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

The 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 ...
The last two decades have seen the rise of viromics, the study of viral communities through the detection and characterization of virus genome sequences. Here we systematically review and summarize the scope and limitations of our current understanding of avian viromes, in both domesticated and wild-bird populations. We compare this viromic work to the broader literature on avian prokaryotic microbiomes, and highlight the growing importance of structured sampling and experimental design for testing explanatory hypotheses. We provide a number of recommendations for sample collection and preliminary data analysis to guide the development of avian viromics. Avian viromes have the potential to inform disease surveillance in poultry and improve our understanding of the risk of zoonotic viruses to human health.
The role and relative importance of intrinsic and extrinsic factors in the development of complex diseases such as cancer still remains a controversial issue. Determining the amount of variation explained by these factors needs experimental data and statistical models. These models are nevertheless based on the occurrence and accumulation of random mutational events during stem cell division, thus rendering cancer development a stochastic outcome. We demonstrate that not only individual genome sequencing is uninformative in determining cancer risk, but also assigning a unique genome sequence to any given individual (healthy or affected) is not meaningful. Current whole-genome sequencing approaches are therefore unlikely to realize the promise of personalized medicine. In conclusion, since genome sequence differs from cell to cell and changes over time, it seems that determining the risk factor of complex diseases based on genome sequence is somewhat unrealistic, and therefore, the resulting data ...
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 ...
Landmarks of the HIV genome 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 ...
Plays a role in viral genome replication by driving entry of quiescent cells into the cell cycle. Stimulation of progression from G1 to S phase allows the virus to efficiently use the cellular DNA replicating machinery to achieve viral genome replication. E7 protein has both transforming and trans-activating activities. Induces the disassembly of the E2F1 transcription factor from RB1, with subsequent transcriptional activation of E2F1-regulated S-phase genes. Interferes with host histone deacetylation mediated by HDAC1 and HDAC2, leading to transcription activation. Plays also a role in the inhibition of both antiviral and antiproliferative functions of host interferon alpha. Interaction with host TMEM173/STING impairs the ability of TMEM173/STING to sense cytosolic DNA and promote the production of type I interferon (IFN-alpha and IFN-beta ...
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 ...
The basic concepts central to understanding virus reverse genetics and molecular clones are summarized in Figures 1 and 2. The central idea is that the virion is an extracellular vehicle that transfers the viral genome (e.g., RNA or DNA genomes) between susceptible cells and protects the nucleic acid genome from degradation in the environment (Figure 2, Part A). Following entry, the viral genome is programmed to initiate a series of events that result in the production of a replicase complex that transcribes mRNA and replicates the genome. As discussed in the previous section, nucleic acid structure and organization determines the pathway of events needed to express mRNA and initiate virus gene expression and infection. Not all viruses, however, require virion attachment and entry to mediate a productive infection. In these cases, viral genomes can be isolated from virions and transfected directly into susceptible hosts cells. If the genome is infectious, viral RNAs and proteins will be ...
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…
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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. ...
We each begin life with a unique genome. As we grow and develop, we are each subjected to a range of factors that influence the way development proceeds. Most of those factors are common to us all, the intracellular and intercellular signals, hormones, birth, milk. But the precise combination and the range and duration of those factors varies between individuals, such as the duration of gestation or the composition and quantity of a mothers milk, for example. In addition we each undergo diff ...
We each begin life with a unique genome. As we grow and develop, we are each subjected to a range of factors that influence the way development proceeds. Most of those factors are common to us all, the intracellular and intercellular signals, hormones, birth, milk. But the precise combination and the range and duration of those factors varies between individuals, such as the duration of gestation or the composition and quantity of a mothers milk, for example. In addition we each undergo diff ...
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
When DNA is used as the starting template, nanogram amounts of cloned template, up to microgram amounts of genomic DNA, or up to 20,000 target copies can be a good starting point for optimization. However, even very low levels of sample (i.e., mRNA from tens of cells, DNA from single cells or individual viral genomes) may be sufficient for PCR amplification ...
Flagship action for the treatment of SARS-COV-2 virus. Epidemiological study in Greece through extensive testing for virus and antibodies for viral genome sequencing and genetic analysis of patients - Εμβληματική δράση για την αντιμετώπιση του ιού SARS-COV-2. Επιδημιολογική μελέτη στην Ελλάδα μέσω εκτεταμένων εξετάσεων ανίχνευσης ιού και αντισωμάτων αλληλούχισης ιικών γονιδιωμάτων και γενετικής ανάλυσης ασθενών - SarsCOV2 ...
There is a lot we still have to learn about SARS-CoV-2 and the disease it causes in humans. One aspect of the virus that we do know a lot about is its underlying molecular blueprint. We have the core viral genome, and broadly speaking we know the parts list of proteins that are translated and…
Hanta Virus- Structure, Genome, Epidemiology, Transmission, Replication, Pathogenesis, Clinical Manifestation, Lab Diagnosis, Treatment, Prevention, Control
Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells. . ...
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
The genomes of DNA tumor viruses regain nuclear localization after nuclear envelope breakdown during mitosis through the action of a viral protein with a chromatin-tethering domain (CTD). Here, we report that the human cytomegalovirus (HCMV) genome is maintained during mitosis by the CTD of the viral IE19 protein. Deletion of the IE19 CTD or disruption of the IE19 splice acceptor site reduced viral genome maintenance and progeny virion formation during infection of dividing fibroblasts, both of which were rescued by IE19 ectopic expression. The discovery of a viral genome maintenance factor during productive infection provides new insight into the mode of HCMV infection implicated in birth defects, organ transplant failure, and cancer.. IMPORTANCE Human cytomegalovirus (HCMV) is the leading infectious cause of birth defects, represents a serious complication for immunocompromised HIV/AIDS and organ transplant patients, and contributes to both immunosenescence and cardiovascular diseases. HCMV is ...
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 ...
Positive-strand RNA infections immediate different virus-specific procedures throughout their infection of sponsor cells. A similar level of theophylline-dependent induction was also observed when a full-length viral genome containing an RE riboswitch was tested. Analysis of this engineered viral genome revealed that this RE, located in the 5 untranslated region, specifically mediates efficient accumulation of plus-strands of the virus genome. Therefore, in addition to allowing for modulation of virus reproduction, the RE riboswitch system also provided insight into RE function. The ability to chemically induce a viral process via modulation of virus genome structure could be useful for basic and applied aspects of research. (15). Specifically, the introduction of mismatches into the lower stem portion of this RE inhibited viral RNA replication, whereas a compensatory mutant containing transposed base pairs was able to replicate to WT levels (15). Importantly, the same study also showed that the ...
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 ...
Human cytomegalovirus (HCMV) in clinical material cannot replicate efficiently in vitro until it has adapted by mutation. Consequently, wild-type HCMV differ fundamentally from the passaged strains used for research. To generate a genetically intact source of HCMV, we cloned strain Merlin into a sel …
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 ...
Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence
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
The genome of phycodnaviridae is not segmented and contains a single molecule of linear double-stranded DNA. The complete genome is 250000-350000 nucleotides long. The genome guanine + cytosine content is 40-52 %. The genome contains unusual bases, varying from 0.1-47 %. These bases are 5-methyl deoxy-cytosine residues and N6-methyl deoxy-adenosine residues in some DNAs. The double-stranded DNA is non-permuted and the genome sequence has termini with cross-linked hairpin ends. The genome, except for the hairpin, has terminally redundant sequences. These sequences have inverted terminal repetitions (ITR) for at least 2000 bases. (source: ICTVdB Descriptions) ...
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A giant virus under a microscope looks like this. To keep abreast of the latest scientific discoveries, subscribe to our news channel in Telegram. In general, researchers believe that the newthe virus comes from an unknown isolated group of viruses or distant relatives of a giant virus, which acquired a reduced form during evolution. Giant viruses were discovered in the twenty-first century. These organisms reach the size of a bacterial cell. Because of capsid - the protein coat that encapsulates viral particles, the virus is called giant. The DNA of a giant virus exceeds 200,000 base pairs and contains Orfan genes that are not found in other organisms.. Read more interesting articles on our channel in Yandex.Zen Yaravirus is composed of small particles with a size of 80 nmand has a unique genome. According to the researchers, it is simple and does not contain giant particles, but at the same time, a significant amount of previously undescribed genes is observed in Yaravirus. Scientists intend ...
The biases we highlight with popular phylogeography methods are much more important than might appear from what is at one level a question of model choice. To underline this, we present an analysis of around 100 Ebola virus genome sequences to investigate the emergence of human outbreaks. Epidemiological studies have found that animals act as a reservoir, maintaining the virus between the sporadic human outbreaks that have unfolded over the past four decades, a scenario that our structured coalescent-based model correctly identifies ...
SATANS SECRET by Brander C. Kitchin, M.D. E-mail: [email protected] The magic of modern molecular biologic techniques allow scientists to peer into the very meaning of living things. Not only are individual chromosomes of body cells identified, but they are teased apart for inspection and characterization of one or another of the thousands upon thousands of individual genes lined up in each. These almost miraculous techniques have enabled a discovery of overwhelming importance to the continued existence of Caucasian White Man, true Homo sapiens. The integrity of his unique genome is dangerously near extinction. His genes are what makes him what he is. It is this genome that created Western Civilization. The survival of earths biosphere may depend upon the preservation of this unique genome free of miscegenated taint. Unquestionably, this discovery is the most important return on the billions of dollars and thousands upon thousands of hours spent on AIDS (Acquired Immunodeficiency Syndrome) ...
2017-02-16 15:06:47] Checking for Bowtie Bowtie version: 2.2.8.0 [2017-02-16 15:06:47] Checking for Bowtie index files (genome).. [2017-02-16 15:06:47] Checking for reference FASTA file [2017-02-16 15:06:47] Generating SAM header for genome [2017-02-16 15:06:47] Preparing reads left reads: min. length=75, max. length=75, 100 kept reads (0 discarded) right reads: min. length=75, max. length=75, 100 kept reads (0 discarded) [2017-02-16 15:06:47] Mapping left_kept_reads to genome genome with Bowtie2 [2017-02-16 15:06:47] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/3) [2017-02-16 15:06:47] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/3) [2017-02-16 15:06:47] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/3) [2017-02-16 15:06:47] Mapping right_kept_reads to genome genome with Bowtie2 [2017-02-16 15:06:47] Mapping right_kept_reads_seg1 to genome genome with Bowtie2 (1/3) [2017-02-16 15:06:48] Mapping right_kept_reads_seg2 to genome genome with Bowtie2 ...
One of the great ongoing myths of evolution is that the genomes of animals and humans are littered with vast amounts of genomic viral DNA fossils. These alleged ancient viral sequences are thought to have entered the genome via viral infection, initially served no purpose in the host, and then later during evolutions long, slow changes were supposedly converted (exapted) to various useful purposes-like aiding in the elaborate process of human reproduction. However, like other evolutionary tales, advancing research in the field of genomics utterly contradicts this popular dogma.. According to evolutionary theory, viruses have repeatedly integrated themselves into the DNA of germline cells (those that produce eggs and sperm) over the past 100 million years of mammalian evolution-with their viral-like DNA proliferating across creatures genomes.1 These are called endogenous retroviruses (ERVs), and 8% of the human genome is populated by these sequences. However, there are least three major ...
and have similar-size icosahedral heads that encapsulate double-stranded DNA genomes (∼65 kb). Their genome sequences are similar to each other but markedly different from those of other sequenced phages. Both are arranged in a modular fashion. These phages can reduce or eliminate foam formation by their host cells under laboratory conditions ...
