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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.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.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.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.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.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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.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.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.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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.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.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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.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.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.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.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.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.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.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.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.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.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.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.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.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Cell Line, Tumor: A cell line derived from cultured tumor cells.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.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.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.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.Gene Expression Regulation, Leukemic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in leukemia.Software: Sequential operating programs and data which instruct the functioning of a digital computer.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.Kinetics: The rate dynamics in chemical or physical systems.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.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.Binding, Competitive: The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.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).Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.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.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.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.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.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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.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)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.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.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.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.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Bacterial Proteins: Proteins found in any species of bacterium.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.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.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.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.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.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.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.Time Factors: Elements of limited time intervals, contributing to particular results or situations.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.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).Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).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.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.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.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.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.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)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.Ligands: A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Mice, Inbred C57BLHeLa 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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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.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.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.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.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.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.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.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.DNA Footprinting: A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)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.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 22.214.171.124.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.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.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.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)Dose-Response Relationship, Drug: The relationship between the dose of an administered drug and the response of the organism to the drug.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.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.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.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.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Receptors, Cell Surface: Cell surface proteins that bind signalling molecules external to the cell with high affinity and convert this extracellular event into one or more intracellular signals that alter the behavior of the target cell (From Alberts, Molecular Biology of the Cell, 2nd ed, pp693-5). Cell surface receptors, unlike enzymes, do not chemically alter their ligands.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.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.Deoxyribonuclease I: An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.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.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.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 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.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.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.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.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.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.Binding Sites, Antibody: Local surface sites on antibodies which react with antigen determinant sites on antigens (EPITOPES.) They are formed from parts of the variable regions of FAB FRAGMENTS.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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.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.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.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.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.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.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.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.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.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.Amino Acid Motifs: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.Genes, Plant: The functional hereditary units of PLANTS.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Radioligand Assay: Quantitative determination of receptor (binding) proteins in body fluids or tissue using radioactively labeled binding reagents (e.g., antibodies, intracellular receptors, plasma binders).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.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.CCAAT-Enhancer-Binding Proteins: A class of proteins that were originally identified by their ability to bind the DNA sequence CCAAT. The typical CCAAT-enhancer binding protein forms dimers and consists of an activation domain, a DNA-binding basic region, and a leucine-rich dimerization domain (LEUCINE ZIPPERS). CCAAT-BINDING FACTOR is structurally distinct type of CCAAT-enhancer binding protein consisting of a trimer of three different subunits.Calcium: A basic element found in nearly all organized tissues. It is a member of the alkaline earth family of metals with the atomic symbol Ca, atomic number 20, and atomic weight 40. Calcium is the most abundant mineral in the body and combines with phosphorus to form calcium phosphate in the bones and teeth. It is essential for the normal functioning of nerves and muscles and plays a role in blood coagulation (as factor IV) and in many enzymatic processes.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.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)Cell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.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.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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Nerve Tissue ProteinsZinc Fingers: Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.Viral Proteins: Proteins found in any species of virus.Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.Genes, Bacterial: The functional hereditary units of BACTERIA.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.Transgenes: Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.Peptides: Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.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.Cell Division: The fission of a CELL. It includes CYTOKINESIS, when the CYTOPLASM of a cell is divided, and CELL NUCLEUS DIVISION.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.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.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.3T3 Cells: Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.Methylation: 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)Fungal Proteins: Proteins found in any species of fungus.Rabbits: The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.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.Nucleotide Motifs: Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.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.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.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.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Autoradiography: The making of a radiograph of an object or tissue by recording on a photographic plate the radiation emitted by radioactive material within the object. (Dorland, 27th ed)Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)
... as a critical regulator of capsule expression. Fis is also involved in the regulation of a range of genes in bacterial ... Two RNA polymerase-binding sites and at least six high-affinity Fis-binding sites are present in the fis promoter region. ... Helices A and B provide the contacts between Fis monomers, facilitating dimer formation, whereas the C and D helices form a ... fis is the E. coli gene encoding FIS protein. The regulation of this gene is more complex than most other genes in the E. coli ...
Nitric oxide synthase
The FMN binding domain is homologous to flavodoxins, and the two domain fragment containing the FAD and NADPH binding sites is ... The gene coding for iNOS is located on Chromosome 17. While evidence for 'baseline' iNOS expression has been elusive, IRF1 and ... gene. Recently, NOS activity has been demonstrated in several bacterial species, including notorious pathogens Bacillus ... This facilitates the conversion of O2 and L-arginine to NO and L-citrulline. The oxygenase domain of each NOS isoform also ...
Bacterial one-hybrid system
Across all living organisms, regulation of gene expression is controlled by interactions between DNA-binding regulatory ... if bound to by the chimeric fusion product, drives expression of downstream reporter genes. This reporter region facilitates ... DNA sequences in or around genes that act as target sites for DNA-binding proteins. By binding to cis-regulatory sequences and ... The bacterial one-hybrid (B1H) system is a method for identifying the sequence-specific target site of a DNA-binding domain. In ...
Type VI secretion system
RsmA is a translational inhibitor that binds to sequences near the ribosome-binding site for T6SS gene expression. This level ... often at their active site, thereby blocking their activity. Some research has gone into regulation of T6SS by two component ... All characterized bacterial-targeting T6SS proteins act as toxins, either by killing or preventing the growth of target cells. ... The mechanism by which secreted proteins facilitate F. tularensis virulence is still unknown. The T6SS of Vibrio cholerae has a ...
Binding of this protein to the consensus sequence represents gene expression by reducing transcription. It is not known what ... "Repressor binding to a regulatory site in the DNA coding sequence is sufficient to confer transcriptional regulation of the vir ... Principles of Bacterial Pathogenesis. Academic Press. pp. 619-674. ISBN 0-12-304220-8. Mattoo S, Cherry J (2005). "Molecular ... where the secretion of toxins causes ciliostasis and facilitates the entry of bacteria to tracheal/bronchial ciliated cells. ...
Activation of gene expression through different promoters results in alternative splicing; however, the physiological ... hypothesize there are other ACC kinases important to its regulation as there are many other possible phosphorylation sites on ... "Carbohydrate response element binding protein directly promotes lipogenic enzyme gene transcription". Proceedings of the ... The enzyme apparently manipulates the pKa to facilitate the deprotonation of bicarbonate. The pKa of bicarbonate is decreased ...
Many proteins involved in the regulation of gene expression contain DNA-binding domains. For example, proteins that regulate ... pathogens of the genus Xanthomonas and are involved in regulating the genes of the host plant in order to facilitate bacterial ... such as DBDs of transcription factors that activate specific genes, or those of enzymes that modify DNA at specific sites, like ... It regulates gene expression. Consisting of about 110 amino acids, the winged helix (WH) domain has four helices and a two- ...
Ren, X.-D. (1999). "Regulation of the small GTP-binding protein Rho by cell adhesion and the cytoskeleton". The EMBO Journal. ... Rosette C, Karin M (March 1995). "Cytoskeletal control of gene expression: depolymerization of microtubules activates NF-kappa ... This configuration is thought to help deliver microtubule-bound vesicles from the Golgi to the site of polarity. Dynamic ... consisting of a hollow tube of protofilaments assembled from heterodimers of bacterial tubulin A (BtubA) and bacterial tubulin ...
... and the NADPH binding site overlaps with the substrate binding site on the flavin group. FMOs contain several sequence motifs ... molecular characterization and regulation of expression". Toxicol. Appl. Pharmacol. 125 (1): 1-6. doi:10.1006/taap.1994.1042. ... Both dinucleotide binding motifs form Rossmann folds. The yeast FMO and bacterial FMO are dimers, with each monomer consisting ... The FMO family of genes is conserved across all phyla that have been studied so far, therefore some form of the FMO gene family ...
YopM may alter host cell growth by binding to RSK (ribosomal S6 kinase), which regulates cell cycle regulation genes. ... A transmembrane protein, invasin, facilitates these functions by binding to host cell αβ1 integrins. Through this binding, the ... A 26-kb "core region" in the pYV contains the ysc genes, which regulate the expression and secretion of Yops. Many Ysc proteins ... Miller, V. (1992). "Yersinia invasion genes and their products". ASM News. 58: 26-33. Bliska JB, Falkow S (1992). "Bacterial ...
Each lobe consists of two subdomains, N1, N2 and C1, C2, and contains one iron binding site and one glycosylation site. The ... Reghunathan R, Jayapal M, Hsu LY, Chng HH, Tai D, Leung BP, Melendez AJ (2005). "Expression profile of immune response genes in ... Lactoferrin binds to lipopolysaccharide of bacterial walls, and the oxidized iron part of the lactoferrin oxidizes bacteria via ... but also in the regulation of their intake. Presence of loose ions of zinc and copper does not affect the iron binding ability ...
Bassler, Bonnie L. "How bacteria talk to each other: regulation of gene expression by quorum sensing". Current Opinion in ... bound to it was also determined. Many bacterial species, including E. coli, an enteric bacterium and model organism for Gram- ... The waiting period is inversely related to the quality of the site; for instance, a worker that has found a poor site will wait ... produces carboxylated acyl homoserine lactone compounds that facilitate the transition from growth as short cells to growth as ...
Outline of cell biology
Transcription - Fundamental process of gene expression through turning DNA segment into a functional unit of RNA. Translation ... or any other membrane-bound organelles, including bacteria. Bacterial cells - A prokaryotic cell belonging to the mostly ... Cell signaling - Regulation of cell behavior by signals from outside. Cell adhesion - Holding together cells and tissues. ... Ribosome - It is a large and complex molecular machine, found within all living cells, that serves as the site of biological ...
A binding site for RNA polymerase *RNA polymerase I: transcribes genes encoding 18s 5.8s 28s ribosomal RNA ... Although co-expression does not necessarily indicate co-regulation, methylation of bidirectional promoter regions has been ... "A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase". Science. 262 (5138): ... A wide variety of algorithms have been developed to facilitate detection of promoters in genomic sequence, and promoter ...
"Differential expression and regulation of the glucokinase gene in liver and islets of Langerhans". Proceedings of the National ... F1P and F6P both bind to the same site on GKRP. It is postulated that they produce 2 different conformations of GKRP, one able ... The ATP binding domain, for example, are shared with hexokinases, bacterial glucokinases, and other proteins, and the common ... Phosphorylation of glucose to glucose-6-phosphate by GK facilitates storage of glucose as glycogen and disposal by glycolysis. ...
The blood glucose level is maintained within well-defined limits in part due to precise regulation of PEPCK gene expression. To ... In addition, hyper-reactive cysteine (C307) is involved in the binding of Mn2+ to the active site. As discussed previously, ... Aich S, Imabayashi F, Delbaere LT (October 2003). "Expression, purification, and characterization of a bacterial GTP-dependent ... which is likely facilitated by the eclipsed conformation of the phosphoryl groups when ATP is bound to PEPCK. Since the ...
Fibronectins also help at the site of tissue injury by binding to platelets during blood clotting and facilitating cell ... Karsenty G, Park RW (1995). "Regulation of type I collagen genes expression". Int. Rev. Immunol. 12 (2-4): 177-185. doi:10.3109 ... doi:10.1016/S1369-5266(02)00286-8. Kostakioti, Maria (2013). "Bacterial Biofilms: Development, Dispersal, and Therapeutic ... "Mechanoregulation of gene expression in fibroblasts". Gene. 391: 1-15. doi:10.1016/j.gene.2007.01.014. PMC 2893340 . PMID ...
