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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

There are several types of genomic instability, including:

1. Chromosomal instability (CIN): This refers to changes in the number or structure of chromosomes, such as aneuploidy (having an abnormal number of chromosomes) or translocations (the movement of genetic material between chromosomes).
2. Point mutations: These are changes in a single base pair in the DNA sequence.
3. Insertions and deletions: These are changes in the number of base pairs in the DNA sequence, resulting in the insertion or deletion of one or more base pairs.
4. Genomic rearrangements: These are changes in the structure of the genome, such as chromosomal breaks and reunions, or the movement of genetic material between chromosomes.

Genomic instability can arise from a variety of sources, including environmental factors, errors during DNA replication and repair, and genetic mutations. It is often associated with cancer, as cancer cells have high levels of genomic instability, which can lead to the development of resistance to chemotherapy and radiation therapy.

Research into genomic instability has led to a greater understanding of the mechanisms underlying cancer and other diseases, and has also spurred the development of new therapeutic strategies, such as targeted therapies and immunotherapies.

In summary, genomic instability is a key feature of cancer cells and is associated with various diseases, including cancer, neurodegenerative disorders, and aging. It can arise from a variety of sources and is the subject of ongoing research in the field of molecular biology.

Polyploidy is a condition where an organism has more than two sets of chromosomes, which are the thread-like structures that carry genetic information. It can occur in both plants and animals, although it is relatively rare in most species. In humans, polyploidy is extremely rare and usually occurs as a result of errors during cell division or abnormal fertilization.

In medicine, polyploidy is often used to describe certain types of cancer, such as breast cancer or colon cancer, that have extra sets of chromosomes. This can lead to the development of more aggressive and difficult-to-treat tumors.

However, not all cases of polyploidy are cancerous. Some individuals with Down syndrome, for example, have an extra copy of chromosome 21, which is a non-cancerous form of polyploidy. Additionally, some people may be born with extra copies of certain genes or chromosomal regions due to errors during embryonic development, which can lead to various health problems but are not cancerous.

Overall, the term "polyploidy" in medicine is used to describe any condition where an organism has more than two sets of chromosomes, regardless of whether it is cancerous or non-cancerous.

Inversions are classified based on their location along the chromosome:

* Interstitial inversion: A segment of DNA is reversed within a larger gene or group of genes.
* Pericentric inversion: A segment of DNA is reversed near the centromere, the region of the chromosome where the sister chromatids are most closely attached.

Chromosome inversions can be detected through cytogenetic analysis, which allows visualization of the chromosomes and their structure. They can also be identified using molecular genetic techniques such as PCR (polymerase chain reaction) or array comparative genomic hybridization (aCGH).

Chromosome inversions are relatively rare in the general population, but they have been associated with various developmental disorders and an increased risk of certain diseases. For example, individuals with an inversion on chromosome 8p have an increased risk of developing cancer, while those with an inversion on chromosome 9q have a higher risk of developing neurological disorders.

Inversions can be inherited from one or both parents, and they can also occur spontaneously as a result of errors during DNA replication or repair. In some cases, inversions may be associated with other genetic abnormalities, such as translocations or deletions.

Overall, chromosome inversions are an important aspect of human genetics and can provide valuable insights into the mechanisms underlying developmental disorders and disease susceptibility.

1. Activation of oncogenes: Some viruses contain genes that code for proteins that can activate existing oncogenes in the host cell, leading to uncontrolled cell growth.
2. Inactivation of tumor suppressor genes: Other viruses may contain genes that inhibit the expression of tumor suppressor genes, allowing cells to grow and divide uncontrollably.
3. Insertional mutagenesis: Some viruses can insert their own DNA into the host cell's genome, leading to disruptions in normal cellular function and potentially causing cancer.
4. Epigenetic changes: Viral infection can also cause epigenetic changes, such as DNA methylation or histone modification, that can lead to the silencing of tumor suppressor genes and the activation of oncogenes.

Viral cell transformation is a key factor in the development of many types of cancer, including cervical cancer caused by human papillomavirus (HPV), and liver cancer caused by hepatitis B virus (HBV). In addition, some viruses are specifically known to cause cancer, such as Kaposi's sarcoma-associated herpesvirus (KSHV) and Merkel cell polyomavirus (MCV).

Early detection and treatment of viral infections can help prevent the development of cancer. Vaccines are also available for some viruses that are known to cause cancer, such as HPV and hepatitis B. Additionally, antiviral therapy can be used to treat existing infections and may help reduce the risk of cancer development.

When a chromosome breaks, it can lead to genetic instability and potentially contribute to the development of diseases such as cancer. Chromosome breakage can also result in the loss or gain of genetic material, which can further disrupt normal cellular function and increase the risk of disease.

There are several types of chromosome breakage, including:

1. Chromosomal aberrations: These occur when there is a change in the number or structure of the chromosomes, such as an extra copy of a chromosome (aneuploidy) or a break in a chromosome.
2. Genomic instability: This refers to the presence of errors in the genetic material that can lead to changes in the function of cells and tissues.
3. Chromosomal fragile sites: These are specific regions of the chromosomes that are more prone to breakage than other regions.
4. Telomere shortening: Telomeres are the protective caps at the ends of the chromosomes, and their shortening can lead to chromosome breakage and genetic instability.

Chromosome breakage can be detected through cytogenetic analysis, which involves staining the cells with dyes to visualize the chromosomes and look for any abnormalities. The detection of chromosome breakage can help diagnose certain diseases, such as cancer, and can also provide information about the risk of disease progression.

In summary, chromosome breakage is a type of genetic alteration that can occur as a result of various factors, including exposure to radiation or chemicals, errors during cell division, or aging. It can lead to genetic instability and increase the risk of diseases such as cancer. Detection of chromosome breakage through cytogenetic analysis can help diagnose certain diseases and provide information about the risk of disease progression.

Tetraploidy can be caused by various factors such as:

1. Polyploidy: This is a condition where an individual has more than two sets of chromosomes, including tetraploidy.
2. Chromosomal abnormalities: Such as aneuploidy, where there is an extra or missing copy of a specific chromosome.
3. Genetic disorders: Such as Down syndrome, which is caused by an extra copy of chromosome 21.
4. Environmental factors: Exposure to certain chemicals or radiation can increase the risk of tetraploidy.

Symptoms of tetraploidy can vary depending on the severity of the condition and may include:

1. Growth delays: Children with tetraploidy may experience slowed growth and development.
2. Intellectual disability: Some individuals with tetraploidy may have cognitive impairments and learning difficulties.
3. Physical abnormalities: Tetraploidy can result in a variety of physical characteristics, such as short stature, thinning hair, and distinctive facial features.
4. Increased risk of health problems: Individuals with tetraploidy may be more susceptible to certain health issues, such as heart defects, hearing loss, and vision problems.

