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.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.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.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.MicroRNAs: Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.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.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.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.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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.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.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.Gene Expression Regulation, Archaeal: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.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.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.RNA Stability: The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.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.Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Gene Regulatory Networks: Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.Down-Regulation: A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.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.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Up-Regulation: A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.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.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Cell Line, Tumor: A cell line derived from cultured tumor cells.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.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Gene Expression Regulation, Leukemic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in leukemia.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.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.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.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Blotting, Northern: Detection of RNA 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.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.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.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)Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.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.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.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.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.Mice, Inbred C57BLDNA, 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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Real-Time Polymerase Chain Reaction: Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Luciferases: Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.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).Homeodomain Proteins: Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.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)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.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.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.Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.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.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.Rats, Sprague-Dawley: A strain of albino rat used widely for experimental purposes because of its calmness and ease of handling. It was developed by the Sprague-Dawley Animal Company.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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Response Elements: Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.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)NF-kappa B: Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.Bacterial Proteins: Proteins found in any species of bacterium.RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.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.Genes, Plant: The functional hereditary units of PLANTS.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Mice, Knockout: Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.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.Green Fluorescent Proteins: Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.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.beta-Galactosidase: A group of enzymes that catalyzes the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-galactosides. Deficiency of beta-Galactosidase A1 may cause GANGLIOSIDOSIS, GM1.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)Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Chloramphenicol O-Acetyltransferase: An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Disease Models, Animal: Naturally occurring or experimentally induced animal diseases with pathological processes sufficiently similar to those of human diseases. They are used as study models for human diseases.Cell Cycle: The complex series of phenomena, occurring between the end of one CELL DIVISION and the end of the next, by which cellular material is duplicated and then divided between two daughter cells. The cell cycle includes INTERPHASE, which includes G0 PHASE; G1 PHASE; S PHASE; and G2 PHASE, and CELL DIVISION PHASE.Transgenes: Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.Epithelial Cells: Cells that line the inner and outer surfaces of the body by forming cellular layers (EPITHELIUM) or masses. Epithelial cells lining the SKIN; the MOUTH; the NOSE; and the ANAL CANAL derive from ectoderm; those lining the RESPIRATORY SYSTEM and the DIGESTIVE SYSTEM derive from endoderm; others (CARDIOVASCULAR SYSTEM and LYMPHATIC SYSTEM) derive from mesoderm. Epithelial cells can be classified mainly by cell shape and function into squamous, glandular and transitional epithelial cells.Electrophoretic Mobility Shift Assay: An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.Genes, Immediate-Early: Genes that show rapid and transient expression in the absence of de novo protein synthesis. The term was originally used exclusively for viral genes where immediate-early referred to transcription immediately following virus integration into the host cell. It is also used to describe cellular genes which are expressed immediately after resting cells are stimulated by extracellular signals such as growth factors and neurotransmitters.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Immediate-Early Proteins: Proteins that are coded by immediate-early genes, in the absence of de novo protein synthesis. The term was originally used exclusively for viral regulatory proteins that were synthesized just after viral integration into the host cell. It is also used to describe cellular proteins which are synthesized immediately after the resting cell is stimulated by extracellular signals.Neoplasm Proteins: Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.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.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Microdissection: The performance of dissections with the aid of a microscope.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.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.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.RNA, Neoplasm: RNA present in neoplastic tissue.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.Cytokines: Non-antibody proteins secreted by inflammatory leukocytes and some non-leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner.Dose-Response Relationship, Drug: The relationship between the dose of an administered drug and the response of the organism to the drug.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.Lac Operon: The genetic unit consisting of three structural genes, an operator and a regulatory gene. The regulatory gene controls the synthesis of the three structural genes: BETA-GALACTOSIDASE and beta-galactoside permease (involved with the metabolism of lactose), and beta-thiogalactoside acetyltransferase.Rats, Wistar: A strain of albino rat developed at the Wistar Institute that has spread widely at other institutions. This has markedly diluted the original strain.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.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.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Tumor Necrosis Factor-alpha: Serum glycoprotein produced by activated MACROPHAGES and other mammalian MONONUCLEAR LEUKOCYTES. It has necrotizing activity against tumor cell lines and increases ability to reject tumor transplants. Also known as TNF-alpha, it is only 30% homologous to TNF-beta (LYMPHOTOXIN), but they share TNF RECEPTORS.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)Embryo, Mammalian: The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.Cell Division: The fission of a CELL. It includes CYTOKINESIS, when the CYTOPLASM of a cell is divided, and CELL NUCLEUS DIVISION.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Gene Transfer Techniques: The introduction of functional (usually cloned) GENES into cells. A variety of techniques and naturally occurring processes are used for the gene transfer such as cell hybridization, LIPOSOMES or microcell-mediated gene transfer, ELECTROPORATION, chromosome-mediated gene transfer, TRANSFECTION, and GENETIC TRANSDUCTION. Gene transfer may result in genetically transformed cells and individual organisms.Breast Neoplasms: Tumors or cancer of the human BREAST.Stress, Physiological: The unfavorable effect of environmental factors (stressors) on the physiological functions of an organism. Prolonged unresolved physiological stress can affect HOMEOSTASIS of the organism, and may lead to damaging or pathological conditions.RNA Processing, Post-Transcriptional: Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.Brain: The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Receptors, Cytoplasmic and Nuclear: Intracellular receptors that can be found in the cytoplasm or in the nucleus. They bind to extracellular signaling molecules that migrate through or are transported across the CELL MEMBRANE. Many members of this class of receptors occur in the cytoplasm and are transported to the CELL NUCLEUS upon ligand-binding where they signal via DNA-binding and transcription regulation. Also included in this category are receptors found on INTRACELLULAR MEMBRANES that act via mechanisms similar to CELL SURFACE RECEPTORS.Proto-Oncogene Proteins: Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Principal Component Analysis: Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Embryo, Nonmammalian: The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.Sp1 Transcription Factor: Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.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.Dexamethasone: An anti-inflammatory 9-fluoro-glucocorticoid.Proto-Oncogene Proteins c-fos: Cellular DNA-binding proteins encoded by the c-fos genes (GENES, FOS). They are involved in growth-related transcriptional control. c-fos combines with c-jun (PROTO-ONCOGENE PROTEINS C-JUN) to form a c-fos/c-jun heterodimer (TRANSCRIPTION FACTOR AP-1) that binds to the TRE (TPA-responsive element) in promoters of certain genes.Histone Deacetylases: Deacetylases that remove N-acetyl groups from amino side chains of the amino acids of HISTONES. The enzyme family can be divided into at least three structurally-defined subclasses. Class I and class II deacetylases utilize a zinc-dependent mechanism. The sirtuin histone deacetylases belong to class III and are NAD-dependent enzymes.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.Nerve Tissue ProteinsMethylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Genes, Bacterial: The functional hereditary units of BACTERIA.Tissue Distribution: Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.Tumor Markers, Biological: Molecular products metabolized and secreted by neoplastic tissue and characterized biochemically in cells or body fluids. They are indicators of tumor stage and grade as well as useful for monitoring responses to treatment and predicting recurrence. Many chemical groups are represented including hormones, antigens, amino and nucleic acids, enzymes, polyamines, and specific cell membrane proteins and lipids.Muscle, Skeletal: A subtype of striated muscle, attached by TENDONS to the SKELETON. Skeletal muscles are innervated and their movement can be consciously controlled. They are also called voluntary muscles.Inflammation: A pathological process characterized by injury or destruction of tissues caused by a variety of cytologic and chemical reactions. It is usually manifested by typical signs of pain, heat, redness, swelling, and loss of function.Transforming Growth Factor beta: A factor synthesized in a wide variety of tissues. It acts synergistically with TGF-alpha in inducing phenotypic transformation and can also act as a negative autocrine growth factor. TGF-beta has a potential role in embryonal development, cellular differentiation, hormone secretion, and immune function. TGF-beta is found mostly as homodimer forms of separate gene products TGF-beta1, TGF-beta2 or TGF-beta3. Heterodimers composed of TGF-beta1 and 2 (TGF-beta1.2) or of TGF-beta2 and 3 (TGF-beta2.3) have been isolated. The TGF-beta proteins are synthesized as precursor proteins.Gene Knockdown Techniques: The artificial induction of GENE SILENCING by the use of RNA INTERFERENCE to reduce the expression of a specific gene. It includes the use of DOUBLE-STRANDED RNA, such as SMALL INTERFERING RNA and RNA containing HAIRPIN LOOP SEQUENCE, and ANTI-SENSE OLIGONUCLEOTIDES.Kinetics: The rate dynamics in chemical or physical systems.Basic Helix-Loop-Helix Transcription Factors: A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.Zebrafish: An exotic species of the family CYPRINIDAE, originally from Asia, that has been introduced in North America. They are used in embryological studies and to study the effects of certain chemicals on development.Macrophages: The relatively long-lived phagocytic cell of mammalian tissues that are derived from blood MONOCYTES. Main types are PERITONEAL MACROPHAGES; ALVEOLAR MACROPHAGES; HISTIOCYTES; KUPFFER CELLS of the liver; and OSTEOCLASTS. They may further differentiate within chronic inflammatory lesions to EPITHELIOID CELLS or may fuse to form FOREIGN BODY GIANT CELLS or LANGHANS GIANT CELLS. (from The Dictionary of Cell Biology, Lackie and Dow, 3rd ed.)Pregnancy: The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.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.Transcription Factor AP-1: A multiprotein complex composed of the products of c-jun and c-fos proto-oncogenes. These proteins must dimerize in order to bind to the AP-1 recognition site, also known as the TPA-responsive element (TRE). AP-1 controls both basal and inducible transcription of several genes.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Enzyme Inhibitors: Compounds or agents that combine with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.Mice, Inbred BALB CViral Proteins: Proteins found in any species of virus.Genes, Insect: The functional hereditary units of INSECTS.Neurons: The basic cellular units of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the NERVOUS SYSTEM.Cell Survival: The span of viability of a cell characterized by the capacity to perform certain functions such as metabolism, growth, reproduction, some form of responsiveness, and adaptability.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.Animals, Genetically Modified: ANIMALS whose GENOME has been altered by GENETIC ENGINEERING, or their offspring.Genes, fos: Retrovirus-associated DNA sequences (fos) originally isolated from the Finkel-Biskis-Jinkins (FBJ-MSV) and Finkel-Biskis-Reilly (FBR-MSV) murine sarcoma viruses. The proto-oncogene protein c-fos codes for a nuclear protein which is involved in growth-related transcriptional control. The insertion of c-fos into FBJ-MSV or FBR-MSV induces osteogenic sarcomas in mice. The human c-fos gene is located at 14q21-31 on the long arm of chromosome 14.Plants, Genetically Modified: PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.Genes, Homeobox: Genes that encode highly conserved TRANSCRIPTION FACTORS that control positional identity of cells (BODY PATTERNING) and MORPHOGENESIS throughout development. Their sequences contain a 180 nucleotide sequence designated the homeobox, so called because mutations of these genes often results in homeotic transformations, in which one body structure replaces another. The proteins encoded by homeobox genes are called HOMEODOMAIN PROTEINS.Genetic Therapy: Techniques and strategies which include the use of coding sequences and other conventional or radical means to transform or modify cells for the purpose of treating or reversing disease conditions.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.Cell Lineage: The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.Animals, Newborn: Refers to animals in the period of time just after birth.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Embryonic Development: Morphological and physiological development of EMBRYOS.

Apontic binds the translational repressor Bruno and is implicated in regulation of oskar mRNA translation. (1/76734)

The product of the oskar gene directs posterior patterning in the Drosophila oocyte, where it must be deployed specifically at the posterior pole. Proper expression relies on the coordinated localization and translational control of the oskar mRNA. Translational repression prior to localization of the transcript is mediated, in part, by the Bruno protein, which binds to discrete sites in the 3' untranslated region of the oskar mRNA. To begin to understand how Bruno acts in translational repression, we performed a yeast two-hybrid screen to identify Bruno-interacting proteins. One interactor, described here, is the product of the apontic gene. Coimmunoprecipitation experiments lend biochemical support to the idea that Bruno and Apontic proteins physically interact in Drosophila. Genetic experiments using mutants defective in apontic and bruno reveal a functional interaction between these genes. Given this interaction, Apontic is likely to act together with Bruno in translational repression of oskar mRNA. Interestingly, Apontic, like Bruno, is an RNA-binding protein and specifically binds certain regions of the oskar mRNA 3' untranslated region.  (+info)

The role of gene splicing, gene amplification and regulation in mosquito insecticide resistance. (2/76734)

The primary routes of insecticide resistance in all insects are alterations in the insecticide target sites or changes in the rate at which the insecticide is detoxified. Three enzyme systems, glutathione S-transferases, esterases and monooxygenases, are involved in the detoxification of the four major insecticide classes. These enzymes act by rapidly metabolizing the insecticide to non-toxic products, or by rapidly binding and very slowly turning over the insecticide (sequestration). In Culex mosquitoes, the most common organophosphate insecticide resistance mechanism is caused by co-amplification of two esterases. The amplified esterases are differentially regulated, with three times more Est beta 2(1) being produced than Est alpha 2(1). Cis-acting regulatory sequences associated with these esterases are under investigation. All the amplified esterases in different Culex species act through sequestration. The rates at which they bind with insecticides are more rapid than those for their non-amplified counterparts in the insecticide-susceptible insects. In contrast, esterase-based organophosphate resistance in Anopheles is invariably based on changes in substrate specificities and increased turnover rates of a small subset of insecticides. The up-regulation of both glutathione S-transferases and monooxygenases in resistant mosquitoes is due to the effects of a single major gene in each case. The products of these major genes up-regulate a broad range of enzymes. The diversity of glutathione S-transferases produced by Anopheles mosquitoes is increased by the splicing of different 5' ends of genes, with a single 3' end, within one class of this enzyme family. The trans-acting regulatory factors responsible for the up-regulation of both the monooxygenase and glutathione S-transferases still need to be identified, but the recent development of molecular tools for positional cloning in Anopheles gambiae now makes this possible.  (+info)