Transcription factors are proteins that bind to specific DNA sequences in order to regulate the expression of a given gene. The ... the majority of gene promoters contain a CpG island with numerous CpG sites. When many of a gene's promoter CpG sites are ... Sigma factors are specialized bacterial proteins that bind to RNA polymerases and orchestrate transcription initiation. Sigma ... Histone rearrangement is facilitated by post-translational modifications to the tails of the core histones. A wide variety of ...
The acetylation of lysine is fundamental to the regulation and expression of certain genes. Oxidative stress creates a ... Formylation is detected most frequently on 19 different modification sites on Histone H1. The genetic expression of the cell is ... This reaction is not used by eukaryotes or Archaea, as the presence of tRNAfMet in non bacterial cells is dubbed as intrusive ... Lysines that are formylated have been shown to play a role in DNA binding. Additionally, formylation has been detected on ...
Binding immunoglobulin protein
"Human gene encoding the 78,000-dalton glucose-regulated protein and its pseudogene: structure, conservation, and regulation". ... BiP's ATPase cycle is facilitated by its co-chaperones, both nucleotide binding factors (NEFs), which facilitate ATP binding ... Yang J, Nune M, Zong Y, Zhou L, Liu Q (Dec 2015). "Close and Allosteric Opening of the Polypeptide-Binding Site in a Human ... Prokaryotic BiP orthologs were found to interact with key proteins such as RecA, which is vital to bacterial DNA replication. ...
Ryu, Keun Woo; Kim, Dae-Seok; Kraus, W. Lee (January 9, 2015). "New Facets in the Regulation of Gene Expression by ADP- ... PARPs use a catalytic triad of His-Tyr-Glu to facilitate binding of NAD+ and positioning of the end of the existing poly-ADP ... and allows for the binding of the PARP and thus ADP-ribosylation which recruits repair factors to interact at the break site. ... Bacterial ADP-ribosylating exotoxins (bAREs) covalently transfer an ADP-Ribose moiety of NAD+ to target proteins of infected ...
IL-1Ra regulates IL-1α and IL-1β proinflammatory activity by competing with them for binding sites of the receptor. All of the ... Its expression is induced by transcription factor NF-κB after exposure of innate immune cells to alarmins. This occurs, for ... This up-regulation is directly controlled by GATA3 transcription factor. IL-33 combined with IL-2, IL-7 or TSLP also stimulates ... Sahoo M, Ceballos-Olvera I, del Barrio L, Re F (2011). "Role of the inflammasome, IL-1β, and IL-18 in bacterial infections". ...
Cytochrome c oxidase
... which indicates the regulation of COX at the level of gene expression. COX distribution is inconsistent across different ... Hydrogen sulfide will bind COX in a noncompetitive fashion at a regulatory site on the enzyme, similar to carbon monoxide. ... Synthesis and assembly of COX subunits I, II, and III are facilitated by translational activators, which interact with the 5' ... or bacterial) membrane. It receives an electron from each of four cytochrome c molecules, and transfers them to one oxygen ...
Oxidized SoxR then induces the expression of SoxS protein, which in turn activates the transcription of structural genes of the ... Reduced OxyR provides autorepression by binding only to the oxyR promoter. Regulation of the soxRS regulon occurs by a two- ... The complexity in bacterial responses appears to be in the number of proteins induced by oxidative stress. In mammalian cells, ... protein disulfide isomerase facilitates disulfide exchange reactions with large inactive protein substrates, besides having ...
The ribosome has three sites for tRNA to bind. They are the aminoacyl site (abbreviated A), the peptidyl site (abbreviated P) ... The entire process is called gene expression. In translation, messenger RNA (mRNA) is decoded in a ribosome, outside the ... The ribosome facilitates decoding by inducing the binding of complementary tRNA anticodon sequences to mRNA codons. The tRNAs ... Regulation of translation can impact the global rate of protein synthesis which is closely coupled to the metabolic and ...
... a DNA-binding protein, which binds to a specific DNA binding site, the promoter, immediately upstream of the genes. Binding of ... The lac gene and its derivatives are amenable to use as a reporter gene in a number of bacterial-based selection techniques ... presence of a second functional site in the same cell makes no difference to expression of genes controlled by the mutant site ... The type of regulation that the lac operon undergoes is referred to as negative inducible, meaning that the gene is turned off ...
Lien, HY; Yu, CH; Liou, CM; Wu, WF (2009). "Regulation of clpQ⁺Y⁺ (hslV⁺U⁺) gene expression in Escherichia coli". The open ... catalyzed by active-site threonine residues. It is inhibited by enzyme inhibitors that covalently bind the threonine. Like the ... Translocation is also facilitated by the C-terminal tails of the HslU subunits, which form a gate closing off the proteolytic ... Both proteins are encoded on the same operon within the bacterial genome. Unlike many eukaryotic proteasomes, which have ...
Gene regulatory network
Schilstra MJ, Bolouri H (2 January 2002). "Modelling the Regulation of Gene Expression in Genetic Regulatory Networks". ... RBS is the RNA ribosome binding site, and Pro i is the promoter region of gene i): RNAP + Pro i ⟶ k i , b a s Pro i ( τ i 1 ... Filloux, AAM (editor) (2012). Bacterial Regulatory Networks. Caister Academic Press. ISBN 978-1-908230-03-4. CS1 maint: Extra ... potentially facilitating the metabolic transition to galactose when glucose is depleted. The feed-forward loop in the arabinose ...
A more likely source of cellular plasticity is through the Regulation of gene expression, such that while two cells may have ... HATs are part of a multiprotein complex that is recruited to chromatin when activators bind to DNA binding sites. Acetylation ... For example, when DNA was amplified in PCR or bacterial cloning techniques, the methylation pattern was not copied and thus the ... Ghosh S, Sinha JK, Raghunath M (September 2016). "Epigenomic maintenance through dietary intervention can facilitate DNA repair ...
More reference expression data. Gene ontology. Molecular function. • nucleotide binding. • DNA binding. • DNA-dependent ATPase ... double-stranded DNA binding. • single-stranded DNA-dependent ATPase activity. Cellular component. • cytoplasm. • site of double ... RAD51 family members are homologous to the bacterial RecA, Archaeal RadA and yeast Rad51. The protein is highly conserved ... regulation of double-strand break repair via homologous recombination. • DNA metabolic process. • telomere organization. • ...
Transcription is initiated at the TATA box in TATA-containing genes. The TATA box is the binding site of the TATA-binding ... TFIID first binds to the TATA box, facilitated by TFIIA binding to the upstream part of the TFIID complex. TFIIB then ... The type of core promoter affects the level of transcription and expression of a gene. TATA-binding protein (TBP) can be ... Gene transcription by RNA polymerase II depends on the regulation of the core promoter by long-range regulatory elements such ...
... the regulation of gene expression, and responses to oxidative stress. The importance of proteolytic degradation inside cells ... Light blue chemical structures are the inhibitor bortezomib bound to the active sites. ... Passage of the unfolded substrate through the opened gate occurs via facilitated diffusion if the 19S cap is in the ATP-bound ... Some prokaryotes, including many archaea and the bacterial order Actinomycetales, also share homologs of the 20S proteasome, ...
Gene expression of hemoglobin before and after birth. Also identifies the types of cells and organs in which the gene ... with the iron ion bound in the center. The iron ion, which is the site of oxygen binding, coordinates with the four ... to facilitate visualization into the molecule. Oxygen is not shown in this model, but, for each of the iron atoms, it binds to ... through problems and mutations in globin gene regulation. All these diseases produce anemia. ...
Other adhesins have also been described, including the genes gfba, fnB, fbBA, fnBB, lmb and gapC; all mediating binding to ... Skerman, V.B.D.M.; Sneath, P.H.A. (1980). "Approved list of bacterial names". Int J Syst Bacteriol. 30: 225-420. doi:10.1099/ ... The M-protein, the most extensively studied SDSE virulence factor, has been documented to facilitate both adherence to and ... and a correlation between the expression of SLO and SLS and disease severity has been inferred. speGdys, a homolog of the S. ...
Polyadenylation site mutations also occur. The primary RNA transcript of a gene is cleaved at the poly-A addition site, and 100 ... Poliovirus mRNA uses a cloverleaf section towards its 5' end to bind PCBP2, which binds poly(A)-binding protein, forming the ... Several roles in gene expression have been attributed to the untranslated regions, including mRNA stability, mRNA localization ... Katz L, Burge CB (September 2003), "Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial Genes ...
By binding to specific sites within the 3'-UTR, miRNAs can decrease gene expression of various mRNAs by either inhibiting ... of Arabidopsis was shown to be involved in the regulation of several genes that control plant shape. In plants, the ... This RNA-binding protein then facilitates the transfer of cleaved siRNAs to the RISC complex. ... "Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction" ...
"Negative regulation of BRCA1 gene expression by HMGA1 proteins accounts for the reduced BRCA1 protein levels in sporadic breast ... incompletely cleared repair sites can cause epigenetic gene silencing. ... Agents (e.g. viruses) and events (e.g. mutations) that cause or facilitate genetic changes in cells destined to become cancer. ... Bacterial infection may also increase the risk of cancer, as seen in Helicobacter pylori-induced gastric carcinoma. ...
Type A HATs are located in the nucleus and are involved in the regulation of gene expression through acetylation of nucleosomal ... For instance, the substrate binding site of the former is more similar to that of the GNAT and MYST HATs. In addition, the ... such as nuclear receptors and other transcription factors to facilitate gene expression. ... Initiation (bacterial,. eukaryotic. *Transcription start site. Elongation. *bacterial RNA polymerase: rpoB. *eukaryotic RNA ...
Interferencia de ARN, a enciclopedia libre
"Inhibition of gene expression in plant cells by expression of antisense RNA". Proc Natl Acad Sci USA 83 (15): 5372-5376. PMC ... "Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction" ... "Nucleic Acids Res 33 (Web Server issue): W589-91. PMC 1160180. PMID 15980542. doi:10.1093/nar/gki419.. ... Matranga C, Tomari Y, Shin C, Bartel D, Zamore P (2005). "Passenger-strand cleavage facilitates assembly of siRNA into Ago2- ...
... paratope is generated by random recombination events of a set of gene segments that encode different antigen-binding sites (or ... "MicroRNA-650 expression is influenced by immunoglobulin gene rearrangement and affects the biology of chronic lymphocytic ... Regulations. Production and testing. Traditionally, most antibodies are produced by hybridoma cell lines through ... Neutralisation, in which neutralizing antibodies block parts of the surface of a bacterial cell or virion to render its attack ...
ATP-binding cassette transporter
... some bacterial ABC proteins are also involved in the regulation of several physiological processes. In bacterial efflux systems ... The ABCG2 gene was discovered in cell lines selected for high level resistance for mitoxantrone and no expression of ABCB1 or ... Each member of the ABCF subgroup consist of a pair of ATP binding domains. Six half transporters with ATP binding sites on the ... formation of a closed dimer upon binding two ATP molecules and dissociation to an open dimer facilitated by ATP hydrolysis and ...
... stimulates the expression of TSG-6 (TNF-stimulated gene 6) in fibroblasts and inflammatory cells. TSG-6, a HA-binding protein, ... and bacterial lipopolysaccharide, also synthesize HA, which has been shown to facilitate primary adhesion of cytokine-activated ... This may contribute to the hydrated microenvironment at sites of synthesis, and is essential for cell migration by facilitating ... Two significant roles of CD44 in skin were proposed. The first is regulation of keratinocyte proliferation in response to ...
Health effects of tobacco
Bruniquel D, Borie N, Hannier S, Triebel F (Jul 1998). "Regulation of expression of the human lymphocyte activation gene-3 (LAG ... The first characterization of the MHC Class II binding sites on LAG-3 were reported by Triebel's group in 1997. The ... Research Center showed in rhesus macaques that Mycobacterium tuberculosis could work through LAG3 to modulate an anti-bacterial ... most LAG3 was housed intracellularly in multiple domains before rapid translocation to the cell surface potentially facilitated ...
