The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The genetic complement of a BACTERIA as represented in its DNA.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
The genetic complement of a plant (PLANTS) as represented in its DNA.
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.
The genetic complement of MITOCHONDRIA as represented in their DNA.
The complete gene complement contained in a set of chromosomes in a fungus.
The amount of DNA (or RNA) in one copy of a genome.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
The relationships of groups of organisms as reflected by their genetic makeup.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The genetic complement of an insect (INSECTS) as represented in its DNA.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The genetic complement of CHLOROPLASTS as represented in their DNA.
Any method used for determining the location of and relative distances between genes on a chromosome.
The genetic complement of a helminth (HELMINTHS) as represented in its DNA.
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).
The genetic complement of PLASTIDS as represented in their DNA.
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.
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.
A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.
Deoxyribonucleic acid that makes up the genetic material of viruses.
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.
The sequential location of genes on a chromosome.
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.
Genotypic differences observed among individuals in a population.
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.
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 devoted to knowledge about specific genes and gene products.
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.
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.
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)
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.
Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.
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).
Ribonucleic acid that makes up the genetic material of viruses.
The functional hereditary units of VIRUSES.
Sequential operating programs and data which instruct the functioning of a digital computer.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
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.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
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.
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.
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.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
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.
Deoxyribonucleic acid that makes up the genetic material of plants.
Proteins found in any species of virus.
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).
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
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.
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 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.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
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.
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.
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)
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.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
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.
An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.
The functional hereditary units of BACTERIA.
The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
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).
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The functional hereditary units of PLANTS.
The genetic complement of a microorganism as represented in its DNA or in some microorganisms its RNA.
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.
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.
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.
Established cell cultures that have the potential to propagate indefinitely.
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.
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.
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)
Proteins found in any species of bacterium.
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.
The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.
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.
The process by which a DNA molecule is duplicated.
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.
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.
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.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
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.
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.
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).
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.
Viruses whose hosts are bacterial cells.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
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.
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.
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.
The portion of an interactive computer program that issues messages to and receives commands from a user.
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.
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.
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.
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).
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 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.
Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.
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.
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).
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.
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.
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.
Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.
Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.
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.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
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.
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 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.
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.
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.
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.
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.
Viruses whose genetic material is RNA.
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.
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.
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.
The functional genetic units of ARCHAEA.
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.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
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)
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.
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.
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).
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.
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.
Low-copy (2-50) repetitive DNA elements that are highly homologous and range in size from 1000 to 400,000 base pairs.
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.
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.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.
A nucleic acid sequence that contains an above average number of GUANINE and CYTOSINE bases.
Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.
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)
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.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
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.
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.
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.
Genetic loci associated with a QUANTITATIVE TRAIT.
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)
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.
Deletion of sequences of nucleic acids from the genetic material of an individual.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
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.
Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.
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.
The chromosomal constitution of cells, in which each type of CHROMOSOME is represented twice. Symbol: 2N or 2X.
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.
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.
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.
The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.
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.
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.
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.
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).
The protein complement of an organism coded for by its genome.
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".
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.
Deoxyribonucleic acid that makes up the genetic material of fungi.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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.
Diseases of plants.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.
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)
Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
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.
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.
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.
Deoxyribonucleic acid that makes up the genetic material of algae.
Genes whose nucleotide sequences overlap to some degree. The overlapped sequences may involve structural or regulatory genes of eukaryotic or prokaryotic cells.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of MAMMALS.
Retroviruses that have integrated into the germline (PROVIRUSES) that have lost infectious capability but retained the capability to transpose.
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.
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.
A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by long, non-contractile tails.
Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Contiguous large-scale (1000-400,000 basepairs) differences in the genomic DNA between individuals, due to SEQUENCE DELETION; SEQUENCE INSERTION; or SEQUENCE INVERSION.

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)

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 ...
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
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. ...
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 - ...
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 ...
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
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 ...
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 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 genus Bacillus comprises spore-forming rod-shaped Gram-positive bacteria, which usually grow aerobically or anaerobically. Members of this genus are common environmental microorganisms. Also, they can be monitored in the food production chain. Genome sequence of Bacillus sp. strain EE-W1 will provide helpful information to understand its ecology and genetics. Draft genome data may be useful in the field of using Bacillus species in industrial biotechnology. Also, these data can be a useful resource for the study of comparative genomics. Here, we present the draft genome sequence of Bacillus sp. strain EE-W1 isolated from a biogas reactor, Kazan, Russia. The assembled genome size was 5,769,164 bp, with a GC content 35.1%. This draft genome data can be accessed at DDBJ/ENA/GenBank under the accession WIPE00000000.
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. ...
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.
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 ...
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= xlink:href=ch1f2 mime-subtype=gif/, ,/fig, ,/p, ... ,/sec ...
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 ...
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
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 ...
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
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 ...
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
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…
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 ...
Draft genome sequences of Candidatus Chloroploca asiatica and Candidatus Viridilinea mediisalina, candidate representatives of the Chloroflexales order: phy
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…
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.
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. ...
Identifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. Using real benchmark datasets we demonstrate that OrthoFinder is more accurate than other orthogroup inference methods by between 8 % and 33 %. Furthermore, we demonstrate the utility of OrthoFinder by providing a complete classification of transcription factor gene families in plants revealing 6.9 million previously unobserved relationships.
Identifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. Using …
Species identification by sequencing the bacterial genome at seven key loci, uncovering achieved similar combinations of sequences with certain bacterial
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 ...
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
Scientists at Harvard have used a modified CRISPR gene editing tool to insert coded sequences into bacterial genomes matching a video clip.
Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on the other, insertions and deletions leave the backbone gene order unchanged but they alter the gene neighborhoods by breaking the syntenic regions. A complete picture about genome organization evolution therefore requires to account for both kinds of events. We developed an approach where we model chromosomes as graphs on which we compute different stability estimators; we consider genome rearrangements as well as the effect of gene insertions and deletions. In a first part of the paper, we fit a measure of
Pan-Genomic Approaches for Comprehensive Screening of Novel or Emerging Infectious Agents in Blood Emerging infectious agents, the latest of which is Zika virus...
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 ...
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 ...
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. ...
All the genome sequences of organisms known throughout the world are stored in a database belonging to the National Center for Biotechnology Information in the United States. As of today, the database has an additional entry: Caulobacter ethensis-2.0. It is the worlds first fully computer-generated genome of a living organism, developed by scientists at ETH Zurich. However, it must be emphasised that although the genome for C. ethensis-2.0 was physically produced in the form of a very large DNA molecule, a corresponding organism does not yet exist.
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 ...
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 …
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 ...
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 ...
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 ...
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 ...
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. ...
Use bioinformatics to explore DNA sequences and protein functions, to find the determinants of virulence in microbes with this free online course.
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 ...
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 ...
TY - JOUR. T1 - Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes. AU - Qu, Hongzhu. AU - Wu, Hao. AU - Zhang, Tongwu. AU - Zhang, Zhang. AU - Hu, Songnian. AU - Yu, Jun. N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: The study was supported by grants awarded to JY (2006CB910404) from the National Basic Research Program (973 Program) and from the National Science and Technology Key Project (2008ZX1004-013), the Ministry of Science and Technology of the Peoples Republic of China.. PY - 2010/12. Y1 - 2010/12. N2 - Nucleotide compositional asymmetry (NCA) between leading and lagging strands (LeS and LaS) is dynamic and diverse among eubacterial genomes due to different mutation and selection forces. A thorough investigation is needed in order to study the relationship between nucleotide composition dynamics and gene distribution biases. Based on a collection of 364 eubacterial genomes that were grouped according to a DnaE-based ...
The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged ... In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell ... The reasons for the presence of so much noncoding DNA in eukaryotic genomes and the extraordinary differences in genome size, ... Data sets representing entire genomes' worth of DNA sequences, such as those produced by the Human Genome Project, are ...
Genome sequencing reveals that obligate bacterial endosymbionts of insects have among the smallest of known bacterial genomes ... Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H (September 2000). "Genome sequence of the endocellular bacterial ... In addition, these insect symbionts have similar patterns of genome evolution to those found in true organelles: genome ... "Genome evolution in bacterial endosymbionts of insects". Nat. Rev. Genet. 3 (11): 850-61. doi:10.1038/nrg931. PMID 12415315. ...
Wernegreen, J.J. (2002). "Genome evolution in bacterial endosymbionts of insects". Nature Reviews Genetics. 3 (11): 850-861. ... The decrease in genome size is due to loss of protein coding genes and not due to lessening of inter-genic regions or open ... There is a drastic reduction in its genome size, as many genes are lost during the process of metabolism, and DNA repair and ... Nair, S. (2005), "Bacterial Associations: Antagonism to Symbiosis", in Ramaiah, N., Marine Microbiology: Facets & Opportunities ...
"EMBL bacterial genomes". Retrieved January 19, 2012. Read, T. D.; Brunham, R. C.; Shen, C.; Gill, S. R.; Heidelberg, J. F.; ... The DNA genome, proteins, and ribosomes are retained in the reticulate body. This occurs as a result of the development cycle ... Table 1. Genome features of selected Chlamydia species and strains. MoPn is a mouse pathogen while strain "D" is a human ... psittaci Chlamydia species have genomes around 1.0 to 1.3 megabases in length. Most encode ~900 to 1050 proteins. Some species ...
... relative to the rest of the Helicobacter genome suggests the island was acquired by horizontal transfer from another bacterial ... The genome of the strain "26695" consists of about 1.7 million base pairs, with some 1,576 genes. The pan-genome, that is a ... Bacterial strains with the cagA gene are associated with an ability to cause ulcers. The cagA gene codes for a relatively long ... The H. pylori bacterial infection persists after remission in these cases. Various antibiotic plus proton pump inhibitor drug ...
Comparative Analysis of Bifidobacterium Genomes (at DOE's IMG system). *Bifidobacterium at BacDive - the Bacterial Diversity ... Genomes[edit]. Members of the genus Bifidobacterium have genome sizes ranging from 1.73 (Bifidobacterium indicum) to 3.25 Mb ( ... Genomes Online Database contains many Bifidobacterium genome projects. * ... Bifidobacterium species genomes of B. longum, B. bifidum, B. breve contain genes that can hydrolyze some of the human milk ...
... and the bacterial genome" (PDF). Cytogenetic and Genome Research. 110 (1-4): 491-9. doi:10.1159/000084982. PMID 16093702. S2CID ... Zimmerly, Steven (2005). "Mobile introns and retroelements in bacteria". In Mullany, Peter (ed.). The Dynamic Bacterial Genome ... Inouye S.; Inouye M. (1993). "Bacterial Reverse Transcriptase". In Goff, Stephen and Anna M. Skalka (ed.). Reverse ... save for the observed fact that msDNA is widely yet sporadically dispersed among bacterial species in a manner suggestive of ...
Ultrastructure of Bacterial Viruses. Plenum Press, New York. OCLC 14492588, ISBN 0-306-30421-X The following have not yet been ... Viral Genome Packaging Machines: Genetics, Structure, and Mechanism. Landes Bioscience/Eurekah, Georgetown, TX; Kluwer Academic ... Studies on Bacterial Viruses. Naya Publishing Co., Tokyo. OCLC 1064505 Jacob, F. 1954. Les bactéries lysogènes et la notion de ... Bacterial and Bacteriophage Genetics. Springer-Verlag, New York. OCLC 41273243, ISBN 0-387-23919-7 Stahl, F. W. 2000. We Can ...
ISBN 978-3-540-38577-6. "Bdellovibrio genome". "Type-strain of Bdellovibrio bacteriovorus at Bac Dive". The Bacterial Diversity ... The genome of Bdellovibrio bacteriovorus HD100 was sequenced in 2004. The HD100 genome is 3782950 nucleotides long, larger than ... November 2012). "Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the ... Bdellovibrio could be considered bacterial predators or parasites. Bdellovibrio bacteriovorus was first described by Stolp and ...