TIF1gamma, a novel member of the transcriptional intermediary factor 1 family. (3/76734)

We report the cloning and characterization of a novel member of the Transcriptional Intermediary Factor 1 (TIF1) gene family, human TIF1gamma. Similar to TIF1alpha and TIF1beta, the structure of TIF1beta is characterized by multiple domains: RING finger, B boxes, Coiled coil, PHD/TTC, and bromodomain. Although structurally related to TIF1alpha and TIF1beta, TIF1gamma presents several functional differences. In contrast to TIF1alpha, but like TIF1beta, TIF1 does not interact with nuclear receptors in yeast two-hybrid or GST pull-down assays and does not interfere with retinoic acid response in transfected mammalian cells. Whereas TIF1alpha and TIF1beta were previously found to interact with the KRAB silencing domain of KOX1 and with the HP1alpha, MODI (HP1beta) and MOD2 (HP1gamma) heterochromatinic proteins, suggesting that they may participate in a complex involved in heterochromatin-induced gene repression, TIF1gamma does not interact with either the KRAB domain of KOX1 or the HP1 proteins. Nevertheless, TIF1gamma, like TIF1alpha and TIF1beta, exhibits a strong silencing activity when tethered to a promoter. Since deletion of a novel motif unique to the three TIF1 proteins, called TIF1 signature sequence (TSS), abrogates transcriptional repression by TIF1gamma, this motif likely participates in TIF1 dependent repression.  (+info)

Telomerase reverse transcriptase gene is a direct target of c-Myc but is not functionally equivalent in cellular transformation. (4/76734)

The telomerase reverse transcriptase component (TERT) is not expressed in most primary somatic human cells and tissues, but is upregulated in the majority of immortalized cell lines and tumors. Here, we identify the c-Myc transcription factor as a direct mediator of telomerase activation in primary human fibroblasts through its ability to specifically induce TERT gene expression. Through the use of a hormone inducible form of c-Myc (c-Myc-ER), we demonstrate that Myc-induced activation of the hTERT promoter requires an evolutionarily conserved E-box and that c-Myc-ER-induced accumulation of hTERT mRNA takes place in the absence of de novo protein synthesis. These findings demonstrate that the TERT gene is a direct transcriptional target of c-Myc. Since telomerase activation frequently correlates with immortalization and telomerase functions to stabilize telomers in cycling cells, we tested whether Myc-induced activation of TERT gene expression represents an important mechanism through which c-Myc acts to immortalize cells. Employing the rat embryo fibroblast cooperation assay, we show that TERT is unable to substitute for c-Myc in the transformation of primary rodent fibroblasts, suggesting that the transforming activities of Myc extend beyond its ability to activate TERT gene expression and hence telomerase activity.  (+info)

Gene expression profiles in HTLV-I-immortalized T cells: deregulated expression of genes involved in apoptosis regulation. (5/76734)

Human T-cell leukemia virus type I (HTLV-I) is the etiologic agent of adult T-cell leukemia, an acute and often fatal T-cell malignancy. A key step in HTLV-I-induced leukemigenesis is induction of abnormal T-cell growth and survival. Unlike antigen-stimulated T cells, which cease proliferation after a finite number of cell division, HTLV-I-infected T cells proliferate indefinitely (immortalized), thus facilitating occurrence of secondary genetic changes leading to malignant transformation. To explore the molecular basis of HTLV-I-induced abnormal T-cell survival, we compared the gene expression profiles of normal and HTLV-I-immortalized T cells using 'gene array'. These studies revealed a strikingly altered expression pattern of a large number of genes along with HTLV-I-mediated T-cell immortalization. Interestingly, many of these deregulated genes are involved in the control of programmed cell death or apoptosis. These findings indicate that disruption of the cellular apoptosis-regulatory network may play a role in the HTLV-I-mediated oncogenesis.  (+info)

Socs1 binds to multiple signalling proteins and suppresses steel factor-dependent proliferation. (6/76734)

We have identified Socs1 as a downstream component of the Kit receptor tyrosine kinase signalling pathway. We show that the expression of Socs1 mRNA is rapidly increased in primary bone marrow-derived mast cells following exposure to Steel factor, and Socs1 inducibly binds to the Kit receptor tyrosine kinase via its Src homology 2 (SH2) domain. Previous studies have shown that Socs1 suppresses cytokine-mediated differentiation in M1 cells inhibiting Janus family kinases. In contrast, constitutive expression of Socs1 suppresses the mitogenic potential of Kit while maintaining Steel factor-dependent cell survival signals. Unlike Janus kinases, Socs1 does not inhibit the catalytic activity of the Kit tyrosine kinase. In order to define the mechanism by which Socs1-mediated suppression of Kit-dependent mitogenesis occurs, we demonstrate that Socs1 binds to the signalling proteins Grb-2 and the Rho-family guanine nucleotide exchange factors Vav. We show that Grb2 binds Socs1 via its SH3 domains to putative diproline determinants located in the N-terminus of Socs1, and Socs1 binds to the N-terminal regulatory region of Vav. These data suggest that Socs1 is an inducible switch which modulates proliferative signals in favour of cell survival signals and functions as an adaptor protein in receptor tyrosine kinase signalling pathways.  (+info)

Anopheles gambiae Ag-STAT, a new insect member of the STAT family, is activated in response to bacterial infection. (7/76734)

A new insect member of the STAT family of transcription factors (Ag-STAT) has been cloned from the human malaria vector Anopheles gambiae. The domain involved in DNA interaction and the SH2 domain are well conserved. Ag-STAT is most similar to Drosophila D-STAT and to vertebrate STATs 5 and 6, constituting a proposed ancient class A of the STAT family. The mRNA is expressed at all developmental stages, and the protein is present in hemocytes, pericardial cells, midgut, skeletal muscle and fat body cells. There is no evidence of transcriptional activation following bacterial challenge. However, bacterial challenge results in nuclear translocation of Ag-STAT protein in fat body cells and induction of DNA-binding activity that recognizes a STAT target site. In vitro treatment with pervanadate (vanadate and H2O2) translocates Ag-STAT to the nucleus in midgut epithelial cells. This is the first evidence of direct participation of the STAT pathway in immune responses in insects.  (+info)

Id helix-loop-helix proteins inhibit nucleoprotein complex formation by the TCF ETS-domain transcription factors. (8/76734)

The Id subfamily of helix-loop-helix (HLH) proteins plays a fundamental role in the regulation of cellular proliferation and differentiation. Id proteins are thought to inhibit differentiation mainly through interaction with other HLH proteins and by blocking their DNA-binding activity. Members of the ternary complex factor (TCF) subfamily of ETS-domain proteins have key functions in regulating immediate-early gene expression in response to mitogenic stimulation. TCFs form DNA-bound complexes with the serum response factor (SRF) and are direct targets of MAP kinase (MAPK) signal transduction cascades. In this study we demonstrate functional interactions between Id proteins and TCFs. Ids bind to the ETS DNA-binding domain and disrupt the formation of DNA-bound complexes between TCFs and SRF on the c-fos serum response element (SRE). Inhibition occurs by disrupting protein-DNA interactions with the TCF component of this complex. In vivo, the Id proteins cause down-regulation of the transcriptional activity mediated by the TCFs and thereby block MAPK signalling to SREs. Therefore, our results demonstrate a novel facet of Id function in the coordination of mitogenic signalling and cell cycle entry.  (+info)

