Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.Genome Size: The amount of DNA (or RNA) in one copy of a genome.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Genome, Protozoan: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Genome, Helminth: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Genome, Plastid: The genetic complement of PLASTIDS as represented in their DNA.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Synteny: The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Gene Order: The sequential location of genes on a chromosome.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Genetic Variation: Genotypic differences observed among individuals in a population.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Genes, Viral: The functional hereditary units of VIRUSES.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Viral Proteins: Proteins found in any species of virus.Gene Transfer, Horizontal: The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Pseudogenes: Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.Genes, Bacterial: The functional hereditary units of BACTERIA.Polyploidy: The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Genes, Plant: The functional hereditary units of PLANTS.Genome, Microbial: The genetic complement of a microorganism as represented in its DNA or in some microorganisms its RNA.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Genome Components: The parts of a GENOME sequence that are involved with the different functions or properties of genomes as a whole as opposed to those of individual GENES.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Oryza sativa: Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.Chromosomes: In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Bacterial Proteins: Proteins found in any species of bacterium.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.DNA Replication: The process by which a DNA molecule is duplicated.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Gene Dosage: The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Bacteriophages: Viruses whose hosts are bacterial cells.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Terminal Repeat Sequences: Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Prophages: Genomes of temperate BACTERIOPHAGES integrated into the DNA of their bacterial host cell. The prophages can be duplicated for many cell generations until some stimulus induces its activation and virulence.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.INDEL Mutation: A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Genes, Mitochondrial: Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.DNA, Chloroplast: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Comparative Genomic Hybridization: A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.Vertebrates: Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.Symbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Interspersed Repetitive Sequences: Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Virulence: The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.Inverted Repeat Sequences: Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.RNA Viruses: Viruses whose genetic material is RNA.Plastids: Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.Virus Integration: Insertion of viral DNA into host-cell DNA. This includes integration of phage DNA into bacterial DNA; (LYSOGENY); to form a PROPHAGE or integration of retroviral DNA into cellular DNA to form a PROVIRUS.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.Genes, Archaeal: The functional genetic units of ARCHAEA.Sorghum: A plant genus of the family POACEAE. The grain is used for FOOD and for ANIMAL FEED. This should not be confused with KAFFIR LIME or with KEFIR milk product.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.DNA, Circular: Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.Chromosomes, Human: Very long DNA molecules and associated proteins, HISTONES, and non-histone chromosomal proteins (CHROMOSOMAL PROTEINS, NON-HISTONE). Normally 46 chromosomes, including two sex chromosomes are found in the nucleus of human cells. They carry the hereditary information of the individual.Short Interspersed Nucleotide Elements: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.Genetic Engineering: Directed modification of the gene complement of a living organism by such techniques as altering the DNA, substituting genetic material by means of a virus, transplanting whole nuclei, transplanting cell hybrids, etc.Segmental Duplications, Genomic: Low-copy (2-50) repetitive DNA elements that are highly homologous and range in size from 1000 to 400,000 base pairs.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.GC Rich Sequence: A nucleic acid sequence that contains an above average number of GUANINE and CYTOSINE bases.Mammals: Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Hybridization, Genetic: The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Pan troglodytes: The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.Eukaryota: One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.Archaea: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.Genes, Duplicate: Two identical genes showing the same phenotypic action but localized in different regions of a chromosome or on different chromosomes. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Angiosperms: Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.Tetraodontiformes: A small order of primarily marine fish containing 340 species. Most have a rotund or box-like shape. TETRODOTOXIN is found in their liver and ovaries.DNA Copy Number Variations: Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Diploidy: The chromosomal constitution of cells, in which each type of CHROMOSOME is represented twice. Symbol: 2N or 2X.Mutation Rate: The number of mutations that occur in a specific sequence, GENE, or GENOME over a specified period of time such as years, CELL DIVISIONS, or generations.Defective Viruses: Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.Chromosome Inversion: An aberration in which a chromosomal segment is deleted and reinserted in the same place but turned 180 degrees from its original orientation, so that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome.Untranslated Regions: The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.Crosses, Genetic: Deliberate breeding of two different individuals that results in offspring that carry part of the genetic material of each parent. The parent organisms must be genetically compatible and may be from different varieties or closely related species.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Likelihood Functions: Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.Tandem Repeat Sequences: Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).Proteome: The protein complement of an organism coded for by its genome.Genomic Islands: Distinct units in some bacterial, bacteriophage or plasmid GENOMES that are types of MOBILE GENETIC ELEMENTS. Encoded in them are a variety of fitness conferring genes, such as VIRULENCE FACTORS (in "pathogenicity islands or islets"), ANTIBIOTIC RESISTANCE genes, or genes required for SYMBIOSIS (in "symbiosis islands or islets"). They range in size from 10 - 500 kilobases, and their GC CONTENT and CODON usage differ from the rest of the genome. They typically contain an INTEGRASE gene, although in some cases this gene has been deleted resulting in "anchored genomic islands".Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.DNA Repair: The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.Plant Diseases: Diseases of plants.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Zea mays: A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Genetic Techniques: Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.Alu Elements: The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.DNA, Algal: Deoxyribonucleic acid that makes up the genetic material of algae.Genes, Overlapping: Genes whose nucleotide sequences overlap to some degree. The overlapped sequences may involve structural or regulatory genes of eukaryotic or prokaryotic cells.Chromosomes, Mammalian: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of MAMMALS.Endogenous Retroviruses: Retroviruses that have integrated into the germline (PROVIRUSES) that have lost infectious capability but retained the capability to transpose.Genome-Wide Association Study: An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.Computer Graphics: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.Siphoviridae: A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by long, non-contractile tails.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.

The Saccharomyces cerevisiae ETH1 gene, an inducible homolog of exonuclease III that provides resistance to DNA-damaging agents and limits spontaneous mutagenesis. (1/8283)

The recently sequenced Saccharomyces cerevisiae genome was searched for a gene with homology to the gene encoding the major human AP endonuclease, a component of the highly conserved DNA base excision repair pathway. An open reading frame was found to encode a putative protein (34% identical to the Schizosaccharomyces pombe eth1(+) [open reading frame SPBC3D6.10] gene product) with a 347-residue segment homologous to the exonuclease III family of AP endonucleases. Synthesis of mRNA from ETH1 in wild-type cells was induced sixfold relative to that in untreated cells after exposure to the alkylating agent methyl methanesulfonate (MMS). To investigate the function of ETH1, deletions of the open reading frame were made in a wild-type strain and a strain deficient in the known yeast AP endonuclease encoded by APN1. eth1 strains were not more sensitive to killing by MMS, hydrogen peroxide, or phleomycin D1, whereas apn1 strains were approximately 3-fold more sensitive to MMS and approximately 10-fold more sensitive to hydrogen peroxide than was the wild type. Double-mutant strains (apn1 eth1) were approximately 15-fold more sensitive to MMS and approximately 2- to 3-fold more sensitive to hydrogen peroxide and phleomycin D1 than were apn1 strains. Elimination of ETH1 in apn1 strains also increased spontaneous mutation rates 9- or 31-fold compared to the wild type as determined by reversion to adenine or lysine prototrophy, respectively. Transformation of apn1 eth1 cells with an expression vector containing ETH1 reversed the hypersensitivity to MMS and limited the rate of spontaneous mutagenesis. Expression of ETH1 in a dut-1 xthA3 Escherichia coli strain demonstrated that the gene product functionally complements the missing AP endonuclease activity. Thus, in apn1 cells where the major AP endonuclease activity is missing, ETH1 offers an alternate capacity for repair of spontaneous or induced damage to DNA that is normally repaired by Apn1 protein.  (+info)

hnRNP C and polypyrimidine tract-binding protein specifically interact with the pyrimidine-rich region within the 3'NTR of the HCV RNA genome. (2/8283)

Like other members of the Flaviviridae family, the 3' non-translated region (NTR) of the hepatitis C virus (HCV) is believed to function in the initiation and regulation of viral RNA replication by interacting with components of the viral replicase complex. To inves-tigate the possibility that host components may also participate in this process, we used UV cross-linking assays to determine if any cellular proteins could bind specifically to the 3'NTR RNA. We demonstrate the specific interaction of two host proteins with the extensive pyrimidine-rich region within the HCV 3'NTR. One host protein migrates as a doublet with a molecular weight of 57 kDa and is immunoreactive with antisera specific for polypyrimidine tract-binding protein (PTB), and the other protein (35 kDa) is recognized by a monoclonal antibody specific for heterogeneous nuclear ribonucleoprotein C (hnRNP C). These results suggest that recognition of the large pyrimidine-rich region by PTB and hnRNP C may play a role in the initiation and/or regulation of HCV RNA replication.  (+info)

