Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Virus Integration: Insertion of viral DNA into host-cell DNA. This includes integration of phage DNA into bacterial DNA; (LYSOGENY); to form a PROPHAGE or integration of retroviral DNA into cellular DNA to form a PROVIRUS.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.HEK293 Cells: A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Single-Cell Analysis: Assaying the products of or monitoring various biochemical processes and reactions in an individual cell.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.Retroviridae: Family of RNA viruses that infects birds and mammals and encodes the enzyme reverse transcriptase. The family contains seven genera: DELTARETROVIRUS; LENTIVIRUS; RETROVIRUSES TYPE B, MAMMALIAN; ALPHARETROVIRUS; GAMMARETROVIRUS; RETROVIRUSES TYPE D; and SPUMAVIRUS. A key feature of retrovirus biology is the synthesis of a DNA copy of the genome which is integrated into cellular DNA. After integration it is sometimes not expressed but maintained in a latent state (PROVIRUSES).Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.HIV Integrase: Enzyme of the HUMAN IMMUNODEFICIENCY VIRUS that is required to integrate viral DNA into cellular DNA in the nucleus of a host cell. HIV integrase is a DNA nucleotidyltransferase encoded by the pol gene.Genes, Viral: The functional hereditary units of VIRUSES.Genome Size: The amount of DNA (or RNA) in one copy of a genome.Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Virus Replication: The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Genome, Protozoan: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.HIV-1: The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Genome, Helminth: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Genome, Plastid: The genetic complement of PLASTIDS as represented in their DNA.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Synteny: The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.Genetic Variation: Genotypic differences observed among individuals in a population.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Gene Order: The sequential location of genes on a chromosome.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Software: Sequential operating programs and data which instruct the functioning of a digital computer.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Viral Proteins: Proteins found in any species of virus.Gene Transfer, Horizontal: The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Pseudogenes: Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.Genes, Bacterial: The functional hereditary units of BACTERIA.Polyploidy: The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Genes, Plant: The functional hereditary units of PLANTS.Genome, Microbial: The genetic complement of a microorganism as represented in its DNA or in some microorganisms its RNA.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Genome Components: The parts of a GENOME sequence that are involved with the different functions or properties of genomes as a whole as opposed to those of individual GENES.Bacterial Proteins: Proteins found in any species of bacterium.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Oryza sativa: Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.Chromosomes: In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.DNA Replication: The process by which a DNA molecule is duplicated.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Gene Dosage: The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Bacteriophages: Viruses whose hosts are bacterial cells.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Terminal Repeat Sequences: Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Prophages: Genomes of temperate BACTERIOPHAGES integrated into the DNA of their bacterial host cell. The prophages can be duplicated for many cell generations until some stimulus induces its activation and virulence.INDEL Mutation: A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Genes, Mitochondrial: Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.DNA, Chloroplast: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Comparative Genomic Hybridization: A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Vertebrates: Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.Symbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Interspersed Repetitive Sequences: Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Virulence: The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Inverted Repeat Sequences: Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.Kidney: Body organ that filters blood for the secretion of URINE and that regulates ion concentrations.RNA Viruses: Viruses whose genetic material is RNA.Genetic Engineering: Directed modification of the gene complement of a living organism by such techniques as altering the DNA, substituting genetic material by means of a virus, transplanting whole nuclei, transplanting cell hybrids, etc.Plastids: Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.Genes, Archaeal: The functional genetic units of ARCHAEA.