Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.MicroRNAs: Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.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.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.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.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.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Gene Expression Regulation, Archaeal: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.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, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Gram-Negative Bacteria: Bacteria which lose crystal violet stain but are stained pink when treated by Gram's method.Gram-Positive Bacteria: Bacteria which retain the crystal violet stain when treated by Gram's method.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.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Bacteria, AnaerobicSignal 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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Gene 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.Bacterial Proteins: Proteins found in any species of bacterium.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.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.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.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.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.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.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.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.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.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.Cell Line, Tumor: A cell line derived from cultured tumor cells.Bacteria, AerobicAlternative 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.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.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.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.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Gene Expression Regulation, Leukemic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in leukemia.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, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.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.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.Genes, Bacterial: The functional hereditary units of BACTERIA.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.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.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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Bacterial Physiological Phenomena: Physiological processes and properties of BACTERIA.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.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.Anti-Bacterial Agents: Substances that reduce the growth or reproduction of BACTERIA.Gram-Negative Aerobic Bacteria: A large group of aerobic bacteria which show up as pink (negative) when treated by the gram-staining method. This is because the cell walls of gram-negative bacteria are low in peptidoglycan and thus have low affinity for violet stain and high affinity for the pink dye safranine.Culture Media: Any liquid or solid preparation made specifically for the growth, storage, or transport of microorganisms or other types of cells. The variety of media that exist allow for the culturing of specific microorganisms and cell types, such as differential media, selective media, test media, and defined media. Solid media consist of liquid media that have been solidified with an agent such as AGAR or GELATIN.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.Gram-Negative Anaerobic Bacteria: A large group of anaerobic bacteria which show up as pink (negative) when treated by the Gram-staining method.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Mice, Inbred C57BLSymbiosis: The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.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.Colony Count, Microbial: Enumeration by direct count of viable, isolated bacterial, archaeal, or fungal CELLS or SPORES capable of growth on solid CULTURE MEDIA. The method is used routinely by environmental microbiologists for quantifying organisms in AIR; FOOD; and WATER; by clinicians for measuring patients' microbial load; and in antimicrobial drug testing.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Anaerobiosis: The complete absence, or (loosely) the paucity, of gaseous or dissolved elemental oxygen in a given place or environment. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Sulfur-Reducing Bacteria: A group of gram-negative, anaerobic bacteria that is able to oxidize acetate completely to carbon dioxide using elemental sulfur as the electron acceptor.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.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.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)Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.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.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.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.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.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)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.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.Genes, rRNA: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.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)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.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.Bacterial Adhesion: Physicochemical property of fimbriated (FIMBRIAE, BACTERIAL) and non-fimbriated bacteria of attaching to cells, tissue, and nonbiological surfaces. It is a factor in bacterial colonization and pathogenicity.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Biodegradation, Environmental: Elimination of ENVIRONMENTAL POLLUTANTS; PESTICIDES and other waste using living organisms, usually involving intervention of environmental or sanitation engineers.Pseudomonas: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.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).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.Virulence: The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.Biofilms: Encrustations, formed from microbes (bacteria, algae, fungi, plankton, or protozoa) embedding in extracellular polymers, that adhere to surfaces such as teeth (DENTAL DEPOSITS); PROSTHESES AND IMPLANTS; and catheters. Biofilms are prevented from forming by treating surfaces with DENTIFRICES; DISINFECTANTS; ANTI-INFECTIVE AGENTS; and antifouling agents.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.Enterobacteriaceae: A family of gram-negative, facultatively anaerobic, rod-shaped bacteria that do not form endospores. Its organisms are distributed worldwide with some being saprophytes and others being plant and animal parasites. Many species are of considerable economic importance due to their pathogenic effects on agriculture and livestock.Aerobiosis: Life or metabolic reactions occurring in an environment containing oxygen.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.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.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.Pseudomonas aeruginosa: A species of gram-negative, aerobic, rod-shaped bacteria commonly isolated from clinical specimens (wound, burn, and urinary tract infections). It is also found widely distributed in soil and water. P. aeruginosa is a major agent of nosocomial infection.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Fermentation: Anaerobic degradation of GLUCOSE or other organic nutrients to gain energy in the form of ATP. End products vary depending on organisms, substrates, and enzymatic pathways. Common fermentation products include ETHANOL and LACTIC ACID.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.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.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).Fatty Acids: Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Kinetics: The rate dynamics in chemical or physical systems.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Bacteriological Techniques: Techniques used in studying bacteria.Lipopolysaccharides: Lipid-containing polysaccharides which are endotoxins and important group-specific antigens. They are often derived from the cell wall of gram-negative bacteria and induce immunoglobulin secretion. The lipopolysaccharide molecule consists of three parts: LIPID A, core polysaccharide, and O-specific chains (O ANTIGENS). When derived from Escherichia coli, lipopolysaccharides serve as polyclonal B-cell mitogens commonly used in laboratory immunology. (From Dorland, 28th ed)Oxidation-Reduction: A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Microbial Sensitivity Tests: Any tests that demonstrate the relative efficacy of different chemotherapeutic agents against specific microorganisms (i.e., bacteria, fungi, viruses).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.Recombinant Proteins: Proteins prepared by recombinant DNA technology.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.Staphylococcus aureus: Potentially pathogenic bacteria found in nasal membranes, skin, hair follicles, and perineum of warm-blooded animals. They may cause a wide range of infections and intoxications.Bacterial Infections: Infections by bacteria, general or unspecified.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.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Microbial Viability: Ability of a microbe to survive under given conditions. This can also be related to a colony's ability to replicate.Bacteroides: A genus of gram-negative, anaerobic, rod-shaped bacteria. Its organisms are normal inhabitants of the oral, respiratory, intestinal, and urogenital cavities of humans, animals, and insects. Some species may be pathogenic.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.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.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.Geologic Sediments: A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)Proteobacteria: A phylum of bacteria consisting of the purple bacteria and their relatives which form a branch of the eubacterial tree. This group of predominantly gram-negative bacteria is classified based on homology of equivalent nucleotide sequences of 16S ribosomal RNA or by hybridization of ribosomal RNA or DNA with 16S and 23S ribosomal RNA.Macrophages: The relatively long-lived phagocytic cell of mammalian tissues that are derived from blood MONOCYTES. Main types are PERITONEAL MACROPHAGES; ALVEOLAR MACROPHAGES; HISTIOCYTES; KUPFFER CELLS of the liver; and OSTEOCLASTS. They may further differentiate within chronic inflammatory lesions to EPITHELIOID CELLS or may fuse to form FOREIGN BODY GIANT CELLS or LANGHANS GIANT CELLS. (from The Dictionary of Cell Biology, Lackie and Dow, 3rd ed.)Host-Pathogen Interactions: The interactions between a host and a pathogen, usually resulting in disease.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.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.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.Rats, Sprague-Dawley: A strain of albino rat used widely for experimental purposes because of its calmness and ease of handling. It was developed by the Sprague-Dawley Animal Company.Intestines: The section of the alimentary canal from the STOMACH to the ANAL CANAL. It includes the LARGE INTESTINE and SMALL INTESTINE.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.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.Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.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.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Vibrio: A genus of VIBRIONACEAE, made up of short, slightly curved, motile, gram-negative rods. Various species produce cholera and other gastrointestinal disorders as well as abortion in sheep and cattle.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.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)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.Salmonella typhimurium: A serotype of Salmonella enterica that is a frequent agent of Salmonella gastroenteritis in humans. It also causes PARATYPHOID FEVER.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.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.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.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.Genes, Plant: The functional hereditary units of PLANTS.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.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.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.Streptococcus: A genus of gram-positive, coccoid bacteria whose organisms occur in pairs or chains. No endospores are produced. Many species exist as commensals or parasites on man or animals with some being highly pathogenic. A few species are saprophytes and occur in the natural environment.Plant Roots: The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990)Cytokines: Non-antibody proteins secreted by inflammatory leukocytes and some non-leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.Betaproteobacteria: A class in the phylum PROTEOBACTERIA comprised of chemoheterotrophs and chemoautotrophs which derive nutrients from decomposition of organic material.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.Mice, Inbred BALB CProtein 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.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.Oxidoreductases: The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)Cytophaga: A genus of gram-negative gliding bacteria found in SOIL; HUMUS; and FRESHWATER and marine habitats.Fungi: A kingdom of eukaryotic, heterotrophic organisms that live parasitically as saprobes, including MUSHROOMS; YEASTS; smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi, commonly known as molds, refer to those that grow as multicellular colonies.Bacillus: A genus of BACILLACEAE that are spore-forming, rod-shaped cells. Most species are saprophytic soil forms with only a few species being pathogenic.Virulence Factors: Those components of an organism that determine its capacity to cause disease but are not required for its viability per se. Two classes have been characterized: TOXINS, BIOLOGICAL and surface adhesion molecules that effect the ability of the microorganism to invade and colonize a host. (From Davis et al., Microbiology, 4th ed. p486)Tumor Necrosis Factor-alpha: Serum glycoprotein produced by activated MACROPHAGES and other mammalian MONONUCLEAR LEUKOCYTES. It has necrotizing activity against tumor cell lines and increases ability to reject tumor transplants. Also known as TNF-alpha, it is only 30% homologous to TNF-beta (LYMPHOTOXIN), but they share TNF RECEPTORS.Archaea: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.Carbohydrate Metabolism: Cellular processes in biosynthesis (anabolism) and degradation (catabolism) of CARBOHYDRATES.Metabolic Networks and Pathways: Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.

*Lactonase

... molecules commonly used as communication signals between bacterial cells in a population to regulate certain gene expression ... This type of gene regulation is known as quorum sensing. Lactonase hydrolyzes the ester bond of the homoserine lactone ring of ... It is still unclear the ecological effects of lactonase but it has been proposed that since bacteria mostly coexist with other ... A dinuclear zinc binding site is conserved in all known lactonases and essential for enzyme activity and protein folding. Zn1 ...

*CrfA RNA

England JC, Perchuk BS, Laub MT, Gober JW (February 2010). "Global regulation of gene expression and cell differentiation in ... Seven affacted gene products were TonB-dependent receptors, outer membrane proteins which facilitate the uptake of external ... Massé E, Majdalani N, Gottesman S (April 2003). "Regulatory roles for small RNAs in bacteria". Curr. Opin. Microbiol. 6 (2): ... Majdalani N, Vanderpool CK, Gottesman S (2005). "Bacterial small RNA regulators". Crit. Rev. Biochem. Mol. Biol. 40 (2): 93-113 ...

*Epigenetics

Morris KL (2008). "Epigenetic Regulation of Gene Expression". RNA and the Regulation of Gene Expression: A Hidden Layer of ... However, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions ... Casadesús J, Low D (September 2006). "Epigenetic gene regulation in the bacterial world". Microbiol. Mol. Biol. Rev. 70 (3): ... Gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA. These ...

*Hemolysin

... s may also mediate bacterial escape from host cells. The regulation of gene expression of hemolysins (such as ... As mentioned above, most hemolysins are protein compounds, but others are lipids biosurfactants. Many bacteria produce ... The regulation of the production of hemolysin in S.aureus(expression of hemolysin) is now possible due to in-vitro mutations ... TDH induces Ca2+ influx from an extracellular environment accompanied by protein kinase C phosphorylation. Activated protein ...

*Xiaoliang Sunney Xie

"Probing Gene Expression in Live Cells, One Protein Molecule at a Time," Science 311, 1600-1603 (2006). Cai, Long; Friedman, Nir ... Gene Expression and Regulation Chong, Shasha; Chen, Chongyi; Ge, Hao; Xie X. Sunney. "Mechanism of Transcriptional Bursting in ... Bacteria," Cell 158, 314-326 (2014). Taniguchi, Yuichi; Choi, Paul J.; Li, Gene-Wei; Chen, Huiyi; Babu, Mohan; Hearn, Jeremy; ... "A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell," Science 322, 442-446 (2008). Elf, Johan; ...

*Αr9 RNA

Expression of Smr9C in free-living bacteria was found to be growth-dependent, being the gene strongly down-regulated when ... Recent co-inmuno precipitation experiments corroborate that Smr9C, does bind the bacterial protein Hfq for efficient target ... whereas no expression was detected in endosymbiotic bacteria. Recent deep sequencing data further revealed up-regulation of ... Parallel studies assessed Smr9C expression in S. meliloti 1021 under different biological conditions; i.e. bacterial growth in ...

*KaiA

... is a gene in the "kaiABC" gene cluster that plays a crucial role in the regulation of bacterial circadian rhythms, such as ... For these bacteria, regulation of kaiA expression is critical for circadian rhythm, which determines the twenty-four-hour ... Kai proteins don't regulate circadian regulated genes, but do regulate genome wide gene expression in the cyanobacterial TTO ... The kaiA gene makes KaiA protein that enhances phosphorylation of KaiC while KaiB inhibits activity of KaiA. Circadian rhythms ...

*Leucine-responsive regulatory protein

In bacteria, it is encoded by the lrp gene. Lrp alternatively activates and represses the expression of acetolactate synthase's ... Lrp, in E. coli, along with DAM plays a role in the regulation of the fim operon, a group of genes needed for successful ... Dorman, C. J.; Corcoran, C. P. (2008). "Bacterial DNA topology and infectious disease". Nucleic Acids Research. 37 (3): 672-678 ... Leucine responsive protein, or Lrp, is a global regulator protein, meaning that it regulates the biosynthesis of leucine, as ...