Comparison of synonymous codon distribution patterns of bacteriophage and host genomes. (3/8283)

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)

Complete genomic sequence of the lytic bacteriophage DT1 of Streptococcus thermophilus. (4/8283)

Streptococcus thermophilus lytic bacteriophage DT1, isolated from a mozzarella whey, was characterized at the microbiological and molecular levels. Phage DT1 had an isometric head of 60 nm and a noncontractile tail of 260 x 8 nm, two major structural proteins of 26 and 32 kDa, and a linear double-stranded DNA genome with cohesive ends at its extremities. The host range of phage DT1 was limited to 5 of the 21 S. thermophilus strains tested. Using S. thermophilus SMQ-301 as a host, phage DT1 had a burst size of 276 +/- 36 and a latent period of 25 min. The genome of phage DT1 contained 34,820 bp with a GC content of 39.1%. Forty-six open reading frames (ORFs) of more than 40 codons were found and putative functions were assigned to 20 ORFs, mostly in the late region of phage DT1. Comparative genomic analysis of DT1 with the completely sequenced S. thermophilus temperate phage O1205 revealed two large homologous regions interspersed by two heterologous segments. The homologous regions consisted of the early replication genes, the late morphogenesis genes, and the lysis cassette. The divergent segments contained the DNA packaging machinery, the major structural proteins, and remnants of a lysogeny module.  (+info)

Interferon-induced human MxA GTPase blocks nuclear import of Thogoto virus nucleocapsids. (5/8283)

Interferon-induced human MxA protein belongs to the dynamin superfamily of large GTPases. It exhibits antiviral activity against a variety of RNA viruses, including Thogoto virus, an influenza virus-like orthomyxovirus transmitted by ticks. Here, we report that MxA blocks the transport of Thogoto virus nucleocapsids into the nucleus, thereby preventing transcription of the viral genome. This interaction can be abolished by a mAb that neutralizes the antiviral activity of MxA. Our results reveal an antiviral mechanism whereby an interferon-induced protein traps the incoming virus and interferes with proper transport of the viral genome to its ultimate target compartment within the infected cell.  (+info)

Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. (6/8283)

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)

Expression of alfalfa mosaic virus coat protein in tobacco mosaic virus (TMV) deficient in the production of its native coat protein supports long-distance movement of a chimeric TMV. (7/8283)

Alfalfa mosaic virus (AlMV) coat protein is involved in systemic infection of host plants, and a specific mutation in this gene prevents the virus from moving into the upper uninoculated leaves. The coat protein also is required for different viral functions during early and late infection. To study the role of the coat protein in long-distance movement of AlMV independent of other vital functions during virus infection, we cloned the gene encoding the coat protein of AlMV into a tobacco mosaic virus (TMV)-based vector Av. This vector is deficient in long-distance movement and is limited to locally inoculated leaves because of the lack of native TMV coat protein. Expression of AlMV coat protein, directed by the subgenomic promoter of TMV coat protein in Av, supported systemic infection with the chimeric virus in Nicotiana benthamiana, Nicotiana tabacum MD609, and Spinacia oleracea. The host range of TMV was extended to include spinach as a permissive host. Here we report the alteration of a host range by incorporating genetic determinants from another virus.  (+info)

Sequence heterogeneity within three different regions of the hepatitis G virus genome. (8/8283)

Two sets of primers derived from the 5'-terminal region and the NS5 region of the hepatitis G virus (HGV) genome were used to amplify PCR fragments from serum specimens obtained from different parts of the world. All PCR fragments from the 5'-terminal region (5'-PCR, n = 56) and from the NS5 region (NS5-PCR, n = 85) were sequenced and compared to corresponding published HGV sequences. The range of nucleotide sequence similarity varied from 74 and 78% to 100% for 5'-PCR and NS5-PCR fragments, respectively. Additionally, five overlapping PCR fragments comprising an approximately 2.0-kb structural region of the HGV genome were sequenced from each of five sera obtained from three United States residents. These sequences were compared to 20 published sequences comprising the same region of the HGV genome. Nucleotide and deduced amino acid sequences obtained from different individuals were homologous from 82.9 to 93. 6% and from 90.4 to 99.0%, respectively. Sequences obtained from follow-up specimens were almost identical. Comparative analysis of deduced amino acid sequences of the HGV structural proteins and hepatitis C virus (HCV) structural proteins combined with an analysis of predicted secondary structures and hydrophobic profiles allowed prediction of processing sites within the HGV structural proteins. A phylogenetic sequence analysis performed on the 2.0-kb structural region supports the existence of three previously identified HGV genetic groups. However, phylogenetic analysis performed on only small DNA fragments yielded inconsistent genetic grouping and failed to confirm the existence of genetic groups. Thus, in contrast to HCV where almost any region can be used for genotyping, only large or carefully selected genome fragments can be used to identify consistent HGV genetic groups.  (+info)