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Mammals: Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.Sorghum: A plant genus of the family POACEAE. The grain is used for FOOD and for ANIMAL FEED. This should not be confused with KAFFIR LIME or with KEFIR milk product.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.DNA, Circular: Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.Chromosomes, Human: Very long DNA molecules and associated proteins, HISTONES, and non-histone chromosomal proteins (CHROMOSOMAL PROTEINS, NON-HISTONE). Normally 46 chromosomes, including two sex chromosomes are found in the nucleus of human cells. They carry the hereditary information of the individual.Short Interspersed Nucleotide Elements: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Segmental Duplications, Genomic: Low-copy (2-50) repetitive DNA elements that are highly homologous and range in size from 1000 to 400,000 base pairs.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.GC Rich Sequence: A nucleic acid sequence that contains an above average number of GUANINE and CYTOSINE bases.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Hybridization, Genetic: The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.Pan troglodytes: The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.Eukaryota: One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.Archaea: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Genes, Duplicate: Two identical genes showing the same phenotypic action but localized in different regions of a chromosome or on different chromosomes. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Angiosperms: Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.Tetraodontiformes: A small order of primarily marine fish containing 340 species. Most have a rotund or box-like shape. TETRODOTOXIN is found in their liver and ovaries.Proteome: The protein complement of an organism coded for by its genome.DNA Copy Number Variations: Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.Diploidy: The chromosomal constitution of cells, in which each type of CHROMOSOME is represented twice. Symbol: 2N or 2X.Mutation Rate: The number of mutations that occur in a specific sequence, GENE, or GENOME over a specified period of time such as years, CELL DIVISIONS, or generations.Defective Viruses: Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.Chromosome Inversion: An aberration in which a chromosomal segment is deleted and reinserted in the same place but turned 180 degrees from its original orientation, so that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome.Untranslated Regions: The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.Endogenous Retroviruses: Retroviruses that have integrated into the germline (PROVIRUSES) that have lost infectious capability but retained the capability to transpose.Crosses, Genetic: Deliberate breeding of two different individuals that results in offspring that carry part of the genetic material of each parent. The parent organisms must be genetically compatible and may be from different varieties or closely related species.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
  • B . DRBP76 immunoblot of HeLa or HEK293 cell lysates (lanes 1-2) or non-fractionated murine tissue extracts of the indicated origin (lanes 3-8). (nih.gov)
  • Figures 1 and 2 show silencing of GAPDH and GFP in HeLa cells after infection with p Silencer adeno 1.0-CMV engineered to express the corresponding siRNAs. (bio-medicine.org)
  • This vector has been used by that lab to silence a number of genes in HeLa cells and adult mice (1). (bio-medicine.org)
  • HeLa cells were infected at an MOI of 80 with adenovirus derived from the p Silencer adeno 1.0-CMV System. (bio-medicine.org)
  • HeLa cells were infected (MOI = 160) with recombinant adenovirus derived from p Silencer adeno 1.0-CMV engineered to express an siRNA targeting GFP. (bio-medicine.org)
  • Fig. 1: High genome editing efficiency using jetCRISPR™ in HeLa cells. (polyplus-transfection.com)
  • Using reporter constructs, we observed that degradation of mRNAs bearing sites imperfectly complementary to the endogenous let-7 miRNA is considerably stronger in human HEK293 than HeLa cells. (unibas.ch)
  • We have experience working with a wide variety of cell backgrounds ranging from easy-to-transfect cell lines (like HEK 293, 293FT, HCT116, or HeLa) to hard-to-transfect cell lines (like fibroblasts, neuroblastoma-derived, hepatocellular carcinoma, bone marrow-derived, and endothelium-derived cells). (thermofisher.com)
  • The resultant plasmids were introduced into Nicotiana benthamiana epidermal leaf cells with a modified Gene Gun protocol. (jove.com)
  • Inside the cell, the plasmids recombine and the recombined genome is replicated and packaged into adenoviral particles. (bio-medicine.org)