... which act as bacterial reservoirs and may help to facilitate transmission between hosts. Salmonella is notorious for its ... See also the National Center for Home Food Preservation. *^ "Reptiles, Amphibians, and Salmonella". Centers for Disease Control ... As Baumler et al. have suggested, Salmonella most likely evolved through horizontal gene transfer, formation of new serovars ... Salmonella further resides within a membrane-bound compartment called the Salmonella-Containing Vacuole (SCV). The ...
Evolution of sexual reproduction
Regulation of gene expression. *Gene regulatory network. *Developmental-genetic toolkit. *Evolutionary developmental biology ... Ronald Fisher also suggested that sex might facilitate the spread of advantageous genes by allowing them to better escape their ... 39 (Web Server issue): W475-8. doi:10.1093/nar/gkr201. PMC 3125724 . PMID 21470960.. ... Bacterial conjugation is a form of genetic exchange that some sources describe as "sex", but technically is not a form of ...
The vestigial gene acts to regulate the expression of the wing imaginal discs in the embryo and acts with other genes to ... In 2020, a dense connectome of half the central brain of Drosophila was released, along with a web site that allows queries ... InaD contains five binding domains called PDZ domain proteins, which specifically bind the C termini of target proteins. ... The transposable P elements, also known as transposons, are segments of bacterial DNA that are transferred into the fly genome ...
T helper cell
... revealed a downgrade in the expression level of both of the genes. Down regulation of such genes has caused Drosophila to ... Some transposases non-specifically bind to any target site in DNA, whereas others bind to specific target sequences. The ... novel gene sequences from being overwritten by similar gene sequences and thereby facilitate the development of new genes. TEs ... Bacterial transposons of this type belong to the Tn family. When the transposable elements lack additional genes, they are ...
... /Cas-mediated gene regulation may contribute to the regulation of endogenous bacterial genes, particularly during ... for sequence-specific control of gene expression". Nature Protocols. 8 (11): 2180-96. doi:10.1038/nprot.2013.132. PMC 3922765. ... the evolution of the Cas gene machinery that facilitates the system evolves through classic Darwinian evolution. ... binding double-stranded fragments of invading DNA, while Cas1 binds the single-stranded flanks of the DNA and catalyses their ...
Roger Wartell | School of Physics
... are important elements in the regulation of gene expression for bacteria. Hfq is a bacterial RNA-binding protein that ... facilitates the hybridization of sRNAs to their target regions on specific mRNAs. Hfq is highly conserved in bacterial phyla ... at understanding the interaction of the RNA-binding protein Hfq with short regulatory RNAs and its specific RNA target sites. ... RNA based regulation of gene expression. RNA-protein interaction. Thermodynamics of DNA and RNA structural motifs ...
List of Accepted Software Demos
This data along with literature-derived knowledge on the regulation of gene expression has opened the way for genome-wide ... We integrated PoSSuMsearch , a fast and statistically sound method to detect transcription factor binding site motifs within ... analysis techniques to bacterial genome sequences provides knowledge to encoded proteins involved in the gene regulation. ... Special graph layout algorithms have been developed and implemented to facilitate the comparison of gene regulatory networks ...
Fis - Wikipedia
Fis as a critical regulator of capsule expression. Fis is also involved in the regulation of a range of genes in bacterial ... Two RNA polymerase-binding sites and at least six high-affinity Fis-binding sites are present in the fis promoter region. ... Helices A and B provide the contacts between Fis monomers, facilitating dimer formation, whereas the C and D helices form a ... fis is the E. coli gene encoding FIS protein. The regulation of this gene is more complex than most other genes in the E. coli ...
Geoff Kneale - University of Portsmouth
A major interest is in the "controller" (C) proteins that regulate the expression of bacterial restriction- modification genes ... we identified the binding sites for the C protein at the promoters controlling the R-M genes. The C protein can act as either ... The Structural basis of gene regulation. We have long-standing interests in the molecular mechanisms that control gene ... Histone chaperones direct the productive assembly and disassembly of nucleosomes by facilitating histone deposition and ...
Vectors bearing a hybrid trp-lac promoter useful for regulated expression of cloned genes in Escherichia coli
A strong promoter has been cloned on a series of plasmid vectors that facilitate the expression of cloned genes. This promoter ... the lac or the lacUV5 promoter can be readily converted to tac promoter gene fusions without changing the ribosome-binding site ... DNA, Bacterial / analysis * Escherichia coli / genetics* * Gene Expression Regulation* * Lac Operon* * Plasmids* ... A strong promoter has been cloned on a series of plasmid vectors that facilitate the expression of cloned genes. This promoter ...
Binding Site Recognition by Rns, a Virulence Regulator in the AraC Family | Journal of Bacteriology
... of the binding sites for these and other regulators would facilitate the identification of virulence genes and their expression ... The potential Rns binding sites we have identified are within regions previously shown to be required for positive regulation ... 1998) The Shigella virulence gene regulatory cascade: a paradigm of bacterial gene control mechanisms. Mol. Microbiol. 29:677- ... 2). Binding site I begins 30 bp upstream of site II, extending from bases −93 to −129. The promoter-proximal site (binding site ...
MicroRNA Expression Profile in RAW264.7 cells in Response to Brucella melitensis Infection
MiRNAs regulate target genes expression by directly binding to complementary sites within the 3′ untranslated region (UTR) to ... melitensis triggers time-dependent modulation of apoptosis and down-regulation of mitochondrion-associated gene expression in ... facilitating Brucella′s latent infection [8, 9]. Previous studies revealed the mRNA expression profiles of macrophages infected ... Bacterial pathogens modulate an apoptosis differentiation program in human neutrophils. Proc Natl Acad Sci U S A. 2003;100: ...
Operons | SpringerLink
... are common features of bacterial genomes. More recently, functional gene clustering has been reported in eukaryotes, from ... clusters of co-regulated genes with related functions) ... Clustering may facilitate co-regulation of gene expression, ... regulation may require the transcription factor gene to be in close proximity to the sites within the genome to which it binds ... Gene clustering may also facilitate co-ordinate regulation of gene expression at the level of chromatin . ...
Small Regulatory RNAs in Bacteria
... genes whose transcripts control expression of distal genes ... some by binding proteins that control gene expression. ... Hfq is the RNA‐binding protein that facilitates the RNA/RNA interaction. RBS is the ribosome‐binding site on the mRNA. ... Vakulskas CA, Potts AH, Babitzke P, Ahmer BM and Romeo T (2015) Regulation of bacterial virulence by Csr (Rsm) systems. ... Some act like sponges that bind and sequester proteins involved in global gene regulation. Many sRNA genes are activated by ...
Trends in Genetics : TIG
The current paradigm in the field of gene regulation postulates that regulatory information for generating gene expression is ... transcription factor binding sites within .... Source: Trends in Genetics : TIG - April 17, 2019 Category: Genetics & Stem ... This modular organization is thought to facilitate the evolution of gene expression by minimizing pleiotropic effects. Here we ... Tools To Live By: Bacterial DNA Structures Illuminate Cancer.. Abstract Holliday junctions (HJs) are DNA intermediates in ...
The putative lytic transglycosylase VirB1 from Brucella suis interacts with the type IV secretion system core components VirB8,...
... which facilitate the assembly of type IV secretion systems via localized lysis of the peptidoglycan. This paper presents the ... Gene Expression Regulation, Bacterial * Genetic Vectors * Glycosyltransferases / chemistry * Glycosyltransferases / genetics * ... The binding sites were localized on a structure model of VirB1, suggesting that different portions of VirB1 may interact with ... VirB1-like proteins are believed to act as lytic transglycosylases, which facilitate the assembly of type IV secretion systems ...
F. Jon Kull | Faculty Directory
... this regulation by environmental stimuli so as to facilitate the development of better strategies to prevent and cure bacterial ... A fourth protein, HapR is a negative regulator of virulence gene expression that functions to repress expression at the aphA ... at their cognate promoters by obtaining high resolution structures of them in the absence and presence of their binding sites. ... Such regulation is widespread among bacterial pathogens and allows productive infections to be mounted only in the appropriate ...
Expansion of the Tetracycline-Dependent Regulation Toolbox for Helicobacter pylori | Applied and Environmental Microbiology
TetR is bound to tetO sites within the tet promoter; thus, it blocks the transcription of the target gene. When tetracycline ... as it would facilitate achieving a closer match to the endogenous expression levels of the target gene of interest. To that end ... allow for studying the physiological role of gene products that are essential for bacterial growth and for studying gene ... Growth phase-dependent regulation of target gene promoters for binding of the essential orphan response regulator HP1043 of ...
Functional Characterization of the Stringent Response Regulatory Gene dksA of Vibrio cholerae and Its Role in Modulation of...
... bacterial cells undergo rapid and complex metabolic adjustments through negative and positive regulation of gene expression ... ppGpp binds to a site adjacent to, but not overlapping, the active site on the β and β′ subunits of the RNA polymerase (RNAP) ... the product of the dksA gene, acts as a coregulator to facilitate the function of (p)ppGpp during the stringent response (39-41 ... Regulation and temporal expression patterns of Vibrio cholerae virulence genes during infection. Cell 99: 625-634. ...
Bacterial one-hybrid system - Wikipedia
Across all living organisms, regulation of gene expression is controlled by interactions between DNA-binding regulatory ... if bound to by the chimeric fusion product, drives expression of downstream reporter genes. This reporter region facilitates ... DNA sequences in or around genes that act as target sites for DNA-binding proteins. By binding to cis-regulatory sequences and ... The bacterial one-hybrid (B1H) system is a method for identifying the sequence-specific target site of a DNA-binding domain. In ...
Nitric oxide synthase - Wikipedia
The FMN binding domain is homologous to flavodoxins, and the two domain fragment containing the FAD and NADPH binding sites is ... The gene coding for iNOS is located on Chromosome 17. While evidence for baseline iNOS expression has been elusive, IRF1 and ... gene. Recently, NOS activity has been demonstrated in several bacterial species, including notorious pathogens Bacillus ... This facilitates the conversion of O2 and L-arginine to NO and L-citrulline. The oxygenase domain of each NOS isoform also ...
Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis | PNAS
2010) Ail binding to fibronectin facilitates Yersinia pestis binding to host cells and Yop delivery. Infect Immun 78(8):3358- ... WT and mutated 5′-UTRs (SI Appendix) were translationally fused to the bgaB reporter gene, and gene expression was measured as ... 2015) Regulation of bacterial virulence by Csr (Rsm) systems. Microbiol Mol Biol Rev 79(2):193-224. ... Our analysis shows that mRNAs tend to have a poorly structured ribosome binding site. Transcripts that deviate from this ...
Proteomic analysis of endothelial cold-adaptation | BMC Genomics | Full Text
... and regulation of translation (PABPC4). There was, however, up-regulation of the non-histone chromatin-binding protein HMGB1, ... SAHH facilitates SAM-dependent DNA and histone methylation and consequently gene silencing  while up-regulating GSH ... Proteins that regulate gene expression. Cold-adaptation induced significant changes in the abundance of proteins that organize ... 14-3-3s are a family of conserved proteins that control many diverse processes by binding to specific phosphorylated sites on ...
Biology | Free Full-Text | Transcriptional Regulation of the Mitochondrial Citrate and Carnitine/Acylcarnitine Transporters:...