Thanks to their expertise in single-molecule imaging of RNAs, researchers from the group of Jeff Chao at the FMI helped to reveal the biological mechanism of a small molecule that restricts Ewings sarcoma cell growth. The study - published in Nature Chemical Biology - is further evidence that each step of the gene expression pathway may be druggable, and a great example of a Novartis-FMI collaboration.
Inflammation involves timed gene expression, suggesting that the fine-tuned onset, amplitude, and termination of expression of hundreds of genes is of critical importance to organismal homeostasis. Recent study of post-transcriptional regulation of inflammatory gene expression led to the suggestion of a regulatory role for pre-mRNA splicing. Here, using a hybrid capture approach to purify incompletely spliced, chromatin-associated pre-mRNAs, we use deep sequencing to study pre-mRNA splicing of the NF-kB transcriptome. By freezing transcription and examining subsequent splicing of complete transcripts, we find many introns splice tens to hundreds of times slower than average. In many cases, this is attributable to poor splice donor sequences that are evolutionarily conserved. When these introns were altered by ~2 base pairs to yield stronger splice donors, gene expression levels increased markedly for several genes in the context of a reporter system. We propose that such splice sites represent a ...
We developed m:Explorer for identifying process-specific transcription factors (TFs) from multiple genome-wide sources, including transcriptome, DNA-binding and chromatin data. m:Explorer robustly outperforms similar techniques in finding cell cycle TFs in Saccharomyces cerevisiae. We predicted and experimentally tested regulators of quiescence (G0), a model of ageing, over a six-week time-course. We validated nine of top-12 predictions as novel G0 TFs, including Δmga2, Δcst6, Δbas1 with higher viability and G0-essential TFs Tup1, Swi3. Pathway analysis associates longevity to reduced growth, reprogrammed metabolism and cell wall remodeling. m:Explorer (http://biit.cs.ut.ee/mexplorer/) is instrumental in interrogating eukaryotic regulatory systems using heterogeneous data.
Introduction: Lung cancer is the number one cancer killer in the United States accounting for nearly 30% of all cancer deaths. Survival rates continue to be abysmal with 5-year survival only 15% despite contemporary therapies, making it clear that novel therapeutic agents need to be discovered. The translation of mRNA into protein, a central control point in the gene expression pathway, has been increasingly implicated as a critical checkpoint in tumor genesis and progression. This checkpoint serves as a traffic signal at the intersection of cell pathways controlling cell division and survival. The cell machinery controlling the first step in protein synthesis, a hetero-trimer designated eIF4F, is stuck in the "on" position in many human cancers. When this happens cells evade restraints on proliferation and survival. The activation state of eIF4F is controlled at multiple levels with the primary mechanism being negative regulation by the 4E binding proteins (4E-BPs). 4E-BPs are inactivated when ...
... :Our work attempts to dissect the myriad roles of RNA binding proteins in mammalian gene expression. RNA p
Translational contributions to tissue specificity in rhythmic and constitutive gene expression. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
The Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases provides an extremely dynamic environment for research into the aging process and its diseases.
The answer, though, is differences in gene expression in a cell. Clones have identical DNA, but the way the DNA is transcribed to RNA, and the way the RNA is translated to making a protein, can be specific to the cell. There are epigenetic factors - basically, chemicals that adhere to certain parts of the genome - that dictate NOT whether the DNA is there, but how often the DNA is read to make RNA and how efficiently that is made into functional proteins. Think about a fertilized egg. It divides into two cells, then 4 cells, then 8 cells, then 16 cells, then 32 cells, etc. Every time the cell divides, it has to make a perfect copy of its DNA. The cell machinery isnt always perfect and little changes in DNA can occur. Also, those chemicals that can affect gene expression can get added or subtracted as cells divide. Many of them, however, are passed on to the daughter cells. Thats how identical cells can have different levels of gene expression, and how people and horses and dogs with identical ...
You need to be familiar with all of the different ways and levels at which cells can control gene expression, including gene expression, Chromatin packing, DNA methylation, Histone acetylation, control elements and transcription factors, alternative RNA splicing, mRNA degredation, translational control by regulatory proteins, proteasomic protein degradation, etc. (Damn, that s a lot of control ...
Biological tissues consist of various cell types that differentially contribute to physiological and pathophysiological processes. Determining and analyzing cell type-specific gene expression under diverse conditions is therefore a central aim of biomedical research. The present study compares gene expression profiles in whole tissues and isolated cell fractions purified from these tissues in patients with rheumatoid arthritis and osteoarthritis. The expression profiles of the whole tissues were compared to computationally reconstituted expression profiles that combine the expression profiles of the isolated cell fractions (macrophages, fibroblasts, and non-adherent cells) according to their relative mRNA proportions in the tissue. The mRNA proportions were determined by trimmed robust regression using only the most robustly-expressed genes (1/3 to 1/2 of all measured genes), i.e. those showing the most similar expression in tissue and isolated cell fractions. The relative mRNA proportions were
RBF1 and E2F2 are components of the Drosophila, Rb, E2F, and Myb‐associated protein (dREAM) complex, a transcriptional silencing complex that represses many E2F target genes (Korenjak et al, 2004). To determine whether components of the Pum complex are targets for dREAM‐mediated repression, we analyzed datasets of published genome‐wide dREAM ChIP experiments from Drosophila Kc cells (Georlette et al, 2007) and found a strong ChIP enrichment for all of the dREAM components (E2F2, Myb, Mip120, Mip130, and Lin‐52) on the pumilio, nanos, and brat genes (Supplementary Fig S1B). To establish the functional significance of E2F2/RBF1 binding to these promoters, we assayed gene expression levels from Drosophila S2 cells and flies containing dsRNA or RNAi sequences targeting E2F/RBF family members. Depletion of RBF1 or E2F2 (but not E2F1) strongly induced the expression of nanos and modestly elevated the levels of pum and brat (Fig 1C, Supplementary Figs S1C and S2A and B). To further assess the ...
Systems biology aims to understand the behavior of and interaction between various components of the living cell, such as genes, proteins, and metabolites. A large number of components are involved in these complex systems and the diversity of relationships between the components can be overwhelming, and there is therefore a need for analysis methods incorporating data integration. We here present a method for exploring gene regulatory mechanisms which integrates various types of data to assist the identification of important components in gene regulation mechanisms. By first analyzing gene expression data, a set of differentially expressed genes is selected. These genes are then further investigated by combining various types of biological information, such as clustering results, promoter sequences, binding sites, transcription factors and other previously published information regarding the selected genes. Inspired by Information Fusion research, we also mapped functions of the proposed method ...
Nashun B, Hill PW, Hajkova P, 2015, Reprogramming of cell fate: epigenetic memory and the erasure of memories past., EMBO Journal, Vol: 34, Pages: 1296-1308, ISSN: 0261-4189 Cell identity is a reflection of a cell type-specific gene expression profile, and consequently, cell type-specific transcription factor networks are considered to be at the heart of a given cellular phenotype. Although generally stable, cell identity can be reprogrammed in vitro by forced changes to the transcriptional network, the most dramatic example of which was shown by the induction of pluripotency in somatic cells by the ectopic expression of defined transcription factors alone. Although changes to cell fate can be achieved in this way, the efficiency of such conversion remains very low, in large part due to specific chromatin signatures constituting an epigenetic barrier to the transcription factor-mediated reprogramming processes. Here we discuss the two-way relationship between transcription factor binding and ...
Mammalian genomic imprinting is an epigenetic gene regulatory mechanism that results in parental‐specific gene expression of a small number of genes in diploid somatic cells (Beechey et al., 2001; Reik and Walter, 2001; Li, 2002; Sleutels and Barlow, 2002). Several features of the imprinting mechanism have been identified; however, it is not yet clear whether imprinting is regulated by a unique process or whether it is part of the general epigenetic apparatus used to regulate mammalian gene expression. Clustering and coordinate regulation is one feature imprinted genes share with non‐imprinted genes (Engemann et al., 2000; Onyango et al., 2000), and it is now clear that many imprinted genes are functionally grouped such that imprinted expression of several genes is regulated by one long‐range imprint control element (Thorvaldsen et al., 1998; Horike et al., 2000; Zwart et al., 2001; Fitzpatrick et al., 2002). The frequent occurrence of an imprinted non‐coding RNA within an imprinted gene ...
Over several decades, the therapeutic use of glucocorticoids have established these molecules as potent inflammation suppressors. The description of transcriptional repression of pro-inflammatory genes as a nuclear receptor mediated mechanism represents a more recent topic of glucocorticoid signaling. However, new evidences suggest that steroidal regulation of inflammation is more complex, including epigenetic and receptor-independent pathways. It is also likely that sets of genes behaves in contradictory ways, making gene repression not a rule, but rather one of the possible modulatory modes. A similar level of complexity might apply to other steroidal hormones, such as those involved in sexually dimorphic immune responses. In fact, some autoimmune diseases are much more prevalent in one gender compared to the other. In addition to well-known steroid hormones, including aldosterone and vitamin D, this review topic intends to cover also non-canonical steroid signaling, including oxysteroids and
99 Tumorigenesis is often attributed to aberrant gene expression control leading to altered cell cycle control, resistance to apoptosis, abnormal differentiation, decreased genomic stability and inefficient DNA repair. The activity of chromatin remodeling complexes is vital to maintaining proper control of gene expression. The SWI/SNF complex is conserved from yeast to man and is responsible for remodeling up to 6% of the human genome, with many of those genes known to be associated with cell cycle control. Therefore, impaired or defective activity of SWI/SNF chromatin remodeling complex, involved in regulation of gene transcription, could encourage tumor development. The complex is composed of 10 or more members but requires only three core members to do the basic task of remodeling nucleosomes: BRG1/BRM, SNF5, and BAF155. BRG1 and SNF5 both lead to tumor development in haploinsufficient mice and embryonic lethality in null mice, and are mutated or inactivated in human tumors. The third and ...
Cancer can be understood as a disease of dysfunctional gene expression control. Research in Chris Vakocs lab investigates how transcription factors and chromatin regulators cooperate to control gene expression and maintain the cancer cell state. This work makes extensive use of genetic screens to reveal cancer-specific functions for transcriptional regulators, as well as genomic and biochemical approaches to identify molecular mechanisms. One theme that has emerged from their efforts is that blood cancers are often vulnerable to targeting transcriptional coactivators, such as BRD4 and the SWI/SNF chromatin remodeling complex. Vakocs team demonstrated that chemical inhibition of BRD4 exhibits therapeutic effects in mouse models of leukemia, a finding that has motivated ongoing clinical trials in human leukemia patients. The Vakoc lab has also developed a CRISPR-Cas9 screening approach that can reveal individual protein domains that sustain cancer cells. Their lab is now deploying this ...
The present study describes a novel cell type-specific mechanism of transcriptional regulation of TSP-1 in vascular cells in response to glucose. We report here that unlike our recently identified short promoter region (−280/+66) responsible for the increased THBS1 transcription in ECs, a longer promoter fragment (−1270/+66) is required for THBS1 regulation in HASMCs, as was described for specialized pericytes and mesangial cells.27 Interestingly, glucose responsiveness in ECs was in fact inhibited by the distal fragment of the promoter,10 suggesting the presence of an inhibitory element in this region, which is not active in either VSMCs or mesangial cells.27 The longer promoter region, −1270/+66, responsible for the increased THBS1 transcription in HASMCs contained distinctly different binding elements, as identified by MatInspector, located in the distal end of the promoter. These binding elements had no similarity to those in the EC-specific THBS1 promoter fragment, −280/+66, ...
Abstract: Interleukin-2 (IL-2) gene regulation was investigated in primary cultures of highly purified human peripheral blood CD28+T cells. Two discrete mechanisms for induction of T-cell proliferation could be distinguished by examining cell cycle progression and the expression of the IL-2 gene. Stimulation of cells by CD3 MoAb induced only transiently expressed, small amounts of IL-2 mRNA that was completely suppressed by cyclosporine. Costimulation of T cells with CD3 MoAb and either CD28 MoAb or PMA, but not calcium ionophore, induced a 50-100-fold increased in IL-2 gene expression and secretion. High levels of IL-2 gene expression could also be achieved by stimulation with calcium ionophore and PMA or CD28 MoAb and PMA, but not by CD28 MoAb plus calcium ionophore. IL-2 gene expression and T-cell proliferation induced by CD3 MoAb plus PMA or calcium ionophore plus PMA were completely suppressible by cyclosporine. In contrast, IL-2 gene expression and T-cell proliferation induced by CD28 MoAb ...
Buffo, A., Carulli, D., Rossi, F. and Strata, P. (2003), Extrinsic regulation of injury/growth-related gene expression in the inferior olive of the adult rat. European Journal of Neuroscience, 18: 2146-2158. doi: 10.1046/j.1460-9568.2003.02940.x ...
Kusakabe T., Yoshida, R., Ikeda, Y., Tsuda, M. (2004). "Computational discovery of DNA motifs associated with cell type-specific gene expression in Ciona." Dev Biol 276:563-580. (PUBMED ...
Antibodies for proteins involved in negative regulation of gene expression pathways, according to their Panther/Gene Ontology Classification
Ca(2+)-dependent gene expression is critical for cell growth, proliferation, plasticity, and adaptation [1-3]. Because a common mechanism in vertebrates linking cytoplasmic Ca(2+) signals with activation of protein synthesis involves the nuclear factor of activated T cells (NFAT) family of transcription factors [4, 5], we have quantified protein expression in single cells following physiological Ca(2+) signals by using NFAT-driven expression of a genetically encoded fluorescent protein. We find that gene expression following CRAC channel activation is an all-or-nothing event over a range of stimulus intensities. Increasing agonist concentration recruits more cells but each responding cell does so in an essentially digital manner. Furthermore, Ca(2+)-dependent gene expression shows both short-term memory and strong synergy, where two pulses of agonist, which are ineffectual individually, robustly activate gene expression provided that the time interval between them is short. Such temporal filtering
Is there a gene or genes that are activated at age 1 that signal to the other genes to perform gene expression appropriate for a one year old? Futhermore, is there a gene or genes that are activated at age 20 that signal to the other genes to perform gene expression appropriate for a twenty year old? Lastly, if there were a gene or genes that signals for twenty year old gene expression regulation, then if that gene were activated in an 80 year old, would the body of the 80 year old begin to exhibit the physiology of a 20 year old, thus increasing lifespan and healthspan? DE. ...
