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.Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.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)DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Comparative Genomic Hybridization: A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.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.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.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.DNA, Ribosomal Spacer: The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).Gene Dosage: The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.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.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)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: 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).Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.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.Oligonucleotides, Antisense: Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.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.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.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.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.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.RNA, Complementary: Synthetic transcripts of a specific DNA molecule or fragment, made by an in vitro transcription system. This cRNA can be labeled with radioactive uracil and then used as a probe. (King & Stansfield, A Dictionary of Genetics, 4th ed)RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Glass: Hard, amorphous, brittle, inorganic, usually transparent, polymerous silicate of basic oxides, usually potassium or sodium. It is used in the form of hard sheets, vessels, tubing, fibers, ceramics, beads, etc.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.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Fixatives: Agents employed in the preparation of histologic or pathologic specimens for the purpose of maintaining the existing form and structure of all of the constituent elements. Great numbers of different agents are used; some are also decalcifying and hardening agents. They must quickly kill and coagulate living tissue.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.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.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.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.Genetic Variation: Genotypic differences observed among individuals in a population.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.DNA Copy Number Variations: Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Software: Sequential operating programs and data which instruct the functioning of a digital computer.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.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)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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Nucleic Acid Amplification Techniques: Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Models, Statistical: Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.Data Interpretation, Statistical: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.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.RNA, Neoplasm: RNA present in neoplastic tissue.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.Chromosome Aberrations: Abnormal number or structure of chromosomes. Chromosome aberrations may result in CHROMOSOME DISORDERS.Genes, Bacterial: The functional hereditary units of BACTERIA.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.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.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.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.Reference Standards: A basis of value established for the measure of quantity, weight, extent or quality, e.g. weight standards, standard solutions, methods, techniques, and procedures used in diagnosis and therapy.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Cell Line: Established cell cultures that have the potential to propagate indefinitely.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Quality Control: A system for verifying and maintaining a desired level of quality in a product or process by careful planning, use of proper equipment, continued inspection, and corrective action as required. (Random House Unabridged Dictionary, 2d ed)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.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.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Cell Line, Tumor: A cell line derived from cultured tumor cells.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.Bacterial Proteins: Proteins found in any species of bacterium.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.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.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.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.DNA, Neoplasm: DNA present in neoplastic tissue.Phosphorothioate Oligonucleotides: Modified oligonucleotides in which one of the oxygens of the phosphate group is replaced with a sulfur atom.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Oligodeoxyribonucleotides, Antisense: Short fragments of DNA that are used to alter the function of target RNAs or DNAs to which they hybridize.Protein Array Analysis: Ligand-binding assays that measure protein-protein, protein-small molecule, or protein-nucleic acid interactions using a very large set of capturing molecules, i.e., those attached separately on a solid support, to measure the presence or interaction of target molecules in the sample.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Neoplasm Proteins: Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.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.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.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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.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.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Thionucleotides: Nucleotides in which the base moiety is substituted with one or more sulfur atoms.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.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.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Oligoribonucleotides, Antisense: Short fragments of RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.Mice, Inbred C57BLMolecular Weight: The sum of the weight of all the atoms in a molecule.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.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Genes, Viral: The functional hereditary units of VIRUSES.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Kinetics: The rate dynamics in chemical or physical systems.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Molecular Probe Techniques: The use of devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.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.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Chromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.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.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.

*  Toward Integration of Biological Noise: Aggregation Effect in Microarray Data Analysis - Batch Effects and Noise in Microarray...

Aggregation effect in microarray data analysis distorts the correlations between gene expression levels and, in some sense, plays a role of technical noise. This aspect is especially important in network and association inference analyses. However, it is possible to construct statistical estimators which take aggregation into account to generate 'clean' covariance of expression levels. Based on this estimator, we provide a method to find gene pairs having essentially different correlation structure. ...
onlinelibrary.wiley.com/doi/10.1002/9780470685983.ch15/summary

*  Microarray technology for tailoring breast canc...( Microarray technology could be used to ...)

Microarray technology could be used to tailor therapy according to the...A team of researchers led by Jonas Bergh from the Karolinska Institute...An analysis of the genes expressed in the tumours of all 159 patients ...The present lack of criteria to help tailor breast cancer treatment to...,Microarray,technology,for,tailoring,breast,cancer,therapy,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
news.bio-medicine.org/biology-news-3/Microarray-technology-for-tailoring-breast-cancer-therapy-9873-1/

*  Plus it

Gene array analysis. The Amersham CodeLink system using the UniSet Human I Expression Bioarray, containing 10,458 gene probes, was used to compare the transcription profiles between parent cells and highly invasive clones. This array contains a broad range of genes derived from publicly available, well-annotated mRNA sequences. The CodeLink array is unique in being capable of detecting minimal differences in gene expression, as low as 1.3-fold with 95% confidence, because of the novel three-dimensional aqueous gel matrix, which the empirically tested 30-mer oligonucleotides are deposited on ( 8). This substantially reduces background, enhances sensitivity, and allows for the detection and quantification of subtle regulatory relationships among genes in parent HNSCC cells and highly invasive clones. Total RNA was isolated from cultures of confluent cells using the RNeasy Mini Kit (Qiagen, ...
cancerres.aacrjournals.org/content/66/14/6928

*  DI-fusion Identification by means of cDNA microarray analyses of gene...

DI-fusion, le Dépôt institutionnel numérique de l'ULB, est l'outil de référencementde la production scientifique de l'ULB.L'interface de recherche DI-fusion permet de consulter les publications des chercheurs de l'ULB et les thèses qui y ont été défendues.
difusion.ulb.ac.be/vufind/Record/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/53540/Details

*  ECHO probes: a concept of fluorescence control for practical nucleic acid sensing - Chemical Society Reviews (RSC Publishing)

An excitonic interaction caused by the H-aggregation of fluorescent dyes is a new type of useful photophysical process for fluorescence-controlled nucleic acid sensing. This critical review points out the recent advances in exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probes,
pubs.rsc.org/en/Content/ArticleLanding/2011/CS/c1cs15025a

*  A multicentre phase II gene expression profiling study of putative relationships between tumour biomarkers and clinical...

Background: Identification of appropriate markers for predicting clinical benefit with erlotinib in non-small-cell lung cancer (NSCLC) may be able to guide patient selection for treatment. This open-label, multicentre, phase II trial aimed to identify genes with potential use as biomarkers for clinical benefit from erlotinib therapy. Methods: Adults with stage IIIb/IV NSCLC in whom one or more chemotherapy regimen had failed were treated with erlotinib (150 mg/day). Tumour biopsies were analysed using gene expression profiling with Affymetrix GeneChip_microarrays. Differentially expressed genes were verified using quantitative RT-PCR (qRT-PCR). Results: A total of 264 patients were enrolled in the study. Gene expression profiles found no statistically significant differentially expressed genes between patients with and without clinical benefit. In an exploratory analysis in responding versus nonresponding patients, three genes on chromosome 7 were expressed at higher levels ...
ddd.uab.cat/record/108162

*  Gene Expression Profiling Reveals Distinct Molecular Signatures Associated With the Rupture of Intracranial Aneurysm | Stroke

Among KLF family, KLF2, KLF12, and KLF15 were downregulated in early RIAs. Klf2-deficient mice died during the embryonic stage from hemorrhage at the site of aneurysmal dilation of arteries.33 It has been reported that KLF2 has an anti-inflammatory function by inhibiting proinflammatory cytokines (interleukin-6 and interleukin-8).34 Additionally, KLF2 represses monocyte/macrophage inflammatory activation as demonstrated by the fact that macrophages of Klf2 heterozygous knockout mice represent enhanced uptake of oxidized low-density lipoproteins,35 and KLF2 inhibits HIF-1α that is essential for macrophage activation.36 Notably, we identified downregulation of KLF2 in concert with upregulations of IL6R, IL8RB, and HIF1A in early RIAs (Figure 3). Motivated by the fact of decreased expressions of KLF15 in human failing hearts and aortic aneurysms, researchers demonstrated that Klf15-deficient mice with infusion of angiotensin II mimicked the human diseases.37 These suggest that KLFs are key ...
stroke.ahajournals.org/content/45/8/2239

*  Global gene expression profiling and senescence biomarker analysis of hESC exposed to H2O2 induced non-cytotoxic oxidative...

Global gene expression profiling and senescence biomarker analysis of hESC exposed to H2O2 induced non-cytotoxic oxidative stress. . Download books free in pdf. Online library with books, university works and thousands of documents available to read online and download.
books.duhnnae.com/2017/aug4/150192868833-Global-gene-expression-profiling-and-senescence-biomarker-analysis-of-hESC-exposed-to-H2O2-induced-non-cytotoxic-oxidative-stress.php

*  Angiotensin-converting enzyme inhibition down-regulates the pro-atherogenic chemokine receptor 9 (CCR9)-chemokine ligand 25 ...

Many experimental and clinical studies suggest a relationship between enhanced angiotensin II release by the angiotensin-converting enzyme (ACE) and the pathophysiology of atherosclerosis. The atherosclerosis-enhancing effects of angiotensin II are complex and incompletely understood. To identify anti-atherogenic target genes, we performed microarray gene expression profiling of the aorta during atherosclerosis prevention with the ACE inhibitor, captopril. Atherosclerosis-prone apolipoprotein E (apoE)-deficient mice were used as a model to decipher susceptible genes regulated during atherosclerosis prevention with captopril. Microarray gene expression profiling and immunohistology revealed that captopril treatment for 7 months strongly decreased the recruitment of pro-atherogenic immune cells into the aorta. Captopril-mediated inhibition of plaque-infiltrating immune cells involved down-regulation of the C-C chemokine receptor 9 (CCR9). Reduced cell migration correlated with ...
zora.uzh.ch/id/eprint/35443/

*  Expoldb: ex pression linked pol ymorphism d atab ase with inbuilt tools for analysis of expression and simple repeats | BMC...

Functional genomics in the post human genome sequencing era is greatly facilitated by correlating expression data with sequences of potential regulatory elements. The primary repositories of gene expression data such as Gene Expression Omnibus (GEO) [1], UniGene [1], Gene Expression Database (GXD) [2], and Gene Expression Atlas (GNF) [3] provide useful information on gene expression obtained from microarrays and other techniques, however, they provide limited information on the role of genetic elements that can potentially modulate gene expression. Thus, there is a need for databases integrating gene expression information with sequence information of potential genetic regulators with propensity for exhibiting sequence variability.. One such potential regulator is the dinucleotide repeat (TG/CA)n. The (TG/CA)n repeats are widely distributed, considered to be cis regulators of transcription, and above 12 repeat units tend to be polymorphic ...
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-7-258

*  Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues - CSHL Scientific...