The Viral Genomes Resource is a collection of viral genomic sequences that is a part of the Entrez Genomes, which provides curated sequence data and annotations of complete genomes to the scientific community.
The NIH is now accepting applications for the Somatic Cell Genome Editing (SCGE) program. The SCGE program aims to improve genome editing technologies to accelerate the translation of this technology into clinical applications and maximize the potential to treat as many diseases as possible. Pending the availability of funds and sufficient numbers of meritorious applications, the NIH expects to fund projects to provide better animal models for assessing genome editing in vivo, tools and assays to detect adverse consequences of genome editing in human cells, new technologies to deliver genome editing machinery into disease relevant cells and tissues in vivo, novel genome editing and engineering systems, and a Dissemination and Coordinating Center. Applications are due April 3, 2018. For additional information on these RFAs visit our Funding Opportunities page.. ...
Synonyms for genom in Free Thesaurus. Antonyms for genom. 3 words related to genome: ordering, ordination, order. What are synonyms for genom?
Genome Hackers. ...alising. By taking a glass from which you have drunk, a genome hacker could obtain a comprehensive scan of your genome, revealing DNA variants that...tional biologist or bioinformatician you hack the entire genome to understand the gods writt... ...
MAGE, the older of the two techniques, made its debut two years ago. It stands for multiplex automated genome engineering, a fancy way of saying that it can easily change a genome many times over. It was originally used to create millions of small variants of bacterial genomes, producing a multitude of strains that can be tested for new abilities. As Jo Marchant puts it in her excellent feature, its an evolution machine. In its debut, within a matter of days, it had evolved a strain of E.coli that would produce large amounts of lycopene, a pigment that makes tomatoes red.. MAGE is a versatile editor. Not only can it create many diverse changes in a group of cells, it can also create many specific changes in a single cell. Thats what Isaacs, Carr and Wang have now done. TAG appears in 314 places throughout the E.coli genome as a stop codon. For each one, the team created a small stretch of DNA that had TAA instead of TAG, surrounded by exactly the same letters. They fed these edited ...
15 Sep 2013. A European consortium has presented the largest-ever study of functional genetic variation in human populations using RNA sequencing. The scientists, led by researchers from the University of Geneva (UNIGE) Faculty of Medicine in the context of the GEUVADIS project, today presented a map that points to the genetic causes of differences between people. The study, published in Nature and Nature Biotechnology, offers the largest-ever dataset linking human genomes to gene activity at the level of RNA.. Understanding how each persons unique genome makes them more or less susceptible to disease is one of the biggest challenges in science today. Geneticists study how different genetic profiles affect how certain genes are turned on or off in different people, which could be the cause of a number of genetic disorders.. Largest-ever human RNA sequencing study. The study presented today, conducted by more than 50 scientists from nine European institutes, measured gene activity (i.e. gene ...
Things to do as of Dec. 2000: look at findglobalcause / we have made subset flexible so that x is a subset of y if / card(x)
Reverse genetics allows the generation of recombinant viruses entirely from cDNA. One application of this technology is the creation of reporter-expressing viruses, which greatly increase the detail and ease with which these viruses can be studied. However, there are a number of challenges when working with reporter-expressing viruses. Both the reporter protein itself as well as the genetic manipulations within the viral genome required for expression of this reporter can result in altered biological properties of the recombinant virus, and lead to attenuation in vitro and/or in vivo. Further, instability of reporter expression and purging of the genetic information encoding for the reporter from the viral genome can be an issue. Finally, a practical challenge for in vivo studies lies in the attenuation of light signals when traversing tissues. Novel expression strategies and the continued development of brighter, red and far-red shifted reporters and the increased use of bioluminescent ...
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Research published in PLoS Genetics today provides insights into how an important fungal disease is able to evade wheats defences. The researchers hope that the study, which reveals the fungus complete genome sequence, ...
Subscribe to Genome magazine! Genome is a quarterly print magazine that covers personalized medicine and the genomic revolution that makes it possible. Your Genome subscription will include four issues each year delivered to your home for free. Subscribe online at: www.genomemag.com ...
Subscribe to Genome magazine! Genome is a quarterly print magazine that covers personalized medicine and the genomic revolution that makes it possible. Your Genome subscription will include four issues each year delivered to your home for free. Subscribe online at: www.genomemag.com ...
The graph GΠΠ of a genome Π. Π is a genome on the set of genes {1,...,14}, containing three chromosomes, two of them being linear and one circular. Its adja
A Whitehead Institute study suggests RNA sequences in the HIV virus might curl and twist in different ways, leading to differences in how they create transcripts for proteins - and introduces a new algorithm that can identify and sort RNA molecules by shape.
Based in San Diego and founded in 2013, Edico Genome develops cutting edge solutions that power the genomic revolution. Our vision is to revolutionize genome sequencing analysis by providing unprecedented speed, scale and accuracy ...
A new Cornell University-led study finds that the genome for a widely researched worm, on which countless studies are based, was flawed. Now, a fresh genome sequence will set the record straight and improve the accuracy of future research.
Map Of Amplified Genome Region Clarified And New Gene Identified As Overexpressed In Oral Cancer, Report University Of Pittsburgh Researchers
Molecular Analysis and Genome Discovery , Molecular Analysis and Genome Discovery , کتابخانه الکترونیک و دیجیتال - آذرسا
SAN DIEGO and CAMBRIDGE, Mass., Dec. 5, 2017 /PRNewswire/ -- Edico Genome and Seven Bridges today announced the availability of Edico Genomes DRAGEN™ pipel...
Genome In biology the genome of an organism is its whole hereditary information and is encoded in the DNA (or, for some viruses, RNA). This includes both the
By Amy Odegard, Manidipa Banerjee, John E. Johnson (auth.), John E. Johnson (eds.). Non enveloped viruses represent an enormous classification of medically major pathogens. They encode their proteins in unmarried (ss) and double strand (ds) RNA and DNA genomes and show a number of sizes and buildings. during this quantity specialists within the box supply brand new descriptions of many features linked to the ssRNA noda, picorna and calciviruses, the dsRNA reo and rotaviruses, the ssDNA parvoviruses and the dsDNA polyoma and adenoviruses. whereas many facets of those viruses were addressed formerly, this quantity in particular specializes in the problem in their access into cells, with specific recognition to the translocation of the viral genome via a membrane, with no assistance from inter-membrane fusion thats universal and fairly good understood in enveloped viruses. enough aspect has been published in many of the viruses mentioned during this quantity to set up a reputable argument for ...
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]. *^ a b Edited by Athel ... Genome comparisons suggest a close relationship between plastids and cyanobacteria.[61]. *Many genes in the genomes of ... genome encoding thousands of proteins.[22] Plastids and mitochondria exhibit a dramatic reduction in genome size when compared ...
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 ...
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 ...
The proteins in a virus can be called a viral proteome. Usually viral proteomes are predicted from the viral genome but some ... The genomes of viruses and prokaryotes encode a relatively well-defined proteome as each protein can be predicted with high ... The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain ... This is very roughly the protein equivalent of the genome. The term proteome has also been used to refer to the collection of ...
... virus genomes, are available online. "ICTV Report Herelleviridae". "Viral Zone". ExPASy. Retrieved 1 July 2015. CS1 maint: ... Genomes are linear, around 130-140kb in length. The genome codes for 190 to 215 proteins. Twort's genome is available on NCBI's ... Viral replication is cytoplasmic. The virus attaches to the host cell using its tail fibers, and ejects the viral DNA into the ... Genomes range between 130k and 149k nucleotides, with 190 to 233 proteins. All complete genomes, as well as several additional ...
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 full genome of the virus is integrated into the genome of the wasp and the virus only replicates in a particular part of ... They promote viral RNA destruction. MicroRNA attach to viral-RNA because they are complementary. Then the complex is recognised ... the genome of each virus is integrated into the host wasp genome ... "Viral Zone". ExPASy. Retrieved 15 June 2015.. *^ a b ICTV. " ... Webb, B. A. (1998). Polydnavirus biology, genome structure, and evolution. In Miller, L.K., Ball, L.A., Eds. The Insect Viruses ...
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, ...
... or through bioinformatics approaches to identify viral contigs or viral genomes from a microbial metagenome. Novel tools to ... The knowledge of variation of viral populations across spatiotemporal and other environmental gradients is supported viral ... "Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome ... viral contigs are generated through direct sequencing of a viral fraction, typically generated after 0.02-um filtration of a ...
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: ...
LAT manages this suppression of the viral genome through miRNAs that block viral transcription factors such as ICP0 and ICP4 ... One epigenetic mechanism employed in the control of latency for CMV is heterochromatization of the viral genome. Studies have ... Cameron, Craig E.; Gotte, Matthias; Raney, Kevin (2009-05-28). Viral Genome Replication. Springer Science & Business Media. ... These miRNAs also change the methylation of the histones in the viral genome. In the latent phase there is a lot of H3K9 ...
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 ...
Genomes are circular, around 2.1kb in length. The genome has 2 open reading frames. Viral replication is nuclear. Entry into ... "Viral Zone". ExPASy. Retrieved 13 August 2015. CS1 maint: discouraged parameter (link) ICTV. "Virus Taxonomy: 2014 Release". ...
... genomes are linear, around 11.1 kb in length. The genome codes for 5 proteins. Viral replication is cytoplasmic. ... The virus exits the host cell by budding, and tubule-guided viral movement. Fish serve as the natural host. "Viral Zone". ... Entry into the host cell is achieved by attachment of the viral G glycoproteins to host receptors, which mediates clathrin- ...
The genome codes for 8 proteins. Viral replication is cytoplasmic. Entry into the host cell is achieved by virus attaches to ... "Viral Zone". ExPASy. Retrieved 13 August 2015. ICTV Report: Paramyxoviridae Viralzone: Ferlavirus. ...
The complete genomes are available from here. Viral replication is cytoplasmic. The virus attaches to the host cell using its ... Genomes are linear, around 65-75kb in length. The genome codes for 90 to 130 proteins. All seven species have been fully ... 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 1 July 2015. CS1 maint: discouraged parameter (link) "Virus Taxonomy: 2019 Release". talk. ...
The genome codes for 12 proteins. Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into ... Genomes are linear and segmented, segments are around 1162 to 3849 base pairs (total size around 26 kb). ... The virus exits the host cell by monopartite non-tubule guided viral movement. The virus is transmitted via a vector (delphacid ... The genus has two species: Echinochloa ragged stunt virus Rice ragged stunt virus "Viral Zone". ExPASy. Retrieved 15 June 2015 ...
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: ...
Replication of the viral genome results in full-length, positive-strand antigenomes that are, in turn, transcribed into genome ... meningitis and other viral haemorrhagic fevers may resemble EVD.[1] Blood samples are tested for viral RNA, viral antibodies or ... Ebolavirus genomes contain seven genes including 3'-UTR-NP-VP35-VP40-GP-VP30-VP24-L-5'-UTR.[33][47] The genomes of the five ... Ebola, also known as Ebola virus disease (EVD) or Ebola hemorrhagic fever (EHF), is a viral hemorrhagic fever of humans and ...
... scientists reported the first genome sequencing of a C. acnes bacteriophage (PA6). The authors proposed applying this research ... "Genome sequence and analysis of a Propionibacterium acnes bacteriophage". Journal of Bacteriology. 189 (11): 4161-7. doi ...