The discovery of the obese gene in the mouse and its conserved homologue in humans has led to important discoveries in energy metabolism. One of the chief findings was the fact that the expression of the leptin gene was regulated and that it, in turn, could regulate metabolism and behavior. Much of the literature has focused on the physiological role of leptin in driving processes as diverse as reproduction, starvation defence, feeding behavior or body weight, all dependent on expression levels of the ob gene. Here, we will describe our work, in which we have begun to elucidate the regulatory processes controlling obese gene expression.. Keywords: Gene Expression Regulation ; Obesity. ...
Summary Basic biological processes require gene expression. Tightly regulated molecules known as transcription factors mediate the expression of genes in development and disease. Signal transduction pathways, which respond to environmental cues or stressors are major regulators of the transcription factors. Use of macromolecular synthesis inhibitors in models of normal neurodevelopment and neurodegenerative cell death has led to the discovery that gene expression is required for these processes to occur (Martin et. al.,(1988), J Cell Biol 106 p829). To date, however, the identities of very few of the genes required in these events have been revealed. Hence, the activation or requirement of specific signaling pathways leading to the expression of known apoptotic genes is not well established. Utilizing the neurothrophic factor deprivation and neurotoxin models of programmed cell death we address these gaps in our understanding of the molecular mechanism of apoptosis as it occurs in neuronal cell death.
Comparison of gene expression from transgenes and endogenous genes with or without introns reveals a time-regulating role of introns in natural biological systems.
Sreenivas was awarded PhD in Biotechnology in 2009 by University of Pune, India for his research work on understanding the genetic determinants of human diseases, undertaken at CSIR-Institute of Genomics and Integrative Biology, India. Subsequently, he undertook postdoctoral studies investigating the role of gene expression regulation in human diseases at the University of Gothenburg, Sweden.. He came to Cambridge in November 2010 as Career Development Fellow to MRC Laboratory of Molecular Biology and has subsequently become an EMBO long-Term fellow. He currently investigates the role of genetic variation on the gene expression regulation and different observable traits in diverse organisms from yeast to humans. He aims to extend the general principles derived by such comprehensive studies to understand the molecular determinants of human diseases.. ...
This study provides a genome-wide screen of neuronal activity-driven gene expression in response to different chemical stimuli and downstream of four important PRTFs (CREB, SRF, EGR1, and FOS). The use of a common approach to manipulate the activity of different PRTFs, making their transactivation activity independent of the upstream signaling cascades that normally would regulate it, provides an alternative and innovative way to explore the neuronal gene programs downstream of these TFs under highly comparable conditions. Furthermore, the integration of PRTF- and stimulation-dependent patterns through meta-analysis has allowed us to gain novel insight into the transcriptional networks underlying neuronal activity-dependent gene expression, which is usually disregarded in single-molecule reductionist approaches.. Our screen identified hundreds of novel stimulus-specific activity-regulated transcripts, including novel stimulus-associated miRNAs and candidate genes that may be differentially ...
This study has confirmed the long-held view that integration of Ca2+ and kinase signaling is needed for efficient activation of inducible gene expression in T cells. We found that for many immune response genes, both signals are needed to open up the chromatin and activate transcription. However, the immune system encompasses other genes that are induced in a range of cell types, by a wide variety of other receptors linked to kinase but not Ca2+ signaling pathways. These include proinflammatory receptors, such as Toll family receptors, and receptors that respond to cytokines such as IL-1 and TNF, which also lead to induction of the TFs AP-1 and NF-κB. For these reasons it makes sense that we find a subset of genes that are induced by PMA via PKC-dependent pathways, in the absence of Ca2+ signaling. Significantly, we found that two-thirds of all of the genes induced 5-fold by TNF were also induced 5-fold by PMA (Table I). In contrast, there appear to be fewer gene-inducing signaling pathways ...
Background Variation in gene expression is extensive among tissues, individuals, strains, populations and species. The interactions among these sources of variation are relevant for physiological...
Effect of the stem-loop element on gene expression in different gene contexts. (A) Cell lines were generated which expressed luciferase under the control of a
A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins. [from MeSH] ...
Transcription factor that is involved in embryonic development, establishment of tissue-specific gene expression and regulation of gene expression in…
IKKα-targeting miRNAs affects noncanonical and canonical NF-κ.B gene expression(a) Real time PCR analysis of ELC mRNA in monocytes and macrophages, normalized
J:99346 Lee CS, Friedman JR, Fulmer JT, Kaestner KH, The initiation of liver development is dependent on Foxa transcription factors. Nature. 2005 Jun 16;435(7044):944-7 ...
J:112202 Krizhanovsky V, Soreq L, Kliminski V, Ben-Arie N, Math1 target genes are enriched with evolutionarily conserved clustered E-box binding sites. J Mol Neurosci. 2006;28(2):211-29 ...
21:47, 20 November 2012 (diff , hist) . . (+4,409)‎ . . N Structural Biochemistry/Modulation of Translation ‎ (Created page with ==Introduction== An effective way gene expression can be controlled is by regulating the translation of RNA. By controlling RNA (primarily mRNA) certain genes can be expresse...) ...
Scientists have made a medical breakthrough which may help bring new insights on how genes are activated. Roughly 3 metres of DNA is tightly folded into the nucleus of every cell in our body. This folding allows some genes to be expressed, or activated, while excluding others.
Gene expression is controlled by transcription factors that regulate the rates at which genes are expressed either by recruiting or inhibiting protein complexes that bind to the promoters or enhancers of target genes. Molecules that can specifically modulate these protein-DNA interfaces show promise as tools for understanding gene regulation pathways and may have application in human medicine. Hairpin pyrrole-imidazole polyamides are programmable oligomers that bind the DNA minor groove in a sequence-specific manner with affinities comparable to those of natural DNA-binding proteins. These cell-permeable small molecules have been shown to enter the nuclei of live cells, disrupt protein-DNA interactions, and downregulate endogenous gene expression. This thesis describes the use of polyamides to modulate gene expression in order to probe gene regulation mechanisms of several different biologically relevant systems. A polyamide is designed to target the glucocorticoid receptor transcription factor ...
A great many aspects of the anatomy and physiology of large animals are constrained by the need to match oxygen supply to cellular metabolism and appear likely to involve the regulation of gene expression by oxygen. Some insight into possible underlying mechanisms has been provided by studies of erythropoietin, a haemopoietic growth factor which stimulates red cell production in response to hypoxia. Studies of hypoxia-inducible cis-acting sequences from the erythropoietin gene have led to the recognition of a widespread transcriptional response to hypoxia based on the activation of a DNA-binding complex termed hypoxia-inducible factor-1 (HIF-1). Perturbation of the transcriptional response by particular transition metal ions, iron chelators and certain redox-active agents have suggested a specific oxygen sensing mechanism, perhaps involving a haem protein in a flavoprotein/cytochrome system. In addition to erythropoietin, HIF-1-responsive genes include examples with functions in cellular energy
Long intergenic non-coding RNAs (lincRNAs) are defined as RNA transcripts that are longer than 200 nucleotides. By definition, these RNAs must not have open reading frames that encode proteins. Many of these transcripts are encoded by RNA polymerase II, are spliced, and are poly-adenylated. This final fact indicates that there is a trove of information about lincRNAs in databases such as the Gene Expression Omnibus (GEO), which is a repository for RNAseq and microarray data. Recent experiments indicate that there are upwards of 15,000 lincRNAs encoded by the human genome. The term "intergenic" refers to the identification of these transcripts from regions of the genome that do not contain protein-encoding genes. These regions coincide with what was once labeled as the "junk DNA" portions of our genomes, which, upon careful examination by whole genome RNA sequencing experiments, clearly encode RNA transcripts. LincRNAs also contain promoter- or enhancer-associated RNAs that are gene proximal and ...
Our present study has provided, for the first time to our knowledge, a systematic analysis of the inflammation-relevant gene expression in ECs and SMCs in their coculture under static condition and in response to shear stress. We demonstrated that SMCs cause an upregulation of proinflammatory gene expression in ECs located in close proximity and that shear stress acts as a negative regulator for these proinflammatory gene expression in ECs cocultured with SMCs. Under static coculture condition, DNA microarray technology identified 23 inflammation-relevant genes that exhibit significant changes (18 increases and 5 decreases) in their expression in ECs cocultured with SMCs, as compared with the control monocultured ECs. All 18 genes upregulated in ECs by the coculture encode products that serve proinflammatory and thrombogenic functions. These functions include: (1) mediation of leukocyte-EC interaction and signal transduction (ICAM-1, VCAM-1, CD44, and NK-4); (2) promotion of chemotaxis and ...
Abstract: In this work, I focus on the development and testing of tools to explore differential gene expression as a molecular mechanism underlying the predisposition to complex disease. By definition, complex diseases (e.g. hypertension, diabetes, asthma) demonstrate both environmental and genetic factors in disease susceptibility, implicating genes that show both environmental response and genetic variability in predisposing disease. Differential gene expression is one important cellular response that reflects both of these factors in complex disease. Given their combined genetic and environmental influences, complex diseases are studied using a variety of analytical approaches. Consequently, the integration of data from diverse sources is a significant and important challenge in modern biomedical science. I demonstrate a statistical approach to integrating differential gene expression and genetic linkage data from multiple sources to reveal candidate genes, metabolic pathways, and DNA ...
Studies spanning the past three decades have revealed that differential gene expression is one of the most widely used modes of cellular regulation in both normal physiological processes such as development and differentiation and aberrant processes such as cancer. The Gene Regulation, Epigenomics and Transcriptomics Home Areas mission is to train students in the principles and concepts of contemporary gene regulation research with an emphasis on developing skills in cellular, proteomic and genome-wide analyses in order to study mechanisms of differential gene expression during cell signaling, differentiation, development and disease. Our program consists of a specialized curriculum focused on generating a comprehensive understanding of current concepts and mechanisms of gene regulation at the fundamental level and in relation to specific biological pathways. Our groups studies range from basic biochemical analysis of chromatin transcription to detailed analysis of RNA-based pathways involved ...
Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS) cells from adult skin primary fibroblasts and attempted to detect tissue-specific cis-regulatory variants using in vitro cell differentiation. We used padlock probes and high-throughput sequencing for digital RNA allelotyping and measured allele-specific gene expression in primary fibroblasts, lymphoblastoid cells, iPS cells, and their differentiated derivatives. We show that allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome. We show that our approach to mapping cis-regulatory variants reduces in vitro experimental ...
Email: [email protected]lberg.de Translation of messenger RNAs into polypeptides represents the interface between the genome and the proteome. Not surprisingly, this step in the gene expression pathway is frequently used for the regulation of biological responses. I will discuss principles by which structural features of mRNAs, regulatory RNA elements and RNA- binding proteins regulate protein synthesis. This will include findings that imply a new role of the poly(A) tail in the translation of messenger RNAs via IRESes (internal ribosome entry sequences), the understanding of an important switch in Drosophila development, and results from whole genome microarray analyses in yeast which suggest that signal-induced changes in the transcriptome are amplified at the translational level. These latter results unveil a novel, higher level of coordinated gene regulation, which we refer to as potentiation .. ...
In recent years, the maturation of microarray technology has allowed the genome-wide analysis of gene expression patterns to identify tissue-specific and ubiquitously expressed (housekeeping) genes. We have performed a functional and topological analysis of housekeeping and tissue-specific networks to identify universally necessary biological processes, and those unique to or characteristic of particular tissues. We measured whole genome expression in 31 human tissues, identifying 2374 housekeeping genes expressed in all tissues, and genes uniquely expressed in each tissue. Comprehensive functional analysis showed that the housekeeping set is substantially larger than previously thought, and is enriched with vital processes such as oxidative phosphorylation, ubiquitin-dependent proteolysis, translation and energy metabolism. Network topology of the housekeeping network was characterized by higher connectivity and shorter paths between the proteins than the global network. Ontology enrichment scoring
Regulation of gene expression is a multi-layered process - from transcription to translation, including regulatory pathways such as epigenetics, chromatin remodeling and splicing, to name a few. A long-standing question in cellular and molecular neuroscience is the establishment of causality between gene expression and neurophysiology. One way to understand causality is to visualize the dynamic behavior of mRNAs and proteins in their native context and in response to neuronal activity. While transcriptomic and proteomic approaches have been the methods of choice to study genome-wide changes in neuronal gene expression, the
Life: The Science of Biology 11th Edition answers to Chapter 16 - Regulation of Gene Expression - 16.2 - Eukaryotic Gene Expression Is Regulated by Transcription Factors - 16.2 Recap - Learning Outcomes - Page 345 2 including work step by step written by community members like you. Textbook Authors: Sadava, David E.; Hillis, David M.; Heller, H. Craig; Hacker, Sally D. , ISBN-10: 1-31901-016-4, ISBN-13: 978-1-31901-016-4, Publisher: W. H. Freeman
Regulation of gene expression includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA), and is informally termed gene regulation. Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein.. Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed. Histone, DNA modifying enzymes and chromatin remodelling factors are major area to concentrate.. Relevant Conferences: Nucleic Acids Conferences , Biochemistry Conferences. 2ndInternational Conference on Transcriptomics, September 12-14, 2016 Philadelphia ...
What is meant by gene expression? Gene expression refers to genes being turned on and producing a product. The product could be an enzyme, a structural protein, or a control molecule. Studies of gene expression typically measure the production of mRNA. Most mechanisms that control gene expression do so by controlling transcription, the synthesis of mRNA. However there are other mechanisms for controlling the rate of protein synthesis that occur downstream (between transcription and translation). Several of these are described in this animation. View the animation below, then complete the quiz to test your knowledge of the concept.. ...