RNA-sequencing (RNA-seq) measures the quantitative change in gene expression over the whole transcriptome, but it lacks spatial context. In contrast, in situ hybridization provides the location of gene expression, but only for a small number of genes. Here we detail a protocol for genome-wide profiling of gene expression in situ in fixed cells and tissues, in which RNA is converted into cross-linked cDNA amplicons and sequenced manually on a confocal microscope. Unlike traditional RNA-seq, our method enriches for context-specific transcripts over housekeeping and/or structural RNA, and it preserves the tissue architecture for RNA localization studies. Our protocol is written for researchers experienced in cell microscopy with minimal computing skills. Library construction and sequencing can be completed within 14 d, with image analysis requiring an additional 2 d.. ...
repository.cshl.edu/31922/

*  Gene expression profiling in the synovium identifies a predictive signature of absence of response to adalimumab therapy in...

We studied synovial tissue from DMARD-resistant RA patients before and 12 weeks after initiation of therapy with adalimumab. Adalimumab therapy resulted in a significant decrease in the number of CD68+ cells and in the expression of genes involved in cell division in all patients. In responders, we found a significant decrease in the numbers of CD68+, CD3+, and CD15+ cells. From a gene expression point of view, responders were characterized by significant changes in the expression of genes involved in cell division and in the regulation of immune responses. Moreover, ANOVAs performed at baseline indicated that overexpression of selected genes belonging to both families was associated with poor response to therapy, an observation that was confirmed by immunostaining experiments. Finally, in vitro experiments performed in FLSs indicated that several cytokines and combinations of cytokines had a significant effect on the expression of a panel of genes overexpressed in poor responders at ...
https://arthritis-research.biomedcentral.com/articles/10.1186/ar2678

*  Plus it

3703 Initial treatment of advanced ovarian cancer includes cydoreductive surgery followed by combination chemotherapy. However, the majority of tumors from women with stage III/IV ovarian cancer recur with poor response to additional chemotherapy or are refractory to their primary chemotherapy regimen. The aim of our study was to develop a gene expression signature predictive for chemoresponse in advanced stage serous papillary ovarian cancer. Gene expression profiling was performed on 52 chemonaive, microdissected advanced stage, high-grade papillary serous ovarian cancers using Affymetrix Human Genome U133 2.0 Plus microarrays. Patient samples were divided into 3 groups based on response to treatment. Nonresponders were considered refractory to chemotherapy (n=19), responders relapsing within 6 months after completion of therapy were defined as chemoresistant (n=14), and responders recurring beyond 6 months were considered chemosensitive (n=19). Each response group was divided into ...
cancerres.aacrjournals.org/content/67/9_Supplement/3703

*  Gene expression profiling of human gliomas reveals differences between GBM and LGA related to energy metabolism and notch...

Toda la información sobre las últimas publicaciones científicas de la Clínica Universidad de Navarra. Gene expression profiling of human gliomas reveals differences between GBM and LGA related to energy metabolism and notch signaling pathways
cun.es/pt/investigacao/publicacoes-cientificas/gene-expression-profiling-of-human-gliomas-reveals-differences-between-gbm-and-lga-related-to-energy-metabolism-and-notch-signaling-pathways

*  Modelling biological responses using gene expression profiling and linear dynamical systems - CUED Publications database

Rangel, C and Wild, DL and Falciani, F and Ghahramani, Z (2001) Modelling biological responses using gene expression profiling and linear dynamical systems. In: The 2nd International Conference on Systems Biology: The Future of Biology in the 21st Century (ICSB), 2001-11-4 to 2001-11-7, California, US pp. 248-256... Full text not available from this repository ...
publications.eng.cam.ac.uk/328947/

*  Plus it

Bladder cancer comprises of highly heterogeneous tumors and is a malignancy requiring a high surveillance because of the frequent recurrences and the poor clinical outcome when tumors progress into invasive disease. Patients also with superficial and invasive tumors have remarkably different 5-year survival rates reflecting their biological differences. The profiles of gene-expression signatures have become an important and promising way for cancer prognosis and treatment. In addition to their application in cancer class prediction and discovery, microarray gene expression signatures can be used for the prediction of patient survival. Gene expression data were collected from tumor specimens from 165 patients with Korean bladder cancer. We selected then genes use Cox proportional hazard model whose expression patterns are proportionally associated the length of cancer-specific survival (CFS). The expression levels of 256 probes were correlated with CFS time (p,0.005). In poor prognosis ...
cancerres.aacrjournals.org/content/72/8_Supplement/4211

*  Plus it

3295 Formalin-fixed, paraffin-embedded (FFPE) tissues represent the most widely available material for retrospective studies of human diseases. In recent years, archival tissues have become an invaluable resource for gene expression analysis for tumor classification and clinical outcome prediction in many cancer types. However, RNA extracted from FFPE tissues is significantly degraded, which makes it hard to work with using current microarray technology. Most gene expression profiling in FFPE tissues has so far been done using quantitative RT-PCR (qPCR), which allows monitoring of only a few genes in the sample. We have developed the DASL™ assay, a flexible, sensitive and reproducible gene expression profiling method. We have used this assay for parallel analysis of hundreds of genes in FFPE samples using universal fiber-optic bead arrays. The method can tolerate RNA degradation because it does not require an intact poly-A tail for cDNA ...
cancerres.aacrjournals.org/content/64/7_Supplement/763.3

*  Robust classification of bacterial and viral infections via integrated host gene expression diagnostics | Science Translational...

Improved diagnostics for acute infections could decrease morbidity and mortality by increasing early antibiotics for patients with bacterial infections and reducing unnecessary antibiotics for patients without bacterial infections. Several groups have used gene expression microarrays to build classifiers for acute infections, but these have been hampered by the size of the gene sets, use of overfit models, or lack of independent validation. We used multicohort analysis to derive a set of seven genes for robust discrimination of bacterial and viral infections, which we then validated in 30 independent cohorts. We next used our previously published 11-gene Sepsis MetaScore together with the new bacterial/viral classifier to build an integrated antibiotics decision model. In a pooled analysis of 1057 samples from 20 cohorts (excluding infants), the integrated antibiotics decision model had a sensitivity and specificity for bacterial infections of 94.0 and ...
stm.sciencemag.org/content/8/346/346ra91

*  Transcriptome-Level Signatures in Gene Expression and Gene Expression Variability during Bacterial Adaptive Evolution | mSphere

Conclusions.Here, we compare transcriptome patterns in heterogeneous adapted and unadapted bacterial populations in order to locate key genes and pathways contributing to adaptive resistance. While others have used mutant library selection approaches to detect genes which convey specific tolerances or resistances (60, 61), only transcriptome profiling allows for the detection of subtle and simultaneous changes across multiple genes. Ascertaining general signatures of adaptation is not trivial, due to the immense potential for heterogeneity in gene expression during adaptation (4, 5, 8). In this study, by intentionally generating diversity at the phenotypic as well as gene expression level via medium-term adaptation to diverse toxins, we identified a subset of 16 genes with significantly different expression characteristics across multiple adaptation conditions. Many of the target genes are supported by previous reports, though several are of unknown function, particularly those genes identified ...
msphere.asm.org/content/2/1/e00009-17

*  Entire transcriptome | Network Glia

USA. Table 28.S2: The astrocyte transcriptome (download). Analysis from Lovatt et al. (2007) was produced by comparing adult cortical GFAP-GFP+/GLT1+ astrocytes to GFAP-GFP-/GLT1- cells (n=3). Analysis from Cahoy et al. (2008) was produced by comparing postnatal (P)16-17 fluorescence activated cell sorting- (FACS) and panning-isolated astrocytes (n=5) to P16-17 panning-isolated neurons (n=3). Analysis from Doyle et al. (2008) was produced by comparing TRAP affinity-purified mRNA from BAC-transgenic Aldh1l1 mice. From Doyle et al. (2008), each sample (n=4) derived from several 8-10 week old mice, and was compared to unbound affinity-purified samples (n=2). Each of the three datasets was normalized individually using the RMA algorithm in R/Bioconductor. The same software was used to calculate statistical values using the limma package. Fold changes are log base 2. P-values are FDR-corrected. A representative probe was chosen for cases where a gene has more ...
networkglia.eu/node/229

*  the proposed action of styrylpyrone derivative in hsv-1 infected vero cells by differential gene expression - UniSZA Repository

This study was done to identify and characterize specific cellular genes expression during infection of host with HSV-1 and treatment with styrylpyrone derivative (SPD). SPD showed antiviral activitywith different modes of action against HSV-1. SPD was effective in inhibiting cell death when the substance was added at 2 hours to 4 hours post infection. Cell death was only observed when treatment was delayed to 5 and 6 hours post infection. Positive effect to this mode of action suggests that SPD were able to treat HSV-1 infected cells at two effective concentration of 1.563x10-7µM and 7.813x10-8µM in treatment mode [S+V]+SPD. Differential gene expression (DEG)method was used to determine and isolate the genes that are differentially expressed inHSV-1 infectedVero cellswith and without treatment with SPD. Results from DEG analysis showed that a total of 177 genes were expressed differentially with 89 cDNAs candidates were induced and 88 cDNAs candidates were repressed. All the genes were ...
erep.unisza.edu.my/3256/

*  Big Data and Drugs: BD2K Centers Solidify Emerging Approaches | Biomedical Computation Review

Mayo Clinic cancer researchers associated with the KnowEnG Center are also perturbing cells but with a different goal: They are most interested in which cells die in response to chemotherapy drugs. "We know that the same drug given to different patients elicits different responses," says Saurabh Sinha, PhD, principal investigator of the KnowEnG Center. "So this is just repeating that observation in a controlled setting in cell lines." The resistant cells are the problem: "You'd like to know why they are resistant," he says. So, for each individual cell line, the researchers also sequence the DNA and measure gene expression and methylation patterns before treatment. The goal: to determine whether these high-dimensional data (millions of gene variants and DNA methylation spots as well as tens of thousands of gene expression measurements) can accurately predict whether a particular drug would or would not work on a particular patient.. To tackle the computational and statistical challenges of ...
biomedicalcomputationreview.org/content/big-data-and-drugs-bd2k-centers-solidify-emerging-approaches

*  Gene expression differences between those of European and African ancestry affect response to drugs and infections - UChicago...