  • Compatible plasmids containing lentivirus genome designed for use with the SnapFast Pro™ LTX Lentivirus Packaging Mix. (oxfordgenetics.com)
  • Based mostly around the Hinf II digestion pat tern, all of the colonies isolated displayed a distinct repertoire of rescued plasmids indicating that each iso lated colony was certainly derived from diverse targeted cells. (phosphorylase-signal.com)
  • Altered subcellular localization and isoform distribution in malignant glioma indicate that tumor-specific changes in DRBP76-related gene products and their regulatory functions may contribute to the formation and/or maintenance of these tumors. (nih.gov)
  • Malignant brain tumors remain refractory to adenovirus type 5 (Ad5)-based gene therapy, mostly due to the lack of the primary Ad5 receptor, the coxsackie and adenovirus receptor, on brain tumor cells. (aacrjournals.org)
  • The therapeutic efficacy of any adenovirus-based cancer gene therapy approach depends on the efficacy of vector-mediated tumor transduction. (aacrjournals.org)
  • This has been understood to result from a relative paucity of the primary adenovirus receptor, the coxsackie and adenovirus receptor (CAR), on brain tumor cells ( 11 - 15 ). (aacrjournals.org)
  • Indeed, a relative paucity of CAR has been shown to limit Ad vector efficacy in a number of tumor contexts, possibly representing a fundamental practical barrier to realizing the full benefit of adenoviruses for cancer gene therapy applications. (aacrjournals.org)
  • Alteration in gene activation, for instance silencing of tumor suppressors or activation of oncogenes, may occur in the case of cancer cells . (termedia.pl)
  • Dysfunction of cell adhesion (metastasis) is characteristic for tumor cells and is regarded as a result of alternation in E-cadherin expression (encoded by CDH1). (termedia.pl)
  • 129 genes with 5-fold changed expression were found in glioblastoma, the most aggressive human brain tumor. (org.ua)
  • B General view of tumor paraffin section, initiated by 293_CHI3L1 cells. (org.ua)
  • Along with superexpressed genes, it was found 85 genes relating to the potential tumor suppressor genes. (org.ua)
  • Tumor lesions and their surrounding normal tissues were separated, snap-frozen in liquid nitrogen immediately after resection, and stored at −80°C. At least 90% of the cells in each tumor specimen were identified as tumor cells. (aacrjournals.org)
  • Cell culture models of normal urothelial cells are valuable for studying urothelial physiology and differentiation, for investigating the function of genetic and epigenetic changes found in urothelial carcinoma and as controls in the evaluation of the tumor specificity of novel cancer drugs. (iospress.com)
  • Primary cultures of urothelial cells, usually established from healthy ureters removed during tumor nephrectomy, provide one valuable model [ 1 ]. (iospress.com)
  • Similarly, antibodies targeting CD137 activation in immune cells have demonstrated potent anti-tumor properties in cancer patients. (bpsbioscience.com)
  • 2008) Multivalent 4-1BB binding aptamers co-stimulate CD8+ T cells and inhibit tumor growth in mice. (bpsbioscience.com)
  • While accurate tumor characterization is crucial for cancer therapy, current sequencing methods are unable to resolve the genetic differences between the heterogeneous cell populations within tumor. (aacrjournals.org)
  • By profiling specific subpopulations of cells from a larger heterogeneous population, single cell sequencing can improve the efficiency of cancer treatments through early detection of rare tumor cells, monitoring of circulating tumor cells, and accurate profiling of intra-tumor heterogeneity. (aacrjournals.org)
  • Thereafter, many more cellular and viral enhancers were described, including a steroid hormone-responsive segment in mouse mammary tumor virus ( 4 ), the particularly strong enhancers associated with immediate-early genes of human and mouse cytomegaloviruses (HCMV and MCMV, respectively) ( 3 , 7 ), and zinc-responsive enhancers associated with human and mouse metallothionein genes ( 28 ). (asm.org)
  • Studies in mice and in human colon cancer cell lines suggest several mechanisms that might account for the tumor suppressive effects of $PPAR{\gamma}$ agonists, although it is not in all cases clear whether these effects are altogether mediated by $PPAR{\gamma}$ . (koreascience.or.kr)
  • In addition to your excellent genomic sequence characterization of both mutant LIF alleles, I have confirmed in our lab that the tumor cells have lost all mouse LIF production. (abmgood.com)
  • Dr. Robert Jackman, Boston University, Mouse LIF CRISPR Knock Out C26 Tumor Cell Line Generation and Screening Service, View case study here . (abmgood.com)
  • Genome-wide analysis of 23,417 piggyBac , 30,303 Sleeping Beauty , and 27,985 TcBuster integrations in HEK-293 cells revealed a uniquely different integration pattern when compared to other transposon systems with regards to genomic elements. (plos.org)