The regulation of the expression of many genes at the level of their transcription has already been analyzed. This review ... Moreover, the mechanism by which the expression of the CIC and CAC genes is modulated by coordinated responses to hormonal and ... of tissue-specific and less tissue-specific transcription factors in activating or repressing CIC and CAC gene expression is ... which are members of the mitochondrial carrier gene family, SLC25. The contribution ...
Protocols and Video Articles Authored by Zongfu Wu
... and Regulation of Virulence Gene Expression Annual Review of Microbiology. 09, 2016 , Pubmed ID: 27482744 Staphylococcus aureus ... SBP2 could also bind fibronectin and laminin, two important extracellular matrix proteins of the host, to facilitate the ... In addition, information can be obtained on the binding site of a ligand (noncoding RNAs, protein, metabolites), and on RNA ... The findings demonstrated that the luxS gene deletion resulted in a significant decrease of bacterial biofilm formation, cell ...
Software - Molecular, Cell and Cancer Biology (MCCB) - UMass Medical School Worcester
cleanUpdTSeq Website. 3′ end processing is important for transcription termination, mRNA stability and regulation of gene ... cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding ... Analyzing composition of ZFP sites. » ZFN target site algorithm for identifying sites for selection using the Bacterial one ... in most human genes. InPAS facilitates the discovery of novel APA sites from RNA-seq data. It leverages the cleanUpdTSeq ...
Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca | PNAS
They are organized into operons and placed under the control of synthetic parts (promoters, ribosome binding sites, and ... Bacterial genes associated with a single trait are often grouped in a contiguous unit of the genome known as a gene cluster. It ... gene. Recoded genes are computationally scanned to eliminate internal regulation. ... Finally, a controller consisting of genetic sensors and circuits regulates the conditions and dynamics of gene expression. We ...
Macosko Group Homepage
Experiments to investigate gene expression and regulation at the single-molecule level One of the simplest known gene ... the sample chamber will be filled with proteins that bind DNA: T7 RNAP binding its promoter sequences, for instance. In this ... T7 lysozyme is produced during a T7 infection to help lyse the bacterial cell wall in order to release the newly formed ... A prototype CFSM will be further developed to facilitate single-molecule manipulation. A sealed gasket encloses the sample ...
JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
The ERs function as transcription factors and regulate gene expression. Whereas ERαs regulation of protein-coding genes is ... We demonstrate the applicability of this method by determining the gene targets and binding site motifs and thus predicting the ... cellular identification and gene expression3,4, monitoring viral multiplication in infected cells5, and bacterial community ... Ribosomes also host chaperones, which facilitate folding of nascent polypeptides, thereby modulating function and stability of ...
Regulation of Gene Expression PowerPoint Presentation, Free Online Download PPT DVHJE5
The recombination sites (inverted repeats) are called hix (yellow). (a) In one orientation, fljB is expressed along with a... ... The recombination sites (inverted repeats) are called hix (yellow). (a) In one orientation, fljB is expressed along with a... ... The hin gene encodes the recombinase that catalyzes inversion of the DNA segment containing the fljB promoter and the hin gene ... The hin gene encodes the recombinase that catalyzes inversion of the DNA segment containing the fljB promoter and the hin gene ...
Biofilms: Microbial Life on Surfaces - Volume 8, Number 9-September 2002 - Emerging Infectious Diseases journal - CDC
... regulation of specific genes. Attachment is a complex process regulated by diverse characteristics of the growth medium, ... Binding of lectins by the cells would minimize the attachment sites and affect cell attachment if polysaccharides were involved ... Abiotic surface sensing and biofilm-dependent regulation of gene expression in Escherichia coli. J Bacteriol. 1999;181:5993- ... Davies and Geesey (34) demonstrated algC up-regulation in individual bacterial cells within minutes of attachment to surfaces ...
Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in...
Careful attention must be paid to the location of transcript start/stop sites, the existence of ribosome binding sites and the ... It is not easy to interpret how their differential regulation affects the bacterial cell (because the biological functions of ... Including sRNA gene annotations in S. aureus GenBank files facilitates global expression analysis of these understudied ... To identify sRNA genes with meaningful differences in expression, we applied cutoffs to eliminate genes expressed at low levels ...
Catalase Expression in Azospirillum brasilense Sp7 Is Regulated by a Network Consisting of OxyR and Two RpoH Paralogs and...
Positive regulation of the target genes of OxyR is carried out by the binding of OxyR to the operator elements which precede ... A novel DNA element that controls bacterial heat shock gene expression. Mol Microbiol 28:315-323. doi:10.1046/j.1365-2958.1998. ... These studies revealed probable binding sites of RpoH5 and OxyR2 in the upstream region of the katAII gene in A. brasilense Sp7 ... Simultaneous and juxtaposed binding of RpoH5 and OxyR2 might facilitate interaction of the α subunit of RpoH5 with the C ...
Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes | Nature...
Using seven bacterial strains, we show that SMALR yields significantly improved resolution and reveals distinct types of ... Bacterial DNA methylation is involved in many processes, from host defense to antibiotic resistance, however current methods ... Bacterial cells in a clonal population can generate epigenetic heterogeneity to increase population-level phenotypic plasticity ... However, existing SMRT sequencing-based methods for studying bacterial methylomes rely on a population-level consensus that ...
Riboswitches and Ribozymes | Sloan Kettering Institute
... bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We ... Pistol Ribozyme Adopts a Pseudoknot Fold Facilitating Site-specific In-line Cleavage. ... Flavin mononucleotide (FMN)-specific riboswitches, also known as RFN elements, direct expression of bacterial genes involved in ... In bacteria, expression of folate related genes is controlled by feedback modulation in response to specific binding of THF and ...
ProteinsRepeated sequencesTranscriptional regulationEncodesVitroRegulatorMutationsPathogenesisMolecularMRNASubunitRegulatorsRNAsTranslationalABSTRACTRepressorPathogenVivoAffinityInteractionsSRNAsOperonsControl of gene expressionTranscription factorsAssaysSpeciesGeneticRibosome bindiMoleculeDifferentially expressedInducibleIntracellularTarget genesNucleotidePlasmidsSpecific genesInduceVibrioToxinsRegulate the expressionMRNAsVirulence factorsActivatorsEssential genesGenomesRiboswitchesMoleculesSRNA genesMechanismOrganismEpigenetic regulationStructuralProtein bindsBacteriumGenetics
- Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions. (wikipedia.org)
- We have long-standing interests in the molecular mechanisms that control gene expression, and how transcriptional regulator proteins (both activators and repressors) recognize their cognate DNA binding sites with varying degrees of specificity. (port.ac.uk)
- A major interest is in the "controller" (C) proteins that regulate the expression of bacterial restriction- modification genes. (port.ac.uk)
- Single-stranded DNA-binding proteins play a key role in DNA replication. (port.ac.uk)
- The expression of CS1 pili by enterotoxigenic strains of Escherichia coli is regulated at the transcriptional level and requires the virulence regulator Rns, a member of the AraC family of regulatory proteins. (asm.org)
- In several other bacterial pathogens, type IV pili are regulated by proteins with homology to Rns. (asm.org)
- The regulatory proteins for these include PerA (BfpT) of enteropathogenic E. coli , AggR of enteroaggregative E. coli , and ToxT (TcpN) of Vibrio cholerae , which control the expression of bundle forming, AAF/I, and toxin-coregulated pili, respectively ( 18 , 30 , 39 ). (asm.org)
- For example, in addition to the activation of genes encoding the bundle-forming pilus, PerA is also needed for expression of eaeA , encoding the membrane protein intimin, which is required for close contact of enteropathogenic E. coli with host epithelial cells, and the esp genes, which encode secreted proteins that induce signal transduction pathways in host epithelial cells ( 13 , 22 ). (asm.org)
- VirF from the genus Yersinia regulates the expression of multiple virulence factors, including secreted Yop proteins encoded by unlinked genes present on the same virulence plasmid that encodes VirF ( 6 ). (asm.org)
- however, some sRNAs bind proteins and can regulate transcription or translation indirectly. (els.net)
- Some act like 'sponges' that bind and sequester proteins involved in global gene regulation. (els.net)
- sRNAs can indirectly regulate the expression of global genes, some by binding proteins that control gene expression. (els.net)
- Molecular motor proteins are practically ubiquitous in cellular activities requiring movement, and mutations in motors or defects in motor regulation can have drastic effects. (dartmouth.edu)
- The expression of its two primary virulence factors, toxin-coregulated pilus and cholera toxin, occurs via a transcriptional cascade involving several activator proteins and serves as a paradigm for the regulation of bacterial virulence. (dartmouth.edu)
- This project aims to explore the structure/function relationships of four cytoplasmic virulence gene regulator proteins in V. cholerae, AphA, AphB, and ToxT, at their cognate promoters by obtaining high resolution structures of them in the absence and presence of their binding sites. (dartmouth.edu)
- In combination with ongoing mutational studies, the work will significantly increase our understanding of how these proteins activate virulence gene expression, will serve as models for these regulatory protein family members in other bacterial pathogens, and will advance efforts to identify molecules that may function as novel therapeutics. (dartmouth.edu)
- VirB1-like proteins are believed to act as lytic transglycosylases, which facilitate the assembly of type IV secretion systems via localized lysis of the peptidoglycan. (nih.gov)
- The binding sites were localized on a structure model of VirB1, suggesting that different portions of VirB1 may interact with other VirB proteins during assembly of the type IV secretion machinery. (nih.gov)
- Across all living organisms, regulation of gene expression is controlled by interactions between DNA-binding regulatory proteins (transcription factors) and cis-regulatory elements, DNA sequences in or around genes that act as target sites for DNA-binding proteins. (wikipedia.org)
- But despite their importance and ubiquity, little is known about where exactly each of these regulatory proteins binds. (wikipedia.org)
- Protein spots were excised from preparative gels and identified by matrix-assisted laser desorption ionization time-of-flight MS (MALDI-TOF-MS) or MALDI-TOF-TOF-MS, which led to the identification of eight immunogenic proteins (arginine deiminase, extracellular solute-binding protein, translation elongation factor Ts, neprilysin, peptide ATP-binding cassette transporter peptide-binding protein, pyruvate kinase, phosphate acetyltransferase, and fructose-bisphosphate aldolase). (jove.com)
- These immunogenic proteins, which are encoded by genes that are reasonably conserved among SS9 strains, could be developed as vaccine candidates. (jove.com)
- Longer time control involves transcriptional regulation that affects the expression levels of key proteins. (mdpi.com)
- Occurs when bacteria are subject to heat stress RNA Pol replaces 70 with 32 Causes RNA Pol to bind to different set of promoters transcription of new products including chaperones that keep proteins in correct conformation, even in heat Small-Molecule Effectors Can Regulate Activators and Repressors Repressors reduce RNA Pol-promoter interactions or block the polymerase. (perdidanautopia.com)
- Once phagocytosed, various bacterial proteins enable Listeria to escape the phagosome, survive within the cytosol, and infect neighboring cells 5 . (jove.com)
- Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. (mskcc.org)
- Adapter/scaffold proteins, through their multidomain structure, perform a fundamental role in facilitating signal transduction within cells. (biomedsearch.com)
- They mediate interactions with several structural and regulatory proteins important for coordinating changes in the actin cytoskeleton associated with cell motility and cell adhesion as well as in the regulation of gene expression. (biomedsearch.com)
- Results from promoter activity assays revealed that expression of rodA3 and ftsW2 is induced in the presence of antibiotics targeting penicillin binding proteins. (imperial.ac.uk)