February 28, 2008: Differences in gene expression levels between people of European versus African ancestry can affect how each group responds to certain drugs or fights off specific infections, report researchers from the University of Chicago Medical Center and the Expression Research Laboratory at Affymetrix Inc. of Santa Clara, CA.
uchospitals.edu/news/2008/20080228-expression.html

*  Plus it

BackgroundBreast carcinoma is one of the most common causes of cancer related death worldwide. However marked differences in outcomes may reflect variation in diagnostic, staging and treatment. Serial Analysis of Gene Expression (SAGE) is a comprehensive profiling method that allows for global, unbiased and quantitative characterization of transcriptomes. A major advantage of SAGE is that once normalized it is possible to directly compare the levels of tags (short nucleotide sequences) generated by a single experiment with any other compatible available.MethodsTo gain an insight on the relationship between breast cancer transcriptomes and the disparate outcomes observed, we retrieve 18 SAGE libraries (4 Normal breast tissues, 11 primary breast tumors and 3 breast cancer metastatic tissues) from Cancer Genome Anatomy Project (CGAP). Data were analyzed by Correspondence Analysis (COA), Hierarchical clustering, Support Tree (ST) and Significance ...
cancerres.aacrjournals.org/content/69/24_Supplement/1165

*  Plus it

Most anticancer drug candidates, currently in clinical trials, have clear targets in molecular and cellular systems. However, such molecular targets are not always affected (or not correlated with efficacious endpoints) when the candidate is evaluated in a clinical setting. The gap between preclinical and clinical drug evaluation remains the bottle neck for anticancer drug development. There is an urgent need to develop better biological tools and models to ease the transition between in vitro and in vivo, and between preclinical and clinical settings. In our translational platforms, 170 human primary tumor models (HuPrimeTM) have been established directly from tumor fragments of the patients with many cancer types. In order to pick the best models for evaluation of targeted therapeutics, we have conducted a comprehensive molecular profiling of our models. This profiling includes Affymetrix whole genome expression, Illumina 1400 SNP of cancer related cancer genes for amplification, deletion, and ...
cancerres.aacrjournals.org/content/70/8_Supplement/637

*  Plus it

Genetic markers for disease and disease states commonly refer to the presence or absence of functional proteins due to genetic causes, a result that is often inferred to reflect the abnormal overexpression of a gene as the cause of excessive appearance of the fully functional gene product. Accepting this viewpoint, measurements of gene expression are currently being used in many aspects of classifying disease state and prognosis. Conversely, cell lines representing different diseases can be classified according to their expression patterns or profiles. As an example, within a panel of immortalized tumor cell lines, characteristics of each disease type's gene expression profile provide a biological readout of the biochemical processes relevant to the maintenance of the tumor cell (Alizadeh et al., 2000; Scherf et al., 2000; Covell et al., 2003). The absence of cellular mRNA is typically not a result of specific DNA mutations preventing translation but rather is a reflection of many factors ...
molpharm.aspetjournals.org/content/69/3/737

*  ActoFactor™ Recombinant Mouse Chemokine (C-X-C motif) ligand 12 (beta) - Creative Bioarray

Creative Bioarray produces the world's most comprehensive list of research-use cells, including tumor cells, primary cells, stem cells AND transformed cells. Creative Bioarray offers ActoFactor™ Recombinant Mouse Chemokine (C-X-C motif) ligand 12 (beta) for your research.
creative-bioarray.com/ActoFactor-Recombinant-Mouse-Chemokine-C-X-C-motif-ligand-12-beta-CSC-CTK0779-item-4105.htm

*  Avoid These Makeup Ingredients If You Want Clear Skin

Could your makeup be causing or making your acne worse? Comprehensive list of ingredients to avoid in makeup and skin care products if you have acne
thelovevitamin.com/19127/ingredients-avoid-makeup-acne/

*  RKO-E6 - Creative Bioarray

Creative Bioarray produces the world's most comprehensive list of research-use cells, including tumor cells, primary cells, stem cells AND transformed cells. Creative Bioarray offers RKO-E6 for your research.
creative-bioarray.com/RKO-E6-CSC-C9244W-item-42177.htm

*  Medical Treatment Services - Alphabet P

The below links are medical procedures that summarize the treatments at Bangkok Hospital Phuket. Browse your medical topic by using the comprehensive list P here.
phukethospital.com/Medical-Services/Medical-Procedures-P.php

*  Gene Expression Literature Detail

J:166689 Danalache BA, Gutkowska J, Slusarz MJ, Berezowska I, Jankowski M, Oxytocin-Gly-Lys-Arg: a novel cardiomyogenic peptide. PLoS One. 2010;5(10):e13643 ...
informatics.jax.org/gxdlit/key/116759

*  Acoperiri metalice

... : acoperiri metalice, constructii metalice, confectii metalice executie, structuri metalice, elemente metalice, produse metalice, profile metalice, sisteme constructii, confectii metalice proiectare, confectii...
ghidul.ro/vanzari-produse-servicii/acoperiri-metalice/

*  Optimal spliced alignments of short sequence reads | BMC Bioinformatics | Full Text

Next generation sequencing technologies open exciting new possibilities for genome and transcriptome sequencing. While reads produced by these technologies are relatively short and error-prone compared to the Sanger method, their throughput is several magnitudes higher. We present a novel approach, called QPALMA, for computing accurate spliced alignments of short sequence reads that take advantage of the read's quality information as well as computational splice site predictions. In computational experiments we illustrate that the quality information as well as the splice site predictions [1] help to considerably improve the alignment quality. Our algorithms were optimized and tested using artificially spliced genomic reads produced with the Illumina Genome Analyzer for the model plant Arabidopsis thaliana. ...
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-S10-O7

*  Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T)

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All general aspects of library construction and sequencing performed at the JGI can be found at Web Site. 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 4,321 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. A hybrid 454/Sanger assembly was made using Arachne assembler. Possible mis-assemblies were corrected and gaps between contigs were closed by custom primer walks from sub-clones or PCR products. Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 437 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of ...
standardsingenomics.org/content/2/1/1/

*  PhD Proposal: Genome scaffolding using emerging sequencing technologies and graph based methods | UMD Department of Computer...

Genome assembly is a critical step in most biological sequence analysis as it gives a nearly complete picture of the genome sequence. All the current sequencing technologies share the fundamental limitation that sequences read from the genome using a sequencer are much smaller than an entire genome.
ssltest.cs.umd.edu/event/2017/04/phd-proposal-genome-scaffolding-using-emerging-sequencing-technologies-and-graph-based

*  Next-Gen Sequencing Is A Numbers Game | August 18, 2014 Issue - Vol. 92 Issue 33 | Chemical & Engineering News

As new technologies such as Pacific Biosciences' rise, others are falling by the wayside. In late 2013, after an unsuccessful $6.8 billion attempt to acquire Illumina, Roche decided to close down its 454 Life Sciences NGS business and sunset its midrange sequencers by the end of 2016. The business still accounts for about 10% of the NGS market. Roche acquired 454 Life Sciences in 2007, two years after 454 launched the first NGS instrument based on a sequencing-by-synthesis method. It is called pyrosequencing and uses a luciferase to detect the release of pyrophosphate and emit light that is detected by a camera.. ...
cen.acs.org/articles/92/i33/Next-Gen-Sequencing-Numbers-Game.html

*  Genomic structure of nucleotide diversity among Lyon rat models of metabolic syndrome | BMC Genomics | Full Text

In this paper we report a simple technique to distinguish genomic regions of identity-by-descent (IBD) from those with different ancestry using genome resequencing results from a group of rat strains that shares a common origin but were selectively inbred for differing phenotypes. Genetic studies in phenotype-selected inbred rodent strains derived from a common ancestor are a common strategy to map loci for many complex disorders, ranging from anxiety [24, 25] to hypertension [26]. The similar genetic background strains minimizes the heterogeneity outside of the regions phenotypically selected, making identity-by-descent (IBD) mapping a means to eliminate disease-causing regions of the genome. However, their similar genetic backgrounds also present problems to the investigator, as their similarities result in a paucity of polymorphic markers available to attain an acceptable marker resolution for mapping. Using next-generation sequencing (NGS) techniques to resequence the genomes of these ...
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-197

*  Kraken Manual

Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers. This database contains a mapping of every k-mer in Kraken's genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer. The set of LCA taxa that correspond to the k-mers in a read are then analyzed to create a single taxonomic label for the read; this label can be any of the nodes in the taxonomic tree. Kraken is designed to be rapid, sensitive, and highly precise. Our tests on various real and simulated data have shown Kraken to have sensitivity slightly lower than Megablast with precision being slightly higher. On a set of simulated 100 bp reads, Kraken processed over 1.3 million reads per minute on a single core in normal operation, and over 4.1 million reads per minute in quick operation.. The latest released version of Kraken will be available at the ...
ccb.jhu.edu/software/kraken/MANUAL.html

*  DNA Sequencing | Contexo.Info

DNA carries the instructions for the processes of life from generation to generation. The goal of DNA research is to decode and understand those instructions
contexo.info/dna_basics/dna_analysis/dna_sequencing/

*  long oligonucleotides

In article ,cchan-2406961604010001 at 128.249.50.79,, cchan at bcm.tmc.edu (The Mighty Shing) says: , ,Could anyone tell me a company to make long oligonucleotides that are more ,than 80 bases long. I know GibcoBRL does not make oligos longer than 60 ,bases, and I've try Genosis but they still failed to make my oligos ,successfully after three attempts. Any help is greatly appreciated. , ,Chi. Try us! we have made ,90mers without problem. Send your postal address if you want any more info. John Fox Alta Bioscience ...
bio.net/bionet/mm/methods/1996-June/046137.html

*  9.8% CAGR for Oligonucleotide Synthesis Market Globally to 2019 Says a New Research Report Available at RnRMarketRe... ((PRWEB)...

