence AlignmentSyntenyHuman Genome ProjectDNA, ViralMolecular Sequence DataGene OrderComputational BiologyGenetic VariationModels, GeneticAmino Acid SequenceDatabases, GeneticRecombination, GeneticSpecies SpecificityMultigene FamilyChromosomes, Artificial, BacterialGene DuplicationRepetitive Sequences, Nucleic AcidRNA, ViralGenes, ViralSoftwareMolecular Sequence AnnotationDNA Transposable ElementsBase CompositionDNA, MitochondrialSequence Homology, Nucleic AcidMutationCloning, MolecularContig MappingDNA, BacterialConserved SequenceDNA, PlantViral ProteinsGene Transfer, HorizontalTranscription, GeneticRetroelementsNucleic Acid HybridizationDatabases, Nucleic AcidChromosomes, PlantExpressed Sequence TagsHigh-Throughput Nucleotide SequencingPseudogenesPhysical Chromosome MappingPolymerase Chain ReactionAlgorithmsBiological EvolutionVirus ReplicationGenomic InstabilityGenes, BacterialPolyploidyGenetic MarkersDNAGene Expression ProfilingSequence Homology, Amino AcidGenes, PlantGenome, MicrobialPlasmidsInternetGenome ComponentsCell LineSequence HomologyOryza sativaChromosomesBacterial ProteinsDNA, IntergenicGene RearrangementNucleic Acid ConformationPolymorphism, Single NucleotideChromosomes, BacterialOligonucleotide Array Sequence AnalysisDNA ReplicationMutagenesis, InsertionalDNA Restriction EnzymesCluster AnalysisGenetic LinkageGene LibraryGene DosageCodonDNA PrimersBacteriophagesPhenotypeRestriction MappingGenotypeSelection, GeneticGenesIntronsTerminal Repeat SequencesUser-Computer InterfaceProphagesBlotting, SouthernINDEL MutationMicrosatellite RepeatsEscherichia coliGenes, MitochondrialDNA, ChloroplastGene DeletionGenomic LibraryComparative Genomic HybridizationArabidopsisRNA, TransferVertebratesProkaryotic CellsSymbiosisSequence Analysis, RNAPromoter Regions, GeneticInterspersed Repetitive SequencesRNA, MessengerPlantsSaccharomyces cerevisiaeVirulenceInverted Repeat SequencesRNA VirusesPlastidsVirus IntegrationBacteriaGenes, ArchaealSorghumGene Expression Regulation, BacterialGene Expression Regulation, ViralDNA, CircularGenetic LociChromosomes, HumanShort Interspersed Nucleotide ElementsGenetic VectorsGenetic EngineeringSegmental Duplications, GenomicDNA, ComplementaryPolymorphism, GeneticDrosophila melanogasterEukaryotic CellsMetabolic Networks and PathwaysGC Rich SequenceMammalsCell NucleusLong Interspersed Nucleotide ElementsTranscriptomeHybridization, GeneticAllelesPan troglodytesEukaryotaArchaeaQuantitative Trait LociGenes, DuplicateAngiospermsSequence DeletionCapsidTetraodontiformesDNA Copy Number VariationsGene Expression RegulationDiploidyMutation RateDefective VirusesChromosome InversionUntranslated RegionsCrosses, GeneticDNA-Binding ProteinsLikelihood FunctionsTandem Repeat SequencesProteomeGenomic IslandsExonsDNA, FungalBinding SitesDNA RepairPlant DiseasesPlant ProteinsZea maysRNAGenetic Techniques5' Untranslated RegionsAlu ElementsChromatinDNA, AlgalGenes, OverlappingChromosomes, MammalianEndogenous RetrovirusesGenome-Wide Association StudyComputer GraphicsSiphoviridaeDNA MethylationGene Expression
Scientists Achieve First Bacterial Genome Transplantation; Promise to Develop First Synthetic Organism | MedgadgetScientists Achieve First Bacterial Genome Transplantation; Promise to Develop First Synthetic Organism | Medgadget
Genes | Free Full-Text | Ecological and Temporal Constraints in the Evolution of Bacterial Genomes | HTMLGenes | Free Full-Text | Ecological and Temporal Constraints in the Evolution of Bacterial Genomes | HTML
Oldest reconstructed bacterial genomes link farming, herding with emergence of new diseaseOldest reconstructed bacterial genomes link farming, herding with emergence of new disease
Fischbach joins project to generate drugs from bacterial genomes | School of Pharmacy | UCSFFischbach joins project to generate drugs from bacterial genomes | School of Pharmacy | UCSF
Blueprints for Anti-cancer Drugs Identified in Bacterial GenomesBlueprints for Anti-cancer Drugs Identified in Bacterial Genomes
Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes « Research Papers «...Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes « Research Papers «...
