The end of a nucleic acid chain that terminates in a free hydroxyl group.
The end of a nucleic acid chain that terminates in a free phosphate group.
The dehydrated form of right-handed helical DNA obtained under non-physiological conditions.
ab initio gene prediction
The prediction of exon structure within a gene using computational algorithms. Exons are ligated to form the structural protein that is encoded by the gene.
The absence of living systems.
An antibody engineered to carry out an enzymatic reaction;a catalytic antibody. Typically the antibody is raised against a transition state analog for the reaction to be catalyzed.
The unique identifier assigned to new sequence information submitted to a major database.
The adaptation of an organism to new environmental conditions.
A compound that may be superimposed on its mirror image. Achiral molecules do not display topological handedness.
A non-heritable genetic change occurring within a somatic cell; a somatic mutation.
Describes a chromosome with a centromere near the end.
The molecular assembly that corresponds to the transition state of a chemical reaction.
A protein that up-regulates gene expression by binding to transcription control sites.
The natural immunological response to an antigen.
The catalytic site of an enzyme.
Vectorial transport of a molecule or ion against a concentration gradient by a membrane-bound protein complex.
The change in the response of a system over time; functional or structural changes that allow an organism to respond to changes in the environment.
The covalent complex formed when a chemical binds a biomolecule, such as DNA or a protein.
A purine that is one of the five bases found in nucleic acids.Adenine base pairs with thymine in DNA and with uracil in RNA.
A virus used to construct vectors that introduce genes into cultured cells.
A cancer of the epthelial cells that form the ducts of glandular organs.
A benign tumor formed by an increase in the number of epithelial cells that form the ducts of glandular organs.
A nucleoside form of adenine.
Adenosine triphosphate (ATP)
A nucleotide that releases energy upon hydrolysis of the phosphate bonds. The energy stored in ATP may drive synthetic processes; be converted to mechanical, light, or electrical energy; or be released as heat.
A group of non-enveloped icosahedral viruses. Recombinant forms of adenovirus are used as gene delivery vectors.
A substance that enhances or diversifies the immune response; a drug that modulates the actions of other drugs.
Procedures for evaluating the absorption, distribution, metabolism, and elimination of pharmaceuticals.
Adult stem cell
A stem cell derived from adult bone marrow. Like embryonic stem cells, adult-derived cells may differentiate into multiple cell types.
A measure of the binding strength between two molecules.
A chromatographic method used to isolate biomolecules that reversibly bind a molecule attached to a solid-phase support.
An amino acid sequence added to a recombinant protein to facilitate purification of the expressed protein.
A carbohydrate polymer used as a matrix for electrophoresis.
The non-carbohydrate component of a glycoside.
A ligand that binds a receptor at a site adjacent to the active site.
A bacterium that is used for plant genetic engineering.
An explicit computational procedure that uses a precise sequence of simple operations to perform a complex operation. Bioinformatics algorithms enable processing, analysis, and visualization of sequence-related data.
A reaction or response that occurs fully or not at all.
A variant form of a given gene that occupies a specific chromosomal locus.
The expression of genes from the maternal or paternal chromosome but not both, due to chromosomal inactivation. In B-lymphocytes, allelic exclusion assures that all antibodies expressed are derived from the same allele.
A chemical or protein antigen that induces an allergic reaction. Allergens typically increase the plasma concentration of IgE which induces mast cells to release histamine.
An inflammatory immune response to a nonpathogenic antigen.
Genetic differences between individuals of the same species.
A graft of tissue between two genetically different members of the same species.
Reversible modification of protein structure and activity by an effector molecule that binds at a site other than the active site.
The ability of an effector molecule (ligand) to change the conformation and activity of a protein.
A protein variant arising from genetic differences between individuals of the same species.
One of the different forms of an enzyme found in individuals of the same species, due to the presence of multiple alleles in the population.
A helical configuration formed by a protein chain in which successive turns are held together by hydrogen bonds between the peptide links.
Alternative splice form
One of the set of proteins with related sequences (isoforms) that may be generated by alternate splicing of exons within a single mRNA.
The process by which alternative exons within a single RNA are combined during the splicing process, resulting in the generation of mRNAs encoding different protein sequences. Alternative splicing may be tissue- or disease-specific.
A 3-5% component of the human genome, consisting of 300-bp repetitive DNA sequences containing an Alu 1 restriction site.
The UAG codon, one of three codons that code for termination of transcription of an mRNA and release of the newly synthesized polypeptide chain from the ribosome.
The -NH2 group, a weakly basic group found in organic molecules.
The end of a polypeptide that contains a free amino group; the N-terminus.
Aminoacyl site (A site)
One of two sites in the large ribosomal subunit involved in protein translation. The aminoacyl site binds the incoming aminoacyl-tRNA during protein synthesis.
A tRNA charged with the appropriate amino acid. The amino acid is esterified to the 3' end of the tRNA. Aminoacyl-tRNAs function as ribosomal adaptors during translation of mRNA into protein.
An enzyme that catalyzes the attachment of the appropriate amino acid to the 3' end of a tRNA.
The abbreviation for adenosine monophosphate; also written as 5' AMP, since the phosphate is attached to ribose moiety at position 5.
An alpha helix that is hydrophobic on one side and hydrophilic on the other.
Describes a molecule containing both hydrophobic and hydrophilic regions.
Capable of photosynthetic or chemotrophic growth.
Ampholyte, carrier ampholyte
One of a set of small electrolytes with differing isoelectric points used to establish a pH gradient in gels.
Describes a molecule that reacts as an acid with bases, and as a base with acids.
A virus that infects a wide range of mammalian host cell types.
Proteins with beta sheet structure that form extracellular aggregates.
An energy-requiring biochemical process that synthesizes complex molecules from simpler reactants.
Any microorganism that grows in the absence of molecular oxygen.
A molecule that is structurally and functionally related to another molecule.
The deduction of the function of a new gene or protein by comparison with genes or proteins of known function using similarity searching and alignment.
An increase in immune response following repeated exposure to an antigen.
The stage of nuclear division when chromatids (homologous chromosomes) move to the poles of the mitotic spindle.
Extreme immune sensitivity produced upon the reintroduction of an antigen.
The reversion of a cell to a simpler, undifferentiated form.
Anaplerotic metabolic pathway
A biochemical pathway that replenishes intermediates needed by a central metabolic pathway.
A deficient immune response due to inactivated B- and T-lymphocytes.
The formation of new blood vessels during embryogenesis, tissue repair, or tumorigenesis. Development of anti-angiogenic agents is a focus of anti-cancer strategies.
A plasminogen fragment with anti-angiogenic properties.
A unit of measure used to measure inter-atomic distances within molecules equal to 10-10 meter.
An ion with a negative charge. Anions migrate to the anode of an electrophoretic gel.
Analysis and commentary added to sequence data in databases. Annotation provides in-context information about coding and non-coding sequence within genes, patterning and motifs, similarities, known or predicted protein structure and function, as well as links to external data, such as clinical observations.
The positive electrode of an electrophoretic system toward which anions migrate.
Ligands that bind to the active site on a protein.
An antibody that recognizes and is complementary to the binding site of another antibody.
A tumor suppressor gene.
A glycoprotein produced by B-lymphocytes of vertebrates capable of recognizing and reversibly binding an antigen. Antibodies consist of four protein chains (two heavy chains and two light chains) and a polysaccharide moiety.
Antibody combining site
The antigen (epitope) recognition and binding site of an antibody. The variable regions of both heavy and light chains contribute to the antibody combining site.
Antibody directed enzyme prodrug therapy (ADEPT)
A two-step treatment protocol that involves the administration of an inactive prodrug that is subsequently activated in a target-specific manner by an antibody linked to an enzyme that activates the prodrug.
Antibody mimetic protein
Proteins selected by directed molecular evolution that have high affinity for a molecular target.
Three-nucleotide sequence of a transfer RNA (tRNA) that is complementary to the three-nucleotide codon of an mRNA.
A glycoprotein found in serum of artic fish that prevents ice crystals from forming.
A molecule, molecular assembly, or organism that is specifically recognized by an antibody.
An unrelated protein that resembles an antibody target protein and cross-reacts with the antibody.
Antigen presenting cell (APC)
A cell that recognizes an antigen to be neutralized, processes it, and incorporates the resulting peptides into the major histocompatibility complex (MHC) molecules on the cell surface. The resulting MHC-peptide complexes are then presented to T-lymphocyte for destruction.
A specific region of an antigenic molecule that binds an antibody (epitope). The antigenic determinants of proteins are typically peptides.
A substance that attenuates the response to hormones.
A substance that prevents utilization of a metabolite.
An agent that decreases the rate of mitosis.
A mutant gene that produces the opposite effect of the wild-type gene at the same locus.
An agent that decreases the rate of mutation.
A mutant gene that reduces the rate of mutation.
A drug that reduces or prevents the growth of a neoplasm.
A compound that inhibits oxidation, often because it is preferentially oxidized. Antioxidants trap free radicals, breaking the chain of reactions and preventing damage to cell components.
Parallel linear structures with directional polarity. DNA strands in double-stranded DNA are antiparallel.
A transmembrane exchange protein that transports two different molecules in opposite directions across a membrane.
Complementary in sequence to an RNA molecule.
Serum that contains a high level of antibodies against a specific antigen.
A mutation that reduces the effects of a gene expression suppressor.
A protein that prevents RNA synthesis termination and allows RNA polymerase to continue transcribing genes.
Lacking a nucleus.
A plasma membrane region of epithelial cells that faces the lumen and is involved in transport.
Incomplete growth or development of a structure.
A small marine organism widely used for neurobiological studies.
The protein part of an enzyme, without prosthetic groups or cofactors.
The protein component of a lipoprotein.
The protein component of a conjugated protein.
A programmed or controlled form of cell death characterized by the loss of cell junctions and microvilli, condensation of the cytoplasm, margination of the nuclear chromatin, and fragmentation of the nucleus.
Short strands of DNA that bind protein targets. Decoy aptamers inactivate DNA-binding proteins, such as transcription factors, resulting in the activation or inactivation of genes.
A DNA site from which the purine base has been lost by cleavage of the glycosidic linkage.
An enzyme with ATPase and ADPase activity used to deplete ATP in reactions.
Arabidopsis thaliana (A. thaliana)
A small plant used as a model organism for the study of plant genetics.
Eicosatetraenoic acid, a precursor for the synthesis of signaling molecules, such as prostaglandins and thromboxanes. Arachidonic acid is released from cell membrane phospholipids, including phosphatidyl inositol, by phospholipases.
A form of parallel synthesis used in combinatorial chemistry in which the reactions take place in a spatially organized array.
Two-dimensional arrays of recombinant clones. Each primary clone is identified by row and column.
A complement-dependent hypersensitivity reaction that occurs when an antigen reacts with a precipitating antibody, forming microprecipitates that damage cells.
A minimal chromosome assembled from cloned DNA sequences and coding for an origin of replication, a centromere, and telomeres.
An accumulation of fluid in the peritoneal cavity. When due to the growth of a hybridoma, the ascites fluid contains a high concentration of monoclonal antibodies.
Procedures that prevent the contamination of cultures, media, animals, and persons by extraneous microorganisms.
A procedure for detecting the presence, estimating the concentration, and determining the biological activity of a macromolecule, molecule, ion, or cell. Assays are based on measurable parameters that enable the evaluation of differences between samples and controls. Sensitivity, the ability to detect small amounts of a substance, and specificity, the ability to detect only the analyte, are essential features of an assay.
The compiling of overlapping gene sequence fragments into a single, continuous sequence.
Association constant (Ka)
The measure of the degree of association of a complex. The larger the Ka, the more tightly the components are bound.
A glial cell found in the brain with a star-like shape. Astrocytes provide physical and metabolic support for neurons.
A tumor arising from astrocytes, glial cells found in the brain.
Atomic force microscopy (AFM)
A form of scanning probe microscopy that provides atom-level information about molecules. The surface of a molecule is scanned with a microprobe in an x-y grid, and the force encountered is measured with piezoelectric sensors.
A vaccine based on an attenuated virus that has low virulence due to genetic inactivation or chemical treatment.
One quintillionth mole; 10-18 mole.
A prefix that indicates self-origin.
The response of the immune system to normal tissues, cells, or molecules within the body.
Derived from the same organism.
Autonomously replicating sequence (ARS)
A plasmid sequence that confers the ability to replicate in a yeast cell.
A technique that uses x-ray film to detect radiolabeled molecules following separation by gel electophoresis. Recently autoradiographs have been supplanted by nonradioactive methods based on the detection of chemiluminescence.
A chromosome not involved in sex determination. The human genome consists of 22 pairs of autosomes, and one pair of sex chromosomes.
A microorganism that synthesizes all organic molecules from inorganic sources.
A microorganism strain that requires nutrients not required by the wild-type strain.
A glycoprotein that binds with high affinity to biotin.
A measure of the affinity of the binding of an antibody to an antigen.
A long part of a cell that transmits nerve impulses from the neuron cell body to the axon terminus, resulting in neurotransmitter release.
The fully hydrated right-handed helical form of DNA seen in vivo.
Bacille Calmette-Guerin (BCG)
An attenuated form of a mycobacterium that activates the immune system. BCG extracts are used in adjuvants to stimulate the immune response.
Bacillus thuringiensis (B. thuringiensis, B.t.)
A microorganism that produces a protein that acts as a biopesticide.
Unicellular prokaryotic organisms that lack a membrane-bounded nucleus.
Bacterial artificial chromosome (BAC)
A vector capable of replication in bacteria that is used to clone 100 to 300 kb DNA fragments into E. coli cells.
A virus that infects bacterial hosts, and may be utilized to introduce genes. Phage are widely used as cloning and expression vectors.
A viral pathogen, such as Autographa californica, that replicates in lepidopteran larvae. Baculovirus expression vectors are widely used for the synthesis of proteins that require post-translational modifications.
Baculovirus expression system
A cellular protein synthesis system based on recombinant baculovirus vectors that is capable of post-translational processing of proteins. Translated proteins are glycosylated, acylated, and proteolytically cleaved in the cytoplasm of the lepidopteran cell.
One of two hybrid proteins used in two-hybrid protein-protein interaction assays.
A single condensed X chromosome. The Barr body is found in the nuclei of female somatic cells.
A relatively undifferentiated cell in an epithelial sheet that forms more specialized cells.
Basal cell carcinoma
A non-metastatic cancer derived from the basal cells of the epithelium.
A proteoglycan and glycoprotein sheet secreted by cells to form the extracellular matrix. The basal lamina, also called the basement membrane, is a three-layer structure that influences cell polarity, differentiation, and migration.
Base pair (bp)
A unit of nucleic acid length, based on the number of paired bases (adenine and thymine, guanine and cytosine) in a DNA double helix.
The order of nucleotide bases in a DNA molecule.
The stacking of base pairs in parallel planes within the interior of a helical double-stranded nucleic acid.
Basic local alignment search tool (BLAST)
A nucleic acid and protein sequence comparison program based on the creation of a matrix of similarity scores for all possible pairs of residues, defining the high-scoring segments, and statistically evaluating the significance of the results.
The region of the cell plasma membrane adjacent to the basal lamina.
A multinucleated leucocyte characterized by cytoplasmic granules that release histamine and other hypersensitivity response effectors.
A microarray technology based on the attachment of individual probes to microbeads. The beads may be embedded in the microwells formed at the tip of a bundle of optical fibers.
Free immunoglobulin light chains synthesized by myeloma cells.
A tumor that is not cancerous and does not metastasize.
A protein structural element consisting of antiparallel beta strands that forms a hydrophobic protein core.
A protein structural element consisting of a hairpin turn between two beta strands.
A protein configuration in which two beta strands are hydrogen bonded to each another.
The protein configuration resulting from the alignment of multiple adjacent beta strands and the formation of hydrogen bonds between them.
A protein region, from 5 to 10 residues in length, in an almost fully extended conformation.
Replication of DNA in two directions from the origin of replication.
Consisting of two layers, often used in reference to lipid bilayer structures.
An assay that uses a living system, such as an intact cell, as a component.
The use of biological systems or their components for chemical synthesis or transformation.
Micro-scale systems for bioanalysis based on integrated circuit technology. Biochips include molecular microarrays (gene chips, protein chips, small molecule chips), microfluidics systems (lab-on-a-chip), and fiber-optic-based arrays.
A compound that is toxic to living systems.
An iterative process consisting of synthesis of combinatorial chemical libraries followed by screening in biological systems to evaluate function.
Biocontrol, biological control
The control of one species by another, as in biological pesticides.
The conversion of one chemical to another by a living system, such as a bacterial cell.
A material that can be broken down to simpler components by a biological process.
The genetic diversity of natural organisms. Collections of millions of microbial genomes harvested from global ecosystems are the starting point for developing new processes and molecules.
The study of intermolecular electron transfer in biological processes. A recent application of bioelectronics is the design of systems that use organic molecules to form electronic circuit elements that detect and quantify target molecules.
A pharmaceutical compound that equals another in bioavailability and potency.
The theory that living systems arise only from pre-existent living systems.
Bioinformatic sequence markup language (BSML)
A data markup language that is a container for bioinformatics data. The goal is to integrate data from multiple platforms and make it possible to interact with and visualize the data. BSML is a form of XML, extensible markup language.
Computational or algorithmic approaches to the analysis and integration of genomic, proteomic, or chemical data residing in databases. Bioinformatics includes applications for the analysis of DNA and protein sequence patterns.
The recovery of precious metals from ore by biological processes.
The high-velocity injection of DNA-coated particles directly into tissues, cells, or organelles using a gene gun.