- Regulation of NF-κB transactivation function is controlled at several levels, including interactions with coactivator proteins. (asm.org)
- Moreover, it suggests that the association of NF-κB with the HDAC1 and HDAC2 corepressor proteins functions to repress expression of NF-κB-regulated genes as well as to control the induced level of expression of these genes. (asm.org)
- NF-κB has typically been thought of as residing in the cytoplasm in an inactive form bound by its inhibitory proteins, members of the IκB family ( 10 , 37 ), although evidence indicates that NF-κB may shuttle between the nucleus and cytoplasm in unstimulated cells ( 5 , 16 ). (asm.org)
- Coregulatory (coactivator and corepressor) proteins have been shown to be required for the regulation of gene expression by many transcription factors. (asm.org)
- These proteins likely function by facilitating or bridging the sequence-specific activators to the basal transcriptional machinery as well as by altering chromatin structure. (asm.org)
- Chen, Zhixiang 2004-10-16 00:00:00 A pathogen- and salicylic acid (SA)-induced DNA-binding activity has been recently identified in tobacco that is related to a previously identified class of WRKY DNA-binding proteins. (deepdyve.com)
- Nonetheless, both tWRKY3 and tWRKY4 are capable of binding DNA molecules with the W-box (TTGAC) element recognized by other WRKY proteins. (deepdyve.com)
- Identification of pathogen- and SA-induced genes encoding WRKY DNA-binding proteins should facilitate future studies on the regulation and functions of this novel group of DNA-binding proteins. (deepdyve.com)
- Support for this assumption comes from reports showing that IRF4 and IRF8 (IFN consensus sequence-binding proteins [ICSBP]) contribute to the control of genes induced by IFN-γ in lymphoid and myeloid cell types, suggesting that members of the IRF family other than IRF1 cooperate with STAT1 in gene regulation ( 16 , 49 ). (asm.org)
- IsrM targets the mRNAs coding for SopA, a SPI-1 effector, and HilE, a global regulator of the expression of SPI-1 proteins, which are major virulence factors essential for bacterial invasion. (prolekare.cz)
- The SECIS acts as a platform for RNA-binding proteins, which mediate or regulate the recoding mechanism. (pubmedcentralcanada.ca)
- In vitro studies support the hypothesis that SBP2 and L30 compete for binding to the SECIS core and that the two proteins act sequentially during UGA recoding ( 10 ). (pubmedcentralcanada.ca)
- The key problem in the production of human recombinant proteins in this bacterial host is related with the lack of post-translational modifications, as glycosylations, and poor protein folding, leading to loss of enzyme activity and the formation of insoluble protein aggregates 14 . (nature.com)
- His lab has extensively studied how the glucan-binding proteins (GBPs) synthesized by Streptococcus mutans contribute to the development of the plaque biofilm and ultimately dental caries. (uiowa.edu)
- Since glucan -- a polymer of glucose derived from the metabolism of sucrose -- is a primary virulence factor that propels the change in microbial ecology that leads to a cariogenic plaque, it has been proposed that proteins that have the property of binding glucan play accessory roles in this process. (uiowa.edu)
- The initial expression of tcpA could be caused by bacterial regulatory proteins sensing a host signal in the upper regions of the gut. (biomedcentral.com)
- These findings suggest that the signals for the actions of HU proteins are located in the DNA regions upstream from the sites near the 5' extremities of the coding regions of the hupB and hupA genes. (labome.org)
- De novo -synthesized RNAs are under the regulation of multiple posttranscriptional processes by a variety of RNA-binding proteins. (asm.org)
- In general, RNA transcripts form ribonucleoprotein (RNP) complexes with a number of RNA-binding proteins. (asm.org)
- The Rab11a-positive recycling endosome is important for the delivery of membranes and core polarity proteins to the lateral cell surface (reviewed in references 25 , 42 , and 74 ), leading to the construction of plasma membrane domains and epithelial cell polarity through binding to motor proteins along the cytoskeleton ( 75 ). (asm.org)
- In addition my laboratory is also interested to study the Mechanism of Ribosome Biogenesis and the Role of Cellular Proteins in Viral gene Expression. (csuohio.edu)
- Cytotoxin K is similar to a class of proteins encoded by genes usually annotated as haemolysin II ( hlyII ) in the majority of genomes of the B. cereus group. (hindawi.com)
- Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. (embl-heidelberg.de)
- Many BRD-containing proteins have been linked to epigenetic regulation of gene expression through their interactions with acetylated histones and have emerged as promising drug targets. (aacrjournals.org)
- All human BRD proteins were subcloned into bacterial expression systems, and the crystal structures of 44 BRDs, representing each of the 8 families, in complex with acetylated peptides were determined. (aacrjournals.org)
- The results of these alterations are reflected in the encoded amino acids sequence of the proteins or in any targeted binding site in the DNA sequence. (els.net)
- The molecular roles of many RNA-binding proteins in bacterial post-transcriptional gene regulation are not well understood. (medworm.com)
- Overall, our generic CLIP-seq approach will bring new insights into post-transcriptional gene regulation by RNA-binding proteins in diverse bacterial species. (medworm.com)
- Although the relatively rigid genetic code that determines the amino acid sequence of proteins was deciphered soon after the discovery of DNA structure, the regulatory code of the genome still remains an unsolved mystery and, as such, understanding the complex interplay between regulatory DNA regions and transcription factors (TF), regulatory RNAs, signalling pathways and epigenetic marks that determine gene expression is among the main current challenges of modern molecular genetics. (royalsocietypublishing.org)
- Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). (biomedcentral.com)
- This research has investigated the regulation of LEE4 translocon proteins, in particular EspA. (asm.org)
- This research demonstrates that while specific environmental conditions are required to induce LEE1-4 expression, a further checkpoint exists before EspA filaments are produced on the bacterial surface and secretion of effector proteins occurs. (asm.org)
- agr is an auto-inducible quorum-sensing system, promoting expression of extracellular virulence factors and down-regulating cell surface proteins. (ukessays.com)
- Many surface proteins/adhesin have been shown to be positively influenced by σB, while the expression of most exoproteins and toxins were down-regulated. (ukessays.com)
- Correspondingly, genes encoding surface proteins were found to be expressed earlier, starting during the transition from stationary to exponential growth while the expression of secreted proteins started at late-exponential growth phase. (ukessays.com)
- E. coli contains at least two different HSP70 proteins, Dnak and HSC66 and 14 different genes encoding HSP70 have been found in the genome of Saccharomyces cereviseae. (thefreelibrary.com)
- Prototypical HSP70 proteins contain a nucleotide binding domain (NBD) and a peptide-binding domain (PBD) that are connected by a flexible linker region that contributes to allosteric regulation of NBD and PBD activity. (thefreelibrary.com)
- Since high concentrations of zinc can be toxic, most bacterial species maintain zinc homeostasis using transcriptional regulatory controls to balance the expression of genes encoding both zinc import and zinc export proteins. (asm.org)
- To circumvent this problem, previous studies have proposed the concurrent use of "orthogonal" Cas9 proteins derived from different bacterial species, each of which interacts with a distinct gRNA that allows users to decide which Cas9 protein is directed to which target site ( 1 ). (addgene.org)
- Consequently, fewer genetic tools for targeted transcriptional and epigenetic regulation have been validated with these proteins. (addgene.org)
- Transcription and translation make up the two-step process by which the coded instructions of genes are used to synthesize proteins. (berkeley.edu)
- In other words, food not only contains carbohydrates, proteins, fat, minerals, vitamins and so forth, it also contains information-in the form of these regulatory snippets of microRNA-which regulate our gene production. (blogspot.com)
- Activators and repressors bind to DNA and those binding sites can lie at some distance from the promoter leading to formation of loops of DNA that bring the regulatory proteins into contact with the transcription complex. (blogspot.com)
- Today, the "epigenome" is generally used to describe the global, comprehensive view of sequence-independent processes that modulate gene expression patterns in a cell and has been liberally applied in reference to the collection of DNA methylation state and covalent modification of histone proteins along the genome (Bernstein et al. (blogspot.com)
- A genetic library, CellPro, based on Probabilistic Timed Automata, simulates gene expression dynamics using simplified and easy to compute digital proteins. (plaswires.eu)
- We investigated five new targets of CsrA regulation, including the genes for 4 ferritin or ferritin-like iron storage proteins (ISPs) and the stress-inducible Fe-S repair protein, SufA. (asm.org)
- The operon is transcribed from two promoters which are subject to both negative and positive control by at least four proteins, Gal repressor, Gal isorepressor, cyclic AMP receptor protein, and bacterial histone like protein, HU. (cancer.gov)
- The present invention further provides a human IGF-I gene which has been sequenced and which encodes at least two preproinsulin-like growth factor-I proteins. (google.com)
- Various genes and DNA sequences useful in producing essentially pure mature IGF-I, preproinsulin-like growth factor I proteins and IGF-I gene related proteins are also provided. (google.com)
- MicroRNA (miRNA) is endogenous small non-coding RNA molecule that functions in post-transcriptional regulation [ 12 , 13 ]. (ijbs.com)
- Circular' regulation: posttranscriptional regulation of lrp mRNA by MicF RNA in nutrient‐rich growth media and transcriptional regulation of micF by Lrp in nutrient‐poor media (after Holmqvist et al . (els.net)
- Alternative polyadenylation (APA) is one of the important post-transcriptional regulation mechanisms, which occur, in most human genes. (umassmed.edu)
- Transcriptional regulation of genes involved in fatty acid metabolism is considered the major long-term regulatory mechanism controlling lipid homeostasis. (mdpi.com)
- The regulation of metabolism occurs through different types of mechanisms: short-term mechanisms involving allosteric control and post- transcriptional modifications, and long-term control by transcriptional regulation. (mdpi.com)
- Hfq fulfills several functions in post-transcriptional regulation. (frontiersin.org)
- This encompasses parts necessary for the development of other systems, such as vectors and translational elements, but with a focus on transcriptional regulation. (diva-portal.org)
- The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. (embl-heidelberg.de)
- Beaudoin J , Ioannoni R , Mailloux S , Plante S and Labbé S (2013) Transcriptional regulation of the copper transporter mfc1 in meiotic cells. (els.net)
- Therefore we are interested in mechanisms of transcriptional regulation in diatoms and other microalgae. (blogspot.com)
- The regulatory gene lacI encodes the lac repressor, which in its active form inhibits the transcription of the structural genes by binding an operator. (springer.com)
- HIS3 encodes a protein required for histidine biosynthesis and thus only those cells containing bait-prey combinations that activate the reporter genes will be able to grow. (wikipedia.org)
- The sRNA LhrA was recently shown to be a post-transcriptional regulator of a single gene, lmo0850, which encodes a small protein of unknown function. (jove.com)
- The MRP1 gene maps to chromosome 16p13.1 and encodes for a protein of 1,531 amino acids. (springer.com)
- Our study highlights that L. monocytogenes encodes a multitude of functional FtsW and RodA enzymes to produce its rigid cell wall and that their expression needs to be tightly regulated to maintain growth, cell division and antibiotic resistance. (imperial.ac.uk)
- This gene encodes a protein that helps form an external protective coating, the loss of which leads to a lack of cellulose production and has adverse effects on these organisms. (eurekalert.org)
- Under normal cellular conditions, dimeric OhrR protein is bound to DNA to repress expression of ohr, which encodes organic hydroperoxide resistance protein. (proteopedia.org)
- The suppressor gene was identified as rpoD, the gene that encodes the major sigma 70. (labome.org)