Diagnosis of tetraploidy is typically made through chromosomal analysis, which can be performed on a blood or tissue sample. Treatment for tetraploidy is not always necessary, but may include:

1. Monitoring growth and development: Regular check-ups with a healthcare provider can help track the child's growth and development.
2. Speech and language therapy: Children with tetraploidy may benefit from speech and language therapy to address any communication difficulties.
3. Occupational therapy: Individuals with tetraploidy may need occupational therapy to help them develop skills and abilities.
4. Medication: In some cases, medication may be prescribed to manage associated health problems, such as heart defects or seizures.

It is important to note that every individual with tetraploidy is unique and may have a different experience and outcome. With appropriate medical care and support, many individuals with tetraploidy can lead fulfilling lives.

Explanation: Genetic predisposition to disease is influenced by multiple factors, including the presence of inherited genetic mutations or variations, environmental factors, and lifestyle choices. The likelihood of developing a particular disease can be increased by inherited genetic mutations that affect the functioning of specific genes or biological pathways. For example, inherited mutations in the BRCA1 and BRCA2 genes increase the risk of developing breast and ovarian cancer.

The expression of genetic predisposition to disease can vary widely, and not all individuals with a genetic predisposition will develop the disease. Additionally, many factors can influence the likelihood of developing a particular disease, such as environmental exposures, lifestyle choices, and other health conditions.

Inheritance patterns: Genetic predisposition to disease can be inherited in an autosomal dominant, autosomal recessive, or multifactorial pattern, depending on the specific disease and the genetic mutations involved. Autosomal dominant inheritance means that a single copy of the mutated gene is enough to cause the disease, while autosomal recessive inheritance requires two copies of the mutated gene. Multifactorial inheritance involves multiple genes and environmental factors contributing to the development of the disease.

Examples of diseases with a known genetic predisposition:

1. Huntington's disease: An autosomal dominant disorder caused by an expansion of a CAG repeat in the Huntingtin gene, leading to progressive neurodegeneration and cognitive decline.
2. Cystic fibrosis: An autosomal recessive disorder caused by mutations in the CFTR gene, leading to respiratory and digestive problems.
3. BRCA1/2-related breast and ovarian cancer: An inherited increased risk of developing breast and ovarian cancer due to mutations in the BRCA1 or BRCA2 genes.
4. Sickle cell anemia: An autosomal recessive disorder caused by a point mutation in the HBB gene, leading to defective hemoglobin production and red blood cell sickling.
5. Type 1 diabetes: An autoimmune disease caused by a combination of genetic and environmental factors, including multiple genes in the HLA complex.

Understanding the genetic basis of disease can help with early detection, prevention, and treatment. For example, genetic testing can identify individuals who are at risk for certain diseases, allowing for earlier intervention and preventive measures. Additionally, understanding the genetic basis of a disease can inform the development of targeted therapies and personalized medicine."


These disorders are caused by changes in specific genes that fail to function properly, leading to a cascade of effects that can damage cells and tissues throughout the body. Some inherited diseases are the result of single gene mutations, while others are caused by multiple genetic changes.

Inherited diseases can be diagnosed through various methods, including:

1. Genetic testing: This involves analyzing a person's DNA to identify specific genetic changes that may be causing the disease.
2. Blood tests: These can help identify certain inherited diseases by measuring enzyme levels or identifying specific proteins in the blood.
3. Imaging studies: X-rays, CT scans, and MRI scans can help identify structural changes in the body that may be indicative of an inherited disease.
4. Physical examination: A healthcare provider may perform a physical examination to look for signs of an inherited disease, such as unusual physical features or abnormalities.

Inherited diseases can be treated in various ways, depending on the specific condition and its causes. Some treatments include:

1. Medications: These can help manage symptoms and slow the progression of the disease.
2. Surgery: In some cases, surgery may be necessary to correct physical abnormalities or repair damaged tissues.
3. Gene therapy: This involves using genes to treat or prevent inherited diseases.
4. Rehabilitation: Physical therapy, occupational therapy, and other forms of rehabilitation can help individuals with inherited diseases manage their symptoms and improve their quality of life.

Inherited diseases are a significant public health concern, as they affect millions of people worldwide. However, advances in genetic research and medical technology have led to the development of new treatments and management strategies for these conditions. By working with healthcare providers and advocacy groups, individuals with inherited diseases can access the resources and support they need to manage their conditions and improve their quality of life.

Some common effects of chromosomal deletions include:

1. Genetic disorders: Chromosomal deletions can lead to a variety of genetic disorders, such as Down syndrome, which is caused by a deletion of a portion of chromosome 21. Other examples include Prader-Willi syndrome (deletion of chromosome 15), and Williams syndrome (deletion of chromosome 7).
2. Birth defects: Chromosomal deletions can increase the risk of birth defects, such as heart defects, cleft palate, and limb abnormalities.
3. Developmental delays: Children with chromosomal deletions may experience developmental delays, learning disabilities, and intellectual disability.
4. Increased cancer risk: Some chromosomal deletions can increase the risk of developing certain types of cancer, such as chronic myelogenous leukemia (CML) and breast cancer.
5. Reproductive problems: Chromosomal deletions can lead to reproductive problems, such as infertility or recurrent miscarriage.

Chromosomal deletions can be diagnosed through a variety of techniques, including karyotyping (examination of the chromosomes), fluorescence in situ hybridization (FISH), and microarray analysis. Treatment options for chromosomal deletions depend on the specific effects of the deletion and may include medication, surgery, or other forms of therapy.

There are several types of chromosome aberrations, including:

1. Chromosomal deletions: Loss of a portion of a chromosome.
2. Chromosomal duplications: Extra copies of a chromosome or a portion of a chromosome.
3. Chromosomal translocations: A change in the position of a chromosome or a portion of a chromosome.
4. Chromosomal inversions: A reversal of a segment of a chromosome.
5. Chromosomal amplifications: An increase in the number of copies of a particular chromosome or gene.

Chromosome aberrations can be detected through various techniques, such as karyotyping, fluorescence in situ hybridization (FISH), or array comparative genomic hybridization (aCGH). These tests can help identify changes in the chromosomal makeup of cells and provide information about the underlying genetic causes of disease.

Chromosome aberrations are associated with a wide range of diseases, including:

1. Cancer: Chromosome abnormalities are common in cancer cells and can contribute to the development and progression of cancer.
2. Birth defects: Many birth defects are caused by chromosome abnormalities, such as Down syndrome (trisomy 21), which is caused by an extra copy of chromosome 21.
3. Neurological disorders: Chromosome aberrations have been linked to various neurological disorders, including autism and intellectual disability.
4. Immunodeficiency diseases: Some immunodeficiency diseases, such as X-linked severe combined immunodeficiency (SCID), are caused by chromosome abnormalities.
5. Infectious diseases: Chromosome aberrations can increase the risk of infection with certain viruses, such as human immunodeficiency virus (HIV).
6. Ageing: Chromosome aberrations have been linked to the ageing process and may contribute to the development of age-related diseases.
7. Radiation exposure: Exposure to radiation can cause chromosome abnormalities, which can increase the risk of cancer and other diseases.
8. Genetic disorders: Many genetic disorders are caused by chromosome aberrations, such as Turner syndrome (45,X), which is caused by a missing X chromosome.
9. Rare diseases: Chromosome aberrations can cause rare diseases, such as Klinefelter syndrome (47,XXY), which is caused by an extra copy of the X chromosome.
10. Infertility: Chromosome abnormalities can contribute to infertility in both men and women.