CS1 maint: discouraged parameter (link) "History of Biology: Dates 1850-1874". Genetics of Bacterial Genomes. Retrieved 2007-01 ...
"Genome Res. 19 (12): 2317-2323. doi:10.1101/gr.096651.109. PMC 2792171 . PMID 19819907.. ... A common marker for human microbiome studies is the gene for bacterial 16S rRNA (i.e. "16S rDNA", the sequence of DNA which ... The human microbiome refers to their genomes.[11] Humans are colonized by many microorganisms; the traditional estimate was ... One drawback of this approach is that many members of microbial communities do not have a representative sequenced genome.[48] ...
... resulted in the first bacterial genome sequence and first commercial genome (the human pathogen Helicobacter pylori) in 1994.[ ... "Personal Genome Project". Retrieved 25 May 2013.. *^ "Okay, You've Sequenced My Genome: Are You Sure You Got it Right?". NGS ... Synthetic biology and genome engineering[edit]. He has co-developed "genome engineering" technologies since 1997 via either ... His team is the first to tackle a genome-scale change in the genetic code.[76] This was done in a 4.7 million basepair genome ...
Billy Bourke; Sherman, Philip M. (2006). Bacterial Genomes and Infectious Diseases. Humana P.,U.S. ISBN 1-59745-152-5. Terio, K ... "Helicobacter pametensis" at the Encyclopedia of Life LPSN Type strain of Helicobacter pametensis at BacDive - the Bacterial ...
Brooks JE, Roberts RJ (February 1982). "Modification profiles of bacterial genomes". Nucleic Acids Research. 10 (3): 913-34. ... but is widespread in bacterial genomes, as part of the restriction modification or DNA repair systems. In Escherichia coli, ... Every sequence of the genome that shares homology or identity with the plasmid may thus appear to be bound by the protein of ... The resolution of DamID is a function of the availability of GATC sequences in the genome. A protein can only be mapped within ...
Billy Bourke; Sherman, Philip M. (2006). Bacterial Genomes and Infectious Diseases. Humana P.,U.S. ISBN 978-1-59745-152-9. ... Its genome has been sequenced. Fox, James G.; et al. (2000). "Helicobacter canadensis sp. nov. isolated from humans with ... 2009). "Genome sequence of the emerging pathogen Helicobacter canadensis". Journal of Bacteriology. 191 (17): 5566-5567. doi: ... "Helicobacter canadensis" at the Encyclopedia of Life LPSN Type strain of Helicobacter canadensis at BacDive - the Bacterial ...
Billy Bourke; Sherman, Philip M. (2006). Bacterial Genomes and Infectious Diseases. Humana P.,U.S. ISBN 1-59745-152-5. Terio, K ... the Bacterial Diversity Metadatabase v t e. ...
Billy Bourke; Sherman, Philip M. (2006). Bacterial Genomes and Infectious Diseases. Humana P.,U.S. ISBN 1-59745-152-5. Terio, K ... Pathogenesis of bacterial infections in animals. John Wiley & Sons, 2008. "Helicobacter brantae" at the Encyclopedia of Life ... LPSN Type strain of Helicobacter brantae at BacDive - the Bacterial Diversity Metadatabase v t e. ...
MICHAEL FONSTEIN AND ROBERT HASELKORN (June 1995). "Physical Mapping of Bacterial Genomes". Journal of Bacteriology. 177 (12): ... Brown TA (2002). "Mapping Genomes". Genomes. Oxford: Wiley-Liss - via NCBI. Alizadeh, F.; Karp, R. M.; Weisser, D. K.; Zweig, G ... "Physical mapping of complex genomes". Genomics : the science and technology behind the Human Genome Project. Wiley. p. 234-284 ... To ensure there is a minimum set of clones that form one config for a genome (i.e. tiling path), the library used will have ...
Kagachi, Chihiro (2007). "A Comparison of Bacterial Genomes". Seikagaku- the Journal of Japanese Biochemical Society. "NTPase [ ... The DUF84 region is found in the genome of a bacterium called Vibrio cholerae. The region consists of approximately 183 amino ...
Genome Center of Wisconsin. 17 January 2007. Archived from the original on 14 December 2013. Retrieved 30 Oct 2012. "Bacterial ... The presence of a soft rot may be an indication of a bacterial disease. However, many other organisms and plant disorders may ... Slawiak, M.; Lojkowska, E.; Van der Wolf, J.M. (2009). "First report of bacterial soft rot on potato caused by Dickeya sp. (syn ... Nelson, S. (2009). "Bacterial leaf blight of aglaonema. Plant Disease: Cooperative Extension Service: College of Tropical ...
"Bacterial genomes and infectious diseases." Pediatric research 54.1 (2003): 1-7. Hau, Jann, and Steven J. Schapiro, eds. ... Pathogenesis of bacterial infections in animals. Wiley. com, 2008. "Helicobacter cholecystus" at the Encyclopedia of Life LPSN ... Type strain of Helicobacter cholecystus at BacDive - the Bacterial Diversity Metadatabase v t e. ...
A database of annotated bacterial genomes and their chromosome/genome maps. Data types. captured. Gene sequence data, protein ... bacterial genome sequence data. All of the genome (chromosome) maps in BacMap were constructed using the program known as ... all of BacMap's bacterial genome maps now have separate prophage genome maps as well as separate tRNA and rRNA maps. Each ... Since it was first introduced, the number of bacterial genomes in BacMap has grown by more than 15X. Essentially BacMap ...
Genome structure[edit]. The E. faecalis genome consists of 3.22 million base pairs with 3,113 protein-coding genes.[26] ... Bacterial small RNAs play important roles in many cellular processes; 11 small RNAs have been experimentally characterised in E ... A genome-wide sRNA study suggested that some sRNAs are linked to the antibiotic resistance and stress response in another ... Type strain of Enterococcus faecalis at BacDive - the Bacterial Diversity Metadatabase ...
"Loman, Nicholas James (2012). Comparative bacterial genomics. University of Birmingham. Ph.D." "Real-time, portable genome ... where gained a PhD in Comparative Bacterial Genomics. On completing his thesis, Loman developed an interest in emerging viral ...
In particular, the DNA extraction method must be good for every bacterial strain, not to have the genomes of the ones that are ... The microbial genome data were extracted by identifying the bacterial specific ribosomal RNA, 16S rRNA. The researchers ... Neither from which genome every contig derives, nor the number of genomes present in the sample are known a priori; the aim of ... The coverage depends on each genome abundance in its specific community; low-abundance genomes may undergo fragmentation if the ...
All families of bacterial viruses that have circular (single-stranded or double-stranded) DNA genomes or replicate their ... A prophage is a bacteriophage (often shortened to "phage") genome inserted and integrated into the circular bacterial DNA ... Menouni R, Hutinet G, Petit MA, Ansaldi M (2015). "Bacterial genome remodeling through bacteriophage recombination". FEMS ... Zygotic induction occurs when a bacterial cell carrying the DNA of a bacterial virus transfers its own DNA along with the viral ...
All families of bacterial viruses with circular (single-stranded or double-stranded) DNA genomes or replicating their genomes ... A provirus is a virus genome that is integrated into the DNA of a host cell. In the case of bacterial viruses (bacteriophages ... Not only eukaryotic viruses integrate into the genomes of their hosts; many bacterial and archaeal viruses also employ this ... A provirus does not directly make new DNA copies of itself while integrated into a host genome in this way. Instead, it is ...
In 2010, scientists at the J. Craig Venter Institute created the first synthetic genome and inserted it into an empty bacterial ... July 2010). "Creation of a bacterial cell controlled by a chemically synthesized genome". Science. 329 (5987): 52-6. Bibcode: ... The frequency of gene targeting can be greatly enhanced through genome editing. Genome editing uses artificially engineered ... "Nation Human Genome Research Institute. 2009.. *^ "GM pigs best bet for organ transplant". Medical News Today. 21 September ...
"Creation of a bacterial cell controlled by a chemically synthesized genome". Science. 329 (5987): 52-6. doi:10.1126/science. ... The M. genitalium genome however is over 100 times larger than that of ΦX174. In 2007, a chemically synthesized genome of ... In March 2010, a synthesized M. mycoides genome was successfully transplanted into M. capricolum.[8][11] The resulting organism ... In 1990 Hutchison began work on Mycoplasma genitalium, which has the smallest known genome that can constitute a cell. It led ...
... genomes and related information at PATRIC, a Bioinformatics Resource Center funded by NIAID Brucella Genome Projects ( ... Bacterial small RNAs (sRNA) are an important class of regulatory molecules. Many Brucella sRNAs have been identified. Infection ... from Genomes OnLine Database) Comparative Analysis of Brucella Genomes (at DOE's IMG system) Brucella Bioinformatics Portal ... The genomes of most Brucella species have been sequenced, and typically encode 3,200 to 3,500 open reading frames (ORFs). ...
The genome of S. pneumoniae is a closed, circular DNA structure that contains between 2.0 and 2.1 million base pairs depending ... Natural bacterial transformation involves the transfer of DNA from one bacterium to another through the surrounding medium. ... The ability of S. pneumoniae to repair the oxidative DNA damages in its genome, caused by this host defense, likely contributes ... van de Beek, Diederik; de Gans, Jan; Tunkel, Allan R.; Wijdicks, Eelco F.M. (5 January 2006). "Community-Acquired Bacterial ...
... virus genomes contain seven genes including 3'-UTR-NP-VP35-VP40-GP-VP30-VP24-L-5'-UTR.[33][47] The genomes of the five ... balance as well as treating any bacterial infections that may develop.[33] Dialysis may be needed for kidney failure, and ... Replication of the viral genome results in full-length, positive-strand antigenomes that are, in turn, transcribed into genome ... Genome-sequencing showed that this outbreak was not related to the 2014-15 West Africa Ebola virus outbreak, but was the same ...
... compact genomes and genes of bacterial origin". BMC Genomics. 16 (1): 204. doi:10.1186/s12864-015-1418-3. PMC 4487195. PMID ... Over time, many parts of the chloroplast genome were transferred to the nuclear genome of the host,[4][7][26] a process called ... Many of the chloroplast's protein complexes consist of subunits from both the chloroplast genome and the host's nuclear genome ... "Genome Biology and Evolution. 10 (10): 2669-2571. doi:10.1093/gbe/evy189. PMC 6166771. PMID 30165616.. ...
The anaerobic bacterial species Cutibacterium acnes (formerly Propionibacterium acnes) contributes to the development of acne, ... scientists reported the first genome sequencing of a C. acnes bacteriophage (PA6). The authors proposed applying this research ... These reinforced the idea amongst dermatologists that bacterial growth on the skin plays an important role in causing acne.[179 ... such as bacterial resistance.[194] Oral and topical probiotics are under evaluation as treatments for acne.[195] Probiotics may ...
The Caulobacter CB15 genome has 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes.[7] The genome ... The bacterial cell's control system has a hierarchical organization.[16] The signaling and the control subsystem interfaces ... Generally, the bacterial species that divides fastest will be most effective at exploiting resources and effectively occupying ... Ausmees, Nora; Kuhn, Jeffrey R.; Jacobs-Wagner, Christine (December 2003). "The bacterial cytoskeleton: an intermediate ...
"DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes. 15 (4): 173-183. doi:10.1093/ ... The government started hailing the use of enamel tanks as easy to clean, lasting forever, and being devoid of bacterial ...
... has been introduced into tomato plants and in vivo studies show significant resistance to bacterial wilt and bacterial spot.[27 ... A second copy of the tomato gene polygalacturonase was inserted into the tomato genome in the antisense direction.[7] The ... In 2000, the concentration of pro-vitamin A was increased by adding a bacterial gene encoding phytoene desaturase, although the ... "Control of Ethylene Synthesis by Expression of a Bacterial Enzyme in Transgenic Tomato Plants". The Plant Cell. 3 (11): 1187- ...