- Interposon mutagenesis experiments identified the ORF as the bchC gene, which encodes an enzyme that catalyses the penultimate step in the biosynthesis of bacteriochlorophyll a, and also showed that the bchC gene formed an operon with the bchA gene. (ubc.ca)
- The deduced amino acid sequence showed that the bchC gene encodes a 33 kDA protein that has hydrophobic segments that could interact with a lipid membrane, and that this putative BchC protein contains a potential bacteriochlorophyll a binding site. (ubc.ca)
- Whereas BC, BCCP, and α-CT are products of nuclear genes, the DNA that encodes soybean β-CT is located in chloroplasts. (plantphysiol.org)
- This gene encodes the regulatory subunit of the inhibitor of kappaB kinase (IKK) complex, which activates NF-kappaB resulting in activation of genes involved in inflammation, immunity, cell survival, and other pathways. (genecards.org)
- In collaboration with Prof. K. Severinov at the Waksman Institute (Rutgers University, NJ, USA), we have demonstrated in vitro activation and repression of gene transcription by the C protein. (port.ac.uk)
- Further analysis of mutants revealed that DksA Vc positively regulates various virulence-related processes, namely, motility, expression of the major secretory protease, called hemagglutinin protease (HAP), and production of cholera toxin (CT), under in vitro conditions. (asm.org)
- Furthermore, in vitro binding experiments show that Hfq stimulates the base pairing of LhrA to chiA mRNA. (jove.com)
- In vitro binding assays showed that purified nucleolin discriminates among SECIS elements in the absence of other factors. (pubmedcentralcanada.ca)
- HSC population is then the ideal target for the correction of hematopoietic genetic diseases and also for the knockout of the responsible genes to in vitro and in vivo model those hematopoietic diseases. (intechopen.com)
- Expression patterns of Vibrio cholerae virulence genes determined during an infection differ dramatically from those observed in conventional in vitro analyses. (biomedcentral.com)
- The regulation of V. cholerae virulence genes has previously been studied only in vitro , because of methodological limitations. (biomedcentral.com)
- This is not particularly satisfactory, as laboratory conditions that facilitate maximum expression of TCP and CT are unlike the conditions in the intestines of an infected animal, and when in vivo conditions are replicated, in vitro virulence gene expression is actually repressed. (biomedcentral.com)
- Furthermore, the virulence genes of the El Tor biotype of V. cholerae , which is responsible for the current global pandemic, are difficult to induce in vitro . (biomedcentral.com)
- have now determined the temporal course of expression of these two genes in the El Tor biotype, both in vivo , during an infection in the mouse, and in vitro . (biomedcentral.com)
- This necessity for tcpA expression was not observed under in vitro conditions, nor is the biphasic expression of tcpA seen in vitro . (biomedcentral.com)
- The expression patterns of tcpA and ctxA within the mutant backgrounds were also found to differ during an infection from their expression in vitro . (biomedcentral.com)
- Site‐directed mutagenesis (SDM) aims to introduce precise alterations in any coding or noncoding deoxyribonucleic acid (DNA) sequence, usually in vitro . (els.net)
- According to the authors, people like me were fooled by studies on individual genes, purified factors, and in vitro binding assays. (blogspot.com)
- A strategy to identify asymmetric binding sites is presented and applied to locate potential binding sites upstream of other genes that Rns can activate, including those encoding the CS2 and CFA/I pili of enterotoxigenic E. coli and the global regulator virB of Shigella flexneri . (asm.org)
- In addition, all pili within the CS1 group require a regulator for their expression. (asm.org)
- One such regulator, Rns, activates transcription of the genes encoding CS1 and CS2 pili ( 3 ). (asm.org)
- Among these genes, we identified lmo0302 and chiA as direct targets of LhrA, thus establishing LhrA as a multiple target regulator. (jove.com)
- We show here that LhrA acts as a post-transcriptional regulator of lmo0302 and chiA by interfering with ribosome recruitment, and we provide evidence that both LhrA and Hfq act to down-regulate the expression of lmo0302 and chiA. (jove.com)
- In addition to its utility in making targeted modifications to DNA, Cas9 can be reprogrammed to serve as a regulator of gene expression. (addgene.org)
- When a bacterial translational regulator is fused to a tna element adaptor, it is able to also regulate transcriptional elongation. (berkeley.edu)
- We have demonstrated that a regulator inhibits or stimulates transcription initiation by disabling or stimulating RNA polymerase activity at a post-binding step by directly or indirectly altering the specific domain of RNA polymerase by a direct GalR-RNA polymerase contact(s) to an unfavorable or to a more favorable state, respectively. (cancer.gov)
- Single point mutations at either the ribosomal binding site or the start codon were introduced to shift the regulatory range of three uPtetO 5 derivatives. (asm.org)
- Our large sample size and precision of measurement allowed us to determine that there are significant differences in fitness between mutations in different genes, between different paralogs, and even between different classes of mutations within the same gene. (stanford.edu)
- Sequence analysis revealed that this region contains a binding site of a transcription factor called AP-2 and, when we induced mutations in this binding site, the expression of cellulose synthase in the ascidian epidermis disappeared. (eurekalert.org)
- Mutations in IsrM result in disregulation of expression of HilE and SopA, as well as other SPI-1 genes whose expression is regulated by HilE. (prolekare.cz)
- The motor neuron disease spinal muscular atrophy (SMA) is caused by recessive, loss-of-function mutations of the survival motor neuron 1 gene (SMN1). (jci.org)
- Alone, such mutations are embryonically lethal, but SMA patients retain a paralog gene, SMN2, that undergoes alternative pre-mRNA splicing, producing low levels of SMN protein. (jci.org)
- A selection system to distinguish and select the molecules with the desired site‐directed mutations from the rest of the molecules has to be planned. (els.net)
- Engineered site‐directed mutations are heritable modifications. (els.net)
- Although this does not mean that physiological and morphological changes cannot be caused by mutations in coding exons [ 6 , 7 ], many characteristics of enhancers and other cis -regulatory regions indicate that organismal evolution is mostly driven by changes in gene regulation, as theorized over 40 years ago [ 1 , 8 , 9 ]. (royalsocietypublishing.org)
- Mutations in this gene result in incontinentia pigmenti, hypohidrotic ectodermal dysplasia, and several other types of immunodeficiencies. (genecards.org)
- Bacterial regulatory RNAs are proving to be remarkable factors in both cell physiology and bacterial pathogenesis and these RNAs have opened a new world in molecular biology. (els.net)
- Much of our current knowledge about bacterial biology and pathogenesis has been attained through the use of deletion mutants in concert with animal models. (asm.org)
- Transition metals, including iron, zinc, manganese, nickel, and copper, participate in many structural and catalytic functions that are necessary to support the pathogenesis of bacterial infections. (asm.org)
- The larger ENase is encoded by three genes (R, M and S) and has 5 subunits (R 2 M 2 S). We have now determined for the first time the molecular structures of a Type I RM enzyme, using electron microscopy (EM), small-angle scattering (neutron and X-ray), and molecular modeling (in collaboration with colleagues in Leeds, Edinburgh and Warsaw). (port.ac.uk)
- Following biophysical analysis of the relevant DNA-protein complexes underpinning the switch, we have determined the 3D molecular structure of each of the complexes by X-ray crystallography, thereby elucidating the mechanism of R-M gene regulation and paving the way to understanding the principles of differential DNA sequence recognition. (port.ac.uk)
- sRNAs can play a major role in bacterial pathogenicity and influence eukaryotic host molecular functions such as levels of host cell microRNA and long noncoding RNA. (els.net)
- The long term goals of the work in this project are to understand the molecular basis for this regulation by environmental stimuli so as to facilitate the development of better strategies to prevent and cure bacterial diseases. (dartmouth.edu)
- Among these bacterial pathogens, Listeria monocytogenes is a Gram positive microorganism that has been used as a paradigm for intracellular parasitism in the characterization of cellular immune responses, and which has played instrumental roles in the discovery of molecular pathways controlling cytoskeletal and membrane trafficking dynamics. (jove.com)
- Dr. Amendt's research focuses on studying the expression and regulation of transcription factor genes and signaling processes involved in craniofacial/tooth development, the molecular basis of selected human genetic disorders, and the role of stem cells and microRNAs in regulating craniofacial and regenerative medicine. (uiowa.edu)
- Molecular basis of bacterial outer membrane permeability revisited. (asmscience.org)
- We also have a new collaboration that seeks to improve upon methods for predicting specificity in protein-DNA interactions based on molecular modeling, combining their expertise in thermodynamic and structural modeling with our extensive models of TF binding specificity. (grantome.com)
- CRISPR/Cas9 technology has revolutionized the fields of molecular biology and bioengineering, as it has facilitated the development of a simple and scalable means of making targeted genetic edits. (addgene.org)
- Genes for carbon metabolism and the ToxA virulence factor in Pseudomonas aeruginosa are regulated through molecular interactions of PtxR and PtxS. (nih.gov)
- Effect of Hfq on RprA-rpoS mRNA pairing: Hfq-RNA binding and the influence of the 5' rpoS mRNA leader region. (gatech.edu)
- fis mRNA levels closely resemble the protein expression pattern, suggesting that regulation occurs largely at the transcriptional level. (wikipedia.org)
- Previous studies revealed the mRNA expression profiles of macrophages infected by Brucella based on microarray [ 10 , 11 ]. (ijbs.com)
- MiRNAs regulate target genes expression by directly binding to complementary sites within the 3′ untranslated region (UTR) to either block or enhance translation or increase degradation of mRNA [ 14 ]. (ijbs.com)
- Regulation is mediated by co-transcription, the lacZYA genes being transcribed in a single mRNA. (springer.com)
- These transcripts, referred to as sRNAs, primarily act at the level of translation where they bind messenger ribonucleic acids (mRNAs) and inhibit or activate a target mRNA. (els.net)
- RBS is the ribosome‐binding site on the mRNA. (els.net)
- sRNAs can also bind to the coding region of the target mRNA and induce cleavage by RNase E (Pfeiffer et al . (els.net)
- When the sRNA is transcribed, it can bind to the 5′ end of the mRNA and produce a conformational change, resulting in the exposure of the RBS. (els.net)
- MicF RNA binds upstream in the 5′ UTR of yahO mRNA (green), disrupts a protective stem loop structure and induces degradation of the message. (els.net)
- b) The binding of DsrA RNA to the upstream sequence of rpoS mRNA exposes the RBS (positions −8 to −12) and creates new RNase III cleavage sites. (els.net)
- LhrA controls the translation and degradation of the lmo0850 mRNA by an antisense mechanism, and it depends on the RNA chaperone Hfq for efficient binding to its target. (jove.com)
- We have focused our RNA regulatory research to metabolite-sensing mRNAs, given the new and unexpected role for non-coding RNA as a riboswitch, and because structural-energetics information will be critical for defining allosteric mRNA transitions associated with the modulation of gene expression levels and metabolic homeostasis. (mskcc.org)
- During initiation , the ribosome is assembled at the initiation codon in the mRNA with a methionyl initiator tRNA bound in the peptidyl (P) site. (hindawi.com)
- GBP2 expression is absent in Stat1 −/− fibroblasts, whereas Irf1 −/− cells still show residual expression of GBP2 mRNA after treatment with IFN-γ ( 36 ). (asm.org)
- We report that in contrast to other NK cell ligands, endoplasmic reticulum (ER) stress upregulates B7H6 mRNA levels and surface expression. (weizmann.ac.il)
- Additionally, Hfq preferentially binds 5' to sRNA-target sites in mRNAs, and 3' to seed sequences in sRNAs, reflecting a simple logic in how Hfq facilitates sRNA-mRNA interactions. (medworm.com)
- How much muscle growth can you side effects of nonprescription and unsupervised the receptor in target tissue and formation of hormone-receptor complex, AAS translocate to binding sites on chromatin, promoting gene transcription and subsequent synthesis of mRNA. (gomiso.com)
- This checkpoint in E. coli O157:H7 translocon expression is controlled by a posttranscriptional mechanism acting on LEE4 - espADB mRNA. (asm.org)