At 4.7 million nucleotides in length, A1::DQ2 is the second longest haplotype identified within the human genome.[1] A1::DQ2 ... or alternatively the result of chronic viral infection which is known to also elevate anti-tranglutaminase antibody. A German ... "Genome-wide association study identifies HLA 8.1 ancestral haplotype alleles as major genetic risk factors for myositis ... "Immunologic features and HLA associations in chronic viral hepatitis". Gastroenterology. 108 (1): 157-64. doi:10.1016/0016- ...
... , also known as Lassa hemorrhagic fever (LHF), is a type of viral hemorrhagic fever caused by the Lassa virus.[1] ... This virus has a both a large and a small genome section, with four lineages identified to date: Josiah (Sierra Leone), GA391 ( ... Viral Hemorrhagic Fever Consortium Lassa fever Archived 4 April 2015 at the Wayback Machine. Page accessed April 6, 2016 ... Clinically, Lassa fever infections are difficult to distinguish from other viral hemorrhagic fevers such as Ebola and Marburg ...
"Genome Research. 14 (7): 1315-23. PMC 442147. . PMID 15231747. doi:10.1101/gr.2122004. ... "Dopamine-dependent neurodegeneration in rats induced by viral vector-mediated overexpression of the parkin target protein, ...
synonym = I ftofti, nazofaringiti akut viral, nazofaringiti, riniti viral, rinofaringjiti, coryza akute, koka e ftohtë,ref,{{ ... www.cnn.com/2009/HEALTH/02/12/cold.genome/,archivedate=26 April 2009,publisher=CNN,language=en,url-status=live,df=dmy-all}},/ ... ref name=Eccles2005/, Izolimi i agjentit viral të përfshirë është kryer rrallë, ,ref name=E51/, dhe në përgjithësi nuk është e ... I ftohti i zakonshëm është një infeksion viral i traktit të sipërm [[ Trakti respirator,respirator]] . Virusi i implikuar më ...
Genomes are circular, around 8kb in length. Viral replication is nuclear. Entry into the host cell is achieved by attachment of ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Viralzone: ... the viral proteins to host receptors, which mediates endocytosis. Replication follows the dsDNA bidirectional replication model ...
The sfRNAs are a result of incomplete degradation of the viral genome by the exonuclease and are important for viral ... After entering the host cell, the viral genome is replicated in the rough endoplasmic reticulum (ER) and in the so-called ... Other viral hemorrhagic fevers, such as Ebola virus, Lassa virus, Marburg virus, and Junin virus, must be excluded as the cause ... Yellow fever is a viral disease of typically short duration.[3] In most cases, symptoms include fever, chills, loss of appetite ...
Its genome is linear, single stranded positive sense RNA with a viral genome-linked protein (VPg) covalently linked at the 5' ... Depending on the type and degree of dehydration the viral particle is around 27-30 nm in diameter. The viral genome is around ... Their genome single-stranded (+) sense RNA is that functions as mRNA after entry into the cell and all viral mRNA synthesized ... Picornaviruses have a viral protein (VPg) covalently linked to 5' end of their genomes instead of 7-methylguanosine cap like ...
The tiny 490,885 base-pair genome of Nanoarchaeum equitans is one-tenth of this size and the smallest archaeal genome known; it ... the impact of viral infection is higher on archaea than on bacteria and virus-induced lysis of archaea accounts for up to one- ... "Genome Biol. Evol. 7 (1): 191-204. doi:10.1093/gbe/evu274. PMC 4316627 . PMID 25527841.. ... "Genome Biol. 3 (2): REVIEWS0003. doi:10.1186/gb-2002-3-2-reviews0003. PMC 139013 . PMID 11864374.. ...
"Genome Research. 11 (5): 677-84. doi:10.1101/gr.gr-1640r. PMC 311086. PMID 11337467.. ... The TATA-binding protein (TBP) could also be targeted by viruses as a means of viral transcription.[6] ... In the 1980s, while investigating nucleotide sequences in mouse genome loci, the Hogness box sequence was found and "boxed in" ... Most research on the TATA box has been conducted on yeast, human, and Drosophila genomes, however, similar elements have been ...
Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment to host receptors, which mediates ... All viruses in this family possess a non-segmented, polyadenylated, positive sense single stand RNA genome of ~7.5-8.5 ... Feline calicivirus "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. ...
"Genome-wide in situ exon capture for selective resequencing". Nat Genet. 39: 1522-7. doi:10.1038/ng.2007.42. PMID 17982454.. ... A.D. Hershey and Martha Chase, "Independent Functions of Viral Protein and Nucleic Acid in Growth of Bacteriophage," J. General ... July 2004). "Large-scale copy number polymorphism in the human genome". Science. 305: 525-8. Bibcode:2004Sci...305..525S. doi: ... Plant genome sequencing; epigenetics and stem cell fate; stem cell signaling; plant-environment interactions; using genetic ...
Wrapping the viroplasm with a membrane, concentrates the viral components required for the genome replication and the ... Viral evolution Viral replication Novoa, R. R.; Calderita, G.; Arranz, R.; Fontana, J.; Granzow, H.; Risco, C. (Feb 2005). " ... A viroplasm is an inclusion body in a cell where viral replication and assembly occurs. They may be thought of as viral ... Some of the membrane components are used for viral replication while some others will be modified to produce viral envelopes, ...
The Spi-B factor was shown to be crucial in initiating viral replication in certain strains of transgenic mice.[10] The protein ... A map of the genome of JC virus, indicating the position of the tumor antigen genes (red), the three capsid protein genes ( ... JC viral DNA can be detected in both non-PML affected and PML-affected (see below) brain tissue.[9] ... "Transcription factor Spi-B binds unique sequences present in the tandem repeat promoter/enhancer of JC virus and supports viral ...
... viral hemorrhagic fever, Q fever and hantavirus pulmonary syndrome. In the United Kingdom, brown rats are an important ... View the rat genome in Ensembl. *View the rn5 genome assembly in the UCSC Genome Browser. ...
The genome of SVNV is a negative sense single stranded RNA virus (Group V) that has three segments (S, M, and L segments). The ... The N protein contributes to viral replication, and coats the genomic RNA within the virion. Presently the soybean thrips ( ... Like other members of Bunyavirales, this virus is enveloped and has a negative sense single-stranded RNA (−ssRNA) genome ...
A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the ... Also rather important are the viral infections to which some of these ectoparasites serve as vectors such as the aphid- ...
... viral burden - viral core - viral culture - viral envelope - viral load - viremia - viricide - virion - virology - virus - ... genome - genotypic assay - germinal centers - giardiasis - globulins - glycoprotein - gonorrhea - gp120 (gp120) - gp160 (gp160 ...
Human GAA genome location and GAA gene details page in the UCSC Genome Browser. ...
Human BDNF genome location and BDNF gene details page in the UCSC Genome Browser. ... of BDNF into the lateral ventricles doubled the population of newborn neurons in the adult rat olfactory bulb and viral ... Variants close to the BDNF gene were found to be associated with obesity in two very large genome-wide association studies of ... January 2009). "Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity". ...
The host cell then treats the viral DNA as part of its own genome, transcribing and translating the viral genes along with the ... This step will also make viral enzymes and capsid proteins (8). Viral RNA will be made in the nucleus. These pieces are then ... When retroviruses have integrated their own genome into the germ line, their genome is passed on to a following generation. ... Both families in Group VII have DNA genomes contained within the invading virus particles. The DNA genome is transcribed into ...
The Institute has contributed to genome-sequencing projects of the common yeast (Saccharomyces cerevisiae, an organism which ... serum which was able to agglutinate the bacteria and neutralize the toxin was supplied by a horse inoculated with the viral ... Currently, an extensive line of research aims at determining the complete genome sequences of several organisms of medical ...
International Human Genome Sequencing Consortium (October 2004). "Finishing the euchromatic sequence of the human genome". ... Hershey, AD; Chase, M (1952). "Independent functions of viral protein and nucleic acid in growth of bacteriophage". The Journal ... "Tandem chimerism as a means to increase protein complexity in the human genome". Genome Research 16 (1): 37-44. doi:10.1101/gr. ... "The Human Genome Project Timeline". Retrieved 13 September 2006. *↑ Avery, OT; MacLeod, CM; McCarty, M (1944). "Studies on the ...
GO:0022415 viral process. • signal transduction. • immune system process. • viral entry into host cell. • negative regulation ... Human CLEC5A genome location and CLEC5A gene details page in the UCSC Genome Browser. ... Viral pathology[edit]. The most known ligand for CLEC5A is dengue virus (DV). Activated CLEC5A by binding to the dengue virion ... The researchers discovered that Japanese encephalitis virus (JEV) also binds to CLEC5A and contributes to viral pathology.[8] ...
Norman Pirie FRS (1907-1997): British biochemist and virologist co-discoverer in 1936 of viral crystallization, an important ... a much more reliable method of altering animal genomes than previously used, and the technique behind gene targeting and ...
Genomes are linear and non-segmented, around 7.8kb in length. Viral replication is cytoplasmic. Entry into the host cell is ... The 3' end of the genome encodes a polyA tail while the 5' end encodes a genome-linked protein. A unique feature of this genus ... "Viral Zone". ExPASy. Retrieved 15 June 2015. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015. Jones, MS.; Lukashov ... Translation takes place by -1 ribosomal frameshifting, viral initiation, and ribosomal skipping. The virus exits the host cell ...
Eigen et al.[76] and Woese[77] proposed that the genomes of early protocells were composed of single-stranded RNA, and that ... Through the process of viral infection into hosts the three domains of life evolved.[83][84] Another interesting proposal is ... In comparison, the genome of the smallest known viruses capable of causing an infection are about 2,000 nucleobases long.[72] ... Genome redundancy would allow a damaged RNA segment to be replaced by an additional replication of its homolog. However, for ...
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- ...
Together, these studies provide preclinical evidence that non-viral genome targeting can enable rapid and flexible experimental ... Here we developed a CRISPR-Cas9 genome-targeting system that does not require viral vectors, allowing rapid and efficient ... 2 using recombinant viral vectors, which do not target transgenes to specific genomic sites3,4. The need for viral vectors has ... A non-viral strategy to introduce large DNA sequences into T cells enables the correction of a pathogenic mutation that causes ...
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 ...
DNA viruses such as bacteriophages and herpesviruses deliver their genome into and out of the capsid through large ... Three-dimensional structure of a viral genome-delivery portal vertex Nat Struct Mol Biol. 2011 May;18(5):597-603. doi: 10.1038/ ... We propose that the barrel domain facilitates genome spooling onto the interior surface of the capsid during genome packaging ... DNA viruses such as bacteriophages and herpesviruses deliver their genome into and out of the capsid through large ...
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, ...
Fig.1: Genome Organization of Dengue. DV genome organization, polyprotein processing scheme and membrane topology of viral ... 1. Genome Organization & Viral Protein Expression. DV belongs to the genus Flavivirus in the family Flaviviridae. These viruses ... B) DV genomic organization and functions of viral proteins. For some proteins their function in the viral life cycle is not yet ... Kliniken & Institute … Institute Zentrum für… Molecular Virology … Research Area DENGUE 1. Genome Organization… ...
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 ...
Detailed analyses of HCV have been hampered by the lack of viral culture systems. Subgenomic replicons of the JFH1 genotype 2a ... Production of infectious hepatitis C virus in tissue culture from a cloned viral genome Nat Med. 2005 Jul;11(7):791-6. doi: ... Here we show that the JFH1 genome replicates efficiently and supports secretion of viral particles after transfection into a ... Detailed analyses of HCV have been hampered by the lack of viral culture systems. Subgenomic replicons of the JFH1 genotype 2a ...