... and Sexual while Living with a Nearly Minimal Bacterial Genome". PLoS Genet. 3 (5): e75. doi:10.1371/journal.pgen.0030075. PMC ... Genome complexity has generally increased since the beginning of the life on Earth.[17][18] Some computer models have suggested ... Sharov, Alexei A (2006). "Genome increase as a clock for the origin and evolution of life". Biology Direct. 1 (1): 17. doi: ... Recently work in evolution theory has proposed that by relaxing selection pressure, which typically acts to streamline genomes ...
Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size. Plant Biology. 8: 770-777. ... Genome sizes[change , change source]. Organism Genome size (base pairs) Note Virus, Bacteriophage MS2 3569 First sequenced RNA- ... First plant genome sequenced, Dec 2000.[9] Plant, Genlisea margaretae 6.34×107 Smallest recorded flowering plant genome, 2006.[ ... For other uses, see Genome (disambiguation).. The genome of an organism is the whole of its hereditary information encoded in ...
Bacterial FISH probes are often primers for the 16s rRNA region. FISH is widely used in the field of microbial ecology, to ... The size of the human genome is so large, compared to the length that could be sequenced directly, that it was necessary to ... Probes are often derived from fragments of DNA that were isolated, purified, and amplified for use in the Human Genome Project ... FISH can also be used to compare the genomes of two biological species, to deduce evolutionary relationships. A similar ...
1967). "The complete genome sequence of the gram-positive bacterium Bacillus subtilis". Nature. 390 (6657): 249-56. doi:10.1038 ... Abel-Santos, E (editor) (2012). Bacterial Spores: Current Research and Applications. Caister Academic Press. ISBN 978-1-908230- ... Further information: Bacterial morphological plasticity. Under conditions of starvation, especially the lack of carbon and ... While the rest of a bacterial cell may stain, the endospore is left colourless. To combat this, a special stain technique ...
Loman, N.J.; Quick, J.; Simpson, J.T. (2015). "A complete bacterial genome assembled de novo using only nanopore sequencing ... accuracy relative to the established 5.4 million base pair genome. Despite earlier skepticism, nanopore sequencing is now ...
Genome[edit]. The genome of MAP strain K-10 was sequenced in 2005 and found to consist of a single circular chromosome of ... Bacterial cultures were regarded as Gold standards for detection of MAP. Detection is very limited in fresh tissues, food, and ... Type strain of Mycobacterium avium subspecies paratuberculosis at BacDive - the Bacterial Diversity Metadatabase ... Gram-positive bacterial infection: Actinobacteria (primarily A00-A79, 001-041, 080-109) ...
"Genome Res. 19 (1): 92-105. doi:10.1101/gr.082701.108. PMC 2612969 . PMID 18955434.. CS1 maint: Multiple names: authors list ( ... RAD51 family members are homologous to the bacterial RecA, Archaeal RadA and yeast Rad51.[5][6] The protein is highly conserved ...
As an example of the relationship between the IMP (in this case the bacterial phototrapping pigment, bacteriorhodopsin) and the ... IMPs comprise a significant fraction of the proteins encoded in an organism's genome.[2] Proteins that cross the membrane are ... "Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms". Protein Science. 7 ...
"Genome Research. 7 (4): 353-8. doi:10.1101/gr.7.4.353. PMC 139146. PMID 9110174.. ... "Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder". Nature Genetics. 40 ... "Case-case genome-wide association analysis shows markers differentially associated with schizophrenia and bipolar disorder and ...
Koonin, E.V.; Mushegian, A.R.; Galperin, M.Y.; Walker, D.R. (1997). "Comparison of archaeal and bacterial genomes: computer ... The tiny 490,885 base-pair genome of Nanoarchaeum equitans is one-tenth of this size and the smallest archaeal genome known; it ... while archaeal flagella appear to have evolved from bacterial type IV pili.[106] In contrast to the bacterial flagellum, which ... "Genome Biol. Evol. 7 (1): 191-204. doi:10.1093/gbe/evu274. PMC 4316627 . PMID 25527841.. ...
"Genome Research. 11 (5): 677-84. doi:10.1101/ PMC 311086. PMID 11337467.. ... The bacterial homolog of the TATA box is called the Pribnow box which has a shorter consensus sequence. ... In the 1980s, while investigating nucleotide sequences in mouse genome loci, the Hogness box sequence was found and "boxed in" ... Most research on the TATA box has been conducted on yeast, human, and Drosophila genomes, however, similar elements have been ...
Cavalier-Smith, T (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial ... "From genomes to function: haloarchaea as model organisms". Microbiology (Reading, Engl.). 152 (Pt 3): 585-90. doi:10.1099/mic. ...
"Genome Res. 11 (3): 422-35. doi:10.1101/gr.GR1547R. PMC 311072. PMID 11230166.. ... cellular response to molecule of bacterial origin. • positive regulation of interferon-gamma production. • embryonic axis ...
The real danger lies that the psyllid can carry a deadly, bacterial tree disease called Huanglongbing (HLB), also known as ... A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the ...
"The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses". PLoS One 8 (2 ... "Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes". FEMS Microbiology ... James, Greg (15 May 2018). "Universal Bacterial Identification by PCR and DNA Sequencing of 16S rRNA Gene". PCR for Clinical ... Kolbert CP, Persing DH (June 1999). "Ribosomal DNA sequencing as a tool for identification of bacterial pathogens". Current ...
Human GAA genome location and GAA gene details page in the UCSC Genome Browser. ...
1997). ""Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and ... "Genome Biol. 3 (2): REVIEWS0003. PMC 139013. PMID 11864374. doi:10.1186/gb-2002-3-2-reviews0003.. ... Ciaramella M, Napoli A, Rossi M (2005). "Another extreme genome: how to live at pH 0". Trends Microbiol. 13 (2): 49-51. PMID ... 1994). "Evolutionary relationships of bacterial and archaeal glutamine synthetase genes". J Mol Evol. (38(6)): 566-576.. ...
"Design and synthesis of a minimal bacterial genome". Science 351 (6280): aad6253. Bibcode:2016Sci...351.....H. doi:10.1126/ ... International Human Genome Sequencing Consortium (October 2004). "Finishing the euchromatic sequence of the human genome". ... "Tandem chimerism as a means to increase protein complexity in the human genome". Genome Research 16 (1): 37-44. doi:10.1101/gr. ... "The Human Genome Project Timeline". Retrieved 13 September 2006. *↑ Avery, OT; MacLeod, CM; McCarty, M (1944). "Studies on the ...
細菌性肺炎(英语:Bacterial pneumonia) *肺炎球菌感染(英语:Pneumococcal infection) ...
"Bacterial glycosidases for the production of universal red blood cells". Nat Biotechnol 25 (4): 454-64. doi:10.1038/nbt1298 ... "Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer" ...
Eigen et al.[76] and Woese[77] proposed that the genomes of early protocells were composed of single-stranded RNA, and that ... Nudler E, Mironov AS (Jan 2004). "The riboswitch control of bacterial metabolism". Trends in Biochemical Sciences. 29 (1): 11-7 ... In comparison, the genome of the smallest known viruses capable of causing an infection are about 2,000 nucleobases long.[72] ... Genome redundancy would allow a damaged RNA segment to be replaced by an additional replication of its homolog. However, for ...
"U.S. National Human Genome Research Institute. 2015년 3월 1일에 확인함.. ... Fisher JF, Meroueh SO, Mobashery S (February 2005). "Bacterial resistance to beta-lactam antibiotics: compelling opportunism, ... "Molecular biology of bacterial bioluminescence". 》Microbiological Reviews》 55 (1): 123-42. PMC 372803. PMID 2030669 ...
Hindra, H; Yang, D; Teng, Q; Dong, LB; Crnovčić, I; Huang, T; Ge, H; Shen, B (17 March 2017). "Genome Mining of Streptomyces ... While potentially effective against bacterial infections, its toxicity prevents its use for this purpose.[1] It has been ...
Dynamics of genome rearrangement in bacterial populations.. Darling AE1, Miklós I, Ragan MA. ... Whole genome alignment of eight Yersinia genomes using Mauve reveals 78 locally collinear blocks conserved among all eight taxa ... Genomes with perfectly balanced replichores have 0% imbalance while a genome with the origin and terminus at the same locus ... Our findings represent the first characterization of genome arrangement evolution in a bacterial population evolving outside ...
A newly sequenced bacterial genome from a team led by the Department of Energys Oak Ridge National Laboratory (ORNL) could ... The new genome, sequenced at the California-based DOE Joint Genome Institute (JGI) and published in the Journal of Bacteriology ... Few bacterial species are capable of this conversion, and exactly how the transformation takes place has been a matter of ... "This is the first Desulfovibrio genome that will methylate mercury thats been published," Brown said. "Now that we have this ...
No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an ... Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude ... For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement ... Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms ( ...
BASys: a web server for automated bacterial genome annotation.. Van Domselaar GH1, Stothard P, Shrivastava S, Cruz JA, Guo A, ... BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic ( ... A) The web server, hosted on the master node, accepts genome data and schedules it for processing by the slave nodes. (B) Each ... Shown are the annotation progress monitor for two genome annotation projects (E.coli and C.trachomatis) in various states of ...
This strategy can also elucidate gene regions that are essential for bacterial survival. ... In a study that twists natures arm to gain clues into the varied functions of the bacterial genome, North Carolina State ... In a study that twists natures arm to gain clues into the varied functions of the bacterial genome, North Carolina State ... Bacterial genome scalpel can identify key gene regions. North Carolina State University ...
Daubin, V., and H. Ochman, 2004 Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res. 14: 1036- ... Daubin, V., E. Lerat and G. Perriere, 2003a The source of laterally transferred genes in bacterial genomes. Genome Biol. 4: R57 ... Garcia-Vallvé, S., A. Romeu and J. Palau, 2000 Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. ... and most of them are transient in bacterial genomes (Lerat and Ochman 2005). Zhaxybayeva et al. (2007) reported that genomes ...
9780521129619 Our cheapest price for The Dynamic Bacterial Genome is $93.12. Free shipping on all orders over $35.00. ... Genome rearrangements are a result of the actions of discrete genetic elements such as conjugative transposons, plasmids, phage ... This book provides an in-depth analysis of the mechanisms and biological consequences of genome rearrangements in bacteria. ... The biological effects of these rearrangements are far-reaching and impact on bacterial virulence, antibiotic resistance and ...
The genomes of a number of bacterial species havebeen fully sequenced ... The genomes of a number of bacterial species have been fully sequenced. Analyses of these genomes are providing useful insights ... Bacterial Genomes. Ronald M Atlas, University of Louisville, Louisville, Kentucky, USA Daniel Drell, US Department of Energy, ... 2000) A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the ...
Bacterial genomes are extremely variable, comprising both a consensus "core" genome, which is present in the majority of ... Stochastic evolution of genome-wide divergence. Genome-wide divergence as a function of time at We have used per base pair per ... Recombination-Driven Genome Evolution and Stability of Bacterial Species. Purushottam D. Dixit, Tin Yau Pang and Sergei Maslov ... Recombination-Driven Genome Evolution and Stability of Bacterial Species. Purushottam D. Dixit, Tin Yau Pang and Sergei Maslov ...
DNA phosphorothioation is widespread and quantized in bacterial genomes. Lianrong Wang, Shi Chen, Kevin L. Vergin, Stephen J. ... DNA phosphorothioation is widespread and quantized in bacterial genomes. Lianrong Wang, Shi Chen, Kevin L. Vergin, Stephen J. ... DNA phosphorothioation is widespread and quantized in bacterial genomes. Lianrong Wang, Shi Chen, Kevin L. Vergin, Stephen J. ... DNA phosphorothioation is widespread and quantized in bacterial genomes Message Subject (Your Name) has sent you a message from ...