Understanding the causes and consequences of chromosome aberrations is important for developing effective treatments and improving human health.

Neoplasm refers to an abnormal growth of cells that can be benign (non-cancerous) or malignant (cancerous). Neoplasms can occur in any part of the body and can affect various organs and tissues. The term "neoplasm" is often used interchangeably with "tumor," but while all tumors are neoplasms, not all neoplasms are tumors.

Types of Neoplasms

There are many different types of neoplasms, including:

1. Carcinomas: These are malignant tumors that arise in the epithelial cells lining organs and glands. Examples include breast cancer, lung cancer, and colon cancer.
2. Sarcomas: These are malignant tumors that arise in connective tissue, such as bone, cartilage, and fat. Examples include osteosarcoma (bone cancer) and soft tissue sarcoma.
3. Lymphomas: These are cancers of the immune system, specifically affecting the lymph nodes and other lymphoid tissues. Examples include Hodgkin lymphoma and non-Hodgkin lymphoma.
4. Leukemias: These are cancers of the blood and bone marrow that affect the white blood cells. Examples include acute myeloid leukemia (AML) and chronic lymphocytic leukemia (CLL).
5. Melanomas: These are malignant tumors that arise in the pigment-producing cells called melanocytes. Examples include skin melanoma and eye melanoma.

Causes and Risk Factors of Neoplasms

The exact causes of neoplasms are not fully understood, but there are several known risk factors that can increase the likelihood of developing a neoplasm. These include:

1. Genetic predisposition: Some people may be born with genetic mutations that increase their risk of developing certain types of neoplasms.
2. Environmental factors: Exposure to certain environmental toxins, such as radiation and certain chemicals, can increase the risk of developing a neoplasm.
3. Infection: Some neoplasms are caused by viruses or bacteria. For example, human papillomavirus (HPV) is a common cause of cervical cancer.
4. Lifestyle factors: Factors such as smoking, excessive alcohol consumption, and a poor diet can increase the risk of developing certain types of neoplasms.
5. Family history: A person's risk of developing a neoplasm may be higher if they have a family history of the condition.

Signs and Symptoms of Neoplasms

The signs and symptoms of neoplasms can vary depending on the type of cancer and where it is located in the body. Some common signs and symptoms include:

1. Unusual lumps or swelling
2. Pain
3. Fatigue
4. Weight loss
5. Change in bowel or bladder habits
6. Unexplained bleeding
7. Coughing up blood
8. Hoarseness or a persistent cough
9. Changes in appetite or digestion
10. Skin changes, such as a new mole or a change in the size or color of an existing mole.

Diagnosis and Treatment of Neoplasms

The diagnosis of a neoplasm usually involves a combination of physical examination, imaging tests (such as X-rays, CT scans, or MRI scans), and biopsy. A biopsy involves removing a small sample of tissue from the suspected tumor and examining it under a microscope for cancer cells.

The treatment of neoplasms depends on the type, size, location, and stage of the cancer, as well as the patient's overall health. Some common treatments include:

1. Surgery: Removing the tumor and surrounding tissue can be an effective way to treat many types of cancer.
2. Chemotherapy: Using drugs to kill cancer cells can be effective for some types of cancer, especially if the cancer has spread to other parts of the body.
3. Radiation therapy: Using high-energy radiation to kill cancer cells can be effective for some types of cancer, especially if the cancer is located in a specific area of the body.
4. Immunotherapy: Boosting the body's immune system to fight cancer can be an effective treatment for some types of cancer.
5. Targeted therapy: Using drugs or other substances to target specific molecules on cancer cells can be an effective treatment for some types of cancer.

Prevention of Neoplasms

While it is not always possible to prevent neoplasms, there are several steps that can reduce the risk of developing cancer. These include:

1. Avoiding exposure to known carcinogens (such as tobacco smoke and radiation)
2. Maintaining a healthy diet and lifestyle
3. Getting regular exercise
4. Not smoking or using tobacco products
5. Limiting alcohol consumption
6. Getting vaccinated against certain viruses that are associated with cancer (such as human papillomavirus, or HPV)
7. Participating in screening programs for early detection of cancer (such as mammograms for breast cancer and colonoscopies for colon cancer)
8. Avoiding excessive exposure to sunlight and using protective measures such as sunscreen and hats to prevent skin cancer.

It's important to note that not all cancers can be prevented, and some may be caused by factors that are not yet understood or cannot be controlled. However, by taking these steps, individuals can reduce their risk of developing cancer and improve their overall health and well-being.

The symptoms of chromosome duplication vary depending on the location and number of extra chromosomes present. Some common symptoms include:

* Delayed development and growth
* Intellectual disability
* Speech and language delays
* Physical abnormalities, such as heart defects or facial dysmorphism
* Increased risk of developing certain health problems, such as autism or epilepsy

Chromosome duplication can be diagnosed through a blood test or by analyzing cells from the body. Treatment is based on the specific symptoms and may include speech therapy, physical therapy, medication, or surgery.

Prognosis for individuals with chromosome duplication varies depending on the location and number of extra chromosomes present, as well as the presence of any other genetic conditions. Some individuals with chromosome duplication may have a good prognosis and lead normal lives, while others may experience significant health problems and developmental delays.

In some cases, chromosome duplication can be inherited from one or both parents, who may be carriers of the condition but do not exhibit any symptoms themselves. In other cases, chromosome duplication can occur spontaneously due to a mistake during cell division.

There is currently no cure for chromosome duplication, but early diagnosis and appropriate interventions can help manage symptoms and improve outcomes for affected individuals.

Types of Adenovirus Infections:

There are over 50 different serotypes of adenoviruses, and each one can cause a specific type of infection. Some of the most common types of adenovirus infections include:

1. Respiratory infections: Adenoviruses can cause upper respiratory tract infections such as bronchitis, bronchiolitis, and pneumonia.
2. Gastrointestinal infections: Adenoviruses can cause gastroenteritis, which is an inflammation of the stomach and intestines.
3. Eye infections: Adenoviruses can cause conjunctivitis, which is an infection of the eye that can lead to redness, swelling, and discharge.
4. Urinary tract infections: Adenoviruses can cause urinary tract infections (UTIs) such as cystitis and pyelonephritis.
5. Inflammatory diseases: Adenoviruses have been linked to certain inflammatory diseases such as arthritis, asthma, and dermatitis.