Control of gene expression is a highly complex process involving the coordinated activity of multiple and heterogeneous biological factors. An underlying and intriguing general phenomenon is that biological molecules may act in a variety of different combinations to modulate cellular activities and to specifically react to changes in the biological milieu. To provide coordinated and multiple complex responses, several mechanisms are known to integrate a number of molecules in a combinatorial way.. Combinatorial post-translational modifications, such as methylation, acetylation, phosphorylation, and/or variations in regulatory trans-factors amounts, can influence the global regulation of gene expression at different levels. For example, the combinatorial epigenetic tagging of DNA and histones may enforce or reverse chromatin remodeling, thus playing a fundamental role in a variety of physiological and diseased cellular states [1, 2]. Such combinatorial patterns of epigenomic modifications were ...
Changes on chromatin accessibility take an important part in the regulation of gene expression. ATAC-seq is proven to be useful in studying chromatin accessibility, and many pipelines have been used in sequencing read analysis. By combining our short read aligner and read quantifier, the Homer peak caller and the Limma/edgeR packages, our pipeline provides a fast yet systematic view to the changes on chromatin accessibility between sample, therefore helping biologists to understand the roles of the key transcription factors in gene expression regulation. In this talk, I will briefly introduce the ATAC-seq technologies and its use in analyses, then present our pipeline for studying the functions of key transcription factors in two real cases ...
View Notes - Control of Gene Expression from BSC BSC1005 at Broward College. mRNA and translational mechanisms control the synthesis of protein after mRNA has been produced. Operons Operons are
Differential cardiac gene expression during cardiopulmonary bypass: ischemia-independent upregulation of proinflammatory genes.s profile, publications, research topics, and co-authors
The spatial information associated with gene expression is important for elucidating the context-dependent transcriptional regulation during development. Recently, high-resolution sampling approaches, such as RNA tomography or single-cell RNA-seq combined with fluorescence in situ hybridization (FISH), have provided indirect ways to view global gene expression patterns in three dimensions. Now in situ sequencing technologies, such as fluorescent in situ sequencing (FISSEQ), are attempting to visualize the genetic signature directly in microscope images. This article will examine the basic principle of modern in situ and single-cell genetic methods, hurdles in quantifying intrinsic and extrinsic forces that influence cell decision-making, and technological requirements for making a visual map of gene regulation, form, and function. Successfully addressing these challenges will be essential for investigating the functional evolution of regulatory sequences during growth, development, and cancer ...
As you learned in BIO101, the cell nucleus is the storage area for all genetic material and constantly full of activity. The nucleus in fact contains not only DNA, but RNA and protein as well. This unit will take a detailed look at chromosomes, the cell nucleus, gene expression, and expression regulation. When we refer to "expression regulation," we are talking about the fact that not all genes are expressed in the cell at the same time. After all, though a liver cell and a nerve cell have the same genome (and thus the same DNA), they look and act completely differently. How does this happen? The answer is regulated gene expression!. ...
Modulation of Host Gene Expression and Innate Immunity by Viruses und Buchbewertungen gibt es auf ReadRate.com. Bücher können hier direkt online erworben werden.
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... emphasizes signal transduction and gene regulation in the hypothalamic-pituitary-gonadal axis. Lectures cover physiologic to molecular actions of peptide, protein and steroid hormones and the intracellular signaling as well as the transcriptional gene regulatory mechanisms that drive reproductive biology. Section 1 laboratories teach methods key to studying hormone action and cell biology. Techniques include quantification of second messengers and transcriptional activity; cell culture and transient transfection; western blot analysis; ELISAs; quantitative RT-PCR; gene silencing; chromatin immunoprecipitation; immunofluorescence and in situ hybridization; mutagenesis; tissue dissection. Principles of microscopy and imaging methods are also discussed and applied.. The schedule for Section 1 of FIR2018 can be downloaded here. ...
Study Regulation of Eukaryotic Gene Expression (Biochem Ch 5) flashcards from dheeraj chintapalli's garranps class online, or in Brainscape's iPhone or Android app. ✓ Learn faster with spaced repetition.
Genomes contain all the genetic information needed by an organism, regardless of the circumstance or environment. Generally, however, even single-cell organisms use only a fraction of their genome at any time; that is, cells generally express only a fraction of their genome at any given time. This is especially true among the individual cells that make up multicellular organisms, where cell specialization (differentiation) dictates that only certain genes be expressed in certain cells, and only at particular times during the organisms life span.. ...
Identification of Single- and Multiple-Class Specific Signature Genes from Gene Expression Profiles by Group Marker Index. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Often transcription is activated when a molecule binds to a protein. What happens next is that bound protein undergoes a change that eventually results in the activation of transcription. The molecule that binds is called a ligand, and the protein that binds the protein is called the receptor protein. Ligands can be small molecules such as protein that pass through the cell membrane and activate transcription, or they can be protein molecules that can not move through the cell membrane and must find a receptor protein that resides in the cell membrane. We will discuss each of these models for gene expression.. Copyright © 1997. Phillip McClean. ...
One common method for profiling the state of a cell is to measure levels of gene expression, the process by which the information within our genes is used to make a gene product. Cells control expression of genes as a way to adapt to their environment. Researchers at the LINCS Transcriptomics Center have released an updated version of the Connectivity Map (CMap) which now contains over 1.3 million gene expression profiles from treating numerous types of human cells with over 42,000 agents that disrupt cellular function (perturbagens). This extremely large set of data is based on the L1000 assay which allows for inexpensive and large-scale analysis of gene expression. CMap is a freely available public resource that any research scientist can use and already has more than 18,000 registered users. For example, researchers can gain insight regarding how a small-molecule drug works in a cell by determining the changes in gene expression it produces. Alternatively, they can find a molecule from all ...
Gene Expression Macro Version 1.1 Instructions Rev B 1 Bio-Rad Gene Expression Macro Users Guide 2004 Bio-Rad Laboratories Table of Contents: Introduction Opening
Mouse polyclonal antibody raised against a full-length human CEBPB protein. CEBPB (AAH21931.1, 1 a.a. ~ 345 a.a) full-length human protein. (H00001051-B01P) - Products - Abnova
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NFAT1 (NFATc2), 0.1 ml. Nuclear factor of activated T cells (NFAT) is a family of transcription factors implicated in multiple biological processes including cytokine gene expression, cardiac hypertrophy and adipocyte differentiation.
Gene, Genes, Glucocorticoids, Prednisolone, Ability, Dimerization, DNA, Elements, Gene Expression, Gene Expression Profiling, Livers, Mice, Regulation, Regulation Of Gene Expression, Transcription Factors, Cell, Drugs, Adaptive Immunity, Blood, Cells
Chapter 18 Regulation of Gene Expression Gene Regulation Is Necessary By switching genes off when they are not needed, cells can prevent resources from being wasted. There should be natural selection
Lyubetsky V., Gorbunov K., Pirogov S., Rubanov L., Seliverstov A., An algorithm and search results for a model of gene expression regulation with RNA secondary structures in bacteria Information Processes, 2005, V. 5, No 5, pp. 337 366. [in Russian] http://www.jip.ru/2005/337-366.pdf ...
In this study we describe the spatial regulation of RNA interference (RNAi) using an RNA-carrier protein labeled with a fluorescent dye and a light source to trigger the RNAi. We demonstrate photo-dependent gene silencing using several dyes with diff
I am fascinated by a fundamental question in biology; How is regulation of gene expression as a response to external stimulus achieved? My laboratory
Akhilesh Bajpai, Sravanthi Davuluri and Acharya KK* (*Correspondence: [email protected]), A comparative account of gene expression resources, feature-validations and application-based categorizations; In: Startbioinfo; 12 Oct 2011, http://www.startbioinfo.com/gene-expression/" ...
Im just not quite sure the answer to this. When we talk about epigenetics and gene expression, does it not matter if we have snps or not? For...
Genotyping & gene expression full services from Eurofins Genomics . Wide range of platforms and assays available ** Call +49 8092 8289-0
An expression system refers to the factors that work together to yield a particular gene product such as a protein, ribozyme or RNA particle.
The need to analyze rare cells is based on the nature of tissue differentiation and regeneration, the initiation and propagation of disease processes in multicellular organisms, and the functional diversity of individual cells
People who want to take free transcription training online can take courses offered by Meditec, Online-medical-transcription-course.com and the eLearn Medical Transcription course. Although these...
This category lists sites for medical transcription associations that inform, and enable the support and advancement of the medical transcription industry. <
I dont have a TV because it seems such a time sink. Nevertheless, over the past few years Ive felt the creep of media convergence. Now I found this site, not quite as bad as channel surfing...but its getting there ...
ON-TARGETplus and siGENOME SMARTpool siRNA reagent and at least 3 of 4 individual siRNAs will silence target gene expression by at least 75% at the mRNA level when used under optimal delivery conditions.. ...
Sources tell TMZ the network has told the cast if they dont accept MTVs deal by the end of business Monday, they will be replaced. And, MTV has told them it does not have to be a package deal -- the cast members who accept the offer will stay ... those who do not can have a nice life ...
The Workshop on Evolutionary Tinkering in Gene Expression which was held at the end of August 1988. was planned to celebrate 20 successful Advanced Study Institutes (A. S. I.) in Molecular and Cell
MicroRNA, also known as miRNA, is a class of non-coding ribonucleic acid (RNA) which plays a vital role in the regulation of gene expression. It founds in
Find info concerning Fairmont State medical transcription. Qualifications for nursing programs vary widely. Learn about the various medical specializations available within technical training programs.
The generation of transgenic mice by DNA microinjection is a powerful tool to investigate the molecular regulation of gene expression, development, and disease
Our daughter, Kezia, came down with Acute Lymphoblastic Leukaemia at the age of two years in 2006 and was evacuated to the UK for treatment. Mum, Nanda, accompanied her and later Nandas son Jaime went to the UK. Dad, Angus, stayed in Africa earning to support them and periodically visited them. Kezia finished treatment in 2008 and the family returned to Sao Tome e Principe mid-2009. Kezia is doing fine and hasnt relapsed but wonnt be considered "clear" until 2013. Meanwhile Dad was made redundant - at the best of times hes a consultant, sometimes a teacher and often unemployed. Poor White Trash. We reserve the right to go off topic and talk about anything we damn well like ...
Artificial transcription factors can be engineered to interact with specific DNA sequences to modulate endogenous gene expression within cells. A significant hurdle to implementation of this approach is the selection of the appropriate DNA sequence for targeting. We reasoned that a good target site should be located in chromatin, where it is accessible to DNA-binding proteins, and it should be, in the close vicinity of known transcriptional regulators of the gene. Here we have explored the efficacy of these criteria to guide our selection of potential regulators of gamma-globin expression. Several zinc finger-based transcriptional activators were designed to target the sites proximal to the -117-position of the gamma-globin promoter. This region is proximal to the binding sites of known and potential natural transcription factors. Design and study of three transcription factors identified the potent transcriptional activator, ggl-VP64-RA. This transcription factor was able to interact directly ...
TY - JOUR. T1 - Antagonistic regulation of type I collagen gene expression by interferon-γ and transforming growth factor-β. T2 - Integration at the level of p300/CBP transcriptional coactivators. AU - Ghosh, Asish K.. AU - Yuan, Weihua. AU - Mori, Yasuji. AU - Chen, Shu Jen. AU - Varga, John. PY - 2001/4/6. Y1 - 2001/4/6. N2 - Among the extracellular signals that modulate the synthesis of collagen, transforming growth factor-β (TGF-β) and interferon-γ (IFN-γ) are preeminent. These two cytokines exert antagonistic effects on fibroblasts, and play important roles in the physiologic regulation of extracellular matrix turnover. We have shown previously that in normal skin fibroblasts, TGF-β positively regulates α2(I) procollagen gene (COL1A2) promoter activity through the cellular Smad signal transduction pathway. In contrast, IFN-γ activates Stat1α, down-regulates COL1A2 transcription, and abrogates its stimulation induced by TGF-β. The level of integration of the two pathways mediating ...
In this study, we provide experimental evidence in favor of the hypothesis that PPARs are involved in the control of renin gene expression. We predicted a role for PPARs in the regulation of renin gene expression using a molecular approach. There was strong initial evidence supporting such a role.7,12 A functional DNA-binding site, similar to the consensus motif for PPARs, was detected in the conserved 5′-renin gene enhancer. The retinoic acid nuclear receptor RXRα, which is the typical interaction partner for PPARs, binds to the mouse renin gene enhancer. Lastly, vitamin A, which is the natural ligand of RXRs, was found to stimulate the transcription of the renin gene.. Renin gene expression is upregulated by cAMP in CaLu-6 cells through stabilization of renin mRNA, although transcriptional mechanisms are also involved.17,21 We provided several lines of evidence that PPARγ stimulates renin gene expression without affecting the stability of renin mRNA (Figures 1, 2, and 5⇑⇑; data not ...
RATIONALE: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is not well known how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart. OBJECTIVE: We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression. METHODS AND RESULTS: We profiled genome-wide transcriptional activity and a variety of epigenetic marks in the regulatory DNA elements using massive RNA-seq (n=12) and ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing; n=84) in human endothelial cells (CD31(+)CD144(+)), cardiac progenitor cells (Sca-1(+)), fibroblasts (DDR2(+)), and their respective induced pluripotent stem cells. We uncovered 2 classes of regulatory DNA elements: class I was ...
Healthy adult cardiomyocytes derive ,60% of their energy from fatty acid oxidation. The nuclear receptor subfamily of peroxisome proliferator-activated receptors (PPAR) regulate cardiac metabolic gene expression by transcriptional activation. Reduced expression of PPARα and its co-activator, PPARγ coactivator-1α (PGC-1α), has been shown in human and animal studies of heart failure and ischemia, concomitant with reduced fatty acid use. PGC-1α regulates mitochondrial biogenesis and energy metabolic gene expression, thus elucidating the transcriptional regulation of PGC-1α gene expression is important for understanding metabolic gene expression in cardiac health and disease. We hypothesized that estrogen related receptor ERRα, which also plays a role in cardiac energy metabolism, regulates expression of PGC-1α by direct interaction with its gene promoter. To examine this possibility we employed a PGC-1α promoter-luciferase reporter in transient transfection assays of COS-7 cells. ERRα ...