This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly. ... have the potential to address limitations associated with genome assembly. Here we combine sequencing data from second- and ... third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain ... Chaisson, M.J. & Pevzner, P.A. Short read fragment assembly of bacterial genomes. Genome Res. 18, 324-330 (2008). ...
We identify 152 gene exchange networks containing 22,963 bacterial genomes. Analysis of ARG-surrounding sequences identify ... Using a separate database with 472,798 genomes from Streptococcaceae, Staphylococcaceae and Enterobacteriaceae, we confirm 34 ... we set out to determine predictive features of ARG transfer among bacterial clades. We use a statistical framework to identify ... putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes. ...
Advances in Bacterial Genome Engineering Conference is for the researchers, scientists, scholars, engineers, academic, ... Advances in Bacterial Genome Engineering. International Conference on Advances in Bacterial Genome Engineering. Advances in ... and concerns as well as practical challenges encountered and solutions adopted in the fields of Advances in Bacterial Genome ... experiences and research results on all aspects of Advances in Bacterial Genome Engineering Conference. It also provides a ...
Construction of MCMV BAC genomes and structural analysis of reconstituted virus genomes. (I) Recombinant BAC genomes were ... The MCMV genome was cloned as a bacterial artificial chromosome (BAC) in Escherichia coli and viral progeny were reconstituted ... The mouse cytomegalovirus genome was cloned and maintained as a 230 kb bacterial artificial chromosome (BAC) in E. coli. ... Cloning and mutagenesis of a herpesvirus genome as an infectious bacterial artificial chromosome. Martin Messerle, Irena ...
They found that bacterial DNA was more likely to integrate in the genome in tumor samples than in normal, healthy somatic cells ... Bacterial DNA may integrate into the human genome more readily in tumors than in normal human tissue, scientists have found. ... analyzed genomic sequencing data available from the Human Genome Project, the 1,000 Genomes Project and The Cancer Genome Atlas ... Bacterial DNA May Integrate Into Human Genome More Readily in Tumor Tissue. ...
This key process remains a bottleneck in synthetic biology, especially for genome engineering strate … ... Genome transplantation (GT) allows the installation of purified chromosomes into recipient cells, causing the resulting ... Impact of donor-recipient phylogenetic distance on bacterial genome transplantation Nucleic Acids Res. 2016 Sep 30;44(17):8501- ... Genome transplantation (GT) allows the installation of purified chromosomes into recipient cells, causing the resulting ...
This course will cover the topic of Whole genome sequencing (WGS) of bacterial genomes which is becoming more and more ... ... Learn Whole genome sequencing of bacterial genomes - tools and applications from Technical University of Denmark (DTU). ... This course will cover the topic of Whole genome sequencing (WGS) of bacterial genomes which is becoming more and more relevant ... Welcome and introduction to typing of bacteria and use of Whole genome sequencing applied to surveillance of bacterial ...
4B, the Pha groups differ not only in genome structure but also in genome size: Pha groups 1 and 2 have small genomes, 2,130 ... Bacterial Phylogenetic Clusters Revealed by Genome Structure. Shu-Lin Liu, Anthony B. Schryvers, Kenneth E. Sanderson, Randal N ... Bacterial Phylogenetic Clusters Revealed by Genome Structure. Shu-Lin Liu, Anthony B. Schryvers, Kenneth E. Sanderson, Randal N ... Bacterial Phylogenetic Clusters Revealed by Genome Structure. Shu-Lin Liu, Anthony B. Schryvers, Kenneth E. Sanderson, Randal N ...
To get the outbreak under control, Clinical Center staff collaborated with investigators at the National Human Genome Research ... Institute, also part of NIH, to use genome sequencing in the middle of this active hospital epidemic to learn how the microbe ... NIH uses genome sequencing to help quell bacterial outbreak in Clinical Center. NIH/National Human Genome Research Institute ... NIH uses genome sequencing to help quell bacterial outbreak in Clinical Center Genomics and microbiology experts collaborate in ...
oryzae ( Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and... ... Genome-wide association Oryza sativa Xanthomonas oryzae bacterial blight (BB) disease resistance genotyping-by-sequencing (GBS ... globally in the 3000 Rice Genomes Project (3k genomes), while they were enriched to 37-97% in the aus subpool of the 3k genomes ... Additional file 4: Figure S3. Genome-wide association analysis of bacterial blight resistance to nine Xoo strains in 198 indica ...
Researchers in Canada and the UK have used data from the Oxford Nanopore MinIon alone to assemble a bacterial genome into a ... Team Demonstrates De Novo Assembly of Bacterial Genome from Nanopore Data Alone. Feb 23, 2015 ... Home » Team Demonstrates De Novo Assembly of Bacterial Genome from Nanopore Data Alone ... and the University of Birmingham in the UK have used data from the Oxford Nanopore MinIon to assemble a bacterial genome into a ...
Genome editing is an important technology for bacterial cellular engineering, which is commonly conducted by homologous ... approach is to conditionally modify the gene expression profile at the posttranscriptional level without altering the genomes. ... recent advances on methods used in genomic engineering and silencing technologies that are advantageously used for bacterial ... "Bacterial Cellular Engineering by Genome Editing and Gene Silencing." Int. J. Mol. Sci. 15, no. 2: 2773-2793. ...
This strategy is based on the recent development of two complementary modelling approaches for B. subtilis: i) a genome-scale ... It is anticipated that validated simpler bacterial strains together with the modelling framework generated by BaSynthec will be ... the development of a new genome-scale metabolic model of B. subtilis which is the most complete and accurate that exists today ...
a bacterial line where the RNAs that decode the genome are also synthetic and which use a different encoding mapping three base ... CREATION OF A BACTERIAL CELL CONTROLLED BY A CHEMICALLY SYNTHESIZED GENOME [1] ... report the creation of a bacterial cell controlled by a chemically synthesized genome. A related News story by E. Pennisi [3] ... The Edge Reality Club discussion on the paper, "Creation Of A Bacterial Cell Controlled By A Chemically Synthesized Genome," is ...
Genome transplantation (GT) allows the installation of purified chromosomes into recipient cells, causing the resulting ... capricolum (Mcap), and the main factors driving the compatibility between a donor genome and a recipient cell are poorly ... Using Mcap as the recipient cell, we successfully transplanted the genome of six bacteria belonging to the Spiroplasma ... This key process remains a bottleneck in synthetic biology, especially for genome engineering strategies of intractable and ...
Here we used splicing-sensitive arrays to assess genome-wide gene- and exon-level expression profiles in human DCs in response ... to a bacterial challenge. We find widespread alternative splicing events and splicing factor transcriptional signatures induced ...
Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost. United States: N. p., 2019. Web. doi: ... Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost. United States. doi:10.1128/mra.00516-19 ... Wed . "Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost". United States. doi:10.1128/mra. ... title = {Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost},. author = {Xue, Yaxin and ...
StrepLab scientists use genome sequences to find connections between invasive group A strep infections in long-term care ... 1 Bacterial samples collected over the course of an outbreak might only be "near" identical because bacteria pick up genome ... 2019: Scientists use bacterial genome sequences to stop a deadly multi-facility outbreak. By Erin Scherer ... This graph shows the similarities between different group A strep genome sequences. On this type of graph, more similar genome ...
Scientists have developed an easy-to-use computer program that can quickly analyse bacterial DNA from a patients infection and ... New laptop program can identify drug resistance from bacterial genomes. HealthResearchGeneticsInnovation ... Genome sequencing has the potential to transform the way we diagnose and treat bacterial infections in NHS hospitals, but one ... One of the barriers to making whole genome sequencing a routine part of NHS care is the need for powerful computers and ...
... Olga L. Voronina,1 Marina S. ... For example, the Mumia flava genome was unexpectedly big: 16.4 Mb, in contrast to the few other Nocardioidaceae genomes that ... Preparation of genomic DNA for the whole genome sequencing was performed as described [9]. Whole genome sequencing of B. ... "The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes," Nucleic Acids Research, vol ...
  • BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. (
  • 2000) The genome sequence of the food‐borne pathogen Campylobacter jejuni reveals hypervariable sequences. (
  • 2000) Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. (
  • Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes. (
  • However, such sequence analyses provide information for only a tiny (though important) portion of the genome, and different choices of sequences for analysis can lead to remarkably variable conclusions ( 10 , 21 ). (
  • Here, 56 prokaryotic metagenome-assembled genome (MAG) sequences from 13 phyla are reported. (
  • article{osti_1572795, title = {Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost}, author = {Xue, Yaxin and Jonassen, Inge and Øvreås, Lise and Taş, Neslihan}, abstractNote = {ABSTRACT Permafrost contains one of the least known soil microbiomes, where microbial populations reside in an ice-locked environment. (
  • Through start-up support from the Advanced Molecular Detection (AMD) program, StrepLab now sequences whole genomes of group A strep and other bacteria. (
  • StrepLab scientists realized they could also use genome sequences to find connections between invasive group A strep infections. (
  • Running the genome sequences through the cluster detection tool at CDC showed the samples were near identical. (
  • The variations in bacterial and archaeal genome DNA sequences are not only explained by neutral mutations. (
  • Therefore, virus resistance systems have resulted in changes in bacterial and archaeal genome DNA sequences during evolution. (
  • I welcome investigators to contribute any types of the tier 1 articles focusing on the evolution and function of bacterial (or archaeal) genome sequences to this Research Topic. (
  • Right now, we have genome sequences from 50 different bacterial phyla and 11 different archaeal phyla. (
  • The genome sequences reveal much diversity in bacteria. (
  • Genome sequences show that parasitic bacteria have 500-1200 genes, free-living bacteria have 1500-7500 genes, and archaea have 1500-2700 genes. (
  • All the genome sequences of organisms known throughout the world are stored in a database belonging to the National Center for Biotechnology Information in the United States. (
  • To investigate the relation between DNA acquisition and phylogenetic incongruence, we selected quartets of related, sequenced genomes whose phylogenetic relationships, based on small subunit ribosomal RNA (SSU rRNA) sequences, display the branching topology shown in Fig. 1 . (
  • The discovery of these three new genomes demonstrates how powerful the public release of raw sequencing data can be," wrote the authors, who have deposited their findings in Genbank, an open repository of genomic sequences. (
  • Complete genome sequences are providing an understanding of how extreme genome reduction affects evolutionary directions and metabolic capabilities of obligate pathogens and symbionts. (
  • This list of sequenced eubacterial genomes contains most of the eubacteria known to have publicly available complete genome sequences. (
  • We also show that there are significant correlations between genomic traits -- such as genome size, repeat content, and number of coding sequences -- and the resulting genome assembly quality. (
  • The researchers identified more than 112,000 bacterial gene sequences, which they then classified and compared. (
  • Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. (
  • It mainly concerned developing a program that reads in the sequences of all genes present on a specified set of bacterial genomes and then creates clusters of related genes. (
  • Optimization of Mutation Pressure in Relation to Properties of Protein-Coding Sequences in Bacterial Genomes. (
  • We observed no substantial differences between the effects of mutational matrices on protein-coding sequences in genomes under study in respect of differently replicated DNA strands, mutational cost types and properties of the referenced artificial matrices. (
  • The template is normally the homologous sequence on a sister chromosome, but when sequences are present in multiple copies within a genome, RecA can promote recombination between paralogs. (
  • Genome rearrangement by homologous recombination between repetitive sequences. (
  • Therefore, bacterial sequences are (anecdotally) quite common in human samples that haven't been processed with care, or are taken from tissues with microbiota. (
  • 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. (
  • We analyze hundreds of bacterial genomes and find that the coding sequences of highly expressed genes systematically contain fewer SD sequences than expected, yielding a robust correlation between the normalized occurrence of SD sites and protein abundances across a range of bacterial taxa. (
  • Modeling of these integrations suggests that the previously identified sequences cover most of the sequence flanking the junction between the bacterial and human DNA. (
  • A necessary step for a genome level analysis of the cellular metabolism is the in silico reconstruction of the metabolic network from genome sequences. (
  • The available methods are mainly based on the annotation of genome sequences including two successive steps, the prediction of coding sequences (CDS) and their function assignment. (
  • Furthermore, two versions of sequences of the bacterium Klebsiella pneumoniae with different genome coverage (3.9 and 7.9 fold, respectively) are examined. (
  • Compared to other gene finding methods such as CRITICA our method is more suitable for exploiting sequences of low genome coverage. (
  • The reversed querying process and the program IdentiCS allow a fast and adequate prediction protein coding sequences and reconstruction of the potential metabolic network from low coverage genome sequences of bacteria. (