  • Despite this level of sequence divergence, Alu elements represent a major source of sequence homology in the human genome and contribute to genomic instability that arises from mutagenic recombination between these elements [ 4 , 5 ]. (prolekare.cz)
  • The dysferlin gene is large, with 55 exons so far identified spanning at least 150 kb of genomic DNA. (plos.org)
  • Sequencing and genomic localization of cis -regulatory regions bound by Elf5 in vivo has identified several potential target genes covering broad functional categories. (biomedcentral.com)
  • TP53 was wild-type and the cell cycle was arrested in response to genomic stress. (iospress.com)
  • Non-small cell lung cancer has emerged as a prototype disease where genomic data from at least several well-documented alterations with approved targeted agents are essential for optimal treatment from diagnosis of advanced disease. (cdc.gov)
  • DICE, an efficient system for iterative genomic editing in human pluripotent stem cells. (appliedstemcell.com)
  • We show that the percentage of mappable reads and regions with more than 1X coverage in whole genome sequencing were similar to that of the genomic DNA data, but the coverage rate of regions with more than 10X was lower in single cell data on both NGS platforms. (aacrjournals.org)
  • One simple approach is to transfect linearized SV40 genomic DNA lacking its own enhancer into monkey host cells together with DNA fragments containing a putative enhancer segment. (asm.org)
  • Here, we present the genomic and functional characterization of a patient with metastatic clear cell RCC (ccRCC) who experienced a partial response to temsirolimus after a poor response to 2 previous lines of treatment. (jnccn.org)
  • Although an earlier report suggested that the cells contained Adenovirus 5 DNA from both the right and left ends of the viral genome [RF it is now clear that only left end sequences are present. (cogforlife.org)
  • The transformation incorporated approximately 4.5 kilobases from the viral genome into human chromosome 19 of the HEK cells. (altogen.com)
  • We found that several oligonucleotides, cotransfected with enhancerless SV40 DNA into host cells, were incorporated into the viral genome via cellular DNA end joining. (asm.org)
  • Here we show that 3 distinct classes of alternatively spliced and/or differentially expressed genes change in an ordered manner as a function of immune activation. (jove.com)
  • Gene expression profiling analysis identified a list of differentially expressed genes in response to BPA exposure in HEK293 cells. (duhnnae.com)
  • To identify endogenous mRNA targets of DRBP76, we performed RNA-immunoprecipitation and genome-wide microarray analyses in HEK293 cells, and identified specific classes of transcripts encoding critical functions in cellular metabolism. (nih.gov)
  • The cell lines were used for microarray analyses to obtain a comprehensive picture of RNA silencing. (unibas.ch)
  • SiRNAs targeting Lamin A/C mRNA or non-silencing control siRNA were transfected into HEK-293 cells following the recommended protocol. (altogen.com)
  • Our studies augment the current view of T and B cell activation in immunity that has been based exclusively upon differential gene expression by providing evidence for a large number of molecular networks populated as a function of time and activation by alternatively spliced genes, many of which are constitutively expressed. (jove.com)
  • Numerous alternatively-spliced genes with varying temporal patterns of expression are revealed, including TGIF1, involved in holoprosencephaly and MARK1, involved in autism. (omicsdi.org)
  • Excision footprints obtained from HEK-293 cells contained small insertions and deletions consistent with a hAT -type repair mechanism of hairpin formation and non-homologous end-joining. (plos.org)
  • Substrates for these homologous and homeologous events include Alu elements, which are approximately 300 bp elements that comprise ~11% of the human genome. (prolekare.cz)
  • However, with more diverged Alu elements, like those typically found in the human genome, repair of DSBs appears to use the Alu/Alu homeology to direct non-homologous end joining in the general vicinity of the Alu elements. (prolekare.cz)
  • Creating nicks favors the higher-fidelity homologous recombination process over non-homologous end joining (NHEJ), with paired nicking shown to reduce off-target activity by 50- to 1,500-fold in cell lines, and to facilitate gene knockout in mice without losing on-target cleavage efficiency 1 . (systembio.com)
  • We demonstrate that guide RNA pairs generate deletions that are repaired with a high level of precision by non-homologous end-joining in mammalian cells. (stanford.edu)