(PRWEB) September 01 2014 The global oligonucleotide synthesis market is expected to reach $1712.1 million by 2019 from $1070.7 million in 2014 growing at a CAGR of 9.8% from 2014 to 2019. The global oligonucleotide synthesis market is categorized on the basis of products and services applications end users and geography. The synthesized oligonucleotides,9.8%,CAGR,for,Oligonucleotide,Synthesis,Market,Globally,to,2019,Says,a,New,Research,Report,Available,at,RnRMarketResearch.com,biological,advanced biology technology,biology laboratory technology,biology device technology,latest biology technology
bio-medicine.org/biology-technology-1/9-8-25-CAGR-for-Oligonucleotide-Synthesis-Market-Globally-to-2019-Says-a-New-Research-Report-Available-at-RnRMarketResearch-com-30207-1/

*  Oligonucleotide Synthesis Market: Latest Trends, Demand and Analysis, 2020 | Medgadget

Oligonucleotides are single-stranded and short RNA or DNA molecule that have a wide range of applications in research forensics and genetic testing. Oligon
https://medgadget.com/2016/10/oligonucleotide-synthesis-market-latest-trends-demand-and-analysis-2020.html

*  Optimal oligonucleotide sequences for TLR9 inhibitory activity in human cells: lack of correlation with TLR9 binding.

Toll-like receptor (TLR)9 performs our innate response to bacterial DNA, warning us of the presence of infection. Inhibitory oligodeoxyribonucleotides (INH-ODN) have been developed that selectively block activation of mouse TLR9. Their inhibitory mot
biomedsearch.com/nih/Optimal-oligonucleotide-sequences-TLR9-inhibitory/21393636.html

*  Full-length messenger RNA sequences greatly improve genome annotation

Background: Annotation of eukaryotic genomes is a complex endeavor that requires the integration of evidence from multiple, often contradictory, sources. With the ever-increasing amount of genome sequence data now available, methods for accurate identification of large numbers of genes have become urgently needed. In an effort to create a set of very high-quality gene models, we used the sequence of 5,000 full-length gene transcripts from Arabidopsis to re-annotate its genome. We have mapped these transcripts to their exact chromosomal locations and, using alignment programs, have created gene models that provide a reference set for this organism. Results: Approximately 35% of the transcripts indicated that previously annotated genes needed modification, and 5% of the transcripts represented newly discovered genes. We also discovered that multiple transcription initiation sites appear to be much more common than previously known, and we report numerous cases of alternative ...
drum.lib.umd.edu/handle/1903/8007

*  Plus it

DNA Samples. DNA samples from 60 CA, 60 AA, 60 HCA, and 60 MA subjects (sample sets HD100CAU, HD100AA, HD100CHI, and HD100MEX) were obtained from the Coriell Cell Repository (Camden, NJ). The present study was reviewed and approved by the Mayo Clinic Institutional Review Board.. DCKandCMPKGene Resequencing. Each of the 240 DNA samples studied was used to perform polymerase chain reaction (PCR) amplifications of all DCK and CMPK exons, splice junctions, and a portion of the 5′-FRs for each gene. This study was powered to make it possible to reliably detect variant alleles with minor allele frequency (MAF) of 2% in the 120 alleles required for studies in each of the four ethnic groups. For CMPK, a region identified by rVISTA (Loots et al., 2002), located upstream of the site of transcription initiation, contained a cluster of putative transcription factor binding sites and showed high sequence homology to orthologous sequences in the dog and mouse genomes. This region was also ...
dmd.aspetjournals.org/content/36/9/1951

*  Microbes & Human Health: Mutation in a primate-conserved retrotransposon reveals a noncoding RNAs a mediator of infantile...

The human genome is densely populated with transposons and transposon-like repetitive elements. Although the impact of these transposons and elements on human genome evolution is recognized, the significance of subtle variations in their sequence remains mostly unexplored. This study reports homozygosity mapping of an infantile neurodegenerative disease locus in a genetic isolate. Complete DNA sequencing of the 400-kb linkage locus revealed a point mutation in a primate-specific retrotransposon that was transcribed as part of a unique noncoding RNA, which was expressed in the brain. In vitro knockdown of this RNA increased neuronal apoptosis, consistent with the inappropriate dosage of this RNA in vivo and with the phenotype. Moreover, structural analysis of the sequence revealed a small RNA-like hairpin that was consistent with the putative gain of a functional site when mutated. This study show here that a mutation in a unique transposable ...
microbes-human-health.blogspot.com/2012/03/mutation-in-primate-conserved.html

*  NGS-resources: Fwd: Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

Here we show that, in a given condition, most protein coding genes have one major transcript expressed at significantly higher level than others, that in human tissues the major transcripts contribute almost 85 percent to the total mRNA from protein coding loci, and that often the same major transcript is expressed in many tissues. We detect a high degree of overlap between the set of major transcripts and a recently published set of alternatively spliced transcripts that are predicted to be translated utilizing proteomic data. Thus, we hypothesize that although some minor transcripts may play a functional role, the major ones are likely to be the main contributors to the proteome. However, we still detect a non-negligible fraction of protein coding genes for which the major transcript does not code a protein ...
ngs-resources.blogspot.com/2013/07/fwd-transcriptome-analysis-of-human.html

*  Stanford Computer Forum - Ali Jos Mashtizadeh: 2015 Security Workshop

The human genome contains the fundamental code that defines the identity and function of all the cell types and tissues in the human body. Genes are functional sequence units that encode for proteins. But they account for just about 2% of the 3 billion long human genome sequence. What does the rest of the genome encode? How is gene activity controlled in each cell type? Where do the regulatory control elements lie and what is their sequence composition? How do variants and mutations in the genome sequence affect cellular function and disease? These are fundamental questions that remain largely unanswered. The regulatory code that controls gene activity is made up complex genome sequence grammars representing hierarchically organized units of regulatory elements. These functional words and grammars are sparsely distributed across billions of nucleotides of genomic sequence and remain largely elusive. Deep ...
forum.stanford.edu/events/2017anshulkundajeinfo.php

*  DNA Sequences

Deoxyribonucleic acid (DNA) represents the most fundamental structure for which genes are composed. A strand of DNA consists of four basic molecules called nucleotides: A,T, G, C. When combined as a sequence, the nucleotides can represent a set of genetic instructions for the development of all cellular forms of life. The molecules are linked as pairs entwined in a double helix forming a chains of DNA strands. Some triplet base pairs of nucleotides are called codons. Codons along with other nucleotides and enzymes generate amino acids - the basic building blocks for proteins. The "expression" of these proteins is encoded ("written") in genes, in other words a gene is a DNA sequence (a string of nucleotides) that generates polypeptides and proteins. The genes provide a genetic code for proteins that an organism can "express." Genes are responsible for defining a species and making individualistic traits. The DNA structure was discovered in 1953 by Watson and Crick. The Human ...
musicalgorithms.ewu.edu/learnmore/DNAseq.html

*  DNATCO v2: Assignment of DNA conformers

Conformers are identified by four-letter symbols. 'A', 'B', 'Z' letters imply stacked bases with first/second nucleotide in A, B, or Z like conformation. 'NS' lables steps with Not Stacked bases. 'S' at 3rd or 4th position means that the 1st or 2nd base is in syn orientation ...
dnatco.org/v2/

*  First Base Is That Way: Teaching Tykes to Play Together : T-Ball Offers 4- and 5-Year Olds Confidence, Coordination, Caps...

Imagine the mortified look on Padre Manager Jack McKeon's face if first baseman Jack Clark were to shove the ball into the stomach of an onrushing baserunner, like a quarterback handing off to a
articles.latimes.com/1989-06-24/sports/sp-1859_1_role-models-tyke-t-ball-t-ball-program

*  hCard 1.0.1 XMDP profile

See section 3.5.4 of RFC 2426. If the value is a vCard, then use a nest hCard. For simplicity in that case, the same element that has the class name of "agent" should use the class name of "vcard ...
microformats.org/profile/hcard

*  Identification of a cDNA clone that contains the complete coding sequence for a 140-kD rat NCAM polypeptide. | JCB

Neural cell adhesion molecules (NCAMs) are cell surface glycoproteins that appear to mediate cell-cell adhesion. In vertebrates NCAMs exist in at least three different polypeptide forms of apparent molecular masses 180, 140, and 120 kD. The 180- and 140-kD forms span the plasma membrane whereas the 120-kD form lacks a transmembrane region. In this study, we report the isolation of NCAM clones from an adult rat brain cDNA library. Sequence analysis indicated that the longest isolate, pR18, contains a 2,574 nucleotide open reading frame flanked by 208 bases of 5' and 409 bases of 3' untranslated sequence. The predicted polypeptide encoded by clone pR18 contains a single membrane-spanning region and a small cytoplasmic domain (120 amino acids), suggesting that it codes for a full-length 140-kD NCAM form. In Northern analysis, probes derived from 5' sequences of pR18, which presumably code for extracellular portions of the ...
jcb.rupress.org/content/105/5/2335

*  Localization of Nox2 N-terminus using polyclonal antipeptide antibodies | Biochemical Journal

Nox2/gp91phox (where phox is phagocyte oxidase) is the catalytic membrane subunit of the NADPH oxidase, an enzyme complex found in phagocytic leucocytes which catalyses the formation of superoxide anion (O2•−), a reactive oxygen species involved in the host defence against pathogens. It is an integral membrane protein of 570 amino acids, which is predicted to contain multiple transmembrane domains [1,2]. The N-terminal part of the protein was shown to be involved in haem binding through histidine residues 101, 115, 209 and 222, located in helices III (101 and 115) and V (209 and 222) [3]. After proteolytic treatment of partially purified cytochrome b558, a spectrally stable fragment comprising the whole N-terminus and ending at amino acids 320 or 363 was recovered [4]. gp91phox has been proposed to contain the binding sites for the NADPH oxidase prosthetic group, FAD, and the substrate, NADPH [5,6]. Based on a weak primary structure similarity between the C-terminal domain of gp91phox and ...
biochemj.org/content/382/3/981

*  Homeo domain of the yeast repressor alpha 2 is a sequence-specific DNA-binding domain but is not sufficient for repression -...