Dynamics of genome rearrangement in bacterial populations. - PubMed - NCBIDynamics of genome rearrangement in bacterial populations. - PubMed - NCBI
Bacterial Genome May Hold Answers To Mercury Mystery - RedorbitBacterial Genome May Hold Answers To Mercury Mystery - Redorbit
One Bacterial Cell, One Complete GenomeOne Bacterial Cell, One Complete Genome
BASys: a web server for automated bacterial genome annotation. - PubMed - NCBIBASys: a web server for automated bacterial genome annotation. - PubMed - NCBI
Inferring Bacterial Genome Flux While Considering Truncated Genes | GeneticsInferring Bacterial Genome Flux While Considering Truncated Genes | Genetics
9780521129619 - The Dynamic Bacterial Genome | eCampus.com9780521129619 - The Dynamic Bacterial Genome | eCampus.com
Bacterial GenomesBacterial Genomes
Recombination-Driven Genome Evolution and Stability of Bacterial Species | GeneticsRecombination-Driven Genome Evolution and Stability of Bacterial Species | Genetics
DNA phosphorothioation is widespread and quantized in bacterial genomes | PNASDNA phosphorothioation is widespread and quantized in bacterial genomes | PNAS
A hybrid approach for the automated finishing of bacterial genomes | Nature BiotechnologyA hybrid approach for the automated finishing of bacterial genomes | Nature Biotechnology
Cloning and mutagenesis of a herpesvirus genome as an infectious bacterial artificial chromosome | PNASCloning and mutagenesis of a herpesvirus genome as an infectious bacterial artificial chromosome | PNAS
Bacterial DNA May Integrate Into Human Genome More Readily in Tumor Tissue | NSF - National Science FoundationBacterial DNA May Integrate Into Human Genome More Readily in Tumor Tissue | NSF - National Science Foundation
Whole genome sequencing of bacterial genomes - tools and applications | CourseraWhole genome sequencing of bacterial genomes - tools and applications | Coursera
NIH uses genome sequencing to help quell bacterial outbreak in Clinical Center | EurekAlert! Science NewsNIH uses genome sequencing to help quell bacterial outbreak in Clinical Center | EurekAlert! Science News
Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm | SpringerLinkGenome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm | SpringerLink
Team Demonstrates De Novo Assembly of Bacterial Genome from Nanopore Data Alone | GenomeWebTeam Demonstrates De Novo Assembly of Bacterial Genome from Nanopore Data Alone | GenomeWeb
IJMS | Free Full-Text | Bacterial Cellular Engineering by Genome Editing and Gene SilencingIJMS | Free Full-Text | Bacterial Cellular Engineering by Genome Editing and Gene Silencing
Bacterial genome - WikipediaBacterial genome - Wikipedia
Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models | npj Systems Biology and...Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models | npj Systems Biology and...
Gut Microbe Studies Expand Bacterial Culture Collections, Reference Genomes | GenomeWebGut Microbe Studies Expand Bacterial Culture Collections, Reference Genomes | GenomeWeb
CREATION OF A BACTERIAL CELL CONTROLLED BY A CHEMICALLY SYNTHESIZED GENOMECREATION OF A BACTERIAL CELL CONTROLLED BY A CHEMICALLY SYNTHESIZED GENOME
JCVI: Impact of Donor-recipient Phylogenetic Distance on Bacterial Genome Transplantation.JCVI: Impact of Donor-recipient Phylogenetic Distance on Bacterial Genome Transplantation.
Design and synthesis of a minimal bacterial genome | ScienceDesign and synthesis of a minimal bacterial genome | Science
Genome-Wide Analysis of Alternative Splicing during Dendritic Cell Response to a Bacterial ChallengeGenome-Wide Analysis of Alternative Splicing during Dendritic Cell Response to a Bacterial Challenge
Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost(Journal Article) | DOE PAGESBacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost(Journal Article) | DOE PAGES
2019: Scientists use bacterial genome sequences to stop a deadly multi-facility outbreak | Advanced Molecular Detection (AMD) |...2019: Scientists use bacterial genome sequences to stop a deadly multi-facility outbreak | Advanced Molecular Detection (AMD) |...