... ​ By IANS , Published on ​ Sun, May 9 2021 22:42 IST , ​ 1 Views ... have been sent for viral genome sequencing to the CSIR-Institute of Genomics and Integrative Biology in New Delhi. ... This is giving rise to a suspicion that a particular viral variant may be circulating in the Civil Lines area of Aligarh in ... section/department of the ICMR to perform analysis of Covid samples sent from our lab to investigate for any particular viral ...
... 13 September 2009. by Vincent Racaniello Hosts: Vincent Racaniello and Dick Despommier. On episode 49 ... The seven types of viral genome. Animation of HIV replication (thanks axiomatically atypical!). Changes in transcript abundance ... Vincent and Dick continue Virology 101 with a discussion of the seven different types of viral genomes, and how to use the ...
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 ...
GENEWIZs viral genome sequencing provides a streamlined approach for adeno-associated virus (AAV) gene therapy applications, ... VIRAL GENOME SEQUENCING. GENEWIZs NGS solutions can be leveraged for adeno-associated virus (AAV) applications, providing a ... Adeno-associated Virus Genome Population Sequencing Achieves Full Vector Genome Resolution and Reveals Human-Vector Chimeras. ... Discover how researchers utilized single molecule, real-time (SMRT®) sequencing to profile rAAV-packaged genomes and assess ...
Meet your viral ancestors - how bornaviruses have been infiltrating our genomes for 40 million years * facebook ... Meet your viral ancestors - how bornaviruses have been infiltrating our genomes for 40 million years ... You find them by taking the viral seqeunces and searching the human genome/proteome for matches. ... The human genome is littered with the remains of viruses that, in ages past, integrated their genes into the DNA of our ...
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). ...
  • Here we developed a CRISPR-Cas9 genome-targeting system that does not require viral vectors, allowing rapid and efficient insertion of large DNA sequences (greater than one kilobase) at specific sites in the genomes of primary human T cells, while preserving cell viability and function. (nature.com)
  • DNA sequences called endogenous retroviruses (ERVs) are abundant in mammalian genomes. (icr.org)
  • 2 These ERVs contain special sequences that act like genetic switches in the genome by binding regulatory proteins (transcription factors) that control genes. (icr.org)
  • Since the discovery of CIV in 1966, many attempts were made to elucidate the viral genome structure and the amino acid sequences of different viral gene products. (springer.com)
  • Twelve more samples had sufficient coverage of redondovirus sequences to allow assembly, yielding 19 complete genomes. (genengnews.com)
  • They compared the BSL RDHV genome to other metagenomic DNA sequences from the Global Ocean Survey, and found strong evidence to conclude that previously undetected BSL RDHV-like viruses could be widespread in the marine environment and are likely to be found in other environments as well. (sott.net)
  • These additions look a lot like the 'fossil' EBLN sequences found in our own genomes. (scienceblogs.com)
  • The study provides definitive proof of a theory that was first proposed in the 1950s by Nobel Laureate in physiology and medicine, Barbara McClintock, who hypothesized that transposable elements, mobile pieces of the genetic material (DNA), such as viral sequences, could be "control elements" that affect gene regulation once inserted in the genome. (redorbit.com)
  • This by itself would be very surprising, but the investigators go further and demonstrate that many of the sites are imbedded within a class of DNA sequences called "transposable" elements because of their ability to move to new places in the genome. (redorbit.com)
  • Research on viral infections is heavily dependent on available genome sequences of both the virus and its human host. (mpg.de)
  • These genome sequences provide the basis for understanding the complex molecular interplay between the pathogen and the patient, knowledge that is crucial for both drug development and therapy optimization. (mpg.de)
  • Recent advances in sequencing technologies allow us to explore microbial diversity in a sample, making metagenomic analysis a promising technique to characterize the viral spectrum (that is, the viral sequences and their abundances) in stool samples. (biomedcentral.com)
  • Currently, reverse transcription followed by polymerase chain reaction (RT-PCR) with primers designed to amplify specific viral RNA sequences is the most common method for amplifying RNA viruses prior to sequencing and other downstream applications. (pubmedcentralcanada.ca)
  • A third clone was generated from primer-extended DNA and contained sequences from the 5' end of the viral RNA. (caltech.edu)
  • These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown' sequence space in viromes. (elifesciences.org)
  • Earlier in 2015, researchers developed a new computational tool called VirSorter that can predict virus genome sequences within the DNA extracted from microbes. (elifesciences.org)
  • VirSorter identifies viral genome sequences based on the presence of 'hallmark' genes that encode for components found in many virus particles, together with a reference database of genomes from many viruses. (elifesciences.org)
  • These data increase the number of viral genome sequences that are publically available by a factor of ten and identify the first viruses associated with 13 new types of bacteria, which include species that are abundant in particular environments. (elifesciences.org)
  • However, research also shows that animal cells can benefit from integrated viral sequences (e.g., to support host cell development or to silence foreign invaders). (diva-portal.org)
  • Here we propose that, comparable with the clustered regularly interspaced short palindromic repeats that provide bacteria with adaptive immunity against invasive bacteriophages, animal cells may co-opt integrated viral sequences to support immune memory. (diva-portal.org)
  • We hypothesize that host cells express viral peptides from open reading frames in integrated sequences to boost adaptive B cell and T cell responses long after replicating viruses are cleared. (diva-portal.org)
  • In support of this hypothesis, we examine previous literature describing (1) viruses that infect acutely (e.g., vaccinia viruses and orthomyxoviruses) followed by unexplained, long-term persistence of viral nucleotide sequences, viral peptides, and virus-specific adaptive immunity, (2) the high frequency of endogenous viral genetic elements found in animal genomes, and (3) mechanisms with which animal host machinery supports foreign sequence integration. (diva-portal.org)
  • Although this ability to gather larger collections of genome sequences has opened up new avenues of research, it has also led to significant problems related to data management and sequence annotation. (biomedcentral.com)
  • The new algorithm excels at metavirome assembly: identifying viral snippets hidden among much longer bacterial sequences and stitching them together into a complete genome. (ucsd.edu)
  • Computational techniques were then used to search for links between variants in the human DNA sequences and variants in the viral sequences. (elifesciences.org)
  • Expanding Virophage Diversity Researchers provided a global analysis of the diversity, distribution, and evolution of virophages - and in doing so, increased the number of known high quality virophage genome sequences 10-fold through computational approaches. (doe.gov)
  • Full-length sequences of HCV genome were determined, and analyzed for changes in each patient. (druglib.com)
  • These observations suggest that signals required for the encapsidation of HSV-1 DNA are located within DNA sequences shared by the inserted fragments and therefore lie within the reiterated 'a' sequence of the viral genome. (gla.ac.uk)
  • The hearts were examined histologically and analyzed for the presence of viral sequences by polymerase chain reaction (PCR) or reverse transcription-PCR. (onlinejacc.org)
  • More than half of the genome is comprised of repeat sequences, they noted, including many repeats not previously detected in other genomes. (genomeweb.com)
  • When they compared these duplication patterns with those in the grape vine, poplar, papaya, and Arabidopsis thaliana sequences, they found evidence for ancient hexaploidization - triplication of the diploid genome - in the dicot common ancestor. (genomeweb.com)
  • But, in the meeting with Anders Nilsson, he said that phage genomes might contain sequences that are the same as the host genome, so a host sequence depletion step can probably not be performed thoughtlessly. (novum.se)
  • Through analysing whole genome sequences, a clearer picture of genome-wide mutation signature patterns can emerge, providing insights into the aetiology of carcinogenesis. (nature.com)
  • The characterization of 4,645 whole‑genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small insertion‑and‑deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development. (nature.com)
  • The researchers identified three viral clades in the Gwangju sequences, namely, GH, GR, and V. Of the seven V isolates, five were from an outbreak within a religious group called the Shincheonji Church of Jesus, and two from another church. (news-medical.net)
  • We describe evidence that SARS-CoV-2 RNAs can be reverse transcribed in human cells by reverse transcriptase (RT) from LINE-1 elements or by HIV-1 RT, and that these DNA sequences can be integrated into the cell genome and subsequently be transcribed," the authors summarized. (medium.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)
  • Their form of parasitism implies the idea that a compact viral genome would carry only the most necessary genes. (asm.org)
  • Many of the SSV1 genes are not homologous to other viral genes, and were assumed to be required for survival under these conditions. (asm.org)
  • The dispensability of these genes, including one of the viral capsid protein genes, vp3 , was unexpected by the scientific team led by senior scientist Kenneth Stedman. (asm.org)
  • To better understand the function of other SSV1 genes, 78 mutant genomes were constructed and tested for their ability to infect Sulfolobus cells. (asm.org)
  • While the number of nonessential genes was surprising, the results allowed the research team to further refine the core fusellovirus viral genome. (asm.org)
  • The dispensable nature of some of the structural genes was particularly surprising, given the importance of structural integrity not only to contain the viral genome, but also to attach and deliver that genome to host cells. (asm.org)
  • The human genome is littered with the remains of viruses that, in ages past, integrated their genes into the DNA of our ancestors. (scienceblogs.com)
  • This process depends on the viral genes jumping into the right place. (scienceblogs.com)
  • It's possible that BDV creates disease-causing mutations by inserting its genes into the wrong parts of our genomes. (scienceblogs.com)
  • Among the tested 31940 gene models a core genome of 14628 genes was identified by hybridization among 16 E. huxleyi strains. (awi.de)
  • Within the variable (non-core) genome we identified genes associated with virus susceptibility and calcification. (awi.de)
  • Previous attempts to investigate intrahost genetic variation in DENV characterized only a few viral genes or a limited number of full-length genomes. (pubmedcentralcanada.ca)
  • Interestingly, a strong association was discerned between the extent of intrahost diversity in a few genes and viral clade identity. (pubmedcentralcanada.ca)
  • It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring reference genome annotations to the target genome. (biomedcentral.com)
  • the genomes of these viruses are far more variable, and contain many non-essential genes not conserved between closely related viruses. (biomedcentral.com)
  • Indeed, genes within a genome have not all followed the same evolutionary path due to events such as incomplete lineage sorting, horizontal gene transfer, gene duplication and deletion, or recombination. (biomedcentral.com)
  • Our method pinpoints viral genes with common evolutionary patterns. (biomedcentral.com)
  • In the genomic era, datasets span several genes (sometimes the whole genome), each available in a variable number of taxa. (biomedcentral.com)
  • a significantly higher than expected number of variants was also seen in genes encoding proteins that directly interact with viral components. (prolekare.cz)
  • Analysis of functional relationships among genes subjected to virus-driven selective pressure identified a complex network enriched in viral products-interacting proteins. (prolekare.cz)
  • Genes involved in anti-viral response have therefore been presumably subjected to an enormous, continuous selective pressure. (prolekare.cz)
  • To help improve the control of Marek's disease, veterinary medical officer John Dunn and his team at the Agricultural Research Service (ARS) Avian Disease and Oncology Laboratory in East Lansing, Michigan, analyzed Marek's disease genomes to find out which genes are mostly associated with virulence. (technologynetworks.com)
  • Using RNA-Seq data for this species and manual annotation of genes of viral origin, we annotated a high-quality gene set including 171 virus-derived protein-coding genes. (usda.gov)
  • Although 10 years have passed since the genome of vaccinia virus was sequenced ( 3 ), the roles of about half of the genes remain entirely unknown. (pnas.org)