TY - BOOK. T1 - Viral genome replication. AU - Cameron, Craig Eugene. AU - Raney, Kevin D.. AU - Götte, Matthias. PY - 2009/1/1. Y1 - 2009/1/1. N2 - Provides the first comprehensive review of viral genome replication strategies, emphasizing not only pathways and regulation but also the structure-function, mechanism, and inhibition of proteins and enzymes required for this process Currently, there is no single source that permits comparison of the factors, elements, enzymes and/or mechanisms employed by different classes of viruses for genome replication. As a result, we (and our students) often restrict our focus to our particular system, missing out on the opportunity to define unifying themes in viral genome replication or benefit from the advances in other systems. For example, extraordinary biological and experimental paradigms that have been established over the past five years for the DNA replication systems of bacteriophage T4 and T7 will likely be of great value to anyone interested in ...
Read "Analysis of the full-length genome sequence of papaya lethal yellowing virus (PLYV), determined by deep sequencing, confirms its classification in the genus Sobemovirus, Archives of Virology" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
There was a thread on this less than a month ago on the bioperl list. CHeck their archives around Feb 14th for a thread titled: [Bioperl-l] Fetching genomic sequences based on HUGO names or GeneIDs There are example scripts and docs available for this kind of activity now via their wiki. hjm On Thursday 02 March 2006 10:45, Ryan Golhar wrote: , Thanks for all your responses, but maybe I need to clarify what Im , trying to do. I have a list of accession #s for genes. I want to get , the full-length genomic sequences (including exons and introns). , , I can get the chromosome and genomic coordinates using NCBIs eutils , efetch method, however Im not sure how to retrieve part of a sequence. , I dont see information on NCBIs eutils documentation and was wondering , if anyone here knew. , , In other words, say I have a gene that occurs on human chromosome 1. , The accession # of chr1 is NC_000001, and I have the genomic , coordinates, say 100 to 5000 on the positive strand. Without retrieving , ...
Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis. Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental
When viruses cross species, serial transmission may lead to the selection for mutations that confer improved replication or transmission in the new host. Identifying such mutations in human viruses is extremely difficult: we cannot conduct the appropriate experiments in humans, and often do not have viral isolates spanning the time from spillover through prolonged circulation. The 2013-2016 outbreak of Ebola virus in West Africa is unique because viral genome sequences were obtained early and throughout the epidemic. The results of two new studies (link to paper one, link to paper two) suggest that some of the observed mutations increase infectivity for human cells. The impact of these mutations on infection of humans, and their role in the West African outbreak, remain unknown.. Many mutations have been identified among the many hundreds of genome sequences obtained during the recent Ebola virus epidemic. One stands out: a mutation that leads to a single amino acid change in the viral ...
Clearly, its time to develop a sophisticated global system to catalog viruses and detect emerging diseases throughout the world. One such system, now being proposed, would routinely screen human blood to identify every human virus and monitor any new viruses that may appear in humans. The viral genomes would be collected in a database called the "human virome.". The proposal goes something like this: Scientists would collect blood from hospitals and labs weekly. Then they would extract viruses from it and sequence the viral genomes. Once a database of viruses is constructed, researchers could use it to screen for new viruses as they appear in the population.. Having a database of genome sequences could speed the characterization of emerging viruses. For instance, genomic information about coronaviruses, collected over many years, helped researchers identify the SARS genome in a matter of weeks. "We want to know whats actually going around, and that is something that nobody knows," says ...
... shows a graphical map of the genes and proteins of HIV-1, including the breakpoints on reference strain HXB2.
Our virulent BAC cloned MDV genome that generates a fully virulent virus will be passed in cell culture, which is known to attenuate the virus. At every 10 passages, the viral population will be used to challenge chickens to determine the amount of MD incidence. This will continue until the viral population is completely avirulent. Preceeding populations will have their viral genome purified and sequenced using next generation sequencers (e.g., Illumina GA or ABI SOLiD) to identify polymorphisms in the genome as well as the allele frequency. In addition, RNAs from the same sequenced populations will be sequenced, which when combined with the genomic sequence information, will confirm polymorphisms and reveal changes in viral gene transcription pattern. Following analysis, key genetic changes will be introduced into the virulent viral genome to address whether the polymorphisms do promote attenuation. ...
One of the more futuristic-sounding ideas for curing HIV involves removing the genome of the virus from the genome of the cells into which it has ...
TORONTO, June 15, 2015- Researchers sequence and assemble first full genome of a living organism using technology the size of smartphone.
Sequence analysis of the 3′ termini of RSV antigenome and genome RNA isolated from RSV infected cells.(A) Putative structures formed by the terminal sequences
The more we get to know about the past, the more obvious it becomes that old Darwinian assumptions have to be discarded. Many species seem to have resisted change for far longer than was thought. A good illustration of this is in a paper recently published in the journal Nature that reports on the full genome sequence of an ancient horse ...
Does anyone have any informations on the positive and negative regulation of HIV genome? I would greatly appreciate any informations send to ptran at po-box.mcgill.ca thank ...
The construct was inserted on the minus strand of the genome. The gene in which ... The construct was inserted on the minus strand of the genome. The gene in which the insertion occurred is also on the minus strand. ...
In this communication, we report a novel strategy for the genetic manipulation of large viral DNA genomes. In a single step we cloned an infectious cytomegalovirus DNA as a bacterial artificial chromosome in E. coli and reconstituted virus progeny after transfection of the BAC plasmid into eukaryotic cells. This approach makes the CMV genome accessible to the genetic techniques established for E. coli. As an example for the power of the mutagenesis procedures, we performed a targeted insertion of four nucleotides into the 230-kb MCMV genome. In principle, any mutation (point mutations, insertions, and deletions) in any region of the genome can now be introduced using the described mutagenesis procedure. Moreover, other procedures, for example a random transposon mutagenesis of the CMV genome are conceivable. Multiple mutations can be introduced in consecutive rounds of mutagenesis without the need to reconstitute infectious viral intermediates. Construction of revertant genomes can be easily ...
387440791 - EP 0832191 A4 2000-11-15 - RECOMBINANT VIRAL NUCLEIC ACIDS - [origin: WO9640867A1] The present invention relates to a recombinant viral nucleic acid selected from a (+) sense, single stranded RNA virus possessing a native subgenomic promoter encoding for a first viral subgenomic promoter, a nucleic acid sequence that codes for a viral coat protein whose transcription is regulated by the first viral subgenomic promoter, a second viral subgenomic promoter and a second nucleic acid sequence whose transcription is regulated by the second viral subgenomic promoter. The first and second viral subgenomic promoters of the recombinant viral nucleic acid do not have homologous sequences relative to each other. The recombinant viral nucleic acid provides the particular advantage that it systematically transcribes the second nucleic acid in the host. Host organisms encompassed by the present invention include procaryotes and eucaryotes, particularly animals and plants. The present invention also relates
The construction of cDNA clones encoding large-size RNA molecules of biological interest, like coronavirus genomes, which are among the largest mature RNA molecules known to biology, has been hampered by the instability of those cDNAs in bacteria. Herein, we show that the application of two strategi …
Given a recent increase in the number of bacteriophage genome sequenced- Nathan ( @NathanMB3) has updated the all-v-all comparison with more genomes (~5500 in total).Image at bottom of page. After reading the recent paper "MASH:fast genome and metagenome distance and estimation using MinHash" and meeting Nathan Brown at the University of Leicester, we discussed using MASH for identification of phage genomes and comparison thereof. The authors of the genome biology paper had included viruses in the microbial comparison in Figure 3 . Here we just focused on bacteriophage genomes.. For rapid identification of phage genomes we first constructed a database of phage genomes that were public. This included all phage genomes from the NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/all.fna.tar.gz) , which were then filtered to remove eukaryotic viruses. In addition phage genomes were collected from the phagesdb.org website. A sketch was made for all of these phages and collated, the mash database of ...
