0 0 0: Biotechnology glossary for those with some background in biology and physical chemistry or chemical engineers. Also intended for those, such as securities analysts, who need to reference such terminology quickly despite having attained some proficiency in the field. In other words, this glossary is not really intended for amateurs. Originally stored as a searchable Unix "man" (manual or online help) file. 14-3-3 PROTEINS: 14-3-3 proteins are a family of proteins that recognize and bind to phosphoserine in specific contexts. 14-3-3 proteins, e.g. bind to the C-terminus of the serine 376-dephosphorylated p53, and by this possibly activate its DNA binding ability and transcriptional activity. 14-3-3 proteins also bind to phosphorylated Bad and prevent it from inhibiting Bcl-2. Transcription of the 14-3-3 proteins 14-3-3-sigma and RAD3 is activated by p53 following DNA damage. RAD3 results in the inactivation of cdc25 and thus G2 arrest, whereas 14-3-3-sigma is important for maintaining G2 arrest by sequestering phosphorylated Cdc2-cyclin B1 from the nucleus into the cytosol 3'-HYDROXYL END: The hydroxyl group that is attached to the 3' carbon atom of the sugar (ribose or deoxyribose) of the terminal nucleotide of a nucleic acid molecule. 5'-PHOSPHATE END: The phosphate group that is attached to the 5' carbon atom of the sugar (ribose or deoxyribose) of the terminal nucleotide of a nucleic acid molecule. 5'CAP: located at the 5' end of the mRNA molecule, the cap helps inhibit degredation and enhances translation ACC: In plants, 1-aminocyclopropane-l-carboxylate (ACC) is the immediate precursor of ethylene. ACC deaminase: A bacterial enzyme that can cleave ACC to ammonia and a-ketobutyrate. ACC oxidase: A plant enzyme that catalyzes the oxidation of ACC to ethylene. Formerly called ethylene-forming enzyme. ACC synthase: A plant enzyme that catalyzes the synthesis of ACC from S-adenosylmethionine. Its activity is stimulated by indoleacetic acid. ACCEPTOR SPLICE SITE: The boundary between the 3' end of an intron and the 5' end of the adjacent exon. ACETATE (ACETIC ACID): CH3-COOH. When in water, the hydrogen is released as H+ to give CH3-COO-. This causes an increase in the concentration of H+ in the water, making the solution more acidic. ACETOBACTER: Bacteria which are strict anaerobes and produce acetate (CH3COOH) from hydrogen and carbon dioxide (CO2). ACETYL GROUP: -CH2-CH3. Often, biological reactions involve the transfer of two carbons of this form. ACETYL-CoA: A compound comprised of an acetyl group (-CH2-CH3) and coenzyme A. ACHIRAL: not chiral. A compound (or object) that is superimposible on its mirror image. For example CH4. ACID-ALCOHOL FAST REACTION: A way of dyeing cells in which carbolfuschin remains bound to cells (Mycobacterium) when washed with acid-alcohol, leaving the cells stained. ACINETOBACTER: Known for their 'twitching motility'; these organisms jump from spot to spot (and are otherwise uninteresting, Gram-negative cocci). ACINUS: A pyknosis inducing factor was identified as Acinus ('apoptotic chromatin condensation inducer in the nucleus'), which is the precursor of an active chromatin condensating factor. Acinus is cleaved by caspase-3. ACTIN: A major protein component of skeletal muscle. ACTINOMYCES: These bacteria form branching filaments as they reproduce, and mostly anaerobic. ACTIVATION ENERGY: The energy required to cause a reaction to proceed ACYL CARRIER PROTEIN: A low-molecular-weight protein that forms part of a larger complex for either fatty acid or polyketide biosynthesis. ADAPTIVE RADIATION: The evolution of new species or subspecies to fill unoccupied ecological niches. ADAPTOR: (1) A synthetic double-stranded oligonucleotide that is blunt ended at one end and at the other has a nucleotide extension that can base pair with a cohesive end created by cleavage of a DNA molecule with a specific type II restriction endonuclease. After blunt-end ligation of the adaptor to the ends of a target DNA molecule, the construct can be cloned into a vector by using the cohesive ends of the adaptor. (2) A synthetic single-stranded oligonucleotide that, after self- hybridization, produces a molecule with cohesive ends and an internal restriction endonuclease site. When the adaptor is inserted into a cloning vector by means of the cohesive ends, the internal sequence provides a new restriction endonuclease site. ADDITION REACTIONS: reactions in which an unsaturated system is saturated or part saturated by the addition of a molecule across the multiple bond. ADENINE: a purine base that codes for heredity information in RNA and DNA ADHESION MOLECULE: These are chemicals on cell surfaces (Proteins or Phospholipids) that enable cells to stick or bind together. These are important on the surface of placental cells to allow them to attach to the uterus and to allow the placental cells to join together to make the placenta. ADIPOSE: of or relating to animal fat ADP (ADENOSINE DIPHOSPHATE): A nucleotide (DNA monomer) which also acts in the cell (along with ATP, which is ADP + phosphate) as the primary cellular energy. AFFERENT: going towards, ie. conveying impulses towards a nerve center such as a brain AGAROSE GEL ELECTROPHORESIS: A matrix composed of a highly purified form of agar that is used to separate larger DNA and RNA molecules ranging 20,000 nucleotides. AGGLUTINATION: The aggregation of particulate antigen by antibodies. Agglutination applies to red blood cells as well as to bacteria and inert particles covered with antigen. AGONIST: A substance capable of binding to a molecular target on the surface of a cell to initiate or enhance a biological response. AGROBACTERIUM TUMEFACIENS. A common soil bacterium that causes crown gall disease by transferring some of its DNA to the plant host. By altering Agrobacterium so that it no longer causes the disease but is still able to transfer DNA, we may they then use this altered Agrobacterium to ferry desirable genes into plants. AICD: Activation Induced Cell Death; Apoptosis of active lymphocytes that have to be removed after an immune response. AIF. Apoptosis Inducing Factor, a 57 kDa flavoprotein with homology to bacterial oxidoreductases: AIF is located in the mitochondria but it translocates to the nucleus when apoptosis is induced: AIF induces chromatin condensation in isolated nuclei and large-scale fragmentation of DNA; AIF also induces dissipation of the mitochondrial transmembrane potential and exposure of phosphatidylserine in the plasma membrane. It induces purified mitochondria to release the apoptogenic proteins cytochrome c and caspase-9. Bcl-2 can prevent the release of AIF from the mitochondrion but does not affect its apoptogenic activity AKT: Akt is a serine-threonine kinase that is implicated in apoptosis suppression induced by Ras, growth factor receptors, neurotrophin receptors and oncogenes. Akt phosphorylates and therfore inactivates pro-Caspase-9 at Ser(196). Akt itself is activated by the PI3K second messenger. ALCALIGENES EUTROPHUS: One of the most studied hydrogen bacteria (i.e. able to oxidize hydrogen to water for energy) and also autotrophic (able to grow on CO2). Also able to grow on fructose and to denitrify. ALGIN: any of a various of colloidal substances derived from marine brown algae and used especially as thickeners or emulsifiers ALGINATE: A polysaccharide polymer produced by different seaweeds and bacteria that is comprised Of P-D-mannuronate and a-L-guluronate. ALKALOID: organic substances occurring naturally, which are basic, forming salts with acids. The basic group is usually an amino function. ALLELE: Alternative form of a genetic locus; a single allele for each locus is inherited separately from each parent (e.g., at a locus for eye color the allele might result in blue or brown eyes). ALLELIC EXCLUSION: The ability of heterozygous lymphoid cells to produce only one allelic form of antigen-specific receptor when they have the genetic endowment to produce both. Genes other than those for the specific receptors are usually expressed codominantly. ALLELIC FREQUENCY: The ratio of the occurrence of one particular allele at a locus to the occurrence of all of the alleles of the locus in a large number of individuals of a population. ALLERGY: This is a condition that involve an immunity in the body against a variety of things that can come into the body including grasses, pollens, molds, etc. The immunity that results is a special one involving an antibody called IgE. This antibody when it combines with the allergen (pollen, mold, antibiotics) causes the immune system to make inflammation that can result in itching, asthma, red eyes etc. ALLOANTIBODY: An antibody in an individual that is directed against another individual of the same species. Blocking antibodies produced during pregnancy are antibodies of this type. ALLOANTIGEN: This is the chemical that induces the immune response in the woman during pregnancy. The alloantigen is provided by the father to the baby's placenta. ALLOGENETIC: The allelic variation seen among members of the same species. ALLOIMMUNITY: A condition characterized by a specific antibody reaction to another human being. Recognition is usually mediated by small polypeptide chains on the cell membrane. Rh sensitivity is set up by this type of immunity. ALLOMETRY EQUATION: Most lines of relative growth conform to y = bxa where y and x are the two variates being compared, b and a are constants. The value of a, the allometric exponent, is 1 one the growth is isometric; allometry is said to be positive when a>1 and negative when a<1. ALLOPOLYPLOIDY: a polyploid individual having a chromosomal set derived more or less complete from different species ALLOSTERIC REGULATION: A catalysis-regulating process in which the binding of a small effector molecule to one site on an enzyme affects the activity at another site of the enzyme. ALLYL GROUP: a group containing 3 carbon atoms and a double bond [C1=C2-C3, where C3 is called the allyliuc position or allylic carbon atom]. ALLYLIC REARRANGEMENT: the migration of a double bond in a 3-carbon system from carbon atoms one and two to carbon atoms two and three, e.g. C1=C2-C3-X X-C1-C2=C3 ALPHA-HELIX Common secondary structure of proteins in which the linear sequence of amino acids is folded into a spiral that is stabilized by hydrogen bonds between the carboxyl oxygen of each peptide bond. ALTERNATION OF GENERATIONS. a life cycle alternating between a diploid (=sporophytic) and haploid (=gametophytic) generation as found in certain protists and plants. ALTERNATIVE SPLICING: Cell-specific removal of an exon(s) during processing of a primary transcript that leads to a functional mRNA. ALTERNATIVE mRNA SPLICING. The inclusion or exclusion of different exons to form different mRNA transcripts: AMINO ACID: H2N-HCR-COOH The R represents an organic side group. There are 26 standard (frequently found) amino acids. In water, these molecules dissociate into the form H3N+-HCR-COO-. The acid form shows the proclivity for two amino acids to associate by bringing together the oppositely charged species (NH3+ and COO-). When these species react to give off water, a peptide bond (-NH-CO-) is formed. Amino acids joined by peptide bond are called polypeptides, or proteins. AMINOACYL SITE: The portion of a ribosome where the anticodon-codon interaction takes place during translation. Also called an A site. AMINOACYL-tRNA: A charged tRNA; a tRNA with its specific amino acid attached to its 3' end. AMNIOTIC EGG. a vertebrate egg with a shell which contains large nutrient and water stores and a number of specialized membranes: Found only in the reptiles, birds and monotremes. AMP (ADENOSINE MONOPHOSPHATE): A nucleotide (DNA monomer) which also acts in the cell as an indicator of cellular energy; this has a single phosphate group, so it's at a (relatively) low energy level, and excessive AMP in a cell indicates the cell is at a low energy state. AMPICILLIN (beta-lactamase). An antibiotic derived from penicillin that prevents bacterial growth by interfering with cell wall synthesis. AMPLICON: A herpes simplex virus type I plasmid vector. AMYLASE. a complex of enzymes which break down starches into sugars AMYLOLYTIC: Agents that are capable of breaking down starch into sugars. ANA (Antinuclear Antibody). This test checks for problems similar to lupus and rheumatoid arthritis or other similar immunological diseases which are associated with pregnancy losses or infertility: This test becomes weakly positive in women with infertility and in women with recurrent pregnancy losses: This antibody causes inflammation in the body or in the uterus when a baby attaches: It is usually reported as ANA positive with at titer of 1:40 or higher with a speckled pattern: This pattern is not typical of lupus or rheumatoid arthritis or other immunological disorders. ANABOLISM: Reactions within an organism which produce cellular components. ANAEROBIC RESPIRATION: The generation of cellular energy (i.e. ATP or NADH) by the flow of electrons from a non-O2 donor (e.g. SO4, NO3, Fe2+). ANAGENESIS. evolutionary change producing a single lineage in which one taxon replaces another without branching ANAPHYLATOXIN: Substance capable of releasing histamine from mast cells. ANAPHYLAXIS: Immediate hypersensitivity response to antigenic challenge, mediated by IgE and mast cells. (Allergic reaction) ANEUPLOIDY: having a chromosome number that is not an exact multiple of the usual chromosome number ANGIOSPERM: a division of vascular plants with ovules and seeds enclosed in an ovary ANKYRIN REPEATS: As has been studied in erythrocytes, the polypeptide ankyrin binds both to transmembrane proteins and to spectrin, and by this links the plasma membrane to the cytoskeleton. Repeats of homologous ankyrin sequences have been found in all IkB family members. It is the interaction between ankyrin repeats of IkB and regions of the RHD of Rel/NF-kB proteins that prevents nuclear translocation of Rel/NF-kB protein dimers. ANNEALING: The process of heating (denaturing step) and slowly cooling (renaturing step) double-stranded DNA to allow the formation of hybrid DNA or DNA-RNA molecules. ANOIKIS. Anoikis is the term for detachment-induced cell death: cells undero apoptosis upon disruption of the cell-matrix interactions. Involved are interactions between integrins and proteins of the extracellular matrix, as well as RGD peptides. ANOMERS: the specific term used to describe carbohydrate stereoisomers differing only in configuration at the hemi-acetal carbon atom. ANT: Adenine Nucleotide Translocator, a member of the PT pore. ANTAGONIST: A substance that blocks the ability of a given agonist to bind to its molecular target so as to prevent or reduce a biological response. ANTHERIDIUM: the male reproductive organ (gametangium) in which gametes develop ANTI-DNA/HISTONE ANTIBODY: If a woman reacts to the broken down DNA (histones) and it is a speckled pattern, then she is showing a reaction to her own embryos. ANTI-IDIOTYPE ANTIBODY: An antibody that has the properties of an antigen. ANTI-SENSE TECHNOLOGY: The use of an RNA molecule to block gene expression by interfering with protein production. ANTIBODY (Immunoglobulin,Ig,Ab): produced in response to antigen, or foreign, immunity-inducing body. ANTIBODY-DEPENDENT, CELL-MEDIATED CYTOTOXICITY (ADCC): A phenomenon in which target cells, coated with antibody, are destroyed by specialized killer cells (NK cells and macrophages), which bear receptors for the Fc portion of the coating antibody (Fc receptors). These receptors allow the killer cells to bind to the anti-body-coated target. ANTICODON: A nucleotide base triplet in a transfer RNA molecule that pairs with a complementary base triplet, or codon, in a messenger RNA molecule. ANTIGEN PROCESSING: Large molecules are broken down (processed) within macrophages into peptides and presented within the groove of MHC molecules. ANTIGEN RECEPTOR: The specific antigen-binding receptor on T or B lymphocytes; these receptors are transcribed and translated from rearrangements of V genes. ANTIGEN-BINDING SITE: The part of an immunoglobulin molecule that binds antigen specifically. ANTIGEN-PRESENTING CELL (APC): A specialized type of cell, bearing cell surface class II MHC (major histocompatibility complex) molecules, involved in processing and presentation of antigen to inducer, or helper , T cells. Examples: macrophage, dendritic cells. ANTIGEN: Any foreign material that is specifically bound by specific antibody or specific lymphocytes; also used loosely to describe materials used for immunization. Antigens may also be immunogens if they are able to trigger an immune response, or haptens if not. ANTIGENIC SWITCHING: The altering of a microorganism's surface antigens through genetic rearrangement, to elude detection by the host's immune system. ANTIPARALLEL: parallel, but oppositely directed or oriented such as DNA ANTISENSE RNA: A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation. ANTISENSE: The in vivo treatment of a genetic disease by blocking translation of a protein with a DNA or an RNA sequence that is complementary to a specific mRNA. ANTISERUM: The fluid portion of the blood that contains the antibodies of an immunized organism. APA (Antiphospholipid Antibody): These are antibodies in the blood that attach to phospholipids that are structures on the surfaces of all cells. A positive APA test indicates that the woman's blood clots too fast cutting off blood flow to the baby. These antibodies can also cause the placenta to attach too weakly to the uterus. The usual treatment is baby aspirin and heparin (a blood thinner). Heparin is given as an injection. Both medications are started before pregnancy during the cycle of conception; these are the least controversial of all the treatments for infertility or recurrent pregnancy losses. APAF-1: Apoptotic Protease Activating Factor 1: Mammalian CED-4 homolog. APAFs: Apoptotic Protease Activating Factors. APICAL DOMINANCE: inhibition of the growth of lateral buds by the terminal bud of a shoot. Responsible for primary growth. APICAL MERISTEM: a region of active mitosis at the stem tip or near the root tip. The meristem responsible for primary growth. APOMIXIS: reproduction involving specialized generative tissues, but not dependent on fertilization. Example: dandelion APOMORPHIC CHARACTER: a derived phenotype that evolved after a branch diverged from the phylogentic tree APOPLAST: the nonliving pathway formed by the extracellular matrix of plant cell walls APOPTOSIS: The term 'apoptosis' describes the molecular and morphological processes leading to controlled cellular self-destruction. Frequently, the terms 'apoptosis' and 'programmed cell death' are used as synonyms. APTAMER: A synthetic nucleic acid that binds to a protein that normally does not bind to a nucleic acid. ARABIDOPSIS THALIANA: A small member of the mustard family (kitchen cress). It has a very small genome (130-140 Mbp), five chromosomes and contains almost no repetitive DNA. Its genome will be completely sequenced by the end of 2000. It is a plant model system of choice because of the additional advantages of short generation time (about five weeks), high seed production (up to 40,000 seeds per plant) and natural self-pollination (as opposed to natural cross-pollination in maize). It has five small chromosomes. ARCHAEBACTERIA: a taxon of primitive bacteria including methane producing forms, red halophilic forms, and others that favor harsh acidic environments. These may be closely related to eukaryotes. ARCHEGONIUM: the flask shaped female sex organ of bryophytes and early vascular plants; it holds and protects the egg ARCHENTERON: the cavity of gastrula forming a primitive gut ARCHEZOA: a recently proposed kingdom characterized by a primitive level of organization in that these organisms have two haploid nuclei but lack other cellular organelles. An example is Giardia spp. ARF: Alternative Reading Frame (also called p14ARF within the p16INK4A locus. ARF is a tumor suppressor which regulates p53 stability, possibly by interacting with p53 and