Biological response modifier (BRM)
A protein or other compound that stimulates immune defense against disease.
Therapies that stimulate the immune system to fight disease.
Production of light by a chemical reaction within an organism. Bioluminescence generated by firefly luciferase is a sensitive assay for ATP, which is utilized during the reaction. Chemiluminescence differs in that it involves a synthetic substrate.
A large biological molecule, such as DNA or protein.
A molecular marker associated with a biological function.
The mass of material produced by living micoorganisms, plants, or animals.
Biologically derived material that is utilized as a structural component.
An ecological community of organisms and environments.
The application of microelectromechanical systems (MEMS) to micro- and nanosystems for genomics, proteomics, and drug delivery analysis; molecular assembly; tissue engineering; biosensor development; and nanoscale imaging.
The statistical study of biological events.
The development of synthetic systems based on information from biological systems.
The deposition of minerals by microorganisms and plant and animal cells.
The use of information derived from living systems to build electromechanical systems.
A single organism.
The study of the application of isotopes to living systems.
Biological applications of photonics, a technology that utilizes light and other forms of radiant energy in which a quantum unit is the photon.
The application of the techniques of physics to biological processes.
A protein, nucleic acid, or polysaccharide molecule.
A method for preparing biological products, for commercial use.
Searching for new plant and microbial strains that may serve as sources for natural products, such as phytopharmaceuticals.
A container used for fermentation or enzymatic reactions. Bioreactors vary in size from benchtop fermentors to standalone units.
The study of the exchange of information between organisms.
A device that uses a biological element, such as an immobilized enzyme or cell, as a sensor.
The sequestering of chemicals by a biological system.
A specialized branch of applied statistics that deals with the statistical evaluation of experimental research or clinical trial results.
The surface structure of individual molecules, cells, and more complex biological systems.
Synthesis by a living system.
Biological techniques applied to research and product development.
Treatment with genetically engineered biological materials.
A small molecule that binds with high affinity to avidin and streptavidin. Biotin is used to label nucleic acids and proteins that may be subsequently detected by avidin or streptavidin linked to a fluorescent or enzymatic reporter molecule.
The covalent linkage of biotin to DNA and proteins. Biotin may be detected with avidin or streptavidin linked to an enzymatic moiety or fluorescent molecule.
An engineered antibody with two different binding sites that recognize two different antigens.
Having two sites available for binding.
An undifferentiated embryonic cell.
A semipermeable membrane that controls diffusion of molecules into the cerebrospinal fluid.
A massively parallel supercomputer with 1 million processors that is under construction and will be capable of 1 petaflop floating point operations/sec. Blue gene is specifically engineered for use in biomolecular simulations.
Flush DNA ends generated by restriction enzymes that cut both DNA strands at the same point.
The joining of DNA ends that have no overhang by a DNA ligase.
A symbol for a protecting group used in polypeptide chemistry.
The tissue in the middle of a bone that is involved in the proliferation and differentiation of stem cells to produce blood cells (hematopoiesis).
A secondary immunization used to increase a weak immune response to a primary immunization.
A solution containing agents that maintain a constant pH during a biochemical reaction.
A reagent used in combinatorial library synthesis.
Secondary effects on adjacent cells and tissues triggered by treatment of a primary target with a therapeutic agent.
CTop Caenorhabditis elegans (C. elegans)
A nematode widely used in cell lineage studies.
An ionophore that surrounds an ion during transport.
A disease characterized by uncontrolled proliferation of cells.
A specialized nucleotide structure present at the 5' end of mRNA consisting of a methlyguanosine residue linked by a triphosphate bridge to the 5' end of the RNA. The cap protects the structure and facilitates transcription initiation.
Capillary electrophoresis (CE), capillary zone electrophoresis
A rapid, high-resolution electrophoresis method based on free zone electrophoresis in tubes of less than 1 mm dia.
The protein coating of a free virus particle.
The polysaccharide outer layer of some bacteria. Also, a connective tissue sheath that encloses a tissue or organ.
The acidic -COOH functional group found in organic molecules.
Carboxyl terminal, C-terminus
The end of a polypeptide that contains a free carboxyl group.
A molecule that can transform normal cells into cancer cells.
The transformation of normal cells into cancer cells.
A cancer that arises in epithelial tissue.
A protein that confers immunogenicity to small molecules (haptens) that are not themselves immunogenic.
A sequence of successive activation reactions.
Genetic material that is spliced into a genome.
An energy-releasing biochemical process that degrades complex molecules into simpler products.
Catabolite activator protein (CAP)
A bacterial transcription factor that is activated by cAMP.
The repression of transcription of the components of a biosynthetic pathway due to the accumulation of the degradation products of the metabolite produced by the pathway.
An antibody engineered to catalyze an enzymatic reaction. Typically the antibody is raised against a transition state analog for thereaction to be catalyzed.
The negative electrode of an electrophoretic system toward which cations migrate.
An ion with a positive charge.
Caviola (plural, caviolae)
Plasma membrane-attached vesicles involved in endocytosis.
A camera that uses CCD (charge coupled device) chips to convert photons to electrical or digital information.
A microfluidics-based array in compact disc format that utilizes centrifugal force to transport molecules through microchannels.
cDNA (complementary DNA)
A single-stranded DNA molecule that is complementary in base sequence to an RNA strand.
A collection of cloned DNA molecules complementary to the complete set of mRNAs obtained from a cell, tissue, or organism.
A basic polypeptide with antibacterial activity.
A microarray consisting of living cells.
The process of growing and maintaining cells and cell lines; a form of tissue culture.
Cell division cycle
The DNA synthesis pattern in dividing cells. The cell division cycle consists of four phases: G1 (Gap), S (Synthesis), G2 (Gap), and M (Mitosis). DNA replication occurs during the S phase and chromosomal separation occurs during the M phase.
The formation of a single hybrid cell from two cells in response to treatment with a fusogen.
The localization of proteins within organelles or protein complexes by purification of the organelle or complex followed by mass spectrometric identification of the components.
The lipid bilayer plasma membrane that forms the cell boundary.
The movement of eukaryotic cells generated by contractile elements of the cytoskeleton. Cells move by protrusion of cell processes, formation of focal contacts, and retraction of the trailing edge. Motility of bacterial cells is due to cilia and flagella.
The increase in cell number due to growth and division.
Cell-free expression system
A mRNA-programmable protein synthesis system.
The immune response mediated by T lymphocytes. Cell-mediated immunity is responsible for allograft rejection, delayed hypersensitivity, and defense against viruses.
A measure of the frequency of genetic recombination. A centimorgan is a unit of genetic mapping equal to 1% crossover of genes between homologous chromosomes as established by genetic studies.
The chromosomal region to which spindle fibers attach when cells divide.
An ion that dissolves membranes, solubilizes proteins, and denatures nucleic acids. Chaotropes, such as guanidium isothiocyanate,are widely used to denature ribonucleases during RNA isolation.
A protein that binds newly synthesized polypeptide chains to prevent incorrect folding during transport to protein assembly sites.
A molecule that binds metal ions.
The analysis of low molecular weight components of a cell by techniques, such as mass spectrometry, gas chromatography, and HPLC.
The use of small molecules to interact with proteins in order to identify the genes involved in a biochemical pathway.
The large-scale study of biological processes based on small-molecule intervention.
Chemical markup language (CML)
A computional language for the management of chemical data.
A method for defining the function of proteins by screening proteins against libraries of small molecules.
The production of light by a chemical reaction.
Chemiluminescent immunoassay (CLIA)
An immunoassay that utilizes a signal generated by light-releasing reactions.
Informatics technologies that integrate chemical data with analytic and molecular design tools. Cheminformatics applications provide access to compound-related information, including chemical structure, properties, structure-activity relationships.
A microorganism that obtains energy from light-independent inorganic reactions.
The integration of genomic, biological activity, and drug molecule data with pharmacology and toxicology information.
A small, soluble protein with a wide range of immunoregulatory functions.
Device for maintaining a bacterial population in the exponential growth phase by controlling nutrient input and cell removal.
The movement of a cell or organism in response to a chemical gradient.
An organism combining tissues derived from two or more genotypes.
A recombinant antibody that combines characteristics of antibodies from two different sources (see Humanized antibody).
A hybrid DNA molecule generated by the ligation of DNA restriction fragments from different sources. Transcription and translation of the chimeric DNA plasmid results in a chimeric protein.
A hybrid protein produced by recombinant DNA technology from a chimeric DNA molecule.
A compound that cannot be superimosed on its mirror image.
The resolution of a mixture of D- and L-enantiomers of a chiral compound.
The production of one enantiomer of a chiral compound, often by stereospecific synthesis by an enzyme.
A cell line derived from the ovary of the Chinese hamster that is used for cytogenetic studies because of the small number of chromosomes.
The identification of chromosomes using combinatorially labeled fluorescent chromosomal probes in a wide array of colors. The chromosomal painting probes specifically hybridize with chromosome sequences and identify known bands.
A DNA sequencer output data file consisting of fluorescent traces for each base and the DNA sequence.
One of the two daughter strands of a duplicated chromosome.
The network of chromosomes, histones, and other proteins found in the eukaryotic nucleus during interphase. The euchromatin corresponds to regions in which the chromosomes are dispersed, and the heterochromatin to the regions in which chromosomes are condensed.
The separation of a mixture of substances by charge, size, or other property by allowing the mixture to partition between a moving phase and a stationary phase.
Pigment-containing cells within the dermis of fish and amphibians.
A molecule with a chromophore that is colorless until the chromophore is modified chemically.
A functional group that absorbs light, giving rise to color.
A protein that contains a chromophore, a molecule that absorbs light.
A physical location on a chromosome in which the inheritance may be monitored. A marker may be a restriction site or a gene.
The translocation of a chromosome fragment to another chromosome.
A structure that carries the heriditary information for an organism and consists of a long DNA molecule with associated proteins.
A chromosome identification method based on the production of a band pattern by staining.
A technique for isolating non-contiguous clones from a genomic library by jumping regions between known points on the chromosome.
A strategy for locating a gene based on sequencing a panel of overlapping clones that span the estimated location of a gene.
Hair-like structures composed of bundled microtubules that drive fluid across the surface of a cell, or drive cell movement.
A biological activity with a periodicity of 24 hrs that is independent of environmental variation.
Describes transcription-factor binding sequences that regulate the transcription of a structural gene located on the same strand of DNA.
Flattened membrane-bound compartment found in the endoplasmic reticulum and Golgi.
A segment of DNA that codes for a single protein chain.
A taxonomic subgroup with similar traits identified by cladistics.
A classification method that constructs phylogenies using characteristics unique to each taxonomic group.
An adaptive evolutionary process that leads to the development of a greater variety of organisms.
Class I proteins
Major histocompatibility antigens that enable the immune system to distinguish self. Also known as transplantation antigens.
Class II proteins
Major histocompatibility antigens that are found only on the surface of specific lymphocyte cell types and some macrophages.
A change in the class of antibody expressed by B lymphocytes (i.e., from IgG to IgM).
The use of informatics to evaluate clinical trial design and to design electronic systems for protocol and data storage.
The evaluation in humans of the effectiveness of a new drug therapy. The phases of a clinical trial are: Phase I, the evaluation of the safety of the drug; Phase II, the determination of optimal dosage and effectiveness; and Phase III, the large-scale evaluation.
Multiple genetically identical animals generated by reproductive cloning techniques.
Multiple identical cells produced by natural cell division processes.
Exact copies of a DNA segments prepared using recombinant DNA technology.
Plasmid or bacteriophage element used to transfect a recipient cell with a DNA fragment that is replicated (cloned).
Characteristic of a clone.
A bioinformatics technique for visualizing patterns in experimental data.
Clusters of differentiation (CD) antigens
A nomenclature used to standardize the naming of human leukocyte differentiation antigens located on the cell surface and recognized by monoclonal antibodies.
Coding region (CDS)
The genomic sequence between start and stop codons.
Three-nucleotide sequence in mRNA that directs the incorporation of a specific amino acid into the protein chain.
A small molecule associated with an enzyme that participates in enzymatic catalysis.
Inorganic ion or coenzyme necessary for the activity of an enzyme.
The single-stranded extensions generated in double-stranded DNA by staggered cuts by restriction endonucleases. Cohesive ends are also known as sticky ends.
The form of the DNA helix in vivo, in which DNA structures are twisted around each other.
A protein expressed at low temperatures that protects cell components. For example, CspA, a cold-shock protein of E. coli, binds RNA and prevents secondary structure formation.
Bacterial proteins that are toxic to closely related strains of bacteria.
Colony stimulating factor (CSF)
A cytokine that controls the differentiation of hematopoietic stem cells in the bone marrow and elsewhere.
Informal term for combinatorial chemistry.
The use of libraries of recombinant microbes to produce complex natural products.
A technique for systematically assembling molecular building blocks in many combinations to create thousands of diverse compounds.
Common object request broker architecture (CORBA)
Specifications for an object computing infrastructure that automates network tasks and enables the interoperability of diverse database systems, such as those used to warehouse bioinformatics data.
The comparison of genomes and of distinct sequences within a genome. Comparative genomics makes possible the application of information gained from a simple genome to a more complex genome, and is the basis for the understanding of genetic variation within a species.
Pretreated bacterial cells that facilitate DNA transfection.
An assay based on the competition of labeled antigen and unlabeled antigen (from the sample) for antibody binding sites.
A plasma protein system involved in immune defense. Following activation by antigen-antibody complexes, complement proteins lyse antigenic cells, attract phagocytic cells, and assist in the destruction of antigenic cells by phagocytosis.
The reverse structural correspondence of one molecule to another, such as an antibody to an antigen, an enzyme to a substrate, or the bases in a base pair.
Complementarity determining region (CDR)
The variable regions of an antibody molecule that form the antigen binding site. The CDR is formed by the combined variable regions of both light and heavy chains.
Complementary DNA (cDNA)
DNA synthesized from an mRNA template.
DNA or RNA sequence that can base pair with another sequence to form a double-stranded structure.
Complex molecular assembly
Multimolecular structure held together by noncovalent bonds.
The study of complex phenomena in natural systems. Basic themes include the dynamics, interactions, emergence, adaptation, learning, and evolution of a system.
Computational biology (bioinformatics)
Computational technologies for the collection, structuring, and mining of biological data that make possible prediction and knowledge discovery.
Computer-based modeling and prediction of the structure of chemical compounds most likely to bind a protein drug target. Known properties are used to calculate properties of new molecules and energy minimization is used to adjust the structure.
Computer-assisted drug design (CADD)
Computational techniques to design and optimize biologically active compounds with desired structure and properties.
Computer-assisted molecular modeling (CAMM)
Computational techniques for the exploration and visualization of molecular structures and properties.
A light microscope technique that constructs an image from information derived from point-by-point scanning of a field.
The spatial determinants of the atoms within a molecule, for example, the 3-D shape of a protein.
Organisms that differ in genotype at a single locus.
Proteins conjugated to other molecules, such as lipids, carbohydrates, heme, or synthetic labels.
A subunit of connexon, a multi-subunit transmembrane channel protein that forms bridges between adjacent cells at gap junctions.
A multi-subunit transmembrane channel protein that forms bridges between adjacent cells at gap junctions.
A sequence pattern derived from the alignment of multiple sequences that represents the nucleotide or amino acid most likely to occur at each position in a sequence.
The retention of sequence and 3-D structure by biomolecules under varying environmental and genetic conditions.
An alteration of the amino acid sequence of a protein with no effect on the function of the protein.
Produced in a constant amount, not subject to regulation. Housekeeping genes are constitutively transcribed.
A group of cloned pieces of DNA representing overlapping regions of a chromosome.
A map depicting the relative order of a series of small overlapping clones representing a chromosomal segment.
A set of genes that are located together on a chromosome and are capable of functioning as a unit to express a trait.
A compound used for in vivo 3-D mapping of tissues by magnetic resonance imaging (MRI).
A standard of comparison by which experimental results are evaluated. A control differs from the experiment in a single variable, and enables the assessment of significance of experimental results.
A gene region that binds transcription regulatory factors.
The endpoint of an iterative or recursive algorithm. Convergence is reached when the difference between predicted and observed data is less than a preset threshold.
A phenomenon by which the binding of a ligand to one site of a receptor or enzyme alters the affinities of the other sites.
A metabolite that combines with and activates a repressor, resulting in the repression of transcription of a gene.
A phage lambda-based vector used for cloning large DNA fragments (45 kb) into E. coli cells.
A stable bond between atoms based on the sharing of electrons.
A DNA region characterized by methlyated cytosine residues in the sequence CpG. Methlated cytosines are correlated with reduced expression of genes.
A phage-based system for the site-specific insertion and deletion of DNA. Tissue-specific knockouts may be generated in transgenics using the Cre-Lox system.
CREB-binding protein (CBP)
A transcriptional co-activator of phosphorylated CREB (Cyclic AMP Response Element Binding Factor).
Critical micelle concentration (CMC)
The lowest concentration of a detergent at which molecules aggregate to form micellar structures.
The binding by an antibody of an antigen that is structurally similar to the antigen that the antibody was raised against.
A technique for filtering thick fluids by flowing the fluid across the filter. The fluid phase becomes more concentrated without blocking the filter.
The study of a population at a point in time. Cross-sectional studies are also known as horizontal studies.
Reciprocal exchange of corresponding segments between homologous chromosomes, resulting in recombination of genetic elements.
A process for storing biological material at very low temperatures for lengthy periods of time. Mixed solvents containing glycerol and dimethyl sulfoxide are used to protect cells from ice crystal formation.