  • Extracellular signals such as growth factors, hormones, and environmental compounds elicit an array of effects on a cell that include proliferation, differentiation, stress, and death (1-3). (thefreelibrary.com)
  • As a consequence, circANRIL induces nucleolar stress and p53 activation, resulting in the induction of apoptosis and inhibition of proliferation, which are key cell functions in atherosclerosis. (nature.com)
  • In concert, circANRIL confers disease protection by modulating apoptosis and proliferation in human vascular cells and tissues, which are key cellular functions in atherosclerosis. (nature.com)
  • This increase resulted in concomitant transactivation of the EGF receptor and sustained activation of extracellular signal related kinase (ERK) 1/2, culminating in enhanced cell proliferation. (rupress.org)
  • It controls cell-fate decisions, coordinates patterning processes and regulates proliferation and differentiation. (uni-wuerzburg.de)
  • CD137:CD137L-mediated signaling has been shown to be important for proliferation, effector functions and survivals of T cells. (bpsbioscience.com)
  • We also have expertise in cardiac punctures, dissection of a variety of tissues for subsequent analysis by FACS, qRT-PCR, primary cell culture and proliferation studies. (ucl.ac.uk)
  • The present disclosure provides novel co-stimulatory domains useful in genetically-modified cells to promote cell proliferation and/or promote cytokine secretion after antigen recognition. (freepatentsonline.com)
  • Overexpression of AChE by an oncolytic adenoviral vector (ZD55-AChE) significantly inhibited gastric cancer cell proliferation and reduced growth of gastric tumors in mice. (biomedcentral.com)
  • Here we show that ZFNs are able to induce DSBs efficiently when delivered directly to mouse liver and that, when co-delivered with an appropriately designed gene-targeting vector, they can stimulate gene replacement through both homology-directed and homology-independent targeted gene insertion at the ZFN-specified locus. (nih.gov)
  • 16. A two vector system in accordance with claim 9, wherein the second vector further comprises a Factor IX gene. (freepatentsonline.com)
  • 19. A two vector system in accordance with claim 18, wherein the second vector further comprises a Factor IX gene disrupting the sequence of the ROSA26 encoding homology arms. (freepatentsonline.com)
  • Taken together, our findings indicate that Ad5/3-RGD may be a superior vector for applications in glioma gene therapy and therefore warrants further attention in the field of neuro-oncology. (aacrjournals.org)
  • The integrase catalyzes an irreversible reaction between the attP site in the genome and attB site in the donor vector, resulting in integration of the gene of interest at the selected H11 locus. (appliedstemcell.com)
  • Furthermore, when AGK transfectants were labeled with [ 3 H]sphingosine, there were no significant increases detected in the formation of [ 3 H]S1P compared with vector-transfected cells (unpublished data). (rupress.org)
  • The modified CMV promoter in the vector efficiently expresses hairpin siRNAs, which elicit gene silencing through the RNAi pathway. (bio-medicine.org)
  • Gastric cancer cells were treated with AChE delivered by replication-deficient adenoviral vector (Ad.AChE) or oncolytic adenoviral vector (ZD55-AChE), respectively, followed by measurement of cell viability and apoptosis by MTT assay and apoptosis detection assays. (biomedcentral.com)
  • AS-605240 Pre-existing neutralizing antibodies dampen gene transfer efficacy and increase vector-mediated toxicity2. (world-of-links.com)
  • To clone the international gene appealing into the Advertisement molecular clone a shuttle vector was utilized including two very uncommon limitation sites I-CeuI and PI-SceI. (world-of-links.com)
  • Using limitation enzyme sites that are exclusive in assembly however not always unique fully AdC6 genome the proper half from the AdC6 genome was after that cloned piecemeal in to the pNEB193 vector. (world-of-links.com)
  • Using the same technique as above the rest from the remaining fragment from the AdC6 genome was constructed in to the pNEB193 vector. (world-of-links.com)
  • Finally using two suitable enzymes the E1-deleted left fragment of the Ad genome was released from the pNEB193 vector and inserted into the vector containing the right fragment of. (world-of-links.com)
  • Lentivirus production is influenced by SV40 large T-antigen and chromosomal integration of the vector in HEK293 cells. (helmholtz-hzi.de)
  • We aimed to exploit single copy integration sites in the HEK293 genome supporting lentiviral vector production. (helmholtz-hzi.de)
  • rather, it seems to impose an indirect effect on the cell thereby enabling lentiviral vector production. (helmholtz-hzi.de)
  • Generation of a packaging cell line for prolonged large-scale production of high-titer HIV-1-based lentiviral vector. (helmholtz-hzi.de)