MDM2. AROMATIC: an aromatic molecule or ion possesses aromaticity. Aromaticity is the special property of planar (or nearly planar) cyclic, conjugated systems having (4n+2) conjugated pi electrons. The delocalisation of the (4n+2) pi electrons gives them special stability. For benzene, the most common aromatic system (n = 1, therefore 6 pi electrons), the aromaticity confers the characteristic reactivity of electrophilic substitution. ARS: Autonomously replicating sequence. ARS is the origin of replication in yeast. ARTHROBACTER: arthro is Greek, meaning 'joint' (like elbow). Common soil organism, coccus shaped, and after budding, the two daughters form a 'V'. ASK1: Apoptosis Signal Regulating Kinase 1; ASK1 is a MAP3k which leads to JNK activation; ASK1 interacts with DAXX. ASYMMETRIC INDUCTION: a term applied to the selective synthesis of one diastereomeric form of a compound resulting from the influence of an existing chiral centre adjacent to the developing asymmetric carbon atom. This usually arises because, for steric reasons, the incoming atom or group does not have equal access to both sides of the molecule. ATM: ATM is the gene mutated in ataxia-telangiectasia (AT) patients. AT is an autosomal recessive disease characterized by high cancer predisposition, radiation sensitivity, increased chromosome breakage, and other physiological symptoms. Cells from AT patients show reduced and delayed accumulation of p53 protein and its transactivational activity in response to ionizing radiation. ATM is one of the major upstream regulators of the p53 response to radiation-induced damage, possibly by regulating the phosphorylation status of p53. ATOPY: A term used by allergists to describe IgE-mediated anaphylactic responses in humans, usually genetically determined. ATP (ADENOSINE TRIPHOSPHATE): A nucleotide (DNA monomer) which acts in the cell (along with ATP, which is ADP + phosphate) as the primary cellular energy source - energy from hydrolysis of the phosphate bond (yielding phosphate and ADP) is coupled to other reactions. ATP-dependence: There are ATP-dependent steps in the apoptotic process, and it was reported that ATP levels might determine the cell death fate by apoptosis or necrosis Known ATP-dependent steps are the activation of caspase-9 by Apaf-1/cyto c and more downstream the active nuclear transport mechanism ATTENUATED VACCINE: A virulent organism that has been modified to produce a less virulent form but nevertheless retains the ability to elicit antibodies against the virulent form. AUTOIMMUNITY (autoallergy): A condition characterized by a specific antibody (antiphospholipid antibody or antibodies to DNA) or cells (such as Natural Killer Cells) which react with molecules or constituents of the body's own tissue and cause disease such as Rheumatoid arthritis and lupus. AUTOLOGOUS: Cells that are taken from an individual, and somehow manipulated before being infused back into the original donor. AUTONOMOUS REPLICATING SEQUENCE (ARS): Any cloned DNA sequence that initiates and supports extrachromosomal replication of a DNA molecule in a host cell; often used in yeast cells. AUTOPOLYPLOIDY: an individual or strain whose chromosome complement consists of more than two complete copies of the genome of a single ancestral species AUTORADIOGRAPHY: A technique that captures the image formed in a photographic emulsion as a result of the emission of either light or radioactivity from a labeled component that is placed next to unexposed film. AUTOSOMAL DOMINANT: A trait that is expressed in an individual who is heterozygous for a particular gene when the mutant allele is on one of the autosomes. AUTOSOMAL MODIFIER GENE: A gene that modifies the action of the autosomes. AUTOSOMAL RECESSIVE: A trait that is expressed in an individual who is homozygous for a particular gene. AUTOSOMES: All members of a chromosome set except the sex chromosomes. AUTOTROPHIC ORGANISM: one that obtains organic food molecules by using energy from the sun or form the oxidation of inorganic substances to make organic substances from inorganic ones AUXOTROPH: A strain which is mutated so that it requires some growth factor which the parent strain does not require. AVIDITY: The summation of multiple affinities, for example when a polyvalent antibody binds to a polyvalent antigen. AXOLOTL (Ambystoma mexicanum): Literally meaning water monster (in Aztec), axolotl is a salamander (amphibian) extensively used in the evolutionary immunogenetic studies. AZOTOBACTER VINELANDII: Aerobically fixes nitrogen and forms cysts. AZOTOBACTER: Bacteria which fix nitrogen (N2) aerobically (Gram-negative, obligately aerobic rods.) B LYMPHOCYTE (B CELL): The precursors of antibody-forming plasma cells; these cells carry immunoglobulin and class II MHC (major histocompatibility complex) antigens on their surfaces. Derived from bone marrow cells. BACILLUS LICHENIFORMIS: A denitrifying soil bacterium - grows on organics, uses nitrate (NO3) as an electron acceptor instead of oxygen (i.e. anaerobic metabolism), producing nitrogen (N2) and carbon dioxide (CO2). BACILLUS SUBTILIS: studied as 'a typical Gram-positive bacterium'. Most of the work on endospore formation has used this organism. BACILLUS THURINGIENSIS: a naturally occurring bacterium with pesticidal properties. Bacillus thuringiensis produces a protein (Bt toxin) that is toxic only to certain insect larvae that consume it. BACILLUS: Latin, for 'little rod'. Aerobic bacteria which form endospores (bacterial spores, since form inside bacteria). BACKCROSS: Crossing an organism with one of its parent organisms. BACMID: A shuttle vector based on the AcMNPV genome that can be propagated in both E. coli and insect cells. BACTERIAL ARTIFICIAL CHROMOSOME (BAC): A vector system based on the Escherichia coli F factor plasmid that is used for cloning large (100- to 300-kb) DNA inserts. BACTERIOPHAGE: A form of virus which attacks bacteria. First observed by d'Herrelle BACTERIOSTATIC: An effect in which bacteria are prevented from growing. BACTERIUM: A single-celled, microscopic prokaryotic organism: a single cell organism without a distinct nucleus. BACTEROIDES: 'little rod'. Inhabitants of the intestinal tract of warm-blooded animals, found more frequently when animals eat lots of meat (may be big protein digesters.) BALANCED TRANSLOCATION: A rearrangement translocation with no apparent loss or gain of chromosomal material, resulting in a clinically normal but genetically "abnormal" person. BANDING: The differential staining of a chromosome by a variety of techniques that results in a specific pattern of positively and negatively stained bands for each chromosomal pair. BARR BODY: Also called sex-chromatin body which represents the inactivated X chromosome in the nucleus of somatic mammalian cells. Normally only seen in female cells and not in male cells. One Barr body is seen in the cells of 46,XX and 47,XXY individuals, and none in the cells of 45,X and 46,XY individuals. BASAL METABOLIC RATE (BMR): The number of kilocalories a resting, endothermic animal requires to maintain minimum function. BASE ANALOGUE: A substance that can mimic the chemical behavior of 1 of the 4 DNA bases. BASE PAIR (bp): A pair of complementary nitrogenous bases in a DNA molecule--adenine-thymine and guanine-cytosine. Also, the unit of measurement for DNA sequences. BASOPHIL: A polymorphonuclear leukocyte., whose basophils granules contain heparin, histamine and other vasoactive amines. Within tissues, these cells are known as mast cells q.v. BATCH FERMENTATION: A process in which cells or microorganisms are grown for a limited time. At the beginning of the fermentation, an inoculum is introduced into fresh medium, and no addition or removal of medium is done for the duration of the process. BCL-10: The Bcl-10 gene was identified and found to be mutated in cases of low-grade MALT lymphoma. Bcl-10 contains a N-terminal CARD, and it confered weak pro-apoptotic effect in 293 cells. In a MALT lymphoma a truncated Bcl-2 without CARD was identified which failed to induce apoptosis. Bcl-10 also activates NF-kB BCL-2: First identified member of the Bcl-2 family; as an oncogene with anti-apoptotic activity Bcl-2 is involved in cancer, e.g. B cell lymphoma. BCL-XL: Member of the Bcl-2 family; closely related Bcl-2 homolog. BENCE-JONES PROTEIN: Dimers of immunoglobulin light chains in the urine of patients with multiple myeloma. BENZENE: C6H6 This molecule has a distributed double bond, drawn as a circle inside a hexagon. The way that the carbons are connected means that the three double bonds are shared around the ring (like -C=C-C= shifting to =C-C=C-). BETA-DNA: The normal form of DNA found in biological systems, which exists as a right-handed helix. BETAINE: A low-molecular-weight compound that acts as a methyl group donor for methionine biosynthesis. BH1, BH2, BH3, and BH4: Bcl-2 homology domains, which are found in members of the Bcl-2 family. BID: BID is a protein which is cleaved by Caspase-8 into truncated BID (tBID). tBID translocates to the mitochondria where it mediates the release of cytochrome c. BILE: a fluid released from the gall bladder into the small intestine that contains detergents to emulsify fats BINARY VECTOR SYSTEM: A two-plasmid system in Agrobacterium for transferring a T-DNA region that carries cloned genes into plant cells. The virulence genes are on one plasmid, and the engineered T-DNA region is on the other plasmid. BIOLISTICS: Delivery of DNA to cells and organelles by means of DNA-coated pellets that are fired under pressure at high speed. BIR: BIR is an approximately 70 amino acid motif which is a common structural feature of all IAP family members. The BIR motif is present in one to three copies, and it may be necessary and sufficient for the anti-apoptotic effect of IAPs. BIVALENT: A pair of homologous chromosomes in association as seen at metaphase of the first meiotic division. BLASTOPORE: During early animal development the opening which remains following gastrulation. In protostomes the blastopore becomes the mouth; in deuterstomes, the anus. BLASTULA: During early animal development, the hollow ball of cells which marks the end of cleavage. BLOCKING ANTIBODY: A functional term for an antibody molecule capable of blocking the interaction of antigen with other antibodies or with cells. BLUNT (FLUSH) END: The end of a DNA duplex molecule in which neither strand extends beyond the other. BLUNT-END CUT: To cleave phosphodiester bonds in the backbone of duplex DNA between the corresponding nucleotide pairs on opposite strands. This cleavage process produces no nucleoticle extensions on either strand. BLUNT-END LIGATION: Joining (ligation) of the nucleotides that are at the ends of two DNA duplex molecules, neither of which has an extension. BMI-1: Bmi-1 was first isolated as an oncogene that cooperates with c-myc in the generation of mouse lymphomas. It is a transcriptional repressor, which e.g. downregulates the expression of the ink4a tumor suppressor genes, p16 and p19ARF, and by this regulates progression into S-phase BOHR SHIFT: the decrease in oxygen affinity of a respiratory pigment in response to decreased blood pH resulting from increased carbon dioxide in the blood. BREWER'S YEAST: Saccharoniyces cerevisiae. BRUSH BORDER: the microscopic finger-like projections on the epithelial cells lining the lumen of the small intestine which are involved in final digestion and absorption of nutrients C (CARBOXY) TERMINUS: The last amino acid of a protein. C-DNA LIBRARY: a collection of cDNA's, each of which has been inserted in a DNA vector (e.g. a circular DNA plasmid) and replicated in a bacterium such as E. coli. The bacteria maintain a ready pool of the cDNA's and can be cultured to make copies of the library for many experiments. A population of bacteria containing a single inserted cDNA is called a clone. To extract a cDNA from the library, the insert from the corresponding clone can be amplified using PCR primed off the vector sequences connected to the ends of the cDNA. CAAT BOX: A highly conserved DNA sequence found about 75 bp 5' to the site of transcription in eukaryotic genes. Its specific (trans-acting) transcription factor is CTF-1 (NF-1) (see also TATA / Goldberg-Hogness box). CAD: Caspase Activated DNase, 40 kDa, is an apoptosis-specific endonuclease that cleaves DNA into the observed olignucleosomal fragments. CAD is a cytoplasmic protein containing a NLS, and it is normally associated with its inhibitor ICAD. The CAD/ICAD complex is inactive, but during apoptosis Caspase-3 cleaves ICAD, CAD enters the nucleus and degrades chromosomal DNA. ICAD is not just inhibitor but also chaperone for CAD, since active CAD is only expressed in presence of ICAD. CAG/CTG repeats: Abbreviation for cytosine-adenine-guanine triplet nucleotide and cytosine-thymine- guanine triplet nucleotide repeats; they are associated with unstable mutations. CALLUS: A cluster of undifferentiated plant cells that have the capacity to regenerate a whole plant in some species. CALMODULIN: An intracellular protein which binds calcium and promotes a specific cellular event, such as protein kinase activity. Example. Calmodulin often acts as a second messenger for a plant hormone. CANONICAL STRUCTURES: any of two or more hypothetical structures of resonance theory which can be written for a molecule simply by rearranging the valence electrons of the molecule. CAP SITE: The site of initiation of transcription. CAP: A modified nucleotide added to the 5' end of a growing mRNA chain, apparently required for normal processing, stability, and the translation of mRNA. CAPSID: A structure that is composed of the coat protein(s) of a virus and is external to the viral nucleic acids. The capsid often determines the shape of the virus. CAPSID: the outer protein coat of a virus. CARCINOEMBRYONIC ANTIGEN (CEA): Antigen present during embryonic development which normally disappears but reappears in malignant tissue. CARCINOMA: A malignant tumor derived from epithelial tissue, which forms the skin and outer cell layers of internal organs. CARD: CAspase Recruitment Domains (CARDs) have been proposed to mediate the recruitment of caspases. CARDs are found in several caspases, e.g. CED-3, Caspase-1, Caspase-2, Caspase-8 and Caspase-9, but also Apaf-1. The DEDs are a specific example for CARDs. CARDIOLIPIN: This is a phospholipid. Some individuals make an antibody to cardiolipin and this causes the blood to clot too quickly. Patients who lose pregnancies through miscarriage sometimes have a false positive test for syphilis because they have antibodies to cardiolipin that were manufactured when the pregnancy miscarried. CASPASES: Cystein Aspartate-specific Proteases: Caspases form a proteolytic network that is of central importance in the initiation and execution of the apoptotic program. CAT ASSAY: Reporter gene assay used to measure activity of a promoter under different conditions, such as to define elements of a promoter or to study signals that activate an intact enhancer/promoter. CAT is the abbreviation for the enzyme, chloramphenicol acetyl transferase, the activity of which is measured in the assay. CATABOLISM: Reactions within an organism which produce cellular energy. CATALYTIC ANTIBODY (abzyme): An antibody selected for its ability to catalyze a chemical reaction by binding to and stabilizing the transition state intermediate. CATALYTIC REFORMING: the process of improving the octane number of straight-run gasoline by increasing the proportion of aromatic and branched chain alkanes. [Catalysts employed are either molybdenum-aluminium oxides or platinum based.] CATALYTIC RNA (ribozyme): A natural or synthetic RNA molecule that cuts an RNA substrate. CBP/p300: CBP/p300 (CBBP = CREB-binding protein) is a histone acetyltransferase. CBP can be phosphorylated by the cyclinE-Cdk2 complex, and by this CBP is activated. The CBP enzymatic activity might result in the activation of S-phase-gene expression and might contribute to G1/S transition. CBP is also target of the transforming protein E1A which binds to CBP: bound E1A renders CPB constitutively active. CBP is a co-activator for E2F and the RelA protein and it is a coactivator for p53-dependent transactivation and- repression. CD (cluster of differentiation) numbers are now used to identify cell surface antigens that can be distinguished by monoclonal antibodies. Some of these (e.g. CD25,35. 71) are clear-cut functional molecules. and several (e.g. CD3,4, 8) are also widely used as markers of particular cell types. The list below shows the major cell type on which they are found and (in brackets) the function where known. It represents the consensus at the last International Workshop (1993). CD no. Cell type CD no. Cell type CD no. Cell type 1 thymocytes, APC 41 platelets 83 dendritic, act T,B 2 T, NK (LFA3R) 42 platelets 84 B, T, mac, leukaemia 3 T 43 myeloid 85 B, plasma cells, mono 4 T hlpr,some mac 44 myeloid, RBC 86 B, mono 5 some T, B 45 all leucocytes 87 myeloid 6 T, some B 46 all leucocytes 88 myeloid (C5aR) 7 T, NK 47 (all cells) 89 T, B, myeloid (Fc alpha R) 8 T cytotoxic 48 all leucocytes 90 thymocytes, brain ('Thy-I') 9 pre-B, mycloid 49a-f all leucyt/adhsn91 mono, mac (alpha2MR) 10 pre-B,leukaemia 50 all leucyt/lCAM392 many cells 11a adhesn (LFA 1) 51 endo, B, mac 93 myeloid 11b adhesion (CR3) 52 leucocytes 94 NK, T 11c adhesion (CR4) 53 all leucocytes 95 B, T 12 myeloid 54 act,TB,mac/ICAM196 act, NK, T 13 myeloid, endo 55 leucocytes 97 act, T, B 14 mono,mac/(LBPR) 56 NK (NCAM) 98 T, B, NK, platelets 15 myeloid 57 NK, some T,B 99 T,B, myeloid 16 myeloid,NK(FCR3)58 leucocyts (LFA3)100 T, B, NK, myeloid 17 myeloid,platelet59 leucocytes 101 T, NK, myeloid 18 as CD11 60 platelet,some T 102 endo (ICAM-2) 19 B 61 platelet(w CD41)103 T (intestinal) 20 B (Ca channel) 62 platelets 104 endo, epi 21 B (CR2l EBVR) 63 platlt, leucyt 105 endo 22 B 64 mono,mac(FCR1) 106 endo(VCAM-1) 23 B, mycloid(FCeR)65 myeloid 107 NK, endo 24 B. granulocyte 66 granulocytes 108 T, NK, endo 25 act,T,B,mac/IL2Ralpha 67 granulocytes 109 mono, endo 26 act,T,B,mac 68 mac 115 mono, mac (MCSFR) 27 T, some B 69 act,T,B,NK, mac 116 mono, mac (GM-CSFR) 28 some T, B 70 act,T,B 117 haemopoietic (SCFR) 29 most cells/adhsn71 prlfrtgcel(TF R)118 act, T 30 act, T, B 72 B 119 many cells (IFNgammaR) 31 myeloid,B,pltlts73 B, some T 120 many (TNFR) 32 myeloid,B(FCR2) 74 B,som mono,mac/Ii 121 T, B (IL-1R) 33 myeloid 75 B, some T 122 T, NK (lL-2Rbeta) 34 stem cells 76 B, NK, some T 124 TB, (IL-4R) 35 mycloid, B(CR1) 77 act, B 126 many (IL-6R) 36 mono,pltlts/LDLR78 B 127 many (IL-7R) 37 B, some T 79alpha,beta B 128 T, myeloid (IL-8R) 38 act,T,B,thymocyt80 act, B, T, mono 130 many (IL-6R-associated) 39 B,act T 81 B,T,NK,mono 40 B, IDC 82 B, T, NK, mono, epi, endo act: activated;APC: antigen-presenting cell; alpha-2M: alpha-2 macroglobulin; CR: complement receptor; EBV:Epstein-Barr virus; endo: endothelial cell; epi, epithelium; FCR: Fc receptor; I/V/N-CAM: intercellular/vascular/neural adhesion molecule; IDC: interdigitating cell; Ii: MHC invariant chain; IL-2R (etc.): IL-2 receptor; LBP: lipopolysaccharide-binding protein; LFA leucocyte function antigen; LDL: low-density lipoprotein; mac: macrophage; mono: monocyte; NK: natural killer cell; RBC, red blood cell: SCF: stem cell factor; TF: transferrin CD4 T Helper Cell: This is a T lymphocyte that helps activate CD3 cells in an immunity response by producing cytokines that cause proliferation, differentiation and growth of other cells necessary for completing the immune reaction. These are usually high normal in women with infertility and recurrent pregnancy losses. CD40: CD40 is involved in regulating T-cell-dependent B-cell activation. Besides on B cells, macrophages and dendritic cells, CD40 is found on endothelial cells nd fibroblasts where it appears to regulate inflammatory cytokine production (e.g via NF-kB) and cell adhesion. There is also evidence for CD40 being involved in regulating normal epithelial cell growth and differentiation, and CD40 might have an impact on the growth and sensitivity to apoptosis of