*Richard Lounsbery Award

... on the regulation of gene expression at both the transcriptional level (structures of the nuclear receptors to retinoic acid ... 2013 Karl Deisseroth, for pioneering the technology called optogenetics in which insertion of a single bacterial protein into a ... 2011 Bonnie L. Bassler, for her pioneering discoveries of the universal use of chemical communication among bacteria and the ... for her fundamental insights into structure and function of cytoskeletal proteins and the relation of these proteins to human ...

*Rhodobacter sphaeroides

"Generalized approach to the regulation and integration of gene expression". Mol Microbiol. 39 (5): 1116-23. doi:10.1111/j.1365- ... Mackenzie, C; Simmons, AE; Kaplan, S. "Multiple chromosomes in bacteria. The yin and yang of trp gene localization in ... Mank, Nils N.; Berghoff, Bork A.; Hermanns, Yannick N.; Klug, Gabriele (2012-10-02). "Regulation of bacterial photosynthesis ... Moreover, many of the open reading frames (ORFs) on CII seem to code for proteins of unknown function. When genes of unknown ...

*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 ... Fis as a critical regulator of capsule expression. Fis is also involved in the regulation of a range of genes in bacterial ... Besides modulating chromatin architecture, it is known to influence numerous promoters of E. coli and several other bacteria. ... The fis gene is cotranscribed with the upstream dusB gene encoding a tRNA-modifying enzyme. DusB protein levels are very low ...

*GalP (protein)

There is also a study on the involvement of NagC in regulation, a protein from the nagC gene which is responsible for N- ... expression, and regulation of GalP along with examples of several of its homologues. Galactose Permease (GalP), is a member of ... 6. Hase, C. C., Fedorova, N. D., Galperin, M. Y., and Dibrov, P. A. (2001). Sodium ion cycle in bacterial pathogens: evidence ... coli and in other bacteria. E. coli has a well-studied GltS glutamate/Na+ symporter that aids in the uptake of glutamate into ...

*Anti-sigma factors

In the regulation of gene expression in prokaryotes, anti-sigma factors bind to sigma factors and inhibit transcriptional ... Sigma Factor is an important protein which starts the transcription by binding with RNAP, anti-sigma factor is a protein which ... Anti-sigma factors have been found in a number of bacteria, including Escherichia coli and Salmonella, and in the T4 ... Paget, Mark S. (2015-06-26). "Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution". ...

*SAM-V riboswitch

Winkler WC, Breaker RR (2005). "Regulation of bacterial gene expression by riboswitches". Annu. Rev. Microbiol. 59: 487-517. ... This regulation controls parts of the sulfur metabolism of marine bacteria. SAM-I riboswitch SAM-II riboswitch SAM-III ... March 2007). "The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families". PLoS Biol. 5 (3): ... October 2004). "A glycine-dependent riboswitch that uses cooperative binding to control gene expression". Science. 306 (5694): ...

*FMN riboswitch

Winkler, WC; Cohen-Chalamish S; Breaker RR (2002). "An mRNA structure that controls gene expression by binding FMN". Proc Natl ... "A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes". Trends Genet. 15 (11): ... "Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation". ... This element is a metabolite-dependent riboswitch that directly binds FMN in the absence of proteins. In Bacillus subtilis, the ...

*Nif gene

In most bacteria, regulation of nif genes transcription is done by the nitrogen sensitive NifA protein. When there isn't enough ... The nif genes can be found on bacterial chromosomes, but in symbiotic bacteria they are often found on plasmids or symbiosis ... R. capsulatus regulates nif gene expression through nifA in the same manner described before, but it uses a different nifA ... Examples of nif gene structure and regulation in different diazotrophs include: Klebsiella pneumoniae-a free-living anaerobic ...

*Cyclic di-GMP

... and cyclic di-GMP-II riboswitch regulate gene expression in response to cyclic di-GMP concentrations in a variety of bacteria, ... Cyclic di-AMP Tamayo R, Pratt JT, Camilli A (2007). "Roles of cyclic diguanylate in the regulation of bacterial pathogenesis". ... Degradation of cyclic di-GMP is effected by proteins with phosphodiesterase activity. These proteins have either an EAL or an ... Cyclic di-GMP is synthesized by proteins with diguanylate cyclase activity. These proteins typically have a characteristic ...

*Carl Woese

... a locus of intense activity on the molecular biology of gene expression and gene regulation. While in Paris, he met Sol ... Archaea Bacterial phyla, the major lineages of Bacteria George E. Fox Karl Stetter Norman R. Pace Otto Kandler Phylogenetics ... This early translation apparatus would have produced a group of similar, yet functionally equivalent, proteins, rather than a ... Bacteria are the major organisms on this planet-in numbers, in total mass, in importance to the global balances. Thus, it is ...

*LONP1

... is also a DNA-binding protein that participates in mtDNA maintenance and gene expression regulation. LONP1 degrades ... Lon protease (LONP1) is a conserved serine peptidase identified from bacteria to eukaryotic cells. In mitochondrial matrix, a ... "A human mitochondrial ATP-dependent protease that is highly homologous to bacterial Lon protease". Proceedings of the National ... A similar protease expressed in E. coli regulates gene expression by targeting specific regulatory proteins for degradation. ...

*PreQ1 riboswitch

... regulation of genetic expression or transcription termination. Translation of protein in prokaryotes is initiated by binding of ... PreQ1 riboswitch activity in Tte bacteria can be measured by the levels of two proteins that are in the coding region of the ... Like any other riboswitch, the two most common types of gene regulation mediated by preQ1 riboswitch are through transcription ... Ligand binding to the transcriptional riboswitch in bacterial causes modification in the structure of riboswitch unit, which ...

*Listeria monocytogenes

This involves a bacterial protein "internalin"(InlA/InlB) which attaches to a protein on the intestinal cell membrane "cadherin ... SigB, an alternative sigma factor, up-regulates Vir genes in the intestines, whereas PrfA up-regulates gene expression when the ... Motility in the intracellular space is provided by actin assembly-inducing protein (ActA) which allows the bacteria to use the ... When this bacterium is present within a host organism, quorum sensing causes the up-regulation of several virulence genes. ...

*John Shine

... and was an important discovery towards understanding gene expression and regulation. Shine undertook post doctoral research at ... During the course of his studies he discovered the RNA sequence necessary for ribosome binding and the initiation of protein ... Shine, J.; Dalgarno, L. (6 March 1975). "Determinant of cistron specificity in bacterial ribosomes". Nature. 254 (5495): 34-38 ... going on to demonstrate that human hormone genes cloned in bacteria could be expressed in a biologically active form. He also ...

*N-Acyl homoserine lactone

Similar pathways occur in other luminescent bacteria. In Vibrio fischeri, AHL binds to the protein product of the LuxR gene and ... They signal changes in gene expression, such as switching between the flagella gene and the gene for pili for the development ... One example of the involvement of AHLs in quorum sensing is in the regulation of the bioluminescent protein luciferase in the ... In bacterial signalling, N-AHLs are produced within the bacterial cell and released into the environment. N-AHLs produced by ...

*Aureolysin

... can cleave a bacterial surface proteins, including clumping factor B, and secreted proteins, i.a. phenol-soluble ... Up-regulation of aureolysin during phagocytosis have also been observed. The aur gene has a high prevalence in the genome of ... a stress response modulator of Gram-positive bacteria). aur expression is highly expressed in post-exponential growth phase. A ... The numerous targets of bacterial proteases, adding the complexity of other virulence factors and their genetic regulation, ...

*Heat shock protein

Gata4 is an essential gene responsible for cardiac morphogenesis. It also regulates the gene expression of hspb7 and hspb12. ... "Characterization and regulation of cold-induced heat shock protein expression in mouse brown adipose tissue". The American ... Some bacterial heat shock proteins are upregulated via a mechanism involving RNA thermometers such as the FourU thermometer, ... from bacteria to humans. Heat-shock proteins are named according to their molecular weight. For example, Hsp60, Hsp70 and Hsp90 ...