A molecule that prevents the formation of ice crystals in frozen cells. Glycerol, dimethyl sulfoxide (DMSO), and sucrose are widely used as cryoprotectants. Antifreeze proteins also have cryoprotectant effects.
An immunological determinant that is hidden.
A structure obtained by x-ray diffraction analysis of a crystal consisting of an ordered array of biomacromolecules.
Large repositories of microorganisms and cell lines, maintained by institutions and countries. Culture collections serve as sources of organisms for scientists, and as a record of ownership for the depositor.
A database developed by a curator with domain expertise. Curators remove redundancy from submitted data, incorporate annotations, and add reference information and links to external databases.
The process of verifying and enhancing data submitted to bioinformatics databases. Curators verify automated annotation of data, and add in-context descriptions of molecular, biochemical, and cellular function.
An agent that eliminates plasmids from a cell.
Cyclic adenosine monophosphate (cAMP)
A 'second messenger' molecule generated from AMP by adenyl cyclase following activation by a G-protein.
Cyclic AMP response element binding factor (CREB)
A leucine zipper transcription factor that is activated by cAMP.
An enzyme involved in thromboxane and prostaglandin synthesis. Inhibition of COX is responsible for the anti-inflammatory action of non-steroidal anti-inflammatory drugs (NSAID), such as ibuprofen and aspirin.
An immunosupressant used in transplant surgery to prevent rejection of transplants.
A nucleoside form of cytosine.
A heme-containing protein involved in electron-transfer reactions.
The study of the appearance, structure, and behavior of chromosomes.
A member of a family of proteins released by cells that act on other cells through specific receptors. Cytokines control cell growth and differentiation, and regulate immune and inflammatory responses. Examples of cytokines include growth factors and colony-stimulating factors.
All the protoplasm of a living cell outside the nucleus and inside the plasma membrane.
A pyrimidine derivative that is one of the five bases found in nucleic acids. Cytosine base pairs with guanine.
An integrated protein framework within eukaryotic cells that provides shape, internal spatial organization, and motility.
The part of the cytoplasm external to the subcellular organelles.
Cytotoxic T cell
A T-lymphocyte subset that recognizes a specific antigen presented by an MHC Class I molecule, and lyses the cell.
A configurational prefix that designates one of two chiral configurations (see L-).
A unit of molecular mass approximately equal to the mass of a hydrogen atom.
Computational processing to remove noise and artifacts from digital data prior to storage.
The automated or semi-automated search for relationships and global patterning within data. Data mining techniques include data visualization, neural network analysis, and genetic algorithms.
A collection of databases combined with a flexible data extraction system.
De novo sequencing
DNA or protein sequencing techniques that do not depend on any prior knowledge of the sequence.
Determining the ligands that bind orphan receptors.
To simplify or render less complex.
An algorithm-based method for eliminating noise and improving the resolution of digital data. For example, deconvolution algorithms are used to remove out-of-focus haze from confocal microscope images.
The release of cellular granule contents.
Delayed fluorescence immunoassay
(DELFIA) A fluorescence technique based on the use of a molecule with a long fluorescence half-life.
The loss of genetic material from a gene or a chromosome.
The use of overlapping deletions to determine the location of a gene on a chromosome.
The loss of the native 3-D structure of a molecule.
To cause a protein to fold into a structure other than the native 3-D conformation; to convert double-stranded DNA to single-stranded DNA.
A branching polymer. Dendrimers are used to transfer genetic material into living cells.
A branching process of a neuron that transmits impulses to the body of the neuron.
A cell found in lymphoid organs and non-lymphoid tissues that presents antigens to T- lymphocytes.
A tree-form diagram that is a graphic depiction of hierarchical relationships between sequences or organisms.
A nucleoside form of adenine.
A nucleoside form of cytosine.
A nucleoside form of guanine.
An enzyme that catalyzes the cleavage of DNA.
Deoxyribonucleic acid (DNA)
A long macromolecule with a duplex structure composed of complementary deoxyribonucleotide strands of opposed polarity.
The removal of protein from a sample.
An agent that reduces the surface tension of a liquid. Detergents are often used to solubilize proteins.
A disease caused by loss of control of glucose homeostasis.
Dibasic cleavage site
A site within proteins specifically recognized and cleaved by endopeptidases.
Dictyostelium discoideum (D. discoideum)
A single-celled ameoba that is a model organism for studies of chemical signaling and chemotaxis.
A chain-termination method for sequencing DNA that utilizes dideoxynucleotides.
A technique for determining differences in gene expression under two different conditions or between two tissues.
The process by which many mRNAs may be generated by selectively joining RNA sequence modules (exons) within a single primary RNA.
The acquisition of specialized structural and functional features by unspecialized cells.
The bending of light caused by the presence of an object.
The hydrolysis of macromolecules resulting in the release of component structures.
The reduction of the luminescence of a sample by dilution.
Two reversibly associated macromolecular structures; two covalently associated molecules.
A two-residue peptide.
A cell or nucleus that has two sets of homologous chromosomes, one derived from each parent.
Directed molecular evolution
A protein engineering technique that uses genetic algorithms to evolve molecules with new functions.
An antigenic determinant created from discontinuous protein segments associated in 3-D space by folding.
Exploratory research that begins with the description of complex networks of interactions within an entire genome.
Displacement loop (D-loop)
The structure formed when a third strand of DNA is taken up by double-stranded DNA.
Dissociation constant (Kd)
Tendency of a complex to dissociate. The smaller the Kd, the less likely is dissociation.
A covalent bond between the sulfur atoms of two cysteines within the same protein or in two different proteins.
Evolutionary process that increases differences in initially similar organisms.
The structure of double-stranded DNA consisting of two polynucleotide chains of opposed polarity linked by hydrogen bonds between complementary base pairs.
The generation of a unique DNA pattern that is a genetic profile for an individual.
The endonucleolytic cleavage of genomic DNA at internucleosomal sites. DNA fragmentation occurs during apoptosis.
Enzymes that initiate DNA repair by hydrolyzing links to bases.
A name for DNA topoisomerase.
An enzyme that catalyzes the unwinding of the DNA helix.
A set of synthetic DNA fragments that differ in length.
An enzyme that catalyzes the joining of DNA strands.
An oligonucleotide containing a sequence that forms a restriction site in the presence of complementary sequence.
DNA melting temperature
The temperature at which DNA undergoes a transition from helix to coil structure.
An enzyme that catalyzes the addition of methyl groups to DNA.
The inactivation of genes by the addition of methyl (-CH3) groups to cytosine.
An enzyme that catalyzes the synthesis of deoxyribonucleotides into a sequence complementary to a pre-existent DNA or RNA template.
A DNA-directed RNA polymerase that synthesizes short RNA primers during DNA replication.
The determination of DNA base sequence order.
An enzyme that changes the superhelix density of supercoiled DNA.
A DNA construct that is introduced into cells and subsequently translated into immunogenic proteins.
A technique for locating the DNA sites bound by proteins that is based on the resistance of protein-DNA complexes to the action of nucleases.
Computational exploration of the possible binding modes of a ligand to an enzyme, receptor, or DNA.
A synonym for signal recognition particle receptor.
A compact structural region within a protein with a distinct function.
An allele with a phenotype that is expressed whether the allele is heterozygous or homozygous.
In the direction of the 3' end of a DNA strand.
Drosophila melanogaster (D. melanogaster)
A fruit fly used as a model organism for genetic studies.
A molecule used to diagnose, treat, mitigate, or prevent disease.
The delivery of a drug to the site of action. The pharmaceutical formulation may target the molecule for transdermal, oral, or nasal/pulmonary delivery. Liposomes deliver molecules through membranes and immunotoxins target antibodies to specific tissues.
Processes for the the identification and development of drugs. High-throughput methods that utilize combinatorial chemistry, genomics, and proteomics information are the starting point. Additional research to characterize lead compounds is followed by clinical trials.
A molecular structure consisting of two strands of opposed polarity.
An early stage of carcinogenesis characterized by changes in epithelial morphology.
E. coli, escherichia coli
A bacterium used extensively for research.
A retrovirus that can replicate only in the host of the species in which it originated.
The outer of the three embryonic germ layers. The ectoderm gives rise to the neural tissue and epidermis.
Occuring in an unusual place or form.
A vaccine based on the engineered expression of an antigenic protein by an edible plant. Following consumption, the protein is recognized by the immune system.
Altering a nucleic acid sequence so as to preserve accuracy of information transfer.
The complex that edits RNA transcripts.
A small molecule that binds a protein in a regulatory manner.
Cells optimized for the introduction of DNA by electroporation.
The transfer of biomolecules from an electrophoresis gel to a membrane surface.
Electron density map
A 3-D representation of the electron density of a molecular structure based on x-ray diffraction data. The map is calculated using a Fourier synthesis, a summation of waves of known frequency, amplitude, and phase.
Bacterial lysis due to electronic pulses.
The movement of a liquid through a material following the application of an electric field.
The movement of charged particles through a fluid following the application of an electric field.
The generation of transient pores in the membrane of living cells by exposing them to brief electrical impulses. Electroporation is used to introduce DNA into cells.
A method for generating a fine spray of highly charged droplets.
Electrospray ionization-mass spectrometry (ESI-MS)
A method for the solution ionization and mass analysis of macromolecules and small polar molecules.
The movement of organisms in response to an electric field.
The structure that develops from the zygote.
Embryonic stem cell (ESC)
A totipotent cell cultured from an early-stage embryo. Genetic modification of embryonic stem cells produces transgenic animals.
Describes a property of a system that is not predictable from the starting conditions.
One of the two stereoisomers of a chiral compound. One enantiomer of a chiral drug may be the basis of the therapeutic effect.
Consisting entirely of one stereoisomer of an enantiomeric compound.
A method for immobilizing cells for use in a bioreactor, usually based on the use of polysaccharides or collagen to coat cells. Also, cell encapsulation is used in tissue engineering.
End group analysis
The determination of the terminal residues of a nucleic acid or protein.
An energy-requiring reaction.
A gland that synthesizes and secretes hormones directly into the circulatory system.
The uptake of extracellular materials by a cell.
The inner germ layer that gives rise to the internal tissues.
Developed from within a cell, tissue, or organism.
A nuclease that cleaves nucleic acids at specific internal sites.
A protease that cleaves peptides and proteins at internal sites.
A microorganism living within plant vascular tissue.
Endoplasmic reticulum (ER)
A membrane system that ramifies throughout the cytoplasm and is involved in the synthesis, processing, transport, and secretion of proteins.
Organelle containing material ingested by endocytosis.
Microbial toxin, such as a cell-surface polysaccharide, that is not easily separated from the cell.
The transfer of energy from one chromophore to another by a process dependent on the distance between the two molecules. Techniques based on energy transfer are useful for structure studies that depend on proximity of two groups.
The capture of energy released in one reaction for use in a second reaction.
DNA sequence that is bound by regulatory proteins that enhance the rate of transcription of a gene that may be thousands of base pairs distal to the enhancer sequence.
A lipoprotein outer layer of enveloped viruses that is derived from the plasma membrane of the host cell.
A protein or glycoprotein component of the viral envelope.
A protein that catalyzes biochemical reactions. Substrates are bound and oriented within the active site of the enzyme in a manner that facilitates the formation of the transition state and the conversion to products.
The loss of the 3-D structure of an enzyme.
An enzyme-linked electrode that senses a substrate or product of the reaction catalyzed by the enzyme.
The synthesis of an enzyme at a greatly increased rate in the presence of an inducer.
Enzyme linked immunosorbent assay (ELISA)
An assay based on the use of an enzyme to catalyze a reaction that generates a product detectable by colorimetric methods. The enzyme is conjugated to an antibody that is specific for the antigen to be detected.
The stabilization of the active structure of an enzyme by binding with antibodies. The binding of monoclonal antibodies targeted to regions other than the active site increases the half-life of the enzyme many times.
A polynucleated granulocyte containing granules filled with hydrolytic enzymes.
Mechanisms controlling gene expression and interaction during development that do not depend on changes in DNA sequence.
The genome-wide study of the distribution of methylated and unmethylated nucleoside residues within the genome.
A phenotype derived by mapping epigenetic parameters, such as DNA methylation.
One of two stereoisomers that differ in configuration at one chiral center.
An enzyme that interconverts epimers.
An extrachromosomal DNA fragment, such as a plasmid.
The blocking of the effects of one gene by the expression of another, non-allelic gene.
A sheet of cells above the basal lamina that is specialized for protection or transport.
The antibody-binding region of an antigenic molecule.
A herpes virus that causes mononucleosis.
A state of balance in which there is no net change.
Equilibrium constant (K)
An expression of chemical equilibrium under defined conditions. K is defined as the ratio of the forward and reverse rate constants for a chemical reaction. At equilibrium K equals the product of the reactant concentrations divided by the product of the reactants.
The production of erythrocytes (red blood cells) in the marrow of adults from pluripotent stem cells.
A cytokine that stimulates differention of bone marrow stem cells, accelerates cell maturation, and maintains the level of circulating erythrocytes.
Required for the normal growth of an organism but not synthesized by the organism.
Essential amino acid
An amino acid that cannot be synthesized by a cell or organism and must be supplied as a nutrient.
Essential fatty acid
A polyunsaturated fatty acid that cannot be synthesized by a cell or organism and must be supplied as a nutrient.
Established cell line
Cultured cells that may be subcultured indefinitely.
Study of the cause of and progression of disease.
The highly dispersed region of chromatin present during interphase. Euchromatin corresponds to regions of the chomosomes containing actively transcribed genes.
Any cell that contain a nucleus, including protists, animals, fungi, and plants. Eukaryotes are characterized by internal membrane systems that partition them into functional zones, such as the nucleus, mitochondria, and endoplasmic reticulum, and cytoskeletal structures that control cell form.
The process of cumulative change occurring over successive generations.
The external alteration of tissue taken from an organism and subsequently returned to the organism.
A prefix indicating 1018; a quintillion.
An adduct between a molecule that has been excited by a photon and a second molecule.
An excision nuclease involved in DNA repair.
A mechanism for the repair of DNA damage.
To raise a molecule from the ground state to the excited state.
A reaction that releases energy.
A gland that utilizes a duct for the secretion of molecules.
The secretion or release of intracellular materials to the extracellular space.
Originating outside a cell, tissue, or organism.
The protein coding sequence of a eukaryotic gene. Exons are separated from introns by splice junction sequences.
The identification of the exons within a gene using hybridization to cDNA.
The recombination of exons by strand crossover.
A nuclease that catalyzes sequential cleavage of nucleotides from the 5' or 3' end of a polynucleotide chain.
A peptide hydrolase that cleaves amino acid residues from the N- or C-terminus of a peptide or protein.
A ribonuclease that catalyzes sequential cleavage of nucleotides from the 5' or 3' end of a ribonucleotide chain.
A toxin released by a microbe.
Expressed sequence tag (EST)
A partial sequence of an expressed gene. EST sequence is obtained by high- throughput methods and is useful in the mapping of genomes.
The transcription and translation of a gene. Microarrays are used to detect patterns of gene transcription in different tissues during development, and in response to a stimulus or disease. Protein chips make possible the analysis of protein levels.
A high-throughput method for evaluating the degree and timing of gene expression in a cell or tissue.
A cell-based protein synthesis system programmed by an expression vector.
Plasmid or virus vector that carries into a cell a DNA sequence that directs the synthesis of a protein.
A protein-splicing product formed after the excision of an intein.
Extensible markup language (XML)
A set of specifications for formatting web documents that allows the creation of custom data tags that enable flexible transmission of data between applications and servers.
Extracellular matrix (ECM)
A complex mixture of polysaccharides (glycosaminoglycans or cellulose) and proteins (collagen) secreted by cells. The extracellular matrix serves as a structural element in tissues.
External to the chromosome.
An organism that grows optimally in extreme conditions, including extreme temperature, pressure, pH, ionic concentration, and pressure.
An enzyme from an extremophile.
F factor (fertility factor)
An episomal genetic element that enables a bacterium to transfer extrachromosomal DNA to a second bacterium.
A disulfide-bonded immunoglobulin fragment obtained by papain digestion that contains both antigen binding sites.
An immunoglobulin fragment obtained by papain digestion that contains a single-antigen binding site.
An organism that grows in the presence or the absence of oxygen.
A test result that wrongly shows an effect to be absent.
A test result that wrongly shows an effect to be present.
An algorithm for identifying sequence similarities.
A long-chain aliphatic acid that is found in natural fats.
The immunoglobulin fragment obtained by papain digestion that contains the complement binding site.
A protein that binds the Fc region of an immunoglobulin.
One quadrillionth mole; 1015.
Bacteria that utilize iron as an energy source.
An embryonic antigen that may be re-expressed in cancer.
A microarray based on the attachment of DNA samples or beads to the micro-scale wells at the distal end of an optical fiber bundle.
An epithelial cell precursor.
A protein that aggregates to form filaments and functions as a structural protein.
The degree to which output reflects input. The extent to which transcripion, translation, and replication represent template information.
Any technique that enables the identification of substances by the comparison of patterns. Examples include DNA, protein, peptide, and chemical fingerprinting.
First principle molecular dynamics
The use of quantum chemical interactions to simulate the motion of molecules.
The analysis and sorting of cells that have been reacted with fluorescent probes. The sorting process is based on detection of fluorescence emitted by single cells within droplets.
Flow field effect (flowFET)
A technology utilized in the design of microfluidics systems that utilizes field effects to control flow.
Dye that fluoresces green when exposed to blue or ultraviolet light.
The emission of electromagnetic radiation following absorption of shorter wave length light.