The alpha 2 protein, the product of the MAT alpha 2 gene, is a regulator of cell type in the yeast Saccharomyces cerevisiae. It represses transcription of a group of cell type-specific genes by binding to an operator located upstream of each target gene. Fifteen in-frame deletions within the coding region of the MAT alpha 2 gene were constructed. The deletion alleles were examined for phenotypes conferred in vivo, and the encoded mutant proteins were assayed for ability to bind specifically to the operator in vitro. This analysis has revealed that the sequence-specific DNA-binding domain of alpha 2 is located within a region of 68 amino acids. This region of alpha 2 has significant homology with the homeo domain, a conserved sequence found in the products of several Drosophila homeotic and segmentation genes. In addition, there is a class of mutant alpha 2 proteins that binds tightly and specifically to the operator in vitro, but fails to repress ...
edoc.unibas.ch/5418/

*  Plus it

alpha 1-Adrenergic receptor (alpha 1-AR) subtypes (alpha 1A and alpha 1B) play a critical role in vascular smooth muscle contraction and circulatory homeostasis. Transcripts for these guanine nucleotide-binding protein-coupled receptors are extremely low in abundance, however, and isolation of their cDNAs is difficult. We have developed a novel technique for identifying rare clones in a cDNA library, which has been used successfully to isolate a cDNA clone encoding an alpha 1D-AR. A 564-bp polymerase chain reaction product encoding a region between the third and sixth transmembrane domains of the alpha 1D-AR was first generated using rat brain mRNA as template and highly degenerate primers. The primers corresponded to those domains but contained mismatches to the alpha 1B-AR sequences. A 3-kb transcript was identified with this polymerase chain reaction probe, by Northern analysis of rat hippocampus. However, traditional plaque hybridization failed to identify a cDNA in a ...
molpharm.aspetjournals.org/content/40/6/876

*  A library of 7TM receptor C-terminal tails. Interactions with the proposed post-endocytic sorting proteins ERM-binding...

Adaptor and scaffolding proteins determine the cellular targeting, the spatial, and thereby the functional association of G protein-coupled seven-transmembrane receptors with co-receptors, transducers, and downstream effectors and the adaptors determine post-signaling events such as receptor sequestration through interactions, mainly with the C-terminal intracellular tails of the receptors. A library of tails from 59 representative members of the super family of seven-transmembrane receptors was probed as glutathione S-transferase fusion proteins for interactions with four different adaptor proteins previously proposed to be involved in post-endocytotic sorting of receptors. Of the two proteins suggested to target receptors for recycling to the cell membrane, which is the route believed to be taken by a majority of receptors, ERM (ezrin-radixin-moesin)-binding phosphoprotein 50 (EBP50) bound only a single receptor tail, i.e. the beta(2)-adrenergic receptor, whereas N-ethylmaleimide-sensitive ...
forskningsdatabasen.dk/catalog/9502549

*  Info - Immune Response - Barnard Health Care

chromosomes, although some members are genetically linked together. For example CD90(Thy-l), CD-56(NCAM) and CD3e, y and 8 are all found on chromosome 11 at band position q23.. One commonly used approach for sequence comparisons with known members of the superfamily utilizes the Dayhoff ALIGN program which scores similarities between the candidate sequence and several sequences from accepted Ig gene superfamily members. The alignments used for such sequence comparisons need careful consideration, taking into account such factors as the 3 strand/loop organization and the repertoire of conserved amino acids. No residue is invariant in all Ig-related domains and the primary structure of the Ig-type domains can be very different. This is vividly illustrated by the Ig variable region genes where even proteins encoded by the same gene family are sometimes ,20% similar. Three domain patterns have been identified in the Ig gene superfamily, namely ...
https://barnardhealth.us/immune-response/info-mij.html

*  The promoter context is a decisive factor in establishing selective responsiveness to nuclear class II receptors | The EMBO...

A major unanswered question concerning control of gene expression is how diverse regulatory proteins bound to their cognate response elements transmit their transactivating or transrepressing signals to the general transcription machinery. Answering this question includes determining the number and character of factors that are involved in transmission of the signal, as well as the spatial relationships and constraints that operate at the promoter for these interactions. Recent evidence from many laboratories indicates a growing complexity of protein-protein as well as protein-DNA interactions, and that the combinatorial aspects, involving cell type‐ and/or factor‐specific co‐activators and co‐repressors, are critical determinants of whether a particular transcription factor elicits a cellular response.. Among many model systems, the ligand‐activated transcription factors that are members of the nuclear receptor superfamily have been of particular importance in the continuing ...
emboj.embopress.org/content/16/10/2861

*  No effect of cancer-associated SNP rs6983267 in the 8q24 region on co-expression of MYC and TCF7L2 in normal colon tissue |...

The strongest correlation between MYC and TCF7L2 expression was observed for assay "ex13-14" of TCF7L2 (r = 0.57- 0.60, p , 10-6), followed by assay "ex11-13" (r = 0.52-0.54, p , 10-6). The weakest correlation was detected for assay "ex11-13a" (r = 0.10 - 0.15, p = 0.12 - 0.28) (Table 1). These assays detect alternative splicing forms that include combinations of exons 11-13-14 and 11-13a-14 in the C-terminal end of the TCF7L2 transcripts (GenBank accession numbers FJ010174 and FJ010167). Both protein isoforms encoded by these splicing forms have long C-terminal reading frames (E-tails) with binding sites for the C-terminal binding protein (CtBP) involved in post-translational regulation of TCF7L2 expression [21, 22]. Protein fragments encoded by the alternative exons 13 and 13a share 68% identity (17 amino acids of 25, Figure 2). The form with exons 11-13-14 encodes a 30-amino-acid highly conserved motif with a CRAR F signature protein sequence, while in the form with exons 11-13a-14 this ...
https://molecular-cancer.biomedcentral.com/articles/10.1186/1476-4598-8-96

*  New information on the waste-disposal units of li... ( Important new information on one of ...)

...Important new information on one of the most critical protein machines... Using electron microscopy and a revolutionary new system for protein ...Says the team's other co-principal investigator and corresponding auth...Nogales who holds appointments with Berkeley Lab UC Berkeley and th...,New,information,on,the,waste-disposal,units,of,living,cells,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
bio-medicine.org/biology-news-1/New-information-on-the-waste-disposal-units-of-living-cells-23262-1/

*  Sense of touch/nerve research( le to use a host of experiments to iden...)

le to use a host of experiments to identify other protein parts of the... This work provides an important first step toward understanding t... The study was supported by the HHMI. ......,Sense,of,touch/nerve,research,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
news.bio-medicine.org/biology-news-2/Sense-of-touch-nerve-research-10869-3/

*  Site directed mutagenesis - Molecular Cloning

Hej guys. I have a big problem with my mutagenesis. I'm supposed to create 12 mutants, each of them one single point mutation. Unfortunateley it doesn't work and I'm very desperate now.. I designed my primers with the Quick change sdm programme. And all of them are above 80°C.And reverse and forward primers bind to the same sequence on opposite strands.. I have two plasmids one 8.5kb and the other one 7.9kb. So I make 6 mutations separatley in each of them. I followed the kit instructions (without having the kit, but having Pfu Turbo) and I could create 2 mutants in the 7.9kb plasmid and one in the 8.5kb very easily. After that eveything went down. I didn't get any colonies or I got some, which I couldn't recover in liquid media.. I begged my supervisor to buy the kit, but even with the kit it didn't work.. I started to optimise my PCR using normal Pfu and DMSO. And running the cycles 20 times (in the kit it says 12 times) to see if I can detect bands on agarose gel and yes I can (correct ...
protocol-online.org/biology-forums-2/posts/29972.html

*  Plus it

Interactions between GPCRs and their cognate G proteins are known to involve several different domains on both the receptor and the G protein heterotrimer. Within Gα, the best characterized GPCR contact site is the extreme C terminus where residues at positions -3 and -4 are particularly important for specific receptor recognition (Conklin et al., 1993, 1996; Kostenis et al., 1997c; Bahia et al., 1998; Blahos et al., 1998; Liu et al., 2002). We have recently demonstrated the importance of the linker I region of Gαq proteins in constraining the fidelity of receptor recognition. A highly conserved glycine residue in linker I (glycine 66) regulates coupling selectivity indirectly by playing a role in the specificity of nucleotide exchange within Gαq induced by ligand-activated GPCRs (Heydorn et al., 2004). Here, we analyzed 1) the relationship between the linker I region and the extreme C terminus of Gα in determining selective GPCR coupling and 2) whether different GPCRs use different Gα ...
jpet.aspetjournals.org/content/313/1/78

*  Biology-Online • View topic - A question about what living organisms are made up of.

I know that living organisms are made up of carbon-based molecules and other molecules, I am wondering what is meant by carbon-based molecules? Is it meant that it consists of more carbon than other elements? What other molecules are a living organism made up of ...
biology-online.org/biology-forum/post-161451.html

*  Recombinant Mouse GRO alpha protein (ab124601) | Abcam

Buy our Recombinant Mouse GRO alpha protein. Ab124601 is a full length protein produced in Escherichia coli and has been validated in SDS-PAGE, MS. Abcam…
abcam.com/recombinant-mouse-gro-alpha-protein-ab124601.html

*  Microbiology | OMNINOGGINOMNINOGGIN

Deoxyribosenucleic acid, as you know in humans and in other eukaryotic organisms codes our chromosomes and makes us the way we are!. Similarly, in prokaryotes, like bacteria, DNA makes up their genetic code or in other words what they are. This includes their function and their appearance.. Universally, DNA contains purines (adenosine, guanine) and pyrimidines (cysteine, thymine, uracil (found in RNA)). These guys are the bases, in which three of it together will code for a codon, that signifies an amino acid. A sequence of these codons assist with making up a peptide chain. As you know, peptides together, after having been rearranged into a 3D structure is a protein.. As you can see in the picture, DNA's backbone is connected by phosphodiester bonds (I can get into this later and why its called what its called). These bonds help create the phosphate backbone of DNA. Since phosphate groups (PO4-) are negatively charged, a chunk of PO4- used as the backbone of the DNA will make the DNA a ...
omninoggin.com/category/microbiology/

*  Amy E. Keating | MIT Biology

The α-helical coiled coil is the simplest of all protein-protein interaction motifs. Coiled coils consist of two or more α-helices that wrap around each other with a superhelical twist. They are characterized by a repeating sequence of seven amino acids, (abcdefg)n, in which the a- and d-position residues are predominantly hydrophobic and the e- and g-position residues are usually polar or charged. The regular sequence makes it possible to predict the occurrence of coiled coils in genomic sequence data. We estimate that ,5% of all proteins in S. cerevisiae, C. elegans, A. thaliana and D. melanogaster contain a coiled-coil region. It is likely that many of these coiled coils mediate protein-protein interactions or oligomerization. An important, unanswered question about coiled coils is how their interaction specificity is encoded in their sequences. We call this the "partnering problem" for coiled coils and are studying it using both ...
https://biology.mit.edu/people/amy_keating

*  NIOSHTIC-2 Publications Search - 20031872 - Identification of a novel domain at the N terminus of caveolin-1 that controls...