*Metabolism

Cohen P (2000). "The regulation of protein function by multisite phosphorylation-a 25 year update". Trends Biochem Sci. 25 (12 ... powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on gene expression ... The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur bacteria and some protists. This ... Bacterial metabolic networks are a striking example of bow-tie organization, an architecture able to input a wide range of ...
Abstract Background Conventional differential gene expression analysis by methods such as students t-test, SAM, and Empirical Bayes often searches for statistically significant genes without considering the interactions among them. Network-based approaches provide a natural way to study these interactions and to investigate the rewiring interactions in disease versus control groups. In this paper, we apply weighted graphical LASSO (wgLASSO) algorithm to integrate a data-driven network model with prior biological knowledge (i.e., protein-protein interactions) for biological network inference. We propose a novel differentially weighted graphical LASSO (dwgLASSO) algorithm that builds group-specific networks and perform network-based differential gene expression analysis to select biomarker candidates by considering their topological differences between the groups. Results Through simulation, we showed that wgLASSO can achieve ...
Gene Expression Profiling Analysis of Bisphenol A-Induced Perturbation in Biological Processes in ER-Negative HEK293 Cells. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
The heterogeneity of prostate cancers extends within clinical states and across states. At the extreme ends of the clinical spectrum are prognostically favorable localized tumors with a low biological potential for metastasis and tumors with a high propensity for early dissemination that are invariably lethal. These clinical phenotypes are related in part to the intrinsic biology of tumor cells and are reflected in the pattern of expression of specific genes. Using comprehensive gene expression analysis of tumor samples representing the nonmetastatic and metastatic phenotypes, we identified genes that were consistently and strongly differentially expressed and represent common and valid biological differences underlying clinical heterogeneity.. Few prior studies have used high-throughput gene expression analysis to study prostate cancer metastases. One ...
Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21) or inv(16). The aim of this gene expression profiling study was to evaluate to what extent suboptimal samples with low leukemic blast load (range, 2-59%) and/or poor quality control criteria could also be correctly identified. Specific signatures were first defined so that all 71 acute promyelocytic leukemia, leukemia with t(8;21) or inv(16)-AML as well as cytogenetically normal acute myeloid leukemia samples with at least 60% blasts and good quality control criteria were correctly classified (training set). The classifiers were then evaluated for their ability to assign to the expected class 111 samples considered as suboptimal because of a low leukemic blast load (n = 101) and/or poor quality control criteria (n = 10) ...
Osteoarthritis (OA) is characterized by alterations to subchondral bone as well as articular cartilage. Changes to bone in OA have also been identified at sites distal to the affected joint, which include increased bone volume fraction and reduced bone mineralization. Altered bone remodelling has been proposed to underlie these bone changes in OA. To investigate the molecular basis for these changes, we performed microarray gene expression profiling of bone obtained at autopsy from individuals with no evidence of joint disease (control) and from individuals undergoing joint replacement surgery for either degenerative hip OA, or fractured neck of femur (osteoporosis [OP]). The OP sample set was included because an inverse association, with respect to bone density, has been observed between OA and the low bone density disease OP. Compugen human 19K-oligo microarray slides were used to compare the gene expression profiles of ...
Since their first use nearly fifteen years ago [1], microarray gene expression profiling experiments have become a ubiquitous tool in the study of disease. The vast number of gene transcripts assayed by modern microarrays (105-106) has driven forward our understanding of biological processes tremendously, elucidating the genes and regulatory mechanisms that drive specific phenotypes. However, the high-dimensional data produced in these experiments--often comprising many more variables than samples and subject to noise--also presents analytical challenges.. The analysis of gene expression data can be broadly grouped into two categories: the identification of differentially expressed genes (or gene-sets) between two or more known conditions, and the unsupervised identification (clustering) of samples or genes that exhibit similar profiles across the data set. ...
Thanks to their expertise in single-molecule imaging of RNAs, researchers from the group of Jeff Chao at the FMI helped to reveal the biological mechanism of a small molecule that restricts Ewings sarcoma cell growth. The study - published in Nature Chemical Biology - is further evidence that each step of the gene expression pathway may be druggable, and a great example of a Novartis-FMI collaboration.
TY - JOUR. T1 - Antagonistic regulation of type I collagen gene expression by interferon-γ and transforming growth factor-β. T2 - Integration at the level of p300/CBP transcriptional coactivators. AU - Ghosh, Asish K.. AU - Yuan, Weihua. AU - Mori, Yasuji. AU - Chen, Shu Jen. AU - Varga, John. PY - 2001/4/6. Y1 - 2001/4/6. N2 - Among the extracellular signals that modulate the synthesis of collagen, transforming growth factor-β (TGF-β) and interferon-γ (IFN-γ) are preeminent. These two cytokines exert antagonistic effects on fibroblasts, and play important roles in the physiologic regulation of extracellular matrix turnover. We have shown previously that in normal skin fibroblasts, TGF-β positively regulates α2(I) procollagen gene (COL1A2) promoter activity through the cellular Smad signal transduction pathway. In contrast, IFN-γ activates Stat1α, down-regulates COL1A2 transcription, and abrogates its stimulation induced by ...
Artificial transcription factors can be engineered to interact with specific DNA sequences to modulate endogenous gene expression within cells. A significant hurdle to implementation of this approach is the selection of the appropriate DNA sequence for targeting. We reasoned that a good target site should be located in chromatin, where it is accessible to DNA-binding proteins, and it should be, in the close vicinity of known transcriptional regulators of the gene. Here we have explored the efficacy of these criteria to guide our selection of potential regulators of gamma-globin expression. Several zinc finger-based transcriptional activators were designed to target the sites proximal to the -117-position of the gamma-globin promoter. This region is proximal to the binding sites of known and potential natural transcription factors. Design and study of three transcription factors identified the potent transcriptional ...
Gene expression is controlled by transcription factors that regulate the rates at which genes are expressed either by recruiting or inhibiting protein complexes that bind to the promoters or enhancers of target genes. Molecules that can specifically modulate these protein-DNA interfaces show promise as tools for understanding gene regulation pathways and may have application in human medicine. Hairpin pyrrole-imidazole polyamides are programmable oligomers that bind the DNA minor groove in a sequence-specific manner with affinities comparable to those of natural DNA-binding proteins. These cell-permeable small molecules have been shown to enter the nuclei of live cells, disrupt protein-DNA interactions, and downregulate endogenous gene expression. This thesis describes the use of polyamides to modulate gene expression in ...
RATIONALE: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is not well known how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart. OBJECTIVE: We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression. METHODS AND RESULTS: We profiled genome-wide transcriptional activity and a variety of epigenetic marks in the regulatory DNA elements using massive RNA-seq (n=12) and ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing; n=84) in human endothelial cells (CD31(+)CD144(+)), cardiac progenitor cells (Sca-1(+)), fibroblasts ...
Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation. The recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation). The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM) detections. At present the database contains ...
A great many aspects of the anatomy and physiology of large animals are constrained by the need to match oxygen supply to cellular metabolism and appear likely to involve the regulation of gene expression by oxygen. Some insight into possible underlying mechanisms has been provided by studies of erythropoietin, a haemopoietic growth factor which stimulates red cell production in response to hypoxia. Studies of hypoxia-inducible cis-acting sequences from the erythropoietin gene have led to the recognition of a widespread transcriptional response to hypoxia based on the activation of a DNA-binding complex termed hypoxia-inducible factor-1 (HIF-1). Perturbation of the transcriptional response by particular transition metal ions, iron chelators and certain redox-active agents have suggested a specific oxygen sensing mechanism, perhaps involving a haem protein in a flavoprotein/cytochrome system. In addition to erythropoietin, HIF-1-responsive ...
The flavonoids comprise a large class of low-molecular-weight plant metabolites ubiquitously distributed in food plants. These dietary antioxidants exert significant antitumor, antiallergic, and anti-inflammatory effects. The molecular mechanisms of their biological effects remain to be clearly understood. We investigated the anti-inflammatory potentials of a safe, common dietary flavonoid component, quercetin, for its ability to modulate the production and gene expression of the proinflammatory cytokine tumor necrosis factor alpha (TNF-α) by human peripheral blood mononuclear cells (PBMC). Our results showed that quercetin significantly inhibited TNF-α production and gene expression in a dose-dependent manner. Our results provide direct evidence of the anti-inflammatory effects of quercetin by PBMC, which are mediated by the inhibition of the proinflammatory cytokine TNF-α via modulation of NF-κβ1 and Iκβ. ...
In this study, we provide experimental evidence in favor of the hypothesis that PPARs are involved in the control of renin gene expression. We predicted a role for PPARs in the regulation of renin gene expression using a molecular approach. There was strong initial evidence supporting such a role.7,12 A functional DNA-binding site, similar to the consensus motif for PPARs, was detected in the conserved 5′-renin gene enhancer. The retinoic acid nuclear receptor RXRα, which is the typical interaction partner for PPARs, binds to the mouse renin gene enhancer. Lastly, vitamin A, which is the natural ligand of RXRs, was found to stimulate the transcription of the renin gene.. Renin gene expression is upregulated by cAMP in CaLu-6 cells through stabilization of renin mRNA, although transcriptional mechanisms are also involved.17,21 We provided ...
Long intergenic non-coding RNAs (lincRNAs) are defined as RNA transcripts that are longer than 200 nucleotides. By definition, these RNAs must not have open reading frames that encode proteins. Many of these transcripts are encoded by RNA polymerase II, are spliced, and are poly-adenylated. This final fact indicates that there is a trove of information about lincRNAs in databases such as the Gene Expression Omnibus (GEO), which is a repository for RNAseq and microarray data. Recent experiments indicate that there are upwards of 15,000 lincRNAs encoded by the human genome. The term "intergenic" refers to the identification of these transcripts from regions of the genome that do not contain protein-encoding genes. These regions coincide with what was once labeled as the "junk DNA" portions of our genomes, which, upon careful examination by whole genome RNA sequencing experiments, clearly encode RNA transcripts. LincRNAs also contain promoter- ...
TY - GEN. T1 - Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes. AU - Huang, Shao-Shan. AU - Fulton, Debra L.. AU - Arenillas, David J.. AU - Perco, Paul. AU - Ho Sui, Shannan J.. AU - Mortimer, James R.. AU - Wasserman, Wyeth W.. PY - 2006/12/1. Y1 - 2006/12/1. N2 - Transcription regulation is mediated by combinatorial interactions between diverse trans-acting proteins and arrays of cis-regulatory sequences. Revealing this complex interplay between transcription factors and binding sites remains a fundamental problem for understanding the flow of genetic information. The oPOSSUM analysis system facilitates the interpretation of gene expression data through the analysis of transcription factor binding sites shared by sets of co-expressed genes. The system is based on cross-species sequence comparisons for ...
Looking for online definition of differential gene expression in the Medical Dictionary? differential gene expression explanation free. What is differential gene expression? Meaning of differential gene expression medical term. What does differential gene expression mean?
TY - JOUR. T1 - Glutathione S-transferase copy number variation alters lung gene expression. AU - Butler, M. W.. AU - Hackett, N. R.. AU - Salit, J.. AU - Strulovici-Barel, Y.. AU - Omberg, L.. AU - Mezey, J.. AU - Crystal, Ronald. PY - 2011/7/1. Y1 - 2011/7/1. N2 - The glutathione S-transferase (GST) enzymes catalyse the conjugation of xenobiotics to glutathione. Based on reports that inherited copy number variations (CNVs) modulate some GST gene expression levels, and that the small airway epithelium (SAE) and alveolar macrophages (AMs) are involved early in the pathogenesis of smoking-induced lung disease, we asked: do germline CNVs modulate GST expression levels in SAE and AMs? Microarrays were used to survey GST gene expression and determine CNVs genotypes in SAE and AMs obtained by bronchoscopy from current smokers and nonsmokers. 26% of subjects were null for both ...
You need to be familiar with all of the different ways and levels at which cells can control gene expression, including gene expression, Chromatin packing, DNA methylation, Histone acetylation, control elements and transcription factors, alternative RNA splicing, mRNA degredation, translational control by regulatory proteins, proteasomic protein degradation, etc. (Damn, that s a lot of control ...
BACKGROUND: Although, systematic analysis of gene annotation is a powerful tool for interpreting gene expression data, it sometimes is blurred by incomplete gene annotation, missing expression response of key genes and secondary gene expression responses. These shortcomings may be partially circumvented by instead matching gene expression signatures to signatures of other experiments. FINDINGS: To facilitate this we present the Functional Association Response by Overlap (FARO) server, that match input signatures to a compendium of 242 gene expression signatures, extracted from more than 1700 Arabidopsis microarray experiments. CONCLUSIONS: Hereby we present a publicly available tool for robust characterization of Arabidopsis gene expression experiments which can point to ...
We previously demonstrated that neuregulin-1 (NRG-1) was neuroprotective in rats following ischemic stroke. Neuroprotection by NRG-1 was associated with the suppression of pro-inflammatory gene expression in brain tissues. Over-activation of brain microglia can induce pro-inflammatory gene expression by activation of transcriptional regulators following stroke. Here, we examined how NRG-1 transcriptionally regulates inflammatory gene expression by computational bioinformatics and in vitro using microglial cells. To identify transcriptional regulators involved in ischemia-induced inflammatory gene expression, rats were sacrificed 24 h after middle cerebral artery occlusion (MCAO) and NRG-1 treatment. Gene expression profiles of brain tissues following ischemia and NRG-1 treatment were examined by microarray technology. The Conserved ...
Large mammals are capable of thermoregulation shortly after birth due to the presence of brown adipose tissue (BAT). The majority of BAT disappears after birth and is replaced by white adipose tissue (WAT). We analyzed the postnatal transformation of adipose in sheep with a time course study of the perirenal adipose depot. We observed changes in tissue morphology, gene expression and metabolism within the first two weeks of postnatal life consistent with the expected transition from BAT to WAT. The transformation was characterized by massively decreased mitochondrial abundance and down-regulation of gene expression related to mitochondrial function and oxidative phosphorylation. Global gene expression profiling demonstrated that the time points grouped into three phases: a brown adipose phase, a transition phase and a white adipose phase. Between the brown adipose and the ...
The human tumor necrosis factor alpha (TNF-alpha) gene is one of the earliest genes transcribed after the stimulation of a B cell through its antigen receptor or via the CD-40 pathway. In both cases, induction of TNF-alpha gene transcription can be blocked by the immunosuppressants cyclosporin A and FK506, which suggested a role for the NFAT family of proteins in the regulation of the gene in B cells. Furthermore, in T cells, two molecules of NFATp bind to the TNF-alpha promoter element kappa 3 in association with ATF-2 and Jun proteins bound to an immediately adjacent cyclic AMP response element (CRE) site. Here, using the murine B-cell lymphoma cell line A20, we show that the TNF-alpha gene is regulated in a cell-type-specific manner. In A20 B cells, the TNF-alpha gene is not regulated by NFATp bound to the kappa 3 element. Instead, ATF-2 and Jun ...
TY - JOUR. T1 - Differentiation-induced gene expression in 3T3-L1 preadipocytes. T2 - CCAAT/enhancer binding protein interacts with and activates the promoters of two adipocyte-specific genes.. AU - Christy, R. J.. AU - Yang, V. W.. AU - Ntambi, J. M.. AU - Geiman, D. E.. AU - Landschulz, W. H.. AU - Friedman, A. D.. AU - Nakabeppu, Y.. AU - Kelly, T. J.. AU - Lane, M. D.. PY - 1989/9. Y1 - 1989/9. N2 - Previous studies have shown that differentiation of 3T3-L1 preadipocytes leads to the transcriptional activation of a group of adipose-specific genes. As an approach to defining the mechanism responsible for activating the expression of these genes, we investigated the binding of nuclear factors to the promoters of two differentiation-induced genes, the 422(aP2) and stearoyl-CoA desaturase 1 (SCD1) genes. DNase I footprinting and gel retardation analysis identified two ...
Biological tissues consist of various cell types that differentially contribute to physiological and pathophysiological processes. Determining and analyzing cell type-specific gene expression under diverse conditions is therefore a central aim of biomedical research. The present study compares gene expression profiles in whole tissues and isolated cell fractions purified from these tissues in patients with rheumatoid arthritis and osteoarthritis. The expression profiles of the whole tissues were compared to computationally reconstituted expression profiles that combine the expression profiles of the isolated cell fractions (macrophages, fibroblasts, and non-adherent cells) according to their relative mRNA proportions in the tissue. The mRNA proportions were determined by trimmed robust regression using only the most robustly-expressed genes (1/3 to 1/2 of all measured ...
RBF1 and E2F2 are components of the Drosophila, Rb, E2F, and Myb‐associated protein (dREAM) complex, a transcriptional silencing complex that represses many E2F target genes (Korenjak et al, 2004). To determine whether components of the Pum complex are targets for dREAM‐mediated repression, we analyzed datasets of published genome‐wide dREAM ChIP experiments from Drosophila Kc cells (Georlette et al, 2007) and found a strong ChIP enrichment for all of the dREAM components (E2F2, Myb, Mip120, Mip130, and Lin‐52) on the pumilio, nanos, and brat genes (Supplementary Fig S1B). To establish the functional significance of E2F2/RBF1 binding to these promoters, we assayed gene expression levels from Drosophila S2 cells and flies containing dsRNA or RNAi sequences targeting E2F/RBF family members. Depletion of RBF1 or E2F2 (but not E2F1) strongly induced the expression of nanos and modestly elevated the levels of pum and brat (Fig ...
Purpose: Retinopathy of prematurity (ROP) is a common blinding disease caused by the abnormal growth of blood vessels in the retina of premature babies with low birth weight and low gestation period. However, the mechanisms and factors contributing to the progression of ROP are still unknown. The present study aimed to identify gene(s) responsible for ROP progression by a global gene expression profiling.. Methods: From a cohort of 600 subjects comprising ROP babies (n=350) and controls (n=250), 15 ROP babies at any stage (gestational age [GA] ≤ 35 weeks and/or birth weight [BW] ≤ 1700 g) and premature babies with no ROP (n=6) (GA ≤ 35 weeks and/or BW ≤ 1700 g) and full term babies of the same age and no ROP (n=3), were screened. RNA was isolated from 0.5-1 ml of blood using RNeasy mini kit from Qiagen and the purity and integrity of RNA was checked with Bioanalyzer 2100 (Agilent). Global gene expression profiling was ...
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene ...
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene ...
ABSTRACT: One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene ...
Looking for online definition of forkhead transcription factor FOXL2 in the Medical Dictionary? forkhead transcription factor FOXL2 explanation free. What is forkhead transcription factor FOXL2? Meaning of forkhead transcription factor FOXL2 medical term. What does forkhead transcription factor FOXL2 mean?
Healthy adult cardiomyocytes derive ,60% of their energy from fatty acid oxidation. The nuclear receptor subfamily of peroxisome proliferator-activated receptors (PPAR) regulate cardiac metabolic gene expression by transcriptional activation. Reduced expression of PPARα and its co-activator, PPARγ coactivator-1α (PGC-1α), has been shown in human and animal studies of heart failure and ischemia, concomitant with reduced fatty acid use. PGC-1α regulates mitochondrial biogenesis and energy metabolic gene expression, thus elucidating the transcriptional regulation of PGC-1α gene expression is important for understanding metabolic gene expression in cardiac health and disease. We hypothesized that estrogen related receptor ERRα, which also plays a role in cardiac energy metabolism, regulates expression of PGC-1α ...
This project is an investigation of whether analysing subsets of time series gene expression data can give additional information about putatively co-regulated genes, compared to only using the whole time series. The original gene expression data set was partitioned into subsets and similarity was computed for both the whole timed series and subsets. Pearson correlation was used as similarity measure between gene expression profiles. The results indicate that analysing co-expression in subsets of gene expression data derives true-positive connections, with respect to co-regulation, that are not detected by only using the whole time series data. Unfortunately, with the actual data set, chosen similarity measure and partitioning of the data, randomly generated connections have the same amount of true-positives ...