Symptoms of Adenovirus Infections:

The symptoms of adenovirus infections can vary depending on the type of infection and the age of the individual. Some common symptoms include:

1. Fever
2. Runny nose
3. Sore throat
4. Coughing
5. Diarrhea
6. Vomiting
7. Abdominal pain
8. Headache
9. Fatigue
10. Muscle aches

Diagnosis of Adenovirus Infections:

Adenovirus infections are typically diagnosed based on the symptoms and medical history of the individual. In some cases, a healthcare provider may perform laboratory tests to confirm the presence of the virus. These tests can include:

1. Polymerase chain reaction (PCR): This test detects the genetic material of the virus in a sample of body fluid or tissue.
2. Viral culture: This test involves growing the virus in a laboratory setting to confirm its presence.
3. Serology tests: These tests measure the levels of antibodies against the virus in the blood.

Treatment and Prevention of Adenovirus Infections:

There is no specific treatment for adenovirus infections, but supportive care can help manage symptoms. This can include:

1. Rest and hydration: Drinking plenty of fluids and getting enough rest can help the body recover from the infection.
2. Medications: Over-the-counter medications such as acetaminophen or ibuprofen can help relieve fever and pain.
3. Antiviral medications: In severe cases, antiviral medications may be prescribed to help reduce the severity of the infection.

Prevention is key to avoiding adenovirus infections. Here are some ways to prevent the spread of the virus:

1. Hand washing: Frequent hand washing, especially after coming into contact with someone who is sick or touching surfaces that may have the virus on them, can help prevent the spread of the virus.
2. Avoiding close contact: Avoiding close contact with people who are sick can help prevent the spread of the virus.
3. Disinfecting surfaces: Regularly disinfecting surfaces and objects that may have the virus on them can help reduce the risk of infection.
4. Vaccination: There is currently no licensed vaccine available to protect against adenovirus infections, but research is ongoing to develop one.

Conclusion:

Adenovirus infections are common and can cause a range of symptoms, from mild to severe. While there is no specific treatment for the infection, supportive care can help manage symptoms. Prevention is key to avoiding adenovirus infections, and this can be achieved through frequent hand washing, avoiding close contact with people who are sick, regularly disinfecting surfaces, and avoiding sharing personal items. Research is ongoing to develop a vaccine against adenovirus infections.

Explanation: Neoplastic cell transformation is a complex process that involves multiple steps and can occur as a result of genetic mutations, environmental factors, or a combination of both. The process typically begins with a series of subtle changes in the DNA of individual cells, which can lead to the loss of normal cellular functions and the acquisition of abnormal growth and reproduction patterns.

Over time, these transformed cells can accumulate further mutations that allow them to survive and proliferate despite adverse conditions. As the transformed cells continue to divide and grow, they can eventually form a tumor, which is a mass of abnormal cells that can invade and damage surrounding tissues.

In some cases, cancer cells can also break away from the primary tumor and travel through the bloodstream or lymphatic system to other parts of the body, where they can establish new tumors. This process, known as metastasis, is a major cause of death in many types of cancer.

It's worth noting that not all transformed cells will become cancerous. Some forms of cellular transformation, such as those that occur during embryonic development or tissue regeneration, are normal and necessary for the proper functioning of the body. However, when these transformations occur in adult tissues, they can be a sign of cancer.

See also: Cancer, Tumor

Word count: 190

https://www.medicinenet.com › Medical Dictionary › G

A genetic translocation is a change in the number or arrangement of the chromosomes in a cell. It occurs when a portion of one chromosome breaks off and attaches to another chromosome. This can result in a gain or loss of genetic material, which can have significant effects on the individual.

Genetic Translocation | Definition & Facts | Britannica
https://www.britannica.com › science › Genetic-tr...

Genetic translocation, also called chromosomal translocation, a type of chromosomal aberration in which a portion of one chromosome breaks off and attaches to another chromosome. This can result in a gain or loss of genetic material. Genetic translocations are often found in cancer cells and may play a role in the development and progression of cancer.

Translocation, Genetic | health Encyclopedia - UPMC
https://www.upmc.com › health-library › gene...

A genetic translocation is a change in the number or arrangement of the chromosomes in a cell. It occurs when a portion of one chromosome breaks off and attaches to another chromosome. This can result in a gain or loss of genetic material, which can have significant effects on the individual.

Genetic Translocation | Genetics Home Reference - NIH
https://ghr.nlm.nih.gov › condition › ge...

A genetic translocation is a change in the number or arrangement of the chromosomes in a cell. It occurs when a portion of one chromosome breaks off and attaches to another chromosome. This can result in a gain or loss of genetic material, which can have significant effects on the individual.

In conclusion, Genetic Translocation is an abnormality in the number or arrangement of chromosomes in a cell. It occurs when a portion of one chromosome breaks off and attaches to another chromosome, resulting in a gain or loss of genetic material that can have significant effects on the individual.