When cells are migrating, caveolin-1, the principal protein component of caveolae, is excluded from the leading edge and polarized at the cell rear. The dynamic feature depends on a specific sequence motif that directs intracellular trafficking of the protein. Deletion mutation analysis revealed a putative polarization domain at the N terminus of caveolin-1, between amino acids 32-60. Alanine subs
https://cdc.gov/niosh/nioshtic-2/20031872.html

*  What are various biochemical tests to identify bacteria? | Reference.com

Biochemical tests for identifying bacteria generally break down into two categories: gram positive tests and gram negative tests. Many tests exist in these two general categories; gram positive tests...
https://reference.com/science/various-biochemical-tests-identify-bacteria-12308e008ba65285

*  Recombinant human IL1 alpha protein (ab73567) | Abcam

Buy our Recombinant human IL1 alpha protein. Ab73567 is an active full length protein produced in Escherichia coli and has been validated in WB, FuncS…
abcam.com/recombinant-human-il1-alpha-protein-ab73567.html

*  Recombinant mouse Urokinase protein (ab92644) | Abcam

Buy our Recombinant mouse Urokinase protein. Ab92644 is an active full length protein produced in Insect cells and has been validated in SDS-PAGE. Abcam…
abcam.com/Recombinant-mouse-Urokinase-protein-ab92644.html

*  Recombinant Human p73 beta protein (ab102553) | Abcam

Buy our Recombinant Human p73 beta protein. Ab102553 is a full length protein produced in Baculovirus infected Sf9 cells and has been validated in WB…
abcam.com/recombinant-human-p73-beta-protein-ab102553.html

*  Recombinant Human FOXA1 protein (ab98301) | Abcam

Buy our Recombinant Human FOXA1 protein. Ab98301 is a full length protein produced in Escherichia coli and has been validated in WB, ELISA, SDS-PAGE. Abcam…
abcam.com/recombinant-human-foxa1-protein-ab98301.html

*  Recombinant Human Ran (mutated Q69 L) protein (ab90208)

Buy our Recombinant Human Ran (mutated Q69 L) protein. Ab90208 is a full length protein produced in Escherichia coli and has been validated in SDS-PAGE. Abcam…
abcam.com/recombinant-human-ran-mutated-q69-l-protein-ab90208.html

*  Recombinant human IL8 protein (ab73858) | Abcam

Buy our Recombinant human IL8 protein. Ab73858 is an active full length protein produced in Escherichia coli and has been validated in WB, FuncS, SDS-PAGE…
abcam.com/recombinant-human-il8-protein-ab73858.html

*  Recombinant Human MAPK11 protein (ab45159) | Abcam

Buy our Recombinant Human MAPK11 protein. Ab45159 is a full length protein produced in Escherichia coli. Abcam provides free protocols, tips and expert support…
abcam.com/recombinant-human-mapk11-protein-ab45159.html

*  Gene Expression Literature Summary - MGI

J:191236 Wang SZ, Ou J, Zhu LJ, Green MR, Transcription factor ATF5 is required for terminal differentiation and survival of olfactory sensory neurons. Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18589-94 ...
informatics.jax.org/gxdlit/marker/MGI:1919643

*  Recombinant Human KAT3B / p300 protein (ab82235) | Abcam

Buy our Recombinant Human KAT3B / p300 protein. Ab82235 is a full length protein produced in Baculovirus and has been validated in SDS-PAGE. Abcam provides…
abcam.com/recombinant-human-kat3b-p300-protein-ab82235.html

*  PROSITE

All these proteins share a number of conserved sequence motifs. Some of them are specific to this family while others are shared by other ATP-binding proteins or by proteins belonging to the helicases `superfamily' [4]. One of these motifs, called the 'D-E-A-D-box', represents a special version of the B motif of ATP-binding proteins. Some other proteins belong to a subfamily which have His instead of the second Asp and are thus said to be 'D-E-A-H-box' proteins [3,5,6]. Proteins currently known to belong to this subfamily are: ...
prosite.expasy.org/doc/PS00039

*  Recombinant Human SMARCA6 protein (ab114875) | Abcam

Buy our Recombinant Human SMARCA6 protein. Ab114875 is a full length protein produced in Wheat germ and has been validated in WB, ELISA, SDS-PAGE. Abcam…
abcam.com/recombinant-human-smarca6-protein-ab114875.html

*  Recombinant human CLK3 protein (ab85759) | Abcam

Buy our Recombinant human CLK3 protein. Ab85759 is an active full length protein produced in Baculovirus infected Sf9 cells and has been validated in WB…
abcam.com/recombinant-human-clk3-protein-ab85759.html

*  Recombinant human MNK2 protein (ab51441) | Abcam

Buy our Recombinant human MNK2 protein. Ab51441 is an active full length protein produced in Baculovirus infected Sf9 cells and has been validated in FuncS…
abcam.com/recombinant-human-mnk2-protein-ab51441.html

*  Recombinant human DCAMKL1 protein (ab101777) | Abcam

Buy our Recombinant human DCAMKL1 protein. Ab101777 is an active full length protein produced in Baculovirus and has been validated in WB, FuncS. Abcam…
abcam.com/recombinant-human-dcamkl1-protein-ab101777.html

*  Plus it

Annexin II can be found in vivo as p36, p36p11, and p362p112, and is involved in endocytosis, exocytosis, and membrane trafficking (8) . p36 belongs to a family of calcium- and lipid-binding proteins and is a substrate for receptor and nonreceptor protein kinases (9 , 10) . Recently, membrane p36 has been shown to mediate steroid rapid action (11) . p11 is a small calcium binding protein and shares sequence homologies with the S-100 family (12) . Overexpression of p36 increases p11 protein level with no change in its mRNA levels (13) , suggesting that p36 has a post-translational stabilizing effect on p11 protein. Thus, it is possible that the lack of p36 in prostate cancer gives rise to substantial degradation of p11 so that the rate of translation from p11 mRNA fails to compensate. The observation that negative p36 expression coexists with a weak expression of p11 in a small number of cancer cells may represent the early stage of p11 degradation. As the loss of p36 and subsequently p11 in ...
cancerres.aacrjournals.org/content/61/17/6331

*  Plus it

Preparation of human Ln-γ2 protein. Human Ln-5 and monomeric Ln-γ2 proteins were purified from culture medium of human gastric carcinoma STKM-1 and malignant melanoma Mum2B cells, respectively, as described previously ( 13).. Construction and expression of DIII, DIII/V, and DI/II. The cDNA of human Ln-γ2 was used as a template to generate DNA fragments encoding DI/II (nucleotides 1830-3580), DIII (nucleotides 1303-1737), and DIII/V (nucleotides 1-1820) by PCR. These PCR products were subcloned into the pcDNA3.1+ expression vector (Invitrogen), and their nucleotide sequences were confirmed. For transient expression of the encoded proteins, each expression plasmid (4 μg) was transfected into COS7 cells (100 mm dish) using Fugene 6 (Roche Diagnostics) and cells were cultured for 48 h in serum-free DMEM after 12 h of transfection. Conditioned medium was collected and concentrated by ammonium sulfate precipitation. Precipitates containing recombinant proteins were collected and dissolved in 20 ...
cancerres.aacrjournals.org/content/68/2/530

*  NIOD - Multi-Molecular Hyaluronic Complex | Ron Robinson LA

This advanced serum combines 12 forms of hyaluronic compounds in a peptide-charged delivery system to offer hydration and to help skin surface look plump, comfortable and uniform. Shop Ron Robinson for Niod serums and more today!
https://ronrobinson.com/niod-multi-molecular-hyaluronic-complex-110111.html

*  Channelpedia

The homology between Slack and Slick is high, especially within the putative six transmembrane domains and proximal carboxy terminal (Bhattacharjee et al., 2003 [1141]). Both channels resemble the Ca2+-activated K+ 'Slowpoke' (Slo) channel by containing very large carboxy termini in addition to the transmembrane domains (Salkoff et al., 2006 [1140]). The large carboxy termini of Slack, Slick and Slo contain "regulate the conductance of K+ (RCK) domains" (Bhattacharjee and Kaczmarek, 2005 [1137]; Salkoff et al., 2006 [1140]). These RCK domains are thought to be essential for ligand binding and concomitant gating for this class of potassium channel (Jiang et al., 2002 [625]; Ye et al., 2006 [1142]). ...
channelpedia.epfl.ch/ionchannels/69

*  Colony Screening PCR - OpenWetWare

We should have assembled Gene 68 and the vector together into one DNA construct which was transformed into bacterial cells to produce colonies. While each colony ought to have the correct DNA construct, both the assembly process and the process of Assembly PCR (templateless and finish PCR) that we used to create Gene 68 are not perfect and do, in fact, produce many smaller DNA fragments. We therefore always need to screen the bacterial colonies to verify that they contain a correct DNA construct. Colonies are checked first by colony PCR, which verifies the size of the gene, and then by DNA sequencing, which verifies that there are no mutations in the DNA sequence. When screening, we want to start with several clones to maximize the likelihood that we have at least one clone that is correct. We will therefore be setting up 8 PCR reactions (6 different DNA clones (bacterial colonies) plus positive and negative controls. Colony PCR is a commonly used method to quickly and directly screen ...
openwetware.org/wiki/Colony_Screening_PCR

*  SHUFFLE! / Characters - TV Tropes

These are the main and secondary characters that appeared in the SHUFFLE! Visual Novel and anime. The Protagonist of the series, Rin Tsuchimi started off …
tvtropes.org/pmwiki/pmwiki.php/Characters/Shuffle

*  Kelly McEvers | WUNC

Kelly McEvers is co-host of All Things Considered, NPR's award-winning afternoon newsmagazine. She hosts the program from NPR West in Culver City,
wunc.org/people/kelly-mcevers

*  CNN.com - Transcripts

Return to Transcripts main page. JOHN KING, USA. Note: This page is continually updated as new transcripts become available. If you cannot find a specific segment, check back later.. ...
cnn.com/TRANSCRIPTS/jkusa.html