  • Meanwhile, their search for genes related to those coding for the toxic protein ricin uncovered 28 genes belonging to a lectin gene family - many of which clustered together in the genome. (genomeweb.com)
  • And while many genes in the genome are present in multiple copies, those involved in oil synthesis and related processes are found in single copies. (genomeweb.com)
  • In discussions with Anders it was advised that this strategy might be possible to do for some of the genes, but not any longer stretches of the phage genome. (novum.se)
  • Cancer is a disease of the genome, caused by a cell's acquisition of somatic mutations in key cancer genes. (nature.com)
  • Until recently, research on the cancer genome was focused on protein-coding genes, which together account for only 1% of the genome. (nature.com)
  • Both HIV-1 RT and LINE1 can integrate parts of certain virus's genes into the human genome. (medium.com)
  • Using various genetic tools, they confirmed the presence of SARS-CoV-2 genes (coding for nucleocapsid protein) in the genome inside the human cell nucleus. (medium.com)
  • In human cells with low LINE-1 or HIV-1 RT expression, SARS-CoV-2 genes were also detected in the genome but at lower levels. (medium.com)
  • These analyses show that LINE-1 (that human cells normally express) and HIV-1 RT can integrate SARS-CoV-2 genes into the human genome inside the cell nucleus. (medium.com)
  • Next, by analyzing the genomes of these published datasets, the study also found traces of SARS-CoV-2 genes. (medium.com)
  • These results show that human cells infected with SARS-CoV-2 exhibit an increase in LINE-1 expression, which integrates SARS-CoV-2 genes into the cell's genome. (medium.com)
  • Viral genomes often encode genes derived from their host. (pnas.org)
  • These genes may allow the virus to manipulate host metabolism to improve viral fitness. (pnas.org)
  • DNA viruses such as bacteriophages and herpesviruses deliver their genome into and out of the capsid through large proteinaceous assemblies, known as portal proteins. (nih.gov)
  • The amino termini of prM, E, NS1 and NS4B are generated upon cleavage by the host ER signal peptidase in the lumen of the ER, whereas the processing of most of the other NS proteins and the C-terminus of the C protein is carried out by the viral two-component protease NS2B-NS3 in the cytoplasm of DV infected cells. (uni-heidelberg.de)
  • DV genome organization, polyprotein processing scheme and membrane topology of viral proteins. (uni-heidelberg.de)
  • B) DV genomic organization and functions of viral proteins. (uni-heidelberg.de)
  • In the Nature study , the researchers imaged the organization of the dsRNA genome and proteins inside the virus. (ucla.edu)
  • These results point to defective interactions between a translation initiation factor and the viral VPg as the most probable cause of host-specific incompatibility, in which other viral factors also participate, and suggest that complex interactions between multiple viral proteins and translation initiation factors not only define resistance to potyviruses in particular varieties of susceptible hosts but also contribute to establish nonhost resistance. (apsnet.org)
  • Viral RNA was detected by in situ hybridization, and five viral proteins were localized using immunohistochemical staining in leaf sections. (apsnet.org)
  • Outside the infection foci, conspicuous signals for VPg were readily and exclusively detected in CC of many veins in all vein classes in the absence of signals for NIapro, other viral proteins, and viral RNA. (apsnet.org)
  • With a genome of only 5.2 kbp, SV40 relies heavily on host cell machinery to propagate, affording investigators a powerful tool to discover key host proteins that the virus manipulates. (prolekare.cz)
  • 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. (elsevier.com)
  • 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. (asmscience.org)
  • HPV31 genomes encoding two of the mutant E1 proteins were not maintained as episomes in immortalized primary keratinocytes, whereas one encoding the third mutant protein was maintained at a very low copy number. (northwestern.edu)
  • We constructed an array of yeast transformants that contained each of the 266 predicted viral ORFs as Gal4 activation domain hybrid proteins. (pnas.org)
  • Vaccinia virus has a genome of approximately 190 kbp and can potentially express more than 200 proteins, allowing an exceptional degree of independence from the host ( 3 ). (pnas.org)
  • Additional viral proteins are needed to maintain adequate levels of deoxyribonucleotides for DNA replication, including a thymidine kinase, a thymidylate kinase, a deoxyribonucleotide reductase, and a deoxyuridine triphosphatase. (pnas.org)
  • Other viral proteins interact with host components to facilitate virus dissemination, prevent apoptosis, and attenuate immune responses ( 8 , 9 ). (pnas.org)
  • Each of the ≈70,000 potential pairwise combinations of proteins was assayed, identifying putative interactions among both characterized viral proteins and those of unknown function. (pnas.org)
  • We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as hnRNPA1, PABPC1 and eIF4b, which may play important roles in the viral life cycle. (cdc.gov)
  • We also detected four viral sequence variants in the spike, polymerase, and nonstructural proteins that correlate with severity of COVID-19. (cdc.gov)
  • These encode the large polyprotein that is cleaved to generate the 16 viral non-structural proteins and take up two-thirds of the whole genome. (news-medical.net)
  • Note: Viral polyprotein is not a single protein, it is a combination of several proteins. (techylib.com)
  • Where to find the proteins in the genome entry? (techylib.com)
  • The human genome can then read and translate this new piece of DNA into new proteins. (medium.com)
  • This supports the hypothesis that the human genome can make SARS-CoV-2-human chimeric transcripts, which may be transcribed into new proteins. (medium.com)
  • Other adjustments to the bacteria's designer genome endowed the bug with the ability to string together non-natural amino acids to produce proteins never before seen inside a living cell. (cdc.gov)
  • The genome and proteins of HIV (human immunodeficiency virus) have been the subject of extensive research since the discovery of the virus in 1983. (wikipedia.org)
  • The HIV genome encodes a small number of viral proteins, invariably establishing cooperative associations among HIV proteins and between HIV and host proteins, to invade host cells and hijack their internal machineries.HIV is different in structure from other retroviruses. (wikipedia.org)
  • Its innermost region consists of a cone-shaped core that includes two copies of the (positive sense) ssRNA genome, the enzymes reverse transcriptase, integrase and protease, some minor proteins, and the major core protein. (wikipedia.org)
  • The genome of human immunodeficiency virus (HIV) encodes 8 viral proteins playing essential roles during the HIV life cycle. (wikipedia.org)
  • Viral structural proteins are encoded by long ORFs, whereas smaller ORFs encode regulators of the viral life cycle: attachment, membrane fusion, replication, and assembly. (wikipedia.org)
  • These viruses have a single stranded RNA genome of positive polarity which is about 11,000 nucleotides long. (uni-heidelberg.de)
  • Evolutionists have long claimed that human chromosomes were infected with many different viruses over millions of years, which then multiplied in the genome. (icr.org)
  • Then evolutionists proclaimed the animal genomes evolved to their present state, in part by repeated infection with viruses initially deemed part of an organism's 'junk' DNA. (icr.org)
  • This software should help researchers design multiplex sets of primers for targeted whole genome enrichment prior to sequencing to obtain better coverage of low titer, divergent viruses. (hindawi.com)
  • Sequencing whole genomes of potentially heterogeneous or divergent viruses can be challenging from a small or complex sample with low viral concentrations. (hindawi.com)
  • Deep sequencing to detect rare viral variants or metagenomic sequencing to genotype viruses from a complex background requires targeted viral amplification. (hindawi.com)
  • Viruses rely on the molecular machinery of their host for many of the functions necessary to generate their viral progeny. (asm.org)
  • A study published in BioMed Central's Biology Direct journal reports the existence of a previously undetected group of viruses and, more importantly, a new type of viral genome that could have huge implications for theories of viral emergence and evolution. (sott.net)
  • Astonishingly, they found a unique viral genome that has never before been reported - a circular, single-stranded DNA virus encoding a major capsid protein seen previously only in RNA viruses. (sott.net)
  • Here, the use of the CODEHOP strategy to identify novel viruses and obtain sequence information for phylogenetic characterization, gene structure determination and genome analysis is reviewed. (nih.gov)
  • Whole genome sequencing of viruses and bacteriophages is often hindered because of the need for large quantities of genomic material. (jcvi.org)
  • In particular, it was discovered that specific types of viruses that inserted themselves in the human genomes millions of years ago have dramatically changed the gene regulatory network in human stem cells. (redorbit.com)
  • These peculiarities compromise the suitability of traditional tools and analysis methods developed for the analysis of the human genome to study infections by viruses. (mpg.de)
  • We have demonstrated the utility of the method on various types and sources of viruses, obtaining near complete genome sequence of viruses ranging in size from 3,000-15,000 kb with a median depth of coverage of 14.33. (biomedcentral.com)
  • The method described is of great utility in generating whole genome assemblies for viruses with little or no available sequence information, viruses from greatly divergent families, previously uncharacterized viruses, or to more fully describe mixed viral infections. (biomedcentral.com)
  • Two overlapping fragments were produced using a newly designed degenerated primer targeting the conserved CRE region for enteroviruses A-D and one degenerated primer set designed to specifically target the conserved region for each enterovirus species (EV-A to -D). This method was capable of sequencing the full genome for all viruses except two, for which nearly 90% of the genome was sequenced. (frontiersin.org)
  • Enteroviruses are non-enveloped viruses, approximately 7500 nucleotides (nt) in length with a positive, single-stranded RNA genome. (frontiersin.org)
  • By studying the genomes of particular viruses that are present in vivo , we may obtain a complete picture of the causes of diarrhea and potentially identify unknown viral pathogens. (biomedcentral.com)
  • In our pipeline, we first assembled the genomes of known diarrhea-causing viruses by aligning the reads with the available references in the National Center for Biotechnology Information database and reconstructing the haplotypes from the mapped reads. (biomedcentral.com)
  • Additional care needs to be taken for RNA viruses because they exist as a set of closely related but nonidentical genomes (quasispecies). (biomedcentral.com)
  • The research demonstrates for the first time how viruses sense environmental conditions inside a host cell to trigger transcription, and presents key findings about how the dsRNA genome is organized inside the virus and RNA's mechanism for self-replication. (ucla.edu)
  • The genomes of many viruses traffic into the nucleus, where they are either integrated into host chromosomes or maintained as episomal DNA and then transcriptionally activated or silenced. (uzh.ch)
  • Viruses use ASCE segregation motors to package their genomes into their protein capsids and provide accessible experimental systems due to their relative simplicity. (sciencemag.org)
  • We have studied the presence of long-range correlations in the complete genomes of ten different dsDNA viruses and Saccharomyces cerevisiae (bakers' yeast) chromosome I. We have also studied the correlation between the distribution of the gene length and the domain of "1/f region" of their genomes. (niscair.res.in)
  • Analogous to observations in RNA viruses such as human immunodeficiency virus, genetic variation associated with intrahost dengue virus (DENV) populations has been postulated to influence viral fitness and disease pathogenesis. (pubmedcentralcanada.ca)
  • The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. (elifesciences.org)
  • Many viruses integrate their genome into the DNA of their host cell, and there are computational tools available that exploit this ability to identify viruses and link them to their host. (elifesciences.org)
  • However, other viruses can live and multiply inside cells without integrating their genome into the host's DNA. (elifesciences.org)
  • These new viral genomes will serve as a useful resource for researchers as they explore the communities of viruses and microbes in natural environments, the human body and in industrial processes. (elifesciences.org)
  • While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics - Canada http://www.virology.ca , we found that researchers were unnecessarily spending time annotating viral genomes that were close relatives of already annotated viruses. (biomedcentral.com)