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The intended therapeutic targets are antibiotic-resistant bacterial infections. The company was founded as a spin-off from ... Harnessing Nature's Toolbox for Genome Engineering". Cell. 164 (1-2): 29-44. doi:10.1016/j.cell.2015.12.035. PMID 26771484. ... 818 million to develop CRISPR-Cas3 drugs targeting two bacterial pathogens. Locus received $20 million upfront and up to $798 ...
... whereas Alveolata and stramenopiles have bacterial ones. Other rearrangements are also possible, since Fungi have bacterial ... this domain does not occur in any other proteins encoded by the genome. The strain has a pleiotropic phenotype including ... Both OPRTase and ODCase have passed through lateral gene transfer, resulting in eukaryotes' having enzymes from bacterial and ...
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Animal Genome Size Database Bacterial genome size C-value Cell nucleus Comparative genomics Comparison of different genome ... Genome reduction, also known as genome degradation, is the process by which an organism's genome shrinks relative to that of ... Genome size is the total amount of DNA contained within one copy of a single complete genome. It is typically measured in terms ... The genome of the endosymbiont B. aphidicola is characterized by a genome size that is seven times smaller than E. coli (643 kb ...
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In 2001, the first genome sequence of Sulfolobus, Sulfolobus solfataricus P2, was published. In P2's genome, the genes related ... This response may be a primitive form of sexual interaction, similar to the more well-studied bacterial transformation that is ... Sulfolobus Genome Projects (from Genomes OnLine Database) (Articles with short description, Short description matches Wikidata ... It showed that both species contained two origins in their genome. This was the first time that more than a single origin of ...
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... is a bacterial species in the genus Streptomyces. Natamycin is an antifungal agent produced during ... Beites, Tiago; Rodríguez-García, Antonio; Moradas-Ferreira, Pedro; Aparicio, Jesús; Mendes, Marta (11 January 2014). "Genome- ...
As of now, the genome of Vampirococcus has not been sequenced, and the phylogeny and taxonomy of the microbe have not been ... They are commonly mentioned as an example of epibionts when discussing strategies employed by bacterial predators. This microbe ... In addition, Vampirococcus specifically preys upon various species within the bacterial genus, Chromatium, a freshwater purple ... Without a pure, isolated culture of this organism, more information regarding its genome, genes, evolutionary relationships ...
Hydrogen peroxide is used to help eliminate bacterial spores in the alcohol; it is "not an active substance for hand antisepsis ... It is 96% identical at the whole genome level to other bat coronavirus samples (BatCov RaTG13). The structural proteins of SARS ...
"Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and ... military contributions to the study of bacterial zoonoses." Military Medicine 170 (2005): 39-48. Bossi, P., Tegnell, A., Baka, ... Flagellar genes, however, are present in the B. suis genome, but are thought to be cryptic remnants because some were truncated ... DelVecchio, VG; Kapatral, V; Elzer, P; Patra, G; Mujer, CV (20 December 2002). "The genome of Brucella melitensis". Veterinary ...
eds.). Novel Genome-Scale Correlation between DNA Replication and RNA Transcription During the Cell Cycle in Yeast is Predicted ... The D period refers to the stage between the end of DNA replication and the splitting of the bacterial cell into two daughter ... Genome-wide studies using high throughput technologies have identified the transcription factors that bind to the promoters of ... This ensures that every portion of the cell's genome will be replicated once and only once. The reason for prevention of gaps ...
The genome sequence of the black truffle was published in March 2010. The black summer truffle (Tuber aestivum) is found across ... Thiophene derivatives appear to be produced by bacterial symbionts living in the truffle body. The most abundant of these, 3- ... "Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis". Nature. 464 (7291): 1033-8. Bibcode: ...
StrepLab scientists use genome sequences to find connections between invasive group A strep infections in long-term care ... 1 Bacterial samples collected over the course of an outbreak might only be "near" identical because bacteria pick up genome ... 2019: Scientists use bacterial genome sequences to stop a deadly multi-facility outbreak. By Erin Scherer ... This graph shows the similarities between different group A strep genome sequences. On this type of graph, more similar genome ...
Analysis of important human pathogen populations is currently under transition toward whole-genome sequencing of growing ... Detection of recombination events in bacterial genomes from large population samples Nucleic Acids Res. 2012 Jan;40(1):e6. doi ... offering an enhanced insight into the diversification of bacterial clones at the level of the whole genome. A data set of 241 ... we introduce here a method for detecting homologous recombination events from whole-genome sequence data for bacterial ...
... and then moves into a short overview of bacterial genome size evolution before spending the remainder of the time on genome ... The seminar that I give most often when I am invited to speak at other universities begins with a brief introduction to genomes ... The main things that I have to say about bacterial genomes are:. 1) Unlike in eukaryotes, bacterial genome size shows a strong ... The 160-kilobase genome of the bacterial endosymbiont Carsonella . Science 314: 267.. 7. Ochman, H. 2006. Genomes on the ...
One hundred and twenty-six of these novel composite genes derived from genetic material from bacterial genomes. These latter ... constitute a different gene pool from the laterally acquired bacterial genes formerly identified. These novel composite genes ... were likely advantageous for their hosts, since they show significant residence times in haloarchaeal genomes-consistent with a ... to test to what extent archaea might have adjusted their lifestyles by incorporating and recycling laterally acquired bacterial ...
Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel ... The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables ... But with two projects, communities are forming to generate high quality genomes to benefit researchers. More ... In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay ...
2012) Bacterial genome mining for novel natural product discovery. Planta Medica, Volume 78 (Number 11). Article number IL7. ... However, a major obstacle to the discovery of novel natural products by genome mining is that many cryptic pathways are ... in several actinomycete genome sequences. Discovery of the metabolic products of such cryptic gene clusters promises to unearth ... system identified in the partial genome sequence of Streptomyces ambofaciens will be described. Activation of expression of the ...
To develop a vaccine against P. gingivalis, herein, we applied a bacterial pan-genome analysis (BPGA) on the bacterial genomes ... Pan-Genome Analysis of Oral Bacterial Pathogens to Predict a Potential Novel Multi-Epitopes Vaccine Candidate.. Rida, Tehniyat ... Currently, no licensed vaccine is available against P. gingivalis and other oral bacterial pathogens. ...
... which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in ... ClonalFrameML can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real ... Clostridium difficile, Computer Simulation, Databases, Genetic, Evolution, Molecular, Genome, Bacterial, Genomics, Phylogeny, ... which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in ...
I am looking at SNP trees for bacterial genomes (mostly N. gonorrhoeae, S. aureus and E. faecium) and I am following outbreaks ... After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, ... Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat ... Variant Analysis and Genome Assembly: Recommended Tools for Next-Level Sequencing Analysis ...
bacterial whole genome analysis good day, how do i upload my fastq files to galaxy server to perform bacterial whole genome ... De-novo assembly of a bacterial genome I am trying to assemble a bacterial genome of length 8Mb in **orione.crs4.it** . I could ... Galaxy for alignment for genomes of bacterial species Galaxy can be used for alignment for genomes of bacterial species or not ... Cant Rsync bacterial genomes Hi everyone, I have a local instance of Galaxy. I am trying to grab some of the reference genome ...