- mRNA expression is well characterized during arrest, recovery, and normal L1 development, providing a metazoan model for nutritional control of gene expression. (genetics.org)
- CsrA binding to the 5′ segments of mRNA targets affects their translation, RNA stability, and/or transcript elongation. (asm.org)
- One is designed to express a DNA-binding protein-of-interest as a fusion construct with a subunit of RNA polymerase (bait). (wikipedia.org)
- Binds 2 calcium ions per subunit. (uniprot.org)
- The type I IFN IFN-α and IFN-β initiate Irf 7 transcription by activating the ISGF3 complex, a tyrosine-phosphorylated STAT1-STAT2 heterodimer in combination with IRF9, which serves as a DNA-binding subunit. (asm.org)
- In addition to facilitating inter-subunit disulfide bond formation, the movement of the α-helix 5 also results in a repositioning of α6. (proteopedia.org)
- Ihara K, Watanabe S, Sugimura K, Katagiri I, Mukohata Y. Identification of proteolipid from an extremely halophilic archaeon Halobacterium salinarum as an N,N'-dicyclohexyl-carbodiimide binding subunit of ATP synthase. (labome.org)
- This mechanism depends on the stimulus dependent release of ribosomal protein L13a from the large ribosomal subunit and formation of an multi-protein RNA-binding complex. (csuohio.edu)
- IKBKG (Inhibitor Of Nuclear Factor Kappa B Kinase Regulatory Subunit Gamma) is a Protein Coding gene. (genecards.org)
- Small non-coding RNAs (sRNAs) that act as regulators of gene expression have been identified in all kingdoms of life, including microRNA (miRNA) and small interfering RNA (siRNA) in eukaryotic cells. (prolekare.cz)
- Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution. (embl-heidelberg.de)
- Response regulators of bacterial sensory transduction systems generally consist of receiver module domains covalently linked to effector domains. (embl-heidelberg.de)
- We have applied CLIP-seq to chart the target landscape of two major bacterial post-transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. (medworm.com)
- The heterogeneity in EspA filamentation could arise from phase-variable expression of regulators that control this posttranscriptional mechanism. (asm.org)
- Activity ofthe agr system is influenced by other gene regulators and may be regulated by cell density. (ukessays.com)
- Application of our adaptor should produce large collections of transcriptional regulators whose inherent composability can facilitate the predictable engineering of complex biological circuits in microorganisms," Arkin says. (berkeley.edu)
- From left, Adam Arkin, Chang Liu and Lei Qi have developed an adaptor that converts bacterial regulators of translation into regulators of transcription, making genetic engineering of microbial components substantially easier and more predictable. (berkeley.edu)
- Current research is directed at understanding the interaction of the RNA-binding protein Hfq with short regulatory RNAs and its specific RNA target sites. (gatech.edu)
- Our analysis profiles the structure of more than 1,750 RNAs at 25 °C, 37 °C, and 42 °C. Average mRNAs tend to be unstructured around the ribosome binding site. (pnas.org)
- RNA structures play a pivotal role in the function of noncoding RNAs (ncRNAs) comprised of rRNAs, tRNAs, and small regulatory RNAs (sRNAs) and in the expression of protein-coding mRNAs. (pnas.org)
- It can stabilize small regulatory RNAs (sRNAs) and facilitate annealing between sRNAs and their target mRNAs. (frontiersin.org)
- Classically small RNAs are known to play a key role in triggering gene silencing by DNA methylation. (blogspot.com)
- We used ABI SOLiD sequencing to further explore the diversity and expression of small RNAs in T. pseudonana . (blogspot.com)
- Transcripts that deviate from this general principle are very good candidates as translational repressor elements, and we identified 16 RNA thermometers able to control gene expression in a temperature-dependent manner. (pnas.org)
- There is increasing elucidation of posttranscriptional and translational regulation. (perdidanautopia.com)
- As selenoprotein transcript levels and localization did not change in siRNA-treated cells, our results suggest that nucleolin selectively enhances the expression of a subset of selenoproteins at the translational level. (pubmedcentralcanada.ca)
- Rhodobacter capsulatus photosynthesis gene was isolated by creating in-frame fusions in a lacZ transcriptional/translational vector, and selecting for those that directed oxygen-regulated levels of β-galactosidase in R. capsulatus. (ubc.ca)
- The paper is titled "An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. (berkeley.edu)
- kel N Abstract The current paradigm in the field of gene regulation postulates that regulatory information for generating gene expression is organized into modules (enhancers), each containing the information for driving gene expression in a single spatiotemporal context. (medworm.com)
- 2015. Urinary microrna expression predicts delayed graft function in kidney transplantation [Abstract] . (cardiff.ac.uk)
- The C protein can act as either an activator or repressor, in a concentration dependent manner, thus controlling the timing of expression of these genes via an elegant genetic switch. (port.ac.uk)
- Effectors can bind to repressor and induce a conformational change. (perdidanautopia.com)
- The regulation of Bvg repressed genes is mediated by the product of a 624-bp open reading frame downstream of bvgA, the so-called Bvg-activated repressor protein, BvgR. (wikipedia.org)
- Furthermore, IsrM is found to be differentially expressed in vivo , with higher expression in the ileum than in the spleen. (prolekare.cz)
- The tcpA gene was induced biphasically in vivo . (biomedcentral.com)
- used a modification of the recombinase-based in vivo expression technology (RIVET). (biomedcentral.com)
- Although this is a very powerful method for monitoring patterns of gene expression in vivo , it is critical that the background expression of the gene under study is minimal, in order to allow construction of the recombinant strain. (biomedcentral.com)
- The improved models will be compared to in vivo location analysis for TFs to better assess which binding sites are indirect or require cooperative binding with other factors. (grantome.com)
- Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP-seq) have begun to revolutionize the transcriptome-wide mapping of eukaryotic RNA-binding protein target sites. (medworm.com)
- Analysis of protein-protein interactions by affinity precipitation revealed that VirB1 bound to VirB9 and VirB11. (nih.gov)
- Using UV crosslinking, we identified a 110 kDa protein, which binds with high affinity to SECIS elements from a subset of selenoprotein mRNAs. (pubmedcentralcanada.ca)
- There was a good correlation between the affinity of nucleolin for a SECIS and its effect on selenoprotein expression. (pubmedcentralcanada.ca)
- The binding affinities were generally low, suggesting that additional modifications may be needed for higher-affinity target binding. (aacrjournals.org)
- CsrA bound with high affinity and specificity to ftnB, bfr , and dps mRNAs and inhibited their translation, while it modestly activated ftnA expression. (asm.org)
- In particular, a total of 25 target genes are involved in regulating apoptosis and autophagy, indicating that these miRNAs may play important regulatory roles in the Brucella -host interactions. (ijbs.com)
- Furthermore, the interactions of miR-1981 and its target genes, Bcl-2 and Bid, were validated by luciferase assay. (ijbs.com)
- The binding interactions are small in length, involving less than ∼20 bp and contain imperfect pairings. (els.net)
- This transition generates an open ligand-binding pocket with L-glutamine selectivity enforced by Mg 2+ -mediated intermolecular interactions. (mskcc.org)
- We will develop models for TFs that allow for higher-order interactions as well as for TFs that can bind in alternative modes and require multiple, independent models to represent them. (grantome.com)
- A new experimental method will be employed to more comprehensively assess the non-independent interactions between protein residues and binding site base-pairs, which should lead to further improvements in recognition modeling. (grantome.com)
- By detecting binding sites at single-nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during their interactions with hundreds of cellular transcripts. (medworm.com)
- 2016. Tumour necrosis factor-stimulated gene (TSG)-6-mediated interactions with the inter-alpha-inhibitor heavy chain 5 facilitate TGF beta1-dependent fibroblast to myofibroblast differentiation. . (cardiff.ac.uk)
- Hfq is a bacterial RNA-binding protein that facilitates the hybridization of sRNAs to their target regions on specific mRNAs. (gatech.edu)
- sRNAs can control gene expression at the level of translation or transcription. (els.net)
- We demonstrate this application, identifying 39 new sRNAs and studying their expression during S. aureus growth in human serum. (asm.org)
- This small, basic, DNA-bending protein has recently been shown to function in many other reactions including phage lambda site-specific recombination, transcriptional activation of rRNA and tRNA operons, repression of its own synthesis, and oriC-directed DNA replication. (wikipedia.org)
- Operons (clusters of co-regulated genes with related functions) are common features of bacterial genomes. (springer.com)
- Operons (clusters of co-regulated genes with related functions) are a well-known feature of prokaryotic genomes. (springer.com)
- Operons usually code for genes in the same functional pathway. (springer.com)
- However, there are also examples of operons that contain genes with no obvious functional relationship. (springer.com)
- The native gene cluster consists of 20 genes in seven operons and is encoded in 23.5 kb of DNA. (pnas.org)
- One of the keys to success in synthetic biology is the design and construction of customized genetic switches in microbes that can control the expression of both coding and non-coding RNA, act on operons (small groups of genes with related functions that are co-transcribed in a single strand of messenger RNA), and be tethered to higher-order regulatory functions (a property called composability). (berkeley.edu)
Control of gene expression4
- Some of them play a crucial role in the control of gene expression involved in a specific pathway. (mdpi.com)
- It has been postulated that epigenetic control of gene expression mediated by phase variation (epigenetic control of a single gene) or phasevarions (multiple genes regulated simultaneously) allows an essentially clonal population to adopt multiple distinct phenotypes 26 . (nature.com)
- Furthermore, we discuss advances in multiplexing different light sensors for achieving multichromatic control of gene expression and indicate developments that could facilitate the construction of efficient systems for light-regulated, multistate control of gene expression. (diva-portal.org)
- We are developing improved computational methods to extract the most important information from high-throughput experiments with the goal of enhancing our understanding and modeling of normal control of gene expression and its variation. (grantome.com)
- FlyFactorSurvey is a database of DNA binding specificities for Drosophila transcription factors (TFs) primarily determined using the bacterial one-hybrid system. (umassmed.edu)
- The contribution of tissue-specific and less tissue-specific transcription factors in activating or repressing CIC and CAC gene expression is discussed. (mdpi.com)
- Following activation, MAPKs induce the expression of IL-1- and TNF-α-responsive genes by phosphorylating a number of transcription factors, including Jun, Fos, and ATF family members. (asm.org)
- Here we show that the Irf7 gene is regulated by transcription factors STAT1 and IRF9 in response to the type II interferon (IFN) IFN-γ. (asm.org)
- Identifying the NA binding sites for all transcription factors (TFs) would greatly facilitate our understanding of regulatory networks and variations in gene expression, both normal and in disease states, that accompany genetic differences. (grantome.com)
- New high-throughput technologies are generating data about the DNA binding specificity of transcription factors at a greatly increased rate, but good computational methods are required to maximize the biological information extracted from those data. (grantome.com)
- Transcription factors control the expression of genes and are essential to the proper functioning of cells. (grantome.com)
- Muscle identity reflects the expression by each PC of a specific combination of identity Transcription Factors (iTFs). (sdbonline.org)
- Chromatin immunoprecipitation (ChIP) assays show that TSA treatment causes hyperacetylation of the wild-type integrated NF-κB-dependent reporter but not of a mutant version in which the NF-κB binding sites were mutated. (asm.org)
- A ) Electrophoretic mobility shift assays for the binding of PtxR to P kgu , P toxA , P gad and P ptxS and of PtxS to P toxA . (nih.gov)
- Hfq is highly conserved in bacterial phyla and has been shown to be a virulence factor in several bacterial species. (gatech.edu)