Leukoregulin (LR), a T-cell-derived growth factor, modulates fibroblast functions in vitro [Mauviel, Rédini, Hartmann, Loyau & Pujol (1991) J. Cell Biol. 113, 1455-1462]. In the present study, incubation of human dermal fibroblasts with LR (0.1-2 units/ml) resulted in decreases in the mRNA steady-state levels for alpha 1(I), alpha 2(I) and alpha 1(III), but not alpha 2(V), collagen genes. LR also down-regulated alpha 2(I) collagen promoter activity in transient cell transfections of control cells as well as those incubated with transforming growth factor-beta, a potent up-regulator of collagen type I gene expression. Thus LR is a strong inhibitor of type I collagen gene expression, acting at the level of transcription. ...
Vibrio parahaemolyticus is an emerging world-wide human pathogen that is associated with food-borne gastroenteritis when raw or undercooked seafood is consumed. Expression of virulence factors in this organism is modulated by the phenomenon known as quorum sensing, which permits differential gene regulation at low versus high cell density. The master regulator of quorum sensing in V. parahaemolyticus is OpaR. OpaR not only controls virulence factor gene expression, but also the colony and cellular morphology associated with growth on a surface and biofilm formation. Whole transcriptome Next Generation sequencing (RNA-Seq) was utilized to determine the OpaR regulon by comparing strains BB22OP (opaR+, LM5312) and BB22TR (∆opaR1, LM5674). This work, using the published V. parahaemolyticus BB22OP genome sequence, confirms and expands upon a previous microarray analysis for these two strains that used an ...
Systems biology aims to understand the behavior of and interaction between various components of the living cell, such as genes, proteins, and metabolites. A large number of components are involved in these complex systems and the diversity of relationships between the components can be overwhelming, and there is therefore a need for analysis methods incorporating data integration. We here present a method for exploring gene regulatory mechanisms which integrates various types of data to assist the identification of important components in gene regulation mechanisms. By first analyzing gene expression data, a set of differentially expressed genes is selected. These genes are then further investigated by combining various types of biological information, such as clustering results, promoter sequences, binding sites, transcription factors and other previously ...
Gene expression network analysis and applications to immunology - We address the problem of using expression data and prior biological knowledge to identify differentially expressed pathways or groups of genes. Following an idea of Ideker et al. (2002), we construct a gene interaction network and search for high-scoring subnetworks. We make several improvements in terms of scoring functions and algorithms, resulting in higher speed and accuracy and easier biological interpretation. We also assign significance levels to our results, adjusted for multiple testing. Our methods are succesfully applied to three human microarray data sets, related to cancer and the immune system, retrieving several known and potential pathways. The method, denoted by the acronym GXNA (Gene eXpression Network Analysis) is implemented in software that is publicly available and can be used on virtually any microarray ...
Nashun B, Hill PW, Hajkova P, 2015, Reprogramming of cell fate: epigenetic memory and the erasure of memories past., EMBO Journal, Vol: 34, Pages: 1296-1308, ISSN: 0261-4189 Cell identity is a reflection of a cell type-specific gene expression profile, and consequently, cell type-specific transcription factor networks are considered to be at the heart of a given cellular phenotype. Although generally stable, cell identity can be reprogrammed in vitro by forced changes to the transcriptional network, the most dramatic example of which was shown by the induction of pluripotency in somatic cells by the ectopic expression of defined transcription factors alone. Although changes to cell fate can be achieved in this way, the efficiency of such conversion remains very low, in large part due to specific chromatin signatures constituting an epigenetic barrier to the transcription factor-mediated reprogramming ...
Biology Assignment Help, Describe how micrornas are able to influence gene expression, 1. Transcriptional analyses of eukaryotic cells reveal widespread production of RNA. Using specific examples describe how: a) microRNAs are able to influence gene expression. b) Long non-coding RNAs are able to influence epigenetics and nuc
Gestational exposure to environmental toxins such as nicotine may result in detectable gene expression changes in later life. To investigate the direct toxic effects of prenatal nicotine exposure on later brain development, we have used transcriptomic analysis of striatal samples to identify gene expression differences between adolescent Lister Hooded rats exposed to nicotine in utero and controls. Using an additional group of animals matched for the reduced food intake experienced in the nicotine group, we were also able to assess the impact of imposed food-restriction on gene expression profiles. We found little evidence for a role of gestational nicotine exposure on altered gene expression in the striatum of adolescent offspring at a significance level of p|0.01 and |log2 fold change |0.5|, although we cannot exclude the possibility of nicotine-induced changes in other ...
Gestational exposure to environmental toxins such as nicotine may result in detectable gene expression changes in later life. To investigate the direct toxic effects of prenatal nicotine exposure on later brain development, we have used transcriptomic analysis of striatal samples to identify gene expression differences between adolescent Lister Hooded rats exposed to nicotine in utero and controls. Using an additional group of animals matched for the reduced food intake experienced in the nicotine group, we were also able to assess the impact of imposed food-restriction on gene expression profiles. We found little evidence for a role of gestational nicotine exposure on altered gene expression in the striatum of adolescent offspring at a significance level of p,0.01 and ,log2 fold change ,0.5,, although we cannot exclude the possibility of nicotine-induced changes in other ...
Purpose To determine whether optic nerve head (ONH) astrocytes, a key cellular component of glaucomatous neuropathy, exhibit differential gene expression in primary cultures of astrocytes from normal African American (AA) donors compared to astrocytes from normal Caucasian American (CA) donors. Methods We used oligonucleotide Affymetrix microarray (HG U133A & HG U133A 2.0 chips) to compare gene expression levels in cultured ONH astrocytes from twelve CA and twelve AA normal age matched donor eyes. Chips were normalized with Robust Microarray Analysis (RMA) in R using Bioconductor. Significant differential gene expression levels were detected using mixed effects modeling and Statistical Analysis of Microarray (SAM). Functional analysis and Gene Ontology were used to classify differentially expressed genes. Differential gene expression was ...
Transcriptional coactivator for steroid receptors and nuclear receptors. Greatly increases the transcriptional activity of PPARG and thyroid hormone receptor on the uncoupling protein promoter. Can regulate key mitochondrial genes that contribute to the program of adaptive thermogenesis. Plays an essential role in metabolic reprogramming in response to dietary availability through coordination of the expression of a wide array of genes involved in glucose and fatty acid metabolism. Induces the expression of PERM1 in the skeletal muscle in an ESRRA-dependent manner. Also involved in the integration of the circadian rhythms and energy metabolism. Required for oscillatory expression of clock genes, such as ARNTL/BMAL1 and NR1D1, through the coactivation of RORA and RORC, and metabolic genes, such as PDK4 and PEPCK. Isoform 4 specifically activates the ...
This unit describes how to use the Transcription Element Search System (TESS). This Web site predicts transcription factor binding sites (TFBS) in DNA sequence using two different kinds of models of sites, strings and positional weight matrices. The binding of transcription factors to DNA is a major part of the control of gene expression. Transcription factors exhibit sequence-specific binding; they form stronger bonds to some DNA sequences than to others. Identification of a good binding site in the promoter for a gene suggests the possibility that the corresponding factor may play a role in the regulation of that gene. However, the sequences transcription factors recognize are typically short and allow for some amount of mismatch. Because of this, binding sites for a factor can typically be found at random every few hundred to a thousand base pairs. TESS has features to help sort through and evaluate the significance of ...
Transcription factors undergo very dynamic binding cycles on promoters (Hager et al., 2009; Michel, 2009). Slow promoters are thought to require more extensive chromatin modification for activation than fast promoters and hence require greater promoter residence time for activation. Consistent with this, increased dwell time on promoters is associated with more active transcription (Stavreva et al., 2004; Hager et al., 2009; Voss et al., 2011). Could differential requirements for transcription factor occupancy be used to differentially control distinct targets of a master regulatory transcription factor in response to a changing cellular environment? We have explored whether such a mechanism might coordinate cell cycle length and differentiation during nervous system development.. The proneural basic helix-loop-helix (bHLH) transcription factor neurogenin 2 (Ngn2) is required for generation of glutamatergic neurons in many regions of the central nervous system (Bertrand et al., 2002) and has ...
The role of DNA methylation in the control of mammalian gene expression has been the subject of intensive research in recent years, partly due to the critical role of CpG island methylation in the inactivation of tumour suppressor genes during the development of cancer. However, this research has also helped elucidate the role that DNA methylation plays in normal cells. At present, it is also clear that DNA methylation forms an important part of the normal cell-regulatory processes that govern gene transcription. Methylation, targeted at CpG islands, is an important part of the mechanisms that govern X-chromosome inactivation; it is also essential for the maintenance of imprinted genes and, at least in some cases, is critical in determining the cell-type-specific expression patterns of genes. Study of these examples will be important in identifying the mechanisms that control targeting of ...
Temporal- and dose-dependent changes in hepatic gene expression were examined in immature ovariectomized C57BL/6 mice gavaged with ethynyl estradiol (EE), an orally active estrogen. For temporal analysis, mice were gavaged every 24 h for 3 days with 100 µg/kg EE or vehicle and liver samples were collected at 2, 4, 8, 12, 24 and 72 h. Gene expression was monitored using custom cDNA microarrays containing 3067 genes/ESTs of which 393 exhibited a change at one or more time points. Functional gene annotation extracted from public databases associated temporal gene expression changes with growth and proliferation, cytoskeletal and extracellular matrix responses, microtubule-based processes, oxidative metabolism and stress, and lipid metabolism and transport. In the dose-response study, hepatic samples were collected 24 h following treatment with 0, 0.1, 1, 10, 100 or 250 µg/kg ...
Several methods have been developed for the comprehensive analysis of gene expression in complex biological systems. Generally these procedures assess either a portion of the cellular transcriptome or a portion of the cellular proteome. Each approach has distinct conceptual and methodological advantages and disadvantages. We have investigated the application of both methods to characterize the gene expression pathway mediated by androgens and the androgen receptor in prostate cancer cells. This pathway is of critical importance for the development and progression of prostate cancer. Of clinical importance, modulation of androgens remains the mainstay of treatment for patients with advanced disease. To facilitate global gene expression studies we have first sought to define the prostate transcriptome by assembling and annotating prostate-derived expressed sequence tags (ESTs). A total of ...
TY - JOUR. T1 - Exendin-4 as a stimulator of rat insulin I gene promoter activity via bZIP/CRE interactions sensitive to serine/threonine protein kinase inhibitor Ro 31-8220. AU - Chepurny, Oleg G.. AU - Hussain, Mehboob. AU - Holz, George G.. PY - 2002. Y1 - 2002. N2 - Signal transduction properties of exendin-4 (Ex-4) underlying its ability to stimulate rat insulin I gene promoter (RIP1) activity were assessed in the pancreatic β-cell line INS-1. Ex-4 acted via glucagon-like peptide-1 receptors to stimulate RIP1 in a glucose-dependent manner, as measured in cells transfected with a -410-bp RIP1-luciferase construct (RIP1-Luc). The action of Ex-4 was independent of cAMP and PKA because it was not blocked by cotransfection with dominant-negative Gαs, was unaffected by pretreatment with the membrane-permeant cAMP antagonist 8-Br-Rp-cAMPS, and remained apparent after treatment with PKA inhibitors H-89 or KT 5720. Similarly, cotransfection with a dominant-negative isoform of ...
TY - JOUR. T1 - Pituitary calcium channel modulation and regulation of prolactin gene expression. AU - Day, Richard N.. AU - Maurer, Richard. PY - 1990/5. Y1 - 1990/5. N2 - The dihydropyridine Ca2+ channel modulators (-) Bay K 8644 (R5417) and nimodipine were used to study the role of voltage-gated Ca2+ channels in the regulation of PRL gene transcription in GH3 cells. Fusion constructs containing 5′-flanking sequences from the rat PRL gene linked to either the bacterial chloramphenicol acetyltransferase (CAT) gene or the firefly luciferase gene were transiently expressed in GH3 cells and the transcriptional response to Ca2+ channel modulators was assessed. The Ca2+ channel agonist R5417 enhanced the transcription of a PRL-CAT fusion gene containing 2.5 kilobase (kb) pairs of the 5′-flanking sequence. This response was completely blocked by ...
TY - JOUR. T1 - Gene expression profile in cerebrum in the filial imprinting of domestic chicks (Gallus gallus domesticus). AU - Yamaguchi, Shinji. AU - Fujii-Taira, Ikuko. AU - Katagiri, Sachiko. AU - Izawa, Ei Ichi. AU - Fujimoto, Yasuyuki. AU - Takeuchi, Hideaki. AU - Takano, Tatsuya. AU - Matsushima, Toshiya. AU - Homma, Koichi J.. PY - 2008/6/15. Y1 - 2008/6/15. N2 - In newly hatched chicks, gene expression in the brain has previously been shown to be up-regulated following filial imprinting. By applying cDNA microarrays containing 13,007 expressed sequence tags, we examined the comprehensive gene expression profiling of the intermediate medial mesopallium in the chick cerebrum, which has been shown to play a key role in filial imprinting. We found 52 up-regulated genes and 6 down-regulated genes of at least 2.0-fold changes 3 h after the training of filial imprinting, ...
Initial physiological adjustments in response to drought stress lead to drastic changes in gene expression. The traditional approaches of assessing such drought-induced changes in gene expression involve measuring the differences in mRNA levels of one or few genes at a time. DNA expression microarray technology is a powerful tool that can monitor changes in expression of a large number of genes simultaneously. Expression microarrays also provide new insights into physiological and biochemical pathways of drought tolerance, and thus can lead to identification of novel candidate genes that can rapidly advance breeding for drought tolerance. This review describes the basic principles and potential applications of gene expression microarrays in understanding and improving drought tolerance in plants. A case ...
Mammalian genomic imprinting is an epigenetic gene regulatory mechanism that results in parental‐specific gene expression of a small number of genes in diploid somatic cells (Beechey et al., 2001; Reik and Walter, 2001; Li, 2002; Sleutels and Barlow, 2002). Several features of the imprinting mechanism have been identified; however, it is not yet clear whether imprinting is regulated by a unique process or whether it is part of the general epigenetic apparatus used to regulate mammalian gene expression. Clustering and coordinate regulation is one feature imprinted genes share with non‐imprinted genes (Engemann et al., 2000; Onyango et al., 2000), and it is now clear that many imprinted genes are functionally grouped such that imprinted expression of several ...
Gene expression is tightly regulated at the level of transcription through cooperation between cis-regulatory elements and trans-factors that bind to the regulatory elements. Together, these factors regulate the higher order chromatin structure which establishes domains that organize the genome and coordinate gene expression. However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood. The cystic fibrosis transmembrane conductance regulator (CFTR) gene provides a paradigm for investigating these mechanisms. CFTR occupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selective cis-regulatory elements for the locus. We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to the CFTR promoter by a looping mechanism to drive gene ...
Seasonal polyphenism demonstrates an organisms ability to respond to predictable environmental variation with alternative phenotypes, each presumably better suited to its respective environment. However, the molecular mechanisms linking environmental variation to alternative phenotypes via shifts in development remain relatively unknown. Here we investigate temporal gene expression variation in the seasonally polyphenic butterfly Bicyclus anynana. This species shows drastic changes in eyespot size depending on the temperature experienced during larval development. The wet season form (larvae reared over 24 degrees C) has large ventral wing eyespots while the dry season form (larvae reared under 19 degrees C) has much smaller eyespots. We compared the expression of three proteins, Notch, Engrailed, and Distal-less, in the future eyespot centers of the two forms to determine if eyespot size variation is associated with heterochronic shifts in ...
The DMP1 transcription factor binds to a single consensus site in the mouse ARF promoter to activate gene expression. Mutation of this binding site abolished DMP1-stimulated expression of a reporter gene driven by a DNA fragment containing residues −225 to +56 of the ARF promoter. Conversely, a DMP1 point mutant that no longer binds to DNA was transcriptionally inert. Ets1 and Ets2 transcription factors can also bind to short oligonucleotides containing the DMP1 consensus binding site, but five Ets family members were unable to activate reporter gene expression driven by the larger 281-bp ARF promoter fragment, suggesting that DMP1 may be the preferred regulator in this context. We have seen similar effects with the promoter of the aminopeptidase-N/CD13 gene on which DMP1-DNA complexes were significantly more stable than those containing Ets factors (32). In agreement with these findings, ...
TY - JOUR. T1 - Platelet-derived growth factor induces interleukin-1 receptor gene expression in Balb/c 3T3 fibroblasts. AU - Chiou, W. J.. AU - Bonin, P. D.. AU - Harris, P. K W. AU - Carter, D. B.. AU - Singh, J. P.. PY - 1989. Y1 - 1989. N2 - Our previous studies have demonstrated that platelet-derived growth factor (PDGF) modulated cellular responses to interleukin-1 (IL-1). In this communication, we show that PDGF regulates expression of IL-1 receptor (IL-1 R) gene. Treatment of quiescent cultures of Balb/c 3T3 fibroblasts with PDGF produced 20-30-fold stimulation of IL-1 R mRNA with a concomitant increase in cell surface 125I-binding. IL-1 R mRNA accumulation occurred after an initial lag period and with a time course preceding the increase in 125I-IL-1 binding to cells. Induction of IL-1 R mRNA was blocked by inhibitors of protein synthesis, suggesting that a product of a gene expressed immediately after PDGF addition ...
The transcription factor p63 plays a pivotal role in keratinocyte proliferation and differentiation in the epidermis. However, how p63 regulates epidermal genes during differentiation is not yet clear. Using epigenome profiling of differentiating human primary epidermal keratinocytes, we characterized a catalog of dynamically regulated genes and p63-bound regulatory elements that are relevant for epithelial development and related diseases. p63-bound regulatory elements occur as single or clustered enhancers, and remarkably, only a subset is active as defined by the co-presence of the active enhancer mark histone modification H3K27ac in epidermal keratinocytes. We show that the dynamics of gene expression correlates with the activity of p63-bound enhancers rather than with p63 binding itself. The activity of p63-bound enhancers is likely determined by other transcription factors that cooperate with p63. Our data show that inactive p63-bound ...
The mechanisms underlying the development and progression of breast cancer are not fully understood, and this is particularly challenging because of its diverse etiologies [20]. However, it is clear that changes in gene expression are essential to drive different processes that occur during tumourigenesis [21]. Transcription factors control gene expression by binding to specific DNA sequences in gene promoters and often regulate multiple target genes. Because of this ability to control different target genes, deregulation of transcription factors can drive events associated with the initiation and progression of diseases such as cancer [22]. Previous studies have shown that the Brn-3b transcription factor is elevated in ,60% of primary breast cancers [1], and when increased, it significantly enhances proliferation and anchorage-independent growth in vitro ...
The developmental transition to motherhood requires gene expression changes that alter the brain to prepare and drive the female to perform maternal behaviors. Furthermore, it is expected that the many physiological changes accompanying pregnancy and postpartum stages will impact brain gene expression patterns. To understand how extensive these gene expression changes are, we examined the global transcriptional response broadly, by examining four different brain regions: hypothalamus, hippocampus, neocortex, and cerebellum. Further, to understand the time course of these changes we performed RNA-sequencing analyses on mRNA derived from virgin females, two pregnancy time points and three postpartum time points. We find that each brain region and time point shows a unique molecular signature, with only 49 genes differentially expressed in all four regions, across the time points. Additionally, ...