CryoEM structure and assembly mechanism of a bacterial virus genome gatekeeper. 26 November 2022 ... Kerfeld, C. A., Aussignargues, C., Zarzycki, J., Cai, F. & Sutter, M. Bacterial microcompartments. Nat. Rev. Microbiol. 16, 277 ... This is accomplished via the assembly of a selectively permeable protein shell that encompasses the phage genome4,5. The shell ... All other data, bacterial strains, and plasmids are available from the corresponding author on a reasonable request. ...
Complete genome sequences of two Bordetella hinzii strains isolated from humans. Genome Announc. 2015;3:1-2. DOIPubMedGoogle ... Spontaneous Bacterial Peritonitis Caused by Bordetella hinzii Grace C. Wang1, Miranda J. Wallace1, Gayathri Krishnan, Patrick D ... After core-genome alignment (58 total core genes), a neighbor-joining phylogenetic tree rooted with Achromobacter xylosoxidans ... the type genomes for B. pertussis, B. parapertussis, and B. bronchiseptica represent an instance of previously established, ...
... delivery of phage genome into the host, phage mechanisms against host defense, phage biosynthesis rate, and phage life cycle, ... The optimization framework should be generally applicable to developing therapeutic phages against bacterial pathogens. ... One can incorporate an optimized phage genome into a bacterial genome, and then induce the lytic phage to generate new phages. ... Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010, 329, 52-56. [Google Scholar] [ ...
Manipulating bacterial communities in carp polyculture - Th next frontier for intensification?. Delamare-Deboutteville, J., ... While the genome-wide association analyses suggested a polygenic genetic architecture for all the measured traits, there were ... Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia (Oreochromis niloticus ...
Several of the dominating bacterial groups in the CR and GS foliage (e.g., Bacillus, Burkholderia, Actinomycetes) are known for ... Several of the dominating bacterial groups in the coast redwood and giant sequoia foliage (e.g. Bacillus, Burkholderia, ... The endophytic bacterial microbiome, with an emerging role in plant nutrient acquisition and stress tolerance, is much less ... The endophytic bacterial microbiome, with an emerging role in plant nutrient acquisition and stress tolerance, is much less ...
Evaluation and genome-wide association study of resistance to bacterial blight race 18 in U.S. Upland cotton germplasm. - Texas ... Evaluation and genome-wide association study of resistance to bacterial blight race 18 in U.S. Upland cotton germplasm. ... Bacterial blight (BB), caused by Xanthomonas citripv.malvacearum (Xcm), is a destructive disease to cotton production in many ... A genome-wide association study (GWAS) based on 26,301 single nucleotide polymorphic (SNP) markers detected 11 quantitative ...
The analysis of cellular transcriptional response at the genome level: Two case studies with relevance to bacterial ... The analysis of cellular transcriptional response at the genome level: Two case studies with relevance to bacterial ...
Genome [‎3]‎. Genome, Bacterial [‎1]‎. Genome, Human [‎10]‎. Genome, Viral [‎11]‎. Genomics [‎14]‎. ...
... phage and other integrated MGE genomes. It also reveals TBSSRs families whose distribution among bacterial taxa suggests they ... we built a set of over 1,300 TBSSR protein sequences tagged with their genome of origin. We organized them in families to ... such as temperate phage genomes, integrated conjugative elements (ICEs) or integron cassettes. TBSSRs are also involved in the ... In bacterial genomes, they play a major role in the comings and goings of mobile genetic elements (MGEs), ...
Categories: Genome, Bacterial Image Types: Photo, Illustrations, Video, Color, Black&White, PublicDomain, CopyrightRestricted ...
Nonevolutionary changes in bacterial genome must also be considered as an explanation. A dramatic increase in EHEC-related HUS ... However, bacterial blood cultures are negative and a Stx-elaborating pathogen is not identified. A viral pathogen is sometimes ... Bacterial genotype and neurological complications of Escherichia coli O157:H7-associated haemolytic uraemic syndrome. Acta ...
4] A. Tasneem et al., Genome Biol 6, R4 (2005).. [5] R. Hilf and R. Dutzler, Nature 452, 375-379 (2008).. [6] N. Bocquet et al ... 113: General view of the crystal structure of the full-length ligand-gated bacterial ion channel GLIC: a) side view, b) top ...
Distinct bacterial species that cause enteric disease can exist as invasive enteropathogens that immediately evoke ... whole-genome sequencing; metagenomics ... or pathobionts that can arise from established bacterial ... The gut is a key conduit for the genesis and spread of antimicrobial resistance in enteric bacterial pathogens. ... Bacterial infections; Bacteria; Antimicrobial resistance; Antimicrobials; Gastrointestinal system; Genomics; Pathogens; Author ...
A Genome-Wide Screen for Bacterial Envelope Biogenesis Mutants Identifies a Novel Factor Involved in Cell Wall Precursor ... Selection for Unequal Densities of σ70 Promoter-Like Signals in Different Regions of Large Bacterial Genomes journal, January ... Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits journal, November 2015 * Freed, Emily F.; ... Genome-scale promoter engineering by coselection MAGE journal, April 2012 * Wang, Harris H.; Kim, Hwangbeom; Cong, Le ...
7 prophages predicted from Helgoland PSA bacterial genomes. *28 prophages predicted from published PSA bacterial genomes ( ... Figure 1. Genome relatedness heatmap.. How many genera of PSA phages exist? And who belongs to those genera?. I will use the ... allPSA,-read.table(/Users/duhaimem/busibee/PostDoc/TMPL/Helgoland_Phages/ecogenomics_project/genome_analysis/JGI/phage/seq_ ...
Screening for genome mobility by Pph 1302A::Tn mutant library showed three Pph 1302A::Tn mutants which may have the ability to ... These mutations were in areas of the genome associated with antibiotic resistance and genes for the Omp family, mobile genetic ... These results demonstrate the identification of many genes involved in key bacterial behaviour and are important for plant ... The use of transposon libraries to investigate the evolution of bacterial pathogenesis ...
bacterial-type DNA replication termination. 0. nuclear DNA replication termination +. 1. Path 2. ... Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data ... OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) (beta) Variant Visualizer Multi-Ontology ...
Genomes at CDC: Man, Mouse, and Microbe-its a Genomic World - Genomics and Precision Health Blog ... Of these, 111 (62%) concerned bacterial, viral, fungal, or parasite genomes; 61 (34%) concerned the human genome; and 6 (3%) ... Of the 111 articles that described research on microbial genomes (bacterial, viral, fungal, or parasite), approximately half (n ... The focus is on pathogen genomes, applying advances in molecular and bioinformatics methods first developed for human genome ...
  • Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
  • Is the Subject Area "Bacterial genomics" applicable to this article? (plos.org)
  • Through start-up support from the Advanced Molecular Detection (AMD) program, StrepLab now sequences whole genomes of group A strep and other bacteria. (cdc.gov)
  • StrepLab scientists realized they could also use genome sequences to find connections between invasive group A strep infections. (cdc.gov)
  • Running the genome sequences through the cluster detection tool at CDC showed the samples were near identical. (cdc.gov)
  • A data set of 241 whole genome sequences from an important pandemic lineage of Streptococcus pneumoniae is used together with multiple simulated data sets to demonstrate the potential of our approach. (nih.gov)
  • Bioinformatics analyses have identified gene clusters encoding cryptic polyketide biosynthetic pathways, not associated with the production of known metabolites, in several actinomycete genome sequences. (warwick.ac.uk)
  • Hi, I want to map a set of sequences (derived from RNA) against a bacterial genome. (usegalaxy.org)
  • Weigand MR , Changayil S , Kulasekarapandian Y , Tondella ML . Complete genome sequences of two Bordetella hinzii strains isolated from humans. (cdc.gov)
  • With the aim of improving the annotation of TBSSR genes in genomic sequences and databases, which so far is far from robust, we built a set of over 1,300 TBSSR protein sequences tagged with their genome of origin. (biomedcentral.com)