*  Homo sapiens integrin subunit beta 3 (ITGB3), mRNA - Nucleotide - NCBI

Opens the Highlight Feature Bar and highlights feature annotations from the FEATURES table of the record. The Highlight Feature Bar can be used to navigate to and highlight other features and provides links to display the highlighted region separately. Links in the FEATURES table will also highlight the corresponding region of the sequence. More... ...
https://ncbi.nlm.nih.gov/nucleotide/47078291

*  Tactio - ReadWrite

Wearables are now a significant part of corporate wellness and remote patient monitoring programs. However, long-term investment from seniors remains a challenge, despite an increasing need for seniors to have better healthcare options. See Also: Richer, sicker seniors to drive medical wearables market growth Garmin and Tactio Health Group, two major companies involved in telehealth… Read more » ...
readwrite.com/tag/tactio/

*  Foods May Block Drug - tribunedigital-sunsentinel

Dear People's Pharmacy: What drugs interact with Glucophage? I take Glucophage at supper, but it's not controlling my blood sugar as well as the doctor thought it would. If I can't get my blood
articles.sun-sentinel.com/1997-08-21/lifestyle/9708200140_1_blood-sugar-glucophage-zoloft

*  Normal and Pathologic Functions of CTCF and Its Distinct Classes of DNA-targets - Victor Lobanenkov

The first US patent issued for CTCF in October 1999 included full length cDNAs sequences coding for exceptionally conserved gene ubiquitously expressed in somat...
grantome.com/grant/NIH/ZIA-AI000860-14

*  Data Model

Life on the cellular level is a network of molecular interactions. Molecules are synthesized and degraded, undergo a bewildering array of temporary and permanent modifications, are transported from one location to another, and form complexes with other molecules. Reactome represents all of this complexity as reactions in which input physical entities are converted to output entities. These reactions can occur spontaneously or be facilitated by physical entities acting as catalysts, and their progress can be modulated by regulatory effects of other physical entities. Reactions are linked together by shared physical entities: a product from one reaction may be a substrate in another reaction and may catalyze yet a third. It is often convenient, if sometimes arbitrary, to group such sets of interlinked reactions into pathways.. The functions of macromolecular entities such as proteins are often determined not only by their primary sequences but by chemical modifications they ...
reactomedev.oicr.on.ca/pages/documentation/data-model/

*  Tools to Calm --or Warn--Parents-to-Be - latimes

For most expecting families, few experiences match the first glimpse of the baby through an ultrasound. For women, it's often a sign that the baby is fine. For fathers, it's sometimes the first
articles.latimes.com/1998/sep/07/health/he-20253

*  Zhou: Shrinkage Estimation of Log Odds Ratios for Comparing Mobility Tables

Zhou: Statistical analysis of mobility tables has long played a pivotal role in comparative stratification research. In this article, I propose a shrinkage ...
https://psc.isr.umich.edu/pubs/abs/8809

*  Life Since Harlie: October 2014

Anyway, the next thing I know Murphy says, "Oh, 134? That's my event!" Oh no. Murphy was in the first heat! There was no way he was going to make it if they were announcing the event already! I told him to run (through a crowded building) but he did not make it. There was no way. Ugh. I wanted to cry. I went over to that area, and he didn't return. I saw his coach doing a lot of talking with a few people. It looked like they were talking about him. So, I was crossing my fingers that they could work him into another heat. When she appeared to be alone for a sec, I went over to her and told her that I was Murphy's mom and that I was really sorry that he missed his event. She was very kind and understanding and said it happens. She said they were looking for a place to put him, but all the heats were full. I stood by the pool and waited while the meet continued, praying that they would work this out for him. To think we sat there for three hours - for nothing?! Ugh! And I knew Tom was never going ...
lifesinceharlie.blogspot.com/2014/10/

Cellular microarray: A cellular microarray is a laboratory tool that allows for the multiplex interrogation of living cells on the surface of a solid support. The support, sometimes called a "chip", is spotted with varying materials, such as antibodies, proteins, or lipids, which can interact with the cells, leading to their capture on specific spots.Allele-specific oligonucleotide: An allele-specific oligonucleotide (ASO) is a short piece of synthetic DNA complementary to the sequence of a variable target DNA. It acts as a probe for the presence of the target in a Southern blot assay or, more commonly, in the simpler Dot blot assay.Gene signature: A gene signature is a group of genes in a cell whose combined expression patternItadani H, Mizuarai S, Kotani H. Can systems biology understand pathway activation?DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Abscription: During normal transcription, RNA polymerase transcribes a number of short nonproductive oligonucleotides, and this process is called abortive transcription. The trapped RNAPs have been named abscriptases and the synthesis of specific length oligonucleotides called abscription.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Coles PhillipsThermal cyclerProtein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Generalizability theory: Generalizability theory, or G Theory, is a statistical framework for conceptualizing, investigating, and designing reliable observations. It is used to determine the reliability (i.Community Fingerprinting: Community fingerprinting refers to a set of molecular biology techniques that can be used to quickly profile the diversity of a microbial community. Rather than directly identifying or counting individual cells in an environmental sample, these techniques show how many variants of a gene are present.Copy number analysis: Copy number analysis usually refers to the process of analyzing data produced by a test for DNA copy number variation in patient's sample. Such analysis helps detect chromosomal copy number variation that may cause or may increase risks of various critical disorders.Mature messenger RNA: Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. Unlike the eukaryotic RNA immediately after transcription known as precursor messenger RNA, it consists exclusively of exons, with all introns removed.Assay sensitivity: Assay sensitivity is a property of a clinical trial defined as the ability of a trial to distinguish an effective treatment from a less effective or ineffective intervention. Without assay sensitivity, a trial is not internally valid and is not capable of comparing the efficacy of two interventions.DNA condensation: DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.Ligation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.Antisense therapy: Antisense therapy is a form of treatment for genetic disorders or infections. When the genetic sequence of a particular gene is known to be causative of a particular disease, it is possible to synthesize a strand of nucleic acid (DNA, RNA or a chemical analogue) that will bind to the messenger RNA (mRNA) produced by that gene and inactivate it, effectively turning that gene "off".YjdF RNA motifEukaryotic transcription: Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells.Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Chromosome regionsBorosilicate glass: Borosilicate glass is a type of glass with silica and boron trioxide as the main glass-forming constituents. Borosilicate glasses are known for having very low coefficients of thermal expansion (~3 × 10−6 /°C at 20 °C), making them resistant to thermal shock, more so than any other common glass.Fixative (drawing): In drawing, a fixative is a liquid, similar to varnish, which is usually sprayed over a finished piece of artwork, usually a dry media artwork, to better preserve it and prevent smudging.CpG OligodeoxynucleotideAlternative splicing: Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene.Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Genetic variation: right|thumbWGAViewer: WGAViewer is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a genome wide association study (GWAS). Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium (LD) with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP.Mac OS X Server 1.0Amplified Ribosomal DNA Restriction Analysis: Amplified rDNA (Ribosomal DNA) Restriction Analysis is the extension of the technique of RFLP (restriction fragment length polymorphism) to the gene encoding the small (16s) ribosomal subunit of bacteria. The technique involves an enzymatic amplification using primers directed at the conserved regions at the ends of the 16s gene, followed by digestion using tetracutter Restriction enzymes.ParaHox: The ParaHox gene cluster is an array of homeobox genes (involved in morphogenesis, the regulation of patterns of anatomical development) from the Gsx, Xlox (Pdx) and Cdx gene families.PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.Polymerase-endonuclease amplification reaction: Polymerase-endonuclease amplification reaction (PEAR) is a DNA amplification technology for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI) cleavage releases monomeric duplex oligonucleotides.Sequence clustering: In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" (ESTs) or protein origin.Pituitary-specific positive transcription factor 1: POU domain, class 1, transcription factor 1 (Pit1, growth hormone factor 1), also known as POU1F1, is a transcription factor for growth hormone.Inverse probability weighting: Inverse probability weighting is a statistical technique for calculating statistics standardized to a population different from that in which the data was collected. Study designs with a disparate sampling population and population of target inference (target population) are common in application.Genetic imbalance: Genetic imbalance is to describe situation when the genome of a cell or organism has more copies of some genes than other genes due to chromosomal rearrangements or aneuploidy.CS-BLASTInfinite alleles model: The infinite alleles model is a mathematical model for calculating genetic mutations. The Japanese geneticist Motoo Kimura and American geneticist James F.DNA-binding proteinCertified reference materials: Certified Reference Materials (CRMs) are ‘controls’ or standards used to check the quality and metrological traceability of products, to validate analytical measurement methods, or for the calibration of instruments.Deletion (genetics)Phenotype microarray: The phenotype microarray approach is a technology for high-throughput phenotyping of cells.GC box: In molecular biology, a GC box is a distinct pattern of nucleotides found in the promoter region of some eukaryotic genes upstream of the TATA box and approximately 110 bases upstream from the transcription initiation site. It has a consensus sequence GGGCGG which is position dependent and orientation independent.List of sequenced eukaryotic genomesExtracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.Analytical quality control: Analytical quality control, commonly shortened to AQC refers to all those processes and procedures designed to ensure that the results of laboratory analysis are consistent, comparable, accurate and within specified limits of precision.analytical quality control (AQC) program to ensure the highest level of confidence in reported data Constituents submitted to the analytical laboratory must be accurately described to avoid faulty interpretations, approximations, or incorrect results.List of strains of Escherichia coli: Escherichia coli is a well studied bacterium that was first identified by Theodor Escherich, after whom it was later named.Gene duplication: Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene.Nucleic acid structure: Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar.Ferric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Transfer-messenger RNA: Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1.Gene polymorphismTriparental mating: Triparental mating is a form of Bacterial conjugation where a conjugative plasmid present in one bacterial strain assists the transfer of a mobilizable plasmid present in a second bacterial strain into a third bacterial strain. Plasmids are introduced into bacteria for such purposes as transformation, cloning, or transposon mutagenesis.Interval boundary element method: Interval boundary element method is classical boundary element method with the interval parameters.
Lattice protein: Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding.Open reading frame: In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of codons that do not contain a stop codon (usually UAA, UAG or UGA).

(1/28523) A novel method for determining linkage between DNA sequences: hybridization to paired probe arrays.