TY - JOUR. T1 - Hyperglycemia modulates angiotensinogen gene expression. AU - Gabriely, Ilan. AU - Yang, Xiao Man. AU - Cases, Jane A.. AU - Ma, Xiao Hui. AU - Rossetti, Luciano. AU - Barzilai, Nir. PY - 2001/10/2. Y1 - 2001/10/2. N2 - Elevated plasma angiotensinogen (AGT) levels have been demonstrated in insulin-resistant states such as obesity and type 2 diabetes mellitus (DM2), conditions that are directly correlated to hypertension. We examined whether hyperinsulinemia or hyperglycemia may modulate fat and liver AGT gene expression and whether obesity and insulin resistance are associated with abnormal AGT regulation. In addition, because the hexosamine biosynthetic pathway is considered to function as a biochemical sensor of intracellular nutrient availability, we hypothesized that activation of this pathway would acutely mediate in vivo the induction of AGT gene expression in fat and ...
Abstract Human β-globin disorders are relatively common genetic diseases cause by mutations in the β-globin gene. Increasing the expression of the γ-globin gene has great benefits in reducing complications associated with these diseases. The Oct-1 transcription factor is involved in the transcriptional regulation of the γ-globin gene. The human γ-globin genes (both Aγ and Gγ-globin genes) carry three Oct-1 transcription factor consensus sequences within their promoter regions. We have studied the possibility of inducing γ-globin gene expression using decoy oligonucleotides that target the Oct-1 transcription factor consensus sequence. A double-stranded 22 bp decoy oligonucleotide containing the Oct-1 consensus sequence was synthesized. The results obtained from our in vitro binding assay revealed a strong competitive binding of the decoy ...
Top performende anti-Hund Sterol Regulatory Element Binding Transcription Factor 2 Antikörper für Immunohistochemistry (Paraffin-embedded Sections) (IHC (p)) vergleichen & kaufen.
A limiting factor of cDNA microarray technology is the need for a substantial amount of RNA per labeling reaction. Thus, 20-200 micro-grams total RNA or 0.5-2 micro-grams poly (A) RNA is typically required for monitoring gene expression. In addition, gene expression profiles from large, heterogeneous cell populations provide complex patterns from which biological data for the target cells may be difficult to extract. In this study, we chose to investigate a widely used mRNA amplification protocol that allows gene expression studies to be performed on samples with limited starting material. We present a quantitative study of the variation and noise present in our data set obtained from experiments with either amplified or non-amplified material. Using analysis of variance (ANOVA) and multiple hypothesis testing, we estimated the impact of amplification on the preservation of ...
View Notes - Lec20 from BCH 110 at UC Riverside. Lecture 20 Eukaryotic Gene Regulation 2 REGULATORY TRANSCRIPTION FACTORS & ACTIVATION MECHANISMS Lodish 6th edition Chapter 7 Lodish 5th edition
Although mutations causing monogenic disorders most frequently lie within the affected gene, sequence variation in complex disorders is more commonly found in noncoding regions. Furthermore, recent genome- wide studies have shown that common DNA sequence variants in noncoding regions are associated with normal variation in gene expression resulting in cell-specific and/or allele-specific differences. The mechanism by which such sequence variation causes changes in gene expression is largely unknown. We have addressed this by studying natural variation in the binding of key transcription factors (TFs) in the well-defined, purified cell system of erythropoiesis. We have shown that common polymorphisms frequently directly perturb the binding sites of key TFs, and detailed analysis shows how this causes considerable (∼10-fold) changes in expression from a single allele in a tissue-specific manner. We also show ...
The HLX gene encoding a diverged homeobox transcription factor has been found to be up-regulated by vascular endothelial growth factor-A (VEGF-A) in endothelial cells. endothelial growth factor-A (VEGF-A) is the major trigger of vasculogenesis and angiogenesis during embryogenesis and blood-vessel formation in the adult.1,2 It has also been implicated in pathologic angiogenesis in diseases such as cancer, chronic inflammatory disorders, and retinopathy.3 Whereas several peptide products are generated from the VEGF-A gene by differential splicing, the available data suggest that isoform VEGF-A165 is the RAB11FIP4 predominant form responsible for the major angiogenic effects.4 The gene repertoire induced by VEGF-A mainly via VEGF receptor 2 has been investigated by several groups5-7; however, the transcription factors up-regulated by VEGF-A and how they mediate its specific ...
In this study, we examined gene expression changes in the amygdala at 3 months of age in three groups of monkeys (1 week separated, 1 month separated, and maternally reared) that differed with respect to the period of early maternal rearing. DNA microarray analysis of the amygdala revealed many interesting gene expression differences (including transcripts of many genes involved in intracellular signaling); we concentrated our follow-up studies on GUCY1A3 because (1) it was the most changed gene between the 1 week separated and maternally reared groups; (2) it was one of the few genes whose expression differed between the 1 week separated and 1 month separated groups; (3) it was one of the highest expressors of the genes identified in the amygdala; and (4) it is part of the NO signaling cascade. The subsequent quantitative in situ hybridization studies ...
Our present study has provided, for the first time to our knowledge, a systematic analysis of the inflammation-relevant gene expression in ECs and SMCs in their coculture under static condition and in response to shear stress. We demonstrated that SMCs cause an upregulation of proinflammatory gene expression in ECs located in close proximity and that shear stress acts as a negative regulator for these proinflammatory gene expression in ECs cocultured with SMCs. Under static coculture condition, DNA microarray technology identified 23 inflammation-relevant genes that exhibit significant changes (18 increases and 5 decreases) in their expression in ECs cocultured with SMCs, as compared with the control monocultured ECs. All 18 genes upregulated in ECs by the coculture encode products that serve proinflammatory and thrombogenic functions. These ...
To explore the molecular mechanisms of PPARgamma1 gene expression in vascular smooth muscle cells (VSMC), we hypothesized that early growth-response factor-1 (Egr-1) might be a transcriptional mediator of the growth factor- and cytokine-induced PPARgamma1 gene expression since a putative Egr-1 binding element was found in the human PPARgamma1 promoter. In this study, we document that overexpression of Egr-1 activates the human PPARgamma1 promoter in both VSMC and HepG2 cells. Using Northern blot analysis, we observed that growth factors and cytokines such as PDGF, bFGF, Ang 11, TNFalpha, and IL-1beta induce Egr-1 expression prior to PPARgamma1 up-regulation in human VSMC. In addition, overexpression of a constitutively active form of Egr-1 by adenoviral gene transfer in VSMC dramatically induced PPARgamma1 gene expression by ...
Inflammation involves timed gene expression, suggesting that the fine-tuned onset, amplitude, and termination of expression of hundreds of genes is of critical importance to organismal homeostasis. Recent study of post-transcriptional regulation of inflammatory gene expression led to the suggestion of a regulatory role for pre-mRNA splicing. Here, using a hybrid capture approach to purify incompletely spliced, chromatin-associated pre-mRNAs, we use deep sequencing to study pre-mRNA splicing of the NF-kB transcriptome. By freezing transcription and examining subsequent splicing of complete transcripts, we find many introns splice tens to hundreds of times slower than average. In many cases, this is attributable to poor splice donor sequences that are evolutionarily conserved. When these introns were altered by ~2 base pairs to yield stronger splice donors, gene ...
Gene Expression Alterations in Biliary Tract Cancers. Heat maps showing the top 40 overexpressed (red) and top 40 underexpressed (green) genes for (a) EHC, (b)
In the present study, we examined the gene expression profile of 25 IGHV4-34 patients including subset #4, #16 and non-subset 4/16 cases. Initially, we compared the gene expression profiles between subset #4 and non-subset 4/16 patients and between subset #16 patients and non-subset 4/16 patients, and detected only few significant differences. This is probably because, overall, non-subset 4/16 IGHV4-34 cases exhibited a more heterogeneous gene expression profile, likely reflecting the structural heterogeneity of their BCR, which would be expected to be responsive to a far wider range of antigens than that recognized by stereotyped subsets. Interestingly, however, we detected distinct differences in gene expression patterns when comparing subset #4 and #16 cases, both of which can be reliably defined at the molecular level based on ...
Objectives: To investigate changes in gene expression in fibrillated and intact human osteoarthritis (OA) cartilage for evidence of an altered chondrocyte phenotype and hypertrophy.. Methods: Paired osteochondral samples were taken from a high-load site and a low-load site from 25 OA joints and were compared with eight similar paired samples from age-matched controls. Gene expression of key matrix and regulatory genes was analysed by quantitative real-time reverse transcription-polymerase chain reaction on total RNA extracted from the cartilage.. Results: There was a major change in chondrocyte gene expression in OA cartilage. SOX9 (38-fold) and aggrecan (4-fold) gene expression were both lower in OA (p,0.001), and collagen I (17-fold) and II (2.5-fold) gene expression were each increased in a subset of OA samples. The major ...
Direct interaction between transcription factors may provide a mechanism for the regulatory function of these proteins on transcription of the responsive genes. These interactions may be facilitated if the target DNA sequences for the participant regulatory proteins are overlapped or positioned in close proximity to each other within the promoter of the responsive genes. In earlier studies, we identified a cellular protein, named Puralpha, which upon binding to the MB1 regulatory DNA sequence of the myelin basic protein (MBP) gene, stimulates its transcription in central nervous system (CNS) cells. Here, we provide evidence for binding of the ubiquitous DNA binding transcription factor, Sp1, to the MB1 DNA motif at the region that partially overlaps with the Puralpha binding site. We demonstrate that binding of Puralpha to its target sequence is enhanced by inclusion of Sp1 in the binding reaction. Under this condition, ...
Fibroblasts are ubiquitous mesenchymal cells with many vital functions during development, tissue repair, and disease. Fibroblasts from different anatomic sites have distinct and characteristic gene expression patterns, but the principles that govern their molecular specialization are poorly understood. Spatial organization of cellular differentiation may be achieved by unique specification of each cell type; alternatively, organization may arise by cells interpreting their position along a coordinate system. Here we test these models by analyzing the genome-wide gene expression profiles of primary fibroblast populations from 43 unique anatomical sites spanning the human body. Large-scale differences in the gene expression programs were related to three anatomic divisions: anterior-posterior (rostral-caudal), proximal-distal, and dermal versus nondermal. A set of 337 genes that varied ...
Abstract: In this work, I focus on the development and testing of tools to explore differential gene expression as a molecular mechanism underlying the predisposition to complex disease. By definition, complex diseases (e.g. hypertension, diabetes, asthma) demonstrate both environmental and genetic factors in disease susceptibility, implicating genes that show both environmental response and genetic variability in predisposing disease. Differential gene expression is one important cellular response that reflects both of these factors in complex disease. Given their combined genetic and environmental influences, complex diseases are studied using a variety of analytical approaches. Consequently, the integration of data from diverse sources is a significant and important challenge in modern biomedical science. I demonstrate a statistical approach to integrating differential ...
Studies spanning the past three decades have revealed that differential gene expression is one of the most widely used modes of cellular regulation in both normal physiological processes such as development and differentiation and aberrant processes such as cancer. The Gene Regulation, Epigenomics and Transcriptomics Home Areas mission is to train students in the principles and concepts of contemporary gene regulation research with an emphasis on developing skills in cellular, proteomic and genome-wide analyses in order to study mechanisms of differential gene expression during cell signaling, differentiation, development and disease. Our program consists of a specialized curriculum focused on generating a comprehensive understanding of current concepts and mechanisms of gene regulation at the fundamental ...
Over several decades, the therapeutic use of glucocorticoids have established these molecules as potent inflammation suppressors. The description of transcriptional repression of pro-inflammatory genes as a nuclear receptor mediated mechanism represents a more recent topic of glucocorticoid signaling. However, new evidences suggest that steroidal regulation of inflammation is more complex, including epigenetic and receptor-independent pathways. It is also likely that sets of genes behaves in contradictory ways, making gene repression not a rule, but rather one of the possible modulatory modes. A similar level of complexity might apply to other steroidal hormones, such as those involved in sexually dimorphic immune responses. In fact, some autoimmune diseases are much more prevalent in one gender compared to the other. In addition to well-known steroid hormones, including aldosterone and vitamin D, this review topic intends ...
Transcriptional regulation of inflammatory gene expression has been at the forefront of studies of innate immunity and is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. The growing evidence for involvement of chromatin in the regulation of gene expression in innate immune cells, has uncovered an evolutionarily conserved role of microbial sensing and chromatin remodeling. Toll-like receptors and RIG-I-like receptors trigger these signaling pathways leading to transcriptional expression of a set of genes involved in inflammation. Tightly regulated control of this gene expression is a paramount, and often foremost, goal of most biological endeavors. In this review, we will discuss the recent progress about the molecular mechanisms governing control of pro-inflammatory gene ...
A Comparative Study of Metallothionein Gene Expression in Peripheral Lymphocytes and Blood Cadmium Level among Die Casting Male Workers
99 Tumorigenesis is often attributed to aberrant gene expression control leading to altered cell cycle control, resistance to apoptosis, abnormal differentiation, decreased genomic stability and inefficient DNA repair. The activity of chromatin remodeling complexes is vital to maintaining proper control of gene expression. The SWI/SNF complex is conserved from yeast to man and is responsible for remodeling up to 6% of the human genome, with many of those genes known to be associated with cell cycle control. Therefore, impaired or defective activity of SWI/SNF chromatin remodeling complex, involved in regulation of gene transcription, could encourage tumor development. The complex is composed of 10 or more members but requires only three core members to do the basic task of remodeling nucleosomes: BRG1/BRM, SNF5, and BAF155. BRG1 and SNF5 both lead to tumor development in ...
Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS) cells from adult skin primary fibroblasts and attempted to detect tissue-specific cis-regulatory variants using in vitro cell differentiation. We used padlock probes and high-throughput sequencing for digital RNA allelotyping and measured allele-specific gene expression in primary fibroblasts, lymphoblastoid cells, iPS cells, and their differentiated derivatives. We show that allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome. We ...
Cancer can be understood as a disease of dysfunctional gene expression control. Research in Chris Vakocs lab investigates how transcription factors and chromatin regulators cooperate to control gene expression and maintain the cancer cell state. This work makes extensive use of genetic screens to reveal cancer-specific functions for transcriptional regulators, as well as genomic and biochemical approaches to identify molecular mechanisms. One theme that has emerged from their efforts is that blood cancers are often vulnerable to targeting transcriptional coactivators, such as BRD4 and the SWI/SNF chromatin remodeling complex. Vakocs team demonstrated that chemical inhibition of BRD4 exhibits therapeutic effects in mouse models of leukemia, a finding that has motivated ongoing clinical trials in human leukemia patients. The Vakoc lab has also developed a CRISPR-Cas9 screening approach that can reveal individual protein ...
The present study describes a novel cell type-specific mechanism of transcriptional regulation of TSP-1 in vascular cells in response to glucose. We report here that unlike our recently identified short promoter region (−280/+66) responsible for the increased THBS1 transcription in ECs, a longer promoter fragment (−1270/+66) is required for THBS1 regulation in HASMCs, as was described for specialized pericytes and mesangial cells.27 Interestingly, glucose responsiveness in ECs was in fact inhibited by the distal fragment of the promoter,10 suggesting the presence of an inhibitory element in this region, which is not active in either VSMCs or mesangial cells.27 The longer promoter region, −1270/+66, responsible for the increased THBS1 transcription in HASMCs contained distinctly different binding elements, as identified by MatInspector, located in the distal end of the promoter. These binding elements had no similarity to those in the EC-specific THBS1 promoter fragment, ...
Email: [email protected] Translation of messenger RNAs into polypeptides represents the interface between the genome and the proteome. Not surprisingly, this step in the gene expression pathway is frequently used for the regulation of biological responses. I will discuss principles by which structural features of mRNAs, regulatory RNA elements and RNA- binding proteins regulate protein synthesis. This will include findings that imply a new role of the poly(A) tail in the translation of messenger RNAs via IRESes (internal ribosome entry sequences), the understanding of an important switch in Drosophila development, and results from whole genome microarray analyses in yeast which suggest that signal-induced changes in the transcriptome are amplified at the translational level. These latter results unveil a novel, higher level of coordinated gene regulation, which we refer to as potentiation .. ...
In recent years, the maturation of microarray technology has allowed the genome-wide analysis of gene expression patterns to identify tissue-specific and ubiquitously expressed (housekeeping) genes. We have performed a functional and topological analysis of housekeeping and tissue-specific networks to identify universally necessary biological processes, and those unique to or characteristic of particular tissues. We measured whole genome expression in 31 human tissues, identifying 2374 housekeeping genes expressed in all tissues, and genes uniquely expressed in each tissue. Comprehensive functional analysis showed that the housekeeping set is substantially larger than previously thought, and is enriched with vital processes such as oxidative phosphorylation, ubiquitin-dependent proteolysis, translation and energy metabolism. Network topology of the housekeeping network was characterized by higher ...
We developed m:Explorer for identifying process-specific transcription factors (TFs) from multiple genome-wide sources, including transcriptome, DNA-binding and chromatin data. m:Explorer robustly outperforms similar techniques in finding cell cycle TFs in Saccharomyces cerevisiae. We predicted and experimentally tested regulators of quiescence (G0), a model of ageing, over a six-week time-course. We validated nine of top-12 predictions as novel G0 TFs, including Δmga2, Δcst6, Δbas1 with higher viability and G0-essential TFs Tup1, Swi3. Pathway analysis associates longevity to reduced growth, reprogrammed metabolism and cell wall remodeling. m:Explorer (http://biit.cs.ut.ee/mexplorer/) is instrumental in interrogating eukaryotic regulatory systems using heterogeneous data.
Regulation of gene expression is a multi-layered process - from transcription to translation, including regulatory pathways such as epigenetics, chromatin remodeling and splicing, to name a few. A long-standing question in cellular and molecular neuroscience is the establishment of causality between gene expression and neurophysiology. One way to understand causality is to visualize the dynamic behavior of mRNAs and proteins in their native context and in response to neuronal activity. While transcriptomic and proteomic approaches have been the methods of choice to study genome-wide changes in neuronal gene expression, the
Introduction: Lung cancer is the number one cancer killer in the United States accounting for nearly 30% of all cancer deaths. Survival rates continue to be abysmal with 5-year survival only 15% despite contemporary therapies, making it clear that novel therapeutic agents need to be discovered. The translation of mRNA into protein, a central control point in the gene expression pathway, has been increasingly implicated as a critical checkpoint in tumor genesis and progression. This checkpoint serves as a traffic signal at the intersection of cell pathways controlling cell division and survival. The cell machinery controlling the first step in protein synthesis, a hetero-trimer designated eIF4F, is stuck in the "on" position in many human cancers. When this happens cells evade restraints on proliferation and survival. The activation state of eIF4F is controlled at multiple levels with the primary mechanism being negative regulation by the 4E ...
... :Our work attempts to dissect the myriad roles of RNA binding proteins in mammalian gene expression. RNA p
Translational contributions to tissue specificity in rhythmic and constitutive gene expression. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
The Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases provides an extremely dynamic environment for research into the aging process and its diseases.
The answer, though, is differences in gene expression in a cell. Clones have identical DNA, but the way the DNA is transcribed to RNA, and the way the RNA is translated to making a protein, can be specific to the cell. There are epigenetic factors - basically, chemicals that adhere to certain parts of the genome - that dictate NOT whether the DNA is there, but how often the DNA is read to make RNA and how efficiently that is made into functional proteins. Think about a fertilized egg. It divides into two cells, then 4 cells, then 8 cells, then 16 cells, then 32 cells, etc. Every time the cell divides, it has to make a perfect copy of its DNA. The cell machinery isnt always perfect and little changes in DNA can occur. Also, those chemicals that can affect gene expression can get added or subtracted as cells divide. Many of them, however, are passed on to the daughter cells. Thats how identical cells can have ...