  • Moreover, because released sequences are not always complete sequences (for both bacterial genomes and metagenomes), sequence analysis and annotation should be performed on contigs or short sequences to detect putative functions, especially for AR genes. (
  • They looked through the genome sequences of thousands of organisms and identified a single gene, chitinase, that appeared in several major bacterial groups, as well as in most species of fungi, which have a well-established fossil record. (
  • The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. (
  • To test whether bacteriophages transfer as single genes or larger regions between coinfections, we sequenced the genome of the obligate intracellular Wolbachia strain w VitB from the parasitic wasp Nasonia vitripennis and compared it against the prophage sequences of the divergent w VitA coinfection. (
  • Often users are not bio-informaticians and, in a black box approach, utilise assembly parameters such as contig length and N50 to generate whole genome sequences, potentially resulting in mis-assemblies. (
  • Background: Being discovered in bacterial genomes as regions with a high density of promoter-like sequences, promoter islands attracted attention due to an unusual combination of their functional features, specific structure and genomic location. (
  • Results: Here we described those features of promoter islands, which had made them transcriptionally inactive, compared their intraspecies polymorphism with other promoters and non-promoter genomic regions, and evaluated the frequency and character of spontaneous mutations in their nucleotide sequences detected in bacterial populations during long-term growth. (
  • The most extraordinary of them was the observation that the frequency and the nature of spontaneous mutations in their sequences depended on the heterogeneity of the bacterial populations, and the number of point mutations in a more diverse community formed during long common growth was lower than in the culture derived from a single cell. (
  • Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. (
  • What is not known are the genes or the proteins that allow these bacteria to mediate the transformation," said ORNL's Steven Brown, who led a research team to sequence the genome of a bacterium in the Desulfovibrio genus that is capable of methylating mercury. (
  • The study was published as "Genome Sequence of the Mercury Methylating Strain Desulfovibrio desulfuricans ND132. (
  • 1998) The genome sequence of Rickettsia prowazekii and the origin of mitochondria. (
  • 1997) The complete genome sequence of Escherichia coli K‐12. (
  • 1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. (
  • 1998) Complete genome sequence of Treponema pallidum, the syphilis spirochete. (
  • 1996) Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. (
  • 1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. (
  • Sequence determination of the entire genome and assignment of potential protein‐coding regions. (
  • 1997) The complete genome sequence of the gram‐positive bacterium Bacillus subtilis. (
  • 1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. (
  • 2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. (
  • 2000) The genome sequence of the plant pathogen Xylella fastidiosa. (
  • 1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. (
  • 2000) Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. (
  • Using the Multi Locus Sequence Typing (MLST) data, we classify a number of bacterial species to be either the divergent or the metastable type. (
  • Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. (
  • Sequence analysis of the human and mouse CMV genomes revealed a similar genetic organization and a coding capacity for presumably more than 220 polypeptides ( 3 - 5 ). (
  • On the other hand, strains of Pasteurella ureae and Pasteurella pneumotropica are very similar to those of P. multocida in both genome structure and 16S rDNA sequence and should be regarded as strains within this species. (
  • Infectious outbreaks happen in every hospital in the world, afflicting millions of patients each year in the United States alone," said NHGRI Director Eric D. Green, M.D., Ph.D. "By marshaling the ability to sequence bacterial genomes in real time to accurately trace the bacteria as it spread among our Clinical Center patients, our researchers successfully elucidated what happened, which in turn has taught us some important lessons. (
  • Where the pulse-field gel electrophoresis technique shows relatively crude patterns, genome sequence data shows precise differences, down to single genetic letters in the bacterial genome. (
  • Genome sequence information allows scientists to track new strains and antibiotic resistance trends. (
  • Mykrobe Predictor streamlines this process by automating genome analysis, cross-checking the bacterium's DNA sequence with previous strains to look for resistance-causing mutations and presenting information about the bug in an easy-to-understand format. (
  • The restriction-modification system, a virus resistance system, has induced palindromic DNA sequence avoidance in the genomes. (
  • I am interested in the relation between bacterial (or archaeal) genome sequence and their functions. (
  • To synthesise the genome segments in the simplest possible way, and then piece together all segments in the most streamlined manner, the scientists radically simplified the genome sequence without modifying the actual genetic information (at the protein level). (
  • Using this algorithm, the researchers computed the ideal DNA sequence for the synthesis and construction of the genome, which they ultimately utilised for their work. (
  • Through our algorithm, we have completely rewritten our genome into a new sequence of DNA letters that no longer resembles the original sequence. (
  • Indeed, the similarities in gene sequence and gene content that define widely accepted bacterial taxa have been proposed to reflect boundaries to gene transfer, rather than vertical transmission and common organismal ancestry ( 10 ). (
  • Wolbachia made headlines a year ago with the publication of the genome sequence of the species Wolbachia pipientis, which lives inside the reproductive cells of the laboratory fruit fly Drosophila melanogaster. (
  • As bacterial homologous recombination DNA degradation by RecBCD exonuclease/helicase from the double‐strand break (g) is attenuated at χ sequence. (
  • Here, we have demonstrated that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species. (
  • These systems can be employed to selectively and quantitatively remove individual bacterial strains based purely on sequence information, creating opportunities in the treatment of multidrug-resistant infections, the control of industrial fermentations, and the study of microbial consortia. (
  • Ca . Sulcia" exhibits much greater genome stability and slower sequence evolution, although the mechanisms underlying these differences are poorly understood. (
  • Comparative full-genome sequencing of bacteria is a powerful method to detect sequence diversity. (
  • Comparative full-genome sequencing has uncovered large numbers of synonymous SNPs and other sequence polymorphisms ( 6 , 24 ). (
  • Using a method the team previously developed to preferentially sequence bacterial DNA (and avoid sequencing only DNA from the tick), the researchers sequenced 148 B. burgdorferi genomes. (
  • The bacterial RecA protein is required for damage to chromosomes - in particular chromosome breaks - to be repaired, and it acts by using a duplicate copy of the damaged sequence as a template for repair. (
  • First Monoploid Reference Sequence of Sugarcane For the highly polyploid sugarcane, an international team of researchers has successfully assembled a first monoploid reference sequence using a targeted approach that focused on the gene rich part of the genome by harnessing information from a sequenced related species - sorghum. (
  • DAS Tool for Genome Reconstruction from Metagenomes Through the JGI's Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. (
  • New Software Tools Streamline DNA Sequence Design-and-Build Process Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. (
  • The sequence of dif sites is widely conserved among many bacterial phyla, and they can be computationally identified using our method. (
  • Recently, the cost has reduced to the extent that routine sequencing of samples is now a feasible alternative to traditional lab methods of bacterial detection and characterization such as microscopy, culture, antibiotic resistance phenotyping and DNA-based methods such as multi-locus sequence typing (MLST). (
  • This PhD seeks to address these gaps through validation and testing of existing analytical methods for whole genome sequence analysis for application to routine surveillance of community acquired pathogens. (
  • Why sequence novel acetogenic bacterial isolates from dechlorinating microbial mixed cultures? (
  • Here, we report the complete genome sequence of the psyllid symbiont Carsonella ruddii, which consists of a circular chromosome of 159,662 base pairs, averaging 16.5% GC content. (
  • 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). (
  • It does not contain a deletion of the viral sequence, and the BAC vector DNA is excised from the viral genome when the BAC plasmid enters mammalian cells. (
  • Previous research identified the Shine-Dalgarno (SD) sequence as a modulator of translation initiation in bacterial genes, while codon usage biases are frequently implicated as a primary determinant of elongation rate variation. (
  • In this work a fast method is proposed to use unannotated genome sequence for predicting CDSs and for an in silico reconstruction of metabolic networks. (
  • Instead of using predicted genes or CDSs to query public databases, entries from public DNA or protein databases are used as queries to search a local database of the unannotated genome sequence to predict CDSs. (
  • The largest barrier to the routine implementation of whole-genome sequencing is the lack of automated, user-friendly interpretation tools that translate the sequence data and rapidly provide clinically meaningful information that can be used by microbiologists. (
  • We applied, for the first time, a targeted sequence capture array to specifically trap the symbiont's DNA from a heterogeneous mixture of eukaryotic, bacterial, and viral DNA. (
  • Examination of the genome sequence revealed the largest transfer of bacteriophage and flanking genes (52.2 kb) to date between two obligate intracellular coinfections. (
  • The draft genome sequence of Nocardia jinanensis, an opportunistic pathogen that can cause skin infections, reveals genes that may contribute to the lifestyle and pathogenicity of N. jinanensis. (
  • The whole genome sequence of a methicillin-resistant Staphylococcus aureus (MRSA) strain (E-MRSA15-CC22-SCC mec IV) was generated on an Illumina HiSeq-2000 via 2X150b paired end sequencing [ 11 ]. (
  • As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. (
  • Although pipelines have been published that group peptides by sequence similarity, no other software performs the large-scale, flexible, full-genome comparative analyses carried out by LS-BSR. (
  • The researchers say that that the same techniques can be used as a template to study essential and non-essential genomic regions in any bacterium of interest -- and can perhaps be used to target unsavory antibiotic resistance genes in bacterial pathogens and occasionally in beneficial bacteria. (
  • Analyses of these genomes are providing useful insights into the evolution and functioning of diverse bacteria and bacterial pathogens. (
  • Give examples of the applications of Whole Genome Sequencing to Surveillance of bacterial pathogens and antimicrobial resistance 3. (
  • Therefore, the ability to efficiently distinguish phylogenetic groups of bacteria within an apparent taxonomic species is desirable, especially for the correct diagnosis and timely treatment of infectious diseases caused by bacterial pathogens. (
  • Obligate bacterial symbionts or pathogens have the smallest genomes and the fewest pseudogenes of the three groups. (
  • Both of these bacteria, which are innocuous goat pathogens, lack an outer membrane, facilitating genome transfer. (
  • During bacterial infections, macrophages play a critical role in eliminating engulfed pathogens. (
  • However, intracellular bacterial pathogens have evolved varying strategies to avoid elimination by host macrophages ( 1 ). (
  • Other bacterial pathogens, such as Listeria monocytogenes , escape the phagocytic vacuole to enter the host cell cytosol where replication occurs ( 3 ). (
  • Whereas numerous bacterial determinants that facilitate intracellular infection have been characterized from diverse bacterial species ( 4 ), less is known about the host factors that are exploited or subverted by intracellular bacterial pathogens. (
  • Particularly relevant in this respect are the studies on the evolution of bacterial pathogens that produce long-lasting chronic infections. (
  • NP303, C2, PS2A] Subobjective 1A: Develop deep proteogenomic data sets to guide the annotation of poorly characterized type strains and field isolates of select strains of bacterial plant pathogens and other plant-associated bacteria. (
  • Blacksburg, Va. The availability of new genome sequencing technology has prompted a Virginia Tech plant scientist to test an intriguing hypothesis about how agricultures early beginnings may have impacted the evolution of plant pathogens. (
  • The emergence and reemergence of infectious diseases, an increasing rate of antibiotic-resistant variants of pathogens, and the threat of bioterrorism underscore the importance of bacterial genomes and infectious diseases. (
  • Also discussed are the genomes of virulent and nonvirulent strains and species, origin and evolution of pathogens, different models of bacteria-host interactions, and diseases mechanisms. (
  • Using a newly developed bacterial screening pipeline called HOPS, Key and colleagues were able to overcome many of the challenges of finding ancient pathogens in metagenomics data. (
  • The immune system works in a similar fashion, Ehrlich says, by continuously realigning the genomes of white blood cells so they can recognize and destroy foreign pathogens. (
  • However there remain barriers to full implementation of whole genome sequencing of clinical samples from community acquired pathogens which make up the vast majority of infectious disease acquisition. (
  • Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. (
  • Although these studies sequenced DNA from multiple cells, they demonstrated that it is technically feasible to analyze the genomes of pathogens taken directly from clinical specimens without the need to culture them, and thus opened the path for single-cell sequencing of pathogens. (