carcinoma cells. CDC25: Cdc25 is an essential regulator of mitosis: it is a nuclear phosphatase which normally dephosphorylates and activates its substrate, the cyclin B/Cdc2 kinase. Dephosphorylation of cyclinB/Cdc2 initiates mitosis. Upon DNA damage, Cdc25 is phosphorylated by the Chk1 serine/threonine kinase and subsequently sequestered into the cytosol by Rad24: cyclinB/Cdc2 remains inactivated and the cell cycle is arrested in the G2 phase. CDNA (cDNA) CLONE: A double-stranded DNA molecule that is carried in a vector and was synthesized in vitro from an mRNA sequence by using reverse transcriptase and DNA polymerase. CDNA (cDNA) LIBRARY: A collection of cDNA clones that were generated in vitro from the mRNA sequences of a single tissue or cell population. CDNA: cDNA: Complementary DNA; created using reverse transcriptase, cDNA is a complement of mRNA, and can be inserted into expression vectors to synthesize foreign proteins in cells. CED-3: CED-3 is the C.elegans caspase; besides CED-4 and CED-9 it plays a central role in C.elegans apoptosis. CED-4: CED-4 activates CED-3 in C.elegans, and it is regulated by CED-9. Its mammalian homolog is Apaf-1 CED-9: CED-9 is a pro-survival member of the Bcl-2 family: it is a crucial regulator of apoptosis in C.elegans. CELL-MEDIATED CYTOTOXICITY (CMC): Killing (lysis) of a target cell by an effector lymphocyte. CELL-MEDIATED IMMUNITY (CMI): Immune reaction mediated by T cells; in contrast to humoral immunity, which is antibody mediated. Also referred to as delayed-type hypersensitivity. CELLULAR ONCOGENE (proto-oncogene): A normal gene that when mutated or improperly expressed contributes to the development of cancer. CENTIMORGAN: A unit of genetic distance between two gene loci, abbreviated cM. Named after T. H. Morgan (1866-1945), who studied Drosophila melanogaster genetics. In humans, 1 cM is approximately 106 base pairs of DNA. CENTROMERE: The central portion of the chromosome to which the spindle fibers attach during mitotic and meiotic division. CEPH FAMILY PANEL: A set of about 65 two- or three-generation families with siblingships of eight or more that are used for the genetic mapping of the human genome. The blood cells from members of these families that provide the source of DNA for genotyping are maintained by the Fondation Jean Dausset Centre d'Etude Polymorphisme Humain in Paris, France. CEPHEM-TYPE ANTIBIOTIC: An antibiotic that shares the basic chemical structure of cephalosporin. CG ISLAND: Unmethylated cytosine-guanine sequences that are often found near the 5' ends of some genes. CHAGAS' DISEASE: A parasitic disease caused by the protozoan Trypanosoma cruzi. CHAIN TERMINATION MUTATION: A mutation that generates a stop codon, thus preventing further synthesis of the polypeptide chain. CHAPERONE: Any protein that binds to an unfolded or partially folded target protein to prevent misfolding, aggegation, and/or degradation of it. Chaperones also facilitate the target protein's proper folding. CHARGED (AMINO ACYL) tRNA: A transfer RNA molecule that is coupled to its specific amino acid. CHEMIOSMOSIS: The use of a chemical gradient (generally hydrogen ions) across the cell wall to drive some other process or reaction. For example, an ADP (low energy) may be converted to ATP (high energy) using the potential available from allowing a hydrogen ion (H+) into the cell, where the hydrogen ion concentration (which we also call pH) is lower (meaning pH is higher). CHEMIOSMOTIC PUMP: a membrane pump which actively transports protons to establish an energy gradient which is then used to drive some other cellular process, such as hormone, ion, or sucrose transport CHEMOKINES: Small, secreted proteins that mediate inflammation by inducing chemotaxis (movement of a cell) and activation of a variety of inflammatory cells. CHEMOSTAT: A continuous growth system for cultures; CSTR (continuous stirred-tank reactor) CHEMOTAXIS: Migration of cells along a concentration gradient of an attractant. CHEMOTAXIS: Motion either up or down a chemical gradient (i.e. towards or away from higher concentrations of the chemical.) CHIMERA: Usually, a plant or animal that has populations of cells with different genotypes. Sometimes it refers to a recombinant DNA molecule that contains sequences from different organisms. CHIRALITY: a term which may be applied to any asymmetric object or molecule. The property of non-identity of an object with its mirror image. CHITIN: A polysaccharide of an amino sugar found in cell walls of some protists and fungi and in the exoskeletons of arthropods. CHITINASE: An enzyme produced by plants in response to infection by fungal pathogens that hydrolyzes the chitin components in fungal cell walls. Some bacteria also produce chitinase. CHLORAMPHENICOL: An antibiotic that interferes with protein synthesis. CHOANOFLAGELLATE: a simple colonial organism in which individual cells are flagellated and which exhibits elemental division of labor. A type of collared, flagellated cell characteristic of the choanoflagellates and also present in sponges. CHORIONIC VILLUS SAMPLING (CVS): A procedure in which a small sample of cells are taken from the placenta through a small catheter placed up through the vagina and the cervix. This is done earlier in pregnancy than amniocentesis and is used to test for chromosomal and other biochemical abnormalities that may affect the health and well being of the baby. CHROMATID: Each of the two daughter strands of a duplicated chromosome joined at the centromere during mitosis and meiosis. CHROMATOGRAPHY: A series of related techniques for the separation of a mixture of compounds by their distribution between two phases. In gas-liquid chromatography the distribution is between a gaseous and a liquid phase. In column chromatography the distribution is between a liquid and a solid phase. CHROMOGENIC SUBSTRATE: A compound or substance that contains a color-forming group. CHROMOSOMAL INTEGRATION SITE: A chromosomal location where foreign DNA can be integrated, often without impairing any essential function in the host organism. CHROMOSOME JUMPING: A technique that allows two segments of duplex DNA that are separated by thousands of base pairs (about 200 kb) to be cloned together. After subcIoning, each segment can be used as a probe to identify cloned DNA sequences that, at the chromosome level, are roughly 200 kb apart. CHROMOSOME WALKING: A technique that identifies overlapping cloned sequences that are about 40 kb long that form one continuous segment of a chromosome. CHROMOSOME WALKING: Working from a flanking DNA marker, overlapping clones are successively identified that span a chromosomal region of interest. CHROMOSOME: A single DNA molecule, a tightly coiled strant of DNA, condensed into a compact structure in vivo by complexing with accessory histones or histone-like proteins. Chromosomes exist in pairs in higher eukaryotes. CHYLOMICRON: a protein coated sphere containing fats which is synthesized by the small intestine. Chylomicrons are transported to the liver via the lacteal and closed circulation CIS-ACTING GENE: A gene acting on or co-operating with another gene on the same chromosome. CISTRON: A DNA sequence that codes for a specific polypeptide; a gene. CITRIC ACID CYCLE (TRICARBOXYLIC ACID (TCA) CYCLE, KREBS CYCLE): A metabolic pathway in which pyruvate (HOOC-CO-CH3) is converted to carbon dioxide (CO2) with the coupled generation of ATP from ADP and NADH from NAD. In most organisms, the primary part of catabolism (energy generation) CLADISTICS: an approach that classifies taxa according to the time when branches appear along the phylogenetic tree. CLEAVE (cut,digest): To break phosphodiester bonds of duplex DNA, usually with a type II restriction endonuclease. CLOSTRIDIUM BUTYRICUM: Used to produce butyric acid, butanol, acetate, acetone and ethanol from amino acids in fermentation. CLOSTRIDIUM PASTEURIANUM: An anaerobic nitrogen fixer. Studied extensively for its ability to fix nitrogen, and considered to be responsible for much of the nitrogen fixation which occurs in soil. CLOSTRIDIUM: Strict (obligate) anaerobes which are Gram-positive, spore-forming rods. Some will produce butyric acid, acetone, and butanol. CO-ORDINATE BOND: The linkage of two atoms by a pair of electrons both electrons being provided by one of the atoms, the donor. Coordinate bonds are covalent bonds. COAT PROTEIN (capsid): The coating of a protein that enclosed the nucleic acid core of a virus. COCCUS (plural: COCCI): bacteria which are spherical CODING TRIPLET: A set of three contiguous nucleotides of the nontranscribed DNA strand of the coding region of a structural gene that is complementary to a transcribed triplet. CODOMINANCE: The expression of both alleles in a heterozygous individual, e.g., presence of both hemoglobin A and S on electrophoresis in an individual heterozygote for sickle-cell disease. CODON OPTIMIZATION: An experimental strategy in which codons within a cloned gene that are not the ones generally used by the host cell translation system are changed to the preferred codons without changing the amino acids of the synthesized protein. CODON: A group of three nucleotides that specifies addition of one of the 20 amino acids during translation of an mRNA into a polypeptide. Strings of codons form genes and strings of genes form chromosomes. COEFFICIENT OF RELATEDNESS: r = n(0.5)L where n is the alternative routes between the related individuals along which a particular allele can be inherited; L is the number of meiosis or generation links. COENZYME: A compound which is involved in a reaction but is not part of the enzyme catalyzing the reaction. These tend to be relatively low molecular weight, and act as carriers of an agent (reduction capacity as in ATP, or an acetyl group as in Acetyl-CoA (CoA stands for Coenzyme A)). COHESIVE ENDS: Complementary single-strand extensions on the ends of duplex DNA molecules. COINTEGRATE VECTOR SYSTEM: A two-plasmid system for transferring cloned genes to plant cells. The cloning vector has a T-DNA segment that contains cloned genes. After introduction into Agrobacterium, the cloning vector DNA undergoes homologous recombination with a resident disarmed Ti plasmid to form a single plasmid carrying the genetic information for transferring the genetically engineered T-DNA region to plant cells. COLIFORM: Gram-negative, non-spore forming rods which produce gas and lactose during fermentation COMPETENCY: An ephemeral state, induced by treatment with cold cations, during which bacterial cells are capable of uptaking foreign DNA. COMPLEMENT RECEPTOR: A structure found on erythrocytes, lymphocytes, neutrophils, monocytes and macrophages that binds C3 fragments. COMPLEMENT: The complement of a nucleic acid sequence replaces each base by its complementary base: adenine (A) by thymidine (T), cytosine (C) by guanine (G), and vice versa. In RNA, adenine is paired not with thymidine but with uracil (U). By convention, DNA and RNA molecules have a consistent orientation (5' to 3') which is used in writing their sequences. To preserve this orientation, the complement of a sequence is written backwards compared to the original. For example, an RNA sequence ACGGUACU has the DNA complement AGTACCGT. COMPLEMENTARITY-DETERMINING REGION (CDR): A part of the variable (V) regions of light and heavy antibody chains that makes contact with the antigen. The amino acid sequences of CDRs are highly variable from one antibody of the same class to another. COMPLEMENTARY DNA (cDNA): A double-stranded DNA complement of an mRNA sequence; synthesized in vitro by reverse transcriptase and DNA polymerase. COMPLEMENTARY HOMOPOLYMERIC TAILING: The process of adding complementary nucleotide extensions to different DNA molecules-e.g., dG (deoxyguanosine) to the 3'-hydroxyl ends of one DNA molecule and dC (deoxycytidine) to the 3'- hydroxyl ends of another DNA molecule-to facilitate, after mixing, the joining of the two DNA molecules by base pairing between the complementary extensions. Also called dG-dC tailing, dA-dT tailing. CONCATEMER: A DNA segment composed of repeated sequences linked end to end. CONCATEMER: A tandem array of repeating unit-length DNA elements. CONFIGURATIONAL ISOMERS: a series of compounds which have the same constitution and bonding of atoms but which differ in their atomic spatial arrangement. Stereoisomers. CONJUGATION: (1) The joining of two bacteria cells when genetic material is transferred from one bacterium to another. (2) Sequence of alternating double (or triple) and single bonds. e.g. C=C-C=C and C=C-C=O. Conjugation can also be relayed by the participation of lone pairs of electrons or vacant orbitals. CONSTANT REGION (C REGION): The invariant carboxyl-terminal portion of an antibody molecule, as distinct from the variable region which is at the amino-terminal of the chain. CONSTITUTIVE PROMOTER: An unregulated promoter that allows for continual transcription of its associated gene. CONTIG: A series of contiguous, overlapping, cloned DNA fragments. CONTIGUOUS (contig) MAP. The alignment of sequence data from large, adjacent regions of the genome to produce a continuous nucleotide sequence across a chromosomal region. COOMBS' TEST: A test named for its originator, R.R.A. Coombs, used to detect non-agglutinating antibodies on red blood cells by addition of an anti-immunoglobulin antibody. COPY NUMBER: The number of copies of a transgene integrated into a host genome; used to describe transgenic animals. COREPRESSOR: A low-molecular-weight compound that combines with an inactive repressor protein to form a complex that binds to an operator region and prevents transcription. CORYNEBACTERIUM: Bacteria characterized by their shape - frequently have a swollen end, giving a club shape, and after budding, the two daughters form a 'V'. COS (cos) ENDS: The 12-base, single-strand, complementary extensions of bacteriophage A DNA. COSEGREGATION: When two genetic conditions appear to be inherited together. COSMID: A vector that uses the cos end sequences of bacteriophage A and in vitro bacteriophage packaging to form, after injection of the vector into a host cell, a plasmid that can carry as much as 45 kb of insert DNA. COSUPPRESSION: The transformation of a plant with a gene in the sense orientation that the plant already possesses. This results in the down regulation of both the endogenous and introduced genes. Also called sense suppression. COTRANSFECTION: The introduction of two different DNA molecules into a eukaryotic cell. In baculovirus expression systems, the procedure by which the baculovirus and the transfer vector are simultaneously introduced into insect cells in culture. COUPLING: The phase state in which either two dominant or two recessive versions of two different genes occur on the same chromosome. Also called cis configuration. CPG (CpG) ISLANDS: Clusters of GC-rich regions that precede many transcribed vertebrate genes. CREB: cAMP-responsive element binding protein. CRMA: Cytokine response-modifier protein produced by cowpox virus: CrmA is a caspase-inhibitor for ICE family members, inhibits preferentially Caspase-1 but also Caspase-8; CrmA shows homology to serpins, a family of serine protease inhibitors. Cyclophilin D Cyp D is a cyclosporin A binding protein and is located in the mitochondrial membrane; it is part of the PT pore. CROSS-HYBRIDIZATION: The hydrogen bonding of a single-stranded DNA sequence that is partially but not entirely complementary to a single-stranded substrate. Often, this involves hybridizing a DNA probe for a specific DNA sequence to the homologous sequences of different species. CROSS-REACTIVITY: The ability of an antibody, specific for one antigen, to react with a second antigen; a measure of relatedness between two different antigenic substances. CROSSING OVER: Reciprocal breaking and rejoining of homologous chromosomes in meiotic prophase I that results in exchange of chromosomal segments. CYANOBACTERIA: Photosynthetic, oxygen-producing bacteria, some of which are capable of nitrogen-fixation (previously known as "blue-green algae"). CYCLIC AMP (cyclic adenosine monophosphate). A second messenger that regulates many intracellular reactions by transducing signals from extracellular growth factors to cellular metabolic pathways. CYTOCHROME: Electron carriers in the electron chain (the mechanism which transport electrons across the cell membrane), made of proteins containing iron sites. CYTOKINE: These are hormones produced by white blood cells (lymphocytes) that communicate with other cells of the immune system, recruiting them to perform more aggressive roles in the fighting off of infection or in the rejection of something from the body such as a baby, a kidney or a bone marrow transplant. Soluble substances secreted by cells, which have a variety of effects on other cells, e.g. Interleukin 1 (Il-1). CYTOKININ: A plant hormone that stimulates cell division. CYTOPLASM: The part of the cell inside the plasma membrane (inner wall membrane) but excluding the nucleus (which is only found in eucaryotes). CYTOSINE: One of the organic bases found in either DNA or RNA. CYTOTOXIC (CYTOLYTIC) T CELL: Cell that kills target cells bearing appropriate antigen within the groove of an MHC class I molecule that is identical to that of the T cell. CYTOTROPHOBLAST: This is a specialized cell of the placenta (also a trophoblast) whose function is to attach the baby to the mother's uterus. It provides the anchor. It grows deeply into the lining of the uterus (decidua) and firmly attaches the placenta for the duration of pregnancy. CpG Island: Repetitive CpG doublets occurring in a sea of DNA sequences low in CpG residues. Usually associated with transcription-initiation regions of genes transcribed at low rates that do not contain a TATA box. The CpG-rich stretch of 20-50 nucleotides occurs within the first 100-200 bases upstream of the start site region (where promoter-proximal elements reside). A trans-acting transcription factor called SP1 recognizes the CpG islands (see also Htf islands). In vertebrates, many of the nontranscribed genes (and the genes on the inactivated X chromosome) have a 5-methyl group on the C residue in CpG dinucleotides in transcription-control regions. D GENE: A small segment of immunoglobulin heavy-chain and T-cell receptor DNA, coding for the third hypervariable region of most receptors. DALTON: A unit of measurement equal to the mass of a hydrogen atom, 1.67E-24 gram/L (Avogadro's number). DCC: DCC is a candidate tumor suppressor gene which is mutated in cases of colonic carcinoma. DCC encodes a receptor for netrin-1 a molecule involved in axon guidance. DCC induces apoptosis in the absence of netrin-1 but blocks apoptosis when bound to netrin-1. DCC is cleaved by Caspase-3 at Asp1290 and this cleavage seems to be required for DCC's apoptotic activity. DD: Death Domain: homologous cytoplasmic domain of Death Receptors; by using their DDs, activated death receptors recruit adaptor molecules like FADD, TRADD or DAXX, which eventually mediate the apoptotic signal to the apoptotic machinery. DEATH PHASE: The final growth phase, during which nutrients have been depleted and the waste products become toxic and cell number decreases. DED: Death Effector Domain: the DED is a specific example of a more global homophilic interaction domain termed CARD, which is found in several caspases with large prodomains. Specific for the DED is, that it is also part of the adaptor protein FADD/MORT 1. DELAYED TYPE HYPERSENSITIVITY (DTH): A T cell-mediated reaction to antigen, which takes 24-48 hours to develop fully, and which involves release of lymphokines and recruitment of monocytes and macrophages. Also called c cell-mediated immunity. DELETION: Loss of part or a whole chromosome or loss of DNA nucleotide bases. DELOCALIZATION: electron systems in which bonding electrons are not localised between two atoms as for a single bond but are spread (delocalized) over the whole group. e.g pi-bond electrons, in particular the delocalised pi-electrons associated with aromatic molecules. DELTAPSI (deltaPsi): Mitochondrial