Fluorescence activated cell sorter (FACS)
A system for sorting cells by flow cytometry, a method based on the analysis and sorting of cells that have been reacted with fluorescent probes. The sorting process is based on detection of fluorescence emitted by single cells within droplets.
Fluorescence energy transfer
Transfer of energy between two fluorophors.
The enhancement of fluorescence by the polarity of the medium.
Fluorescence immunoassay (FIA)
An assay technique based on a fluorescent-labeled antigen.
Fluorescence in situ hybridization (FISH)
The use of fluorescent probes that emit light of different colors to tag DNA probes that hybridize specific chromosomal regions.
The partial polarization of light emitted from fluorescent molecules.
Molecules that change in fluorescence upon interacting with another structure.
Fluorescence resonance energy transfer (FRET)
A technique useful for analyzing intermolecular distances based on the transfer of energy from a donor molecule to an acceptor molecule without the emission of a photon.
An autofluorescent protein that is used as a reporter molecule, for example, green fluorescent protein (GFP).
A fluorescent molecule or group.
The acquisition of 3-D structure by a protein; the pattern of the 3-D structure that is the result of the folding process.
The addition or deletion of a nucleotide to a DNA sequence, causing out-of-phase translation.
A mutation that suppresses a frameshift mutation by correcting the phase of translation.
Functional complementation (genetic complementation)
The restoration of function by the introduction of exogenous DNA.
The large-scale exploration of gene function that includes the analysis of regulatory networks, biochemical pathways, protein-protein interactions, the effects of gene knockouts, and the results of functional complementation of knockouts.
A group within a molecule that confers characteristic properties.
The large-scale study of protein function, especially protein-protein interaction networks, biochemical pathways, and post-translational modifications.
The expressed protein resulting from the fusion of two genes.
A substance that induces membrane fusion.
A metabolic cycle that converts energy to heat.
G protein, GTP binding protein
A heterotrimeric guanine nucleotide binding protein that transduces a signal derived from a transmembrane receptor; also, small cytoplasmic proteins that regulate intracellular process.
Mature reproductive cell with a haploid set of chromosomes.
A space introduced into a sequence within a multiple sequence alignment that allows similar or conserved sequence regions to be aligned in columns.
A specialized area of apposed plasma membranes containing connexons, proteins that bridge the extracellular space and that allow the cytoplasm of one cell to communicate with that of the other cell.
A penalty subtracted from a sequence alignment score due to the introduction of a gap or the elongation of a gap.
G1 and G2 phases in cell division, during which there is no DNA synthesis.
The repair of a gap (or nick) introduced into a DNA strand by the loss of one or more nucleotides.
An ion channel that allows ion entry under specific conditions.
Gated ion channel
A transmembrane protein that allows ion fluxes to pass under defined conditions. Voltage-gated channels respond to the transmembrane potential difference, and ligand-gated channels to the presence of specific neurotransmitters.
A technique for the separation of nucleic acids or proteins based on the movement of molecules through a gel matrix under the influence of an applied electrical field.
Gel retardation assay (gel shift assay, electrophoretic shift assay)
A gel electrophoresis technique that detects DNA sequences that bind proteins.
A DNA region that corresponds to a single protein, a set of alternately spliced protein isoforms, or an RNA. The sequence of a gene consists of the entire functional unit and includes noncoding regulatory sequences and introns, as well as coding regions.
Increased replication of a gene.
A gene expression microarray.
The number of times a gene occurs within a genome.
The duplication of DNA sequences corresponding to genes.
The conversion of DNA sequence information to a phenotype. Gene expression involves activation of transcription, processing of the transcript, translation of structural genes, and assembly of the protein products.
Gene expression markup language (GEML)
An Extensible Markup Language (XML) tag set that provides a standard method for exchanging gene expression data and annotation.
A measure of the occurrence of an allele in a population.
A device used for the high-velocity injection of DNA-coated particles directly into tissues, cells, or organelles.
A DNA segment or phenotypic trait that serves as a marker for a gene.
The sum of genetic information for a population.
The protein or RNA encoded by a gene. A single gene may have multiple protein products, due to extensive post-translational modification. The large-scale study of all possible gene products is the goal of the Human Proteome Project (HUPO).
Multiple copies of a single gene.
The acronym or abbreviation corresponding to a given gene name. Genes and markers may have multiple symbols and names due to rediscovery or correlation to function following discovery.
The synthesis of an entire gene by hybridizing oligonucleotides, which are subsequently joined enzymatically.
The inactivation of a specific gene.
The delivery of genes to cells in order to correct genetic mutations associated with hereditary disease, to stimulate the immune system, or to target a tumor for subsequent drug therapy.
The time interval between successive cell divisions.
An algorithm for optimizing a property based on an evolutionary mechanism that uses replication, deletion, and mutation processes carried out over many generations.
The deposit of an individual's genetic information to a database that enables the individual to control access.
The code by which a nucleotide sequence is translated into an amino acid sequence. Each three nucleotide triplet constitutes a codon; the 64 codons correspond to 20 amino acids and to signals for the initiation and termination of transcription.
Genetic complementation (functional complementation)
The restoration of function by the introduction of exogenous DNA.
A change of gene frequencies within a population over time.
Analyzing gene expression patterns using computational techniques, such as artificial neural networks.
A map of relative chromosomal locations based on recombination data.
An observable characteristic useful for genetic analysis.
The presence of two genotypes in a population.
The exchange of genetic material between homologous chromosomes in meiosis.
Testing of individuals for a gene or metabolite.
Genetic heterogeneity in a population.
The biology of heredity and variation.
The total genetic information of an organism.
The linear arrangement of genes and markers within the chromosomes of a genome.
The genome-wide study of the relation between genetic variation and disease.
A set of clones consisting of ramdomly generated overlapping DNA fragments representing the entire genome of an organism.
The large-scale investigation of the structure and function of genes. Understanding the structure and function of genomes aids in drug discovery and development, agroscience research, and other fields.
The genetic information for an organism that is carried on the chromosomes and extrachromosomally.
A region of the endoplasmic reticulum involved in the packaging of molecules. The GERL includes the Golgi, smooth endoplasmic reticulum, and lysosomes.
Any cell of the germ line. Germ cells are the reproductive cells and include the egg and sperm cells.
A cell line that gives rise to gametes.
Germ line mutation
A heritable genetic change in the germ line cells.
A plant hormone that regulates growth.
A specialized cell that surrounds neurons, providing metabolic and physical support.
A malignant brain tumor of glial origin.
A non-metastatic brain tumor of glial origin.
A sequence alignment over the entire length of two nucleic acid or protein sequences.
A protein that is rounded in shape.
A polysaccharide consisting of monosaccharides joined by glycosidic linkages.
A non-enzymatic reaction that adds a carbohydrate group to a protein or peptide.
The biochemistry of glycoconjugates.
A cell coating consisting of glycoproteins and proteoglycans.
A complex carbohydrate attached to a lipid, peptide, or protein.
A glycoprotein variant that differs in the oligosaccharide moiety.
A molecule consisting of a short carbohydrate chain attached to a lipid.
The total carbohydrate complement of a cell.
A protein with covently bound carbohydrates.
A carbohydrate-bearing transmembrane protein found on the surface of erythrocytes.
A protein with covalently bound carbohydrates.
The removal of oligosaccharides from a glycoprotein by a glycosidase.
A polysaccharide containing aminomonosaccharide residues.
An enzyme that hydrolyzes glycosidic bonds between monosaccharide components of a polysaccharide.
A compound in which a glycosyl group has been substituted for a hydroxyl group.
The post-translational addition of carbohydrate groups to a molecule. Glycosylation of proteins occurs via the amide group within the sequence Asn-X-Ser/Thr (or through the hydroxyl of the serine or threonine residue in the sequence).
A system to which only preselected components, organisms and nutrients are introduced.
Golgi body, Golgi apparatus
Intracellular stack of vesicles in which glycosylation and packaging of proteins and peptides destined to be secreted takes place. Proteins are processed as they progress from the cis- to the trans-Golgi region.
Graft-versus-host response (GVH)
A reaction that occurs when lymphocytes of a different MHC class are introduced into a host, resulting in the reaction of the lymphocytes against the host.
The degree to which a system contains separate components. Systems with greater granularity are more flexible.
A white blood cell containing large granules.
Granulocyte-colony stimulating factor (G-CSF)
A cytokine that controls the differentiation of granulocytes and macrophages.
A substance that promotes the growth of cells. Growth factors include epidermal growth factor (EGF), fibroblast growth factor (FGF), erythropoietin (EPO), hematopoietic cell growth factor (HCGF), platelet-derived growth factor (PDGF), stem cell factors, and neurotrophins.
A purine that is one of the five main bases found in nucleic acids. Guanine base pairs with cytosine.
A nucleoside form of guanine.
Guide RNA (gRNA)
A small RNA involved in a specialized form of RNA editing.
A structure in which adjacent segments of DNA or RNA fold together and are stabilized by base pairing, creating a loop of single-strand DNA or RNA.
Hairy root culture
A plant culture system based on highly branched roots generated by plant tissue with agrobacterium rhizogenes. The hairy root cultures grow on simple media and produce secondary metabolites at normal levels.
The time that it takes for half of the activity of a molecule to decay.
A microorganism that grows optimally in a highly saline environment.
Genetic material consisting of a single chromosome set (half of the diploid number). Egg and sperm cells of animals and egg and pollen cells of plants are haploid.
A set of genes on a single chromosome.
A small molecule that is not immunogenic unless attached to a carrier protein.
A mathematical statement of the concept that gene and genotype frequencies are constant from generation to generation in a large, interbreeding population with random mating in the absence of selection, mutation, or migration.
Heat shock protein
A protein synthesized in response to cellular stress, including high temperature. Heat shock proteins function as molecular chaperones to protect proteins from premature folding.
The heavier of the two types of immunoglogulin chains.
A protein that unwinds the DNA double helix during replication.
An amino acid residue that interrupts alpha helical structure.
Helix destabilizing protein
A protein that binds single-stranded DNA.
An amino acid residue that favors the formation of alpha helix.
Helix loop helix (Helix turn helix)
A structure characteristic of DNA-binding proteins.
The transition of a nucleic acid or protein from the native to the denatured state.
A T-lymphocyte that binds antigens on the surface of presenting cells and secretes lymphokines that activate cytotoxic cells.
A virus that provides functions missing in a defective virus.
Hematologic growth factor
A colony stimulating factor that stimulates the production of some types of white and red blood cells.
The proliferation and differentiation of stem cells to produce blood cells. Hematopoeisis occurs in the bone marrow in adults.
An iron-porphyrin compound that occurs as a prosthetic group in hemoproteins.
A protein bound to an iron-porphyrin compounds such as hemoglobin, myoglobin, and members of the cytochrome group.
A cancer of the liver that is derived from hepatocytes.
An epithelial cell of the liver responsible for the synthesis, degradation, and storage of a variety of materials.
A virus group that includes the Epstein-Barr Virus and Herpes Simplex.
The highly condensed region of chromatin present during interphase. Chromosomes in this region are transcriptionally inactive.
A dimer composed of two different molecules.
A double-stranded DNA in which the base sequences are not completely complementary due to recombination or mutation.
Heterogeneous RNA (hnRNA)
A mixture of different molecular weight RNAs synthesized by RNA polymerase II.
Heterogeneous RNP (hnRNP)
The complex of heterogeneous nuclear RNA with proteins.
A cell with more than one nucleus.
Consisting of different elements.
The presence of different alleles on homologous chromosomes.
An organism with different alleles on homologous chromosomes.
A method based on empirical information that has no explicit rationalization.
A programming strategy based on trial-and-error methods and feedback evaluation.
Hidden Markov Model
A probabilistic model used to align and analyze sequence datasets by generalization from a sequence profile.
High field NMR
A high-resolution NMR method based on higher field magnets that enables the analysis of large molecules.
Simultaneous multiparametric analysis of complex systems, such as living cells.
High-throughput system, High-throughput screening (HTS)
A massively parallel screening technique for the simultaneous assay and evaluation of large numbers of samples.
A proline-rich region that allows an antibody to flex upon binding antigen.
The ability of a host to tolerate a tissue graft.
A genetically determined antigen that determines the immune response to grafts.
A graphic representation of a frequency distribution.
Abundant small protein rich in arginine and lysine that associates with DNA and enables the packaging of DNA into chromosomes.
Abbreviation for human leukocyte-associated antigen.
Refers to systems based on hollow semi-permeable fibers that are used for protein separation and cell culture. Hollow-fiber bioreactors are used to maintain mammalian cells in culture, particularly cells producing monoclonal antibodies.
A catalytically active enzyme that includes cofactors.
A highly conserved nucleotide sequence that is important to the orchestration of gene expression during development.
A protein motif encoded by DNA sequence within the homeobox.
A homeobox- or homeodomain-encoding gene.
A dimer composed of identical molecules.
Exchange of sequence information between two homologous DNA molecules. Homologous recombination contributes to DNA repair and is essential for maintaining genome stability.
The presence of identical alleles on homologous chromosomes.
An organism with identical alleles on homologous chromosomes.
The study of a population at a point in time. Horizontal studies are also known as cross-sectional studies.
A substance formed in a specialized gland or group of cells that has regulatory effects on another gland or group of cells. Hormones are usually transported in the circulation.
A cell used for the reproduction of foreign DNA, such as a plasmid or virus.
A system for the propagation of a DNA vector in a host cell.
A constitutively expressed gene. Housekeeping genes are continuously transcribed at low basal levels.
Human immunodeficiency virus (HIV)
The retrovirus that causes AIDS, acquired immune deficiency syndrome.
Contained in a bodily fluid.
Immunity mediated by humoral antibodies.
An immunoglobulin produced by fusing hybridomas producing two different antibodies, resulting in the production of a third, heterophile antibody.
A cell formed by fusion of two cells. Hybrid antibodies may also be produced by combining two antibodies.
The annealing of two complementary nucleic acid strands to form a double-stranded molecule; a technique for detecting specific nucleic acid sequences.
A permanent cell line generated by cell fusion that secretes a specific monoclonal antibody.
The rupture of a chemical bond by a reaction that involves water.
A polar compound that forms hydrogen bonds with water and dissolves easily in water.
A nonpolar compound that does not form favorable binding interactions with water, and is insoluble in water.
An increase in tissue due to enhanced cell division. Hyperplasia may be reversed by removal of the stimulus.
An excessive immune response that results from previous exposure to an antigen. Immediate responses are antibody-mediated and occur in minutes; delayed responses are mediated by T-cells and occur about 24 hrs later.
An antigenic determinant within the variable region of an antibody.
The antigenic specificity defined by the idiotopes within the antigen combining site of an antibody.
A chemical that is readily detectable by a medical imaging system. Imaging agents include electron-opaque molecules, such as gold particles, radioisotopes, such as technetium, and stable isotope-labeled molecules.
Immobilized cell biosensor
A biosensor that uses living cells as the detection system. The cell signal is read out by a system that produces fluorescence, or by direct electrochemical coupling.
The generation of cells that undergo an infinite number of division cycles. Immortalization of cells may be brought about by transfection with oncogenes, transfection with telomerase reverse transcriptase, induction by mutagens, or may be spontaneous.
Immune complex disease
A disorder characterized by the presence of immune complexes in bodily fluids.
Immune deficiency disease
A disorder characterized by the suppression of the immune reaction.
The total immunological reaction of an organism. The immune response includes antibody production, cell-mediated immunity, and complement activation.
An antibody-based technique for the qualitative and quantitative characterization of samples. Different antibody labels and imaging agents used to detect antibody-antigen interactions distinguish the different assay types: ELISA (enzyme-linked immunosorbent assay) uses an enzyme that produces a colorimetric product, RIA (radioimmunoassay) uses a radioactive label, FIA (fluorescent immunoassay) uses a fluorescent molecule, CLIA (chemiluminescent immunoassay) uses a light-generator.
An antibody conjugated to a molecule, such as a fluorescent label or an enzyme, that produces a colorimetric product.
A molecule, molecular assembly, or organism that is specifically recognized by an antibody; an antigen.
Capable of stimulating an immune response.
A protein produced by lymphocytes that consist of two heavy chains, two light chains, and an oligosaccharide moiety.
Activation or suppression of the immune response.
The typing of cells with antibody markers.
The precipitate formed in a reaction between an antibody and an antigen.
The precipitation of a multivalent antigen by a bivalent antibody.
A microelectronic sensor used on a biochip that senses when a molecule binds to an attached antibody.
The use of antibodies or antigens attached to a solid support to purify antigens or antibodies, respectively, from a mixture.
Suppression of the immune response.
A genetically engineered protein, such as an interferon, interleukin, or a colony-stimulating factor, that enhances the immune response.
The use of antibodies, proteins derived from antibodies, or immune cells to treat disease.
An antibody joined to a toxic molecule that is used to target toxins to specific tissues.
The differential expression of genes due to differential methylation of nucleosides.
In silico biology
The use of computational algorithms to create virtual systems that emulate molecular pathways, entire cells, or more complex living systems.
In situ hybridization
A technique that uses x-ray film to detect labeled molecules after hybridization of a labeled DNA or RNA probe to DNA or RNA within tissue specimens.
In situ oligonucleotide synthesis
On-chip synthesis of oligonucleotides or peptide nucleic acids.
Occurring outside an organism, in culture, or in an extract.
Occurring in a living organism.
Inborn error of metabolism
An inherited biochemical variation due to genetic alterations in the genes encoding metabolic enzymes.
Bodies formed within bacterial cells for the storage of various materials. Bacterial systems that express proteins within the cytoplasm form protein-filled inclusion bodies due to the aggregation of misfolded proteins.