New laptop program can identify drug resistance from bacterial genomes | University of OxfordNew laptop program can identify drug resistance from bacterial genomes | University of Oxford
Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial GenomesBurkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes
Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial GenomesBurkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes
Evolution and function of bacterial and archaeal genome sequences | Frontiers Research TopicEvolution and function of bacterial and archaeal genome sequences | Frontiers Research Topic
AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsTechnology, Industry, AgricultureInformation ScienceHealth Care
GenomeGenome, BacterialGenome, ViralGenome, PlantGenome, HumanGenome, MitochondrialGenome, FungalGenome SizeSequence Analysis, DNAGenome, ArchaealPhylogenyBase SequenceGenome, InsectEvolution, MolecularGenome, ProtozoanGenomicsGenome, ChloroplastChromosome MappingGenome, HelminthOpen Reading FramesGenome, PlastidSequence AlignmentSyntenyHuman Genome ProjectDNA, ViralMolecular Sequence DataGene OrderComputational BiologyGenetic VariationModels, GeneticAmino Acid SequenceDatabases, GeneticRecombination, GeneticSpecies SpecificityMultigene FamilyChromosomes, Artificial, BacterialGene DuplicationRepetitive Sequences, Nucleic AcidRNA, ViralGenes, ViralSoftwareMolecular Sequence AnnotationDNA Transposable ElementsBase CompositionDNA, MitochondrialSequence Homology, Nucleic AcidMutationCloning, MolecularContig MappingDNA, BacterialConserved SequenceDNA, PlantViral ProteinsGene Transfer, HorizontalTranscription, GeneticRetroelementsNucleic Acid HybridizationDatabases, Nucleic AcidChromosomes, PlantExpressed Sequence TagsHigh-Throughput Nucleotide SequencingPseudogenesPhysical Chromosome MappingPolymerase Chain ReactionAlgorithmsBiological EvolutionVirus ReplicationGenomic InstabilityGenes, BacterialPolyploidyGenetic MarkersDNAGene Expression ProfilingSequence Homology, Amino AcidGenes, PlantGenome, MicrobialPlasmidsInternetGenome ComponentsCell LineSequence HomologyOryza sativaChromosomesBacterial ProteinsDNA, IntergenicGene RearrangementNucleic Acid ConformationPolymorphism, Single NucleotideChromosomes, BacterialOligonucleotide Array Sequence AnalysisDNA ReplicationMutagenesis, InsertionalDNA Restriction EnzymesCluster AnalysisGenetic LinkageGene LibraryGene DosageCodonDNA PrimersBacteriophagesPhenotypeRestriction MappingGenotypeSelection, GeneticGenesIntronsTerminal Repeat SequencesUser-Computer InterfaceProphagesBlotting, SouthernINDEL MutationMicrosatellite RepeatsEscherichia coliGenes, MitochondrialDNA, ChloroplastGene DeletionGenomic LibraryComparative Genomic HybridizationArabidopsisRNA, TransferVertebratesProkaryotic CellsSymbiosisSequence Analysis, RNAPromoter Regions, GeneticInterspersed Repetitive SequencesRNA, MessengerPlantsSaccharomyces cerevisiaeVirulenceInverted Repeat SequencesRNA VirusesPlastidsVirus IntegrationBacteriaGenes, ArchaealSorghumGene Expression Regulation, BacterialGene Expression Regulation, ViralDNA, CircularGenetic LociChromosomes, HumanShort Interspersed Nucleotide ElementsGenetic VectorsGenetic EngineeringSegmental Duplications, GenomicDNA, ComplementaryPolymorphism, GeneticDrosophila melanogasterEukaryotic CellsMetabolic Networks and PathwaysGC Rich SequenceMammalsCell NucleusLong Interspersed Nucleotide ElementsTranscriptomeHybridization, GeneticAllelesPan troglodytesEukaryotaArchaeaQuantitative Trait LociGenes, DuplicateAngiospermsSequence DeletionCapsidTetraodontiformesDNA Copy Number VariationsGene Expression RegulationDiploidyMutation RateDefective VirusesChromosome InversionUntranslated RegionsCrosses, GeneticDNA-Binding ProteinsLikelihood FunctionsTandem Repeat SequencesProteomeGenomic IslandsExonsDNA, FungalBinding SitesDNA RepairPlant DiseasesPlant ProteinsZea maysRNAGenetic Techniques5' Untranslated RegionsAlu ElementsChromatinDNA, AlgalGenes, OverlappingChromosomes, MammalianEndogenous RetrovirusesGenome-Wide Association StudyComputer GraphicsSiphoviridaeDNA MethylationGene Expression
SequencesBacteriaGenesSpeciesPathogensEukaryoticGenomicsGeneStrainsChromosomeOrganismsGeneticsGeneticChromosomesViralPlasmidsArchaeal genomesSequencingNucleotideResearchersPathogenHuman genome containsAssembliesSalmonellaSequenceMicrobial GenomesGenes in bacterial genomesGeneGeneticsIsolatesObligateCore genomeCharacterizationResearchersAntibioticPhylogeneticFull-genomeArchaeaEvolution of bacterialPathogen genomePhylogenyComparativeMycoplasmaIntracellularPathogenicSymbiontEntire bacterial genomeMinimal genomeMechanismsEukaryotic genomesBioinformaticsArchaeal genomeCRISPR-CasHuman somatic genomePopulationsMutationsAnalysesRecombinationClinicalLarge genomesLargest genomesReplicationMicrobiomeEndosymbiontsStability
Sequences17
Bacteria5
Genes3
  • These bacterial genes encode molecules that could yield narrow-spectrum antibiotics, immune system regulators, and neuroactive drugs. (ucsf.edu)