Generation of wt genomes by excision of the BAC vector from the MCMV BAC genome.After transfection of the MCMV BAC plasmid into eukaryotic cells we expected homologous recombination via the duplicated sequences leading to excision of the vector sequences and generation of a wt genome (see Fig. 2 and Fig. 3A, maps 4 and 5). During construction of the original MCMV BAC plasmid pSM3 we had observed that overlength genomes are not stable in cells (22), suggesting that overlength genomes are poorly packaged into viral capsids. Similar observations have been made for other DNA viruses. An overlength of more than 5% over the adenovirus wt genome leads to unstable genomes (2), and Epstein-Barr virus preferentially packages genomes within a very narrow size range (3). Thus, we expected that even when rare recombination events occur at the created target site, preferential packaging of unit length genomes should lead to an accumulation of viruses with the wt genome.. For reconstitution of virus progeny ...
Adeno-associated virus 2 ATCC ® 37215™ Designation: pAV1 TypeStrain=False Application: Contains the complete viral genome for use in site-specific mutagenesis.
Adeno-associated virus 2 ATCC ® 37215™ Designation: pAV1 TypeStrain=False Application: Contains the complete viral genome for use in site-specific mutagenesis.
Read "Complete genomic sequence of a Tobacco rattle virus isolate from Michigan-grown potatoes, Archives of Virology" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Hi all, I am looking for a way or a tool to map all the GC rich (of given percentage say, 60% or 70% GC) short stretches of nucleotides anywhere between 20-80 base pairs in Bacteriophage T4 and other Phage genomes.I could not find such a tool at NCBI website. I highly appreciate your help. Thank you so much Kiran ...
VIROME: Goal is to characterize the whole viral population. (Lambda control gave quantitative recovery.) 10^10 phage per gram of stool! Circular contigs (genomes?) all about 5-6 kb. Linear ones very diverse lengths. 7000 new virus genomes! 19-785 per individual sample. Lots of unknown! No contigs of eukaryotic viruses at all, but bits of eukaryotic viral genomes in phage genomes. He thinks there has been lots of misidentification - what appears to be DNA indicating presence of a eukaryotic virus is really jsut a bit of phage genome. See CRISPR system used to compete with other phage (I forget what CRISPR does ...
In a recent article, I go into more detail about ERVs and why the evolutionary story is completely backwards when it comes to explaining their presence in the genome. (4) In brief, these elements are clearly part of the original created genomic blueprint for each creature and not the result of numerous viral infestations over eons of time. As I and several other creationist researchers have proposed, its far more likely that ERVs were part of Gods original genomic blueprint for different kinds of animals and humans, and that external viral genomes were derived from human and animal ERVs only after God cursed the creation for mans sin. This began a process of degeneration and corruption, yet His amazing handiwork is still seen in fully functional genomes ...
This is an application for renewal of a grant to study picornavirus genome replication. All positive-strand RNA viruses hijack and/or remodel host membranes to...
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Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
Zalckvar, E., C. Paulus, D. Tillo, A. Asbach-Nitzsche, Y. Lubling, iv, C. Winterling, N. Strieder, K. Mücke, F. Goodrum, E. Segal, et al., Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein., Proc Natl Acad Sci U S A, vol. 110, issue 32, pp. 13126-31, 2013 Aug 6. PMCID: PMC3740854 PMID: 23878222 ...
Using Beagle, one of the fastest supercomputers devoted to life sciences, the complete genome analysis can be radically accelerated, a new study reveals.
Two newly discovered giant viruses are bigger than many bacteria and carry massive and largely unique genomes that hint at new branches of life.
Replication in P2P architectures No proactive replication (Gnutella) - Hosts store and serve only what they requested - A copy can be found only by probing a host with a copy Proactive replication of
Today I was looking at ScienceDaily.com and found 3 really exciting developments. Bound to change medicine and our lives forever. Cancer detection, full genome sequencing on a small budget and fixing the broken Fixer responsible for the bad effects of Aging. Cancer Detection In the early 70s President Nixon launched the War On Cancer. While…
One view of evolution is that it is a process by which simple organisms become more complex. The simplicity of many viruses lead to their placement at the origin of life. This long-standing hypothesis ignores the fact that viral genomes are subject to selective pressure to maintain minimal size to ensure rapid replication rates. The authors conclude that viral simplicity is a consequence of parasitism, not antiquity.. Even though viruses are not living and should not be included in the tree of life, they play an important role in evolution of their cellular hosts by regulating population and biodiversity.. Are you convinced by these arguments? Post a comment and let us know whether you think viruses or living or not.. Moreira, D., & López-García, P. (2009). Ten reasons to exclude viruses from the tree of life Nature Reviews Microbiology, 7 (4), 306-311 DOI: 10.1038/nrmicro2108. ...
In a breakthrough that experts say will help feed the growing global population in the coming decades, scientists Thursday revealed they have cracked the f
This Application Note shows how the Dual luciferase assay can help to assess the Replication of the Hepatitis C Virus subgenomic replicon. Read more.
Kaposis sarcoma-associated herpesvirus (KSHV) is thought to be an oncogenic member of the γ-herpesvirus subfamily. The virus usually establishes latency upon infection as a default infection pattern. The viral genome replicates according to the host cell cycle by recruiting the host cellular replication machinery. Among the latently expressing viral factors, LANA seems to play pivotal roles in viral genome replication, partitioning, and maintenance. LANA binds with two LANA-binding sites (LBS1/2) within a terminal repeat sequence and is indispensable for viral genome replication in latency. The nuclear matrix region seems to be important as a replication site, since LANA as well as cellular replication factors accumulate there and recruit the viral replication origin in latency (ori-P) by its binding activity to LBS. KSHV ori-P consists of LBS followed by a 32 bp GC-rich segment (32GC). Although it has been reported that LANA recruits cellular pre-replication complexes (pre-RC) such as origin
Several metagenomic projects have been accomplished or are in progress. However, in most cases, it is not feasible to generate complete genomic assemblies of species from the metagenomic sequencing of a complex environment. Only a few studies have reported the reconstruction of bacterial genomes from complex metagenomes. In this work, Binning-Assembly approach has been proposed and demonstrated for the reconstruction of bacterial and viral genomes from 72 human gut metagenomic datasets. A total 1156 bacterial genomes belonging to 219 bacterial families and, 279 viral genomes belonging to 84 viral families could be identified. More than 80% complete draft genome sequences could be reconstructed for a total of 126 bacterial and 11 viral genomes. Selected draft assembled genomes could be validated with 99.8% accuracy using their ORFs. The study provides useful information on the assembly expected for a species given its number of reads and abundance. This approach along with spiking was also ...
We aim to determine how cells faithfully complete genome replication. Accurate and complete genome replication is essential for all life. A single DNA replication error in a single cell division can give rise to a genomic disorder. However, almost all experimental data are ensemble; collected from millions of cells. We used a combination of high-resolution, genomic-wide DNA replication data, mathematical modelling and single cell experiments to demonstrate that ensemble data mask the significant heterogeneity present within a cell population; see [1-4]. Therefore, the pattern of replication origin usage and dynamics of genome replication in individual cells remains largely unknown. We are now developing cutting-edge single molecule methods and allied mathematical models to determine the dynamics of genome replication at the DNA sequence level in normal and perturbed human cells.. [1] de Moura et al., 2010, Nucleic Acids Research, 38: 5623-5633. [2] Retkute et al, 2011, PRL, 107:068103. [3] ...
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 ...
Chikungunya (CHIK-un-goon-ya) virus (also known as CHIKV) is a mosquito-transmitted alphavirus that has spread around the world and is currently infecting people in about 60 countries globally. CHIKV is rarely fatal, but causes severe joint pain for months to years that can debilitate affected patients for long periods of time. There are currently no known drugs to treat CHIKV infection, primarily due to a lack of understanding of the structure of CHIKV proteins involved in viral genome replication. The Geiss lab has worked on developing drug targeting the membrane bound CHIKV nsP1 protein, which is the anchor for the viral genome replication complex on cellular membranes and a multifunctional enzyme that forms a 5 RNA cap structure on the end of the CHIKV RNA genome. Solving the structure of the CHIKV nsP1 protein would provide critical information for designing drugs that inhibit nsP1 function and abort viral genome replication ...
The C11-13 strain from the Siberian subtype of tick-borne encephalitis virus (TBEV) was isolated from human brain using pig embryo kidney (PEK), 293, and Neuro-2a cells. Analysis of the complete viral genome of the C11-13 variants during six passages in these cells revealed that the cell-adapted C11-13 variants had multiple amino acid substitutions as compared to TBEV from human brain. Seven out of eight amino acids substitutions in the high-replicating C11-13(PEK) variant mapped to non-structural proteins; 13 out of 14 substitutions in the well-replicating C11-13(293) variant, and all four substitutions in the low-replicating C11-13(Neuro-2a) variant were also localized in non-structural proteins, predominantly in the NS2a (2), NS3 (6) and NS5 (3) proteins ...