A genotype that is not uniformly expressed as a phenotype.
The immediate defense of tissue against infection or injury.
Information RNA (iRNA)
An RNA sequence that does not encode a protein, but provides regulatory information.
Inhibitor RNA (iRNA)
An RNA that interferes with normal RNA function.
A protein that promotes the association of ribosomes with mRNA and the initiation of protein synthesis.
A non-contact method for delivering biomolecules to substrate surfaces. Ink-jet technologies rely on piezoelectric propulsion to transfer small molecules to solid surfaces.
A lipid family characterized by phosphorylated inositol derivatives. Inositol phospholipids are a minor component of the plasma membrane important in signal transduction.
The internal protein sequence that is excised during protein splicing.
A protein liberated by cells following exposure to viruses and other microorganisms. Interferons induce protein synthesis inhibitors that block translation of viral mRNA.
A cytokine that acts as a signal between different leukocyte populations.
Ability of different types of databases, applications, operating systems, and platforms to function in an integrated manner.
The stage of a cell not undergoing mitosis or meiosis. Interphase includes G1, S, and G2 phases of the cell division cycle.
A connective tissue cell.
Within a single protein domain.
Within an epithelial cell layer.
Within the liver.
A transmembrane protein.
The non-coding (intervening) sequence of a gene that is transcribed into RNA but then excised by splicing to produce an mRNA transcript. Recently eukaryotic nuclear introns have been found to encode proteins.
Tending to penetrate healthy tissue.
Identical copies of a sequence of double-stranded DNA repeated in inverse order.
An atom or molecule with a positive or negative electrical charge. Positively charged ions are cations, and negatively charged ions are anions.
Transmembrane protein complex that forms a channel through which specific inorganic ions diffuse.
A small hydrophobic molecule that dissolves in lipid bilayer membranes and increases permeability to inorganic ions.
A receptor that mediates its effects by regulating ion channels.
The transfer of ions across cell membranes due to the application of an electrical potential.
A synthetic molecule designed to bind the active site of an enzyme and form a covalent bond with the enzyme.
An inadequate flow of oxygen (hypoxia) due to insufficient blood supply.
An antigen that elicits an immune response in other individuals of the same species but not in the individual from which the antigen is derived.
Isoelectric focusing (IEF)
An electrophoresis technique based on the movement of proteins through a stable pH gradient established using carrier ampholytes. Isoelectric focusing is the first dimension of 2-D electrophoresis.
The pH of a solution in which a protein has no net charge and does not migrate in an electric field.
Multiple related proteins that differ in sequence due to alternate splicing of exons within a single primary RNA transcript or due to derivation from two related genes.
Different restriction enzymes that recognize the same sequence, but do not necessarily cut at the same site.
A form of an atom that differs from other forms of the atom in atomic weight. Isotopes may be stable (for example, deuterium) or radioactive (for example, tritium). Isotopes are incorporated into tracer molecules used in imaging molecular function in tissues.
Macromolecules with common structural and functional features, such as the IgG, IgM, IgA, IgD, and IgE antibody isotypes.
One of several forms of an enzyme that differ in primary sequence.
A single round of data processing. During iterative data processing, a loop of instructions is executed in a repetitive manner until some threshold is reached.
A term used to refer to stretches of DNA within the genome that do not encode genes and are likely to play a structural, regulatory, or undefined role.
Kappa (K) chain
One of the two types of light chains that occur in antibodies.
A photomicrograph of size-ordered, banded chromosomes that enables low-resolution physical mapping of features.
A unit of DNA length; 1 kb is equal to 1,000 base pairs.
The study of the rate of change.
A pair of structures adjacent to the chromosomal centromere to which spindle microtubules attach.
The large fragment of E. coli DNA Polymerase I. The Klenow fragment retains DNA polymerase activity and 3'-5' exonuclease activity, and is used for DNA sequencing.
An alteration of a gene so that it may be expressed conditionally.
An alteration of a gene in a way that results in a gain of function.
An alteration of a gene that results in loss of function; a transgenic organism in which a gene has been inactivated.
The extraction of useful knowledge from data patterns that have been rendered meaningful by the integration of information derived from external sources.
A DNA sequence that surrounds the ATG start signal for the translation of an mRNA.
A conserved protein domain whose 2-D representation resembles a Scandinavian pastry known as a kringle.
Specialized non-motile macrophages in the liver sinusoidal regions.
A configurational prefix that designates one of two chiral configurations (see D-).
A microfabricated fluidics system designed to perform high-resolution biochemical analyses.
A bacteriophage vector that is widely used as a DNA cloning vector.
One of two types of light chains that occur in antibodies.
A lipid bilayer on the surface of water.
A device that emits an intense coherent monochromatic light beam.
Laser capture microdissection
A technique for isolating single cells from tissues. Laser microdissection makes possible the collection of pure populations of cells for the analysis of molecular function.
Protein knockout technique based on the binding of a chromophore to a specific protein followed by laser irradiation to inactivate the protein.
An approach to genomics that emphasizes lateral gene transfer.
A peptide or small molecule that optimally modulates the activity of a receptor or other target protein. A successful lead compound becomes a drug candidate for further development.
A short amino acid sequence that determines the localization of a protein within the cell.
A group that departs during a substitution reaction.
A glycoprotein that binds sugars and agglutinates cells.
A retrovirus utilized for gene therapy vectors.
Insects such as butterflies and moths.
A structural motif characteristic of DNA-binding proteins consisting of a protein dimer formed by two interacting a helices from separate proteins.
A group of neoplastic diseases of leukocytes, often resulting in proliferation of leukocytes.
A small molecule that binds to a receptor/protein.
An enzyme that ligates (joins) two molecules in an energy-dependent process.
Light chain (L chain)
The shorter of the two protein chains that comprise antibodies.
The co-inheritance of two DNA loci that are near each other on the same chromosome.
A map of the relative positions of genetic markers, based on how often they are inherited together.
An oil-soluble molecule such as a fatty acid or steroid.
The use of liposomes to transfect cells with DNA.
Lipophilic molecule A
nonpolar compound that readily mixes with lipids or other low polarity substances.
A lipid attached to a polysaccharide.
A protein conjugated to lipids.
A synthetic lipid bilayer vesicle that fuses with the outer cell membrane and is used to transport small molecules into cells.
A microorganism that synthesizes all organic molecules from inorganic sources.
Live cell array
A micro-system for the high-throughput analysis of intact cells.
Locus (plural, loci)
The specific position of a gene or other chromosomal marker.
Long terminal repeat (LTR)
A long DNA sequence that is repeated at each end of retrotransposon and retrovirus DNA.
A study that follows a population forward over time.
A region of protein sequence enriched for a single amino acid.
A mono-oxygenase enzyme that catalyzes bioluminescent reactions. Firefly luciferase used in combination with substrate luciferin is a sensitive assay for ATP.
Any bioluminescent substrate for luciferase.
The volume enclosed by the endoplasmic reticulum or the mitochondrial inner membrane; the interior space of a tubular organ such as a blood vessel.
Lumenal protein, luminal protein
A protein that is retained in the rough endoplasmic reticulum due to the presence of a four amino acid signal (KDEL).
A luminescent substance.
A membrane-bound particle isolated from marine organisms that contains proteins that produce luminescence.
Bioluminescent marine proteins that are the counterpart of the luciferase system.
A small organ that is a component of the lymphatic system and consists of lymphocytes, macrophages, and dendritic cells. The lymph nodes filter lymph from peripheral nodes, and ultimately empty into the thoracic duct.
A leukocyte (white blood cell) that functions in specific immunity.
A factor released by lymphocytes that modulates other cell types.
A malignant tissue neoplasm that produces a tumor mass, often associated with lymphoid tissue.
Cell disintegration due to membrane rupture or the breakdown of the cell wall.
A virus capable of becoming a prophage and integrating into a bacterial genome.
The ability of a phage to integrate into the bacterial DNA chromosome.
A eukaryotic organelle containing hydrolases active at pH 5. The enzymes break down particles ingested by vacuoles following fusion.
An enzyme that hydrolyzes glycosidic linkages within peptidoglycans in prokaryote cell walls.
A viral infection that results in the lysis of the host cell and release of viral progeny.
A virus that lyses the host cell.
A single-stranded bacteriophage vector that is used in the Sanger dideoxy sequencing method.
A visible aggregrate of macromolecules.
A low-density “microarray” on a nylon transfer membrane.
A crystal whose lattice structure is based on macromolecules.
A molecule larger than about 10 kDA.
A cell characterized by prominent lysosomes and the ability to phagocytose foreign material. Macrophages are involved in both non-specific immunity, due to the phagocytosis of foreign materials, and in specific immunity, due to the presentation of the antigen.
Macrophage-colony stimulating factor (M-CSF)
A growth factor that stimulates macrophage colonies.
A linear map of the order of restriction sites on a chromosome and the distance between sites.
Visible to the unaided eye.
Magnetic resonance imaging (MRI)
An imaging technique that produces cross-sectional images for medical research. The object to be viewed is exposed to a radio frequency field in the presence of a varying electromagnetic field.
Major histocompatibility antigen, Class I
A cell-surface glycoprotein that enables the immune system to distinguish self; a transplantation antigen.
Major histocompatibility antigen, Class II
A cell-surface glycoprotein found only on the surface of specific lymphocyte cell types and some macrophages.
Major histocompatibility complex (MHC)
The genetic loci that encode the histocompatibility antigens, cell-surface proteins that bind peptide fragments of foreign proteins, present them to T-lymphocytes, and induce an immune response.
The abbreviation for Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry, a high-throughput protein sequencing method based on embedding samples in a matrix from which they are desorbed by laser light.
Invasive, capable of metastasis.
A unit of genetic length derived from recombination frequency. One map unit corresponds to a recombination frequency of 1%.
The culture of marine organisms.
The recovery of genetic markers due to recombination events that restore function.
Mass spectrometer (MS)
An instrument that determines the exact mass of charged particles or ions by measuring the flight path through a set of magnetic and electric fields. Mass spectrometers specialized for protein and peptide sequencing are used for high-throughput identification.
A method for identifying molecules based on the detection of the mass-to-charge ratio of ions generated from the molecule by vaporization and electron bombardment. Deflection of the ions through a magnetic field results in a characteristic pattern used to identify the molecule.
The ratio of the mass of an ion being analyzed to its charge.
Massively parallel computing
High-performance computing based on the development of parallel processing algorithms and applications that can be executed simultaneously by many separate processors.
A non-circulating leukocyte characterized by histamine-filled granules. Mast cells are involved in hypersensitivity reactions.
A medium in which things are formed, developed, or embedded.
Matrix attachment region (MAR)
A region of a chromosome that binds nuclear matrix proteins.
A unit of DNA length: 1 Mb equals 1,000,000 base pairs.
Nuclear division that occurs in eukaryotes to produce haploid eggs and spermocytes from a diploid cell. Meiosis consists of two reductive divisions.
A skin cell that produces and stores the pigment melanin.
A melanocyte with contractile properties that causes the translocation of melanosomes (melanin-containing organelles), resulting in rapid adaptive changes in coloration.
The thermal denaturation of a macromolecule.
A single- or double-layer lipid sheet that separates two compartments.
Transmembrane protein complex that allows inorganic ions to diffuse passively across the membrane bilayer.
The electric potential difference across a membrane.
A hereditary process explainable in terms of the segregation of chromosomes, independent assortment, and homologous exchange.
A characteristic that is transmitted according to the laws of genetics formulated by Mendel.
Mesenchymal stem cell (MSC)
A pluripotent cell that differentiates into connective tissue.
Embryonic tissue of medodermal orgin that develops into connective tissue, lymphatic tissues, and blood vessels.
The middle of the three germ layers of an embryo that forms the connective, musculoskeletal, and vascular tissue.
Messenger RNA (mRNA)
The RNA template for protein synthesis. mRNA is formed by transcription of the template DNA strand, followed by the excision of introns and the joining of exons to form mature mRNA.
A method for the statistical re-analysis of experimental and correlational results from independent studies that address related research questions.
Metabolic burst, respiratory burst
The response of phagocytes to the uptake of particles that involves the production of hydrogen peroxide, superoxide anions, and hydroxyl radicals.
The measurement of biochemical intermediates within a tissue in order to describe the functioning of metabolic pathways.
Processes for the synthesis, modification, and breakdown of molecules within a living organism.
A molecule synthesized or modified by metabolic processes within an organism.
The total small molecule complement of whole cells.
A supramolecular assembly of sequential metabolic enzymes.
A receptor that mediates its effects by activating enzymes.
A chromosome with a centromere near the center.
Information about data that facilitates access and use of the data.
The stage in mitosis and meiosis during which chromosomes align along the equatorial plane of the cell.
The development of a secondary tumor at a site remote from a primary tumor.
Multicellular animals with a nervous system and tissues.
The structure formed by amphipathic molecules in solution that places the polar group toward the solution and the hydrophobic group toward the interior.
Micro chemical system (MiCS)
A miniature system for the synthesis and analysis of chemicals.
Micro total analytical system (µTAS)
A miniature biochemical analysis system based on microsystems technology.
Oligonucleotides, cDNAs, proteins, peptides, or other small molecules organized in a grid on a glass or plastic slide, silicon chip, fiber optic array, or filter membrane.
A membrane-bounded cytoplasmic organelle that contains oxidative enzymes.
Nontoxic, finely particulate material used to grow cells in suspension culture.
Dissection of organisms by mechanically controlled instruments monitored using a microscope.
Microelectromechanical systems (MEMS)
A technology that combines computers with micro-scale sensors, actuators, valves, gears, and mirrors embedded in semiconductor chips.
A microarray that uses microelectrodes to concentrate DNA samples and accelerate probe hybrization.
A fibril identifiable only by electron microscopy.
Lab-on-a-chip technology based on the transport of nanoliter or picoliter volumes of fluids through microchannels within a glass or plastic chip. Microfluidics systems evolved from MEMS research.
Device used with a microscope for the generation of micropipets.
The graphic representation of a microscope image.
A rotating wall vessel bioreactor used for tissue engineering that neutralizes gravitational effects on cells. Cells self-associate and grow three-dimensionally to generate tissues.
The injection of a single cell using a micropipet.
Instrument used with a microscope for manipulating small instruments and specimens.
Post-translational modification of a protein.
A unit of length equal to 10-6 meter.
An integrated electronic circuit designed to carry out a specific set of operations.
A minitiarized reaction system used for chemical synthesis.
A device for sequencing small amounts of sample.
A small closed vesicle created by mechanical disruption of the rough endoplasmic reticulum.
A contact-based transfer method that utilizes pins or capillaries to deposit biomolecules on a solid surface.
The movement of a cell over a surface.
A molecule that replicates essential features of another molecule.
A compound that mimics the structure of an epitope and provokes an identical antibody response. Mimotopes are useful in the development of vaccines.
A plasmid that contains a chromosomal origin of replication.
Minimum recognition unit (MRU)
The complementarity determining region of an antibody.
The end of an actin filament to which monomers are added more slowly.
A DNA or RNA strand that is complementary to a viral plus strand.
A cell-based enzymatic mechanism that corrects nucleotide insertion errors made during DNA replication by excising the defective sequence and replacing it with the correct sequence.
A codon altered so that it codes for a different amino acid.
A base substitution that changes a codon into a codon corresponding to a different amino acid.
The insertion of an amino acid not specified by the corresponding mRNA codon.
Mitochondrial DNA (mtDNA)
Double-stranded DNA contained within mitochondria that encodes mitochondrial tRNAs, rRNAs, and proteins. Several copies of the mitochondrial genome are found in each organelle.
Mitochondrial intermembrane space
The mitochondrial compartment between the outer and the inner membranes.
The inner mitochondrial compartment that contains enzymes associated with the oxidation of fatty acids and the tricarboxylic acid cycle.
RNA transcribed from mitochondrial DNA.
Mitochondrion (plural, mitochondria)
A self-replicating organelle bound by two bilayer membranes that is found in the cytoplasm of eukaryotic cells. Mitochondria produce ATP via oxidative phosphorylation reactions carried out by respiratory enzymes located in the inner membrane.
A stimulant of cell division.
The mitochondrial inner membrane and matrix.
A mitochondrial ribosome. Mitoribosomes resemble prokaryotic ribosomes rather than the cytoplasmic ribosomes of the cells containing the mitochondria, giving rise to the symbiont hypothesis.
The process of chromosome segregation that occurs during the division of eukaryotic cells. During mitosis, DNA is condensed into visible chromosomes (prophase) that arrange at the cell midplane (metaphase), separate (anaphase), and decondense into the interphase.
A relatively simple organism that duplicates some critical aspect of a more complex system that would be difficult to manipulate experimentally. Examples of widely used model systems include Saccharomyces cerevisiae, Caenorhabditis elegans, and Arabidopsis thaliana.
A component part of a complex molecule.
A single-stranded DNA molecule with a fluorescent reporter group on one end and fluorescence quencher on the other. Unfolding of the self-quenched DNA structure occurs upon hybridization to a complementary sequence and results in the emission of a fluoresence.
The interpretation of biological events in terms of the physics and chemistry of molecules within cells.
An evolutionary hypothesis based on the assumption that mutations occur in a regular manner.
The study of intramolecular conformations and molecular motions, using computational simulations.
Electronic devices based on components consisting of individual molecules.
The study of the molecular structure and function of genes.
The computational visualization of macromolecules for the purpose of molecular design, protein engineering, and structural refinement.
Chemical compounds that resemble biomolecules and recognize and bind their targets.