  • One potential application of bacterial single-cell genomics is the detection of hospital pathogens during those phases of their life cycle when they persist at very low levels in environmental reservoirs and can be transmitted but not detected easily. (
  • Few bacterial species are capable of this conversion, and exactly how the transformation takes place has been a matter of debate for decades. (
  • The genomes of a number of bacterial species have been fully sequenced. (
  • Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. (
  • The finding means researchers may be able to predict the types of microbes that thrive in specific marine environments by sampling the genomes of just a few dominant species, according to research co-author Rick Cavicchioli of the University of New South Wales. (
  • Better still, sampling the genomes of a small number of species should enable scientists to gain useful new insights into the dynamics of whole marine ecosystems. (
  • It's not practical to sample every species in a given area so the model we have described is useful for studying the collective genomes of whole marine microbial communities - or metagenomes - to better understand how they have evolved in specific locations," he says. (
  • This key process remains a bottleneck in synthetic biology, especially for genome engineering strategies of intractable and economically important microbial species. (
  • Using Mcap as the recipient cell, we successfully transplanted the genome of six bacteria belonging to the Spiroplasma phylogenetic group but including species of two distinct genera. (
  • Apply the tools for species identification, MLST typing and resistance gene detection in real cases of other bacterial and pathogen genomes. (
  • In marked contrast, the Pasteurella strains have very different genome structures among and even within individual species. (
  • If criteria for defining bacterial species or genera similar to those used for Salmonella and Escherichia coli were applied, the striking phylogenetic diversity would allow bacteria in the currently recognized species of P. multocida and P. haemolytica to be divided into different species, genera, or even higher ranks. (
  • Bacterial genera or species, as defined by current taxonomic approaches ( 18 , 44 ), may include bacteria that in fact are not closely related phylogenetically. (
  • The bacterial species Streptococcus pyogenes , or group A strep, is known for causing strep throat. (
  • Bacterial genomes are generally smaller and less variant in size among species when compared with genomes of eukaryotes. (
  • Furthermore, amongst species of bacteria, there is relatively little variation in genome size when compared with the genome sizes of other major groups of life. (
  • Genome size is of little relevance when considering the number of functional genes in eukaryotic species. (
  • With enough data from genomes of one genus, algorithms are executed to categorize species. (
  • The group chose to work with these species of mycoplasmas for several reasons - the small genomes of these organisms which make them easier to work with, their lack of cell walls, and the team's experience and expertise with mycoplasmas. (
  • The ability to transfer the naked DNA isolated from one species into a second microbial species paves the way for next experiments to transplant a fully synthetic bacterial chromosome into a living organism and if successful, "boot up" the new entity. (
  • Although the incidence of recently acquired DNA in bacterial genomes is the most direct indication of extensive LGT among species ( 1 ), the question of whether the incongruence in gene phylogenies is linked to the amount of new DNA in a genome has not been addressed. (
  • When scientists finished sequencing the genomes of seven species of fruit fly last year, little did they know that they had also sequenced the genes of several bacteria that dwell undetected inside fruit fly embryos. (
  • Because he s a fruit fly geneticist and not an expert on bacteria, Eisen contacted bacterial geneticists at The Institute for Genomic Research (TIGR) in Maryland, and together they pulled out genes from three species of Wolbachia - all of them new to science. (
  • The existence of these bacterial species inside the fruit fly genome database is an artifact of the way the fly was sequenced, Eisen said. (
  • They were able to reconstruct 95 percent (1,440,650 base pairs) of the genome of one new species from D. ananassae, which they called Wolbachia wAna. (
  • Researchers transformed one bacterial species into another by swapping. (
  • Researchers transformed one bacterial species into another by swapping their genomes, a move that will accelerate the race to develop custom-built synthetic bugs, a pioneer on genetics said Thursday. (
  • Craig Venter, who had a hand in mapping the human genome, said a team of his researchers had transplanted the entire genetic code of one bacterial organism into another closely related species. (
  • All Vibrio species have genome constituted of two circular chromosomes with distinct dynamic characteristics, and we aim at understanding both the selective benefit of this organization as well as the specific machinery in charge of their maintenance. (
  • To understand how symbiont genome degeneration proceeds, we compared the genomes of symbionts in two leafhopper species, Homalodisca vitripennis (glassy-winged sharpshooter [GWSS]) and Graphocephala atropunctata (blue-green sharpshooter [BGSS]) (Hemiptera: Cicadellidae). (
  • To understand whether genome evolution impacts symbiont types equally and whether lineages follow the same evolutionary path, we sequenced the genomes of two coresident symbiotic bacteria from a plant sap-feeding insect and compared them to the symbionts from a related host species. (
  • Combatting this threat will require significant improvement in our understanding of how bacteria develop antibiotic resistance, and how resistance can spread within and between bacterial species. (
  • Researchers at the University of Hawaiʻi recently finished sequencing the genome of a bacterium a new species discovered from the Lōʻihi underwater volcano located more than 4,000 feet below the surface of the Pacific Ocean off the island of Hawaiʻi. (
  • Very soon, the public will be able to see the entire genetic code of the bacterium, the first new bacterial species discovered in Hawaiʻi. (
  • An argument for high N e values for bacteria has been the high genetic diversity within many bacterial "species," but this diversity may be due to population structure: diversity across subpopulations can be far higher than diversity within a subpopulation, which makes it difficult to estimate N e correctly. (
  • Inversions and translocations distinguish the genomes of closely related bacterial species, but most of these rearrangements preserve the relationship between the rearranged fragments and the axis of chromosome replication. (
  • Third, chromosomal rearrangements are less common within species, but a dramatic increase in the frequency of inversions and translocation seems to be associated with the ability of bacteria to infect eukaryotic hosts, possibly reflecting a bacterial response to the challenges posed by the immune system. (
  • The availability of a rapidly increasing number of completely sequenced bacterial genomes makes it possible to explore gene order conservation in related and distant species. (
  • For example, the genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. (
  • Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. (
  • 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. (
  • The capture of bacterial genomes has been a long-standing challenge in microbiology research because the great majority of bacterial species cannot be readily cultivated. (
  • however, few vaginal isolates of uropathogenic bacterial species are available as fully sequenced deposited isolates. (
  • Thus, there is still a need for accurate in silico prediction methods to identify sRNAs within a given bacterial species. (
  • Genome rearrangements are a result of the actions of discrete genetic elements such as conjugative transposons, plasmids, phage, and non-conjugative transposons. (
  • Rice diversity panels can be exploited as reservoirs of useful genetic variation for bacterial blight (BB) resistance. (
  • The program can analyse the entire genetic code of a bacterium in under 3 minutes, once a bacterial sample has been cultured and its DNA sequenced. (
  • Mobile genetic elements may have played a role in the plasmid and virus genesis, which is related to genome reduction. (
  • The Average Nucleotide Identity method quantifies genetic distance between entire genomes by taking advantage of regions of about 10,000 bp. (
  • There is ample latitude for the simplification of genomes, because biology has built-in redundancies for storing genetic information. (
  • Agroscope researchers have cracked an especially tricky bacterial genome code and published an analysis of the complexity of genetic information of nearly 10,000 bacteria. (
  • As whole genome sequencing of bacteria becomes a routine part of clinical microbiological diagnosis, understanding the genetic determinants of antibiotic resistance will allow microbiologists to predict accurately which drug treatments are most likely to be effective in managing each patient's infection. (
  • The evolution of biological diversity through genetic change raises questions about how much variation one can expect among closely related genomes. (
  • To these phenomena one can add the acquisition of new DNA by horizontal transfer from another genome, which in addition to introducing new genetic information may upset the stability of a genome and trigger other compensating rearrangements. (
  • Insights into Functional Diversity in Neurospora This proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi. (
  • 1989 . Physical and genetic maps of the genome of the heterocyst-forming cyanobacterium Anabaena sp. (
  • We have created a concise database for BLAST using a Bio-Edit interface that can detect AR genetic determinants in bacterial genomes and can rapidly and easily discover putative new AR genetic determinants. (
  • This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. (
  • LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. (
  • The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. (
  • LS-BSR is a method to not only compare the complete genetic content between bacterial genomes, but can also be used for screening a set of genomes for a known set of genes. (
  • Apply the phylogenetic tool to construct phylogenetic trees and explain the relatedness of bacterial or pathogen strains 13. (
  • For decades, we used pulsed-field gel electrophoresis to differentiate bacterial strains," said Tara N. Palmore, M.D., the NIH Clinical Center's deputy hospital epidemiologist who led the outbreak investigation. (
  • This test produces a barcode-like pattern of bacterial DNA that shows whether strains are genetically similar. (
  • A genome-wide association study (GWAS) of BB resistance using a diverse panel of 285 rice accessions was performed to identify loci that are associated with resistance to nine Xoo strains from the Philippines, representative of eight global races. (
  • It is anticipated that validated simpler bacterial strains together with the modelling framework generated by BaSynthec will be used as generic biotechnological platforms to better control and exploit cell metabolism in industrial processes. (
  • NEW YORK (GenomeWeb) - Two independent research teams have cultured and characterized thousands of bacterial strains from fecal samples of healthy humans, generating reference genomes for hundreds of organisms not sequenced in the past. (
  • Participating ABCs sites then send patients' bacterial strains to CDC's StrepLab. (
  • Before genome sequencing, scientists only knew the type of group A strep strains, not if they were identical or near identical. (
  • B. contaminans clinical and LBP strains were analyzed by whole genome sequencing and bioinformatics resources. (
  • Then, in order to address the role of genomic variability on genome assembly quality, we selected a clade of closely related Escherichia coli strains and assessed how strain-level genomic variation leads to differences in genome assembly quality. (
  • NP303, C2, PS2A] Subobjective 2A: Extend comparative genomics methods to propagate the experimentally-supported genome annotate updates from targeted bacterial strains to related strains. (
  • Unfortunately, most of these approaches offer constrained opportunities to selectively remove individual bacterial strains (e.g., antibiotics and antimicrobial peptides) or require detailed knowledge of the genetics, metabolism, and physiology of each constituent of the population (e.g., selective growth conditions). (
  • The result is a group of highly-related bacterial strains that are changing genetically so fast that it is likely nearly impossible for the host's immune system to effectively track and eradicate it, says Garth Ehrlich, PhD, scientific director of the Center for Genomic Sciences and the paper's senior author. (
  • Using advanced high throughput bacterial DNA sequencing, Ehrlich and his colleagues investigated the tempo and relevance of horizontal gene transfer among nasopharyngeal strains of Streptococcus pneumoniae recovered from a child with chronic respiratory and middle ear infections. (
  • Comparing the original strain that started the infection with strains sequenced at its end, approximately 7.5 percent of the entire genome had changed. (
  • The genome size of Bacillus cereus strains varies from 5.5 to 6.3 Mb, and great diversity is seen in the number and organization of the chromosomes. (
  • The lack of reference strains and corresponding reference genomes of urogenital bacteria hinders research progress aimed at understanding how bacteria cause infection in the genital and urinary tracts. (
  • Each chromosome has been laid out horizontally and homologous blocks in each genome are shown as identically colored regions linked across genomes. (
  • The textual annotations and images that are provided by BASys can be generated in approximately 24 h for an average bacterial chromosome (5 Mb). (
  • The mouse cytomegalovirus genome was cloned and maintained as a 230 kb bacterial artificial chromosome (BAC) in E. coli . (
  • The MCMV genome was cloned as a bacterial artificial chromosome (BAC) in Escherichia coli and viral progeny were reconstituted by transfection of the MCMV BAC plasmid into eukaryotic cells that support virus production. (
  • They set out to chemically synthesise this genome from scratch as a continuous ring-shaped chromosome. (