- Small regulatory RNA genes have been found in most bacterial species. (els.net)
- The AP-2 binding site in ascidians is actually GC-rich, suggesting it originated from another species. (eurekalert.org)
- Other collaborations, both within and outside the College of Dentistry, foster work to identify novel agents to specifically target cariogenic bacterial species, to coat dental materials with antimicrobials, to examine the microflora associated with localized aggressive periodontitis, and to investigate potential cariogenic properties associated with multiple bacterial species common to dental plaque. (uiowa.edu)
- We have established that a TPP-sensing riboswitch is present in the 3′ untranslated region (UTR) of the thiamin biosynthetic gene THIC of all plant species examined. (plantcell.org)
- The nucleotide sequences of the ligand binding core and supporting architectures of each aptamer class are highly conserved among different species as a result of their need to form a precise receptor for a specific ligand. (plantcell.org)
- By contrast, the expression platforms for riboswitches can vary considerably among species or even among multiple representatives of a riboswitch class in a single organism. (plantcell.org)
- Herein, we report that TPP riboswitches are present in a variety of plant species where they reside in the 3′ untranslated regions (UTRs) of THIC genes. (plantcell.org)
- Expression of genes in microorganisms is a highly regulated process and often involves complex genetic circuits controlling several phenotypes for their growth and survival under various environmental conditions. (asm.org)
- Finally, a controller consisting of genetic sensors and circuits regulates the conditions and dynamics of gene expression. (pnas.org)
- Identifying the DNA sequences that they bind to can lead to a better understanding of the normal regulatory network and how it can be altered in genetic variation and disease. (grantome.com)
- During induction of excision of this prophage with mitomycin C, intact hlyII gene is formed, thus providing to cells a genetic ability to synthesize the active toxin. (hindawi.com)
- A relatively small number of genes affecting starvation survival during L1 arrest are known, and many of them also affect adult lifespan, reflecting a common genetic basis ripe for exploration. (genetics.org)
- Cas9 is a DNA binding protein that can be directed to virtually any genetic locus when complexed with an appropriately designed small RNA, or guide RNA (gRNA). (addgene.org)
- Consider, for instance, the challenge of attempting to simultaneously and selectively induce both cutting and regulation of expression at different genetic loci within a single cell. (addgene.org)
- Structure-based genetic analysis have indicated that GalR homodimers interact directly and form a V-shaped stacked tetramer in repressosome, which is further stabilized by HU binding to an architecturally critical position on the DNA. (cancer.gov)
- Single molecule, real-time (SMRT) sequencing enables the detection of N6-methyladenine and N4-methylcytosine, two major types of DNA modifications comprising the bacterial methylome. (nature.com)
- Tight nucleotide binding occurs when domains of lobes I and II collapse around an ATP molecule. (thefreelibrary.com)
- As such, there has been increasing interest in generating conditional knockouts, based on the inducible expression of the target gene, to address these important questions ( 10 - 18 ). (asm.org)
- The inducible isoform, iNOS, is involved in immune response, binds calmodulin at physiologically relevant concentrations, and produces NO as an immune defense mechanism, as NO is a free radical with an unpaired electron. (wikipedia.org)
- Such genes are inducible. (perdidanautopia.com)
- We also report the regulation of an inducible catalase by a cascade of alternative sigma factors and an OxyR. (asm.org)
- NF-κB is an inducible transcription factor that plays a role in the expression of a variety of genes involved in immune and inflammatory responses and cell survival ( 3 , 13 ). (asm.org)
- At higher dxs expression levels, the intracellular concentration of 2-C-methyl-d-erythritol-2,4-cyclopyrophosphate (MEcPP) increased substantially in contrast to the other MEP pathway intermediates, which were linearly dependent on the abundance of Dxs. (sun.ac.za)
- Virtually every adaptation and developmental process originates at the level of gene regulation by transduction of extra- or intracellular signals. (cancer.gov)
- Small molecules generally activate or inhibit gene transcription as externally added substrates or as internally accumulated end-products, respectively, Rarely has a connection been made that links an intracellular intermediary metabolite as a signal of gene expression. (cancer.gov)
- At each site, Rns recognizes asymmetric nucleotide sequences in two regions of the major groove and binds along one face of the DNA helix. (asm.org)
- In this way, researches can gauge how strongly bait binds its prey (correlated with the level of expression of HIS3) and thus determines which nucleotide binding-sites have strong or weak preferences for a given base. (wikipedia.org)
- Among its related pathways are Antigen processing-Cross presentation and Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways . (genecards.org)
- Transformation of a bacterial host with two different plasmids is required. (wikipedia.org)
- Still no evidence exists for the association between phages and toxicity genes in the B. cereus group, although the presence in plasmids of genes for highly effective toxins, like that of anthrax, entomotoxic crystal protein, or emetic toxin, was well documented [ 4 - 6 , 11 , 15 ]. (hindawi.com)
- These include gene clusters for use of different carbon and nitrogen sources in yeasts, for production of antibiotics, toxins, and virulence determinants in filamentous fungi, for production of defense compounds in plants, and for innate and adaptive immunity in animals (the major histocompatibility locus). (springer.com)
- Unlike most other Bordetella toxins, tracheal cytotoxin is expressed constitutively, being a normal product of the breakdown of the bacterial cell wall. (wikipedia.org)
- The expression of many Bordetella adhesins and toxins is controlled by the two-component regulatory system BvgAS. (wikipedia.org)
- Activation of NF-κB is induced by a number of stimuli, including inflammatory cytokines, phorbol esters, bacterial toxins (such as lipopolysaccharides), viruses, UV light, and a variety of mitogens ( 13 ). (asm.org)
Regulate the expression1
- Our analysis shows that mRNAs tend to have a poorly structured ribosome binding site. (pnas.org)
- In summary, we present a dynamic bacterial RNA structurome and find that the expression of virulence-relevant functions in Y. pseudotuberculosis and reprogramming of its metabolism in response to temperature is associated with a restructuring of numerous mRNAs. (pnas.org)
- Metabolite-sensing mRNAs, or riboswitches, specifically interact with small ligands and direct expression of the genes involved in their metabolism. (mskcc.org)
- See commentary " Nucleolin binds to a subset of selenoprotein mRNAs and regulates their expression " in volume 39 on page 6844. (pubmedcentralcanada.ca)
- CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs. (medworm.com)
- Riboswitches are metabolite-sensing gene control elements typically located in the noncoding portions of mRNAs. (plantcell.org)
- Many of the virulence factors discussed below are encoded by genes located in the variable region. (ukessays.com)
- In any case, it would be interesting to see how host immunological activity 'feedback' on S. aureus regulation of its virulence factors, especially immune evasion molecules. (ukessays.com)
- We propose that H. pylori exploits down-regulation of Cav1 to subvert the host's immune response and to promote signalling of its virulence factors in host cells. (plos.org)
- Activators with significant homology to Rns have also been shown to control expression of ETEC pili unrelated to the CS1 group, including the Pap-related pili CS5 and 987P, which are dependent upon CsvR and FapR, respectively ( 7 , 23 ). (asm.org)
- Despite opposite effects on transcription, both are negative regulation Positive Regulation Positive regulation involves activators. (perdidanautopia.com)
- Dynamic, condition-dependent structural changes are able to modulate gene expression as shown for riboswitches and RNA thermometers. (pnas.org)
- Amino acid recognition and gene regulation by riboswitches. (mskcc.org)
- Besides protein receptors, there are bacterial riboswitches that selectively recognize cyclic dinucleotides. (mskcc.org)
- These findings highlight the importance of metabolite sensing by riboswitches in plants and further reveal the significance of alternative 3′ end processing as a mechanism of gene control in eukaryotes. (plantcell.org)
- In most instances, riboswitches can be divided into aptamer and expression platform regions that represent two functionally distinct but usually physically overlapping domains responsible for ligand binding and gene control, respectively. (plantcell.org)
- our philosophy is that by combining structural and biophysical analysis with biochemical and functional studies, we will be able to build up a complete picture of the mechanism of action of the relevant macromolecules and their role in fundamental biological processes, particularly those related to gene expression and DNA replication. (port.ac.uk)
- Moreover, the mechanism by which the expression of the CIC and CAC genes is modulated by coordinated responses to hormonal and nutritional changes and to epigenetics is highlighted. (mdpi.com)
- Analysis of the gene and protein expression showed that this system likely has an autoregulation mechanism to express the toxin and antitoxin in the most beneficial ratio for the cell to oppose stress. (frontiersin.org)
- The team has revealed the likely mechanism by which this gene ended up being expressed in a functionally important and tissue-specific way. (eurekalert.org)
- The mechanism may involve binding of HBD3 to HagB: HBD3 binds to immobilized HagB via surface plasmon spectroscopy and via ELISA and HBD3 inhibits binding of rHagB via surface plasmon spectroscopy and via ELISA and HBD3 inhibits binding of rHagB to cells via confocal microscopy and immunoelectron microscopy. (uiowa.edu)
- Using cellular and tissue-specific gene knockout mice model we discovered a unique translation regulation mechanism in the cells of innate immune systems. (csuohio.edu)
- The second mechanism of protection therefore is Effector Triggered Immunity (ETI) whereby plants monitor effectors or their targets with Resistance (R) gene products. (biomedcentral.com)
- constantly expressed in approximately all cells Regulated gene Levels of the gene product rise and fall with the needs of the organism. (perdidanautopia.com)
- Tsukuba, Japan - The transfer of genes from one organism to another is potentially a rapid way for evolution to occur and for complicated novel functions to emerge. (eurekalert.org)
- This finding suggested that the unusual cytoplasmic localization of the E. coli phosphatidylserine synthase plays a role in the regulation of the phospholipid polar headgroup composition in this organism. (labome.org)
- Importantly, the DNA-binding domains of the reduced dimers do not themselves undergo and structural rearrangements. (proteopedia.org)
- Arai H, Igarashi Y, Kodama T. The structural genes for nitric oxide reductase from Pseudomonas aeruginosa. (labome.org)
- Human bromodomains were classified based on structural and binding properties. (aacrjournals.org)
- Structural data may facilitate the rational design of selective bromodomain protein inhibitors. (aacrjournals.org)
- This comprehensive structural analysis allowed the identification of common BRD structural elements, such as a hydrophobic acetylated-lysine binding pocket formed by 4 α-helices, as well as family-specific motifs and surface properties. (aacrjournals.org)
- Site-directed mutagenesis and protein modeling studies revealed a structural basis for preferential LDC activity, suggesting an evolutionary implication of L/ODC in the QA-producing plants. (plantcell.org)
- We do not yet know how the expression of multiple catalases is regulated in any bacterium. (asm.org)
- We found that K locus polysaccharides facilitate resistance to multiple antibiotics, and, unexpectedly, that the bacterium responds to certain antibiotics at subinhibitory concentrations by increasing production of capsule, the principal K locus polysaccharide. (prolekare.cz)
- In a new discovery that increases our understanding of gene transfer, a research team centered at University of Tsukuba has studied a gene in marine invertebrates called ascidians originally came from a common bacterium. (eurekalert.org)
- We have developed a systematic approach to completely specify the genetics of a gene cluster by rebuilding it from the bottom up using only synthetic, well-characterized parts. (pnas.org)
- This work demonstrates the potential for synthetic biology tools to rewrite the genetics encoding complex biological functions to facilitate access, engineering, and transferability. (pnas.org)