  • This lab bioinformatics program, ClusterFinder, analyzes bacterial genomic data to identify physically clustered groups of genes in a particular genome that together encode enzymes which interact in sequence to produce drug-like small molecules (i.e., biosynthetic gene clusters). (ucsf.edu)
  • The genome includes both the genes (the coding regions ) and the noncoding DNA , as well as the genetic material of the mitochondria and chloroplasts . (readtiger.com)
Species7
Pathogens3
Eukaryotic1
Genomics1
  • Genome transplantation is an essential enabling step in the field of synthetic genomics as it is a key mechanism by which chemically synthesized chromosomes can be activated into viable living cells. (medgadget.com)
Gene4
Strains2
  • Luckily, researchers have a valuable resource on TSRI's Florida campus, where Shen heads the Natural Products Library Initiative, a library consisting of purified natural products, partially pure fractions, crude extracts and bacterial strains collected from all over the globe that are available for screening. (technologynetworks.com)
  • A potential user ('customer') of our sequencing platform asked how to generate reference genomes for his 4 bacterial strains. (wordpress.com)
Chromosome1
  • As a test of the success of the genome transplantation, the team used two methods - 2D gel electrophoresis and protein sequencing, to prove that all the expressed proteins were now the ones coded for by the M. mycoides LC chromosome. (medgadget.com)
Organisms1
Genetics1
Genetic1
Chromosomes1
Viral1
  • In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome ( Bacteriophage MS2 ). (readtiger.com)
Plasmids1
Archaeal genomes1
Sequencing3
Nucleotide1
Researchers2
  • The researchers screened 2,739 ancient human remains in total, eventually reconstructing eight Salmonella genomes up to 6,500 years old-the oldest reconstructed bacterial genomes to date. (phys.org)
  • The researchers were able to determine that all six Salmonella genomes recovered from herders and farmers are progenitors to a strain that specifically infects humans but is rare today, Paratyphi C. Those ancient Salmonella, however, were probably not yet adapted to humans, and instead infected humans and animals alike, which suggests the cultural practices uniquely associated with the Neolithization process facilitated the emergence of those progenitors and subsequently human-specific disease. (phys.org)
Pathogen2
  • These results illuminate what was likely a serious health concern in the past and reveal how this bacterial pathogen evolved over a period of 6,500 years. (phys.org)
  • This highlights an inherent difficulty in the field of ancient pathogen research, as hundreds of human samples are often required to recover just a single microbial genome. (phys.org)
Human genome contains1
  • Just as a cookbook gives the instructions needed to make a range of meals including a holiday feast or a summer picnic, the human genome contains all the instructions needed to make the full range of human cell types including muscle cells or neurons. (readtiger.com)
Assemblies1
Salmonella1
  • A new study published in Nature Ecology & Evolution led by Felix M. Key, Alexander Herbig, and Johannes Krause of the Max Planck Institute for the Science of Human History studied human remains excavated across Western Eurasia and reconstructed eight ancient Salmonella enterica genomes-all part of a related group within the much larger diversity of modern S. enterica. (phys.org)
Sequence61
Microbial Genomes3
Genes in bacterial genomes2
Gene23
  • Bacterial gene content variation during the course of evolution has been widely acknowledged and its pattern has been actively modeled in recent years. (genetics.org)
  • Gene truncation or gene pseudogenization also plays an important role in shaping bacterial genome content. (genetics.org)
  • Analysis using the new model not only provides more accurate estimates on gene gains/losses (or insertions/deletions), but also reduces any concern of a systematic bias from applying simplified models to bacterial genome evolution. (genetics.org)
  • reported that genomes with truncated homologs might erroneously lead to false inferences of "gene gain" rather than multiple instances of "gene loss. (genetics.org)
  • This will not only yield more accurate estimates of the rates of gene insertions/deletions, but also provide a quantitative view of the effect of truncated genes on rate estimation, which has been understudied in bacterial genome evolution. (genetics.org)
  • The feasibility to introduce targeted mutations into the BAC cloned virus genome was shown by mutation of the immediate-early 1 gene and generation of a mutant virus. (pnas.org)
  • Genome editing is an important technology for bacterial cellular engineering, which is commonly conducted by homologous recombination-based procedures, including gene knockout (disruption), knock-in (insertion), and allelic exchange. (mdpi.com)