  • With recent advances in DNA sequencing technology and reductions in sequencing costs, it has become relatively easy to sequence the complete genomes of many viruses and it is not uncommon for researchers to determine the sequence of multiple virus isolates as part of a single experiment. (biomedcentral.com)
  • Computer scientists at UC San Diego and Saint Petersburg State University have developed a new approach to genome assembly that will help scientists identify new viruses in complex samples. (ucsd.edu)
  • The technique, called metaviralSPAdes, allows researchers and clinicians to delineate a single viral genome, even when it is mixed with thousands of others viruses and bacteria. (ucsd.edu)
  • The challenge with viral sequencing is that a sample from a patient, like the saliva from the COVID-19 patient used to assemble the first SARS-COV-2 genome, contains genomes from many other viruses. (ucsd.edu)
  • We must recognize the importance of ongoing viral surveillance, such as collecting samples from animals and studying this huge repertoire of viruses before they move to humans and trigger the next outbreak. (ucsd.edu)
  • In Hot Spring Microbial Mat, Viruses Ride "Piggyback" In The ISME Journal, scientists have used sequencing methods for the first time to comprehensively characterize viral-host interactions. (doe.gov)
  • In particular, viruses have affected humans before they emerged as a species, as testified by the fact that roughly 8% of the human genome is represented by recognizable endogenous retroviruses [2] which represent the fossil remnants of past infections. (prolekare.cz)
  • 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. (fjmu.edu.cn)
  • To increase our understanding of the poxvirus life cycle and to evaluate an approach that would be generally applicable to other large viruses, we initiated a genome-wide yeast two-hybrid analysis to identify vaccinia virus protein-protein interactions. (pnas.org)
  • We use cryo-electron microscopy to study the structures of viruses and viral vaccine candidates to help develop vaccines and antiviral agents. (utmb.edu)
  • When mixed together with a cocktail of five different bacteriophages - viruses that prey on bacteria - their genetically reformulated E. coli rebuffed the viral onslaught. (cdc.gov)
  • NS3 acts as the viral serine protease, which requires the protein NS2B as cofactor for activity. (uni-heidelberg.de)
  • Because s2m plays an essential role for the viral RNA to substitute host protein synthesis, we hypothesize the disruption of s2m could alter the viral viability or infectivity dramatically. (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 found significant inhibition of virus replication and viral protein expression in cells recipient of Cas9 together with JCPyV-specific single-guide RNA delivered prior to or after JCPyV infection. (harvard.edu)
  • Moreover, EGR1 protein co-localizes with EV71 RNA in the cytoplasm of infected cells to facilitate viral replication. (sigmaaldrich.com)
  • Applications can propose delivery of genome editors in the form of DNA, RNA, and/or protein. (sbir.gov)
  • With 5 million reads, we capture 96 to 100% of the viral protein coding region of HIV, respiratory syncytial and West Nile viral samples from as little as 100 copies of viral RNA. (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)
  • Genome-linked viral protein (VPg) mutations similar to those involved in the breakdown of eIF4E-mediated resistance to other potyviruses allow some PPV chimeras to infect A. thaliana . (apsnet.org)
  • Our goal was to develop a quantitative, high-throughput functional profiling system to identify viral cis -elements and protein subdomains critical for virus replication in the context of the herpesvirus genome. (asm.org)
  • Additionally, the abundance of viral variants within a host, as well as the impact of viral mutations on amino acid encoding and predicted protein function, determined whether intrahost variants were observed at the interhost level in circulating Nicaraguan DENV-2 populations, strongly suggestive of purifying selection across transmission events. (pubmedcentralcanada.ca)
  • Indeed, a single multifunctional viral protein, the large tumor (T) antigen (Tag) ( Figure 1A ), is sufficient to orchestrate the replication of the viral mini-chromosome in infected monkey cells [2] , [3] . (prolekare.cz)
  • We investigated interactions between PI(4,5)P2 and hepatitis C virus (HCV) nonstructural protein 5A (NS5A) and effects on the viral life cycle. (ntu.edu.sg)
  • By sequencing the plant's genome, researchers hope to learn more about producing the plant's economically valuable oil without making a toxic protein called ricin in the process. (genomeweb.com)
  • There were four mutations in the N protein, which is essential for the packaging of the viral RNA genome, which must happen before the virions can be released from the host cells. (news-medical.net)
  • We confirm that the viral transporter protein is expressed during infection and show that the protein functions to take up sources of nitrogen. (pnas.org)
  • This gene is transcribed during infection and when expressed in yeast mutants the viral protein is located to the plasma membrane and rescues growth when cultured with ammonium as the sole nitrogen source. (pnas.org)
  • HIV-1 is composed of two copies of noncovalently linked, unspliced, positive-sense single-stranded RNA enclosed by a conical capsid composed of the viral protein p24, typical of lentiviruses. (wikipedia.org)
  • envelope]] of the virion is formed by a plasma membrane of host cell origin, which is supported by a matrix composed of the viral p17 protein, ensuring the integrity of the virion particle. (wikipedia.org)
  • The density is high as the glycans shield underlying viral protein from neutralisation by antibodies. (wikipedia.org)
  • A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. (hindawi.com)
  • Targeted enrichment should preferentially amplify the target virus over host or environmental DNA/RNA, in contrast to random amplification commonly used prior to whole genome sequencing. (hindawi.com)
  • Primers designed to tile amplicons across a set of related viral genomes prior to sequencing can enrich whole viral genomes or large regions. (hindawi.com)
  • Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing," Virology Journal , vol. 9, article 261, 2012. (hindawi.com)
  • In order to analyse the severity of Covid and its suspected new variant that wreaked havoc in Aligarh, the samples collected at the ICMR approved Covid Testing Laboratory of the Department of Microbiology, Jawaharlal Nehru Medical College (JNMC), Aligarh Muslim University (AMU) have been sent for viral genome sequencing to the CSIR-Institute of Genomics and Integrative Biology in New Delhi. (prokerala.com)
  • New Delhi, Aug 1 (IANS) Union Health Minister Harsh Vardhan, here on Saturday, announced the completion of pan-India 1000 genome sequencing of SARS-CoV-2. (prokerala.com)
  • Sequence-confirm rAAV vectors and identify DNA contaminants in AAV library preparation by employing the power of GENEWIZ's short- and long-read whole genome sequencing solutions. (genewiz.com)
  • Discover how researchers utilized single molecule, real-time (SMRT ® ) sequencing to profile rAAV-packaged genomes and assess full-length integrity for rAAV quality control. (genewiz.com)
  • In this study, learn how short-read sequencing technology can extensively characterize the rAAV genome while simultaneously detecting the presence of DNA contaminants. (genewiz.com)
  • Sequencing viral genomes from a single isolated plaque. (jcvi.org)
  • This method can be used for de novo whole genome next-generation sequencing of any cultivable virus without the need for large-scale production of viral stocks or viral purification using centrifugal techniques. (jcvi.org)
  • The advent of next-generation sequencing technologies resulted in a dramatic drop in cost and increase in throughput of genome sequencing. (mpg.de)
  • Next-generation sequencing is also used to analyze the complex interaction of the hepatitis B virus with the host's immune system on the basis of the viral genome. (mpg.de)
  • this will require rapid and flexible methods for complete viral genome sequencing. (biomedcentral.com)
  • Given the success of earlier efforts for the identification of novel viral nucleic acids using SISPA, we sought to adapt and optimize this method as a general and cost effective technique for large scale de novo viral genome sequencing (Figures 1 and 2 ). (biomedcentral.com)
  • Development of rapid and broadly applicable methods for complete viral genome sequencing is highly desirable to fully understand all aspects of these infectious agents as well as for surveillance of viral pandemic threats and emerging pathogens. (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)
  • Massively parallel sequencing allows for rapid and low-cost deep sequencing of viral genomes and provides an opportunity to gain greater insight into viral evolution, fitness, emergence and transmission. (pubmedcentralcanada.ca)
  • However, standard RT-PCR methods are not adequate for the generation of templates suitable for sequencing low-copy viral RNA samples, where labor-intensive methods such as nested PCR ( 15 ) or single-genome amplification (SGA) ( 16 , 17 ) are typically required. (pubmedcentralcanada.ca)
  • Development of high-throughput methods for viral sequencing from low-copy viral samples presents challenges. (pubmedcentralcanada.ca)
  • We developed a whole-genome amplification approach coupled with deep sequencing to capture intrahost diversity across the entire coding region of DENV-2. (pubmedcentralcanada.ca)
  • Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral genomes have been sequenced. (biomedcentral.com)
  • This can be particularly challenging when sequencing a new pathogen, like the novel coronavirus, without a reference genome. (ucsd.edu)
  • took samples of both human and viral genomes from 1071 individuals infected with HIV, the AIDS virus, and used genotyping and sequencing technology to obtain a comprehensive description of the genetic variation in both. (elifesciences.org)
  • Here we applied a novel, comprehensive bioinformatic strategy to public RNA sequencing and viral genome sequencing data, to better understand how SARS-CoV-2 interacts with human cells. (cdc.gov)
  • Rabinowicz and his co-workers isolated nuclear DNA from castor bean seedlings and used Sanger sequencing to do paired-end sequencing of the roughly 350 million base castor bean genome to 4.6 times coverage. (genomeweb.com)
  • To address this issue, the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Project performed whole‑genome sequencing and integrative analysis on more than 2,600 primary cancers and their matching normal tissues across 38 distinct tumour types. (nature.com)
  • One of the advantages of sequencing whole genomes is the ability to move beyond characterization of point mutations. (nature.com)
  • PCAWG researchers use the information obtained from whole‑genome sequencing to delineate more precisely the parameters that influence tumour evolution, and how it shapes the cancer genome. (nature.com)
  • Analysis of mitochondrial genomes (mtDNA) using whole‑genome sequencing data from 2,658 cancer samples across 38 cancer types identifies hypermutated mtDNA cases, frequent somatic nuclear transfer of mtDNA and high variability of mtDNA copy number in many cancers. (nature.com)
  • Scientists in the Broad community are sequencing and analyzing the genomes of a wide range of insects and microorganisms to understand their genetic regulation, population variation, and specialized genomic mechanisms. (broadinstitute.org)
  • Using next-generation sequencing (NGS) methods, they identified point mutations in the genome. (news-medical.net)
  • Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome. (hdbr.org)
  • 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. (icr.org)
  • As I and several other creationist researchers have proposed, it's far more likely that ERVs were part of God's 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 man's sin. (icr.org)
  • Viral discovery has been aided by the development of sequence independent methodologies for the generation of genomic data [ 10 ]. (biomedcentral.com)
  • 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)
  • This phenomenon is likely a consequence of genomic differences, or transcriptomic responses, to environmental conditions or threats such as viral infections. (awi.de)
  • We used an E. huxleyi genome microarray based on the sequenced strain CCMP1516 (reference strain) to perform comparative genomic hybridizations (CGH) of 16 E. huxleyi strains of different geographic origin. (awi.de)
  • In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. (elifesciences.org)
  • Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. (elifesciences.org)
  • When genomic sequencers "read" a genome, it's not a linear process, like reading a book. (ucsd.edu)
  • 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)
  • The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host-pathogen interaction. (elifesciences.org)
  • A genome-wide association study (GWAS) was performed using the phenotypes time to death (TD) and binary survival (BS), along with the genotypes of the challenged fish using a Bayesian model (Bayes C). Heritabilities for resistance to IPNV estimated using genomic information, were 0.53 and 0.82 for TD and BS, respectively. (g3journal.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)