The UAB investigators went on to molecularly clone and sequence the complete viral genomes from four individual chimpanzees. According to UAB post-doctoral researcher Brandon Keele, Ph.D., lead author of the report, this allowed for unprecedented genetic comparisons to be done between HIV-1 and its closest simian virus counterpart. He went on to say that finding this cluster of naturally infected chimpanzees will allow us to explore the natural history and behavior of SIVcpz in its natural host and help us begin to unravel how and why SIVcpz made the jump to humans ...
Students working in pairs or small groups receive a simulated virus: two paper cups taped together, enclosing a strip of paper listing an RNA or DNA sequence (an abbreviated viral genome). The students break open the cups (simulating viral uncoating in the host cell) and decide how host and/or viral enzymes will convert the genome into viral proteins and new genomes. The sequences provided describe a double-stranded DNA virus, single-stranded RNA viruses (+ or - strand), a retrovirus, and a double-stranded RNA virus. Templates for photocopying the genomes, sample worksheets, and an instructors answer key are included.
Sequencing RNA genomes was difficult in the 1980s, and cDNA cloning was just emerging. The first complete genome sequence of a coronavirus was for infectious bronchitis virus in 1987 (Boursnell et al., 1987) and a few years later it was completed for MHV (Lee et al., 1991). These genomes were assembled from many short cDNA clones and, when completed, indicated that the genome was ∼30 kb, significantly longer than had been estimated previously by sucrose gradient centrifugation, and that it was the longest of any known RNA virus. These sequences revealed two long open reading frames, ORF1a and 1b encoding 16 nonstructural proteins. It was also shown that both ORF1a and ORF1ab proteins were translated from genome RNA, and ORF1b via a translational frame shift at the end of ORF1a revealing new mechanisms of translational control (Bredenbeek et al., 1990). Alexander Gorbalenyas insightful analyses of the proteins encoded in ORFs1a and 1b revealed several protease and other enzymatic domains (for ...
Background New sequencing technologies possess opened up the true method towards the discovery as well as the characterization of pathogenic infections in scientific samples. in 1337532-29-2 supplier all full cases, our pre-processed technique improved genome set up, just its combination by using SPAdes allowed us to get the full-length from the viral genomes examined in a single contig. Conclusions The suggested pipeline can overcome drawbacks because of the era of chimeric reads through the amplification of viral RNA which significantly boosts the assembling of full-length viral genomes. Electronic supplementary materials The online edition of this content (doi:10.1186/s40659-016-0099-y) contains supplementary materials, which is open to certified users. and in 1983 from sp, a types owned by rodents (Gerbilinae), respectively, had been amplified by serial passing in the mind of new-born mice. After many passages, the brains were centrifuged and homogenized before a lyophilisation of every ...
Background New sequencing technologies possess opened up the true method towards the discovery as well as the characterization of pathogenic infections in scientific samples. in 1337532-29-2 supplier all full cases, our pre-processed technique improved genome set up, just its combination by using SPAdes allowed us to get the full-length from the viral genomes examined in a single contig. Conclusions The suggested pipeline can overcome drawbacks because of the era of chimeric reads through the amplification of viral RNA which significantly boosts the assembling of full-length viral genomes. Electronic supplementary materials The online edition of this content (doi:10.1186/s40659-016-0099-y) contains supplementary materials, which is open to certified users. and in 1983 from sp, a types owned by rodents (Gerbilinae), respectively, had been amplified by serial passing in the mind of new-born mice. After many passages, the brains were centrifuged and homogenized before a lyophilisation of every ...
Common plasmids are simple DNA molecules which contain a few genes and regulatory elements. Most viral genomes are more complex. For example, the genome of phage lambda contains approximately 50 genes. About 4,000 genes are present in the E. coli genome while there is approximately 1,000 times more DNA in the genome of a mammal. This progression in genome complexity is the topic of this exercise. Here, students compare the electrophoretic patterns of restriction digests of a plasmid, phage lambda DNA, and cow DNA from thymus and kidney as shown in the figure below. The exercise serves as a good introduction for determining the size of DNA molecules and provides an appreciation for the complexity of genomes from different organisms.. ...
The genes encoding the two major structural proteins and a putative NTPase belong to a cluster of five genes/ORFs (genes 3, 4 and 8; ORFs 6 and 7 of Halorubrum pleomorphic virus 1) that are collinear and conserved among members of the family Pleolipoviridae (Figure 2.Pleolipoviridae; (Senčilo et al., 2012). Pleolipoviruses have non-lytic life cycles. Although there is no direct evidence for the entry mechanism, it has been proposed that the entry of pleolipoviral genomes occurs by membrane fusion of the viral envelope with the host cell cytoplasmic membrane (Pietilä et al., 2009). Viruses are predicted to employ different genome replication strategies, including rolling circle replication (RCR; circular genomes) and protein-primed replication carried out by family B-type polymerase (linear genomes), although direct experimental evidence is missing (Pietilä et al., 2009, Roine et al., 2010, Bath et al., 2006). Viruses exit the cells continuously starting 3-4 hours post infection (Pietilä et ...
View Notes - Lecture 2 from PLB 40175 at UC Davis. PLB 113 Lecture 2 II. Genome Organization and Gene Expression A. Plants have big (and small genomes) B. Genomes consist of single (LOW) copy and
Viral DNA is an example of extrachromosomal DNA. Understanding viral genomes is very important for understanding the evolution ... Some viruses, such as HIV and oncogenetic viruses, incorporate their own DNA into the genome of the host cell. Viral genomes ... viral dsRNA by TLR3, viral ssRNA by TLR7/TLR8, viral or bacterial unmethylated DNA by TLR9. TLR9 has evolved to detect CpG DNA ... The recognition of viral DNA is an important part of immune responses. For this virus to persist, the circular genome must be ...
Genomes are linear and non-segmented, around 4kb in length. The genome codes for 4 proteins. Entry into the host cell is ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Viralzone: ...
Genomes are circular, around 3.2kb in length. The genome codes for 7 proteins. Viral replication is nucleo-cytoplasmic. ... "Viral Zone". ExPASy. Retrieved 12 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 12 June 2015. Guo, Haitao; Mason, ...
Genomes are circular, around 3.2kb in length. The genome codes for 7 proteins. Viral replication is nucleo-cytoplasmic. ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Viralzone: ...
The genome codes for 9 proteins. Below are a few of the essential proteins of Bornaviridae that have been characterized. Viral ... Borna disease was first identified in 1926 and its genome was isolated in 1990. The viral family is named after the city of ... "Viral Zone". ExPASy. Retrieved 12 June 2015. Amarasinghe, Gaya K.; Bào, Yīmíng; Basler, Christopher F.; Bavari, Sina; Beer, ... Entry into the host cell is achieved by attachment of the viral GP glycoproteins to host receptors, which mediates clathrin- ...
The genome codes for 40 proteins. Viral replication is nuclear. Entry into the host cell is achieved by attachment of the viral ... Import of the viral genome into host nucleus mediated by core protein VII. Transcription of early genes (E genes) by host RNA ... Microtubular transport toward nucleus of the viral genome still protected by the core protein VII and a partial capsid mainly ... "Viral Zone". ExPASy. Retrieved 1 July 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 1 July 2015. taxonomy. "Taxonomy ...
The genome codes for 12 proteins. Viral replication is cytoplasmic. Replication follows the double-stranded RNA virus ... They were able to identify viral plaques from this and then subsequently sequence their genomes. "ICTV Report Cystoviridae". " ... Genomes are linear and segmented, and labeled as large (L) 6.4kb, Medium (M) 4 kb and Small (S) 2.9 kb in length. ... "Viral Zone". ExPASy. Retrieved 15 June 2015. "NCBI Taxonomy Browser: Cystoviridae". NCBI. Retrieved 19 June 2016. Silander OK, ...
Genomes are linear and have 2 segments, around 2.7-3.4kb in length. The genome codes for 6 proteins. Viral replication is ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Viralzone: ...
The complete genomes, as well as two other similar, unclassified genomes are available here. The virus attaches to the host ... and degrades the cell wall using viral exolysin enough to eject the viral DNA into the host cytoplasm via long flexible tail ... Once the viral genes have been replicated, the procapsid is assembled and packed. The tail is then assembled and the mature ... Genomes are linear, around 121kb in length. The type species, Enterobacteria phage T5, and several other species have been ...
The complete genome is available here Viral replication is cytoplasmic. The virus attaches to the host cell's adhesion ... Once the viral genes have been replicated, the procapsid is assembled and packed. The tail is then assembled and the mature ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. NCBI (February 2015 ... "N15likevirus Complete Genomes". ICTV. "Virus Taxonomy: 2013 Release". Retrieved 18 February 2015. Viralzone: N15likevirus ICTV ...