Roger Wartell | School of PhysicsRoger Wartell | School of Physics

... are important elements in the regulation of gene expression for bacteria. Hfq is a bacterial RNA-binding protein that ... RNA based regulation of gene expression. RNA-protein interaction. Thermodynamics of DNA and RNA structural motifs ... Hfq is highly conserved in bacterial phyla and has been shown to be a virulence factor in several bacterial species. The ... Current research is directed at understanding the interaction of the RNA-binding protein Hfq with short regulatory RNAs and its ...
more infohttps://www.physics.gatech.edu/user/roger-wartell

Amsterdam UMC Locatie AMC - Dr. A. van der Ende PhDAmsterdam UMC Locatie AMC - Dr. A. van der Ende PhD

Molecular epidemiology and Genotyping of pathogenic bacteria. *Bacterial Gene Expression Regulation. *Antigenic Variation of ... We are particularly interested in the bacterial stress response and its regulation by small RNAs (ribo-regulation) in ... The research on Bacterial Meningitis benefits strongly from the Netherlands Reference Laboratory for Bacterial Meningitis ( ... The NRLBM gives access to a collection of over 10,000 bacterial isolates form patients and carriers and of human clinical ...
more infohttps://www.amc.nl/web/research-75/person-1/dr.-a.-van-der-ende-phd.htm

Cyclic Diguanylate Is a Ubiquitous Signaling Molecule in Bacteria: Insights into Biochemistry of the GGDEF Protein Domain |...Cyclic Diguanylate Is a Ubiquitous Signaling Molecule in Bacteria: Insights into Biochemistry of the GGDEF Protein Domain |...