  • In this study, using a set of over 1,300 TBSSR protein sequences tagged with their genome of origin, we attempt to investigate: i) whether TBSSRs tend to be more conserved within than between classes of MGE types, that is, whether (sub)families of TBSSRs are specific to one (sub)type of MGE and ii) whether these (sub)families may help in understanding more about the function of the plasmid encoded TBSSRs. (biomedcentral.com)
  • This approach has been called " genomic epidemiology "-using pathogen genome sequences to detect emerging diseases, assess their potential virulence and resistance to antibiotics, and monitor their spread in populations. (cdc.gov)
  • data are preliminary and based on broth microdilution susceptibility testing and/or presence of resistance genes and mutations found in whole genome sequences of bacterial DNA. (cdc.gov)
  • has been identified as the 2nd most consensus (ERIC) sequences which · 60 environmental samples were tak- frequent organism causing ventilator- are common to Gram-negative enteric en throughout the ICU, including associated pneumonia, the 4th most bacteria [11,12]. (who.int)
  • Because genome size is primarily determined by the number of genes in bacteria, the question to be addressed is why symbionts have fewer genes in their genomes. (scitizen.com)
  • So, on the one hand, there are processes that can add genes (duplication and lateral gene transfer), whereas in the absence of these processes, and if there are no adverse consequences to losing DNA (i.e., there is no selective constraint occurring), genomes should tend to get smaller as a result of this deletion bias. (scitizen.com)
  • One hundred and twenty-six of these novel composite genes derived from genetic material from bacterial genomes. (biomedcentral.com)
  • These latter genes, largely involved in metabolic functions but also in oxygenic lifestyle, constitute a different gene pool from the laterally acquired bacterial genes formerly identified. (biomedcentral.com)
  • These novel composite genes were likely advantageous for their hosts, since they show significant residence times in haloarchaeal genomes-consistent with a long phylogenetic history involving vertical descent and lateral gene transfer-and encode proteins with optimized isoelectric points. (biomedcentral.com)
  • Overall, our work encourages a systematic search for composite genes across all archaeal major groups, in order to better understand the origins of novel prokaryotic genes, and in order to test to what extent archaea might have adjusted their lifestyles by incorporating and recycling laterally acquired bacterial genetic fragments into new archaeal genes. (biomedcentral.com)
  • Within a genome, genes are connected to each other through a complex network of interactions. (nature.com)
  • After core-genome alignment (58 total core genes), a neighbor-joining phylogenetic tree rooted with Achromobacter xylosoxidans as the outgroup demonstrates the isolates from this study cluster with other previously deposited B. hinzii genomes. (cdc.gov)
  • As a demonstration of this approach, we constructed a Dub-seq library with total Escherichia coli genomic DNA, performed 155 genome-wide fitness assays in 52 experimental conditions, and identified 813 genes with high-confidence overexpression phenotypes across 4,151 genes assayed. (osti.gov)
  • A total of 960 mutants in Pph strains 1302A and 1448A were tested for their phenotypic characterisation and for identification of genome mobility in Pph 1302A and competence genes in Pph 1448A. (bl.uk)
  • To investigate genes involved in Pph colonisation of plants and evolution of Pph pathogenesis by HGT, the Tn mutant libraries were screened for changes in bacterial phenotypic characteristics such as colony morphology, motility, biofilm formation, growth rate in bean apoplastic fluid and conjugation. (bl.uk)
  • These results demonstrate the identification of many genes involved in key bacterial behaviour and are important for plant colonisation and therefore disease in bean plants. (bl.uk)
  • These mutations were in areas of the genome associated with antibiotic resistance and genes for the Omp family, mobile genetic elements and type III effector protein and conserved hypothetical and adhesion protein. (bl.uk)
  • Genome sequence information allows scientists to track new strains and antibiotic resistance trends. (cdc.gov)
  • By harnessing the power of recent advances in Bayesian modeling techniques, we introduce here a method for detecting homologous recombination events from whole-genome sequence data for bacterial population samples on a large scale. (nih.gov)
  • Our statistical approach can efficiently handle hundreds of whole genome sequenced population samples and identify separate origins of the recombinant sequence, offering an enhanced insight into the diversification of bacterial clones at the level of the whole genome. (nih.gov)
  • The discovery of the stambomycins, a new family of 51-membered macrolides with promising anti-cancer activity, as the products of a novel type I modular polyketide synthase (PKS) system identified in the partial genome sequence of Streptomyces ambofaciens will be described. (warwick.ac.uk)
  • How genome sequence ca. (usegalaxy.org)
  • Even when scientists can acquire sequence data, parasitic genomes are so large that they require specialized computer programs to decipher. (cdc.gov)
  • The genome sequence of Sii strain CJ18 was compared with that of other Streptococcus species to identify dairy adaptations including genome decay such as in Streptococcus thermophilus , traits for its competitiveness in spontaneous milk fermentation and to assess potential health risks for consumers. (biomedcentral.com)
  • repetitive sequence elements in the members had been in contact with bacterial genome have shown con- patients for several hours. (who.int)
  • The population of P. aeruginosa in the Philippines was diverse, with clonal expansions of XDR genomes belonging to multi-locus sequence types ST235, ST244, ST309, and ST773. (who.int)
  • How entire genomic alignment of bacterial species can be carried out? (usegalaxy.org)
  • In the present genomic era, TBSSR annotation is far from homogenous, whether for genomes or in databases. (biomedcentral.com)
  • What genomic studies are CDC public health scientists doing-and which genomes are they writing about? (cdc.gov)
  • Genomes are found at all three corners of the epidemiologic triangle: human or animal hosts are engaged in genomic contests with pathogens of all kinds, played out in an environment teeming with the genomes of other people, animals, plants, and microbes. (cdc.gov)
  • Scientists have done this before for viruses, but viruses typically have much smaller genomes than bacteria. (cdc.gov)
  • 1 Bacterial samples collected over the course of an outbreak might only be "near" identical because bacteria pick up genome mutations over time. (cdc.gov)
  • The seminar that I give most often when I am invited to speak at other universities begins with a brief introduction to genomes, sets up some comparisons between bacteria and eukaryotes, and then moves into a short overview of bacterial genome size evolution before spending the remainder of the time on genome size diversity and its importance among animals. (scitizen.com)
  • Genome size and gene number in bacteria and archaea. (scitizen.com)
  • 3) The major pattern in bacteria is that, on average, free-living species have larger genomes than parasitic species which in turn have larger genomes than obligate endosymbionts (Mira et al. (scitizen.com)
  • Genome sizes among bacteria with differing lifestyles. (scitizen.com)
  • In order to explain these patterns, it was sometimes argued that some bacteria have small genomes because there is selection for rapid cell division, with larger DNA contents taking longer to replicate and thereby slowing down the cell cycle. (scitizen.com)
  • 2001) compared doubling time and genome size in bacteria that could be cultured in the lab, they found no significant relationship between them. (scitizen.com)
  • In other words, selection for small genome size is probably not responsible for the highly compact genomes of some bacteria, even though it seems plausible that, more generally, selection does prevent the accumulation of non-coding DNA to eukaryote levels in bacterial cells. (scitizen.com)
  • While many factors contribute to phage efficiency in killing bacteria, such as phage attachment to host, delivery of phage genome into the host, phage mechanisms against host defense, phage biosynthesis rate, and phage life cycle, this paper focuses only on the optimization of phage mRNA for efficient translation. (mdpi.com)
  • This bacterium lacks a cell wall, so many of the antimicrobials that are typically used to treat bacterial infections are not effective against this bacteria. (cdc.gov)