inner transmembrane potential DENATURE: To induce structural alterations that disrupt the biological activity of a molecule. Often refers to breaking hydrogen bonds between base pairs in double-stranded nucleic acid molecules to produce in single-stranded polynucleotides or altering the secondary and tertiary structure of a protein, destroying its activity. DENITRIFY: To convert nitrate (NO3) to ammonia (NH3) DENSITY GRADIENT CENTRIFUGATION: High-speed centrifugation in which molecules "float" at a point where their density equals that in a gradient of cesium chloride or sucrose. DEOXYRIBOSE: The 5-carbon sugar component of DNA. DESULFO-: named for sulfur. Anaerobic organisms which reduce sulfate (SO3) or sulfur (elemental, to sulfide (H2S)) to get their energy. DEXTROROTATORY: the phenomenon in which plane polarised light is turned in a clockwise direction. DFF45: DNA Fragmentation Factor (45 kDa), human homolog to ICAD (from mouse). It is an inhibitor of a specific endonuclease which cleaves DNA to oligonuceosomal fragments as one of the main features of the apoptotic preocess. DIAMINOPIMELIC ACID: The immediate precursor to L-lysine in bacteria and plants, and a component of some bacterial cell walls. DIASTEREOMERS (DIASTEREOISOMERS): stereoisomeric structures which are not enantiomers (mirror images) of one another. Often applied to systems which differ only in the configuration at one carbon atom, e.g. meso- and d- or l-tartaric acids are diastereoisomeric. DIAUXIC GROWTH: A pattern of growth observed in batch studies in which two growth compounds are available. The more favored compound (giving a higher growth rate) is used first, and then the second compound is used, resulting in a lower rate of growth. DIAZOTROPH: An organism that can fix nitrogen. DICENTRIC: Refers to an aberrant chromosome that contains 2 centromeres. DICISTRONIC VECTOR: A mammalian cloning vector that is specially designed to carry two functional genes. DIDEOXYNUCLEOTIDE (ddNTP): A deoxynucleotide that lacks a 3' hydroxyl group, and is thus unable to form a 3'-5' phosphodiester bond necessary for chain elongation. DIHEDRAL ANGLE: the angle between groups attached on adjacent carbon atoms when viewed in a Newman projection. DIHYDROFOLATE REDUCTASE: An enzyme that catalyzes the formation of tetrahydrofolic acid. DIKARYONS: A fungal mycelium that possesses two separate haploid nuclei per cell which eventually fuse to form a diploid nucleus. A unique fungal characteristic. DIPLOBLASTIC: having two layers, an endoderm and an exoderm. Example: Hydra DIPLOID. The number of chromosomes in most somatic cells, which is double the number found in the gametes (the haploid number). In humans, the diploid chromosome number is 46. DIRECTIONAL CLONING. DNA insert and vector molecules are digested with two different restriction enzymes to create noncomplementary sticky ends at either end of each restriction fragment. This allows the insert to be ligated to the vector in a specific orientation and prevents the vector from recircularizing. DISACCHARIDE. A double sugar, consisting of two monosaccharides joined by dehydration synthesis. Example: fructose DISC. Death Inducing Signaling Complex. DISCORDANT. A twin pair (or set of individuals) in which one member exhibits a certain trait and the other does not. DISPROPORTIONATION: a process in which a compound of one oxidation state changes to compounds two or more oxidation states e.g. 2Cu+ --> Cu + Cu2+ DISSOCIATION CONSTANT: the measure of the extent of dissociation, measured by the dissociation constant K. For the process: AB = A + B, K = ([A][B])/[AB] DISSYMMETRIC: chiral DITHIOTHREITOL: A low-molecular-weight thiol-containing reducing agent. It is added to buffers in low concentrations to prevent protein sulfhydryl groups from being oxidized. At higher concentrations, it is used to reduce disulfide linkages in proteins. DIZYGOTIC. The product of fertilization of 2 separate eggs by 2 separate sperm; nonidentical twin pair. DNA CODON: A set of three contiguous deoxyribonucleotide pairs of the coding region of a structural gene where the bases of one strand are transcribed into a codon. DNA LIGASE. An enzyme that rejoins cut pieces of DNA. DNA POLYMERASE: An enzyme that links an incoming deoxyribonucleotide, which is determined by complementarity to a deoxyribonucleotide in a template DNA strand, with a phosphodiester bond to the X-hydroxyl group of the last incorporated nucleotide of the growing strand during replication. DNA POLYMORPHISM. One of two or more alternate forms (alleles) of a chromosomal locus that differ in nucleotide sequence or have variable numbers of repeated nucleotide units. DNA PROBE. A molecule that has been labeled with a radioactive isotope, dye or enzyme and is used to locate a particular portion of a DNA molecule. DNA REARRANGEMENTS. Recombination of DNA segments, eg, in cells of the immune system, the variable (V), diversity (D), and joining (J) regions somatically rearrange to generate functional antibody genes. DNA-PK. DNA-dependent Protein Kinase. DNA-PK is a substrate for caspases (-3) and is activated upon DNA damage. One of its substrates is p53. DNASE I: An enzyme that degrades DNA, used to remove DNA from RNA preparations and from cell free extracts. Also called deoxyribonuclease 1. DOMAIN. A compact segment of an immunoglobulin molecule, made up of about 110 amino acids around an S-S bond, and encoded by a unique segment of DNA, surrounded by nontranslated sequences. DONOR SITE. Guanine-thymidine sequence that defines the splice site at the 5' end of an intron. DOUBLE FERTILIZATION. A mechanism of fertilization in angiosperms, in which two sperm cells unite with two cells in the embryo sac to form the zygote and endosperm. DOUBLE-STRANDED COMPLEMENTARY DNA (dscDNA). A duplex DNA molecule copied from a cDNA template. DOWN SYNDROME. This is a genetic disorder caused by the presence of an extra chromosome 21. (Called trisomy 21). Affected children have mental retardation and characteristic features of the body, face and limbs. Affected children also have many medical problems such has heart defects. DOWNSTREAM. The region extending in a 3' direction from a gene. DQ ALPHA. These are HLA antenna present on certain white blood cells (lymphocytes). They are part of the white blood cell type of an individual. When couples are compatible for these factors (share the same DQ numbers), it is an unfavorable combination for pregnancy. These tests give you back two numbers for each member of the couple. In a normal pregnancy the father's DNA in the baby signals the mother's body to protect the developing embryo. If the father's DNA is too closely matched to the mother's, there is a good chance that the embryo created by them cannot differentiate itself from the mother's body. The mother's body then rejects the embryo because it cannot identify and protect the embryo as a baby. DQ BETA. The DQ antennae have an alpha limb (chain) and beta limb (chain). If a man is DQ alpha 2 (0201) and DQ beta 2 (0201) and the sperm carrying this information fertilizes the egg, the embryo will be a blighted ovum. Donor sperm is considered in this situation. DR ANTIGENS. MHC class II molecules found on B cells and antigen-presenting cells of humans. DRD. DED-Recruiting Domain; a domain of modest homology to the DED domain, DRD was found in FLASH, which binds to the DEDs of DADD and caspase-8. E1A. E1A is a transforming viral protein produced by adenovirus. E1A forces cells through the restriction point of the cell cycle into the S phase by forming complexes with Rb and CBP/p300. By binding Rb it activates E2F, and by binding CBP it activates its histone acetyltransferase activity, both inducing S-phase-gene expression. E1A has transforming activity only when cell proliferation is not blocked, e.g. by p53. E1A stimulated proliferation normally would trigger p53-dependent cell cycle arrest what results in apoptosis. For that reason, adenovirus additionally expresses E1B which blocks p53 function. E1B. E1B (55 kDa) is an adenovirus oncogene, which blocks the function of p53. E1B shares sequence and functional homology with Bcl-2 E1B19K. Anti-apoptotic adenovirus protein, which indirectly prevents Fas-mediated activation of caspase-8, possibly by its interaction with FLASH. E2F. E2F is a key transcription factor for S-phase-gene induction. E2F is strictly regulated during the cell cycle: it is inactive when bound in a complex with the Rb protein. E6 and E7. Viral onogenes produced by papillomavirus: E6 inactivates Rb, while E7 inactivates p53. ECLIPSED: a conformation in which substituents on two attached saturated carbon atoms overlap when viewed as a Newman projection. ECTOTHERM. An animal that must use an external energy source to regulate its body temperature. Cold-blooded. EFFECTOR CELLS: Cells of the immune system that degrade antigens. EFFECTOR: A low-molecular-weight compound that modifies the function of a regulatory protein. ELECTRON CHAIN: The mechanism which transports electrons across the cell membrane, establishing the proton-motive force. Often, this chain converts ATP to ADP while moving hydrogen ions out of the cell. ELECTRON DONOR: The compound which is oxidized during metabolism ELECTROPHILIC SUBSTITUTION: an overall reaction in which an electrophile binds to a substrate with the expulsion of another electrophile. The most common example is the electrophilic substitution of a proton by another electrophile, such as a nitronium ion, on an aromatic substrate such as benzene. ELECTROPORATION. Application of a short, high-voltage electric pulse to cells in the presence of DNA to permit DNA to enter the cells. ELISA (enzyme-linked immunosorbent assay). This is a laboratory test method to analyze blood for the presence and the amount of antibodies in the woman to DNA, phospholipids, and other things. The test tubes are coated with the substance such as the phospholipid. Then the serum to be tested is added. If there are antibodies in the serum against the phospholipid, they attach and in the process of attachment a color (dye) is released that turns the fluid in the test tube a different color. The intensity of the color tells you how high the immunity is (how much antibody is present). ELONGATION: Sequential addition of one monomer at a time to a polymer. EMBRYONIC STEM CELLS: Cells of an early embryo that can give rise to all differentiated cells, including germ line cells. EMSA. Electrophoretic Mobility Shift Assay ENANTIOMERS: a pair of isomers which are related as mirror images of one another. e.g. isomers differing only in the configuration about the chiral atoms. ENCAPSIDATION. Process by which a virus' nucleic acid is enclosed in a capsid. ENCODE: To specify, after decoding by transcription and translation, the sequence of amino acids in a protein. ENDOMETRIOSIS. A disease condition of women when the tissue that normally lines the uterus each month preparing for a baby (endometrium) leaks out of the uterus inside the body cavity and begins to grow (and menstruate) in locations such as the ovaries, fallopian tubes, bowel, bladder and abdominal cavity. This causes pain, inflammation, scar tissue, and autoimmunity response in the woman that may make it difficult for her to become pregnant. ENDONUCLEASE. Enzyme that cleaves bonds between nucleotides of single- or double-stranded DNA or of RNA at specific sequences of nucleotides. ENDOPHYTE. A plant that lives inside another. ENDOPROTEASE: An enzyme that cleaves the peptide bonds between amino acids within a protein. Cleavage is usually at one or more specific sites. ENDOSKELETON. A hard skeleton present beneath soft external tissues, such as the spicules of sponges, the plates of echinoderms, and the internal skeleton of all vertebrates. ENDOSYMBIOSIS. a hypothesis that the creation of the eukaryotic cell resulted from the symbiotic inclusion of prokaryotes into a host cell ENDOTHERM. An animal that uses its own metabolic energy to maintain a constant body temperature, such as in a bird, mammal and some insects. ENDOTOXIN: A component of the cell wall of gram-negative bacteria that elicits, in humans, an inflammatory response and fever. ENOLASE: An enzyme that catalyzes the conversion of 2-phosphoglycerate to phosphoenolpyruvate. ENOYLREDUCTASE. An enzyme involved in the synthesis of polyketicle antibiotics. ENTEROBACTER AEROGENES: A coliform (Gram-negative, non-spore forming rods which produce gas and lactose during fermentation) bacterium which is not usually found in the intestine. ENTEROGASTRONE. a hormone secreted by the wall of the small intestine which slows stomach digestion and emptying ENTHALPY: a thermodynamic state function, generally measured in kilojoules per mole. In chemical reactions the enthalpy change (deltaH) is related to changes in the free energy (deltaG) and entropy (deltaS) by the equation: deltaG = deltaH - T.deltaS ENTROPY: a thermodynamic quantity which is a measure of the degree of disorder within any system. The greater the degree of order the higher the entropy; for an increase in entropy S is positive. Entropy has the units of joules per degree K per mole. ENV GENE. Encodes capsule or envelope protein of a retrovirus. ENZYME-LINKED IMMUNOSORBENT ASSAY (ELISA): A primary antibody is bound to the target molecule; a secondary antibody, which binds to the primary antibody, is added later, and has attached to it an enzyme that can convert a colorless substrate into a colored product. If the target molecule is not present in the sample, washing steps will remove both antibodies and no colored product will be produced. ENZYMES. Proteins that control the various steps in all chemical reactions. Biocatalysts. End in -ase. EOSINOPHIL CHEMOTACTIC FACTOR OF ANAPHYLAXIS (ECF-A): A substrate released from mast cells during anaphylaxis which attracts eosinophils. EOSINOPHIL. A polymorphonuclear leukocyte with large eosinophilic (i.e. red) cytoplasmic granules. EPB virus. Epstein-Barr virus EPIGENETIC. A factor that changes the phenotype without changing the genotype. EPIMERIZATION: a process in which the configuration about one chiral centre of a compound, containing more than one chiral atom, is inverted to give the opposite configuration. The term epimers is often used to describe two related compounds which differ only in the configuration about one chiral atom. EPISOME. A plasmid that can exist either independently in the cytoplasm or as an integrated part of the genome of its bacterial host. EPISTASIS. The influence of a gene on the expression of another (non-allelic) gene. EPITOPE: A specific chemical domain on an antigen that is recognized by an antibody. Each epitope on a molecule such as a protein elicits the synthesis of a different antibody. EPOXIDATION: the addition of an oxygen bridge across a double bond to give an oxirane. Achieved by use of a peracid or, in a few cases, by use of a catalyst and oxygen. EQUILIBRIUM CONSTANT: according to the law of mass action, for any reversible chemical reaction: aA + bB = cC + dD, the equilibrium constant (K)is defined as: K = ([C]c[D]d)/([A]a[B]b) EQUIVALENCE ZONE. In a precipitin reaction, the region in which the concentration of antigen and antibody leads to maximal precipitation. ERYTHROMYCIN: An antibiotic produced by Streptomyces ES. Embryonic Stem cells ESCHERICHIA COLI. A commensal bacterium inhabiting the human colon that is widely used in biology, both as a simple model of cell biochemical function and as a host for molecular cloning experiments. ESCHERICIA: Inhabitants of the intestinal tract of warm-blooded animals, grow on a wide variety of carbon and energy sources. ETHIDIUM BROMIDE. A fluorescent dye used to stain DNA and RNA. The dye fluoresces when exposed to UV light. Carcinogenic to touch. ETHYLENE: A gaseous compound that acts as a plant hormone. It is important in fruit ripening, flower senescence, seed germination, rooting of cuttings, root elongation, and the response of the plant to environmental stress. EUBACTERIA: One of the two kingdoms of bacteria. Bacteria in this kingdom have ester-linked lipids (CH2-O-CO-) and a single form of RNA polymerase consisting of four subunits. The lineage of prokaryotes that includes the cyanobacteria and other contemporary bacteria, but excludes the archaebacteria (=Archea), such as the halophiles and thermophiles. EUKARYOTES: Organisms, including animals, plants, fungi, and some algae, that have (1) chromosomes enclosed within a membrane-bounded nucleus and (2) functional organelles, such as mitochondria and chloroplasts, in the cytoplasm of their cells. EXCISION: The natural or in vitro enzymatic release (removal) of a DNA segment from a chromosome or cloning vector. EXCITED STATE: the state of an atom, molecule or group when it has absorbed energy and become excited to a higher energy state as compared to the normal ground state. The excited state may be electronic, vibrational, rotational, etc. EXOCYTOSIS. The cellular secretion of macromolecules by the fusion of vesicles with the plasma membrane. EXON TRAPPING: A protocol for the isolation of exons from genomic clones. Genomic DNA (I to 6 kb) is cloned into an intron that is flanked by two exons (artificial gene) in a vector. When an exon is present in the cloned DNA, reverse transcriptase polymerase chain reaction (RT-PCR) shows that the mRNA from the artificial gene is longer than expected. The cloned DNA can be amplified, subcIoned, and characterized. Also called exon entrapment, exon amplification. EXON. A DNA sequence that is ultimately translated into protein. EXONUCLEASE III (ExoIII, exodeoxyribonuclease III): An Escherichia coli enzyme that removes nucleotides from the 3'hydroxyl ends of double-stranded DNA. EXONUCLEASE. An enzyme that cleaves nucleotide chains at their terminal bonds only. EXOPOLYSACCHARIDE: A high-molecular-weight polymer that is composed of sugar residues and is secreted by a microorganism into the surrounding environment. EXPONENTIAL PHASE: A growth phase observed during batch growth in which the rate of growth is described by an exponential equation (dX/dt = kXt, so that X(t) = X(0) exp(kt)). (The entire process, however, is a sigmoidal, hyperbolic tangent) EXPRESSED SEQUENCE TAG (EST). a sequence from a transcribed mRNA for a possibly unknown gene. Individual EST's are neither especially informative nor highly accurate; however, they are easy to collect in large numbers. A database of EST's can be helpful for picking protein-coding sequences out of a long stretch of DNA, or for providing a larger context for very short sequences, such as the small pieces of protein sequence obtainable by mass spectrometry. EST's are compiled by the National Center for Biotechnology Information in a database called dbEST. EXPRESSION VECTORS. Sequences of DNA into which cDNA fragments are inserted to encourage cells to more efficiently transcribe desired cDNA sequences. EXTENSION (protruding end, sticky end, overhang, cohesive end): A single-stranded DNA region consisting of one or more nucleotides at the end of a strand of duplex DNA. (3' extension on the 3'-hydroxyl end; 5'extension on the 5'-phosphate). EXTRACELLULAR MATRIX: The organized carbohydrate and protein structure that is secreted by animal cells when they are part of a tissue. F(ab')2. A fragment of an antibody containing two antigen-binding sites generated by cleavage of the antibody molecule with the enzyme pepsin which cuts at the hinge region C-terminally to the inter-H-chain disulphide bond. F1 HYBRIDS. The first generation of animals generated from 2 different inbred strains. These animals are genetically identical to one another but different from either inbred parent. F2 HYBRIDS. The progeny produced from matings between F1 animals. These animals are different from one another and will contain different mixtures of the genetic variations that were present in the original inbred progenitors. FADD. Fas-Associating protein with Death Domain (also called MORT 1). FATTY ACIDS: Molecules having a hydrophobic section (usually a chain of (-CH2-)) and an end with a carboxylic acid (-COOH) which is hydrophilic. One