Cooperative hybridization has been used to establish physical linkage between two loci on a DNA strand. Linkage was detected by hybridization to a new type of high-density oligonucleotide array. Each synthesis location on the array contains a mixture of two different probe sequences. Each of the two probes can hybridize independently to a different target sequence, but if the two target sequences are physically linked there is a cooperative increase in hybridization yield. The ability to create and control non-linear effects raises a host of possibilities for applications of oligonucleotide array hybridization. The method has been used to assign linkage in 50:50 mixtures of DNA containing single nucleotide polymorphisms (SNPs) separated by 17, 693, 1350 and 2038 bp and to reconstruct haplotypes. Other potential uses include increasing the specificity of hybridization in mutation detection and gene expression monitoring applications, determining SNP haplotypes, characterizing repetitive sequences, such as short tandem repeats, and aiding contig assembly in sequen-cing by hybridization.  (+info)

(2/28523) Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents.

The effect of alkyltrimethylammonium ions on the thermostability of natural and modified DNA duplexes has been investigated. We have shown that the use of tetramethylammonium ions TMA+along with the chemical modification of duplexes allow the fine adjustment of T m and the possibility of obtaining several duplex systems with varied isostabilizedtemperatures, some of which show greater stability than those of natural DNA. This approach could be very useful for DNA sequencing by hybridization.  (+info)

(3/28523) Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes.

Comparing patterns of gene expression in cell lines and tissues has important applications in a variety of biological systems. In this study we have examined whether the emerging technology of cDNA microarrays will allow a high throughput analysis of expression of cDNA clones generated by suppression subtractive hybridization (SSH). A set of cDNA clones including 332 SSH inserts amplified by PCR was arrayed using robotic printing. The cDNA arrays were hybridized with fluorescent labeled probes prepared from RNA from ER-positive (MCF7 and T47D) and ER-negative (MDA-MB-231 and HBL-100) breast cancer cell lines. Ten clones were identified that were over-expressed by at least a factor of five in the ER-positive cell lines. Northern blot analysis confirmed over-expression of these 10 cDNAs. Sequence analysis identified four of these clones as cytokeratin 19, GATA-3, CD24 and glutathione-S-transferase mu-3. Of the remaining six cDNA clones, four clones matched EST sequences from two different genes and two clones were novel sequences. Flow cytometry and immunofluorescence confirmed that CD24 protein was over-expressed in the ER-positive cell lines. We conclude that SSH and microarray technology can be successfully applied to identify differentially expressed genes. This approach allowed the identification of differentially expressed genes without the need to obtain previously cloned cDNAs.  (+info)

(4/28523) Identification of the genes responsive to etoposide-induced apoptosis: application of DNA chip technology.

DNA chip technology was used in an attempt to identify target genes responsible for apoptosis induced by etoposide, a p53 activating topoisomerase II inhibitor used clinically as an antitumor agent. 62 Individual mRNAs whose mass changed significantly were identified after screening oligonucleotide arrays capable of detecting 6591 unique human mRNA species. 12 (Nine induced and three repressed) of the etoposide-responsive genes were further studied by Northern analysis and an agreement rate of 92%, was reached. Among the 12 genes studied, two (WAF1/p21 and PCNA) are known p53 regulatory genes, two (glutathione peroxidase and S100A2 calcium-binding protein) appear to be the novel p53 target genes and the others appear to be p53-independent. Based upon these findings, the signalling pathways that possibly mediate etoposide-induced apoptosis are proposed.  (+info)

(5/28523) Development of an oligonucleotide-specific capture plate hybridization assay for detection of Haemophilus parasuis.

An oligonucleotide-specific capture plate hybridization assay has been developed to rapidly, specifically, and sensitively detect Haemophilus parasuis from nasal swabs. Several in vitro studies have been performed to determine the sensitivity and specificity of the test, and in vivo studies have validated this technique in pigs. Results suggest that the assay detects <100 colony-forming units/ml in a pure culture and gives a positive result when H. parasuis is present in a ratio of 1:10(3)-10(4) in a mixed culture, and the probe does not hybridize with other related species found in the upper respiratory tract. This assay is more sensitive than culture for detection of the microorganism from nasal swabs and lesions.  (+info)

(6/28523) Versatile derivatisation of solid support media for covalent bonding on DNA-microchips.

A chemistry was developed that permits on DNA-arrays both the covalent immobilisation of pre-fabricated nucleic acids-such as oligonucleotides, PCR-products or peptide nucleic acid oligomers-and the in situ synthesis of such compounds on either glass or polypropylene surfaces. Bonding was found to be stable even after some 30 cycles of stripping. Due to a dendrimeric structure of the linker molecule, the loading can be modified in a controlled manner and increased beyond the capacity of glass without negative effects on hybridisation efficiency. Also, the chemistry warrants the modulation of other surface properties such as charge or hydrophobicity. Preferentially, attachment of nucleic acids takes place only via the terminal amino-group of amino-modified oligonucleotides or the terminal hydroxyl-group of unmodified molecules so that the entire molecule is accessible to probe hybridisation. This derivatisation represents a support chemistry versatile enough to serve nearly all current forms of DNA-arrays or microchips.  (+info)

(7/28523) Timely toxicology.

The ToxChip, a DNA microarray chip, allows the monitoring of the expression levels of thousands of different genes at a time, thereby condensing months of painstaking laboratory tasks into a day's work. For toxicology researchers in particular, this tool is important because it promises a more effective way to identify environmental hazards and their effects on DNA. The ToxChip, developed by NIEHS scientists J. Carl Barrett, Cynthia Afshari, and Emile F. Nuwaysir, could transform the way toxicologists approach environmental problems.  (+info)

(8/28523) DNA microarray technology: the anticipated impact on the study of human disease.

One can imagine that, one day, there will be a general requirement that relevant array data be deposited, at the time of publication of manuscripts in which they are described, into a single site made available for the storage and analysis of array data (modeled after the GenBank submission requirements for DNA sequence information). With this system in place, one can anticipate a time when data from thousands of gene expression experiments will be available for meta-analysis, which has the potential to balance out artifacts from many individual studies, thus leading to more robust results and subtle conclusions. This will require that data adhere to some type of uniform structure and format that would ideally be independent of the particular expression technology used to generate it. The pros and cons of various publication modalities for these large electronic data sets have been discussed elsewhere [12], but, practical difficulties aside, general depositing must occur for this technology to reach the broadest range of investigators. Finally, as mentioned at the beginning of this review, it is unfortunate that this important research tool remains largely restricted to a few laboratories that have developed expertise in this area and to a growing number of commercial interests. Ultimately the real value of microarray technology will only be realized when this approach is generally available. It is hoped that issues including platforms, instrumentation, clone availability, and patents [20] will be resolved shortly, making this technology accessible to the broadest range of scientists at the earliest possible moment.  (+info)



directed oligonucleotide synthesis


  • 3. The method of claim 2 wherein spatially directed oligonucleotide synthesis is performed by light-directed oligonucleotide synthesis. (google.com)
  • 8. The method of claim 3 wherein spatially directed oligonucleotide synthesis comprises deprotecting oligonucleotides by exposure to an acid, and the test condition is the identity of the acid. (google.com)

nucleic


  • 1. A method of manufacturing oligonucleotide arrays comprising manufacturing oligonucleotide arrays by spatially directed nucleic acid synthesis in high volume and testing selected arrays wherein the selected arrays are tested for the amount of depurination of oligonucleotides. (google.com)
  • Oligonucleotides also have its application in nucleic acid array based technology, diagnostics, genetic engineering, next-generation sequencing, synthetic biology, genomics, cloning and nucleic acid based detection. (medgadget.com)

Genes


  • Rise importance of personalized medicine, rising innovation in genomics and increasing demand for synthetic genes are some of the key factors driving the growth for global oligonucleotide synthesis market. (medgadget.com)
  • Using a combination of spatial molecular network and gene ontology enrichment analyses, it is shown that genes involved in cell wall metabolism are found in multiple modules, but cluster into two main groups that exhibit peak expression at 3 DAP to 4 DAP and 5 DAP to 8 DAP. (edu.au)
  • Cryptococcus gattii virulence composite: candidate genes revealed by microarray analysis of high and less virulent Vancouver island outbreak strains. (nih.gov)
  • By expression microarray analysis, 202 genes showed at least a 2-fold difference in expression with 108 being up- and 94 being down-regulated in strain R265 compared with strain R272. (nih.gov)

molecular


  • In addition, increasing researches in molecular biology is also fuelling the growth of global oligonucleotide synthesis market. (medgadget.com)

Genome


  • Specifically, we performed genome wide analysis of DNA methylation in samples of chorionic villus (CVS) and maternal blood cells (MBC) using both commercially available and custom designed microarrays. (nih.gov)
  • We analyzed transcriptome profile of different oocyte and CC samples using Affymetrix GeneChip Bovine Genome array containing 23000 transcripts. (nih.gov)

microarray analysis


  • We explored the effects of human immunodeficiency virus-1 (HIV-1) and its Tat transactivator on these primary antigen-presenting cells using DNA microarray analysis and functional assays. (nih.gov)

transcripts


  • b) Quantitative RT-PCR analysis of post-switched Iμ-CH transcripts (PST) in Batf+/+ or Batf−/− B-cells stimulated for 4 days as in Supplementary figure 10a, b. (nih.gov)

functional


  • We have carried out a detailed structural and functional analysis of the placental epigenome at its maternal interface. (nih.gov)

expression


  • a) FACS analysis for IgA, IgM and B220 expression by lymphocytes from Peyer's patches (PP) or Lamina propria (LPL) of Batf+/+ or Batf−/− mice was performed. (nih.gov)
  • We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies. (labome.org)

test


  • 6. The method of claim 3 comprising synthesizing at least two ensembles of the same sequence-specific oligonucleotide in at least two areas of the substrate and exposing each ensemble to a different test condition. (google.com)

experiments


  • The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time. (labome.org)

high


  • Asia is expected to show high growth rates in the next five years in global oligonucleotide synthesis market. (medgadget.com)
  • However, manufacturing high-quality RNA-interference oligos and large scale synthesis of oligonucleotides could lead challenges for the global oligonucleotide synthesis market. (medgadget.com)

factors


  • However, stringent regulations and continuous downward price pressure are some of the major factors restraining the growth for global oligonucleotide synthesis market. (medgadget.com)

primary


  • Epigenetics can be loosely defined as the study of cellular "traits" that influence biological phenotype in a fashion that is not dependent on the underlying primary DNA sequence. (nih.gov)