Both complete genomes are available here Viral replication is cytoplasmic. The virus attaches to the host cell's adhesion ... and viral exolysin degrades the cell wall enough to eject the viral DNA into the host cytoplasm via long flexible tail ejection ... Genomes are linear, around 22kb in length. Both species have been fully sequenced. They range between 22k and 23k nucleotides, ... "Viral Zone". ExPASy. Retrieved 18 February 2015. ICTV. "Virus Taxonomy: 2013 Release". Retrieved 18 February 2015. NCBI. " ...
Genomes are linear. Viral replication is cytoplasmic. Entry into the host cell is achieved by adsorption into the host cell. ... "Viral Zone". ExPASy. Retrieved 13 August 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 13 August 2015. Viralzone: ...
Firstly, the viral genome enters the cytoplasm. The viral DNA forms supercoiled mini-chromosome structures upon entering the ... they do not require the integration of viral genome into the host's in order to replicate and for this reason their genome does ... Harper G, Hull R, Lockhart B, Olszewski N (2002). "Viral sequences integrated into plant genomes". Annu Rev Phytopathol. 40: ... It can either be used as a template for viral protein synthesis, or it can undergo reverse transcription by viral encoded ...
Genomes are linear, around 40.5kb in length. The genome has 67 open reading frames. Viral replication is cytoplasmic. Entry ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Viralzone: ...
Genomes are linear and non-segmented. Viral replication is cytoplasmic, and is lysogenic. Entry into the host cell is achieved ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Viralzone: ... The virus exits the host cell by tubule-guided viral movement. Commercial cultivars of euphorbia pulcherrima serve as the ...
Genomes are linear, around 8.4-9.3kb in length. The genome codes for 5 proteins. Viral replication is cytoplasmic, and is ... The virus exits the host cell by tripartite non-tubule guided viral movement. Plants serve as the natural host. Transmission ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Viralzone: ...
Genomes are linear, around 6.8kb in length. The genome has 2 open reading frames. Viral replication is cytoplasmic. Entry into ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Howitt, R. L.; ... Beever, R. E.; Pearson, M. N.; Forster, R. L. (2001). "Genome characterization of Botrytis virus F, a flexuous rod-shaped ...
Viral genomes[change , change source]. Viral genomes, which are usually RNA, take over the cell machinery and make both new ... viral RNA and the protein coat of the virus.. Phage genomes[change , change source]. Phage genomes are quite varied. The ... Phage genomes may code for as few as four genes,[10] and as many as hundreds of genes. ... The DNA copy is then inserted into the genome in a new position. Retrotransposons behave very similarly to retroviruses, such ...
Organellar genomes[edit]. Plastomes and mitogenomes[edit]. The human mitochondrial genome has retained genes encoding 2 rRNAs, ... Viral eukaryogenesis, hypothesis that the cell nucleus originated from endosymbiosis. References[edit]. *^ "Mereschkowsky's ... Genome comparisons suggest a close relationship between plastids and cyanobacteria.[61]. *Many genes in the genomes of ... genome encoding thousands of proteins.[21] Plastids and mitochondria exhibit a dramatic reduction in genome size when compared ...
Genomes are linear, around 6.5-9kb in length. The genome codes for 2 to 6 proteins. Viral replication is cytoplasmic, and is ... The virus exits the host cell by tripartite non-tubule guided viral movement, and tubule-guided viral movement. Plants and ... "Viral Zone". ExPASy. Retrieved 12 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 12 June 2015. Viralzone: ...
Genomes are linear, around 15.9kb in length. The TTV1 virion contains four virus-encoded proteins, TP1-4. The proteins do not ... Viral replication is cytoplasmic. Entry into the host cell is achieved by adsorption into the host cell. DNA-templated ... "Viral Zone". ExPASy. Retrieved 12 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 12 June 2015. Janekovic, D.; ...
... the viral genome is also replicated. The viral genome is mostly silent within the host. However, at some point, the provirus or ... viral protein synthesis, possible assembly of viral proteins, then viral genome replication mediated by early or regulatory ... The smallest viral genomes - the ssDNA circoviruses, family Circoviridae - code for only two proteins and have a genome size of ... This membrane is studded with proteins coded for by the viral genome and host genome; the lipid membrane itself and any ...
Genomes are linear, around 9-13kb in length. The genome has 1 or 2 open reading frames. Viral replication is cytoplasmic. ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Peever, Tobin; Liu, ... "Hypovirulence of Chestnut Blight Fungus Conferred by an Infectious Viral cDNA". Science. 257: 800-803. doi:10.1126/science. ...
The viral oncogene was derived from cellular genome. Thus, KRAS gene in cellular genome is called a proto-oncogene. ...
Genomes are linear and non-segmented. Viral replication is cytoplasmic. Replication follows the positive stranded RNA virus ... "Viral Zone". ExPASy. Retrieved 15 June 2015. Viralzone: Narnavirus ICTV. ...
Xin-Cheng Qin et al.: A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors, in: ... Fusariviridae, auf: NCBI Genomes *↑ D. F. Quito-Avila, P. M. Brannen, W. O. Cline, P. F. Harmon, R. R. Martin: Genetic ... Marion Heller-Dohmen et al.: The nucleotide sequence and genome organization of Plasmopara halstedii virus, in: Virol J. 2011; ... Henxia Xia et al.: A dsRNA virus with filamentous viral particled, in: Nature Communicationsvolume 8, Nr. 168 (2017), [[doi: ...
The chapters of this book concentrate on the biochemistry, enzymology and structural aspects of the genome packaging machinery ... Viral Genome Packaging focuses on the process of genome packaging within a pre-formed viral procapsid. ... Viral Genome Packaging focuses on the process of genome "packaging" within a pre-formed viral procapsid. The chapters of this ... Viral Genome Packaging: Genetics, Structure, and Mechanism. Editors. * Carlos E. Catalano Series Title. Molecular Biology ...
Viral capsids: mechanical characteristics, genome packaging and delivery mechanisms.. Roos WH1, Ivanovska IL, Evilevitch A, ... Viral capsids: Mechanical characteristics, genome packaging and delivery mechanisms. Cell Mol Life Sci. 2007 Jun;64(12):1484- ... Viral capsids: Mechanical characteristics, genome packaging and delivery mechanisms. Cell Mol Life Sci. 2007 Jun;64(12):1484- ... Viral capsids: Mechanical characteristics, genome packaging and delivery mechanisms. Cell Mol Life Sci. 2007 Jun;64(12):1484- ...
Additionally, we provide evidence that the functionality of one of these sequences has been maintained in the host genome over ... Unexpectedly, however, we identified a large and diverse population of sequences in animal genomes that are derived from non- ... Analysis of these sequences-which represent all known virus genome types and replication strategies-reveals new information ... many millions of years, raising the possibility that captured viral sequences may have played a larger than expected role in ...
... connect the wealth of existing osmotic pressure data for DNA in the bulk with the DNA encapsidation curves within small viral ...
These alleged ancient viral sequences are thought to have entered the genome via viral infection, initially served no purpose ... over the past 100 million years of mammalian evolution-with their viral-like DNA proliferating across creatures genomes.1 ... the great ongoing myths of evolution is that the genomes of animals and humans are littered with vast amounts of genomic viral ... So, where do viruses come from that essentially share the same sequences as those found in their host genomes? Perhaps the ...
... thus preserving viral genome integrity during lytic reactivation. ... to APOBEC3B-mediated deamination as evidenced by lower viral ... Epstein-Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity. *Adam Z. Cheng ORCID: orcid.org/0000- ... The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 ... Ebrahimi, D., Anwar, F. & Davenport, M. P. APOBEC3 has not left an evolutionary footprint on the HIV-1 genome. J. Virol. 85, ...
Viral Genome Junk Hits the Trash by Jeffrey P. Tomkins, Ph.D. * Evidence for Creation › Evidence from Science › Evidence from ... Viral Genome Junk Is Bunk. Acts & Facts. 44 (4): 12. *Dr. Tomkins is Director of Life Sciences at the Institute for Creation ... and that external viral genomes were derived from human and animal ERVs only after God cursed the creation for mans sin. This ... Genome Biology and Evolution. 7 (4): 1082-1097.. * Chuong, E. B., N. C. Elde, and C. Feschotte. 2016. Regulatory evolution of ...
Buy a discounted Paperback of Viral Genome Methods online from Australias leading online bookstore. ... Booktopia has Viral Genome Methods by Kenneth W. Adolph. ... Viral Genome Methods is a practical guide to the newest ... Molecular biology and genetics techniques now dominate viral research in attempts to cure diseases such as AIDS. ... Recognized authorities and pioneers in viral research pass on their expertise to you. ...
... many attempts were made to elucidate the viral genome structure and the amino acid sequences of different viral gene products. ... Molecular Anatomy of Chilo Iridescent Virus Genome and the Evolution of Viral Genes. ... The identification of several putative viral gene products including a DNA ligase and a viral antibiotic peptide is a powerful ... Koonin E.V., Wolf Y.I., and Aravind L., Genome Res 11, 240-252, 2001.PubMedGoogle Scholar ...