  • Lentiviral vector transduction of NOD/SCID repopulating cells results in multiple vector integrations per transduced cell: risk of insertional mutagenesis. (helmholtz-hzi.de)
  • Lentiviral vector integration sites in human NOD/SCID repopulating cells. (helmholtz-hzi.de)
  • 5. The vector according to claim 2 wherein said selected gene is a reporter gene. (google.com)
  • According to searches in the PubMed citation database, during the last 15 years 80% of all recombinant genes reported on in the literature were expressed in either the enterobacterium Escherichia coli or the methylotropic yeast Pichia pastoris . (biomedcentral.com)
  • Citation data are presented for the last 15 years for PubMed and the last 5 years for Microbial Cell Factories . (biomedcentral.com)
  • The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines. (nih.gov)
  • F . DRBP76 immunoblot from fractionated extracts of the indicated cell lines. (nih.gov)
  • Ad5/3-RGD showed a 10-fold increase in gene expression in passaged cell lines and up to 75-fold increase in primary tumors obtained from patients relative to the control. (aacrjournals.org)
  • DDT and its metabolites alter gene expression in human uterine cell lines through estrogen receptor-independent mechanisms. (thefreelibrary.com)
  • Using two Ishikawa human endometrial adenocarcinoma cell line variants that we confirmed to be estrogen responsive [Ishikawa(+)] and estrogen unresponsive [Ishikawa(-)], we generated stably transfected AP-1 luciferase cell lines to identify the role of an estrogen-responsive mechanism in AP-1-mediated gene expression by various stimuli. (thefreelibrary.com)
  • EBV produces EBNA2, EBNA3 and EBNA-LP, as well as EBERs, EBNA1, LMP1 and LMP2 in immunosuppression-related lymphoma or lymphoblastoid cell lines (LCLs) (type III latency). (frontiersin.org)
  • We systematically investigated the exon structure of circANRIL in human cell lines and primary cells ( Fig. 1a and Supplementary Fig. 1 ). (nature.com)
  • It combines the scalability, affordability, and ease-of-use of bacterial/ yeast systems and the advantages of using mammalian cells (closer to human environment and post-translational modifications) for efficient and stable gene knock-in into cell lines and for library generation. (appliedstemcell.com)
  • Karyographs of the cell lines 293 and 293_CHI3L1 clone 2. (org.ua)
  • Clinical samples and cell lines. (aacrjournals.org)
  • Beyond primary cultures with their limitations in lifespan, interindividual heterogeneity and supply, few conditionally immortalized cell lines with limited applicability due to partial transformation or impaired differentiation capacity are available. (iospress.com)
  • Thus, several immortalized cell lines have been generated from such cultures by introducing viral oncogenes (SV-HUC1, UROtsa) or telomerase (TERT-NHUC) [ 4, 5 ]. (iospress.com)
  • In cell lines, both read-throughs influenced molecular mechanisms (i.e. target gene expression or migration/invasion) in a way that counteracted the effect of the respective parent transcript GATM or KLK4 . (biomedcentral.com)
  • The authors of these studies used deposited data from EST data bases and confirmed their predictions only in normal human tissues and a few cell lines. (biomedcentral.com)
  • Cell lines are developed with doxycycline‐inducible expression of specific mi RNA s. (embopress.org)
  • The TARGATT™ technology enables faster and efficient site-specific integration of large DNA fragments in cell lines. (appliedstemcell.com)
  • Stable cell lines expressing recombinant antibodies are generated by experienced scientists working on antibody and cell line development services for decades. (sydlabs.com)
  • Other mammalian stable cell lines, such as HEK 293 cells, can be used if requested. (sydlabs.com)
  • If requested, the antibody variable regions (including both VL and VH) of hybridoma cell lines will be cloned and sequenced . (sydlabs.com)
  • Despite significant overlap in the ligand-independent genes between Y537S and D538G, the number of mutant ERα-target genes shared between the two cell lines was limited, suggesting context-dependent activity of the mutant receptor. (biomedcentral.com)
  • In fact, there are very few cell lines that cannot be infected. (vectorbiolabs.com)
  • Some lymphoid cell lines may be more resistant to adenoviral infection, and may need higher viral quantities to achieve sufficient infection levels. (vectorbiolabs.com)
  • development of stable cell lines for recombinant antibody expression. (sydlabs.com)
  • Pricing for premade cell lines are for customers in the US and Canada only. (genecopoeia.com)
  • This study describes a patient with metastatic clear cell RCC (ccRCC) refractory to multiple lines of anti-vascular endothelial growth factor (VEGF) therapy that, on temsirolimus treatment, exhibited an exceptional clinical response. (jnccn.org)
  • Creating stable cell lines is time-consuming and complex. (thermofisher.com)