... and regulation of gene expression. However, biochemical activities of only a few GGDEF domain proteins have been tested. These ... Phosphorylation of bacterial response regulator proteins by low molecular weight phospho-donors. Proc. Natl. Acad. Sci. USA 89: ... Slr1143 protein. Top, full-length protein; middle, protein fragment corresponding to the CC-plus-GGDEF domains; bottom, protein ... In V. cholerae and Synechococcus elongatus, the proteins anticipated to be involved in c-di-GMP turnover affect gene expression ...
more infohttps://jb.asm.org/content/187/5/1792?ijkey=a1b6ca42a03ce31e21d47158139fe3894549e83e&keytype2=tf_ipsecsha

Gene Function in Prokaryotes
	Gene Function in Prokaryotes

Genetic Analysis of Protein Localization. Membrane mediated Regulation of Gene Expression in Bacteria. Bacterial Chemotaxis: ... Protein mediated Translational Repression. Recombinational Regulation of Gene Expression in Bacteria. Some Bacterial ... Introduction to Prokaryotic Gene Function. Precision of Protein Biosynthesis. Attenuation in Bacterial Operons. Inducible ... Gene Function in Prokaryotes. (Cold Spring Harbor Monograph Series 15). Book Series: Cold Spring Harbor Monograph Series. ...
more infohttps://www.cshlpress.com/default.tpl?action=full&cart=156826408021166254&--eqskudatarq=651&typ=ps&newtitle=Gene%20Function%20in%20Prokaryotes

Gene Function in Prokaryotes
	Gene Function in Prokaryotes

Genetic Analysis of Protein Localization. Membrane mediated Regulation of Gene Expression in Bacteria. Bacterial Chemotaxis: ... Protein mediated Translational Repression. Recombinational Regulation of Gene Expression in Bacteria. Some Bacterial ... Introduction to Prokaryotic Gene Function. Precision of Protein Biosynthesis. Attenuation in Bacterial Operons. Inducible ... Gene Function in Prokaryotes. (Cold Spring Harbor Monograph Series 15). Book Series: Cold Spring Harbor Monograph Series. ...
more infohttps://cshlpress.com/default.tpl?action=full&cart=1550599699226622270&--eqskudatarq=651&typ=ps&newtitle=Gene%20Function%20in%20Prokaryotes

Gene Function in ProkaryotesGene Function in Prokaryotes

Genetic Analysis of Protein Localization. Membrane mediated Regulation of Gene Expression in Bacteria. Bacterial Chemotaxis: ... Protein mediated Translational Repression. Recombinational Regulation of Gene Expression in Bacteria. Some Bacterial ... Introduction to Prokaryotic Gene Function. Precision of Protein Biosynthesis. Attenuation in Bacterial Operons. Inducible ... Gene Function in Prokaryotes. (Cold Spring Harbor Monograph Series 15). Book Series: Cold Spring Harbor Monograph Series. ...
more infohttps://www.cshlpress.com/default.tpl?cart=1524468611142341775&fromlink=T&linkaction=full&linksortby=oop_title&--eqSKUdatarq=651

UAB - Graduate Biomedical Sciences - CourseworkUAB - Graduate Biomedical Sciences - Coursework

This includes new areas of epigenetic regulation of gene expression and post-translational regulation of protein function. ... The students will learn the fundamental principles how structural components of bacterial cells are built and how bacteria- ... regulation of gene expression, transport mechanisms and protein export. ... GBSC 707- Metabolic Regulation of Gene Expression- Natalia Kedishvili. This course will focus on the impact of various ...
more infohttps://www.uab.edu/gbs/home/requirements/coursework

Frontiers | A Two-Component Regulatory System in Transcriptional Control of Photosystem Stoichiometry: Redox-Dependent and...Frontiers | A Two-Component Regulatory System in Transcriptional Control of Photosystem Stoichiometry: Redox-Dependent and...

... which couples photosynthetic electron transport to gene transcription. Hik2 function is so important that it has survived the ... which couples photosynthetic electron transport to gene transcription. Hik2 function is so important that it has survived the ... We report on regulation and interactions of a unique histidine sensor kinase, Hik2. Hik2 is found in all known cyanobacteria, ... No part of it is submitted for publication elsewhere.We report on regulation and interactions of a unique histidine sensor ...
more infohttps://www.frontiersin.org/articles/10.3389/fpls.2016.00137/full

Dynamic features of gene expression control by small regulatory RNAs | PNASDynamic features of gene expression control by small regulatory RNAs | PNAS

... in eukaryotes and bacteria play an important role in the regulation of gene expression either by binding to regulatory proteins ... Quantifying the sequence-function relation in gene silencing by bacterial small RNAs ... Dynamic features of gene expression control by small regulatory RNAs. Namiko Mitarai, Julie-Anna M. Benjamin, Sandeep Krishna, ... Dynamic features of gene expression control by small regulatory RNAs. Namiko Mitarai, Julie-Anna M. Benjamin, Sandeep Krishna, ...
more infohttps://www.pnas.org/content/106/26/10655.abstract

Squaring up to DNA: pentapeptide repeat proteins and DNA mimicry | SpringerLinkSquaring up to DNA: pentapeptide repeat proteins and DNA mimicry | SpringerLink

Pentapeptide repeats are a class of proteins characterized by the presence of multiple repeating sequences five amino acids in ... Dorman CJ, Deighan P (2003) Regulation of gene expression by histone-like proteins in bacteria. Curr Opin Genet Dev 13(2):179- ... Cox MM (2007) Motoring along with the bacterial RecA protein. Nat Rev Mol Cell Biol 8(2):127-138PubMedGoogle Scholar ... Grove A (2011) Functional evolution of bacterial histone-like HU proteins. Curr Issues Mol Biol 13(1):1-12PubMedGoogle Scholar ...
more infohttps://link.springer.com/article/10.1007/s00253-014-6151-3

pGLO™ Bacterial Transformation Kit | Life Science Education | Bio-RadpGLO™ Bacterial Transformation Kit | Life Science Education | Bio-Rad

Students will glow with excitement when they transform bacteria with pGLO plasmid. Ideal for AP Biology Lab 6. ... protein, gene, expression, plasmid, regulation, bioengineer, bacteria, ap, biology, science, education, products, classroom 06/ ... Gene Regulation. Gene regulation. With pGLO, students analyze the growth of bacteria on various media and examine the roles ... protein, expression, gfp, green fluorescence, gene, regulation, bioengineer, bacteria, plasmid, lab, prep, map, pglow, sequence ...
more infohttp://www.bio-rad.com/en-us/product/pglo-bacterial-transformation-kit?ID=619b8f74-9d3f-4c2f-a795-8a27e67598b7

Beatty Lab - Principal Investigator | Microbiology & Immunology @ UBCBeatty Lab - Principal Investigator | Microbiology & Immunology @ UBC

... with an emphasis on the regulation of gene expression, and protein structure and function. Most of the research in my ... laboratory is on photosynthetic bacteria. These organisms use membrane proteins that bind chlorophylls and other cofactors to ... My laboratorys research activities are centered on the general areas of bacterial molecular biology, physiology and genetics, ... In one such protein called the reaction center, the light energy excites chlorophyll electrons, which hop to nearby cofactors ...
more infohttp://microbiology.ubc.ca/research/labs/beatty/pi

Koch, StefanKoch, Stefan

Animals, Axin Protein/metabolism, Cyclins/metabolism, Epididymis/*metabolism, *Gene Expression Regulation, Glycogen Synthase ... Gene Expression Regulation, Bacterial, Mice, Mice, Inbred C57BL, Mice, Knockout, Microbiota, *Signal Transduction, Specific ... Open this publication in new window or tab ,,Gut commensal bacteria and regional Wnt gene expression in the proximal versus ... Gene Expression Regulation, Homeostasis/*immunology, Humans, Intestinal Mucosa/*immunology/*metabolism, Mice, Protein Transport ...
more infohttp://liu.diva-portal.org/smash/person.jsf?pid=authority-person:55744

pGLO™ Bacterial Transformation Kit | Life Science Education | Bio-RadpGLO™ Bacterial Transformation Kit | Life Science Education | Bio-Rad

Students will glow with excitement when they transform bacteria with pGLO plasmid. Ideal for AP Biology Lab 6. ... protein, gene, expression, plasmid, regulation, bioengineer, bacteria, ap, biology, science, education, products, classroom 06/ ... Gene Regulation. Gene regulation. With pGLO, students analyze the growth of bacteria on various media and examine the roles ... protein, expression, gfp, green fluorescence, gene, regulation, bioengineer, bacteria, plasmid, lab, prep, map, pglow, sequence ...
more infohttp://www.bio-rad.com/en-us/product/pglo-bacterial-transformation-kit?ID=619b8f74-9d3f-4c2f-a795-8a27e67598b7&pcp_loc=catprod

Publications | Ned WingreenPublications | Ned Wingreen

Quorum sensing is the regulation of gene expression in response to changes in cell density. To measure their cell density, ... Broedersz, Chase P, et al. "Condensation and localization of the partitioning protein ParB on the bacterial chromosome.". Proc ... Individual bacteria internally represent the external concentration of autoinducers via the level of monitor proteins. In turn ... Here, we highlight the effects of mechanics on bacterial behaviors on surfaces at multiple length scales, from single bacteria ...
more infohttps://scholar.princeton.edu/wingreenlab/publications

NAVER Academic > Search...NAVER Academic > Search...

Bacterial Proteins, genetics, metabolism, Binding Sites, DNA, Bacterial, Gene Expression Regulation, Bacterial, physiology, ... Gene Expression Regulation, Bacterial, Gram-Negative Bacteria, Molecular Sequence... ... Amino Acid Sequence, Escherichia coli Proteins, genetics, metabolism, Gene Expression Regulation, Bacterial, physiology, Models ... Amino Acid Sequence, Escherichia coli Proteins, genetics, metabolism, Gene Expression Regulation, Bacterial, physiology, Models ...
more infohttps://academic.naver.com/search.naver?field=3&query=Journal+of+Bacteriology+193%EA%B6%8C+7%ED%98%B8

Enteric Dysbiosis Associated with a Mouse Model of Alcoholic Liver Disease | J. Craig Venter InstituteEnteric Dysbiosis Associated with a Mouse Model of Alcoholic Liver Disease | J. Craig Venter Institute

The aims of our study were to investigate bacterial translocation, changes in the enteric microbiome, and its regulation by ... Intestinal bacterial overgrowth is common in patients with alcoholic liver disease. ... The translocation of bacteria and bacterial products into the circulation contributes to alcoholic liver disease. ... With respect to the hosts transcriptome, alcohol feeding was associated with down-regulation in gene and protein expression of ...
more infohttps://www.jcvi.org/enteric-dysbiosis-associated-mouse-model-alcoholic-liver-disease

Regulation of Bacterial Gene Expression by Transcription Attenuation | Microbiology and Molecular Biology ReviewsRegulation of Bacterial Gene Expression by Transcription Attenuation | Microbiology and Molecular Biology Reviews

A wide variety of mechanisms that control gene expression in bacteria are based on conditional transcription termination. ... protein, or RNA. The most common type of regulation involving conditional termination is transcription attenuation, in which ... Regulation of Bacterial Gene Expression by Transcription Attenuation Message Subject (Your Name) has forwarded a page to you ... Regulation of Bacterial Gene Expression by Transcription Attenuation. Charles L. Turnbough, Jr. ...
more infohttps://mmbr.asm.org/content/83/3/e00019-19

Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli.Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli.