  • Scientists at the J. Craig Venter Institute (JCVI), a genomics research facility, transplanted a bacterial chromosome from one type of bacteria into another, and have completely replaced an entire bacterial genome and its expression. (
  • 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. (
  • We first preface our research by discussing the benefits and challenges surrounding assembly of single chromosome bacterial genomes. (
  • Gene clustering plays an important role in the organization of the bacterial chromosome and several mechanisms have been proposed to explain its extent. (
  • Because there is only one origin of replication on bacterial circular chromosomes, replication generally terminates in a specific region of the chromosome. (
  • The full-length genome of human cytomegalovirus strain AD169 was cloned as an infectious bacterial artificial chromosome (BAC) plasmid, pAD/Cre. (
  • By mapping the sequencing reads to a reference genome, a subset of the paired-end reads will support the chromosomal rearrangement by spanning the break point between the two chromosomes with one of the paired-end reads mapping to chromosome A, while the respective other paired-end read maps to chromosome B (Fig. 1 ). (
  • It is the world's first fully computer-generated genome of a living organism, developed by scientists at ETH Zurich. (
  • But this is the first time that researchers have transplanted an entire genome into a living organism and shown that the cell can express the foreign DNA. (
  • In this experiment, the scientists at the J. Craig Venter Institute in Rockville, Maryland, used naturally-occurring DNA from a living organism, but they believe the transplantation techniques could be used on artificial, or man-made genomes, once they are developed. (
  • 1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. (
  • C. ethensis-2.0 is based on the genome of a well-studied and harmless freshwater bacterium, Caulobacter crescentus, which is a naturally occurring bacterium found in spring water, rivers and lakes around the globe. (
  • The genome of this bacterium contains 4,000 genes. (
  • With this method, they have built the first genome of a bacterium entirely designed by a computer algorithm. (
  • For the first time, the full genomes of the Lyme disease bacterium , Borrelia burgdorferi, were sequenced from deer ticks to reconstruct the history of this invading pathogen. (
  • This strategy can also elucidate gene regions that are essential for bacterial survival. (
  • The approach offers a rapid and effective way to identify core and essential genomic regions, eliminate non-essential regions and leads to greater understanding of bacterial evolution in a chaotic pool of gene loss and gene acquisition. (
  • Bacterial gene content variation during the course of evolution has been widely acknowledged and its pattern has been actively modeled in recent years. (
  • Gene truncation or gene pseudogenization also plays an important role in shaping bacterial genome content. (
  • 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. (
  • reported that genomes with truncated homologs might erroneously lead to false inferences of "gene gain" rather than multiple instances of "gene loss. (
  • 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. (
  • We identify 152 gene exchange networks containing 22,963 bacterial genomes. (
  • Mapping recent gene transfers across ~2700 genomes found overlapping ecological habitats to be a major factor in shaping HGT among microbes 12 . (
  • Analysis of mobile ARGs and their neighbouring mobilisation elements across 23,425 genomes found that phylogeny is another major variable shaping networks for resistance gene transfer 13 . (
  • 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. (
  • 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. (
  • 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. (
  • 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. (
  • As single-gene comparisons have largely given way to genome comparisons, phylogeny of bacterial genomes have improved in accuracy. (
  • Gene acquisition is an ongoing process in many bacterial genomes, contributing to adaptation and ecological diversification. (
  • We measured the extent of phylogenetic conflict and alien-gene acquisition within quartets of sequenced genomes. (
  • 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 ). (
  • 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. (
  • 2005). "Extensive DNA inversions in the B. fragilis genome control variable gene expression" (PDF). (
  • 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. (
  • 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. (
  • IMPORTANCE In obligate animal-bacterial symbioses, bacteria experience extreme patterns of genome evolution, including massive gene loss and rapid evolution. (
  • We found that the older symbiont has a highly reduced genome with low rates of mutation and gene loss. (
  • 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. (
  • 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. (
  • 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. (
  • The genome has a high coding density (97%) with many overlapping genes and reduced gene length. (
  • ARG-ANNOT (Antibiotic Resistance Gene-ANNOTation) is a new bioinformatic tool that was created to detect existing and putative new antibiotic resistance (AR) genes in bacterial genomes. (
  • 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. (
  • 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. (
  • The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. (
  • Single Molecule, Real-Time (SMRT) Sequencing offers affordable characterization of complete microbial genomes and populations. (
  • The obligate host-associated bacteria (with the exception of Candidatus Hodgkinia cicadicola) have short and low GC content genomes. (
  • Unlike with most obligate endosymbionts, genome reduction has not played a major role in the evolution of the Barbulanympha ectosymbionts. (
  • 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. (
  • 1995) Whole‐genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512. (
  • Third-generation sequencing technologies, which can yield longer multikilobase reads, have the potential to address limitations associated with genome assembly. (
  • The researchers, affiliated with the University of Maryland School of Medicine's Institute for Genome Sciences, analyzed genomic sequencing data available from the Human Genome Project, the 1,000 Genomes Project and The Cancer Genome Atlas. (
  • This course will cover the topic of Whole genome sequencing (WGS) of bacterial genomes which is becoming more and more relevant for the medical sector. (
  • To get the outbreak under control, Clinical Center staff collaborated with investigators at the National Human Genome Research Institute (NHGRI), also part of NIH, to use genome sequencing in the middle of this active hospital epidemic to learn how the microbe spread. (
  • We were already trying to develop clinical molecular diagnostics tools," Dr. Segre said, "We thought we could use genome sequencing to tell whether the K. pneumoniae from the first patient was the same strain as the one that infected the second patient. (
  • This webinar will discuss an optimized protocol for methyl-CpG binding domain sequencing (MBD-seq), which enables comprehensive, adequately powered, and cost-effective large-scale methylome-wide association studies (MWAS) of almost all 28 million CpG sites in the genome. (
  • One of the barriers to making whole genome sequencing a routine part of NHS care is the need for powerful computers and expertise to interpret the masses of complex data. (
  • The software is now being evaluated in hospitals in Oxford, Brighton and Leeds in a project led by Professor Derrick Crook, which in collaboration with parallel programmes at UCL and Cambridge University aims to develop whole genome sequencing as a routine tool for the diagnosis and control of infections within the NHS. (
  • third-generation sequencing might eventually yield a complete genome in a few hours. (
  • A significant achievement in the second decade of bacterial genome sequencing was the production of metagenomic data, which covers all DNA present in a sample. (
  • What's more, the sequencing technology used has led to the conclusion that some of these genomes are not fully decoded, and still contain errors. (
  • Excellent course with a wealth of information about tools and applications of whole genome sequencing. (
  • Adequate recommendations for the amount and types of sequencing data necessary to optimize the recovery of single chromosomes from bacterial sequencing projects do not exist. (
  • Broad estimates for coverage depths needed to recover complete bacterial genomes are present in the literature, but required sequencing depths across bacterial and archaeal phylogenies needed for high-quality assembly are not known. (
  • Furthermore, the capabilities of multiplexing (sequencing more than one sample simultaneously on one flow cell) with long-read sequencing platforms in order to recover complete bacterial chromosomes are poorly documented. (
  • Furthermore, we simulated long-read data based on standard multiplexed read profiles of a phylogenetically diverse array of bacteria and archaea and found that although limitations due to genome size and repeat complexity exist, long-read x8 multiplexed data are able to complete many bacterial genomes without the need for additional short-read sequencing. (
  • This research provides a series of criteria for why short-read sequencing and assembly often does not result in the generation of complete genome assemblies, and how multiplexed, long-read data can greatly reduce time and financial resources for many bacterial and archaeal sequencing projects. (
  • Researchers from the Sanger Institute have used whole genome sequencing to identify changes in the genome of nearly 4000 S. pneumoniae samples . (
  • The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. (
  • It is the first microbial genome-sequencing project in the state of Hawaiʻi. (
  • One, complete genome sequencing, is providing detailed blueprints of one or a few examples of each genome of interest. (
  • Whole genome sequencing (WGS) has been used successfully to understand outbreaks of infection in hospitals e.g. (
  • We will use the datasets to compare different methods for selecting samples for routine whole genome sequencing and inform the optimal method, taking into account cost-considerations, for detecting population level changes in strain types. (
  • The potential of bacterial whole-genome sequencing (WGS) to complement existing diagnostic infrastructures in clinical microbiology has been shown in proof-of-principle examples and extensively discussed. (
  • From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic. (
  • The advent of next generation sequencing has enabled the interrogation of the human genome and transcriptome with base pair resolution. (
  • A comprehensive understanding of the metabolic network at the system level is particularly important for both biotechnological and biomedical research and is now made possible by rapid advances in genome sequencing and functional genomics. (
  • Next-generation sequencing technologies have greatly reduced the cost for sequencing bacterial genomes and metagenomes and have increased the likelihood of rapid whole-bacterial-genome sequencing in clinical microbiology laboratories ( 1 ). (
  • Chaisson, M.J. & Pevzner, P.A. Short read fragment assembly of bacterial genomes. (
  • We demonstrate the utility of whole genome mapping (WGM) as a tool to identify mis-assemblies and to guide k-mer selection and higher quality de novo genome assembly of bacterial genomes. (
  • Multiple factors shape the diversification of the core genome. (
  • The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. (
  • The core genome was extracted from the output of Mugsy (Angiuoli & Salzberg 2010) and the phylogeny was inferred with FastTree2 (Price et al. (
  • Our findings represent the first characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. (
  • We show that the strong selective pressure acting on the function of persistent genes, in a permanent state of flux of genes in bacterial genomes, maintaining their size fairly constant, that drives persistent genes clustering. (
  • The task is considered to be a true tour de force: The chemically synthesised bacterial genome presented 11 years ago by the American genetics pioneer Craig Venter was the result of 10 years of work by 20 scientists, according to media reports. (
  • 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. (
  • In a study that twists nature's arm to gain clues into the varied functions of the bacterial genome, North Carolina State University researchers utilize a precision scalpel to excise target genomic regions that are expendable. (
  • In a paper published in Proceedings of the National Academy of Sciences , the NC State researchers harness the power of customized genome editing utilizing the system known as CRISPR-Cas. (
  • Advances in Bacterial Genome Engineering Conference aims to bring together leading academic scientists, researchers and research scholars to exchange and share their experiences and research results on all aspects of Advances in Bacterial Genome Engineering Conference. (
  • It also provides a premier interdisciplinary platform for researchers, practitioners, and educators to present and discuss the most recent innovations, trends, and concerns as well as practical challenges encountered and solutions adopted in the fields of Advances in Bacterial Genome Engineering Conference. (
  • 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. (
  • 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. (
  • 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. (
  • Researchers have developed several theories to explain the patterns of genome size evolution amongst bacteria. (
  • 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 . (
  • Naturally, the rewritten genome can contain only information that the researchers have actually understood. (
  • This enables researchers to choose the optimal strategy for completely decoding even the genomes of bacteria with very complex DNA. (
  • Replacing a Genome Boosts Race to Develop Designer Bugs: Study ( Researchers transformed one bacterial s. (
  • The researchers took the genome of a simple, one-celled organism called Mycoplasma mycoides and transplanted it into a close relative, M. capricolum. (
  • The researchers acknowledged that they were not sure how the one genome displaced the other. (
  • 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. (
  • 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. (
  • 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. (