Computational analysis and modeling of the physicochemical properties of a molecule or biomacromolecule.
Molecular pattern recognition
Computational methods for the analysis of genome-wide expression patterns and and phenotypes.
A method for solving biomacromolecular structure based on the use of a model derived from a related, previously solved structure.
A material with pores capable of separating molecules on the basis of size.
Derived from a single clone.
Monoclonal antibody (Mab)
A monospecific immunoglobulin produced by a single clone of cells.
A leukocyte found in bone marrow and in the circulatory system. Monocytes differentiate into macrophages in the tissues.
One of the component units of a polymeric molecule.
Characterized by a single set of chromosomes.
The component unit of an oligosaccharide or polysaccharide.
A chromosome in a diploid set with no homolog.
An antibody that recognizes a single antigen or epitope.
Possessing a single charge or valency.
Developmental changes in the inner structure and outer form of an organism.
A nucleic acid or protein sequence that is associated with a function.
A protein that moves along filament or polymer substrates in an ATP-dependent manner.
mRNA binding site
A ribosomal region that binds mRNA.
Three- and four-dimensional NMR methods for the detailed characterization of protein structure.
A set of sequence-related genes within a genome that evolved from a single ancestral gene by gene duplication and subsequent mutations.
A molecular aggregate held together by noncovalent bonds.
An alignment of multiple sequences that inserts gaps into the individual sequences in order to align conserved sequences in the same column.
Multiple anomalous dispersion (MAD), multiple wavelength anomalous dispersion
An x-ray crystallographic phasing method that utilizes heavy atom information to solve biomacromolecular structures.
Multiple codon recognition
The ability of a tRNA to recognize more than one mRNA codon.
A procedure for the parallel analysis of pooled samples.
Multiplex fluorescent in situ hybridization (M-FISH)
The identification of chromosomes using combinatorially labeled fluorescent chromosomal probes in a wide array of colors. Chromosomal painting probes specifically hybridize with chromosome sequences and identify known bands.
Multiplicity of infection
The ratio of virus particles to cells in a system.
A cell or tissue able to form several different kinds of cells or tissues.
A lysosomal structure containing inner vesicles.
An agent that increases the frequency of mutation.
The production of changes in DNA sequence that affect the expression of genes or the structure of gene products.
A heritable change in DNA sequence at the level of the gene, the chromosome, or the genome.
A tumor caused by the proliferation of immunoglobulin-synthesizing cells. Myelomas produce large amounts of a single (monoclonal) antibody, or the individual heavy or light chains.
Purified DNA with no associated proteins.
The use of silicon-based nanostructures capable to analyze single molecules with features comparable in size to DNA and proteins.
One billionth mole; 10-9 mole.
A high-throughput technique for the detection of differences in single DNA strands based on the use of an ionic current to pull DNA through a pore created by a channel protein.
A miniaturization technology based on the development of nanometer-scale machines to operate in molecular environments.
The 3-D structure of a protein in a living system.
Changes in the occurrence of alleles within a population over time due to differential reproductive success of individual genotypes.
The down-regulation or shutdown of gene transcription in response to the binding of negative regulatory elements.
A cellular antigen acquired after transformation by an oncogenic virus.
A tissue growth or tumor that may be benign or malignant.
Nerve growth factor (NGF)
A protein that stimulates the growth of neurons and the formation of neural networks.
A second round of PCR amplification that utilizes primers located internally to those used in the first round of amplification.
A computational method for optimizing for a desired property based on previous learning cycles (training).
A tumor arising in nerve cells.
A cell specialized for the transmission of nerve impulses.
A chemical released from the pre-synaptic terminus of an axon that diffuses across the synapse and binds to receptors in the post-synaptic membrane. Neurotransmitters are released from synaptic vesicles near the presynaptic cell membrane in response to the action potential.
Phagocytic white blood cell produced in the bone marrow that plays a role in immune defense.
New chemical entity (NCE)
A compound capable of being patented.
A space introduced into a DNA strand by the loss of one or more nucleotides.
A DNA probe labeling technique based on the introduction of nucleotide gaps into one strand of double-stranded DNA by a treatment with a nuclease, followed by the use of a DNA polymerase with exonuclease activity to extend the gaps and replace the nucleotides.
A nucleic acid segment that has no gene product and may play a role in structural organization.
Nonessential amino acid
An amino acid that may be synthesized by a cell or organism from simple chemical precursors. Nonessential amino acids are not required as nutrients.
Lacking in polarity; characterized by an even distribution of positive and negative charges.
The non-reactive binding of a substrate to the active site of an enzyme.
Nonprotein amino acid
An amino acid that is not a component of proteins.
A database in which redundant entries have been noted and merged.
One of three codons (UAA, UAG, UGA) that signal the termination of translation and release of the protein chain from the ribosome.
A mutation that causes the formation of a nonsense codon and the truncation of the protein product.
A database refinement process that organizes a database so that results obtained from queries to the database are always unambiguous.
Technique in which RNA fragments separated by electrophoresis are transferred to a membrane and probed with a labeled nucleic acid probe to detect a specific RNA.
Nuclear localization signal (NLS)
A short amino acid sequence that functions as a nuclear localization signal.
Nuclear magnetic resonance (NMR)
A spectroscopic technique used to determine the 3-D structure of small- to medium-sized proteins. NMR is based on resonant absorption of electromagnetic radiation by the magnetic dipole moments of atomic nuclei in an applied magnetic field.
Nuclear Overhauser effect (NOE)
A multidimensional NMR method for measuring spatial relationships within molecules based on the interaction between dipole moments of two nuclei in spatial proximity.
An opening in the nuclear envelope that joins the inner and outer nuclear membranes.
An enzyme that hydrolyzes ester linkages in nucleic acids.
A polynucleotide polymer consisting of deoxyribunucleotide units (DNA) or ribonucleotide units (RNA) joined by phosphodiester bonds.
Relating the nucleus to the cytoplasm.
A compact body within a bacterium containing the genome.
A dense body found in the cell nucleus. The nucleolus functions to transcribe and process ribosomal RNA and to assemble ribosomal precursors.
The protoplasm within the nuclear envelope.
Any complex of a protein with a nucleic acid (DNA or RNA).
A molecule consisting of a nitrogen-containing purine or pyrimidine base attached to a ribose or a deoxyribose sugar.
A chromosomal packing unit composed of a length of DNA wrapped around a histone core.
The fundamental unit of nucleic acids. A nucleotide consists of a nitrogen-containing base attached to a pentose monosaccharide with one, two, or three phosphate groups attached by ester linkages to the saccharide moiety.
Nucleus (plural, nuclei)
An organelle containing chromosomes that is the site of cellular DNA synthesis and RNA replication.
A single isotope.
A mutant mouse strain that lacks a thymus gland and T lymphocytes. Nude mice are hairless due to a mutation at a linked locus.
A mutation that does not produce a transcript or protein product.
The phenotype corresponding to a null mutation.
A nutrient that confers beneficial effects.
The UAA codon, one of three codons that code for termination of transcription of a mRNA and release of the newly synthesized polypeptide chain from the ribosome.
A mutation that produces a tRNA that inserts an amino acid at the site of the ochre termination codon, and allows translation to continue.
Ockham's razor, Occam's razor
A maxim stating an explanation should be based on a minimal number of assumptions.
An eight-base sequence element typical of eukaryotic promoters that binds transcription factors; the set of eight histones that forms the nucleosome core.
Short DNA fragments produced as DNA replication intermediates that are subsequently joined to form a single continuous strand of DNA.
Derived from a small number of clones.
A molecule containing a small number of covalently linked units; a multisubunit protein.
A molecule consisting of a small number of nucleotide units.
A molecule consisting of a small number of amino acid units.
A molecule consisting of a small number of monosaccharide units.
Any gene associated with cancer. Oncogenes are derived by the mutation of proto-oncogenes, normal cellular genes involved in growth control.
One hybrid system
A method for detecting protein-DNA interactions.
The creation of a systematically ordered data structure that enhances exchange of information between computers and scientists. Ontologies enable the definition and sharing of domain-specific vocabularies.
The UGA codon, one of three codons that code for the termination of transcription of a mRNA and release of the newly synthesized polypeptide chain from the ribosome.
Open reading frame (ORF)
The length of DNA sequence between the translation start signal and the termination codon that can be translated into a protein; the phase in which nucleotides can be read in sets of three that results in a protein.
A regulatory DNA sequence that controls the transcription of structural genes.
A prokaryotic DNA region that coordinates the regulatory and structural sequences for a gene or set of related genes.
A serum protein that renders microorganisms and other foreign material more susceptible to phagocytosis.
Coating a particle with opsonin proteins.
A sensor that uses light to detect the effect of a chemical on a biological system.
A glass or plastic fiber surrounded by a material with a lower index of refraction. Optical fibers transmit light from one end to the other by internal reflection.
A laser-based technique that utilizes minute forces exerted by light waves to measure and to manipulate biomolecules.
A discrete subcellular structure with specialized function.
Origin of replication
A region of DNA necessary for the initiation of replication.
A drug that treats a rare disease.
Receptor for which an in vivo ligand is not yet known.
A gene with similar function to a gene in an evolutionarily related species. The identification of orthologs is useful for gene function prediction.
A cell that secretes the bone matrix.
A mononucleate macrophage that breaks down the bone matrix and plays a role in bone remodeling.
A gene whose sequence overlaps that of another gene in the same or a different reading frame.
The phosphorylation of ADP to ATP in a process driven by the generation of a proton gradient in the mitochondrial inner membrane that drives ATP synthase.
The encapsulation of DNA by viral coat proteins.
An arrangement of symbols that reads the same backward as forward.
A double-stranded DNA sequence with a two-fold rotational axis of symmetry (dyad symmetry).
An iterative method for selecting cells or clones based on successive rounds of target selection.
Simultaneous analysis of thousands of samples.
A gene related to a similar gene by duplication within a genome. Paralogs tend to evolve new, related functions.
User-derived values used to set the boundaries of an algorithm.
The use of algorithms to analyze data into components.
Immunity acquired by transfer of antibodies or T-lymphocytes from another individual.
A technique that uses a microelectrode to record current flow across a membrane.
A microorganism or other agent that causes disease.
A series of related biochemical reactions.
A nucleic acid or protein motif that is computationally detectable within aligned sequences.
The degree to which a genotype is expressed as a phenotype; also used to characterize the likelihood that a gene will result in a disease.
A protease that hydrolyzes peptide bonds.
Two or more amino acids joined by a peptide bond.
An amide bond formed between two amino acids by the linkage of the amino group of one amino acid to the carboxyl group of a second amino acid.
Peptide map, peptide fingerprint
A pattern produced by hydrolysis of a protein and 2-D mapping of the resulting peptide fragments.
Peptide nucleic acid (PNA)
A DNA mimic that incorporates a peptide-like polyamide backbone.
A polymer that contains equal amounts of peptide and polysaccharide.
Peptidyl site (P site)
One of two sites in the large ribosomal subunit involved in protein translation.
A ribosomal enzyme that catalyzes peptide bond formation during protein synthesis.
The space between the bacterial cell membrane and the cell wall. Recombinant proteins secreted into the periplasmic space are readily released.
A molecule or peptide that disrupts intracellular processes, providing information about the operation of pathways and networks within the cell.
A prefix indicating 1015; a quadrillion.
A theoretical measure of computer speed that corresponds to a thousand trillion (1015) floating point operations per second.
A region of lymphoid tissue in the submucosa of the intestine that is rich in B cells and germinal centers.
A virus that infects bacterial hosts and may be utilized to introduce genes. Phages are widely used as cloning and expression vectors.
Phage display (peptide phage display)
A technique that fuses peptides to capsid proteins on the phage surface. Libraries of phage-displayed peptides may be screened for binding to specific ligands; determination of the gene sequence of the selected phage identifies the peptide sequence.
A phage-plasmid vector able to replicate as single- or double-stranded DNA.
An endocytic process based on the extension of cellular pseudopods that engulf target cells and tissue debris, forming phagosomes. Subsequent fusion with lysosomes generates phagolysosomes and results in the digestion of the particles.
The organelle formed by the fusion of a phagosome with a lysosome.
A cellular inclusion formed by the engulfment of cells or tissue debris during phagocytosis.
Proteins manufactured for use as drugs.
The evaluation of individual genomic variation in relation to the delivery and effectiveness of drugs. Knowledge of individual genotype and hence phenotype makes it possible to customize drugs and drug delivery methods for specific subgroups.
The study of the absorption, distribution, metabolism, and elimination of drugs.
The 3-D coordinates of atoms corresponding to pharmacologically active components of a drug molecule.
The production of large quantities of useful proteins by transgenic animals or plants.
All biochemical, physiological, and morphological characteristics of an organism.
The study of all possible phenotypes; the subject of functional genomics.
Measurable functional and structural characteristics of an organism as determined by the interaction of the genotype with the environment.
The overall biochemical, physiological, and morphological profile of an organism.
Two fatty acids linked via glycerol phosphate to one of several polar groups.
A label with a photoactivatable group that forms a covalent link with an adjacent protein upon illumination.
The study of the effects of light on living systems.
Photodynamic therapy (PDT)
A treatment based on the uptake by target cells of photoactivatable molecules that destroy the cells upon exposure to a specific light source.
A process that utilizes selective masking to generate light patterns that direct chemical transformations within a photosensitive surface.
The light-activated repair of DNA damage by DNA photolyase.
A biochemical process in which light absorbed by chlorophyll is utilized to build carbohydrate molecules.
Photosynthetic reaction center
The bacterial photosynthetic complex that transduces light to ATP.
An organism that uses light as a primary source of energy, synthesizing all organic requirements directly from inorganic precursors.
Blue pigment found in cyanobacteria and red algae.
Red pigment found in cyanobacteria and red algae.
A method for predicting the function of a protein that is based on the correlation of protein inheritance across different species. Any two proteins having similar phylogenetic profiles are likely to be involved in a common pathway or multi-protein complex.
Phylum (plural, phyla)
A major group within a kingdom. Members of a phylum share a common structure and organization.
The mapping of restriction fragments or overlapping clones onto a chromosome.
The study of the complete set of interactions that produce the physiology of an organism.
A biologically active molecule derived from herbs, vegetables, fruits, flowers, etc.
A plant chromoprotein involved in the regulation of light-dependent growth processes.
A plant hormone.
One trillionth mole; 10-12 mole.
A material capable of transducing mechanical output to electrical signals or, alternatively, electrical signals to mechanical output. Piezoelectric devices are used in microsystems.
A plant cell culture technique that produces plant embryos from small pieces of plant tissue. Plant embryogenesis is a form of somatic cell embryogenesis, in which an embryonic program is initiated in a cell from an adult tissue.
Plant storage proteins
Proteins stored in seeds that are utilized as a source of amino acids during germination.
Antibody produced by genetically engineered plants.
A clear zone in a layer of cells produced by the action of an agent that lyses the cells, such as a virus.
A technique that uses a membrane to “lift” expressed proteins from clones growing on a plate. Screening of the membrane identifies the proteins, and the active clones.
An antibody-secreting B-lymphocyte.
The lipid bilayer membrane that forms the boundary of a cell.
A plasma cell tumor.
A DNA element that is able to replicate independently. Elements of bacterial plasmids are utilized in vectors.
The treatment of cells with a substance that interferes with plasmid replication.
The ability to develop or adapt in response to the environment.
A double membrane-bound cytoplasmic organelle containing DNA found in plants. Plastids include chloroplasts and chromoplasts.
The total plastid complement of a cell.
The intertwining of the two strands of a double helix such that separation of the strands requires uncoiling.
Having the ability to change shape.
Having multiple effects on phenotype.
Capable of differentiating into several final differentiated cell types.
The end of an actin filament to which monomers are added more rapidly.
A virus-specified RNA, or any strand of DNA or RNA with equivalent sequence. The complementary sequence is the minus strand.
A single base change.
The uneven distribution of postive and negative charges in small molecules, resulting in an electric dipole moment.
A protein structural motif consisting of interactions between polar residues on separate subunits or separate proteins.
An abbreviation for polyadenylate, or polymerized adenosines. Most mRNAs are terminated by poly(A) stretches. Binding of poly(A) regions by poly(T) is a widely used technique for the isolation of mRNA from cells.
A matrix of acrylamide polymers cross-linked using bis-acrylamide. Polyacrylamide gels are used for the separation of nucleic acids and proteins by gel electrophoresis.
Polyacrylamide gel electrophoresis (PAGE)
Electrophoresis of nucleic acids and proteins through polyacrylamide gels.
A processing signal at the 3' end of an RNA that specifies the addition of a stretch of adenines.
A macromolecule with multiple positive charges conjugated to a protein that binds a cell receptor. Polycation conjugates are used to transport DNA into cells.
Derived from multiple clones.
An antibody generated by the immune response to an antigen. Each epitope on the antigen is capable of causing the formation of a clone of B lymphocytes that will produce an antibody to that epitope.
Polyethylene glycol (PEG)
A water-soluble polymer used to solubilize proteins, and as a cell fusogen.
Caused by the combined action of alleles of multiple genes.
Polymerase chain reaction (PCR)
A techique for the cyclic amplification of DNA segments by thermostable DNA polymerase. Following heat denaturation of the DNA, oligonucleotide primers complementary to flanking regions are annealed and extended, resulting in the synthesis of replicated DNA.
The existence within a population of two alleles of a gene, where the frequency of the rare allele is greater than 1%, and not attributable to recurrent mutation.
A collective name for neutrophils, basophils, and eosinophils.
Polymorphonuclear leukocytes (PMN)
Phagocytic white blood cells with a lobed nucleus.