  • The focus is on pathogen genomes, applying advances in molecular and bioinformatics methods first developed for human genome research. (cdc.gov)
  • Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. (ox.ac.uk)
  • After performing dozens of tests, CDC identified the cancer-like cells as being from the dwarf tapeworm, Hymenolepis nana , and AMD proved the mutations were in the tapeworm genome. (cdc.gov)
  • 1) Unlike in eukaryotes, bacterial genome size shows a strong positive relationship with gene number (in other words, bacterial genomes contain little non-coding DNA). (scitizen.com)
  • Nucleoprotein complexes play a key role in the genome organization of eukaryotes and prokaryotes, some of which are known to influence global organization by mediating long-range anchored chromosomal loop formation leading to spatial segregation of large sections of DNA. (genomeweb.com)
  • The gut is a key conduit for the genesis and spread of antimicrobial resistance in enteric bacterial pathogens. (cdc.gov)
  • In this review, we present a comprehensive discussion on circulating resistance profiles and gene mobilization strategies of the most problematic species of enteric bacterial pathogens. (cdc.gov)
  • This approach has already led CDC researchers to discover additional novel tickborne bacterial pathogens, not associated previously with human infection. (cdc.gov)
  • The bacterial species Streptococcus pyogenes , or group A strep, is known for causing strep throat. (cdc.gov)
  • Comparative genome analysis of Streptococcus infantarius subsp. (biomedcentral.com)
  • In bacterial genomes, they play a major role in the comings and goings of mobile genetic elements (MGEs), such as temperate phage genomes, integrated conjugative elements (ICEs) or integron cassettes. (biomedcentral.com)
  • The simple in silico procedure described here, which uses a set of reference TBSSRs from defined MGE types, could contribute to greatly improve the annotation of tyrosine-based site-specific recombinases in plasmid, (pro)phage and other integrated MGE genomes. (biomedcentral.com)
  • ClonalFrameML: efficient inference of recombination in whole bacterial genomes. (ox.ac.uk)
  • Using AMD, CDC scientists sequenced the full genome of the newly discovered bacterium, providing a critical foundation for diagnostic development. (cdc.gov)
  • The diversity of archaeal, bacterial, and eukaryotic genome sizes as currently known from more than 10,000 species. (scitizen.com)
  • Galaxy can be used for alignment for genomes of bacterial species or not? (usegalaxy.org)
  • As previously observed ( 8 ), the type genomes for B. pertussis , B. parapertussis , and B. bronchiseptica represent an instance of previously established, distinct species that exceed the species-level ANI threshold relative to each other. (cdc.gov)
  • Distinct bacterial species that cause enteric disease can exist as invasive enteropathogens that immediately evoke gastrointestinal distress, or pathobionts that can arise from established bacterial commensals to inflict dysbiosis and disease. (cdc.gov)
  • and 6 (3%) concerned genomes of other animal species (Figure). (cdc.gov)
  • We sequenced the whole genomes of 176 P. aeruginosa isolates collected in 2013-2014 by the Antimicrobial Resistance Surveillance Program. (who.int)
  • Complemento genético de un microorganismo arqueal (ARCHAEA) como está representado en su ADN. (bvsalud.org)
  • The Active Bacterial Core surveillance (ABCs) system collects clinical and demographic information about patients with bacterial infections. (cdc.gov)
  • A genome-wide association study (GWAS) based on 26,301 single nucleotide polymorphic (SNP) markers detected 11 quantitative trait loci (QTL) anchored by 79 SNPs, including three QTL on each of the three chromosomes A01, A05 and D02, and one QTL on each of D08 and D10. (tamu.edu)
  • Participating ABCs sites then send patients' bacterial strains to CDC's StrepLab. (cdc.gov)
  • Before genome sequencing, scientists only knew the type of group A strep strains, not if they were identical or near identical. (cdc.gov)
  • But AMD is helping CDC scientists explore the complex parasitic genome in new and faster ways. (cdc.gov)
  • The endophytic bacterial microbiome, with an emerging role in plant nutrient acquisition and stress tolerance, is much less studied in natural plant populations than in agricultural crops. (frontiersin.org)
  • The discovery of a transcription factor involved in bacterial genome organization is detailed in Nature Genetics this week . (genomeweb.com)
  • Examination of the loss of competence in Pph 1448A showed two changes i.e. growth rate reduction in vitro in LB liquid media and plasmid genome alteration by bean pod passage. (bl.uk)
  • We demonstrate that Cas3 helicase activity is not essential for immunity against MGE in vivo and explore applications of the Thioalkalivibrio sulfidiphilus Cascade effector for genome engineering in Escherichia coli . (bvsalud.org)
  • The genome of the African dairy isolate Sii CJ18 clearly differs from the human isolate ATCC BAA-102 T . CJ18 possesses a high natural competence predisposition likely explaining the enlarged genome. (biomedcentral.com)
  • Evaluation and genome-wide association study of resistance to bacterial blight race 18 in U.S. Upland cotton germplasm. (tamu.edu)
  • Since the completion of the human genome, the growth of DNA sequencing databases has exploded, currently exceeding 20 petabases. (genomeweb.com)
  • Most of the ST235 genomes formed a distinct Philippine lineage when contextualized with international genomes, thus raising the possibility that this is a lineage unique to the Philippines. (who.int)
  • After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we're wrapping up with a discussion about tools for differential gene expression analysis and data visualization. (seqanswers.com)
  • Continuing from our previous article , we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming 'Tommy' Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line . (seqanswers.com)
  • Dear Sir or Madam, May I know how to add some other genome information for custemerized analysis. (usegalaxy.org)
  • Hallo Galaxy users, I would like to annotate variants (in vcf file) found in my bacterial genome. (usegalaxy.org)
  • Until recently, only the simplest genomes were available to public health scientists and even those were generally known only by their fingerprints. (cdc.gov)
  • While the genome-wide association analyses suggested a polygenic genetic architecture for all the measured traits, there were significant QTL identified for BWG and FI on chromosomes seven and five respectively. (worldfishcenter.org)
  • The resulting "cluster detection tool" accurately and efficiently identifies outbreaks of the same bacterial strain. (cdc.gov)
  • however, they are typically limited either to only a few samples or to data from relatively short regions of a total genome. (nih.gov)
  • I have my ChIP-Seq data on Galaxy but can't map it because the bacterial genome that I am working on, Burkholderia cenocepacia genome does not exist in Galaxy database. (usegalaxy.org)
  • less is known about the role and diversity of their bacterial counterparts. (frontiersin.org)
  • Shigellosis is an acute enteric infection that is an important cause of domestically acquired and travel-associated bacterial diarrhea in the United States. (cdc.gov)
  • But with two projects, communities are forming to generate high quality genomes to benefit researchers. (doe.gov)
  • It also reveals TBSSRs families whose distribution among bacterial taxa suggests they mediate lateral gene transfer. (biomedcentral.com)
  • The Jan. 13, 2021 event celebrated the 25th anniversary of the first complete bacterial genome, the 20th anniversary of the publication of the human genome, and the 15th anniversary of the first human metagenome. (nih.gov)
  • Tracing the Evolution of Shiitake Mushrooms Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. (doe.gov)
  • ClonalFrameML can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real datasets. (ox.ac.uk)
  • How to add a bacterial genome to Galaxy database? (usegalaxy.org)
  • Could you add reference genomes into the database? (usegalaxy.org)
  • I have been running 0.2-2M 150 bp kraken jobs on the bacterial database on a private cloudman clu. (usegalaxy.org)
  • Repurposing the atypical type I-G CRISPR system for bacterial genome engineering. (bvsalud.org)
  • Dairy adaptations in CJ18 are reflected by a high percentage of pseudogenes (4.9%) representing genome decay which includes the inactivation of the lactose phosphotransferase system ( lacIIABC ) by multiple transposases integration. (biomedcentral.com)