example of fatty acids are the components of soap which make it possible to dissolve oils in water. FERMENTATION: Breakdown of carbon compounds by cells or organisms to ATP without using molecular oxygen. FERREDOXIN: An iron-sulfur protein that acts as an electron carrier. FIBERS. A lignified cell type that reinforces the xylem of angiosperms and functions in mechanical support; slender, tapered sclerenchyma cells that usually form bundles. FIBRINOLYSINS. These are special proteins in the blood of all normal persons that help blood clots that formed dissolve. FISCHER PROJECTION: a convention for drawing carbon chains so that the relative 3-dimensional stereochemistry of the carbon atoms is relatively easy portrayed on a 2-dimensional drawing. FISH (FLUORESCENCE IN SITU HYBRIDIZATION): A physical mapping approach that uses fluorescein tags to detect hybridization of probes with metaphase chromosomes and with the lesscondensed somatic interphase chromatin. FLANKING REGION. The DNA sequences extending on either side of a specific locus or gene. FLASH. FLice-ASsociated Huge protein (220 kDa): FLASH is a component of the DISC; it contains a motif structurally related to CED-4/Apaf-1 and two tandem-repeated DED homologous domains (DRDs) which mediate its interaction with caspase-8 and FADD. FLASH self-associates through its CED-4-homologous domains (in analogy to CED-4/Apaf-1). FLASH is required for the activation of Caspase-8 during Fas-meditated apoptosis. Overexpression of FLASH deletion mutants inhibited Fas- and TNF-mediated apoptosis. FLASH also interacts with the anti-apoptotic adenovirus protein E1B19K FLAVOBACTERIUM: Known for moving by gliding (not wiggling); a psychrophilic (cold-loving) organism. FLAVONOID: A member of a class of plant phenolic compounds containing two aromatic rings connected by a 3-carbon bridge. FLICE. also called MACH or Caspase-8. FLIP. FLICE Inhibitor Protein; inhibitor of Death Receptor induced apoptosis; aliases for FLIP are among others Casper, Usurpin, CASH. FLOW CYTOMETRY. This is a laboratory method where blood is placed into a machine that separates blood cells by size, shape, density and epitope (antennae) on their surface. The immunophenotype assay and the NK assay are tested by using this machine. Each cell in the machine passes a laser eye and the reflected light is analyzed by the machine. Each type of cell reflects light differently. An NK ( CD 56+) cell gives a different reflection than a B cell (CD 19+). FLOW CYTOMETRY: Analysis of biological material by detection of the lightabsorbing or fluorescing properties of cells or subcellular fractions (i.e., chromosomes) passing in a narrow stream through a laser beam. An absorbance or fluorescence profile of the sample is produced. Automated sorting devices, used to fractionate samples, sort successive droplets of the analyzed stream into different fractions depending on the fluorescence emitted by each droplet. FLOW KARYOTYPING: Use of flow cytometry to analyze and separate chromosomes on the basis of their DNA content. FLUORESCEIN: A fluorescent dye often used to label antibodies so that they may be visualized after they have reacted with antigens in cells. FLUOROGRAPHY: Detection of the emission of light on X-ray film from a labeled source. FOLLICLE STIMULATING HORMONE (FSH). This brain hormone is produced in the pituitary gland deep in the brain. It is responsible for making the ovary grow and produce eggs. It is also important in telling the ovary when to release the egg (ovulate) and when to begin the production of estrogen by the ovary. In the male FSH does a similar thing to the testicles. It stimulates them to produce and to release the sperm to the site where they are ready to be ejaculated. FOOTPRINTING. (DNA footprinting) Assay used to study DNAbinding proteins. FOUR-CUTTER: A type II restriction endonuclease that binds and cleaves DNA at sites that contain four nucleotide pairs. FRAGMENTATION. a method of asexual reproduction in the fungi where a hypha breaks apart to form two new mycelia. In plants, a method of asexual reproduction. FRAMESHIFT MUTATION: In chromosomal DNA, an insertion or deletion of base pairs that changes the reading frame of a gene. FREE ENERGY (deltaG): a thermodynamic state function; the free energy change (deltaG) in any reaction is related to the enthalpy and entropy: deltaG = deltaH - T*deltaS FREUND'S COMPLETE ADJUVANT. A water-in-oil emulsion that contains an immunogen, an emulsifying agent, and killed mycobacteria which enhance the immune response to the immunogen; termed "incomplete" Freund's adjuvant if mycobacteria are not included. FRONTIER ORBITAL SYMMETRY: the theory that the site and rates of reaction depend on the geometries, sign of the wave function and relative energies of the highest occupied molecular orbital (HOMO) of one molecule and the lowest unoccupied molecular orbital (LUMO) of the other. FUNGUS: Eucaryotes which do not contain chlorophyll (that is, which aren't algae). There are three primary fungal groups: yeast, molds, and mushrooms FUSION PROTEIN: The product of two or more coding sequences from different genes that have been cloned together and that, after translation, form a single polypeptide sequence. Also called hybrid protein, chimeric protein. Fab. Fragment of antibody containing the antigen-binding site, generated by cleavage of the antibody with the enzyme papain, which cuts at the hinge region N-terminally to the inter-H-chain disulphide bond and generates two Fab fragments from one antibody molecule. Fc receptor (FcR). A receptor on a cell surface with specific binding affinity for the Fc portion of an antibody molecule. Fc receptors are found on many types of cells. Fc. Fragment of antibody without antigen-binding sites, generated by cleavage with papain; the Fc fragment contains the C-terminal domains of the heavy immunoglobulin chains. G CAP: The 5'-terminal methylated guanine nucleotide that is present on many eukaryotic mRNAs; it is joined, after transcription, to the mRNA in a 5'-to-5' linkage. G Proteins. A class of intracellular proteins that bind to the internal surface of receptors and are involved in the signal transduction process. GAMETE: A cell with a haploid chromosome content. In animals, sperm or egg; in plants, pollen or ovum. GASTRIN. a hormone secreted by the wall of mammalian stomach which activates digestive processes in the stomach GATA-1. GATA-1 is a gene regulatory protein that is found in red blood cells and contributes to cell-type specific expression of the á-globin gene and for the maturation of erythroblasts. Absence of GATA-1 leads to apoptosis and to a block in maturation. GATA-1 upregulates the expression of Bcl-XL and was found to be cleaved in a caspase-dependent manner upon activation of death receptors on the surface of erythroid cells, or alternatively, following deprivation of erythropoietin. Thus, GABA-1 appears to be involved in a complex regulation system determining the red blood cell's fate: differentiation, reversible maturation arrest or death GAUCHE: a conformational isomer in which the groups are neither eclipsed nor trans to one another. Often taken as the conformation where the dihedral angle between the groups is 60'. GEL ELECTROPHORESIS: a DNA separation technique that is very important in DNA sequencing. Standard sequencing procedures involve cloning DNA fragments into special sequencing cloning vectors that carry tiny pieces of DNA. The next step is to determine the base sequence of the tiny fragments by a special procedure that generates a series of even tinier DNA fragments that differ in size by only one base. These nested fragments are separated by gel electrophoresis, in which the DNA pieces are added to a gelatinous solution, allowing the fragments to work their way down through the gel. Smaller pieces move faster and will reach the bottom first. Movement through the gel is hastened by applying an electrical field to the gel. GEL-SHIFT ASSAY. An assay used to detect specific protein binding to DNA. Such binding creates complexes that migrate more slowly during gel electrophoresis than free DNA. Also known as mobility-shift assay. GENETIC POLYMORPHISM: When two or more alleles of a locus in a population of individuals occur at a frequency greater than one per cent. GEOMETRICAL ISOMERISM: a term describing isomerism owing to the presence of restricted rotation about a bond. The major example is (Z) and (E) isomers of unsymmetrically substituted alkenes. GLD MUTATION. gld = generalized lymphoproliferative disease; spontaneous loss-of-function mutation in the FasL gene of mice. Leads to accumulation of lymphocytes. GLYCOGEN. the storage carbohydrate of animals; in mammals it is found in high concentration in the muscles and in the liver GLYCOLYSIS: The splitting of sugar into smaller organic acids, yielding cellular energy. GLYCOSYLATION: The covalent addition of sugar or sugar-related molecules to proteins or polynucleotides. GRAM-NEGATIVE: Cells which stain red when Gram-stained This arises from the inability of iodine to bind to the cell's peptidoglycan (rigid layer comprised of sugar and amino acid residues) because it is covered by another layer of wall (the outer wall, made of lipopolysacharide and proteins.) GRAM-POSITIVE: Cells which stain purple when Gram-stained This arises from the binding of iodine to the cell's peptidoglycan (rigid layer comprised of sugar and amino acid residues.) GROWTH PHASE (curve). The characteristic periods in the growth of a bacterial culture, as indicated by the shape of a graph of viable cell number versus time. GUANINE: One of the organic bases found in either DNA or RNA. H-2 complex. The major histocompatibility complex situated on chromosome 17 of the mouse; contains subregions K, I and D. HAPLOID CELL. A cell containing only one set, or half the usual (diploid) number, of chromosomes. HAPLOTYPE: The alleles of the loci of a chromosome. HAPTEN. A compound, usually of low molecular weight, that is not itself immunogenic but that, after conjugation to a carrier protein or cells, becomes immunogenic and induces antibody, which can bind the hapten alone in the absence of carrier. HARD AND SOFT ACIDS AND BASES: a classification of acids and bases depending on their polarizability. Hard bases include fluoride ions; soft bases include triphenylphosphine. Hard acids include Na+, whilst an example of a soft, polarisable acid is Pt2+; hard-hard and soft-soft interactions are favoured. Hardness and softness can be described in terms of the HOMO and LUMO interactions. HEAT SHOCK PROTEINS: The proteins synthesized in the nearly universal response of organisms to environmental stress such as high temperature. HEAVY CHAIN (H chain). The larger of the two types of chains that comprise a normal immunoglobulin or antibody molecule. HELPER PLASMID: A plasmid that provides a function(s) to another plasmid in the same cell. Some helper plasmids are used to mobilize nonconjugative plasmids from a donor cell into a recipient cell. HELPER T CELLS. A class of T cells which help trigger B cells to make antibody against thymus-dependent antigens. Helper T cells also help generate cytotoxic T cells. HERITABILITY. the proportion of the total phenotypic variance that is attributable to genetic causes: h2 = genetic variance / total phenotypic variance Natural selection tends to reduce heritability because strong (directional or stabilizing) selection leads to reduced variation. HETEROCHROMATIN. Dark-stained regions of chromosomes thought to be for the most part genetically inactive. HETERODUPLEX. A double-stranded DNA (dsDNA) molecule or DNA-RNA hybrid, where each strand is of a different origin. HETEROGENEOUS NUCLEAR RNA (hnRNA). The name originally given to large RNA molecules found in the nucleus, which are now known to be unedited mRNA transcripts, or pre-mRNAs. HETEROLOGOUS PROBE: A DNA probe that is derived from one organism and used to screen for a similar DNA sequence in a clone bank derived from another organism. HETEROLYTIC REACTION: a reaction in which a covalent bond is broken with unequal sharing of the electrons from the bond. HETEROPHILE ANTIGEN. A cross-reacting antigen that appears in widely ranging species such as humans and bacteria. HETEROPLASMY. The existence of more than 1 mitochondrial type in the cells of an individual, i.e., the presence of both normal and mutant mt DNA in a single individual. HETEROPLOID. An individual with an abnormal number of chromosomes (as compared to euploid, which is the normal number of chromosomes). HETEROTETRAMER. A molecule consisting of 4 subunits, at least 1 of which differs from the others. HIGH THROUGHPUT SCREENING. The process of using automated assays to search through large numbers of substances for desired activity, resulting in less costly and faster systematic processes. HINGE REGION. A flexible, open segment of an antibody molecule that allows bending of the molecule. The hinge region is located between Fab and Fc and is susceptible to enzymatic cleavage. HISTOCOMPATIBILITY. Literally, the ability of tissues to get along; in immunology, it means identity in all transplantation antigens. These antigens, in turn, are collectively referred to as histocompatibility antigens. HLA (Human Leukocyte Antigen). These are molecules on the surface of human cells that determine a person's white blood cell type. Ten numbers make up this system. There are two A numbers, two B numbers, two C numbers, two DR numbers and two DQ numbers. One number at each locus (A,B,C, DR and DQ) comes from your mother the other one comes from your father. Couples with infertility and recurrent pregnancy losses share too many DR and DQ HLA factors. They are too compatible. This is referred to as the unlucky match for a successful pregnancy to occur. HOLOENZYME: A catalytically active enzyme containing all of the necessary cofactors and subunits. HOMEOBOX: A short stretch of nucleotides whose base sequence is virtually identical in all the genes that contain it. It has been found in many organisms from fruit flies to human beings. In the fruit fly, a homeobox appears to determine when particular groups of genes are expressed during development. HOMODIMER: A protein with two identical polypeptide chains. HOMOLOGOUS CHROMOSOMES. Chromosomes that have the same linear arrangement of genes--a pair of matching chromosomes in a diploid organism. HOMOLOGOUS RECOMBINATION. The exchange of DNA fragments between two DNA molecules or chromatids of paired chromosomes (during crossing over) at the site of identical nucleotide sequences. HOMOLOGY. a similarity in a characteristic due to a shared ancestry HOMOLYTIC REACTION: a reaction in which a covalent bond is broken with equal sharing of the electrons from the bond. HOMOMER: A protein with two or more identical protein chains. Also called homomeric polypeptide, homomeric protein. HOMOPLASMY. The presence of a single population of mt DNA in the cells of a single individual. This is normal. HOMOPOLYMER: A nucleic acid strand that is composed of one kind of nucleotide. HOMOTETRAMER. A molecule consisting of 4 identical subunits. HOUSE-KEEPING GENES. Genes which are constitutively expressed in most cells because they provide basic functions. HPA-II (HpaII) TINY FRAGMENTS (HTF): Small DNA fragments that are generated from a genomic clone after treatment with the restriction endonuclease HpalI, which cleaves within the CpG islands. HUMAN ARTIFICIAL CHROMOSOME (HAC): A chromosome that is assembled from telomere, centromere, and human genomic DNA sequences. HUMAN CHORIONIC GONADOTROPIN (hCG). A hormone that increases early in pregnancy. It is produced by the cells of the placenta that attach the baby to the uterus. Its detection is the basis of all pregnancy tests. It is also used as a drug given to the woman to time ovulation. Once this drug, is given the woman predictably ovulates in 36-40 hours. HUMAN GROWTH HORMONE (HGH, somatotrophin). A protein produced in the pituitary gland that stimulates the liver to produce somatomedins, which stimulate growth of bone and muscle. HUMAN MINISATELLITE DNA: Human DNA that is noncoding and generally G+C rich and contains tandem repeats of short (9- to 40-base-pair) stretches of DNA. HUMEGON. This drug is used to stimulate ovulation. It contains biologically active FSH an LH. Humegon and hCG are given sequentially for induction of ovulation. It, like Pergonal, is also used in men to treat testicular dysfunction. HUMORAL IMMUNE RESPONSE: The production of antibody by B cells of the immune system in response to the presence of a foreign antigen. HYBRID CELL. A cell formed by fusion of 2 cells of different origin in which the 2 nuclei have merged into 1. Can be cloned to produce hybrid cell lines. HYBRID GENE: The combination of two genes or the parts of two genes in the correct reading frame that encodes a single protein that has amino acid sequences from both genes. HYBRID SELECTION: A protocol for determining which genomic clones hybridize to a cDNA or mRNA molecule. HYBRIDIZATION: (1) The pairing of two polynucleotide strands, often from different sources, by hydrogen bonding between complementary nucleotides. (2) The process whereby atomic orbitals of different type but similar energies are combined to form a set of equivalent hybid orbitals. These hybrid orbitals do not exist in the atoms but only in the formation of molecular orbitals by combining atomic orbitals from different atoms. HYBRIDOMA: The product of the fusion of a myeloma cell with an antibody-producing lymphocyte. This cell combination (hybridoma) can continue to divide in cell culture and secrete a single type of antibody. HYDROBORATION: the cis-addition of B-H bonds across double (or triple) carbon-carbon bonds. HYDROGEN UPTAKE POSITIVE (HUP): A term describing a microorganism that is capable of assimilating hydrogen gas. HYDROGENOLYSIS: the cleaving of a chemical bond by hydrogen. Generally carried out in the presence of a hydrogenation catalyst. HYDROLYSIS: the addition of the elements of water to a substance, often with the partition of the substance into two parts, such as in the hydrolysis of an ester to an acid and an alcohol. HYDROPHILIC: Describing compounds which are highly soluble in water. Generally, such compounds have a charge or are polar (having a dipole). HYDROPHOBIC; Describing compounds with a lower water solubility (and high solubility in oils). Typically, these are neutral compounds. On a molecular thermodynamic level, hydrophobic compounds would like to be in among water molecules, but not as much as other water molecules would like to be in the same place; hydrophilic compounds would like to be in with water molecules more than other water molecules. HYPERVARIABLE REGIONS. Portions of the light and heavy immunoglobulin chains that are highly variable in amino acid sequence from one immunoglobulin molecule to another, and that, together, constitute the antigen-binding site of an antibody molecule. Also, portions of the T-cell receptor which constitute the antigen-binding site. HYPHA (plural. HYPHAE). A single fungal filament; Collectively, the hyphae make up the mycelium. HYPOCOTYL. the portion of an early developing plant which is below the cotelydon (s) (=seed leaf) but above the root system. Its elongation helps the young plant to break away from the ground. HYPOTHALAMUS. This is a thumb-sized gland near the base of the brain that controls the pituitary gland. It releases messages called releasing hormones that stimulate the pituitary gland to release its hormones (FSH and LH) in the proper amounts to achieve ovulation. In some women the hypothalamus is dysfunctional and infertility results. HYSTEROSALPINIGOGRAM (HSG). This is an x-ray test that involves the injection of a liquid dye into the uterus and into the tubes. It allows the doctor to see the size and the shape of the uterus, whether there are any abnormalities and whether the tubes are open to take the sperm to the egg and to deliver the fertilized egg into the uterus. IAPs. Inhibitor of Apoptosis Proteins: a family of proteins with antiapoptotic effect, probably