  • The trusted, experienced developers of Invitrogen GeneArt TALs and GeneArt CRISPR products can custom-design stable cell lines using one of the most robust and reliable technologies on the market. (thermofisher.com)
  • We have successfully completed many knockout projects in a variety of cell lines, including fibroblasts, blood cells, ovarian cells, hepatocytes, and many more. (abmgood.com)
  • These cell lines are available as Cas-9 expressing versions or parental versions. (abmgood.com)
  • In this case you may have to try different cell lines. (idtdna.com)
  • TGF-β is the main inducer of the contractile gene program that drives myofibroblast differentiation from various precursor cell types. (biologists.org)
  • Here, we report the discovery of a novel MKL1 variant/isoform, MKL1_S, transcribed from an alternative promoter and uncover a novel translation start for the published human isoform, MKL1_L. Using a human adipose-derived mesenchymal stem cell differentiation model, we show that TGF-β specifically upregulates MKL1_S during the initial phase of myofibroblast differentiation. (biologists.org)
  • Differentiation of a variety of cell types into myofibroblasts defines a major physiological process that facilitates wound healing and tissue repair. (biologists.org)
  • In both tissue repair and tumorigenesis, TGF-β represents the prototypic inducer of myofibroblast differentiation from all precursor cell types. (biologists.org)
  • Cell culture models of normal urothelial cells are important for studying differentiation, disease mechanisms and anticancer drug development. (iospress.com)
  • It has been widely reported that aberrant IFN-α/β production of pDCs triggered by self-RNA/DNA is responsible for the development or perpetuation of autoimmune diseases, such as systemic lupus erythematodes, psoriasis, dermatomyositis, and type I diabetes, through maturation of DCs and differentiation of autoreactive T and B cells ( 5 - 8 ). (jimmunol.org)
  • Using a modified differentiation protocol and RNA-Seq technology with computational analysis, we identified sets of genes and long non-coding RNAs that significantly change during corticogenesis, and those enriched for disease-associations. (omicsdi.org)
  • Collective advantages of availability from donors without age restriction, capabilities in expansion and differentiation, and no concern of tumorigenesis, let hiMEPs have the considerable application potentials on cell therapies of diseases such as liver failure and diabetes, as well as personalized drug-screenings. (omicsdi.org)
  • In addition, we recommend testing 3 or more crRNAs per target gene. (valuegene.com)
  • For the prices described above, target gene constructs must be supplied by clients. (sydlabs.com)
  • It is also possible that your target gene is vital to your cells, and thus its knockout results in cell death. (idtdna.com)
  • Some of the previous studies demonstrated the ability of ascites to modulate the gene expression, which is associated with changes in the cellular behavior of ovarian cancer cell [5, (termedia.pl)
  • In this study, we performed RNA-seq to characterize BPA-induced cellular and molecular impacts on ER-negative HEK293 cells. (duhnnae.com)
  • The first example of a cellular enhancer discovered was the immunoglobulin heavy chain (IgH) enhancer, which was a cell-type-specific regulatory sequence since it was active only in B-lymphocyte-type cells and not in other cell types ( 1 , 9 ). (asm.org)
  • These genes were involved in variable important biological processes including ion transport, cysteine metabolic process, apoptosis, DNA damage repair, etc. (duhnnae.com)
  • Consistent with the repair defect, these cells displayed increased apoptosis, abnormal chromosome segregation, aneuploidy, centrosome amplification, and significant accumulation of γH2AX signals. (jci.org)
  • These are mainly other TF involved in e.g. developmental processes, apoptosis, cell migration and cell cycle. (uni-wuerzburg.de)
  • E3 gene items subvert immune reactions by changing antigen demonstration and cytokine and apoptosis pathways but are unneeded for viral replication11. (world-of-links.com)
  • Our results show that FUS and EWS bind to a subset of actively transcribed genes, that binding often is downstream the poly(A)-signal, and that binding overlaps with RNA polymerase II. (biomedcentral.com)
  • However, in CM the repressive effect of Hey binding on a subset of genes can be annulled, likely due to binding of cardiac specific activators like Srf, Nkx2-5 and Gata4. (uni-wuerzburg.de)
  • While traditional lipid and amine based reagents work well for transfecting some cultured cells, they can be inefficient for transfecting many primary cells, neural cells, etc. (bio-medicine.org)
  • Purified human CD2(+) T or CD19(+) B cells were activated using protocols to model the early events in post-transplant allograft immunity and sampled as a function of time during the process of immune activation. (jove.com)