  • Apart from these methods, which directly modify the genomic structure, an alternative approach is to conditionally modify the gene expression profile at the posttranscriptional level without altering the genomes. (mdpi.com)
  • Analysis of over 2000 Escherichia coli genomes reveals an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. (wikipedia.org)
  • As single-gene comparisons have largely given way to genome comparisons, phylogeny of bacterial genomes have improved in accuracy. (wikipedia.org)
  • Gene acquisition is an ongoing process in many bacterial genomes, contributing to adaptation and ecological diversification. (sciencemag.org)
  • We measured the extent of phylogenetic conflict and alien-gene acquisition within quartets of sequenced genomes. (sciencemag.org)
  • In all but the most reduced bacterial genomes, there is a substantial fraction of genes whose distributions and compositional features indicate that they originated by lateral gene transfer (LGT) ( 1 ). (sciencemag.org)
  • It "is a landmark in biological engineering taking us from moving one gene or a set of genes to the ability to move an intact genome," said Barbara Jasny, deputy editor of the journal Science, which first reported the experiment in this week's issue. (bio-medicine.org)
  • We study the mechanisms responsible of the bacterial genome variability, with a special interest for those involved in exogenous gene acquisition - the horizontal gene transfer. (pasteur.fr)
  • In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. (mdpi.com)
  • Reconstructions of the gene set of the shared ancestor of the γ- Proteobacteria provide strong evidence that B. aphidicola genomes are derived from larger genomes through loss of most genes ( 12 , 19 ). (asm.org)
  • Once we have verified that horizontal gene transfer is indeed a common occurrence in chronic bacterial infections, and we expect that to be the case, it opens the door to a realm of promising new directions in the study and treatment of these diseases,' he said. (infectioncontroltoday.com)
  • Models proposed to explain clustering did not take into account the function of the gene products nor the likely presence or absence of a given gene in a genome. (biomedcentral.com)
  • We propose a model accounting specifically for such clustering, and show that indispensability in a genome with frequent gene deletion and insertion leads to the transient clustering of these genes. (biomedcentral.com)
  • The genome has a high coding density (97%) with many overlapping genes and reduced gene length. (semanticscholar.org)
  • Finally, the analysis of 178 Acinetobacter baumannii and 20 Staphylococcus aureus genomes allowed the detection of a significantly higher number of AR genes than the Resfinder gene analyzer and 11 point mutations in target genes known to be associated with AR. (asm.org)
  • This tenet of bacterial genome evolution generally does not extend to obligate intracellular bacteria owing to their reduced contact with other microbes and a predominance of gene deletion over gene transfer. (oup.com)
Genetics2
  • Published Dec. 18, 2017 in Nature Genetics, a team led by researchers at Joint Genome Institute (JGI) and the Howard Hughes Medical Institute at the University of North Carolina at Chapel Hill (UNC) have exploited a catalog of bacterial genomes to identify and characterize candidate genes that aid bacteria in adapting to plant environments, specifically genes involved in bacterial root colonization. (eurekalert.org)
  • Such a task was previously seen as a true tour de force: The chemically synthesised bacterial genome presented eleven years ago by the American genetics pioneer Craig Venter was the result of ten years of work by 20 scientists, according to media reports. (teknoscienze.com)
Isolates3
Obligate5
  • The obligate host-associated bacteria (with the exception of Candidatus Hodgkinia cicadicola) have short and low GC content genomes. (frontiersin.org)
  • Unlike with most obligate endosymbionts, genome reduction has not played a major role in the evolution of the Barbulanympha ectosymbionts. (osti.gov)
  • Buchnera aphidicola , the obligate symbiont of aphids, has an extremely reduced genome, of which about 10% is devoted to the biosynthesis of essential amino acids needed by its hosts. (asm.org)
  • In diverse bacteria, as well as archaea and eukaryotes, a drastic reduction in overall genome size is associated with obligate dependence on a host (e.g., see references 1 , 10 , 17 , and 34 ). (asm.org)
  • In addition to discovering an evolutionary recent and large-scale horizontal phage transfer between coinfecting obligate intracellular bacteria, we demonstrate that "targeted genome capture" can enrich target DNA to alleviate the problem of isolating symbiotic microbes that are difficult to culture or purify from the conglomerate of organisms inside eukaryotes. (oup.com)
Core genome3