Perelman School of Medicine team identifies previously unknown viral family that appears to be the second-most common DNA virus ... Home Genomics Metagenomics Virus Hunters Stalk Through Genome and ID New Disease Associated Viral Family ... Virus Hunters Stalk Through Genome and ID New Disease Associated Viral Family. May 9, 2019. 0 ... allowing us to identify seven genomes," they stated. "These genomes were then used as alignment targets to interrogate publicly ...
Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving ... Each group is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget ... i,Conclusions,/i,. This software should help researchers design multiplex sets of primers for targeted whole genome enrichment ... tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes ...
... Shea N. Gardner,1 Crystal J. ... M. K. Borucki, J. E. Allen, H. Chen-Harris et al., "The role of viral population diversity in adaptation of bovine coronavirus ... "Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing," Virology ...
Read more about the manipulation of the SSV1 genome and how it may lead to discovery of a minimal SSV genome for future studies ... Researchers have found its genome is surprisingly tolerant of mutation, including loss of one of its structural capsid genes, ... given the importance of structural integrity not only to contain the viral genome, but also to attach and deliver that genome ... Their form of parasitism implies the idea that a compact viral genome would carry only the most necessary genes. A new report ...
Em futuro próximo, a análise do genoma humano será capaz de elucidar o curso natural de uma hepatite viral, bem como a sua ... Os mecanismos que determinam o clearance ou a persistência da infecção viral nas hepatites virais crônicas não estão ainda bem ...
... Published on ​ Sat, Aug 1 2020 19:06 IST , ​ 19 Views ... announced the completion of pan-India 1000 genome sequencing of SARS-CoV-2. ...
... a new type of viral genome that could have huge implications for theories of viral emergence and... ... a new type of viral genome that could have huge implications for theories of viral emergence and evolution. Viruses are the ... Virus Evolution Theory Could Change With Newly Discovered Viral Genome Author. Mediaclnewstoday.com. Fri, 20 Apr 2012 10:20 UTC ... Astonishingly, they found a unique viral genome that has never before been reported - a circular, single-stranded DNA virus ...
The general approach to use CODEHOP-mediated PCR to identify novel viral genomes from a target virus family is shown ... CODEHOP-mediated PCR - a powerful technique for the identification and characterization of viral genomes.. Rose TM1. ... CODEHOP-mediated PCR - A powerful technique for the identification and characterization of viral genomes ... CODEHOP-mediated PCR - A powerful technique for the identification and characterization of viral genomes ...
... genome next-generation sequencing of any cultivable virus without the need for large-scale production of viral stocks or viral ... Whole genome sequencing of viruses and bacteriophages is often hindered because of the need for large quantities of genomic ...
There are a number of such elements believed to be the evolutionary remnants of viral genomes, but it was very surprising to ... Scientists Finding Of An Ancient Viral Invasion That Shaped The Human Genome An Important Step Towards Advancement In ... such as viral sequences, could be "control elements" that affect gene regulation once inserted in the genome. ... By comparing the genomes of mouse with human, the scientists were able to show that the binding sites for gene regulatory ...
Now that we have created synthetic Gene 68, we need to combine that synthetic gene with the rest of the phage genome. We will ... Today we will introduce the native phage genome and synthetic gene 68 into the bacterial cells and then plate those cells onto ... If it is infectious, the semi-synthetic phage genome will burst the initial host bacterial cell, causing it to rupture and ... The method that we will use to introduce the phage genome and synthetic gene into bacteria is called electroporation; rather ...
... epigenetic de-repression of the viral genome, and enhanced viral early gene expression. The coordination of viral gene ... As the cells differentiate, YY1 protein expression and recruitment to the viral genome is dramatically reduced. This results in ... required for replication of the viral genome. In normal epithelia, cellular migration away from the basal layer induces cell ... supporting amplification of the viral DNA. In this study, we show that the HPV genome recruits the cellular transcriptional ...
DENV genome was detected in 75% (15/20) of marmosets after primary DENV infection. No DENV genome was detected in urine samples ... Levels of DENV genome were determined in 228 urine samples from 20 primary DENV-inoculated marmosets and in 56 urine samples ... Presence of DENV genome in urine samples and pathological changes in kidneys were examined in the present study. ... In comparison to detection of viral genome in urine samples, DENV genome was detected on days 2-7 in serum samples (Table 2). ...
Emerging viral mutants in Australia suggest RNA recombination event in the SARS-CoV-2 (COVID-19) genome. Med J Aust 2020; https ... Emerging viral mutants in Australia suggest RNA recombination event in the SARS-CoV-2 (COVID-19) genome. ... The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol 2005; 3: e5. ... viral mutations are located at the stem loop-II (s2m) motif, an extremely conserved RNA element in the 3 untranslated region ( ...
"Inhibition of JCPyV infection mediated by targeted viral genome editing using CRISPR/Cas9." Scientific Reports 6 (1): 36921. ... Inhibition of JCPyV infection mediated by targeted viral genome editing using CRISPR/Cas9. ... We utilized CRISPR/Cas9 to target the noncoding control region and the late gene open reading frame of the JCPyV genome. We ... is a genome editing tool capable of introducing sequence specific breaks in double stranded DNA. Here we show that the CRISPR/ ...
Early growth response-1 facilitates enterovirus 71 replication by direct binding to the viral genome RNA.. [Yu Song, Xin Cheng ... Our results reveal an important new role of EGR1 in viral infection, provide new insight into the novel mechanism underlying ... Unfortunately, there is currently no effective treatment for EV71 infection due to the lack of understanding of viral ... Moreover, EGR1 protein co-localizes with EV71 RNA in the cytoplasm of infected cells to facilitate viral replication. ...
  • The coding capacity of the CIV genome was determined by the analysis of the complete DNA nucleotide sequence consisting of 212,482 bp that represent 468 open reading frames encoding for polypeptides ranging from 40 to 2432 amino acid residues. (springer.com)
  • Subsequent analysis of metagenomics sequence datasets from more than 7,500 samples held in 173 datasets covering 51 different organisms and environments indicated that the redondovirus family was found exclusively in humans, and was localized to the human oral cavity and lung, although rarely the viral DNA was also found in gut samples. (genengnews.com)
  • Viral metagenomics, however, is becoming an increasingly useful tool with which to glimpse virus evolution, as it makes available vast amounts of new sequence data for analysis. (sott.net)
  • Phylogenetic analysis showed that SARS with 30 other coronaviruses and astroviruses all possess the s2m motif, suggesting that this motif is conserved in both nucleotide sequence and secondary structure folding during evolution in an otherwise rapidly mutable RNA genome. (mja.com.au)
  • The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system (CRISPR/Cas9) is a genome editing tool capable of introducing sequence specific breaks in double stranded DNA. (harvard.edu)
  • We aim to fill this methodological gap by developing "Virana", a software package and associated web service for viral next-generation sequence analysis. (mpg.de)
  • We used this technique to generate full viral genome sequence in the presence of host contaminants, using viral preparations from cell culture supernatant, allantoic fluid and fecal matter. (biomedcentral.com)
  • Viral discovery has been aided by the development of sequence independent methodologies for the generation of genomic data [ 10 ]. (biomedcentral.com)
  • In addition to its utility for viral discovery and viral surveillance, the DNase-SISPA method has utility in obtaining full genome sequence from uncharacterized viral isolates or viral isolates from highly divergent families. (biomedcentral.com)
  • Additionally, in order to capture 5' ends of viral RNA, a random hexamer primer tagged with a conserved sequence at the 5' end was added to the Klenow reaction (Figure 2 shows a 5' oligo specific for rhinoviruses). (biomedcentral.com)
  • Viral sequence integration into the mammalian genome has long been perceived as a health risk. (nih.gov)
  • viral sequence integration. (nih.gov)
  • However, traditional viral detection methods rely on prior sequence or antigen knowledge. (pubmedcentralcanada.ca)
  • In this study, we describe sequence-independent amplification for samples containing ultra-low amounts of viral RNA coupled with Illumina sequencing and de novo assembly optimized for viral genomes. (pubmedcentralcanada.ca)
  • The methods presented here are scalable to large numbers of samples and capable of generating full or near full length viral genomes from clone and clinical samples with low amounts of viral RNA, without prior sequence information and in the presence of substantial host contamination. (pubmedcentralcanada.ca)
  • Obtaining genomic sequence from such samples can provide valuable insights into viral attenuation, response to host immune pressure and drug treatment during infection, disease severity, transmission and epidemic spread. (pubmedcentralcanada.ca)
  • Finally, it should consistently generate sequence coverage for the entire target region, typically the protein coding region, CDS, of a viral genome. (pubmedcentralcanada.ca)