... also imply that functions of lysine acetylation beyond regulation of gene expression are evolutionarily conserved from bacteria ... None of the proteins has been previously associated with this modification. Among the identified proteins are transcriptional ... Furthermore, we demonstrate that bacterial lysine acetylation is regulated in response to stress stimuli. ... European Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics. UniProt is an ELIXIR core ...
more infohttps://www.uniprot.org/citations/18723842

Plus itPlus it

... also imply that functions of lysine acetylation beyond regulation of gene expression are evolutionarily conserved from bacteria ... Lysine Acetylation Motifs in Bacterial Substrate Proteins and Bioinformatics Analysis-. Conserved protein sequence motifs are ... These proteins include 7 proteins involved in amino acid metabolism and 7 proteins in nucleotide metabolism. ... Protein Data Bank code 1dfo) (56), isocitrate dehydrogenase (Protein Data Bank code 1hqs) (57), and IMP cyclohydrolase (Protein ...
more infohttp://www.mcponline.org/content/8/2/215

Functional Profiling Of Metabolic Regulation In Marine BacteriaFunctional Profiling Of Metabolic Regulation In Marine Bacteria

... focusing on the regulation of gene and protein expression in heterotrophic marine bacteria. ... Most of the ocean surface is often limited by nutrients, influencing bacterial growth and activities. Bacterial adaptation to ... Functional Profiling Of Metabolic Regulation In Marine Bacteria. Muthusamy, Saraladevi Linnéuniversitetet, Institutionen för ... Concomitantly, inorganic sulfur oxidation gene expression increased with thiosulfate compared to controls. Moreover, ...
more infohttp://umu.diva-portal.org/smash/record.jsf?pid=diva2:1140829

Novel Strategy to Overcome Antibiotic ResistanceNovel Strategy to Overcome Antibiotic Resistance

Antibiotics used to inhibit the growth of bacteria may become ineffective. However, a new strategy discovered helps in ... production is the key to controlling the regulation of bacterial gene expression. Gene expression is the term used to describe ... how a gene product coded by a gene is formed . These products are often proteins, or RNA molecules.. In bacteria, the RNA is ... The early phase of RNA production may help to control the regulation of bacterial gene expression. ...
more infohttps://www.medindia.net/news/novel-strategy-to-overcome-antibiotic-resistance-179271-1.htm?utm_source=medindia&utm_medium=widget&utm_content=&utm_campaign=punchline

Laboratory Experiments in Microbiology - Johnson - 0 reviews - Benjamin Cummings -  - English - AnobiiLaboratory Experiments in Microbiology - Johnson - 0 reviews - Benjamin Cummings - - English - Anobii

Regulation of Gene Expression, Isolation of Bacterial Mutants, Transformation of Bacteria, DNA Fingerprinting, Genetic ... Protein Catabolism, Respiration, Rapid Identification Methods; Microbial Growth: Oxygen and the Growth of Bacteria, ... Bacteria of the Skin, Bacteria of the Respiratory Tract, Bacteria of the Mouth, Bacteria of the Gastrointestinal Tract, ... Cultivation of Bacteria: Microbes in the Environment, Transfer of Bacteria: Aseptic Techniques, Isolation of Bacteria by ...
more infohttp://www.anobii.com/books/Laboratory_Experiments_in_Microbiology/9780805382921/003a9293d9c68920ba

Joanna Hicks - Faculty of Science and Engineering: University of WaikatoJoanna Hicks - Faculty of Science and Engineering: University of Waikato

Firstly we focus on bacterial metabolism and regulation of gene expression to understand how pathogenic bacteria (such as ... In the applied direction we are engineering proteins for biotechnology applications, such as RNA sequencing. ... Bacteria; Biochemistry; Biology; Biotechnology. Contact Details. Email: [email protected] Room: C.2.14. Phone: +64 7 ...
more infohttps://sci.waikato.ac.nz/about-us/people/jmckenzi2

Bacteria as Plant PathogensBacteria as Plant Pathogens

... gene expression and gene regulation. These discoveries are occurring both with natural bacterial variants and mutants ... 2003). Similarly, methods for characterizing the entire protein complement of an organism (proteomics) are becoming available ( ... which are chemicals effective against deleterious bacteria or fungi. Storage granules can be seen in some bacteria. Bacterial ... you are observing bacterial streaming (Figure 19) which is an indicator of a bacterial disease. However, not all bacterial ...
more infohttps://www.apsnet.org/edcenter/intropp/PathogenGroups/Pages/Bacteria.aspx
  • To investigate specificity of the GGDEF domains in Bacteria , six GGDEF domain-encoding genes from randomly chosen representatives of diverse branches of the bacterial phylogenetic tree, i.e. (asm.org)
  • The bacterial genes encoding the enzymes needed to metabolize the simple sugar arabinose are a perfect example. (bio-rad.com)
  • A promoter region upstream of these genes acts as molecular on/off switch that regulates their expression. (bio-rad.com)
  • Bio-Rad's pGLO plasmid incorporates the arabinose promoter, but the genes involved in the breakdown of arabinose have been replaced with the jellyfish gene encoding GFP. (bio-rad.com)
  • Sequencing of 16S ribosomal RNA genes revealed a relative abundance of Bacteroidetes and Verrucomicrobia bacteria in mice fed alcohol compared with a relative predominance of Firmicutes bacteria in control mice. (jcvi.org)
  • However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. (springer.com)
  • The Bacillus cereus group (consisting of B. cereus, B. thuringiensis, B. mycoides, and B. anthracis) was found to contain nine genes homologous to the AiiA gene that encode AHL-inactivating enzymes, with the catalytic zinc-binding motif conserved in all cases. (wikipedia.org)
  • Expression of virulence genes in E. Carotovora is regulated by N-(3-oxohexanoyl)-l-homoserine lactone (OHHL). (wikipedia.org)
  • At this moment he is Associate Professor in Medical Microbiology, head of the Laboratory for Experimental Bacteriology and head of the Netherlands Reference Laboratory for Bacterial Meningitis (all at the Dept. of Medical Microbiology, Academic Medical Centre, University of Amsterdam). (amc.nl)
  • Processes mediated by more elaborate two-component systems include bacterial chemotaxis ( 2 ), in which chemoeffectors are sensed by a complex of transmembrane chemoreceptor, CheW, and the cytoplasmic histidine kinase CheA. (pnas.org)
  • It is still unclear the ecological effects of lactonase but it has been proposed that since bacteria mostly coexist with other microorganisms in the environment, some bacteria strains could have evolved its feeding strategies and utilize AHLs as their main resource for energy and nitrogen. (wikipedia.org)
  • Hfq is a bacterial RNA-binding protein that facilitates the hybridization of sRNAs to their target regions on specific mRNAs. (gatech.edu)
  • Two of the best-characterized bacterial sRNAs, Spot42 and RyhB, form a complementary pair with the ribosome binding region of their target mRNAs, thereby inhibiting translation or promoting mRNA degradation. (pnas.org)
  • To investigate the steady-state and dynamic potential of such sRNAs, we examine the 2 key parameters characterizing sRNA regulation: the capacity to overexpress the sRNA relative to its target mRNA and the speed at which the target mRNA is irreversibly inactivated. (pnas.org)
  • Retinoic acid inducible gene I (RIG-I) and melanoma differentiation associated gene 5 (MDA5) are part of the RIG-I-like helicase (RLH) family of sensors that recognize RNA in the cytoplasm and signal through the adaptor protein mitochondrial antiviral signaling (MAVS) (IPS1) to induce type I IFNs ( 32 ). (asm.org)
  • 2003). Similarly, methods for characterizing the entire protein complement of an organism (proteomics) are becoming available (Graves and Hayward 2002). (apsnet.org)
  • The use of DNA arrays and proteomics will transform the scale of our ability to describe the patterns of gene expression as bacteria respond to their environments. (whsmith.co.uk)
  • Stk33 expression first appears in primary spermatocytes, and targeted deletion of Stk33 in these cells recapitulates the defects observed in constitutive knockout mice, confirming a germ cell-intrinsic function. (diva-portal.org)
  • Acetyl-coenzyme A (CoA) synthetase, CheY, and Alba are the only proteins in prokaryotes known to be lysine-acetylated ( 4 , 21 - 24 ). (mcponline.org)
  • Topics include the mitogen activated protein kinase cascade, transforming growth factor beta, insulin, and cytokines. (uab.edu)
  • Bacterial biofilms display remarkable changes during their development from initial attachment to maturity, yet the cellular architecture that gives rise to collective biofilm morphology during growth is largely unknown. (princeton.edu)
  • Most of the ocean surface is often limited by nutrients, influencing bacterial growth and activities. (diva-portal.org)
  • MED193 showed that the addition of thiosulfate enhanced the bacterial growth yields. (diva-portal.org)
  • The presentation provides educators with background on the pGLO Transformation and Green Fluorescent Protein Chromatography Kits and includes instructions for using the kits. (bio-rad.com)
  • Using the classic pGLO Bacterial Transformation Kit, students transform bacteria by introducing a gene from the bioluminescent jellyfish Aequorea victoria . (bio-rad.com)
  • Asensio JL, Perez-Lago L, Lazaro JM, Gonzalez C, Serrano-Heras G, Salas M (2011) Novel dimeric structure of phage phi29-encoded protein p56: insights into uracil-DNA glycosylase inhibition. (springer.com)
  • DNA gyrase-targeting pentapeptide repeat proteins can both inhibit DNA gyrase-a potentially useful therapeutic property-and contribute to resistance to quinolone antibacterials (by acting to prevent them forming a lethal complex with the DNA and enzyme). (springer.com)
  • These organisms use membrane proteins that bind chlorophylls and other cofactors to capture light energy in the form of photons. (ubc.ca)
  • In one such protein called the reaction center, the light energy excites chlorophyll electrons, which hop to nearby cofactors that form a chain across the membrane domain of the protein. (ubc.ca)
  • Hemolysins or haemolysins are lipids and proteins that cause lysis of red blood cells by destroying their cell membrane. (wikipedia.org)
  • Belogurov AA, Delver EP, Rodzevich OV (1992) IncN plasmid pKM101 and IncI1 plasmid ColIb-P9 encode homologous antirestriction proteins in their leading regions. (springer.com)
  • Most of the research in my laboratory is on photosynthetic bacteria. (ubc.ca)
  • Individual bacterial cells cannot be seen without the use of a microscope, however, large populations of bacteria become visible as aggregates in liquid, as biofilms on plants, as viscous suspensions plugging plant vessels, or colonies on petri dishes in the laboratory. (apsnet.org)
  • Many bacteria produce hemolysins that can be detected in the laboratory. (wikipedia.org)
  • Guzman LM, Belin D, Carson MJ, Beckwith J (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose pBAD promoter. (springer.com)
  • However, biochemical activities of only a few GGDEF domain proteins have been tested. (asm.org)
  • The receiver protein CheY carries the signal to the flagellar switch. (pnas.org)
  • Type I IFNs are induced upon cytosolic detection of microbial nucleic acids, including DNA, RNA, and the bacterial second messenger cyclic-di-GMP (c-di-GMP). (asm.org)
  • In collaborative studies with Dr. D. van de Beek (Department of Neurology, AMC) we investigate clinical aspects of bacterial meningitis as well correlation between clinical features, outcome and host and bacterial factors. (amc.nl)
  • Arsène S, Leclercq R (2007) Role of a qnr-like gene in the intrinsic resistance of Enterococcus faecalis to fluoroquinolones. (springer.com)
  • New drugs could now be developed on the basis of our findings that kill the bacteria that cause illnesses', hopes Dr. David Dulin from the Interdisciplinary Centre for Clinical Research at FAU. (medindia.net)
  • To illustrate this potential, I begin with a brief review of some of the key findings made with bacteria. (biologists.org)
  • When bacteria transformed with pGLO are grown in the presence of arabinose, the GFP gene switches on, causing the bacteria to express GFP and to fluoresce brilliant green. (bio-rad.com)
  • In the applied direction we are engineering proteins for biotechnology applications, such as RNA sequencing. (waikato.ac.nz)
  • The genetic potential of such organisms is exploited in synthetic biology approaches to engineer novel combinations of proteins with new light-harvesting properties. (ubc.ca)
  • Finally, we are also studying a novel bacteriophage-like genetic exchange element called the "gene transfer agent", or GTA. (ubc.ca)
  • By genetic mapping and complementation experiments, we found that Gt mice harbor a single nucleotide variant (T596A) of Sting that functions as a null allele and fails to produce detectable protein. (asm.org)
  • Although we found no difference after 1 day or 1 week, intestinal bacterial overgrowth was observed in the gastrointestinal tract of mice fed alcohol for 3 weeks compared with control mice fed an isocaloric liquid diet. (jcvi.org)
  • The early phase of RNA production may help to control the regulation of bacterial gene expression. (medindia.net)
  • For beneficial purposes or as pathogens, populations of 106 CFU (colony-forming units/milliliter) or higher are normally required for bacteria to function as biological control agents or cause infectious disease. (apsnet.org)
  • Over time, these types of medication become ineffective, and multi-resistant bacteria become even more widespread as a result. (medindia.net)
  • Participation of chromosome segregation protein ParAI of Vibrio cholerae in chromosome replication. (naver.com)
  • 2003), in bacterial viruses integrated in the chromosome or in a 'carrier' state, and on one or more extra-chromosomal elements (plasmids). (apsnet.org)
  • Population development must normally occur for many bacteria to survive and infect plants. (apsnet.org)
  • One reason for the ecological success of bacteria is their remarkable ability to sense and respond to changing environmental conditions. (frontiersin.org)