A chain of amino acids connected by peptide linkages. A polypeptide is longer than an oligopeptide, and may constitute an entire protein.
Multiple ribosomes actively translating a single mRNA into polypeptides.
Organisms of the same species that occupy the same area.
Population diffusion coefficient
The tendency of motile cells to diffuse through the environment.
A trimeric transmembrane protein that forms channels in the bacterial outer membrane. Similar porins are found in the mitochondrial outer membrane.
A change in the expression of a gene due to translocation of the gene to a new position in the genome.
The activation or up-regulation of transcription in response to the binding of a regulatory element.
Positive negative selection (PNS)
A laboratory technique that accelerates the identification of genetically engineered organisms that possess desired genetic changes by selecting against the organisms that do not have the desired characteristics.
Superhelical turns of a DNA double helix molecule.
Alteration of newly transcribed RNA within the nucleus, such as 5' capping, the splicing out of introns, and 3' polyadenylation.
Covalent modification of proteins following translation, including glycosylation, phosphorylation, sulfation, acetylation, and ribosylation.
Small molecule transport across cell membranes by caveolae.
Pre-steady state kinetics, transient phase kinetics
The brief phase of an enzymatic reaction during which the concentration of the reactant-catalyst complex rises to the steady state value.
The additon of a prenyl moiety to a protein. The addition of prenyl groups regulates protein-membrane interactions.
One of two hybrid proteins used in two-hybrid protein-protein interaction assays.
One of the two consensus sequences in the 5' promoter region of prokaryotic RNA that control the binding of RNA polymerase.
An antibody generated against an antigenic target (a protein, peptide, carbohydrate, or other small molecule).
The culture of cells obtained directly from the tissue source.
Primary immune response
The response of the immune system to the first challenge by an antigen.
Primary RNA, pre-RNA
Newly transcribed RNA that has not been processed to mRNA. Primary RNAs undergo processing by spliceosomes to remove introns and ligate exons, resulting in a continuous mRNA sequence.
An RNA polymerase that forms oligoribonucleotide primers in the 5' to 3' direction. During DNA replication, primase primes the RNA-DNA sequences that become the Okazaki fragments.
Oligonucleotide that may be extended by DNA polymerase.
A method for finding the start site for gene transcription. Reverse transcriptase is used to extend a primer to the 5' region of a gene and the resulting fragments compared on a gel.
A protein complex, consisting mainly of DNA helicase and primase, that unwinds the DNA helix prior to replication and synthesizes RNA primer sequences.
An abnormally folded protein that causes disease by inducing normal counterparts within the cell to fold in an abnormal manner and aggregate.
The first person to be studied, from whom genetic descent may be traced.
A virion precursor that consists only of the viral capsid without the nucleic acid.
The activity of an enzyme that progressively synthesizes or breaks down a polymeric molecule using successive cyclic reactions but does not dissociate from the template between cycles.
The number of nucleotides polymerized before a polymerase dissociates from the template.
An inactive drug precursor that is activated by a biological process, such as enzymatic cleavage.
The inhibition of an enzymatic reaction by the accumulation of the products of the reaction.
The binding of a substrate to the active site of an enzyme in a reactive manner.
An inactive enzyme precursor that is activated by proteolysis; a zymogen.
Programmed cell death
A form of cell death essential for development that is based on a mechanism that requires protein synthesis.
An peptide hormone that is inactive until proteolytic cleavage.
An organism lacking a nucleus and other membrane-bounded compartments.
The DNA sequence bound by RNA polymerase and transcription factors during the initiation of transcription.
An enzymatic mechanism that corrects errors in DNA synthesis.
A copyrighted database accessible by subscription.
A non-protein structure that is bound tightly to a protein and is essential to the activity of the protein.
An enzyme that degrades proteins by hydrolyzing peptide bonds.
A large protein complex that degrades proteins that have been tagged for elimination, particularly those tagged by ubiquitination.
A linear biomacromolecule synthesized by ribosomes and consisting of a chain of amino acids in peptide linkage. Intracellular proteins have structural, regulatory, and catalytic functions; proteins secreted by cells have, in addition, intercellular signaling functions.
Protein affinity chromatography
A method for the direct characterization of protein-protein interactions.
Microarrays used to identify proteins and characterize protein function.
A structurally and functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein.
The translation and post-translational processing of proteins.
A group of proteins related by evolution that share highly conserved sequence regions, 3-D structure, and function.
The pattern of proteins in a cell or organism as determined by 2-D gel electrophoresis.
Protein linkage map
A protein-protein interaction network map.
Protein primary structure
The sequence of amino acid residues that form a protein.
Protein quaternary structure
The interaction of protein subunits to form functional multi-subunit proteins.
Protein secondary structure
The interactions between amino acids within a protein chain to form an a helix and b sheet structure.
Protein tertiary structure
The folding of a protein into a 3-D structure.
The network of interactions between proteins based on two-hybrid assays and other protein-binding data.
One or more glycosaminoglycans attached to a core protein.
Cleavage of proteins by proteases.
The dynamic protein complement of an organism, including all post-translational modifications and protein interactions.
Proteome-wide analysis of protein regulation, expression, structure, post-translational modification, interactions, and function. This study of proteins is important in biotechnology and drug discovery, because proteins are responsible for most tasks in the cell.
Normal cellular gene, usually involved in growth control, from which an oncogene is derived as the result of a somatic mutation or viral recombination.
A subunit of an oligomeric protein.
An ionophore that transports protons.
A plant, fungal, or bacterial cell from which the outer cell wall or membrane has been removed.
A microorganism strain that requires the same nutrients as the wild-type strain.
A virus that is integrated into the host chromosome and does not cause lysis.
A nonfunctional gene sequence that is related to a known gene but cannot be transcribed or translated due to mutations.
A transient protrusion or retractile process associated with cell movement and feeding.
Process for changing the cell binding specificity of a virus by changing the capsid (envelope) proteins.
A minor nucleoside component of tRNA formed by post-transcriptional modification of uridine. Pseudouridine within the anticodon base pairs with adenine.
An organism that grows optimally at low temperatures.
Pulsed field gel electrophoresis (PFGE)
A gel electrophoretic method for the separation of megabase fragments of DNA based on continuous alteration of the angle at which the electrical field is applied.
A double-ring basic compound that contains nitrogen. Adenine and guanine are purines found in DNA and RNA.
A nucleoside antibiotic that interrupts protein synthesis by incorporating into the polypeptide and causing premature release from the ribosome.
A single-ring basic compound that contains nitrogen. Cytosine and thymine are pyrimidines found in DNA; cytosine and uracil are pyrimidines in RNA.
Describes a biological system capable of only two responses.
Quantitative structure activity relationship (QSAR)
The relationship between the structure of a chemical and its pharmacologic action.
Quantitative trait locus (QTL)
The chromosomal location of one of a set of genes that collectively encode a quantitative trait that varies continuously across a population.
A theory that explains the behavior of elementary particles, atoms, and energy in terms of probabilities.
Quantum yield, quantum efficiency
The probability of luminescence in a system.
A substance that deactivates excited molecules by processes such as resonance energy transfer and complex formation.
The reduction of luminescence of a sample by the addition of a quencher.
The nucleic acid or protein sequence used to search sequence databases in order to identify similar sequences from which function may be deduced.
A structure formed when a complementary RNA pairs with one strand of double-stranded DNA at the start of transcription.
Racemic mixture, racemate
A mixture of equal amounts of the D- and L- enantiomers of a chiral compound.
An assay that utilizes radiolabeled antigens or antibodies to quantitate antibody-antigen interactions.
A radioactive ligand incorporated into a small molecule or biomolecule that enables detection and quantification of the molecule.
A restriction enzyme that cuts at sites that occur infrequently within chromosomes.
Rational drug design (RDD)
The design of a drug molecule based on knowledge of the pharmacologically relevant characteristics of the target protein structure, as obtained by x-ray crystallographic methods.
The extended protein that results when an RNA termination codon is read through by a suppressor tRNA.
A protein that binds an extracellular ligand. Binding of ligand to a cell-surface receptor alters the structure and activity, resulting in the initiation of a series of signal transduction events that modulate intracellular biochemical pathways.
The use of the known 3-D structure of a ligand to predict features of the complementary structure of the receptor. The model is continuously refined as data are acquired.
An allele that is expressed in the phenotype of the organism only when present in the homozygous form.
DNA molecules generated by cloning DNA fragments into vectors, transforming cells, and isolating clones that express the DNA fragment.
A protein generated using recombinant DNA technology.
The formation of a new genotype by chromosome re-assortment or intrachomosomal crossing over.
The repetition of a data-processing algorithm until a pre-set threshold is reached.
A chromatographic technique for the rescue of misfolded proteins that have aggregated and become insoluble.
A gene encoding a DNA-binding protein that functions as an enhancer, a transcription factor, a repressor, or other modifier of gene expression.
A network of interactions between molecules that is inferred from computational algorithms that identify relationships within data derived from large-scale gene expression and proteome analysis.
A DNA sequence that controls the expression of a gene.
The total interactions of the regulatory networks within a cell.
The self-adjustment of a molecular system to a new minimum free energy state after the perturbation of the system.
Circular DNA that has an unwound loop. Relaxed DNA is less compact than supercoiled DNA and migrates more slowly during gel electrophoresis.
Relaxed form (R form)
A quaternary protein structure that has higher affinity for a ligand than the taut form.
Release factor (R factor)
A protein involved in the release of nascent polypeptide chains from the ribosome.
The return of a denatured molecule to the original native conformation.
Repeated polynucleotide sequences. Repetive sequence is characteristic of satellite DNA, minisatellite DNA, transposons, and Alu sequences.
The production of identical bacterial colony patterns on a series of agar plates.
The synthesis of new deoxypolynucleotide strands.
A large multi-protein complex that performs DNA replication.
A gene used to reveal the function of potential regulatory sequences.
A DNA-binding protein that prevents transcription of an adjacent gene.
An enzyme involved in the replicative transposition of elements in E. coli.
An endonuclease that recognizes specific nucleotide sequences and cleaves DNA at these sites.
Restriction fragment length polymorphism (RFLP)
Variation in DNA sequence between individuals that is detectable by variation in the length of DNA fragments generated by digestion with restriction endonucleases.
A diagram of DNA indicating sites of cleavage by restriction enzymes.
The DNA sequence recognized and cleaved by a restriction endonuclease.
A tumor of the retina.
A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.
The use of phenotype or protein information to identify the gene encoding the protein.
An enzyme with a DNA helicase and DNA topoisomerase domains that induces positive supercoiling into DNA.
The structure formed by amphipathic molecules in a nonpolar solvent. The hydrophilic regions of the molecules are sequestered in the interior of the micelle, and the hydrophobic regions are at the surface.
An enzyme that catalyzes the synthesis of deoxyribonucleotides into a sequence complementary to a pre-existent RNA template.
Reverse transcriptase-PCR (RT-PCR)
A technique based on the use of reverse transcriptase to copy cellular RNA sequences into DNAs that are subsequently amplified by the polymerase chain reaction.
Reverse two hybrid system
A method for studying protein-protein interactions in which interactions result in the increased transcription of a toxic marker causing growth inhibition. Reverse two hybrid methods can select for conditions that cause the dissociation of proteins.
A second mutation that reverses a previous single point mutation.
rho (R) factor
A bacterial protein that facilitates transcription termination. rho factor is an ATP-dependent helicase that upon activation causes release of the mRNA from the DNA template.
rho (R) protein
A small GTPase that controls the polymerization of actin into filaments.
Any nuclease that cleaves phosphodiester bonds in RNA. All ribonucleases are proteins, with the exception of Ribonuclease P, which is a ribonucleoprotein with ribozyme activity.
Ribonuclease P (rNase P)
A ribozyme that forms the 5'-phosphate terminus of tRNA by cleaving bases from the 5' end of the primary transcript. rNase P is a ribonucleoprotein complex.
Ribonucleic acid (RNA)
A long macromolecule formed from ribonucleotides. Functional classes include messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), small nucleolar RNA (snoRNA), and other small RNAs.
A complex of a protein with RNA. Examples include snRNP, small nuclear ribonucleoprotein and hnRNP, heterogeneous nuclear ribonucleoprotein.
A ribosome-binding protein found in the endoplasmic reticulum.
The systematic characterization of RNA-protein interactions that affect the splicing, transport, lifetime, and translation of RNAs.
A pentose sugar that is a structural component of ribonucleic acid, riboflavin, and other nucleosides and nucleotides.
Any protein component of a ribosomal subunit. S proteins are derived from the small ribosomal subunit, L proteins from the large ribosomal subunit.
Ribosomal RNA (rRNA)
An integral structural component of the large and small ribosomal subunits. The rRNA associated with the large subunit has been shown to be a ribozyme with peptidyl transferase activity.
A structure consisting of small and large ribonucleoprotein units that is the site of intracellular protein biosynthesis.
A glycosyl group derived from ribose.
The addition of a ribosyl residue.
An RNA molecule that catalyzes RNA splicing.
A derivative of rifamycin that inhibits bacterial transcription without affecting eukaryotic transcription.
The alteration of RNA transcripts to produce RNAs with sequences different from those encoded in the genome.
An enzyme that catalyzes the synthesis of ribonucleotides into a sequence complementary to a pre-existent DNA template.
RNA polymerase I
The RNA polymerase that transcribes ribosomal RNA (rRNA).
RNA polymerase II
The RNA polymerase that transcribes messenger RNA (mRNA).
RNA polymerase III
The RNA polymerase that transcribes transfer RNA (tRNA).
The excision of introns from RNA during the formation of mRNA.
A method for the replication of circular double-stranded DNA.
Rosetta Stone method
A comparative genomics method that utilizes information about fused multi-domain proteins in one species to predict potential interactions of homologous proteins in other species that correspond to the individual domains.
Rough endoplasmic reticulum (RER)
A region of the endoplasmic reticulum associated with ribosomes and involved in the synthesis of membrane proteins and secreted proteins.
The stage of the cell division cycle during which DNA is synthesized.
S1 mapping (S1 nuclease mapping)
A technique for the removal of single-stranded regions of DNA and RNA from double-stranded hybrids of DNA and RNA.
An endonuclease that degrades single-stranded RNA or DNA to mononucleotides. S1 nuclease is useful for the removal of unpaired regions following hybridization.
Saccharomyces cerevisiae (S. cerevisiae), Baker's yeast
A budding yeast widely studied as a simple model for eukaryotic cells.
A DNA sequencing method based on controlled interruption of replication by dideoxynucleotides.
A glycosidic surfactant produced by plant cells.
A malignant tumor of the connective tissue.
Highly repetitive, non-transcribed DNA regions in eukaryotic chromosomes that have a different sedimentatin coefficient than other nuclear DNA.
The molecular core common to all members of a combinatorial library; also proteins that are instrumental in the assembly of large 3-D structures.
A mediator that is generated within a cell in response to a signal transduction event at the cell surface.
An antibody that recognizes and binds a primary antibody. Secondary antibodies conjugated to enzymes and labels are key components of detection systems.
The immune response that follows the second exposure to a substance.
The arrangement of a protein chain into regular hydrogen-bonded structures such as a helix or b sheet.
A small single-membrane vesicle formed from the Golgi apparatus that transports newly synthesized proteins to the cell periphery, fuses with the cell membrane, and delivers the proteins to the extracellular space.
A cell culture method that enables cells with specific characteristics to be isolated from a mixture of cells.
The intensity of natural genetic selection processes. Selection pressure may be measured by changes in gene frequency.
The dynamic organization and interaction of the molecular components of living systems; the development of complex structures by the iteration of simple behaviors by individual components using only local information.
The strand of DNA that acts as the template for RNA synthesis.
Device for determining the sequence of monomeric residues of a polymeric molecule.
The determination of the sequence of a nucleic acid, protein, or carbohydrate based on the fragmentation of the original molecule, the analysis of sequence, and the assembly and interpretation of the sequence information.
A sequence pattern representation emerging from comparison of multiple aligned sequences.
Sequence tagged site (STS)
A short DNA sequence with a known chromosomal location that occurs once within the human genome.
Device for determining the sequence of monomeric residues of a polymeric molecule.
Sequestration enabling reagent
A reagent that sequesters starting materials or reaction by-products, in order to simplify removal from a reaction mixture.
Serial analysis of gene expression (SAGE)
A quantitative gene expression analysis method based on the concept that an mRNA transcript may be identified by a short subfragment or tag derived from the 3' region of the transcript.
The 23rd pair in a karyotype; females have two X chromosomes, males have an X and a Y chromosome.
The genetic specification of the sex of an individual by the genes of the X and Y chromosomes.
An mRNA sequence that precedes the translation initiation codon and is complementary to a ribosomal RNA .
A genomic cloning method based on the generation of random DNA fragments that are cloned into vectors to form a genome library.
A DNA plasmid capable of replication in multiple host organisms.
Sigma (S) factor (sigma subunit)
A bacterial transcription initiation factor that promotes association of RNA polymerase to specific initiation sites.
An endopeptidase that removes the signal peptide following translocation of a protein.
A short amino acid sequence that determines the localization of a protein within the cell.
Relaying a signal by conversion from one form to another. The transduction of an extracellular signal to the cytoplasm by a cell surface receptor or a cytoplasmic receptor.
An alternative term for motif or pattern.
A mutation in a codon that does not cause a change in the amino acid sequence of the translation product.
A molecular dynamics method that simulates the heating and cooling of a system in order to describe the most stable state.
An emulation of biological systems with predictive value for research; a virtual biological system.