  • Analysis of clinical samples of patients with new viral infections is critical to confirm the diagnosis, provide viral load and sequence data necessary for characterizing viral kinetics, transmission and evolution of the virus. (flutrackers.com)
  • The challenge for bioinformaticians is to ensure the final genomic assembly includes the unknown virus they're trying to identify, making sure this sequence is not lost among the other genomes. (ucsd.edu)
  • 3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. (elifesciences.org)
  • Students working in pairs or small groups receive a simulated virus: two paper cups taped together, enclosing a strip of paper listing an RNA or DNA sequence (an abbreviated viral genome). (asmscience.org)
  • Whole Genome Sequence of the Parasitoid Wasp Microplitis demolitor that Harbors an Endogenous Virus Mutualist. (usda.gov)
  • Many bioinformatics tools use reference data, such as genome assemblies or sequence databanks. (biomedcentral.com)
  • Advances in next generation sequencing make it possible to obtain high-coverage sequence data for large numbers of viral strains in a short time. (biomedcentral.com)
  • The complete sequence of the HIV-1 genome, extracted from infectious virions, has been solved to single-nucleotide resolution. (wikipedia.org)
  • The identification of several putative viral gene products including a DNA ligase and a viral antibiotic peptide is a powerful tool for the investigation of the phylogenetic relatedness of this evolutionary and ecologically relevant eukaryotic virus. (springer.com)
  • Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving strains or variants in a gene family. (hindawi.com)
  • By comparing these gene lists, the researchers determined the core genome to be less tolerant of mutagenesis than the overall genome. (asm.org)
  • By comparing the genomes of mouse with human, the scientists were able to show that the binding sites for gene regulatory factors are very often not in the same place between the two species. (redorbit.com)
  • We utilized CRISPR/Cas9 to target the noncoding control region and the late gene open reading frame of the JCPyV genome. (harvard.edu)
  • For example, Sequin can be used to transfer annotations between highly similar HIV genomes that have identical gene content. (biomedcentral.com)
  • In the case of papillomaviruses, gene clusters match well our knowledge on viral biology and life cycle, illustrating the potential of our approach. (biomedcentral.com)
  • For the less known TuMV, our results trigger new hypotheses about viral evolution and gene interaction. (biomedcentral.com)
  • The viral eukaryogenesis hypothesis depicts a model of eukaryotic evolution in which a virus, similar to a modern pox virus, evolved into a nucleus via gene acquisition from existing bacterial and archaeal species. (wikipedia.org)
  • The lysogenic virus then became the information storage center for the cell, while the cell retained its capacities for gene translation and general function despite the viral genome's entry. (wikipedia.org)
  • The role of viral population diversity in adaptation of bovine coronavirus to new host environments," PLoS ONE , vol. 8, no. 1, Article ID e52752, 2013. (hindawi.com)
  • The situation is further complicated by the fact that viral genomes differ from the genomes of multicellular organisms such as humans in their very high evolutionary rate and intra-species diversity, resulting in an especially complex genotype. (mpg.de)
  • Being able to simultaneously amplify the whole genome and identify enteroviruses in samples is important for studying the viral diversity in different geographical regions and populations. (frontiersin.org)
  • In live, attenuated vaccines, such contaminants are not inactivated, and endogenous retroviruses by their very nature as Mendelian transmitted genomes are particularly difficult to eliminate. (cdc.gov)
  • GATU transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. (biomedcentral.com)
  • The recommended way of joining contigs is to align them to a related reference genome. (novum.se)
  • This will probably not be possible in this case, though, since phages evolve to fast which makes it impossible to use a reference genome. (novum.se)
  • Evidence for infectivity came from the detection of viral DNA in newly emerged leaves and the precise excision of the viral genome from the multimeric clones in inoculated leaves. (canterbury.ac.nz)
  • The new study opens new perspectives for the use of computer simulations to discover heretofore unimagined properties of viral RNAs and thus providing, in perspective, possible mechanistic clues for novel therapeutic approaches. (news-medical.net)
  • There may also be hundreds, or even thousands, of bacterial genomes. (ucsd.edu)
  • second, the amount of viral early RNAs yielded by a single integrated copy appears to be very similar to that associated with several thousands of extrachromosomal copies of the viral genome. (asm.org)
  • Virana is specifically tailored to the analysis of clinical data and takes the complex viral genotype as well as the longitudinal character of antiviral therapies into account. (mpg.de)
  • In contrast, treatment of MHV-CXCL10-infected CXCL10 −/− mice with anti-CXCL10 Ab resulted in increased clinical disease correlating with enhanced viral recovery from the brain and liver as well as increased serum alanine aminotransferase levels. (jimmunol.org)
  • Examples of low-copy viral RNA samples include the following: HIV controllers (capable of controlling the virus in the absence of antiretroviral therapy) ( 18 ), dengue virus (DENV) clinical samples collected after peak viremia ( 19 ), and West Nile virus (WNV) surveillance samples ( 20 ). (pubmedcentralcanada.ca)
  • Dr Eddy Rubin, Director of the U.S. Department of Energy Joint Genome Institute and Director of the Genomics Division at Lawrence Berkeley National Laboratory in Berkeley added, "This study using a comparative genomics strategy discovered important human specific properties of the regulatory network in human ES cells. (redorbit.com)
  • This work identified the areas of the human genome that put pressure on the AIDS virus, and the regions of the virus that serve to escape human control. (elifesciences.org)
  • The aim of this study was to investigate the frequency of viral nucleic acid detection in the myocardium of human immunodeficiency virus (HIV)-infected children to determine whether an association exists with the development of heart disease. (onlinejacc.org)
  • The immunization rates hpv viral genome Human papillomavirus are generally lower than for other human papillomavirus viral genome papilloma 6 vaccines, and further implementation of appropriate strategies is still needed. (natural-aloevera.ro)
  • Keywords Human papillomavirus, immunization strategies Rezumat Infecţia cu virusul papiloma uman HPV rămâne un factor important în producerea cancerelor de col uterin, vaginale, vulvare, anale hpv viral genome de orofaringe. (natural-aloevera.ro)
  • Oncoproteinele E6 si E7 perturba ciclul celular human papillomavirus viral genome legarea si inactivarea a doua proteine ale gazdei cu rol important in reglarea diviziunii celulare normale: proteina supresoare tumorala p53 si proteina retinoblastomului pRb. (natural-aloevera.ro)
  • Virusul papiloma uman poate fi clasificat în funcţie de capacitatea de oncogeneză, în genotipuri de HPV cu risc scăzut, asociate în principal cu verucile ano-genitale, şi HPV cu risc înalt, asociate human papillomavirus viral genome leziuni premaligne hpv viral genome maligne. (natural-aloevera.ro)
  • Cuvinte cheie Human papillomavirus strategii imunizare Introducere Virusul papiloma uman HPV este hpv viral genome de o treime dintre cazurile de neoplazii induse de agenţi infecţioşi cancere de col uterin, vaginale, vulvare, hpv viral genome şi de orofaringe 1. (natural-aloevera.ro)
  • Interestingly, direct qPCR analysis of lung samples from 60 healthy adults and 69 critically ill individuals indicated that although redondoviruses were present in healthy people, viral levels were also elevated in the critically ill patients. (genengnews.com)
  • Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation. (jcvi.org)
  • Analysis of mapped nanopore reads alone, despite an average individual error rate of 24 % (range 8-49 %), permitted identification of the correct viral strain in all four isolates, and 90 % of the genome of CHIKV was recovered with 97-99 % accuracy. (biomedcentral.com)
  • I am not sure if I need to play around with some settings or if there are specific ChIP analysis programs that cater to small genomes such as viral genomes. (biostars.org)
  • I then use only the viral aligned reads for peak analysis. (biostars.org)
  • I think your analysis is correct, and the tools are optimised for large genomes. (biostars.org)
  • Never had to do small genome chip-seq analysis, thankfully. (biostars.org)
  • 2,600 whole cancer genomes and their matching normal tissues across 38 tumour types, including data, portals, analysis pipelines and downstream integrative analyses. (nature.com)
  • In Genome Biology this week: peopling of the Sahara, epigenetic reprogramming analysis of liverwort, and more. (genomeweb.com)
  • Antonio Suma, lead author of the study, explains: 'By using modelling and simulations we have shed light on the unusual mechanical properties of Zika genome and complemented experiments by providing a detailed description of the underpinning atomistic processes. (news-medical.net)
  • The COVID-19 pandemic is a wake-up call for biologists studying viral transmission from animals to humans," said Pevzner. (ucsd.edu)
  • The SSV1 genome tolerates the DNA insertions necessary to generate shuttle vectors, allowing manipulation of its genome via traditional cloning methods. (asm.org)
  • The biochemical, biophysical and structural aspects of genome packaging are examined in detail. (springer.com)
  • The chapters of this book concentrate on the biochemistry, enzymology and structural aspects of the genome packaging machinery. (springer.com)