  • In gamma-2 herpesviruses, the transactivating factor RTA is essential for initiation of lytic gene expression and viral reactivation. (asm.org)
  • In some cases, integration translates to chronic viral infection, and in other instances, oncogenic gene mutations occur. (diva-portal.org)
  • 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)
  • Fig. 3: Monogenic autoimmune mutations corrected by non-viral genome targeting. (nature.com)
  • 3 Except for the NSW03 and NSW01 isolates, viral mutations are located at the stem loop-II (s2m) motif, an extremely conserved RNA element in the 3' untranslated region (Figure 1A). (mja.com.au)
  • There were 21 non-synonymous mutations and one frameshift mutation (deletion), as compared to the reference genome downloaded from the GISAID database. (news-medical.net)
  • Is the Subject Area "Viral genomics" applicable to this article? (plos.org)
  • 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)
  • The genome-scale expansion of the genetic profiling approach will expedite the functional genomics research on herpesvirus. (asm.org)
  • Picking Up Threads of Cotton Genomics High quality genomes of the five major cotton lineages have been assembled by a multi-institutional team and are available for comparative analysis on JGI's plant data portal Phytozome. (doe.gov)
  • We believe that the castor bean genome sequence and its annotation constitute the foundation for identifying the regulatory and metabolic networks controlling castor-oil biosynthesis," senior author Pablo Rabinowicz, a plant genomics researcher with the University of Maryland Institute for Genome Sciences and formerly with JCVI, and his colleagues wrote. (genomeweb.com)
  • The goals of the Broad Viral Genomics Group are to pioneer the application of these technologies to address the crucial unanswered biological questions in viral disease, and to foster a community of research leaders focused on using genomics to advance preventative and therapeutic strategies for viral diseases. (broadinstitute.org)
  • We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU), to transfer annotations from a previously annotated reference genome to a new target genome, thereby greatly reducing this laborious task. (biomedcentral.com)
  • 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)
  • GATU also detects open reading frames present in the target but not the reference genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. (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)
  • including some of the researchers from the earlier work-use VirSorter to predict viral DNA from publicly available bacteria and archaea genome data. (elifesciences.org)
  • The subsequent annotation of these genomes by multiple researchers, who may lack bioinformatics experience, is a tedious and time-consuming process. (biomedcentral.com)
  • Scaling Microbial Traits From Genomes to Watersheds Using remote sensing, metagenomics and machine learning, researchers are building new ways to predict of how plant and microbial metabolism interact to influence biogeochemistry across watersheds in the headwaters of the Colorado River. (doe.gov)
  • How to Target a Microbial Needle within a Community Haystack Enabled by the JGI's Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes. (doe.gov)
  • NEW YORK (GenomeWeb News) - An international team led by researchers at the University of Maryland and the J. Craig Venter Institute reported in the early, online edition of Nature Biotechnology yesterday that they have sequenced a draft version of the castor bean, Ricinus communis , genome. (genomeweb.com)
  • The researchers also looked for evidence of past genome duplications in castor bean genome. (genomeweb.com)
  • With the castor oil genome in hand, researchers are planning to undertake such studies, looking, for instance, at metabolome and transcriptome patterns in the castor beans to find metabolites and regulatory networks that can be manipulated in the castor beans themselves or transplanted into other plants to try to produce ricin-free castor oil. (genomeweb.com)
  • In addition, researchers say, the genome is expected to serve as tools for "developing improved diagnostic and forensic methods for ricin detection and cultivar identification for tracing sample origins. (genomeweb.com)
  • Thus researchers have spent much time tracing the changes in the viral genome over time. (news-medical.net)
  • On Thursday, that same group of researchers at the Medical Research Council Laboratory of Molecular Biology reported in Science that with continued tinkering, they've made their artificial life form virtually invincible to viral infection. (cdc.gov)
  • GATU greatly simplifies the initial stages of genome annotation by using a closely related genome as a reference. (biomedcentral.com)
  • In order to facilitate the process of annotation, we have developed a tool, Genome Annotation Transfer Utility (GATU), which makes use of the fact that most unannotated genomes are closely related to previously annotated genomes. (biomedcentral.com)
  • Look for the latest entry with complete genome and good functional annotation. (techylib.com)
  • Molecular biology and genetics techniques now dominate viral research in attempts to cure diseases such as AIDS. (booktopia.com.au)
  • Viral Genome Methods is a practical guide to the newest molecular techniques, providing step-by-step protocols to be used in the laboratory. (booktopia.com.au)
  • This could help better define the minimal SSV1 genome, which would improve the molecular tools scientists have to study both the bacteriophage itself and the Sulfolobus bacteria that they infect. (asm.org)
  • Research performed on model herbaceous hosts has been useful to unravel the molecular mechanisms that control viral infections. (apsnet.org)
  • Its discovery coincided with an explosion of knowledge in the new field of molecular biology, and SV40 was quickly adopted as a model to study eukaryotic genome structure, expression, replication, and cell growth regulation in cultured cells [1] . (prolekare.cz)
  • The molecular structure of the viral spike has now been determined by X-ray crystallography and cryo-electron microscopy. (wikipedia.org)
  • We propose that the barrel domain facilitates genome spooling onto the interior surface of the capsid during genome packaging and, in analogy to a rifle barrel, increases the accuracy of genome ejection into the host cell. (nih.gov)
  • The binding energy of capsid subunits on the genome is moderate (~7k B T 0 , with k B the Boltzmann constant and T 0 = 298 K, the room temperature), while the energy barrier separating the complexes and the virions is high (~ 20k B T 0 ). (cea.fr)
  • Depending on the size of the capsid enclosing the genome, three principles of viral nucleic acids import are discussed. (uzh.ch)
  • Second, the genome is injected from a capsid that is docked to the pore complex, and third, import factors are recruited to cytosolic capsids to increase capsid affinity to the pore complex, mediate translocation and allow disassembly in the nucleoplasm. (uzh.ch)
  • Each virion comprises a viral envelope and associated matrix enclosing a capsid, which itself encloses two copies of the single-stranded RNA genome and several enzymes. (wikipedia.org)
  • However, the association between disease symptoms from appearance of DENV genome in urine, renal injury (occurrence rate of 2.9-13.3% of dengue patients) and haemolytic uraemic syndrome in the pathogenesis of dengue fever is unclear [ 1 , 2 ]. (mdpi.com)
  • Studies of the relationship of the complete HIV-1 genome to pathogenesis therefore need to focus on plasma virions. (elsevier.com)
  • I request you to instruct the concerned section/department of the ICMR to perform analysis of Covid samples sent from our lab to investigate for any particular viral variants of Covid virus circulating in Aligarh, which may be giving rise to greater severity of the disease, so that we may consider other epidemiological links and measures to control the same as per advice and recommendations", wrote Mansoor. (prokerala.com)
  • We utilized the marks left by selection on allele frequency to identify viral infection-associated allelic variants. (prolekare.cz)
  • The novel approach to the study of infectious disease epidemiology presented herein may represent an alternative to classic genome-wide association studies and provides a large set of candidate susceptibility variants for viral infections. (prolekare.cz)
  • Despite the relevance of viral infection for human health, only few genome-wide association studies (GWAS) have been performed in the attempt to identify variants associated with increased susceptibility to infection or faster disease progression [4] - [5] . (prolekare.cz)
  • An alternative approach to discover variants that modulate susceptibility to viral infection is based on the identification of SNPs subjected to virus-driven selective pressure. (prolekare.cz)
  • and viral infections have emerged as an imperative global hazard. (sigmaaldrich.com)
  • Viral infections are considered the most frequent cause of myocarditis and dilated cardiomyopathy (DCM). (termedia.pl)
  • 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)
  • Since dual infections and recombination can occur in vivo, cloning an intact plasma virus genome as a single full-length molecule is desirable. (elsevier.com)
  • However, research addressing the effect of host innate immune evasion on the pathology caused by viral infections is less prevalent in the literature, though very relevant and interesting. (mdpi.com)
  • We have recently used a reverse genetics approach to generate a recombinant MHV capable of expressing CXCL10 (MHV-CXCL10) to characterize how CXCL10 signaling regulates innate immune responses to viral infection ( 21 ). (jimmunol.org)
  • Viral capsids: mechanical characteristics, genome packaging and delivery mechanisms. (nih.gov)
  • The main functions of viral capsids are to protect, transport and deliver their genome. (nih.gov)
  • This review focuses on the mechanical properties of viral capsids in general and the elucidation of the biophysical aspects of genome packaging mechanisms and genome delivery processes of double-stranded DNA bacteriophages in particular. (nih.gov)
  • In this way we directly connect the wealth of existing osmotic pressure data for DNA in the bulk with the DNA encapsidation curves within small viral capsids. (springer.com)
  • Here, we use timeresolved small-angle X-ray scattering to uncover the nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging their full RNA genome. (cea.fr)
  • A) Schematic of the single stranded RNA genome with highly structured RNA elements in the 5' and 3' NTRs. (uni-heidelberg.de)
  • In dengue fever patients, urine samples contain dengue virus (DENV) genomes and virus antigens were present in renal biopsies. (mdpi.com)
  • 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)
  • 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)
  • Once the DNA complex is complete, it is transcribed in a manner that does amplify the viral genome. (cueflash.com)
  • Two different strategies were employed to amplify the full-length genome: one amplified a 9-kb fragment, and the other amplified two overlapping 5-kb fragments. (elsevier.com)
  • As used here, the term "genome editing machinery" includes an editing enzyme, or other genome editing entity, as well as nucleic acids if applicable. (sbir.gov)
  • 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)
  • These data suggest that the presence of viral nucleic acid in the myocardium is common in HIV-infected children, and may relate to the development of myocarditis, DCM or CHF and may contribute to the rapid progression of HIV disease. (onlinejacc.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)
  • Our data illustrate the value of high-coverage genome-wide analysis of intrahost diversity for high-resolution mapping of the relationship between intrahost diversity and clinical, epidemiological, and virological parameters of viral infection. (pubmedcentralcanada.ca)
  • This extensive genetic variability originates from the accumulation of genetically distinct genomes in individual hosts (referred to here as intrahost diversity) due to the error-prone nature of the enzyme responsible for viral RNA replication, the viral RNA-dependent RNA polymerase (RdRp) ( 16 ). (pubmedcentralcanada.ca)
  • For their newly reported work, the team queried metagenomic datasets from multiple BAL samples, and were able to construct additional complete redondovirus genomes. (genengnews.com)
  • These genomes were then used as alignment targets to interrogate publicly available datasets. (genengnews.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)
  • To illustrate the applicability of the method, we have chosen two viral datasets, namely papillomaviruses and Turnip mosaic virus (TuMV) isolates, largely dissimilar in genome, evolutionary distance and biology. (biomedcentral.com)
  • The analysis of the coding capacity of the CIV genome revealed that 50% (234 ORFs) of all identified ORFs (468 ORFs) were non-overlapping. (springer.com)
  • SSV1 is a fusellovirus with a 15.5-kilobase, double-stranded DNA genome containing 35 open reading frames (ORFs). (asm.org)
  • The team observed that the Boiling Springs Lake RNA-DNA hybrid virus (BSL RDHV) genome is circular, but its size is roughly double that of typical circoviruses, with the ORFs arranged in an uncommon orientation. (sott.net)
  • The PCV2 genome encodes four ORFs. (biomedcentral.com)
  • Together, these studies provide preclinical evidence that non-viral genome targeting can enable rapid and flexible experimental manipulation and therapeutic engineering of primary human immune cells. (nature.com)