Characterization1
Researchers14
  • The researchers found that while only 63.5 percent of TCGA samples analyzed were from tumors, the tumor samples contained 99.9 percent of reads supporting bacterial integration. (nsf.gov)
  • NEW YORK (GenomeWeb) - In a proof-of-principle demonstration that genomes can be assembled from long, noisy nanopore reads alone, researchers at the Ontario Institute for Cancer Research in Toronto and the University of Birmingham in the UK have used data from the Oxford Nanopore MinIon to assemble a bacterial genome into a single contig. (genomeweb.com)
  • Over the years, researchers have proposed several theories to explain the general trend of bacterial genome decay and the relatively small size of bacterial genomes. (wikipedia.org)
  • Researchers have developed several theories to explain the patterns of genome size evolution amongst bacteria. (wikipedia.org)
  • This enables researchers to choose the optimal strategy for completely decoding even the genomes of bacteria with very complex DNA. (admin.ch)
  • Replacing a Genome Boosts Race to Develop Designer Bugs: Study ( Researchers transformed one bacterial s. (bio-medicine.org)
  • The researchers took the genome of a simple, one-celled organism called Mycoplasma mycoides and transplanted it into a close relative, M. capricolum. (bio-medicine.org)
  • The researchers acknowledged that they were not sure how the one genome displaced the other. (bio-medicine.org)
  • To better understand this balance, National Institutes of Health researchers have set out to explore the skin's microbiome, which is all of the DNA, or genomes, of all of the microbes that inhabit human skin. (genome.gov)
  • Our work has laid an essential foundation for researchers who are working to develop new and better strategies for treating and preventing skin diseases," said Julia A. Segre, Ph.D., of the National Human Genome Research Institute (NHGRI), who was the study's senior author. (genome.gov)
  • While Venter's team made an exact copy of a natural genome, the researchers at ETH Zurich radically altered their genome using a computer algorithm. (teknoscienze.com)
  • The researchers screened 2,739 ancient human remains in total, eventually reconstructing eight Salmonella genomes up to 6,500 years old-the oldest reconstructed bacterial genomes to date. (phys.org)
  • The researchers were able to determine that all six Salmonella genomes recovered from herders and farmers are progenitors to a strain that specifically infects humans but is rare today, Paratyphi C. Those ancient Salmonella, however, were probably not yet adapted to humans, and instead infected humans and animals alike, which suggests the cultural practices uniquely associated with the Neolithization process facilitated the emergence of those progenitors and subsequently human-specific disease. (phys.org)
  • Hidden Giants in Forest Soils In Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. (doe.gov)
Antibiotic7
Phylogenetic5
Full-genome2
  • This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly. (nature.com)
  • Using full-genome microarrays for B. aphidicola of the host Schizaphis graminum , we examined transcriptome responses to changes in dietary amino acid content and then verified behavior of individual transcripts using quantitative reverse transcriptase PCR. (asm.org)
Archaea4
Evolution of bacterial3
  • These findings might help shed light on the evolution of bacterial endosymbionts and on the mechanisms these organisms use to alter the cell cycle of the host in order to reproduce. (innovations-report.com)
  • In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods. (mdpi.com)
  • This book imparts fundamental knowledge on the structure, organization, and evolution of bacterial genomes. (springer.com)
Pathogen genome2
Phylogeny1
Comparative2
Mycoplasma4
Intracellular3
  • In addressing genome evolution of protist ectosymbionts, our data suggest that the ecological pressures influencing the evolution of extracellular symbionts clearly differ from intracellular symbionts and organelles. (osti.gov)
  • One of the best-studied cases of genome reduction is that of the intracellular bacterial symbiont Buchnera aphidicola , which shows a long evolutionary history of strict maternal transmission in its aphid hosts (Insecta: Homoptera: Aphidoidea) ( 18 ). (asm.org)
  • Genome size of Pachypsylla venusta (Hemiptera: Psyllidae) and the ploidy of its bacteriocyte, the symbiotic host cell that harbors intracellular mutualistic bacteria with the smallest cellular genome. (semanticscholar.org)
Pathogenic1
Symbiont1
Entire bacterial genome1
Minimal genome3
  • One way to approach this is to build a minimal genome that includes only the genes essential for life. (sciencemag.org)
  • Bacteria with this minimal genome are viable under laboratory conditions. (teknoscienze.com)