by inhibiting Caspase-3 and -7. ICAD. Inhibitor of CAD (Caspase-activated DNase), identified in mouse cells, ICAD is homologous to human DFF45. ICAD binds to CAD, and inhibits its DNase activity. Active Caspase-3 cleaves ICAD and by this activates CAD what results in oligonucleosomal DNA cleavage. ICAD is not just inhibitor of CAD but probably also chaperone for CAD, since active CAD is only expressed in presence of ICAD. ICE NUCLEATION PROTEIN: A protein around which ice crystals form. ICE-MINUS BACTERIA: Bacteria that do not synthesize ice nucleation proteins. IDIOTYPE. The combined antigenic determinants (idiotopes) found on antibodies of an individual that are directed at a particular antigen; such antigenic determinants are found only in the variable region. IFN-gamma. Interferon-gamma; cytokine with antiviral effect produced by cytotoxic CD8+ T lymphocytes and CD4+ Th1 cells but not by Th2 lymphocytes. It inhibits proliferation of T2h cells, activates macrophage functions and regulates antibody production of B lymphocytes. IKAP. IKK-complex-Associated Protein is a scaffold component of the heigh molecular weight IKK complexes. Like NEMO/IKK-gamma, IKAP binds to IKKs directly, but it also binds to NIK. It might direct the assembly or disassembly of IKK complexes in response to signalling, and control deactivation of the kinase complex after stimulation. IKKs. Two IkB kinases (IKKs) have been cloned : IKK-alpha and -beta. They are the only kinases known to phospphorylate IkB-alpha at the same residues that are modified in response to agents that activate NF-kB. IKKs are part of multi-protein complexes (800 kDa) which include the IKK-alpha and -beta, NEMO/IKK-gamma, IKAP and NIK. IL (Interleukin). This is a generic term for cytokines produced by white blood cells when they are activated and in the process of killing or rejecting something such as an embryo, a kidney transplant or an infection. CD3-IL2 Receptor + cells are T cells in the process of rejection in the body. They should be below 5% of the total T cells in the immunophenotype testing. IMMEDIATE-EARLY GENE: A viral gene that is expressed promptly after infection. IMMORTALIZING ONCOGENE. A gene that upon transfection enables a primary cell to grow indefinitely in culture. IMMUNE RESPONSE (Ir) GENE. A gene controlling an immune response to a particular antigen; most genes of this type are in the MHC (major histocompatibility complex), and the term is rarely used to describe other types of Ir genes outside the MHC. IMMUNOAFFINITY CHROMATOGRAPHY: A purification technique in which an antibody is bound to a matrix and is subsequently used to bind a specific protein and separate it from a complex mixture. IMMUNOGEN (ANTIGEN, Ag): induces antibody response. IMMUNOGLOBULIN (Ig). A general term for all antibody molecules. Each Ig unit is made up of two heavy chains and two light chains and has two antigen- binding sites. IMMUNOGLOBULIN CLASS. There are five different classes or families of antibodies (immunoglobulins). IgM is the first antibody produced when an immune response is initiated. It lives in the blood system. IgG lives in the lymphatic system and is made by IgM. IgA lives in the organs and protects them. IgD which is present as a memory antibody in the blood once a person is immune or immunized. IgE is the antibody that causes allergies and asthma. It is present throughout the body. IMMUNOGLOBULIN FOLD. The immunoglobulin fold is one of the most versatile and widely-used structural units of proteins. The immunoglobulin fold was originally characterized as the globular modules that form the homology domains of immunoglobulins. Its secondary structure consists of a barrel that is composed of a three- and a four-stranded antiparallel beta-sheet which are linked by a disulfide bond. IMMUNOTHERAPEUTIC PROCEDURE: The use of an antibody or a fusion protein containing the antigen binding site of an antibody to treat a disease and enhance the well-being of a patient. IMMUNOTOXIN: A fusion protein that has separate domains with antibody and toxin activity. The antibody portion of the molecule facilitates binding to a target molecule or cell, and the toxin inactivates the target molecule or kills the cell. IN SITU HYBRIDIZATION: Use of a DNA or RNA probe to detect the presence of the complementary DNA sequence in cloned bacterial or cultured eukaryotic cells. IN VITRO TRANSLATION: Protein synthesis that is directed by either purified DNA with bacterial extracts or mRNA with wheat germ or rabbit reticulocyte extracts that provide ribosomes, tRNAs, and protein synthesis factors. The reaction mixture is often supplemented with ATP, GTP, and amino acids. INBRED MOUSE STRAIN. A strain of mice that has been maintained by successive brother to sister matings over many generations, e.g., BALB/c and C57BL/6 mice strains. INBREEDING DEPRESSION. Reduction in offspring fitness resulting from mating between blood relatives. INCLUSION BODY: A protein that is overproduced in a recombinant bacterium and forms a crystalline array inside the bacterial cell. INCOMPATIBILITY GROUP: A classification scheme indicating which plasmids can coexist within a single cell. Plasmids must belong to different incompatibility groups to coexist within the same cell. Plasmids that belong to the same incompatibility group are unstable when placed into the same cell. A plasmid cloning vector should always belong to an incompatibility group different from that of the host bacterium's endogenous; plasmids. INCOMPLETE DOMINANCE. A condition where a heterozygous off- spring has a phenotype that is distinctly different from, and intermediate to, the parental phenotypes. INCOMPLETE PENETRANCE: When some individuals in a population have a specific genotype that causes an abnormality but are not affected. INDEPENDENT ASSORTMENT: The formation of all possible gene combinations in gametes with genes on different chromosomes, followed by the random joining of male and female gametes. Also called Mendel's second law of inheritance. INDUCER. A molecule that induces the expression of a gene. INITIATION CODON: The codon AUG, which specifies the first amino acid (methionine [N-formylmethionine in prokaryotes]) of a protein. Also called initiator, translational start codon, translational initiation signal. INITIATION COMPLEX: The fMet-tRNA'Fet-mRNA-small ribosomal subunit-large ribosomal subunit combination in prokaryotes or the Met-tRNA let-mRNA-small ribosomal subunit-large ribosomal subunit combination in eukaryotes that is ready for the elongation phase of translation. INITIATOR tRNA: The fMet-tRNA'Fet in prokaryotes and Met-tRNA Met in eukaryotes that starts translation. INOSITOL LIPID. A membrane-anchored phospholipid that transduces hormonal signals by stimulating the release of any of several chemical messengers. INTEGRATION-EXCISION (I/E) REGION: The portion of bacteriophage A DNA that enables bacteriophage A DNA to be inserted into a specific site in the Escherichia coli chromosome and excised from this site. INTERFERON. A protein produced naturally by the cells of our bodies. It increases the resistance of surrounding cells to attacks by viruses. One type of interferon, alpha interferon, is effective against certain types of cancer. Others may prove effective in treating autoimmune diseases. INTERNAL RIBOSOMAL ENTRY SITE: A nontranslated sequence following a coding region of a polycistronic RNA that binds to a small ribosomal subunit and forms an initiation-of-translation complex. INTERPHASE: The period in the cell cycle when DNA is replicated in the nucleus; followed by mitosis. INTROGRESSION. Backcrossing of hybrids of two plant populations to introduce new genes into a wild population. INTRON (INTERVENING SEQUENCE): Segment of gene transcribed but then excised from primary transcript during processing to a functional RNA molecule. INVERSION. A structural rearrangement of a chromosome in which 2 breaks occur, followed by the reinsertion of the chromosome segment but in reversed order. It may be either paracentric, i.e., it does not include the centromere, or pericentric, i.e., it does include the centromere. ION CHANNEL: An integral protein, within a cell membrane, that facilitates selective ion transport. IPTG (Isopropylthiogalactopyranoside): an inducer of the lac (lactose) operon. In recombinant DNA technology, IPTG is often used to induce cloned genes that are under the control of the lac repressor-lac promoter system. ISOCHROMOSOME. A structural chromosome rearrangement caused by the division of a chromosome along an axis perpendicular to the usual axis of division; results in chromosomes with either 2 short arms or 2 long arms. ISODISOMY. The presence of 2 identical homologues of a transmitted chromosome from only 1 of the parents. junk DNA with no apparent function. ISOGRAFT. A tissue transplanted between two genetically identical individuals. ISOHEMAGGLUTININS. Antibodies to major red blood cell antigens present normally as a result of inapparent immunization by cross-reactive antigens in bacteria, food, etc. ISOTYPE SWITCH. The shift of a B cell or its progeny from the secretion of antibody of one isotype or class of antibody with the same V regions but a different heavy- chain constant region and, hence, a different isotype (class switch). ISOTYPES. Classes of antibody that differ in the constant region of their heavy chain (Fc portion); distinguishable also on the basis of reaction with antisera raised in another species. These differences also result in different biological activities of the antibodies. IVIg (Intravenous Immunoglobulin G Infusion). This gamma globulin preparation is made just like Rhogam, the gamma globulin that is given to Rh negative women during pregnancy. It is made from pooled blood that is washed and processed (it comes out clear in the end). It takes approximately 2-4 hours to administer in the vein. The first dose in given preconception in a doctor's office. The next doses if they are needed in women with the highest levels of Natural Killer Cells, are given by a nurse in the home. Before it is administered, the nurse will give the patient an injection of Benadryl to avoid an allergic reaction (this makes the patient very sleepy). Some common reactions include: headaches, joint pain, flu like symptoms and occasionally fever. The Natural Killer test is done again 7-10 days afterwards to make sure it is working and enough IVIg has been given. Ia. "Immune response-associated" proteins, found on B cells and antigen-presenting cells of mice; an old term now replaced with MHC (major histocompatibility complex) class II molecules. IgG (Immunoglobulin G). This is a protein in the blood produced by B lymphocytes (CD19+). It is an antibody that is present primarily in the lymph system. It is produced by IgM (Immunoglobulin) that resides in the blood. One IgM produces five IgG antibody molecules in a balanced system. It is a Y shaped molecule consisting of two heavy and two light chains, each having variable and constant regions. The variable regions determine the fit with the antigen that initiated the response like a key-in-lock situation. IkB-proteins. IkB-proteins (IkB-alpha, beta, and epsilon) are inhibitor proteins of NF-kB, which keep cytosolic NF-kB under tight control by binding to NF-kB and blocking its transport into the nucleus. For NF-kB activation, IkB-alpha is phosphorylated by IKKs at two serine residues what results in the binding of ubiquitin to and degradation of IkB-alpha by the proteasome. J chain (joining chain). A polypeptide involved in the polymerization of immunoglobulin molecules IgM and IgA. J gene. A gene segment coding for the J or joining segment in immunoglobulin DNA; V genes translocate to J segments in L chains, and to D and J segments in H chains. Also, codes for a portion of the T-cell receptor. K cell. An effector lymphocyte with Fc receptors which allow it to bind to and kill antibody-coated target cells. KANAMYCIN. An antibiotic of the aminoglycoside family that poisons translation by binding to the ribosomes. KARYORRHEXIS. fragmentation of nucleus during apoptosis. KARYOTYPE. All of the chromosomes in a cell or an individual organism, visible through a microsope during cell division. KETOSYNTHASE: A low-molecular-weight enzyme involved as part of a larger complex in polyketide biosynthesis. KILLER T CELL. A T cell with a particular immune specificity and an endogenously produced receptor for antigen, capable of specifically killing its target cell after attachment to the target cell by this receptor. Also called cytotoxic T cell. KILOBASE PAIR (kb,kbp, 1000 base pairs): unit of length of DNA. KINASES. Enzymes which phosphorylate proteins. KINETOCHORE. A structure at the centromere to which the spindle fibers are attached. KLEBSIELLA: Named for T.A.E. Klebs (who isolated the cause of diphtheria). Another enteric bacterium (gastric tract inhabitant), but produces butanediol. KLENOW FRAGMENT: A product of proteolytic digestion of the DNA polymerase I from E. coli that retains both polymerase and 3'-exonuclease activities but not 5'-exonuclease activity. KNOCKOUT: The targeted disruption of a gene by homologous recombination. LAC OPERON. A structural unit in the E.coli genome that consists of three structural genes (encoding different enzymes involved in sugar metabolism) transcribed together and their common promoter and operator genes. Provides a good model for studying the interactions between promoters and repressors. LACTEAL. a blind-ended tube which forms the basic element of the lymphatic system; in the digestive system of mammals, lacteals transport fats from the small intestine to the closed circulatory system LACTOBACILLUS: named for milk. These are often found in dairy products (fermenters of food) LAG PHASE. The initial growth phase, during which cell number remains relatively constant prior to rapid growth. LAGGING STRAND OF DNA. The new strand of a DNA replicating in the 3' to 5' direction. It is synthesized in short fragments in the 5'to 3' direction that are subsequently joined together. LATERAL MERISTEM. A continuous cylinder of meristematic cells surrounding the xylem and pith that produces secondary xylem and phloem. Responsible for secondary growth. LCAO: a method for the calculation of molecular orbitals from a linear combination of atomic orbitals. LEUKOCYTE ANTIBODY DETECTION (Cross Match). A close DQ Alpha match will be indicated by this test. Low numbers on this test tell the doctor you need LIT (Lymphocyte Immune Therapy). This is an immunization given to the woman made from the husband's white blood cells. IVIg (Intravenous Gamma Globulin) is used by some doctors for this problem. Others choose to put in more embryos to increase the chances of having an embryo that will be accepted because it is too compatible to the mother's DNA. The immunization is made from the husband's or a donor's white blood cells (lymphocytes). A donor is used for the woman if the couple's DQ alpha numbers are very close. The immunization is known to be working when the woman's antibodies to her husband's T and B lymphocytes climb to over 30% and the woman's microcytotoxicity test becomes positive. LEWIS ACID: an agent capable of accepoting a pair of electrons to form a coordinate bond. LICHEN: A symbiote of algae and fungus able to grow in extreme conditions. The alga makes carbohydrates out of carbon dioxide, which are used by the fungus to grow. The fungus extracts minerals and fixes nitrogen, which are used by the alga to grow. LIGAND. A molecule that can bind to a receptor and thereby induce a signal in the cell, e.g., a hormone. LIGASE (DNA ligase). An enzyme that catalyzes a condensation reaction that links two DNA molecules via the formation of a phosphodiester bond between the 3' hydroxyl and 5' phosphate of adjacent nucleotides. LIGATE. The process of joining two or more DNA fragments. LIGATION: Joining of two DNA molecules by the formation of phosphodiester bonds. In vitro, this reaction is usually catalyzed by the enzyme T4 DNA ligase. LIGHT CHAIN (L chain). The light chain of immunoglobulin is a structural feature that occurs in two forms: kappa and lambda. LIGNOCELLULOSE: The combination of lignin, hemicellulose, and cellulose that forms the structural framework of plant cell walls. LINKAGE DISEQUILIBRIUM. The frequency, in a population of linked genes, which is governed by factors other than change. LINKAGE MAP. A chromosome map showing the relative positions of genetic markers of a given species, as determined by linkage analysis; not the same as a physical, or gene, map, which uses linkage analysis, cytogenetic examination, and physical techniques to generate the map. LINKAGE PHASE. The arrangement of alleles of linked loci on chromosomes. LINKER DNA. A synthetic DNA that carries the recognition site for a restriction enzyme and that can bind 2 DNA fragments. Also, the stretch of DNA between 2 nucleosomes. LINKER. A short, double-stranded oligonucleotide containing a restriction endonuclease recognition site, which is ligated to the ends of a DNA fragment. LIPASE. an enzyme which digests fats LIPOFECTION: Delivery into eukaryotic cells of DNA, RNA, or other compounds that have been encapsulated in an artificial phospholipid vesicle. LIPOPOLYSACCHARIDE (LPS): A combination of sugars and fatty acids which is found in the outer wall or slime layer of some bacteria. It has the property of being partially soluble in water and also in oils. LIPOSOME: A circular collection of lipid molecules in which the hydrophobic portions of the molecule are facing inward; a lipid vesicle with an aqueous interior that can carry nucleic acids, drugs, or other therapeutic agents. LISTERIA MONOCYTOGENES: Bacterium which causes listeriosis. LIT (Lymphocyte Immunization Therapy). Lymphocyte immune therapy is used in women with recurrent spontaneous abortions. This immunization is made from the father-to-be's blood or sometimes from a donor's blood. It is injected under the skin of the mother's forearm. This is done twice, separated by one month. Testing to see that it has worked is done one month after the second treatment. Common reactions to this treatment include: swelling, irritation, and itching at the injection site. Some women run a fever after this treatment. LITHOTROPH: An organism able to use inorganic compounds as an electron acceptor. Thus, denitrifyers, sulfur bacteria, and iron bacteria are lithotrophs; also lithotrophs tend to be anaerobes. LOD (Z) SCORE: The logarithm of the ratio of the likelihood of the odds that two loci are linked with a recombination fraction equal to or greater than 0 and less than 0.5, to the likelihood of the odds for independent assortment. LOGARITHMIC PHASE. The steepest slope of the growth curve--the phase of vigorous growth during which cell number doubles every 20-30 minutes. LONE PAIR: a pair of electrons in a molecule which is not shared by two of the constituent atoms. LONG TERMINAL REPEATS (LTR): Similar blocks of genetic information that are found at the ends of the genomes of retroviruses. LONG-RANGE RESTRICTION MAPPING: Restriction enzymes are proteins that cut DNA at precise locations. Restriction maps depict the positions on chromosomes of restriction enzyme cutting sites. These are used as biochemical "signposts", or markers of specific areas along the chromosomes. The map will detail the positions on the DNA molecule that are cut by particular restriction enzymes. LOSS OF HETEROZYGOSITY. Describes a locus (or loci) at which a deletion or other process has converted the locus from heterozygosity to homozygosity or hemizygosity. Phenomenon can lead to cancers by loss of tumor suppressor genes. LPR MUTATION. lpr = Lymphoproliferation; spontaneous loss-of-function mutation in the Fas gene of mice. Leads to accumulation of lymphocytes. LUMO: the lowest unoccupied molecular orbital in a molecule or ion. LUTEINIZING HORMONE (LH). This pituitary hormone works in concert with FSH. FSH starts the development of the egg, and LH finishes the development and starts progesterone production. FSH is important to stimulate the cells of