  • Fig. 1: Efficient non-viral genome targeting in primary human T cells. (nature.com)
  • Here we show that the JFH1 genome replicates efficiently and supports secretion of viral particles after transfection into a human hepatoma cell line (Huh7). (nih.gov)
  • Therefore, the objective of this FOA is to support the development and evaluation of innovative approaches to deliver genome editing machinery into somatic cells, with the ultimate goal of enabling the use of genome editing therapeutics to treat human disease. (sbir.gov)
  • Non-viral vector technologies could include, but are not limited to: Nanoparticles Liposomes Electroporation Physical delivery methods (devices) Prokaryotic systems Human cells that are modified to deliver genome editing machinery to target cells in vivo Synthetic viral-like particles Projects proposing the use of high-throughput, combinatorial, or barcoding-based screening approaches to develop cell-type specific delivery vehicles are encouraged. (sbir.gov)
  • Metagenomic analysis of human diarrhea: viral detection and discovery. (biomedcentral.com)
  • 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)
  • The most common type of genetic variation found in the human genome is a single nucleotide polymorphism, or SNP for short: a SNP is produced when a single nucleotide - an A, C, G or T - is replaced by a different nucleotide. (elifesciences.org)
  • 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)
  • allows the interactions between a microbe and a human host to be studied by looking at the genome of the microbe and the genome of the infected person. (elifesciences.org)
  • Due to the limited coding capacity of their small genomes, human papillomaviruses (HPV) rely extensively on host factors for the completion of their life cycles. (northwestern.edu)
  • Viral diseases have an enormous impact on human health worldwide. (broadinstitute.org)
  • A few days ago, a preprint titled " SARS-CoV-2 RNA reverse-transcribed and integrated into the human genome " was released in bioRxiv . (medium.com)
  • In simpler language, the study shows that human cells can turn coronavirus's RNAs into DNAs - in a process called reverse transcription - which are integrated into the human genome. (medium.com)
  • In contrast, long interspersed element 1 (LINE-1) is derived from evolutionary ancient virus remnants that make up about 17% of the human genome. (medium.com)
  • 2010. Endogenous non-retroviral RNA virus elements in mammalian genomes. (scienceblogs.com)
  • Assembly of shotgun metagenomic reads yielded complete circular genomes, which were then used to interrogate our collection of lung virome samples, allowing us to identify seven genomes," they stated. (genengnews.com)
  • Lead author Kenneth M Stedman said, "As more viral metagenomic data are generated and analyzed, additional evidence of recombination between RNA and DNA virus groups will likely be discovered. (sott.net)
  • To investigate whether the phenotype was associated with a potential viral agent, we shotgun sequenced viral particles that were isolated from kelp with normal (healthy) and bleached phenotypes. (frontiersin.org)
  • It is proposed that this pressure helps driving the genome into the host, but other mechanisms also seem to play an important role in ejection. (nih.gov)
  • The elucidation of the coding capacity and strategy of CIV was the first step towards understanding the underlying mechanisms of viral infection, replication and virus-host interaction. (springer.com)
  • We show by cryo-EM-focused image reconstruction that ASCE ATPases in viral double-stranded DNA (dsDNA) packaging motors adopt helical symmetry complementary to their dsDNA substrates. (sciencemag.org)
  • Double-stranded poliovirus cDNA was synthesized and inserted into the Pst I site of plasmid pBR322, and three clones were derived that together provided DNA copies of the entire poliovirus genome. (caltech.edu)
  • 3) more than 125 SARS genomes submitted since the first two SARS coronavirus genomes were published in May, 2003. (biomedcentral.com)
  • Alternative way to find SARS coronavirus genome. (techylib.com)
  • Genome Biology and Evolution. (icr.org)
  • 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)
  • This unusual genome provides proof that integration of an RNA virus into a DNA virus may have occurred between two unrelated virus groups at some point in evolution - something that has not been observed before. (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)
  • Through multiple rounds of selection and escape, host and pathogen genomes are imprinted with signatures of co-evolution that are governed by Darwinian forces. (elifesciences.org)
  • The most important take aways were that phages are difficult to assemble and annotate because their evolution are very fast, so when a phage genome is assembled and annotated it becomes irrelevant to use as a reference for other phage genomes. (novum.se)
  • BAsE-Seq is readily applicable for monitoring quasispecies evolution in viral diseases. (biomedcentral.com)
  • The SSV1 genome tolerates the DNA insertions necessary to generate shuttle vectors, allowing manipulation of its genome via traditional cloning methods. (asm.org)
  • For applications proposing delivery technologies for organs and cell types that are currently accessible to in vivo genome editing by available methods, emphasis will be placed on technologies that produce substantial qualitative improvements in clinical application. (sbir.gov)
  • However, traditional viral detection methods rely on prior sequence or antigen knowledge. (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)
  • Computationally Classifying Fungal Lifestyles Machine learning methods were applied on sequenced fungal genomes, generated in part through the 1000 Fungal Genomes Project, to classify them by lifestyles. (doe.gov)
  • CRISPR has developed into a core tool to facilitate genome editing, inspiring transformative ideas in engineering biology. (genomeweb.com)
  • These advances in structural biology were made possible due to the development of stable recombinant forms of the viral spike by the introduction of an intersubunit disulphide bond and an isoleucine to proline mutation in gp41. (wikipedia.org)
  • Together with our collaboration partners from the university hospital in Düsseldorf, we analyze the entire viral population within a host of multiple patients at several characteristic points in time. (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)
  • Blocking CXCL10 signaling results in increased mortality, accompanied by diminished T cell infiltration into the CNS, and enhanced viral recovery from the brain suggesting that CXCL10 is an important sentinel molecule in host defense following viral infection of the brain ( 13 , 16 ). (jimmunol.org)
  • Also, many of the fragments of viral genomes that have been identified have not yet been linked to their host microbes. (elifesciences.org)
  • What can be said about the nature of the viral genome and its tendency to gravitate to certain parts of the host cell? (cueflash.com)
  • But in case of these two kit , a big problem will face me that the host RNA will interfer with the viral RNA and this will make big noisy in my data in analysis stage. (seqanswers.com)
  • This means that the reads are first aligned to the host genome and only the unmapped reads are used for de novo assembly. (novum.se)
  • This work demonstrates how a virus can amend host-viral dynamics by modulating acquisition of nutrients from the environment. (pnas.org)
  • We identify in the genome of a phytoplankton virus, which infects the small green alga Ostreococcus tauri , a host-derived ammonium transporter. (pnas.org)
  • Env is responsible for binding to its primary host receptor, CD4, and its co-receptor (mainly CCR5 or CXCR4), leading to viral entry into its target cell. (wikipedia.org)
  • The two copies of RNA strands are vital in contributing to HIV-1 recombination, which occurs during reverse transcription of viral replication. (wikipedia.org)
  • The need for viral vectors has slowed down research and clinical use as their manufacturing and testing is lengthy and expensive. (nature.com)
  • 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)
  • Although many causative agents are known, as many as 40% of clinical cases are attributed to unknown viral pathogens. (biomedcentral.com)
  • 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)
  • Since interferons have been implicated in inflammatory diseases and immunopathology in addition to their protective role in infection, antagonizing the immune response may have an ambiguous effect on the clinical outcome of the viral disease. (mdpi.com)
  • Applying BAsE-Seq to a clinical sample, we obtained over 9,000 viral haplotypes, which provided an unprecedented view of hepatitis B virus population structure during chronic infection. (biomedcentral.com)
  • In hepatitis C virus (HCV) infection, serum viral load is important in the prediction of therapeutic efficacy. (druglib.com)
  • Replication of the viral genome is the primary goal of any viral infection, and thus obtaining structural information on the flavivirus replicase complex is an important step in understanding the virus replication mechanism and in developing antiviral therapeutics. (utmb.edu)
  • This novel feature of SARS-CoV-2 infection may explain why patients can continue to produce viral RNA after recovery and suggest a new aspect of RNA virus replication. (medium.com)
  • The biochemical, biophysical and structural aspects of genome packaging are examined in detail. (springer.com)
  • They were thus able to trace the phylogenetic descent of the isolates and to classify the viral strains from these patients. (news-medical.net)
  • 2,226 entries of viral genomes (1,524 distinct virus strains) in the database. (techylib.com)
  • The mutation in certain positions of the HCV genome may be determinant factors of the viral load in a relatively homogeneous patient population. (druglib.com)
  • On episode 49 of the podcast 'This Week in Virology", Vincent and Dick continue Virology 101 with a discussion of the seven different types of viral genomes, and how to use the pathway to mRNA to understand viral replication. (virology.ws)
  • A 535 base pair DNA fragment which maps entirely within the IRS/TRS regions of the herpes simplex virus type 1 (HSV-1) genome and contains all the cis-acting signals necessary for it to function as an origin of viral DNA replication has previously been identified (N.D. Stow and E.C. McMonagle, Virology, in press). (gla.ac.uk)
  • a powerful technique for the identification and characterization of viral genomes. (nih.gov)
  • 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)
  • In this study, we demonstrate the utility of the SISPA method and its use as a rapid and cost effective method for generating full genome coverage of a wide range of viral types from several sources. (biomedcentral.com)
  • 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)
  • Many copies of partial or complete ALV genomes were located in chicken DNA ( 1 ). (cdc.gov)
  • The complete 7410 nucleotide sequence of the poliovirus type I genome was obtained from cloned cDNA. (caltech.edu)
  • After this process is complete, GATU saves the newly annotated genome as a GenBank, EMBL or XML-format file. (biomedcentral.com)
  • Unfortunately, however, a large number of the complete virus genomes submitted to GenBank lack annotations, severely limiting the usefulness of the data. (biomedcentral.com)
  • This method provides a tool for studying complete HIV-1 genomes in relation to pathogenic processes. (elsevier.com)
  • One big issue with de novo assemblies are that they consist of a multitude of contigs and not the complete genome. (novum.se)
  • 1,193 entries of complete viral genome. (techylib.com)
  • The complete sequence of the HIV-1 genome, extracted from infectious virions, has been solved to single-nucleotide resolution. (wikipedia.org)
  • The viral genome is present within tumor cells either as abundant nonrandomly deleted extrachromosomal copies or as a single copy integrated into cellular DNA. (asm.org)
  • In this study, small RNA libraries were constructed from two tissues of subclinically PCV2 infected pigs to explore if PCV2 can encode viral miRNAs. (biomedcentral.com)
  • Virus-specific siRNA responses are amplified via the reverse transcription of viral RNA to viral DNA (vDNA). (archives-ouvertes.fr)
  • Today, these " endogenous retroviruses ", or ERVs, make up around 8% of our genome. (scienceblogs.com)
  • Endogenous retroviruses are weird, but how they got into our genomes and what they mean, evolutionarily, isnt too hard to understand (unless youre an IDiot). (scienceblogs.com)
  • 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)
  • We investigated the changes in viral presence and the impact of viral genome persistence in the myocardium on echocardiographic parameters, functional status and some laboratory parameters in a 6-month follow-up. (termedia.pl)
  • Local Mutagenesis: A Method for Generating Viral Mutants with Base Substitutions in Pr. (nih.gov)
  • Together these findings illustrate the value of mining viral signal from microbial genomes. (elifesciences.org)
  • The study identifies over 12,000 viral genomes and links them to their microbial hosts. (elifesciences.org)
  • s findings demonstrate the value of searching publicly available microbial genome data for fragments of viral genomes. (elifesciences.org)