  • As a result, the scientists seeded many small modifications into the minimal genome, which in their entirety are, however, impressive: more than a sixth of all of the 800,000 DNA letters in the artificial genome were replaced, compared to the "natural" minimal genome. (teknoscienze.com)
Mechanisms8
Eukaryotic genomes2
  • The main reason for the relative density of bacterial genomes compared to eukaryotic genomes (especially multicellular eukaryotes) is the presence of noncoding DNA in the form of intergenic regions and introns. (wikipedia.org)
  • These findings add to our understanding of how mutation risk is distributed across bacterial and likely also eukaryotic genomes, owing to their highly conserved replication and repair machinery. (asm.org)
Bioinformatics1
  • The team led by Christian Ahrens - a bioinformatician at Agroscope and a member of the Swiss Institute of Bioinformatics - has now succeeded in revealing the unexpected complexity of bacterial genomes. (admin.ch)
Archaeal genome1
  • We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads. (igsb.org)
CRISPR-Cas1
Human somatic genome2
  • The data present a compelling case that LGT occurs in the human somatic genome, and that it could have an important role in cancer and other human diseases associated with mutations. (nsf.gov)
  • Cancer is a disease driven by the accumulation of genomic alterations, including the integration of exogenous DNA into the human somatic genome. (biomedcentral.com)
Populations3
  • Dynamics of genome rearrangement in bacterial populations. (nih.gov)
  • In this study, the ability to distinguish between these bacterial 'sub-populations' gave Mykrobe an advantage over conventional testing in detecting resistance to second-line TB drugs. (ox.ac.uk)
  • CGMs are preidentified by making comparisons among a relatively small number of completely or nearly completely sequenced genomes and then applied to analyze larger bacterial populations by targeted identification techniques. (asm.org)
Mutations2
Analyses1
Recombination3
Clinical3
  • The Active Bacterial Core surveillance (ABCs) system collects clinical and demographic information about patients with bacterial infections. (cdc.gov)
  • Furthermore, categorization of subjects based on the similarity or dissimilarity of their microbiota into groups by clustering techniques will not only help to reveal the bacterial distribution pattern in the population, but also facilitate our understanding of the underlying causes or the clinical association of specific types of microbial distributions. (biomedcentral.com)
  • Scientists on the Florida campus of The Scripps Research Institute (TSRI) who had previously discovered the prostate cancer-killing compound LNM E1 have now brought the family of LNM molecules even closer to clinical testing by "mining" the information stored in bacteria genomes. (technologynetworks.com)
Large genomes1
  • The myxobacteria have very large genomes, relative to other bacteria, e.g. 9-10 million nucleotides except for Anaeromyxobacter and Vulgatibacter. (wikipedia.org)
Largest genomes1
Replication4
  • The origin of replication in each genome is approximately at coordinate 1 and the terminus dif sites are approximately midway through each genome, as marked by grey vertical bars. (nih.gov)
  • There is a lack of CMV mutants because due to the large genome size and slow replication kinetics construction of CMV recombinants turned out to be difficult. (pnas.org)
  • It is our working model of a minimal cell, the result of a compromise between small genome size and an experimentally useful replication rate. (geoset.info)
  • Bacterial origins regulate orisome assembly, a nuclei-protein complex assembled on the origin responsible for unwinding the origin and loading all the replication machinery. (wikipedia.org)
Microbiome2
Endosymbionts3
Stability1
Scientists Achieve First Bacterial Genome Transplantation; Promise to Develop First Synthetic Organism | Medgadget
Scientists Achieve First Bacterial Genome Transplantation; Promise to Develop First Synthetic Organism | Medgadget (medgadget.com)
Welcome lecture - Module 1 | Coursera
Welcome lecture - Module 1 | Coursera (coursera.org)
Genome-Wide Analysis of Alternative Splicing during Dendritic Cell Response to a Bacterial Challenge
Genome-Wide Analysis of Alternative Splicing during Dendritic Cell Response to a Bacterial Challenge (journals.plos.org)
Microbiology and immunology | Cambridge University Press
Microbiology and immunology | Cambridge University Press (cambridge.org)
Experimental Biology/ASBMB | Cambridge University Press
Experimental Biology/ASBMB | Cambridge University Press (cambridge.org)
Genomics, bioinformatics and systems biology | Cambridge University Press
Genomics, bioinformatics and systems biology | Cambridge University Press (cambridge.org)
Pathogen genomics and microbiota (8 entities) | Institut Pasteur
Pathogen genomics and microbiota (8 entities) | Institut Pasteur (pasteur.fr)
Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in...
Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in... (link.springer.com)
CTC Capture Device
CTC Capture Device (genengnews.com)
More Than One: The Transition to Multicellularity
More Than One: The Transition to Multicellularity (genengnews.com)
News | Communications of the ACM
News | Communications of the ACM (cacm.acm.org)
CiteSeerX - Search Results - Allowing mismatches in anchors for wholw genome alignment: Generation and effectiveness
CiteSeerX - Search Results - Allowing mismatches in anchors for wholw genome alignment: Generation and effectiveness (citeseerx.ist.psu.edu)
Inferring Bacterial Genome Flux While Considering Truncated Genes | Genetics
Inferring Bacterial Genome Flux While Considering Truncated Genes | Genetics (genetics.org)
Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models | npj Systems Biology and...
Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models | npj Systems Biology and... (nature.com)
Bacterial DNA May Integrate Into Human Genome More Readily in Tumor Tissue | NSF - National Science Foundation
Bacterial DNA May Integrate Into Human Genome More Readily in Tumor Tissue | NSF - National Science Foundation (nsf.gov)
Recombination-Driven Genome Evolution and Stability of Bacterial Species | Genetics
Recombination-Driven Genome Evolution and Stability of Bacterial Species | Genetics (genetics.org)
2019: Scientists use bacterial genome sequences to stop a deadly multi-facility outbreak | Advanced Molecular Detection (AMD) |...
2019: Scientists use bacterial genome sequences to stop a deadly multi-facility outbreak | Advanced Molecular Detection (AMD) |... (cdc.gov)
Week in Review: March 10-14 | The Scientist Magazine®
Week in Review: March 10-14 | The Scientist Magazine® (the-scientist.com)
Frontiers | Whole Genome Sequencing and Metabolomic Study of Cave Streptomyces Isolates ICC1 and ICC4 | Microbiology
Frontiers | Whole Genome Sequencing and Metabolomic Study of Cave Streptomyces Isolates ICC1 and ICC4 | Microbiology (frontiersin.org)
Difference between revisions of Synergistes jonesii - microbewiki
Difference between revisions of "Synergistes jonesii" - microbewiki (microbewiki.kenyon.edu)
NYC, NY State Promote Cluster-Building with $1B+ in Incentives, New Startup Spaces
NYC, NY State Promote Cluster-Building with $1B+ in Incentives, New Startup Spaces (genengnews.com)
Whole genome sequencing of bacterial genomes - tools and applications | Coursera
Whole genome sequencing of bacterial genomes - tools and applications | Coursera (coursera.org)
Frontiers | Acinetobacter Plasmids: Diversity and Development of Classification Strategies | Microbiology
Frontiers | Acinetobacter Plasmids: Diversity and Development of Classification Strategies | Microbiology (frontiersin.org)
Leprosy: History of a Bacterial Scourge | Medieval Diseases | Live Science
Leprosy: History of a Bacterial Scourge | Medieval Diseases | Live Science (livescience.com)
News Desk - All News | ORNL
News Desk - All News | ORNL (ornl.gov)
Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality | PNAS
Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality | PNAS (pnas.org)
Birth of a W sex chromosome by horizontal transfer of Wolbachia bacterial symbiont genome | PNAS
Birth of a W sex chromosome by horizontal transfer of Wolbachia bacterial symbiont genome | PNAS (pnas.org)