The human tumor necrosis factor alpha (TNF-alpha) gene is one of the earliest genes transcribed after the stimulation of a B cell through its antigen receptor or via the CD-40 pathway. In both cases, induction of TNF-alpha gene transcription can be blocked by the immunosuppressants cyclosporin A and FK506, which suggested a role for the NFAT family of proteins in the regulation of the gene in B cells. Furthermore, in T cells, two molecules of NFATp bind to the TNF-alpha promoter element kappa 3 in association with ATF-2 and Jun proteins bound to an immediately adjacent cyclic AMP response element (CRE) site. Here, using the murine B-cell lymphoma cell line A20, we show that the TNF-alpha gene is regulated in a cell-type-specific manner. In A20 B cells, the TNF-alpha gene is not regulated by NFATp bound to the kappa 3 element. Instead, ATF-2 and Jun proteins bind to the composite kappa 3/CRE site and NFATp binds to a newly identified second NFAT site centered at -76 nucleotides relative to the ...
TY - GEN. T1 - Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes. AU - Huang, Shao-Shan. AU - Fulton, Debra L.. AU - Arenillas, David J.. AU - Perco, Paul. AU - Ho Sui, Shannan J.. AU - Mortimer, James R.. AU - Wasserman, Wyeth W.. PY - 2006/12/1. Y1 - 2006/12/1. N2 - Transcription regulation is mediated by combinatorial interactions between diverse trans-acting proteins and arrays of cis-regulatory sequences. Revealing this complex interplay between transcription factors and binding sites remains a fundamental problem for understanding the flow of genetic information. The oPOSSUM analysis system facilitates the interpretation of gene expression data through the analysis of transcription factor binding sites shared by sets of co-expressed genes. The system is based on cross-species sequence comparisons for phylogenetic footprinting and motif models for binding site prediction. We introduce a new set of analysis algorithms for the ...
Gene regulation[edit]. Main article: Regulation of gene expression. At the cellular level, homeostasis is carried out by ... receptors include nuclear receptors that bring about changes in gene expression through up-regulation or down-regulation, and ... Main articles: Blood sugar regulation and Glycolysis § Regulation of the rate limiting enzymes ... Copper regulation[edit]. Main article: Copper in health § Homeostasis. This section needs expansion. You can help by adding to ...
Morris KL (2008). "Epigenetic Regulation of Gene Expression". RNA and the Regulation of Gene Expression: A Hidden Layer of ... There are several layers of regulation of gene expression. One way that genes are regulated is through the remodeling of ... They control gene expression including virulence genes in pathogens and are viewed as new targets in the fight against drug- ... transposase activity and regulation of gene expression.[110][116] There exists a genetic switch controlling Streptococcus ...
Hilbert, J. L.; Martin, F. (1988). "Regulation of gene expression in ectomycorrhizas". New Phytologist. 110 (3): 339-346. doi: ... 2004). "Differential gene expression during pre-symbiotic interaction between Tuber borchii Vittad. and Tilia americana L". ... Comparative analyses of the mRNAs from both free-living mycelium and the EcM mycobionts showed many changes in gene expression ... A few fungal genes that appear to be expressed before plant contact include PF6.2 and ras from Laccaria bicolor, and ras from ...
Pays, E. (2005). "Regulation of antigen gene expression in Trypanosoma brucei". Trends Parasitol. 21 (11): 517-20. doi:10.1016/ ... According to this model, new genes are created by non-adaptive processes, such as by random gene duplication. These novel ... All changes in the gene frequencies of populations--and quite often in the traits those genes influence--are by definition ... how new alternative spliced isoforms of genes arise, how gene scrambling in ciliates evolved, and how pervasive pan-RNA editing ...
"Gonadotropin regulation by pulsatile GnRH: Signaling and gene expression". Molecular and Cellular Endocrinology. 463: 131-141 ... "Role of glucocorticoid negative feedback in the regulation of HPA axis pulsatility". Stress. 21 (5): 403-416. doi:10.1080/ ...
"Expression profiling reveals off-target gene regulation by RNAi". Nature Biotechnology. 21 (6): 635-637. doi:10.1038/nbt831. ... Toxic effects due to over-expression of shRNAs: High level expression of shRNAs has been shown to be toxic. Strategies to ... Woods, N. B.; Bottero, V.; Schmidt, M.; Von Kalle, C.; Verma, I. M. (2006). "Gene therapy: Therapeutic gene causing lymphoma". ... or diseases associated with altered expression of endogenous genes such as drug-resistant lung cancer, neuropathic pain, ...
Global regulation of gene expression and chromosomal topologyEdit. In eukaryotes, about 10-20% of the genes are rhythmically ... Circadian orchestration of gene expression in cyanobacteria. Genes Dev. 9, 1469-1478. ... No significant similarity was found among the kai genes and any other previously reported genes in eukaryotes, but there are ... The mechanism by which this global gene regulation is mechanistically linked to the circadian clock is not known, but it may be ...
Leslie MC, Bar-Eli M (January 2005). "Regulation of gene expression in melanoma: new approaches for treatment". J. Cell. ... with both unfavorable genes where high expression is correlated to poor survival and favorable genes where high expression is ... Some rare genes have a relatively high risk of causing melanoma; some more common genes, such as a gene called MC1R that causes ... Examples of unfavorable genes are MCM6 and TIMELESS; an example of a favorable gene is WIPI1.[44][45] ...
Karsenty G, Park RW (1995). "Regulation of type I collagen genes expression". International Reviews of Immunology. 12 (2-4): ... "Mechanoregulation of gene expression in fibroblasts". Gene. 391 (1-2): 1-15. doi:10.1016/j.gene.2007.01.014. PMC 2893340. PMID ... Effect on gene expression[edit]. Differing mechanical properties in ECM exert effects on both cell behaviour and gene ... The stiffness and elasticity of the ECM has important implications in cell migration, gene expression,[29] and differentiation. ...
"Global regulation of erythroid gene expression by transcription factor GATA-1". Blood. 104 (10): 3136-47. doi:10.1182/blood- ... GATA1 regulates the expression (i.e. formation of the genes' products) of an ensemble of genes that mediate the development of ... regulation of transcription, DNA-templated. • regulation of primitive erythrocyte differentiation. • positive regulation of ... positive regulation of peptidyl-tyrosine phosphorylation. • negative regulation of bone mineralization. • negative regulation ...
Tomilin N. V. (2008). "Regulation of mammalian gene expression by retroelements and non-coding tandem repeats". BioEssays. 30 ( ... It is probable that short sequence repeats in those locations are also involved in the regulation of gene expression.[42] ... Effects on gene regulation[edit]. Length changes of microsatellites within promoters and other cis-regulatory regions can ... A genome-wide study estimates that microsatellite variation contributes 10-15% of heritable gene expression variation in humans ...
Thus, codon usage can introduce an additional level of transcriptional regulation for appropriate gene expression under ... "Importance of codon usage for the temporal regulation of viral gene expression". Proceedings of the National Academy of ... Fox JM, Erill I (June 2010). "Relative codon adaptation: a generic codon bias index for prediction of gene expression". DNA Res ... Heterologous gene expression is used in many biotechnological applications, including protein production and metabolic ...
"Regulation of gene and protein expression in cardiac myocyte hypertrophy and apoptosis". Advances in Enzyme Regulation. 45 (1 ... and a crucial step in gene expression profiling.. For protein detection, it is advantageous to use fluorescent labels ... "Down-regulation of the strawberry Bet v 1-homologous allergen in concert with the flavonoid biosynthesis pathway in colorless ...
Regulation of gene expression. DNA is transcribed into mRNA, introns are spliced during post-transcriptional regulation, and ... "Gene Regulation in Eukaryotes". Eastern Michigan University. Retrieved 7 April 2013.. *^ a b c "Gene Regulation in Eukaryotes" ... Enhancers function as a "turn on" switch in gene expression and will activate the promoter region of a particular gene while ... untranslated region of the ANP gene and acts as a mediator for its appropriate expression. The protein encoded by the ANP gene ...
Gene regulation[edit]. Main article: Regulation of gene expression. The genome of a given organism contains thousands of genes ... The tryptophan repressor blocks the transcription and expression of the genes, thereby creating negative feedback regulation of ... 2002), II.3. Control of Gene Expression - The Tryptophan Repressor is a Simple Switch That Turns Genes On and Off in Bacteria ... "Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals" (PDF). Nature Genetics ...
"Seizures and the regulation of neurotrophic factor and neuropeptide gene expression in brain". Epilepsy Research. Supplement. 4 ... positive regulation of receptor binding. • regulation of protein localization to cell surface. • regulation of receptor ... Expression[edit]. The BDNF protein is encoded by a gene that is also called BDNF, found in humans on chromosome 11.[6][7] ... The calcium influx triggered through NMDA receptors can lead to expression of BDNF, as well as other genes thought to be ...
Ngo P, Ozga JA, Reinecke DM (July 2002). "Specificity of auxin regulation of gibberellin 20-oxidase gene expression in pea ... "Phytochrome regulation and differential expression of gibberellin 3beta-hydroxylase genes in germinating Arabidopsis seeds". ... genes coding for GA 20-oxidase and GA 3-oxidase) and the SLENDER1 gene (a GA signal transduction gene) are found in growing ... Regulation[edit]. Regulation by other hormones[edit]. The auxin indole-3-acetic acid (IAA) regulates concentration of GA1 in ...
"Prospects for inhibiting the post-transcriptional regulation of gene expression in hepatitis B virus". World Journal of ...
"The regulation of arginine biosynthesis: its contribution to understanding the control of gene expression". Genetics. 128 (3 ... "Regulation of the Escherichia coli glyA gene by the purR gene product". J. Bacteriol. 172 (7): 3799-803. PMC 213358. PMID ... "Regulation of the Escherichia coli glyA gene by the metR gene product and homocysteine". J. Bacteriol. 171 (9): 4958-62. PMC ... which is where the product of a structural gene regulates the expression of the operon in which the genes reside. The ...
2004) „Oxygen-dependent and tissue-specific regulation of erythropoietin gene expression". American Journal of Physiology. ... Goldwasser, Eugene. A Bloody Long Journey: Erythropoietin and the Person Who Isolated It. Xlibris (2011. április 15.). ISBN 978 ...
Atkins KB, Troen BR (July 1995). "Regulation of cathepsin D gene expression in HL-60 cells by retinoic acid and calcitriol". ... Cathepsin D is a protein that in humans is encoded by the CTSD gene.[5][6] This gene encodes a lysosomal aspartyl protease ... The CTSD gene is one of the identified eight genes the deficiency of which is responsible for NCLs.[10] It has been reported ... Gene[edit]. The CTSD gene is located at chromosome 4q32.1, consisting of 8 exons. ...
Génin P, Lin R, Hiscott J, Civas A (Jun 2009). "Differential regulation of human interferon A gene expression by interferon ... The gene encoding IFNα2, the IFNA2 gene, is clustered with all other type I IFN genes on chromosome 9 and as all type I IFN ... Paul F, Pellegrini S, Uzé G (2015). "IFNA2: The prototypic human alpha interferon". Gene. 567 (2): 132-7. doi:10.1016/j.gene. ... Interferon alpha-2 is a protein that in humans is encoded by the IFNA2 gene. Human interferon alpha-2 (IFNα2) is a cytokine ...
... he researched the regulation of bacterial gene expression by cyclic AMP. In 1970, he began postdoctoral research in Bishop's ... Jacks, T. and Varmus, H.E. Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting. Science 230:1237, 1985. ... Their best-known accomplishment[7] was the identification of a cellular gene (c-src) that gave rise to the v-src oncogene of ... Varmus and Jacob have performed a series of lecture-concerts entitled "Genes and Jazz" at the Guggenheim[47] and Smithsonian ...
Regulation of gene expression, the means by which a gene product is either induced or inhibited ... Enzyme induction and inhibition, a process in which a molecule induces the expression of an enzyme ...
Tonnelle C, DeMars R, Long EO (1986). "DO beta: a new beta chain gene in HLA-D with a distinct regulation of expression". EMBO ... The DO beta gene is a divergent member of the class II beta gene family". J. Biol. Chem. 262 (18): 8759-66. PMID 3036827. ... HLA class II histocompatibility antigen, DO beta chain is a protein that in humans is encoded by the HLA-DOB gene. HLA-DOB ... 1992). "DNA sequence analysis of 66 kb of the human MHC class II region encoding a cluster of genes for antigen processing". J ...
"Regulation of HIV-1 gene expression by histone acetylation and factor recruitment at the LTR promoter". EMBO J. 22 (24): 6550- ... Hatch CL, Bonner WM (Oct 1990). "The human histone H2A.Z gene. Sequence and regulation". J Biol Chem. 265 (25): 15211-8. PMID ... This article on a gene on human chromosome 4 is a stub. You can help Wikipedia by expanding it.. *v ... "Entrez Gene: H2AFZ H2A histone family, member Z".. *^ Bargaje R., Alam P., Patowary A., Sarkar M., Ali T., Gupta S., Garg M., ...
Manohar CF, Salwen HR, Furtado MR, Cohn SL (1996). "Up-regulation of HOXC6, HOXD1, and HOXD8 homeobox gene expression in human ... This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors ... consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located in a cluster on ... regulation of transcription, DNA-templated. • negative regulation of transcription from RNA polymerase II promoter. • positive ...
"Complex expression pattern of the TNF region gene LST1 through differential regulation, initiation, and alternative splicing". ... "Entrez Gene: LST1 leukocyte specific transcript 1". Abraham LJ, Grimsley G, Zhang WJ, et al. (1992). "Polymorphism in the human ... 2000). "LST1: a gene with extensive alternative splicing and immunomodulatory function". J. Immunol. 164 (6): 3169-76. doi: ... 2001). "Functional analysis of B144/LST1: a gene in the tumor necrosis factor cluster that induces formation of long filopodia ...
"Gene modulation" redirects here. For information on therapeutic regulation of gene expression, see therapeutic gene modulation. ... Main article: Gene regulatory network. Up-regulation and down-regulation[edit]. Up-regulation is a process that occurs within a ... Regulated stages of gene expression[edit]. Any step of gene expression may be modulated, from the DNA-RNA transcription step to ... can silence expression of the gene. Regulation of transcription in cancer[edit]. Main article: Regulation of transcription in ...
Regulation of MHC gene expression.. Ting JP1, Baldwin AS.. Author information. 1. Department of Microbiology and Immunology, ... allow the functional analysis of these molecules in MHC gene regulation. The application of new techniques, such as genomic in ... The better characterization of proteins that interact with MHC class I and II promoters and the isolation of genes encoding ... New insights have also been gained in the understanding of MHC-associated genes. ...
This application proposes to study the molecular basis of retinal development using the regulation of rhodopsin gene expression ... Studies on the regulation of expression of retina-specific genes, in addition to their importance at the basic level, will also ... The definition of retina-specific promoters will make possible targeted expression of heterologous and altered genes to the ... have identified cis-acting DNA regulatory sequences that are capable of directing photoreceptor cell-specific gene expression. ...
Gene expression converts the information coded by our genes into proteins. These determine the structure and function of an ... Gene expression converts the information coded by our genes into proteins. These determine the structure and function of an ... Sorting and Intracellular Transport of RNA in Neurons: Regulation of Gene Expression at Synaptic Sites ... s Syndrom Gene Expression Messenger RNA Parkinson Translation genes hybridization neurons transcription ...
Nitrogen-dependent regulation of photosynthetic gene expression. F. Gerald Plumley and Gregory W. Schmidt ... Regulation of nuclear-encoded photosynthetic proteins by nitrogen is achieved through mechanisms affecting transcription and/or ...