the follicle to produce Estrogen. LH is important to stimulate the cells of the follicle that produce Progesterone during the second half of the menstrual cycle. A certain ratio of FSH to LH tells the ovary when to release the egg (ovulation). In the male, LH stimulates the testicles to produce the male hormone testosterone. LYMPHOCYTE. This is a white blood cell that is in charge of starting antigen specific immunity responses. There are many types of lymphocytes in the immune family. These consist of T cells, B cells, granulocytes, basophils, mast cells, eosiniophils, Natural Killer Cells, etc. Each cell type has a CD designation. Small cell with virtually no cytoplasm, found in blood, in all tissue, and in lymphoid organs, such as lymph nodes, spleen, and Peyer's patches, and bears antigen-specific receptors. LYMPHOKINES. Soluble substances secreted by lymphocytes, which have a variety of effects on lymphocytes and other cell types. LYSOGENIC. A type or phase of the virus life cycle during which the virus integrates into the host chromosome of the infected cell, often remaining essentially dormant for some period of time. LYSOGENY: A condition in which a bacteriophage genome (prophage) survives within a host bacterium either as part of the host chromosome or as part of an extrachromosomal element and does not initiate lytic functions. LYTIC. A phase of the virus life cycle during which the virus replicates within the host cell, releasing a new generation of viruses when the infected cell lyses. MACH. MORT 1 associated CED-3 homolog; also called FLICE or Caspase-8. MACROPHAGE. A type of white blood cell that ingests dead tissue and cells and is involved in producing Interleukin 1. MACRORESTRICTION MAP: Map depicting the order of and distance between sites at which restriction enzymes cleave chromosomes. MALT LYMPHOMAS. B cell lymphomas of Mucosa-Associated Lymphoid Tissue, in most cases arising in the gastric mucosa, either as low-grade or high-grade form. High-grade MALT lymphoma might result from transformation of low-grade disease. There is an etological link between low-grade gastric malt lymphoma and infection with Helicobacter pilori. Cytogenetic studies of low-grade MALT lymphomas identified abnormalities of chromosome 1p22, in particular translocation t(1;14)(p22,q32): on 1p22 the gene Bcl-10 was cloned and found to be mutated in MALT lymphomas but also in other tumor types MALTOSE BINDING PROTEIN: An abundant bacterial protein located within the periplasmic space and involved in the uptake of maltose. Fusion with other proteins often results in the fusion protein being secreted to the periplasm. MAP UNIT: A measure of genetic distance between two linked genetic loci; usually 1% recombination corresponds to one map unit. MAP3K. Mitogen-Activated Protein kinase kinase kinase. MARKOWNIKOW'S RULE: in the ionic addition of hydrogen halides to a carbon-carbon double bond the halogen attaches itself to the carbon atom bearing the least number of hydrogen atoms. The rule is useful in the prediction of the major product from such reactions. Free radical reactions proceed in the opposite sense, giving rise to anti-Markownikow addition. MASS SPECTROMETRY: a form of spectrometry in which, generally, high energy electrons are bombarded onto a sample and this generates charged fragments of the parent substance; these ions are then focused by electrostatic and magnetic fields to give a spectrum of the charged fragments. MAST CELL. Tissue located cell probably derived from basophils. Possesses receptor for Fc of IgE. Participates in MAXAM-GILBERT METHOD. A method for determining the exact nucleotide sequence via a chemical degradation process. MDM-2. The mdm-2 gene was identified by virtue of its amplification in transformed mouse lines. Its overexpression was shown to be tumourigenic. Homologous deletion of mdm-2 in mice is lethal at early stages of embryogenesis but is completely rescued by additional deletion of the p53 gene. By binding to p53, the mdm-2 gene product MDM2 can target p53 for nuclear export and degradation. Moreover, it can block transcriptional activity of p53. Interestingly, mdm-2 is a transcriptional target of p53, what gives rise to a feedback loop MEIOSIS: The process of two consecutive cell divisions in the diploid progenitors of sex cells. Meiosis results in four rather than two daughter cells, each with a haploid set of chromosomes. MENDEL'S FIRST LAW (law of segregation). The two alleles received one from each parent segregate independently in gamete formation, so that each gamete receives one or the other with equal probability. MENDEL'S SECOND LAW (law of recombination). Two characters determined by two unlinked genes are recombined at random in gametic formation, so that they segregate independently of each other, each according to the first law. (Note that recombination here is not used to mean crossing-over in meiosis). MERISTEM. A plant cell line capable of continuous cell division, such as cambium in the stem or pericycle in the root MESOPHILE: A microorganism that is able to grow within the temperature range of 20 to 50'C; optimal growth often occurs at about 37C. MESSENGER RNA (mRNA). The class of RNA molecules that copies the genetic information from DNA, in the nucleus, and carries it to ribosomes, in the cytoplasm, where it is translated into protein. METACENTRIC CHROMOSOME. A chromosome with its centromere near the centre. If the centromere is slightly off-centre, the chromosome is said to be submetacentric (see also acrocentric and telocentric). METALLOTHIONEIN. A protective protein that binds heavy metals, such as cadmium and lead. METAPHASE: A stage in mitosis or meiosis during which the chromosomes are aligned along the equatorial plane of the cell. METHYLATION. The addition of a methyl group (-CH3) to DNA. Methylated DNA is inactivated and not transcribed. Most frequently occurs at CpG doublets (see genomic imprinting and CpG islands). METRODIN. This drug contains FSH. It is given in a sequential manner with hCG for ovulation induction. MHC (Major histocompatibility complex). A genetic system of man that determines the antennae (cell surface molecules) on lymphocytes that are responsible for antigen presentation to T lymphocytes in the elicitation and the expression (the beginnings) of an immune response. This genetic system is responsible for rapid rejection of grafts between individuals that are not appropriately matched. This system is responsible for the rejection of pregnancies and embryos in individuals that are too closely matched at DR and DQ. A cluster of genes on chromosome 6 in humans, encoding cell surface molecules that are polymorphic and that code for antigens which lead to rapid graft rejection between members of a single species which differ at these loci. Several classes of protein such as MHC class I and II proteins are encoded in this region. These in humans, are known as 'Human leukocyte antigens' (HLA). MHC CLASS I MOLECULE. A molecule encoded to genes of the MHC which participates in antigen presentation to cytotoxic T (CD8+) cells. MHC CLASS II MOLECULE. A molecule encoded by genes of the MHC which participates in antigen presentation to helper T (CD4+) cells. MHC RESTRICTION. The ability of T lymphocytes to respond only when they 'see' the appropriate antigen in association with "self" MHC class I or class II proteins on the antigen presenting cells. MICELLE. a very small globule of digested fatty acids, glycerides, and glycerol which is found in the lumen of the small intestine. MICHAELIS CONSTANT: Dissociation constant that characterizes the binding of an enzyme to a substrate. The lower the constant, the tighter the binding of the enzyme to the substrate. MICROBIAL MATS (biofilms). Layered groups or communities of microbial populations. MICROINJECTION. A means to introduce a solution of DNA, protein, or other soluble material into a cell using a fine microcapillary pipet. MIGRATION INHIBITION FACTOR (MIF). A lymphokine that inhibits the motility of macrophages in culture. MINIMAL PROMOTER. The minimal elements of a promoter, including the TATA box and transcription initiation site, which is inactive unless regulatory elements that enhance promoter activity are placed upstream; used to test candidate sequences for enhancer activity. MINOR HISTOCOMPATIBILITY ANTIGENS. These antigens, encoded outside the MHC, are numerous, but do not generate rapid graft rejection or primary responses of T cells in vitro. They do not serve as restricting elements in cell interactions. MISSENSE MUTATION: A genetic mutation that changes a codon for one amino acid into a codon specifying another amino acid. MITOCHONDRIA. A small, intracellular, spherical to rod-shaped cytoplasmic organelle, enclosed by Z membranous spaces; the inner membrane is folded, forming a series of projections called cristae. Mitochondria are the principal sites of ATP synthesis; they contain enzymes of the tricarboxylic acid cycle and enzymes for fatty acid oxidation, oxidative phosphorylation, and many other biochemical pathways. They contain their own nucleic acids and ribosomes, replicate independently, and code for the synthesis of some of their own proteins. MITOGEN. A substance that stimulates the proliferation of many different clones of lymphocytes. MITOSIS. A process of cell division in eukaryotic cells conventionally divided into the growth period (interphase) and four stages: prophase, metaphase, anaphase, and telophase. The stages conserve chromosome number by equally allocating replicated chromosomes to each of the daughter cells. MIXED LYMPHOCYTE REACTION (MLR). When lymphocytes from two individuals are cultured together, a proliferative response is generally observed, as the result of reactions of T cells of one individual to MHC antigens on the other individual's cells. MMPs. Matrix MetalloProteinases (MMPs) break down collagen and other proteins that form connective tissue. This is important for cell mobility, e.g. during embryonic development and for the migration of immune cells or the cells necessary for wound healing to places where they are needed. But overactivity of MMPs can be involved in disorders such as arthritis and cancer. MMP-2 was found to be overexpressed in metatstatic tumors, obviously helping the tumors to spread by degrading collagen in basement membranes, which usually are a first barrier for tumor cells during the metastatic process. MOBILE ELEMENTS. DNA sequences that are capable of inserting themselves into other locations in the genome. MOBILITY-SHIFT ASSAY. An assay used to detect specific protein binding to DNA. Such binding creates complexes that migrate more slowly during gel electrophoresis than free DNA. Also known as gel-shift assay. MOBILIZING FUNCTIONS: The genes on a plasmid that facilitate the transfer of either a nonconjugative or conjugative plasmid from one bacterium to another. MODIFIER GENE. A gene that alters the expression of a gene at another locus. MONOCLONAL ANTIBODY (MAb): A single type of antibody that is directed against a specific epitope (antigenic determinant) and is produced by a hybridoma cell line, which is formed by the fusion of a lymphocyte with a myeloma cell. Some myeloma cells synthesize single antibodies naturally. MONOCYTE. Large circulating white cell, 2-10% of total white cells, phagocytic, indented nucleus. Migrates to tissues, where it is known as a macrophage. MONOGENIC. Describing a single gene or mendelian trait. MONOKINES. Soluble substances secreted by monocytes, which have a variety of effects on other cells. MONOPHYLETIC. A taxon (or taxa) derived from a single ancestral line MONOSOMY. An aneuploid condition in which a specific chromosome is present in only single copy, giving the individual a total of 45 chromosomes. MONOZYGOTIC. Refers to twins derived from a single fertilized egg. MORPHOGEN. A protein present in embryonic tissues in a concentration gradient that induces a developmental process. MOSAIC. An individual or tissue with at least 2 cell lines differing in genotype or karyotype, derived from a single zygote. MRNA. mRNA: Messenger ribonucleic acid; the complementary strand of RNA transcribed from DNA and translated by the ribosomes into proteins. MULTI-LOCUS PROBE. A probe that hybridizes to a number of different sites in the genome of an organism. MULTIGENIC. Many genes are involved in the expression of a trait. MULTIPOINT (MULTILOCUS) LINKAGE ANALYSIS: The determination of the order and map distances of many loci on a chromosome at one time. MURINE. Relating to mice or rats. MYCELIUM: A mass of interwoven thread-like filaments of a fungus or bacteria. MYCOBACTERIUM: named after fungus (= myco, Latin). Primarily characterized by their ability to be stained by the acid-alcohol fast reaction MYCORRHIZAE. Fungi that form symbiotic relationships with roots of more developed plants. MYELOMA. A tumour of plasma cells, generally secreting a single species of immunoglobulin. N (AMINO) TERMINUS: The first amino acid(s) of a protein. NAD/NADH (NICOTINAMIDE ADENINE DINUCLEOTIDE): A compound used in some cellular energy processes. NADH carries a greater reducing potential than does ATP (One NADH can convert 3 ATDP to ATP), and so it is used for reducing potential for high-energy metabolic conversions. The actual compound is one AMP bonded to a nucleotide (nicotinamide) which is not a component of DNA or RNA. NEMO/IKK-gamma. NEMO (NF-kB Essential Modifier, found in mouse) and its human homologue IKK-gamma are part of the IKK complex and are essential in the acivation of NF-kB. They probably link IkB kinases (IKKs) to upstream activators. NEOMYCIN PHOSPHOTRANSFERASE: An enzyme that inactivates the antibiotics neomycin and kanamycin. This enzyme is often used as a selective marker for transgenic plants. NEPHRIDIUM. A general term for an invertebrate excretory organ as found in the segmented worms and mollusks NEUROFIBROMIN. The protein product of the neurofibromatosis type 1 gene. NEUTROPHIL. A type of leukocyte (white blood cell) involved in early inflammatory response. NEWMAN PROJECTION: a projection obtained by viewing along a carbon-carbon single (double) bond. NF-kB. NF-kB is a transcription factor that coordinates the activation of numerous genes in response to pathogenes and pro-inflammatory cytokines. NF-kB is critical for proper immune function, cell growth and survival, and anomalous activation is associated with inflammatory and neoplastic diseases and viral infection. NF-kB is activated by several exogeneous stimuli. NGF RECEPTOR FAMILY. Nerve Growth Factor receptor family. NICK TRANSLATION. A procedure for making a DNA probe in which a DNA fragment is treated with DNase to produce single-stranded nicks, followed by incorporation of radioactive nucleotides from the nicked sites by DNA polymerase I. NICK: break phosphodiester bond in backbone of one of the strands of a duplex DNA molecule. NICKED CIRCLE (relaxed circle). During extraction of plasmid DNA from the bacterial cell, one strand of the DNA becomes nicked. This relaxes the torsional strain needed to maintain supercoiling, producing the familiar form of plasmid. NIK. NF-kB-inducing kinase, which is activated by TRADD or TRAFs upon TNFR- or IL-ligation. NIK is an essential component in the phosphorylation of IKKs. NITROCELLULOSE. A membrane used to immobilize DNA, RNA, or protein, which can then be probed with a labeled sequence or antibody. NITROGEN FIXATION: Conversion of atmospheric nitrogen to ammonia. Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which is found only in prokaryotes. NITROGENOUS BASES. The purines (adenine and guanine) and pyrimidines (thymine, cytosine, and uracil) that comprise DNA and RNA molecules. NK cell. Naturally occurring, large, granular, lymphocyte-like killer cells that kill various tumour cells; they may play a role in resistance to tumours. Also, they participate in ADCC. They do not exhibit antigenic specificity, and their number does not increase by immunization. NLS. Nuclear Localization Signals can be located almost anywhere in the aminoacid sequence and generally consists of a short sequence (4 to 8 aa) which is rich in the positively charged aminoacids lysine and arginine and frequently contains proline. NMDA RECEPTOR. The N-methyl-D-Aspartate receptor is a subtype of glutamate-activated ionotropic channels, that is implicated in synaptic mechanisms underlying learning, memory and the perception of pain. It is also believed to be a target of the intravenous general anaesthetic agent ketamine and possibly nitrous oxide. Also xenon was reported to exert its anaethetic effects by inhibiting NMDA receptors. NOD BOX: A DNA sequence that controls the transcriptional regulation of Rhizobium nodulation genes. NONDISJUNCTION. The failure of homologous chromosomes (in mitosis or meiosis 1) or sister chromatics (in meiosis 11) to separate properly into different progeny cells. NONPENETRANCE. Lack of clinical expression of the mutant phenotype in an individual with the appropriate genotype. NORTHERN BLOTTING: Similar to Southern blotting, except that RNA that has been separated by gel electrophoresis is transferred from a gel onto a matrix such as a nitrocellulose or nylon membrane, and the presence of a specific RNA molecule is detected by DNA-RNA hybridization. NOTOCHORD. a stiff dorsal rod found in all chordates at some devlopmental stage; the notochord is replaced by the vertebral column in most chordates NUCLEASE. A class of enzymes that degrades DNA and/or RNA molecules by cleaving the phosphodiester bonds that link adjacent nucleotides. In deoxyribonuclease (DNase), the substrate is DNA. In endonuclease, it cleaves at internal sites in the substrate molecule. Exonuclease progressively cleaves from the end of the substrate molecule. In ribonuclease (RNase), the substrate is RNA. In the S1 nuclease, the substrate is single-stranded DNA or RNA. NUCLEIC ACIDS. The two nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are made up of long chains of molecules called nucleotides. NUCLEOPHILE: a substance which donates a pair of electrons in the reaction considered. NUCLEOPHILIC SUBSTITUTION: an overall reaction in which a nucleophile reacts with a compound displacing another nucleophile. Such reactions commonly occur in aliphatic chemistry. If the reaction is unimolecular they are known as SN1 reactions; for reactions which are bimolecular, they are known as SN2 reactions. NUCLEOSIDE: A base (purine or pyrimidine) that is covalently linked to a five-carbon (pentose) sugar. NUCLEOTIDE: A nucleoside with one or more phosphate groups linked to the 5' carbon of the pentose sugar. Ribose- containing nucleosides are often called ribonucleoside monophosphate (NMP), ribonucleoside diphosphate (NDP), or ribonucleoside triphosphate (NTP). When the nucleoside contains the sugar deoxyribose, the nucleotides are called deoxyribonucleoside mono-, di-, or triphosphates (dNMP, dNDP, or dNTP). OLIGONUCLEOTIDE LIGATION ASSAY (OLA): A diagnostic technique for determining the presence or absence of a specific nucleotide pair within a target gene which indicates whether a gene is wild type (normal) or mutant (defective). OLIGONUCLEOTIDE: A short molecule (usually 6 to 100 nucleotides) of singlestranded DNA. Oligonucleoticles are sometimes called oligodeoxyribonucleotides or oligomers and are usually synthesized chemically. OLIGOPROBE. A short DNA probe whose hybridization is sensitive to a single base mismatch. ONCOGENE: A gene, one or more forms of which is associated with cancer. Many oncogenes are involved, directly or indirectly, in controlling the rate of cell growth. OPEN READING FRAME (ORF). a DNA sequence which is believed, on the basis of statistical evidence, to code for protein, but for which no matching protein or mRNA is known. ORFs can often be confirmed by matching their sequences to a database of known genes or EST's. OPERATOR. A prokaryotic regulatory element that interacts with a repressor to control the transcription of adjacent structural genes. OPERON: A cluster of genes that are coordinately regulated. OPINE: The condensation product