  • 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. (
  • 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. (
  • A genome alignment of eight Yersinia isolates. (
  • Three individual amplified genomes were obtained for Porphyromonas gingivalis , a human pathogen whose genome had previously only been sequenced from cultured isolates from patients. (
  • Escherichia coli is the most common cause of UTI ( 16 ), and there are many dozens of available isolates and genomes of E. coli available for study. (
  • Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes. (
  • Genome transplantation (GT) allows the installation of purified chromosomes into recipient cells, causing the resulting organisms to adopt the genotype and the phenotype conferred by the donor cells. (
  • 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. (
  • Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. (
  • The general trends of bacterial evolution indicate that bacteria started as free-living organisms. (
  • 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. (
  • Deoxyribonucleic acid (DNA) double‐strand breaks, which are caused by many factors such as chemical treatments, radiations and, often, biological factors, are lethal events in organisms carrying DNA as their genome, which include bacteria. (
  • However, genomes harbor two very different categories of genes: those genes present in a majority of organisms - persistent genes - and those present in very few organisms - rare genes. (
  • For this purpose, we have devised a strategy enabling us to resolve phylogenetic clusters of bacteria by comparing their genome structures. (
  • We conclude that large-scale genome structure can be a sensitive indicator of phylogenetic relationships and that, therefore, I- Ceu I-based genomic mapping is an efficient tool for probing the phylogenetic status of bacteria. (
  • The physical structure of bacterial genomes as revealed by endonuclease mapping, on the other hand, could provide an alternative parameter to be employed in phylogenetic studies ( 26 , 29 ). (
  • The claim that the history of bacteria might be more faithfully depicted as a net than as a tree ( 7 ) relies upon the postulate that the substantial incidence of acquired DNA within genomes is the basis for findings of phylogenetic incongruence among genes. (
  • This image depicts a phylogenetic tree of over 3,800 high quality and non-redundant bacterial genomes. (
  • Phylogenetic analysis using these "comparative-genome markers" (CGMs) produced a highly unusual phylogeny with a complete absence of secondary branches. (
  • These comparative-genome marker (CGM) SNPs represent a distinct class of phylogenetic markers that has unique advantages. (
  • Genome size and GC content are weakly correlated in bacteria and archaea. (
  • Projects such as the Genomic Encyclopedia of Bacteria and Archaea (GEBA) intend to add more genomes. (
  • For the genomes of archaea see list of sequenced archaeal genomes. (
  • Defining a Pan-Genome for Antarctic Archaea Some Antarctic lakes have salinities 10 times that of seawater. (
  • Dr. Segre had been working with the Clinical Center's Clinical Microbiology Department to study the evolution of bacterial antibiotic resistance when she heard about the outbreak. (
  • 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. (
  • This book imparts fundamental knowledge on the structure, organization, and evolution of bacterial genomes. (
  • A team led by Steven L. Salzberg of TIGR and including Eisen of UC Berkeley s Center for Integrative Genomics published their discovery in the most recent issue of the open access journal Genome Biology, published this week. (
  • Boris Vinatzer, assistant professor of plant pathology, physiology, and weed science in the College of Agriculture and Life Sciences, has received a $1 million, five-year Faculty Early Career Development (CAREER) award from the National Science Foundation (NSF) to investigate the pathogen that causes bacterial speck disease of tomatoes and to develop a new undergraduate course in microbial genomics. (
  • The value and power of comparative genomics and proteomics, bioinformatics, microarrays, and knockout animal models in analyzing genomes, bacteria-host interactions and disease are demonstrated. (
  • At this early stage in comparative genomics, the main generalizations that are emerging concerning rearrangements in bacterial genome organization are as follows. (
  • This chapter summarizes the recent findings of bacterial genomics and comments on the themes and trends which are emerging. (
  • Several applications of single-cell genomics to the infectious disease field are developing, such as tracking pathogen persistence and transmission, targeted and untargeted pathogen-genome recovery, and the identification of novel bacteria that have pathogenic potential from the human microbiome. (
  • In this application of single-cell genomics, roughly 400 amplified genomes of interest from 25 different genera from the indoor environment of a health care facility were captured using an automated process. (
  • Shown are the annotation progress monitor for two genome annotation projects ( E.coli and C.trachomatis ) in various states of completion, a full-scale and expanded graphical genome map for E.coli and a sample annotation report. (
  • The approach allows mutagenesis of the MCMV genome as one entity in E. coli using standard procedures, and the highly efficient generation of viral mutants. (
  • Utilize the tools for Salmonella and E.coli typing, plasmid replicon detection and plasmid typing in real cases of other bacterial and pathogen genomes. (
  • Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in ~60h using 16 processors. (
  • 2010) . This phylogeny contains labels that can be used to identify specific genomes in Figures 2 and 3. (
  • Addgene: RNA-guided editing of bacterial genomes using CRISPR-Cas systems. (
  • Furthermore, he introduces the adaption of the CRISPR-Cas system into a potent molecular biology tool, which is used heavily for genome editing. (
  • 1999) Global transposon mutagenesis and a minimal Mycoplasma genome. (
  • The enhanced Mycoplasma mycoides genome was added to a test-tube of M. capricolum, and the contents of the tube were exposed to an antibiotic. (
  • In 2010, we chemically synthesized the 1078 Kb Mycoplasma mycoides genome and transplanted it into a recipient cell cytoplasm to create a 'synthetic cell', JCVI-syn1.0 (Science, 329, 52-56, 2010). (
  • Aligning against bacterial genomes is a good quality control routine, especially when considering the prevalence of laboratory contaminants such as Mycoplasma . (
  • 1999) Comparative genomes of Chlamydia pneumoniae and C. trachomatis. (
  • It also supports a comparative analysis with the annotated genomes maintained in the SEED environment. (
  • Beat Christen, Professor of Experimental Systems Biology at ETH Zurich, and his brother, Matthias Christen, a chemist at ETH Zurich, took the minimal genome of C. crescentus as a starting point. (
  • Their motivation was twofold: one, to make it much easier to produce genomes, and two, to address fundamental questions of biology. (
  • Analysis of the genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of Wolbachia. (
  • 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. (
  • 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. (
  • In contrast, the younger symbiont has a larger genome that exhibits higher mutation rates and varies dramatically in the retention of genes related to cell wall biogenesis, cellular replication, and stress response. (
  • It is our working model of a minimal cell, the result of a compromise between small genome size and an experimentally useful replication rate. (
  • Biofilm formation is the principal reason for bacterial stability in CF patients' respiratory tracts. (
  • Thus, temporal changes in bacterial communities (community stability) are also an important component of microbiome variation. (
  • Here, we report a genome-wide RNA interference screen to identify host factors required for intracellular bacterial pathogenesis. (
  • 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. (
  • 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. (
  • This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly. (
  • Given these findings, incompatibility of phylogenies within and among bacterial phyla based on different genes has routinely been ascribed to LGT ( 3 - 10 ). (
  • Bacterial Genomes and Infectious Diseases presents major findings about bacterial genomes and their impact on strategy and approach for investigating mechanisms of pathogenesis of infectious diseases. (
  • 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. (
  • The well-annotated genome of Salmonella typhimurium LT2 is used as an example to demonstrate the applicability of the method. (
  • The new genome, sequenced at the California-based DOE Joint Genome Institute (JGI) and published in the Journal of Bacteriology, lays the foundation for future research to examine the little understood mechanisms behind the production of methylmercury. (
  • This book provides an in-depth analysis of the mechanisms and biological consequences of genome rearrangements in bacteria. (
  • Each chapter examines the mechanisms involved in genome rearrangements and the direct biological consequences of these events. (
  • Studies applying this approach to additional cancer genome projects could be fruitful, leading us to a better understanding of the mechanisms of cancer. (
  • The relationship between life-styles of bacteria and genome size raises questions as to the mechanisms of bacterial genome evolution. (
  • Therefore, the molecular mechanisms and the evolutionary pressures shaping the bacterial responses to subinhibitory concentrations of antibiotics merit to be extensively studied. (
  • Therefore, studies on bacterial evolution are of increasing interest to understand the basic mechanisms of evolution. (
  • 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. (
  • 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. (
  • We conclude that while symbiotic bacteria evolve toward tiny genomes, this process is shaped by different selection intensities that may reflect the different ages and metabolic roles of symbiont types. (
  • The bacterial essence of tiny symbiont genomes. (
  • A strategy for cloning and mutagenesis of an infectious herpesvirus genome is described. (
  • The described approach should be generally applicable to the mutagenesis of genomes of other large DNA viruses. (
  • 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. (
  • Cancer is a disease driven by the accumulation of genomic alterations, including the integration of exogenous DNA into the human somatic genome. (
  • Dynamics of genome rearrangement in bacterial populations. (
  • 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. (
  • It has also become evident that subinhibitory concentrations of antibiotics, which pollute all kind of terrestrial and aquatic environments, have a non-negligible effect on the evolution of antibiotic resistance in bacterial populations. (
  • 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. (
  • 1 Bacterial samples collected over the course of an outbreak might only be "near" identical because bacteria pick up genome mutations over time. (
  • In bacterial genomes, mutations from GC to adenosine-thymine (AT) are more common than mutations from AT to GC. (
  • By comparing the genomes of S. pneumoniae samples known to be resistant to beta lactam antibiotics with those that responded to treatment, they identified 50 regions of the genome in which mutations appeared to confer antibiotic resistance. (
  • In addition, the experts have made analyses of the repeat complexity of almost 10,000 bacterial genomes freely available. (
  • Together, these technologies are providing insights into the dynamics of genome plasticity that are both detailed and broad. (
  • Outbreaks are caused by spreading the same bacterial strain from person-to-person. (
  • The resulting "cluster detection tool" accurately and efficiently identifies outbreaks of the same bacterial strain. (
  • Search for details on specific genomes by organism name and strain. (
  • Employing a strategy similar to that used to create the PRV BAC, we cloned the full-length genome of HCMV strain AD169 into a BAC vector to generate pAD/Cre. (
  • The 235-kb genomes of both human and mouse CMV are the largest genomes of mammalian DNA viruses. (
  • The sequencers of other genomes, especially the human genome, were more careful to eliminate any endosymbionts or parasites, he said, but secrets may still lie hidden inside these other genomes. (
  • There is a lot of unexplored stuff out there in the genome databases - it s certainly not out of the question that other genomes have these lurking endosymbionts," Eisen said. (
  • In particular, we investigated the structure of ectosymbiont genomes, which, in contrast to those of endosymbionts, has been little studied to date, and tested the hypothesis that these ectosymbionts fix nitrogen. (
  • Correct reconstitution of the viral genome can only be verified after growth and isolation of the mutant virus. (
  • Construction of the mutant genome is completely independent of the biological fitness of the mutant virus and the recombinant genome can be characterized and controlled prior to reconstitution of viral progeny. (
  • In the earlier HCMV BACs, portions of the viral genome, Us2 to Us6 ( 3 ) or Us1 to Us12 ( 14 ), were deleted to accommodate insertion of the BAC vector. (
  • 2000) A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. (
  • By comparing B. burgdorferi genomes collected from different areas and over a 30-year period, the team built an evolutionary tree and reconstructed the history of the pathogen's spread. (
  • Earlier studies of the evolutionary history of B. burgdorferi have relied upon short DNA markers rather than full genomes. (
  • These may bring about death, restoration or recombinational/mutational changes in the genome. (
  • When you use pinpointed targeting of a specific portion of the genome, you expect a smaller deletion to occur. (
  • We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. (
  • They found that bacterial DNA was more likely to integrate in the genome in tumor samples than in normal, healthy somatic cells. (
  • LGT from bacteria to animals was only described recently, and it is exciting to find that such transfers can be found in the genome of human somatic cells and particularly in cancer genomes,' says Julie Dunning Hotopp of the University of Maryland School of Medicine and lead author of the paper. (
  • Somatic genome variations occur during normal development and ageing, contribute to pathogenesis and are the cause of diseases such as cancer, as well as autoimmune, brain and other disorders. (