The bacterium Escherichia colicarries approximately 3000 genes, but this total repertoire... ... It presents the cell with the signals that ultimately lead to gene regulation-the turning on or off of gene expression. ... Zieg, J., Hilmen, M., and Simon, M., 1978a, Regulation of gene expression by site-specific inversion, Cell 15: 237-244.Google ... Nieuwkoop, A. J., Boylan, S. A., and Bender, R. A., 1984, Regulation of hutUHoperon expression by the catabolite gene activator ...
Disturbed Placental Imprinting in Preeclampsia Leads to Altered Expression of DLX5, a Human-Specific Early Trophoblast Marker ... Disease Risk Variants Disrupt TEAD Transcription Factor-Dependent Transforming Growth Factor β Regulation of p16 Expression in ...
Regulation of beta-cell glucose transporter gene expression.. L Chen, T Alam, J H Johnson, S Hughes, C B Newgard, and R H Unger ... We conclude that GLUT-2 expression in beta cells, but not liver, is subject to regulation by certain perturbations in blood ... Regulation of beta-cell glucose transporter gene expression.. L Chen, T Alam, J H Johnson, S Hughes, C B Newgard, R H Unger ... Regulation of beta-cell glucose transporter gene expression.. L Chen, T Alam, J H Johnson, S Hughes, C B Newgard, R H Unger ...
Vitamin A and regulation of gene expression.. Nagpal S1, Chandraratna RA. ... These therapeutic effects are achieved by their ability to regulate complex programs of gene expression in target cells by ... This article reviews retinoid regulated genes and recently identified mechanisms which play important roles in the regulation ... Gene. *Gene Expression Omnibus (GEO) Database *Gene Expression Omnibus (GEO) Datasets. *Gene Expression Omnibus (GEO) Profiles ...
... novel anticode oligomers and methods of using them for controlling the growth of cancer cells expressing the bcl-2 gene. ... bcl-2 gene expression refers to bcl-2 protein production from the human bcl-2 gene; e.g. reduced bcl-2 gene expression means ... Regulation of bcl-2 gene expression. EP0058146A1. Feb 5, 1982. Aug 18, 1982. U C B, S.A.. 2-(4-(Diphenylmethyl)-1-piperazinyl)- ... Regulation of bcl-2 gene expression. US5932697 *. Dec 23, 1991. Aug 3, 1999. Virginia Tech Intellectual Properties, Inc.. ...
Ireland Regulation of Gene Expression study abroad course, Fall 4 2020. Experience the best study abroad programs in Dublin, ... pertaining to general and specialised mechanisms of gene expression and transcriptional regulation in various prokaryotic and ... obtain a detailed understanding of the general and more specific mechanisms involved in the control of gene expression in both ...
Gene regulation. Gene regulation is a label for the cellular processes that control the rate and manner of gene expression. A ... Gene expression. Gene expression is the process by which the genetic code - the nucleotide sequence - of a gene is used to ... Mechanisms of gene regulation include:. *Regulating the rate of transcription. This is the most economical method of regulation ... You are here: Home / Projects / VGEC / Genetics for Higher Education / Topics for Higher Education / Gene expression and ...
You are here: Home / Academic Departments / Molecular and Cell Biology / Research / Regulation of Gene Expression ... must be countered in order to activate a gene. We study fundamental aspects of gene regulation, from transcriptional initiation ... Structural biology of signal transduction and epigenetic gene regulation. *Andrey Revyakin - Single molecule dynamics of gene ... There are nine research groups working in the area of gene expression. We utilize bacterial and human cells to produce ...
Conversely, down-regulation is a process resulting in decreased gene and corresponding protein expression. Up-regulation occurs ... Often, one gene regulator controls another, and so on, in a gene regulatory network. Gene regulation is essential for viruses, ... and is informally termed gene regulation. Sophisticated programs of gene expression are widely observed in biology, for example ... Regulation of gene expression includes a wide range of mechanisms that are used by cells to increase or decrease the production ...
They act as regulatory molecules as well, preventing other genes from making protein by marking their mRNA molecules for ... A novel mechanism for fast regulation of gene expression Messenger RNA normally tells cellular machinery which protein to make ... So the gene that codes for a sodium channel regulates the expression of the potassium channel gene. And it does so after the ... Does RNA interference regulate gene expression? But the scientists had also noticed that the two genes overlapped a bit at ...
... novel anticode oligomers and methods of using them for controlling the growth of cancer cells expressing the bcl-2 gene. ... bcl-2 gene expression refers to bcl-2 protein production from the human bcl-2 gene; e.g. reduced bcl-2 gene expression means ... Regulation of BCL-2-gene expression. US6977244 *. 4 Oct 1996. 20 Dec 2005. Board Of Regents, The University Of Texas Systems. ... Regulation of bcl-2 gene expression. US6841541. 28 Nov 2000. 11 Jan 2005. The Trustees Of The University Of Pennsylvania. ...
Regulation of eukaryotic gene expression will be discussed. Selected examples where gene expression has been disrupted will ... BIOL3015 Regulation of Gene Expression. Module Overview. To provide an understanding of i) the regulation of transcription in ... In subsequent lectures the role of microRNAs in gene regulation and disease will be discussed, together with the factors and ... To provide an understanding of i) the regulation of transcription in eukaryotic organisms, ii) post-transcriptional regulation ...
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Microarray-based gene expression analysis identified genes showing ploidy-dependent expression in isogenic Saccharomyces ... Moreover, ploidy regulation of the FLO11 gene had direct consequences for yeast development. ... These genes were induced or repressed in proportion to the number of chromosome sets, regardless of the mating type. Ploidy- ...
... Fumiko Taniuchi, Koji Higai, Tomomi ... supported Elk-1-dependent transcriptional regulation of FUT1 gene expression in DLD-1 cells. These results suggest that a ... which has high expression of Lewis B and Lewis Y antigens, expresses the FUT1 gene, and shows α1,2-fucosyltransferase (FUT) ... FUT1 gene expression was shown to be regulated at the region −91 to −81 nt to the transcriptional start site, which contains ...
Functional Relevance of CpG Island Length for Regulation of Gene Expression Message Subject (Your Name) has forwarded a page to ... Functional Relevance of CpG Island Length for Regulation of Gene Expression. Navin Elango and Soojin V. Yi ... Functional Relevance of CpG Island Length for Regulation of Gene Expression. Navin Elango and Soojin V. Yi ... Functional Relevance of CpG Island Length for Regulation of Gene Expression. Navin Elango and Soojin V. Yi ...
Deep venous thrombosis (DVT) and secondary pulmonary embolism cause approximately 100,000 deaths per year in the United States. Physical immobility is the most significant risk factor for DVT, but a molecular and cellular basis for this link has not been defined. We found that the endothelial cells surrounding the venous valve, where DVTs originate, express high levels of FOXC2 and PROX1, transcription factors known to be activated by oscillatory shear stress. The perivalvular venous endothelial cells exhibited a powerful antithrombotic phenotype characterized by low levels of the prothrombotic proteins vWF, P-selectin, and ICAM1 and high levels of the antithrombotic proteins thrombomodulin (THBD), endothelial protein C receptor (EPCR), and tissue factor pathway inhibitor (TFPI). The perivalvular antithrombotic phenotype was lost following genetic deletion of FOXC2 or femoral artery ligation to reduce venous flow in mice, and at the site of origin of human DVT associated with fatal pulmonary ...
... an international research team compared the expression of genes in the brains of honey bees that had different ages, genotypes ... Expression Study Links Gene Regulation and Evolution of Aggression in Bees Aug 18, 2009 ... Home » Expression Study Links Gene Regulation and Evolution of Aggression in Bees ... NEW YORK (GenomeWeb News) - Short-term aggressive behavior in European honey bees involves many of the same gene expression ...
Eukaryotic Gene ExpressionBasics Benefits by Prof.PN RANGARAJAN,Department of Biochemistry,IISC Bangalore. For more details on ... byexpressiongenekinaseofproteinbyexpressiongenekinaseofproteinregulation ... Mod-05 Lec-18 Regulation of gene expression by Protein Kinase C. More details ... Eukaryotic Gene Expression:Basics & Benefits by Prof.PN RANGARAJAN,Department of Biochemistry,IISC Bangalore. For more details ...
  • In multicellular organisms, gene regulation drives cellular differentiation and morphogenesis in the embryo, leading to the creation of different cell types that possess different gene expression profiles from the same genome sequence. (wikipedia.org)
  • Embryonic development requires exquisite control of the expression of large numbers of genes, integrating components from the genome, transcriptome and proteome. (findaphd.com)
  • Animal viruses are providing scientists with relatively simple models to study the molecular biology of genome replication and gene expression. (waterstones.com)
  • Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression. (genetics.org)
  • Whole transcriptome shotgun sequencing (RNA-seq) analyses based on the v.2.2 P. chrysosporium genome identified 356 genes whose transcripts accumulated to relatively high levels at 96 h and were at least four times the levels found at 40 h. (usda.gov)
  • Our comprehension of the way that the genome is packaged into the nucleus in eukaryotes and of how some genes are expressed or "read" in some cells but not in others in order to produce cellular diversity, has been more challenging. (europa.eu)
  • We analyzed genome-wide mRNA expression and DNA methylation in cervical and anterior thoracal spinal cord segments of five human fetuses and show development-dependent gene expression asymmetries. (mpi.nl)
  • To achieve this Broad is leveraging FireCloud , our cloud platform for hosting data from The Cancer Genome Atlas (TCGA) that was funded through the National Cancer Institute's Cloud Pilots program , and extending it to manage data and run pipelines for RNA sequencing and expression Quantitative Trait Loci (eQTL) analyses, that were developed as part of the Genotype Tissue Expression (GTEx) project . (broadinstitute.org)
  • Zhou X, Feng H, Guo Q, Dai H. Identification and characterization of the first reptilian CD9, and its expression analysis in response to bacterial infection. (labome.org)
  • To get further information on bacterial surface sensing and biofilm-dependent regulation of gene expression in Escherichia coli K-12, random insertion mutagenesis with Mu dX, a mini-Mu carrying the promoterless lacZ gene, was performed with an ompR234 adherent strain, and a simple screen was developed to assess changes in gene expression in biofilm cells versus planktonic cells. (asm.org)
  • However, there is still limited information available on bacterial surface sensing at the gene expression level. (asm.org)
  • Furthermore, in many bacterial species, regulation of metabolic functions, particularly those relating to virulence, involves cell-to-cell signalling molecules (such as N -acylhomoserine lactones in gram-negative bacteria). (asm.org)
  • In addition to their ability to disrupt the integrity of bacterial, viral and fungal membranes, AMPs bind lipopolysaccharides, act as chemoattractants for immune cells and bind to cellular receptors and modulate the expression of cytokines and chemokines. (oregonstate.edu)
  • However, a key discovery was that genes encoding proteins involved in interaction with the host coagulation/fibrinolysis system and bacterial-host interactions were rapidly up-regulated. (nih.gov)
  • An experimental‐computational approach is applied to dissect the contribution of specific transcription factor‐mediated versus global growth‐dependent regulation to bacterial gene expression, and obtain a quantitative understanding of dynamic adaptations in arginine biosynthesis of E. coli . (embopress.org)
  • We present a model‐based approach to quantitatively dissect simultaneous contributions from specific transcription factors and the global growth status to bacterial gene expression, based on parameter inference from GFP‐based promoter activity measurements. (embopress.org)
  • In each plasmid a different promoter controls the transcription rate of the same reporter gene, gfp , and thus rate of transcript production from the promoter is proportional to the rate of GFP accumulation. (pnas.org)
  • Finally, despite pervasiveness of established ABA-responsive promoter elements in Arabidopsis SR and SR-like genes, their expression is likely governed by additional, yet unidentified cis -acting elements. (mdpi.com)
  • Repressors bind to the Operator, coding sequences on the DNA strand that are close to or overlapping the promoter region, impeding RNA polymerase's progress along the strand, thus impeding the expression of the gene.The image to the right demonstrates regulation by a repressor in the lac operon. (wikipedia.org)
  • Though the promoter binds transcription factors and drives some aspects of CFTR gene expression, it cannot alone account for tissue specific control. (luriechildrens.org)
  • Changes in the level of pattern of reporter gene activity in cadmium-exposed nematodes will be used to identity functional promoter elements. (epa.gov)
  • The LFY transcription factor binds to a sequence, with dyad symmetry, that lies within a region of the AP3 promoter required for early expression of AP3 . (biologists.org)
  • Lastly, ectopic expression of wild type CNBP but not a mutant form that could not be phosphorylated together with c-Rel led to synergistic activation of an IL12 promoter driven reporter gene. (jimmunol.org)
  • By using fluorescent promoter reporters, we show that global regulation is growth rate dependent not only during steady state but also during dynamic changes in growth rate and can be quantified through two promoter‐specific parameters. (embopress.org)
  • We thereby uncover two principles of joint regulation: (i) specific regulation by repression dominates the transcriptional response during metabolic steady states, largely repressing the biosynthesis genes even when biosynthesis is required and (ii) global regulation sets the maximum promoter activity that is exploited during the transition between steady states. (embopress.org)
  • This ERC project set out to study how differential gene expression can occur not only between cell types, but even between two copies of a gene within the same cell. (europa.eu)
  • In addition to the differential expression of endogenous H. armigera PIs, we also observed a distinct novel isoform of endogenous PI in CanPI-7 fed H. armigera larvae. (mcponline.org)
  • Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis. (umassmed.edu)
  • It was determined that adenoviral E4orf4, splicing proteins SRp30c and PTB as well as HPV-16 E2 can induce the expression of the late HPV genes and these were shown to alter the ratio of expression of HPV L1 mRNAs, demonstrating that these proteins may play a role in the differential expression of proteins during the HPV life-cycle. (dit.ie)
  • Inhibition or depletion of PAD4 elevated the expression of a subset of p53 target genes, including p21/CIP1/WAF1, leading to cell cycle arrest and apoptosis. (environmental-expert.com)
  • The modulation of mdr gene expression in sparse and confluent cells was not related to cell division, nutrient depletion, inhibition of protein synthesis, gap junction status, extracellular ATP, or the presence of various extracellular matrixes, but may be related to cell-density and cell-contact mediated changes in phosphatase activity. (spandidos-publications.com)
  • We show that in the mandibular arch, as in the limb, Fgf-8 functions in combination with CD44, a cell surface binding protein, and that blocking CD44 binding results in inhibition of Fgf8-induced expression of Clim-2 and Lhx-6. (biologists.org)
  • This volume presents a didactic approach to the understanding of the basic processes of gene expression and their involvement in certain brain diseases, such asAlzheimer's disease and schizophrenia. (springer.com)
  • Eukaryotic gene expression is more complex than prokaryotic gene expression because the processes of transcription and translation are physically separated. (oercommons.org)
  • The widespread IL-18 mRNA distribution and the special relationship with ICE lead us to the hypothesis that IL-18 expression may be coupled with apoptotic processes involving activation of ICE or ICE-like proteinase. (jimmunol.org)
  • Much of the literature has focused on the physiological role of leptin in driving processes as diverse as reproduction, starvation defence, feeding behavior or body weight, all dependent on expression levels of the ob gene. (epfl.ch)