Single cell capture
The isolation of single cells from a tissue using laser microdissection.
Single chain antibody
A synthetic antibody based on a single chain.
Single domain antibody (Dab)
A synthetic antibody based on a single chain.
Single molecule detection
Observations of the dynamics of single molecules. Single molecule methods complement high-resolution information obtained by averaging molecular ensembles using NMR and from static molecules using x-ray crystallography.
Single nucleotide polymorphism (SNP)
Scattered single-base pair variations within the genetic code of the individuals of a population. SNPs determine ways that subpopulations within a species differ and provide information about variations of protein expression.
A protein with a single transmembrane sequence.
Single strand binding protein (SSB)
A protein that binds single-stranded DNA and stabilizes unwinding of the double helix.
Single stranded conformation polymorphism analysis (SSCP)
A method for identifying mutations using the rate of DNA migration in denaturing gels.
Small molecule array
A microarray for the screening of small molecules derived from combinatorial synthesis.
A sensitive algorithm for identifying sequence similarities.
Smooth endoplasmic reticulum (SER)
A region of the endoplasmic reticulum involved in lipid synthesis.
A model for vesicular fusion.
Abbreviation for Small Nucleolar Ribonucleoprotein.
Abbreviation for Small Ribonuclear Particle.
One of three distinct nucleolar regions that contain small nuclear ribonucleoproteins (snRNPs).
Solid phase extraction
A sample purification method based on the affinity of either the desired or undesired components of a reaction mixture for a solid material and subsequent filtration of the solid material from the reaction.
An insoluble material to which reagents may be attached so that they may be readily separated from reaction by-products and solvents by filtration.
A combinatorial chemical synthesis technique for the creation of libraries of diverse compounds that utilizes solid supports to separate compounds during synthesis, thus simplifying the identification of the resulting compounds.
A support for a reaction that is soluble under reaction conditions, but readily separable by some simple process. Examples of soluble supports include linear polymers such as polyethylene glycol and dendrimers.
Liquid-phase combinatorial chemical synthesis techniques for the creation of libraries of diverse compounds.
Any cell of an organism that is not a germ cell.
Somatic cell hybrid
A hybrid cell formed from the fusion of cells from different species. Somatic cell hybrids are utilized for gene mapping.
Somatic gene therapy
The delivery of genetically engineered genes to somatic cells in order to treat a disease.
A non-heritable genetic change occurring within a somatic cell, also known as an acquired mutation.
Proteins vital to pattern formation in several metazoan groups.
A technique that utilizes labeled DNA probes to identify DNA fragments that have been transferred to membrane filters following electrophoretic separation.
A blotting technique for the detection of DNA-protein interactions based on the use of labeled DNA to probe proteins transferred to membrane filters.
The development of new species as a result of evolutionary processes.
The study of molecular or atomic structure of a substance by observation of its interaction with electromagnetic radiation.
Microtubules extending from each chromatid to opposite poles of the cell during mitosis. Spindle fibers separate the chromatids into daughter cells.
The RNA sequence at the exon-intron boundary.
The base sequence at each end of an intron that determines the splice point. The site at the 5' end of the intron is the donor site and the site at the 3' end is the acceptor site.
A ribonucleoprotein complex consisting of RNA and small nuclear ribonucleoproteins (snRNPs). The spliceosome accomplishes the splicing of primary RNA transcripts by excising introns and ligating the ends of exons, resulting in a mRNA transcription.
The covalent linkage of DNA by DNA ligase; the process by which the spliceosome excises introns from RNA; the post-translation cleavage and ligation process that results in the excision of a protein intein and ligation of the ends created to form an extein.
An interrupted gene.
Array generated by microspotting nucleic acids on a glass, plastic, or filter substrate.
Flat cells that constitute the surface of the skin.
An isotope that does not undergo radioactive decay.
The codon (AUG) that codes for the first amino acid residue of all proteins (formylmethionine).
Steady state kinetics
The analysis of an enzyme reaction during the interval when the concentration of intermediates is steady.
Hindrance of an enzymatic reaction by structural features of the substrate or the enzyme.
One of three codons (UGA, UAG, UAA) that code for termination of transcription of a mRNA and release of the newly synthesized polypeptide chain.
An organism that is geneticaly different from others of the same species. Also known as a cultivar.
A tetrameric biotin-binding protein capable of binding four molecules of biotin per molecule. Streptavidin may be labeled with a fluorophore, an enzyme, or gold particle to facilitate detection.
The process of predicting the 3-D structure of a protein from comparison of primary sequence alignment, secondary structure prediction, homology modeling, threading prediction, NMR data, and crystallographic data.
A gene that encodes a protein.
The prediction of the structure of a protein based on homology to a known protein structure.
The proteome-wide study of protein structure and function, based on the selection of a set of proteins representative of each major protein family, development of high-throughput approaches to crystallization screening, and x-ray diffraction analysis.
Structure based drug design (SBDD)
The design of a drug molecule based on knowledge of the pharmacologically relevant characteristics of the target protein structure, as obtained by x-ray crystallographic methods.
The isolation of intracellular organelles and and sub-organellar compartments.
A DNA clone generated by transferring a cloned DNA fragment from one plasmid to another.
Submitochondrial particle (SMP)
An inside-out particle formed by the sonication of mitochondria. Inverted mitochondrial inner membrane vesicles are used to study processes that involve oxidative phosphorylation.
A chemical component that exists at a lower level of complexity than individual molecules (electrons, ions, free radicals).
A molecular group that replaces another in a chemical reaction.
A molecule acted upon by an enzyme.
A library prepared by subtractive hybridization that allows the detection of differentially expressed RNAs.
A process that eliminates cDNAs shared by two libraries by hybridization. Unhybridized cDNAs represent RNAs that are differentially expressed in one library.
A single unit of a multi-subunit protein.
A gene that processes an inactive prodrug to a toxic form.
An antigen that activates a large percentage of T-lymphocytes.
A group of functionally or structurally related proteins.
The form of the DNA helix in vivo, in which DNA duplex structures are twisted around each other to form a superhelical structure.
A gene that reverses the effect of a mutation in another gene.
A secondary mutation that restores function lost due to mutation at another site.
A transfer RNA that recognizes a termination codon in an RNA and adds an amino acid residue instead of terminating the chain, generating a readthrough protein.
Any chemical system that exists at a higher level of complexity than individual molecules (multi-enzyme complexes, organelles, membranes).
Surface plasmon resonance (SPR)
A biosensor system used for analyzing ligand binding and kinetics of specific molecules within complex mixtures without prior purification. Binding of a ligand to a biomolecule immobilized on a membrane results in changes in membrane surface plasmon resonance.
Surfactant, surface active agent
A substance that reduces the surface tension of a liquid. Detergents and emulsifiers are surfactants.
A curated protein sequence base.
The concept that mitochondria are the descendants of bacteria that once lived as symbionts within eukaryotic cells.
A long-term association of different species that provides mutual benefit.
The site of communication between neurons. The synapse may transmit an action potential by the release of a neurotransmitter that binds a ligand-gated channel on the post-synaptic cell, or may make a direct connection between cells via gap junctions.
Syncytium (plural, syncytia)
Multi-nucleate cells formed by the fusion of neighboring cells. Syncytia may form due to the expression of a viral fusion protein during viral replication.
A pattern of recognizable symptoms or signs characteristic of a disease.
An agent that increases the effectiveness of a ligand or other agent.
An antigenically identical organism.
Systematic evolution of ligands by exponential enrichment (SELEX)
A process that identifies aptamers by iterative enrichment for molecules capable of binding a target.
In enzyme nomenclature, a name that precisely defines the catalytic activity of an enzyme. The systematic name for an enzyme describes the substrate(s) and provides a description of the nature of the reaction (a word ending in “-ase”).
Biological classification and nomenclature.
Affecting the entire body rather than a single part.
Systems-level understanding of biological systems that takes into account complex interactions of gene, protein, and cell elements.
T cell receptor
A transmembrane protein on the surface of T cells that recognizes antigens associated with MHC proteins on the surface of phagocytes.
T suppressor cell
A cell that suppresses helper cells.
A white blood cell derived from lymphoid stem cells in the thymus that is responsible for cell-mediated immunity and for stimulating B lymphocytes. T-lymphocyte subtypes include helper, suppressor, and cytotoxic T cells.
Tandem MS (MS/MS)
A mass spectroscopic method used for high-throughput analysis of protein sequence. Two mass spectrometers are linked in tandem so that the first fragments proteins into peptides, and the second fragments the peptides, enabling the determination of the amino acid sequence.
Multiple copies of the same base sequence on a chromosome.
A DNA, RNA, or protein that is involved in a disease process and is a suitable target for therapeutic compound development.
Verifying that a DNA, RNA, or protein is involved in a disease process and is a suitable target for therapeutic compound development.
A consensus sequence in the 5' region of eukaryotic transcription promoter regions that controls the binding of RNA Polymerase II. The TATA box is also known as the Goldberg-Hogness box.
Taut form (T form)
A quaternary protein structure that has lower affinity for a ligand than the relaxed form.
One of a set of possible alternative structures.
Telomerase reverse transcriptase (TERT)
A ribonucleoprotein reverse transcriptase involved with telomere formation and elongation.
A cap structure at the ends of chromosomes consisting of short repeated sequences with strand asymmetry in GC content, resulting in one G-rich strand and one C-rich strand.
The final stage of mitosis or meosis during which nuclei form in the daughter cells.
A molecule whose structure is a pattern for the synthesis of a complementary molecule.
A gene that programs the development of a system, determining the activation of structural and regulatory genes in various cell types.
A prefix indicating 10 to the power of 12; a trillion.
A measure of supercomputer speed equivalent to 10 to the power of 12 floating point operations per second.
An agent that causes congenital malformations in embryos.
One of three codons (UGA, UAG, UAA) that code for termination of transcription of an mRNA and release of the newly synthesized polypeptide chain.
Any protein involved in the termination of transcription or translation.
A microorganism that grows optimally in high-temperature environments.
Three-dimensional quantitative structure-activity relationship (3-D QSAR)
The statistical correlation of 3-D structure of a compound with its biological activity.
A technique for the detection of complexes that involve three proteins; also used to refer to a technique for the detection of RNA-protein interactions.
A nucleoside form of thymine.
A pyrimidine base present in DNA. Thymine base pairs with adenine.
A microarray consisting of thousands of overlapping oligonucleotides defining a continuous chromosomal region.
Arrays consisting of tissue specimen cores.
A target validation process that compares gene expression in normal and disease tissues.
An attenuation of response to an agent or antigen.
Macromolecular isomers that differ in topology.
The study of the deformability of intact structures.
Conformations that share the same backbone topology.
Total gene expression analysis (TOGA)
An automated gene expression analysis technique that is a hybrid of differential display and serial analysis of gene expression (SAGE).
A cell with the potential to become any other cell of an organism.
The genome-wide study of the effects of toxic substances on gene and protein expression.
The rate of uptake and transformation of potentially toxic substances within a living system.
A protein transcription factor.
The splicing of RNA exons generated from both strands of DNA into a single transcript.
Activation of transcription by the binding of a transcription factor to a DNA regulatory sequence.
An RNA synthesized from a DNA template.
The synthesis by RNA polymerase of an RNA complement from a DNA template.
Transcription factor binding site
The DNA sequence that is recognized and bound by a transcription factor.
A regulatory element that binds a DNA transcription control sequence to activate the transcription of genes.
A regulatory element that binds a DNA transcription control sequence to repress the transcription of genes.
A large multi-protein complex that carries out the transcription of RNA.
All transcribed mRNAs within a cell.
The genome-wide study of mRNA expression levels.
The transfer of bacterial genetic material between bacteria by a bacteriophage or phage vector.
The introduction of DNA into a cell or organism using recombinant DNA technology.
Transfer RNA (tRNA)
An RNA class characterized by a three-nucleotide sequence (the anticodon) that is complementary to a three-nucleotide sequence in mRNA (the codon). Attachment of an amino acid forms the active aminoacyl tRNA which functions as a ribosomal adaptor during translation.
A bacterial cell that has undergone transformation.
The alteration of the heritable properties of a cell.
A gene incorporated into the germline that functions as a normal gene.
A genetically altered organism that stably incorporates genes from another organism and can pass them on to succeeding generations.
The transfer of a glycosyl residue to a molecule with the formation of a new glycosidic linkage.
A mutation that consists of the replacement of one purine by another purine or one pyrimidine by another pyrimidine.
The initial state of a substrate molecule bound to the active site of an enzyme. The transition state is followed by the formation of more stable intermediates prior to product formation.
Transition state analog
A molecule that mimics the transition state of an enzymatic reaction.
The process of protein synthesis, carried out by ribosomes, and directed by the sequence of mRNA as read out by tRNA adaptors.
The transfer of a molecule across a membrane.
A protein that traverses a membrane.
A protein that transports a molecule within a cell or within a biological fluid.
A DNA segment that moves from one region of a genome to another.
An enzyme involved in the transfer of transposons within a genome.
A transposable genetic element that moves as a unit and inserts at new locations.
A mutation that consists of the replacement of a purine by a pyrimidine or vice versa.
A disaccharide found in microorganisms that is used to stabilize protein structure.
A triple-stranded form of DNA generated by binding an oligo that recognizes a DNA region to double-stranded DNA.
The movement response of an organism to an external stimulus, such as heat or light.
A growth consisting of differentiated cancer cells.
A diagnostic marker for cancer.
Tumor necrosis factor
A cytokine produced by many cell types that causes cytolysis of tumor cells, and mediates the expression of genes involved in the defense against disease.
The number of product molecules produced per minute by an enzyme catalyzing a reaction at the maximum rate.
A technique used for the separation of complex protein mixtures. Proteins are separated in the first dimension on an isoelectric focusing gel, rotated 90 degrees, then separated by molecular weight using standard gel electrophoresis.
A method for studying protein-protein interactions. The “bait” protein is fused to one domain of a transcription factor and the “prey” to the other domain. Interaction between bait and prey proteins brings the two domains of the transcription factor into proximity.
A protein that is covalently attached to lysines of other proteins, tagging them for proteolysis within proteasomes. Multiple ubiquitin units may be ligated to the protein, forming a multiubiquitin chain.
The covalent modification of a protein by conjugation to ubiquitin, a process which targets the protein-ubiquitin complex for degradation by the proteasome.
Ultra-high-throughput system (UHTS)
A high-throughput system capable of processing 100,000 samples a day.
Consisting of one layer, often used in reference to lipid monolayer structures.
A protein that binds single-stranded DNA, and stabilizes the unwinding of the helical structure.
In the 5' direction from a given transcription start point.
A nitrogenous base found in RNA. Uracil base pairs with adenine.
A nucleoside form of uracil.
Immunogenic material capable of stimulating active immunity or, in the case of DNA vaccines, of directing the synthesis of proteins that stimulate immunity. Vaccines may elicit both prophylactic (preventative) and therapeutic responses.
A cytosolic membrane-bounded structure containing liquids.
Van der Waals forces
Weak, long-range forces between nonpolar molecules.
Variable numbers of tandem repeats (VNTR)
A polymorphism resulting in variability in the number of sequence repeats between two individuals.
An automously replicating DNA element that is used to transfer genes into organisms and to shuttle genes between organisms.
A membrane-bound structure used to shuttle molecules within the membrane.
A complete viral particle comprising a nucleic acid core and a protein capsid.
An autonomously replicating plant pathogen.
A computational simulation of a living cell.
An combinatorial chemical library that is built in silico with the goal of evaluating possible structures.
A combinatorial chemistry technique for the computational screening of compounds.
A nucleoprotein structure consisting of DNA or RNA surrounded by a protein capsid. Viruses are unable to synthesize proteins or generate energy and are dependent on host cells for the production of progeny.
The graphic representation of data, patterns within data, or knowledge based on analysis of data patterns.
Voltage-gated ion channel
A transmembrane ion channel controlled by membrane potential.
A technique for the separation, immobilization, and detection of proteins, usually by a labeled antibody.
The naturally occurring phenotype of an organism.
Non-specific base-pairing of the base at the 5' end of a tRNA anti-codon to alternative bases at the 3' end of a mRNA codon.
The sex chromosome that exists in paired form in females.
X chromosome inactivation
The inactivation of one of the two X chromosomes carried by females. The inactivation of the X chromosome occurs randomly throughout the embryo, resulting in cells that are mosaic with respect to which chromosome is active.
An energy beam of very short wavelengths (0.1 to 1000 Å) produced by the bombardment of various materials with high velocity electrons.
A technique for determining the 3-D structure of a molecule, based on the diffraction of x-rays by the crystallized form of the molecule. Computational analysis of the diffraction pattern produces an electron density map.
The scattering of x-rays from a crystal, resulting in an interference pattern used to determine the structure of the crystal.
A synthetic chemical that affects living systems.
A graft between individuals of different species.
Xenopus laevis (X. laevis)
An African clawed toad used to study developmental biology.
A virus that can be grown in a species different from the normal host species.
One septillionth mole; 10-24 mole.
A prefix indicating 1024; a septillion.
A left-handed helical form of DNA. Z-DNA has been found for sequences containing alternating C and G bases.
One-sextillionth mole; 10-21 mole.
A prefix indicating 1021; a sextillion.
A DNA-binding protein motif that contains residues that coordinate a zinc ion which creates a finger-like loop.
A Northern blot of mRNA from multiple organisms.
A disease that may be transmitted to humans from animals.
A hypothetical pattern of gene expression shared across all animal phyla.
A dipolar ion containing ionic groups of opposite charge.
An inactive enzyme precursor that is activated by proteolysis; a proenzyme.