  • Genes coding for the neuropeptide hormone pituitary adenylate cyclase activating polypeptide (PACAP) and the enzyme that processes PACAP's precursor to the mature form, peptidylglycine alpha-amidating monooxygenase, were upregulated by inositol depletion. (broadinstitute.org)
  • The expression of at least four other mitochondrially encoded cytochrome subunits is dependent upon specific translation factors, raising the potential for translational regulation as a general mechanism. (asm.org)
  • Upregulation of these genes was completely blunted in type 2 diabetic patients. (diabetesjournals.org)
  • Genes encoding cellulases showed little apparent upregulation and thus may be expressed constitutively. (usda.gov)
  • However, strong upregulation of the same genes can be induced in Purkinje cells after colchicine injection into the uninjured adult cerebellum, indicating that their expression could be controlled by retrograde signals. (jneurosci.org)
  • Application of IN-1 antibodies induces the upregulation of c-Jun, JunD, and NADPH diaphorase in Purkinje cells, showing that their expression is suppressed constitutively by myelin-associated neurite growth inhibitors. (jneurosci.org)
  • The bacterium Escherichia coli carries approximately 3000 genes, but this total repertoire describes its potential properties and, in reality, only a small subset of this genetic information is expressed at any given moment. (springer.com)
  • Gene expression is the process by which the genetic code - the nucleotide sequence - of a gene is used to direct protein synthesis and produce the structures of the cell. (le.ac.uk)
  • This module covers the structure and expression of genetic material in eukaryotic cells. (southampton.ac.uk)
  • This new method for studying globally regulated genetic systems in E. coli combines detection, cloning, and physical mapping of a battery of coregulated genes in one step. (asm.org)
  • Using real-time RT-qPCR, we analyzed total steady-state transcript levels of the 18 SR and two SR-like genes from Arabidopsis thaliana in seedlings treated with ABA and in genetic backgrounds with altered expression of the ABA-biosynthesis ABA2 and the ABA-signaling ABI1 and ABI4 genes. (mdpi.com)
  • In this paper, we propose an innovative method for finding gene specific co-regulations using genetic algorithm (GA). A sliding window is used to delimit the allowed length of conditions in which gene co-regulations occur and an ad hoc GA, called the progressive GA, is performed in each window position to find those condition subsets having high fitness. (hindawi.com)
  • A methodology to dissect the genetic architecture of quantitative variation of numerous gene products simultaneously is proposed. (genetics.org)
  • Such a genetic reprogramming of gene expression in biofilms seems to result from changes in multiple environmental physicochemical conditions. (asm.org)
  • He concluded that a gene that controls the development of a mammalian eye can be transplanted to control the development of the insect eye, demonstrating how the "genetic toolkit" remains constant throughout most animal groups. (gradesaver.com)
  • each of the 23 pairs of human chromosomes encodes thousands of genes. (oercommons.org)
  • Importantly, we observed up-regulation of four genes encoding LPXTG proteins after 30 min of incubation in blood, including gbs0428, gbs1087 (fbsA) encoding a major receptor for fibrinogen, gbs1420 (bsp) which encodes a putative choline-binding protein, and gbs2018 (bibA) which encodes a protein that binds to human C4-binding protein and contributes to survival in human blood (Fig. 4A and Table 2). (nih.gov)
  • 1995 ) The mouse Fgf8 gene encodes a family of polypeptides and is expressed in regions that direct outgrowth and patterning in the developing embryo. (biologists.org)
  • Here, we report that peptidylarginine deiminase 4, a histone citrullination enzyme, is involved in the repression of p53 target genes. (environmental-expert.com)
  • The signals that determine activation and repression of specific genes in response to appropriate stimuli are one of the most important, but least understood, types of information encoded in genomic DNA. (psu.edu)
  • Heme repression is achieved through the action of the ROX1 repressor, the expression of which is transcriptionally activated by heme. (asm.org)
  • In addition, animal virus genomes contain elements and encode proteins that are very useful for the design of vectors for gene cloning and expression in mammalian cells. (waterstones.com)
  • In addition to largely expanding the coding capacity of genomes, AS represents an important means of regulating gene expression, for instance by introducing premature termination codons (PTCs) that then target these transcripts for degradation by a process known as nonsense-mediated mRNA decay (NMD) [ 1 ]. (mdpi.com)
  • These different components of the tumor microenvironment could have stimulatory and inhibitory effects on tumor progression by regulating the gene expression repertoire within the tumor cells on one hand and the stroma cells on the other. (springer.com)
  • The initiating event leading to a change in gene expression includes activation or deactivation of receptors . (wikipedia.org)
  • Histone Arg methylation has been correlated with transcriptional activation of p53 target genes. (environmental-expert.com)
  • Our findings suggest that activation of INO80-associated Uch37 by transient association of proteasomes with the INO80 complex could be one way proteasomes help to regulate gene expression," said Tingting Yao, Ph.D., Postdoctoral Research Fellow and lead author on the paper. (phys.org)
  • stimulated activation of genes downstream of NF-?B. J Cell Sci. (labome.org)
  • Here we show that the floral meristem identity genes LEAFY ( LFY ) and APETALA1 ( AP1 ) are required for the activation of AP3 . (biologists.org)
  • Experiments using a steroid-inducible form of LFY show that, in contrast to its direct transcriptional activation of other floral homeotic genes, LFY acts in both a direct and an indirect manner to regulate AP3 expression. (biologists.org)
  • LFY is required for AP3 expression, since a loss-of-function lfy-6 mutant shows a dramatic reduction in the levels and domain of AP3 activation ( Weigel and Meyerowitz, 1993 ). (biologists.org)
  • The objective of the present study was to investigate whether differences in the temporal dynamics of the second messenger Ca 2+ and integration by downstream signaling elements could contribute to specific activation of genes in response to specific patterns of neuronal firing. (jneurosci.org)
  • and genes encoding proteins implicated in binding/activation of plasminogen: gbs0608 (eno), gbs1811 (gapC), and gbs1195 (ska). (nih.gov)
  • In addition, many chromosomal regions containing no previously known regulated genes were discovered that responded to various stimuli. (asm.org)
  • When the flies are too hot, they make more transcripts of the sei gene and fewer of ppk29. (eurekalert.org)
  • Alternative splicing (AS) occurs when splice sites are differentially recognized, allowing for the production of multiple transcripts from a single gene that can potentially result in different protein isoforms. (mdpi.com)
  • Computational biologists at Carnegie Mellon University have developed a more accurate computational method for reconstructing the full-length nucleotide sequences of the RNA products in cells, called transcripts, that transform information from a gene into proteins or other gene products. (outlookseries.com)
  • Their software, called Scallop, will help scientists build a more complete library of RNA transcripts and thus help scientists better understand the regulation of gene expression. (outlookseries.com)
  • When compared to two leading assemblers, StringTie and TransComb, Scallop is 34.5 percent and 36.3 percent more accurate for transcripts consisting of multiple exons subunits of a gene that encode part of the gene product. (outlookseries.com)
  • Transcripts corresponding to 165 genes of unknown function accumulated more than 4-fold after oxidation commenced, and some of them may merit investigation as possible contributors to ligninolysis. (usda.gov)
  • The expression level of mdr-1 mRNA transcripts (analyzed by Northern blot and in situ hybridization) and P-glycoprotein (analyzed by flow cytometry) inversely correlated with cell density. (spandidos-publications.com)
  • Most (83%) of the significantly altered transcripts were down-regulated after 30 minutes of incubation in blood, and all functional categories of genes were abundantly represented. (nih.gov)
  • The transcripts of relatively few proven virulence genes were up-regulated during the first 90 minutes. (nih.gov)
  • Most known and putative virulence genes were either down-regulated or their transcript level was not altered, although after 90 min of incubation in blood the level of many transcripts was increased (Fig. 4). (nih.gov)
  • Precursor messenger RNA (pre-mRNA) splicing is an essential step in gene expression mediated by the spliceosome, a large protein complex in the cell nucleus that interacts with specific intronic sequences in the pre-mRNA called splice sites for the proper removal of introns and correct joining of exons. (mdpi.com)
  • In vivo footprinting of the rhodopsin gene and the transgene will also be performed. (hopkinsmedicine.org)
  • A model was developed, using human tumours grown as xenografts in immune deficient mice, in which the in vivo regulation of human P450 genes could be examined. (bl.uk)
  • Importantly, we also showed that such monoallelic expression can be seen in vivo and that some of the genes affected have been associated with human autosomal dominant disorders. (europa.eu)
  • The functional significance of each modification will be determined in vivo (inside the organism) by creating transgenic nematodes containing a ß-galactosidase reporter gene. (epa.gov)
  • To assess whether myelin-associated neurite growth inhibitory proteins contribute to this regulation, we applied the neutralizing antibodies IN-1 against one of the main inhibitory components of central myelin (NI-250) either in vivo or in vitro to organotypic cerebellar cultures. (jneurosci.org)
  • Methods: The present review examines published data from both in vitro and in vivo studies reporting effects of nutrients and byproducts of microbial metabolism on the expression of antimicrobial peptide genes in order to highlight an emerging appreciation for the role of dietary compounds in modulating the innate immune response. (oregonstate.edu)
  • These data may explain some of the discrepancies in results obtained when analyzing mdr gene expression in tumors growing in vivo or in vitro, and why mdi expression in tumors is localized to the periphery of the lesions. (spandidos-publications.com)
  • NEW YORK (GenomeWeb News) - Short-term aggressive behavior in European honey bees involves many of the same gene expression patterns found in the inherently more aggressive Africanized bees, according to research scheduled to appear online this week in the Proceedings of the National Academy of Sciences . (genomeweb.com)
  • A basic challenge in systems biology is to understand the dynamical behavior of gene regulation networks. (pnas.org)
  • Determining the dynamic behavior of these systems requires specifying not only the network connectivity, but also the kinetic parameters for the various regulation reactions. (pnas.org)
  • One of the chief findings was the fact that the expression of the leptin gene was regulated and that it, in turn, could regulate metabolism and behavior. (epfl.ch)
  • Compared to the almost infinite complexity of vertebrate cognition and behavior, the number of genes influencing central nervous system development is staggeringly small ( Kadakkuzha and Puthanveettil, 2013 ). (elifesciences.org)
  • Positive regulation by GABA(B)R1 subunit of leptin expression through gene transactivation in adipocytes. (sigmaaldrich.com)
  • Our results indicate that GABA(B)R1 subunit is constitutively expressed by adipocytes to primarily regulate leptin expression at the transcriptional level through a mechanism not relevant to the function as a partner of heterodimeric assembly to the functional GABA(B)R. (sigmaaldrich.com)
  • Given the possible association between VPA, CEBPα and adipokine gene regulation, we hypothesized that they would alter the expression of resistin (rstn) , fasting-induced adipose factor (fiaf) and suppressor of cytokine signaling-3 (socs-3) , genes implicated in the development of leptin and insulin resistance. (karger.com)
  • CHIP assays proved that the translocation of MLL1 to chromatin was dependent on NF-?B. Our results suggest that MLL1 is recruited to its target genes by activated NF-?B and regulates their transcription. (labome.org)
  • Previous work has shown that PACAP can increase tyrosine hydroxylase (TH) activity and dopamine release, and we found that the gene for GTP cyclohydrolase, which effectively regulates TH through synthesis of tetrahydrobiopterin, was also upregulated by inositol depletion. (broadinstitute.org)
  • In both the developing face and the limb buds we identify Fgf-8 as the likely candidate signalling molecule that regulates Clim-2 expression. (biologists.org)
  • 1995 ) The expression pattern of the distal-less homeobox-containing gene Dlx-5 in the developing chick limb bud suggests its involvement in apical ectodermal ridge activity, pattern-formation, and cartilage differentiation. (biologists.org)
  • It presents the cell with the signals that ultimately lead to gene regulation-the turning on or off of gene expression. (springer.com)
  • The ability to switch protein-coding genes 'on' and 'off' is a fundamental process shared by all cell types. (le.ac.uk)
  • The α 1,2-fucosyltransferase I (FUT1) enzyme is important for the biosynthesis of H antigens, Lewis B, and Lewis Y. In this study, we clarified the transcriptional regulation of FUT1 in the DLD-1 colon cancer cell line, which has high expression of Lewis B and Lewis Y antigens, expresses the FUT1 gene, and shows α 1,2-fucosyltransferase (FUT) activity. (hindawi.com)
  • We observed concordant expression of IL-18 and ICE mRNAs in a wide range of cell types, unlike the more restricted expression of IL-12 p40 mRNA. (jimmunol.org)
  • the total cell lysates were analyzed for RAD23B expression. (aacrjournals.org)
  • C, Western blot analysis for RAD52 expression was performed on whole-cell lysates in MCF-7 cells following pretreatment (24 h) with anti-miR-210, anti-miR-373, or negative control #1 anti-miR ( anti-miR-NC ) and exposure to normoxia or hypoxia (48 h, 0.01% O 2 ), as described in Materials and Methods. (aacrjournals.org)
  • Specifically, the analysis showed that bivalent domains which were thought to be a defining characteristic of pluripotent stem cells are equally prevalent in B cells, suggesting that the epigenetic marking of silent genes is quite similar in these two very different cell types. (bl.uk)
  • The results obtained in this study demonstrate the complex and diverse nature of histone modifications at tissue-restricted genes and suggest that trans-acting factors are responsible for generating highly specific combinations of histone modifications at each individual gene at different stages of cell differentiation. (bl.uk)
  • This suggests that if monoallelic expression becomes clonally heritable it might sometimes have severe consequences, because if one copy of a gene is mutated, while the other normal copy is silent, then some cells will not express the gene at all and this could be deleterious in a cell or organ. (europa.eu)
  • The Centre aims to enhance our understanding of how genes are regulated at both the single cell and whole organism level. (wikipedia.org)
  • In an attempt to understand the antiproliferative effects of progestins in endometrial cancer, we have examined the effects of the potent progestin, medroxyprogesterone acetate (MPA), on the cell proliferation and the expression of transforming growth factor (TGF) α and β genes in human endometrial adenocarcinoma cell lines. (aacrjournals.org)
  • How specificity is maintained between stimulus and transcription of specific genes is a fundamental problem in cell biology. (jneurosci.org)
  • The increased VDR gene expression in the parathyroid cell would amplify the effect of 1,25(OH)2D3 to decrease PTH gene transcription. (jci.org)
  • MYC/BCL2 protein coexpression contributes to the inferior survival of activated B-cell subtype of diffuse large B-cell lymphoma and demonstrates high-risk gene expression signatures: a report from The International DLBCL Rituximab-CHOP Consortium Program. (duke.edu)
  • Diffuse large B-cell lymphoma (DLBCL) is stratified into prognostically favorable germinal center B-cell (GCB)-like and unfavorable activated B-cell (ABC)-like subtypes based on gene expression signatures. (duke.edu)
  • The effect of a number of these proteins on transcription of the late HPV genes was evaluated in modified HeLa cell lines (pBEL and pBELM) by transfection studies, with effects evaluated using real-time PCR and Northern blot analyses. (dit.ie)