of an amino acid with either a keto acid or a sugar. OPSONIN. A substance, usually antibody or complement component, which coats a particle such as a bacterium and enhances phagocytosis by phagocytic cells. OPSONIZATION. Literally means "preparation for eating". The coating of a bacterium with antibody and/or complement that leads to enhanced phagocytosis of the bacterium by phagocytic cells. OPTICAL ACTIVITY: the property of certain substances to rotate plane polarized light. It is associated with asymmetry. Compounds that possess a chiral carbon atom of all the same 'handedness' will rotate plane polarized light. Isomers that rotate light in equal but opposite directions are sometimes called 'optical isomers', although the better term to use is 'enantiomers'. ORGANELLES. Membrane-bound intracellular, cytoplasmic structures having specialized functions, e.g., mitochondria, plastics, Golgi apparatus, lysosomes. ORGANOCHEMICAL NOMENCLATURE: The number of carbons and associated names are: meth-: 1; eth-: 2; prop-: 3; but-: 4; -ane: no non-hydrogens; -ol: alcohol; -diol: two alcohols; -anate, -oic acid: carboxylic acid (COOH); -anone: ketone (C=O); -amine: NH2; -ene: carbonn-carbon double bond (C=C); Phen-: benzyne; Phosphate: P(O4)2-; -ose: Sugar (CH2O)n; Deoxy sugars are missing one OH group; Sulfate: SO42-; Sulfide: -SH; -ase: enzyme. ORIGIN OF REPLICATION (ori): The nucleotide sequence at which DNA synthesis is initiated. OUTBRED MOUSE STRAINS. Strains of mice propagated by nonstandardized matings. These mice retain substantial genetic variability. OVERLAPPING READING FRAMES. Start codons in different reading frames generate different polypeptides from the same DNA sequence. OXIDATION: a chemical process in which the proportion of electronegative substituents in a compound is increased, or the charge is made more positive, or the oxidation number is increased. P-BR322. A derivation of ColE1, one of the first plasmid vectors widely used. P-UC. A widely used expression plasmid containing a -galactosidase gene. P1 ARTIFICIAL CHROMOSOME (PAC): A plasmid vector system based on bacteriophage P1 that uses electroporation for introducing a vector with a large DNA insert (100 to 300 kb) into Escherichia coli. P1 CLONING SYSTEM: A plasmid vector system based on bacteriophage P1 that uses in vitro bacteriophage P1 packaging for introducing a vector with a large DNA insert (80 to 100 kb) into Escherichia coli. P1-DERIVED ARTIFICIAL CHROMOSOME (PAC): A vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. Based on bacteriophage (a virus) P1 genome. P14ARF. p14ARF (or just ARF) is a human tumor-suppressor gene (the mouse homolog is p19ARF); it is activated by E2F-1 and stabilizes p53. Abnormal proliferation (due to defect of Rb, expression of oncogenes such as Ras, E1A, or Myc) results in deregulated E2F-1 activity, which induces p14ARF and stabilizes p53. This would lead to cell-cycle arrest or apoptosis unless a second lesion occurred such as mutation in p14ARF or p53 itself. P16INK4A. p16INK4a is a tumor-suppressor which inhibits the cyclin-dependent kinases 4 and 6. Its inhibitory effect results from its binding to CDk4/6 and by this preventing the formation of the Cdk4/6-cyclin D complex. INK4 inhibitors (p16INK4a and the related p19INK4a) also distort the Cdk4/6 kinase catalytic cleft and interfere with its ATP binding. P35. Caspase-inhibitor from insect Baculovirus; inhibits ICE family members with broader specificity than CrmA: it inhibits Caspase-1 and caspase-3 equally well. P53. p53 is a tumor-suppressor gene which codes for a transcriptionally active protein involved in cell cycle arrest, DNA repair and apoptosis. Almost 50% of human cancers contain a p53 missense mutation -- including cancers of the breast, cervix, collon, lung, liver, prostate, bladder, and skin -- and these cancers are more aggressive, more apt to metastasize, and more often fatal. A number of tumor-promoting viruses and environmental carcinogens act via p53. Carcinogenic aflatoxins produced by fungi that contaminate foods such as corn and peanuts are known to alter one specific amino acid in p53, while carcinogens in cigarette smoke also cause a characteristic alteration. Strains of human papilloma virus (HPV) linked with cervical cancer -- in particular HPV 16 and 18 -- produce proteins that promote the destruction of p53. Two other DNA tumor viruses -- simian virus 40 and adenovirus -- also produce proteins that target p53, eliminate its activity as a transcription factor, and initiate cell transformation. P53 knockout mice are highly susceptible to spontaneous tumor formation. Because p53 suppresses abnormal cell proliferation, it may represent an important mechanism for protection against cancer. p53 is induced by DNA damage or stress (heat shock, viral infection) and results in G1 cell cycle arrest or apoptosis. Several response genes (p21, mdm-2, GADD45, bax ...) have been identified that are transcriptionally activated by p53, but p53 also can repress transcription of genes with promoters lacking p53-binding sites (e.g. hsp70, c-fos, c-jun, Rb, bcl-2..) In apoptosis, p53 may also have transcription-independent functions. When a mutation in the p53 gene results in the substitution of one amino acid for another, p53 loses its ability to block abnormal cell growth. Indeed, some mutations produce a p53 molecule that actually stimulates cell division and promotes cancer. P73. p73 is a homologue of p53; p73 can induce cell cycle arrest and apoptosis. It also transcriptionally induces the expression of some (but not all) known p53 target genes such as p21. PAC T.he artificial chromosome vector derived from the temperate bacteriophage, P1, used for cloning 100- to 200-kb DNA fragments. PALINDROMIC SEQUENCES: Complementary DNA sequences that are the same when each strand is read in the same direction (e.g., 5' to 3'). PALISADE PARENCHYMA. the major photosynthetic layer of a leaf characterized by tightly packed columns of parenchymal cells just beneath the upper dermal layer PARACOCCUS DENITRIFICANS: A strong denitrifyer. PARASPORAL CRYSTAL: Tightly packaged insect protoxin molecules that are produced by strains of Bacillus thuringiensis during the formation of resting spores. PARATOPE. An antibody combining site that is complementary to an epitope. PARENCHYMA. the undifferentiated ground tissue in plants which is capable of some mitotic activity, especially in wound-healing. This tissue is also involved in storage of nutrient and in photosyntesis. PARP. Poly(ADP-Ribose) Polymerase; PARP catalyses the poly(ADP-ribosyl)ation (PARation) of nuclear proteins such as histones, topoisomerases I and II, SV40T antigen, DNA polymerase alpha, PCNA, and it also automodifies itself. PARP is activated following DNA strand breakage during DNA repair. PARP also was reported to modify p53 early during apoptosis and by this possibly stabilizing p53. At later stages PARP is cleaved (= inactivated) by caspase-3 and PAR is removed from p53, concomitant with the onset of the execution phase of apoptosis. PARP-/- fibroblasts did not show PARation and no signs of apoptosis after anti-Fas treatment, suggesting an essential role for PARP and PARation in the early stages of apoptosis PARTIAL DIGEST: Treatment of a DNA sample with a type II restriction endonuclease under conditions that result in a limited number of cuts in each DNA molecule to yield many possible combinations of cleaved pieces in the final sample. PASSIVE IMMUNIZATION. Immunization by the administration of preformed antibody into a nonimmune individual. PBL. Peripheral Blood Lymphocyte. PCD. Programmed Cell Death: the term programmed cell death is usually reserved for physiological conditions during which disposal of cells takes place, such as development and morphogenesis, clonal selection of lymphocytes, and cell renewal in epithelia. On the contrary, the term apoptosis indicates a form of active cell death triggered by pathological conditions such as inflammation, cancer, viral infections, or exposure to a wide variety of chemical and physical stimuli. PENETRANCE: A certain fraction, usually expressed as a percentage, of individuals with a mutant gene(s) at a locus that show the expected abnormal (mutant) phenotype. PEP. Abbreviation for primer extension preamplification. PEPSIN. enzymes secreted by the mammalian stomach lining which assist in digestion of proteins PEPTIDE BOND: The covalent bond between the free carboxyl group of the a carbon of one amino acid and the free amino group of the a carbon of an adjacent amino acid in a peptide or protein. PEPTIDE EXPRESSION LIBRARY. A collection of peptide molecules in which the amino acid sequences are varied and which are produced by recombinant cells. PEPTIDE FINGERPRINT. The chromatographic pattern of peptides obtained after partial hydrolysis of a protein or peptide. The technique also may be applied to DNA and RNA. PEPTIDE: A short chain of amino acids that are linked with peptide bonds. PEPTIDOGLYCAN: A part of the cell wall which is a rigid layer comprised of sugar and amino acid residues. The term actually refers to the chemical structure of this wall. PEPTIDYL (P) SITE: The portion of a ribosome where the tRNA with the peptide chain participates in peptide bond formation with the aminoacyl-tRNA during translation. PEPTIDYL-tRNA: The tRNA that has a growing peptide chain attached to it during translation. PERGONAL. This is a drug used to stimulate ovulation. It contains equal amounts of FSH and LH. It is administered by injection and is used to stimulate the development of the follicle and the egg in the ovary in women undergoing ovulation induction. This preparation is also used in men with infertility due to primary or secondary problems of sperm production to stimulate sperm production. PERICYCLE. A layer of cells just inside the endodermis of a root that may become meristematic and begin dividing again. PERINATOLOGIST. This is an Obstetrician/Gynecologist who has had extra training in maternal fetal medicine. They treat high risk pregnant women and manage their pregnancies and deliveries. PERIPLASM: The space (periplasmic space) between the cell (cytoplasmic) membrane of a bacterium or fungus and the outer membrane or cell wall. PEROXISOMAL ENZYMES. Enzymes localized to the peroxisomes. These enzymes are initially synthesized by the free polyribosomes and then enter the cytoplasm and eventually are localized to the peroxisomes. There are at least 40 enzymes. Some are involved in the production and decomposition of hydrogen peroxide and some are concerned with lipid and amino acid metabolism. PEROXISOME. A subcellular organelle surrounded by a single membrane containing at least 40 enzymes involved in energy production. PHAGOCYTOSIS. The engulfment of a particle or a microorganism by leukocytes. PHARYNGEAL SLITS. the numerous openings between the throat (=pharynx) and exterior which are present at some developmental stage of all chordates. PHASE STATE: The coupling or repulsion of two linked genes. PHASE-KNOWN: A double heterozygous genotype that is known to be in either a cis or trans configuration. PHASE-UNKNOWN: The gene arrangement of a double heterozygous genotype that is not known. PHENETICS. An approach to taxonomy based on measurable similarities and differences in phenotypic characters, but without consideration of homology, analogy, or phylogeny. Numerical taxonomy, where many, many characters are measured on all taxa, is a form of phenetics. PHENOCOPY: A nongenetic condition that closely resembles a genetic disorder. PHENOTYPE: An observable feature or set of traits that is determined by a gene or combination of genes of an organism. PHENYLKETONURIA (PKU): An autosomal recessive disorder in humans that is due to the lack of the liver enzyme phenylalanine hydroxylase and that causes phenylalanine to accumulate. PHLOEM. the vascular tissue in plants which transports food from the leaf to the roots. Phloem is living tissue PHOSPHATASE. An enzyme that hydrolyzes esters of phosphoric acid, removing a phosphate group. PHOSPHODIESTER BOND. A bond in which a phosphate group joins adjacent carbons through ester linkages. A condensation reaction between adjacent nucleotides results in a phosphodiester bond between 3' and 5' carbons in DNA and RNA. PHOSPHOLIPID: Lipids consisting of a phosphate-containing group and two fatty acids, each ester-linked to a glycerol PHOSPHOROTHIOATE LINKAGE: The linkage between nucleotides after a sulfur group replaces an available oxygen of a phosphodiester linkage. PHOSPHORYLATION. The addition of a phosphate group to a compound. PHOTOPERIODISM. the ability of organisms to read the light:dark cycle when making seasonal adjustments PHYTOCHROME. a light-sensitive pigment found within the plant cell. Phytochromes are involved in a number of light-related events, such as seasonal flowering, but are not considered hormones. PHYTOHEMAGGLUTININ. Lectin isolated from the red bean used to agglutinate red blood cells and stimulate lymphocytes to divide; used in preparation of peripheral blood karyotypes. PINOCYTOSIS. Ingestion of liquid or very small particles by vesicle formation in a cell. PITUITARY GLAND. A small hormone producing gland just beneath the hypothalamus at the base of the brain. The hormones produced control the ovaries, the thyroid and the adrenal glands of the woman. FSH, LH and TSH are some of the hormones produced. Disorders of this gland leads to irregular or absent ovulation in the female and abnormal or absent sperm production in the male. PLASMA CELL. End-stage differentiation of a B cell to an antibody-producing cell. PLASMID. A small circular piece of bacterial or yeast DNA which is found in the cytoplasm and which is replicated independently of the rest of the cell's genome. Plasmids are used to establish a transgenic strain. typically carries one or more genes encoding antibiotic resistance proteins. A store of ancient genetic material not well understood. PLASMODESMATA. the pores between two plant cells which permit cytoplasmic flow between adjacent cells. Plasmodesmata are not present in animals cells. PLASMOVIRUS; A combined retrovirus packaging-and-vector system that is confined to a plasmid. PLASTID: In plants, a double-membrane-bound organelle such as a chloroplast. PLATELET-DERIVED GROWTH FACTOR (PDGF). A protein, produced by platelets and other cells, that strongly stimulates cell growth and division and is involved in normal wound healing. The gene for PDGF is identical to the proto-oncogene sis. PLEIOTROPHY. The effect of a particular gene on several different traits. PML GENE. The PML gene was first identified as being translocated (and fused with the retinoic acid receptor alpha, RAR-alpha) in acute promyelocytic leukaemia (APL). PML encodes a cell growth and tumor suppressor which was reported to be a mediator of multiple apoptotic signals, including Fas, TNF-alpha, and interferons type I and II. PML was reported to be required for caspase-1 and -3 activation upon exposure to these stimuli. PML also might be involved in the expression of genes required for the formation of functional MHC class I receptors: malfunction of PML thus may affect the susceptibility of tumor cells to be recognized by T cells, what may allow tumors to escape the immune system POLLEN: Microspores of plants that carry male gametes. POLY(A) POLYMERASE. Catalyzes the addition of adenine residues to the 3' end of pre-mRNAs to form the poly(A) tail. POLYACRYLAMIDE GEL ELECTROPHORESIS. Electrophoresis through a matrix composed of a synthetic polymer, used to separate proteins, small DNA, or RNA molecules of up to 1000 nucleotides. Used in DNA sequencing. POLYADENYLATION SIGNAL: A sequence that terminates transcription and provides a recognition site at the end of an mRNA for the enzymatic addition of adenine residues. POLYADENYLATION. The addition of approximately 200 adenosine residues at the 3' end of messenger RNAs, apparently involved in their transport of the nucleus and stability. POLYADENYLATION; POLY(A) TAILING: Addition of adenine residues to the 3' end of eukaryotic mRNAs. Adenine-rich 3'-terminal segment is called a poly(A) tail. POLYCISTRONIC RNA: An mRNA that encodes two or more proteins. POLYCLONAL ACTIVATOR. A substance that induces activation of many individual clones of either T or B cells. POLYCLONAL ANTIBODY: A serum sample that contains antibodies that bind to different antigenic determinants of one antigen. POLYGENIC. Controlled by or associated with more than one gene. POLYHYDROXYALKANOATE: Biodegradable polymers produced by microorganisms as a carbon and energy storage material. POLYKETIDE: A class of antibiotics Polyketide synthase. An enzyme involved in the biosynthesis of polyketicle antibiotics. POLYLINKER (MULTIPLE CLONING SITE): Synthetic DNA sequence that contains a number of different restriction endonuclease sites. POLYLINKER. A short DNA sequence containing several restriction enzyme recognition sites that is contained in cloning vectors. POLYMERASE (DNA). Synthesizes a double-stranded DNA molecule using a primer and DNA as a template. POLYMERASE CHAIN REACTION (PCR). a technique for making many copies of a specific DNA sequence. The reaction is initiated using a pair of short primer sequences which match the ends of the sequence to be copied. Thereafter, each cycle of the reaction copies the sequence between the primers. Primers can bind to the copies as well as the original sequence, so the total number of copies increases exponentially with time. POLYMORPHIC SITE (LOCUS): A chromosome location that has two or more identifiable allelic DNA sequences that each occur with a frequency of 1% (0.01) or greater in a large population. POLYMORPHONUCLEAR LEUKOCYTE. White cell, granular cytoplasm. Neutral staining (neutrophil) - most frequent, phagocytic. Basophilic staining - basophil q.v. Eosinophilic staining - eosinophil q.v. POLYPEPTIDE (PROTEIN): Linear series of amino acids linked together with peptide bonds. POLYPLOID. A multiple of the haploid chromosome number that results from chromosome replication without nuclear division. POLYSACCHARIDE. A polymer composed of multiple units of monosaccharide (simple sugar). POLYSOMES (POLYRIBOSOMES). Structures composed of multiple ribosomes attached to mRNA in the process of translation. POLYVALENT VACCINE. A recombinant organism into which has been cloned antigenic determinants from a number of different disease-causing organisms. POSITIONAL GENE CLONING: A strategy for isolating an unknown disease gene. The disease gene is mapped to a chromosome site. A contig or genomic clone that covers the site of the disease gene is tested for exons. Examination of exons and mutation detection assays establish which gene is the disease gene. POSITIONAL-CANDIDATE GENE CLONING: A strategy for isolating an unknown disease gene. The disease gene is mapped to a chromosome site. The genes and expressed sequence tags that have been mapped to the same interval (bin) as the disease gene become candidates for the disease gene. Examination of exons and mutation detection assays establish which gene is the disease gene. POSITIVE-NEGATIVE SELECTION: A protocol that both selects for cells that carry a DNA insert integrated at a specific targeted chromosomal location (positive selection) and selects against cells that carry a DNA insert integrated at a nontargeted chromosomal site (negative selection). POSTTRANSLATIONAL MODIFICATION: The specific addition of phosphate groups, sugars (glycosylation), or other molecules to a protein after it has been synthesized. PREDNISONE. This is a steroid that blocks inflammation of an allergic reaction. A common reaction from this drug is bloating. It is a drug that can cause many side effects. Ask your doctor many questions about its many side effects. PRIMARY LYMPHOID ORGANS. Organs in which the maturation of T and B lymphocytes take place and antigen-specific receptors are first acquired. PRIMARY RESPONSES. The immune response to a first encounter with antigen. The primary response is generally small, has a long induction phase or lag period, consists primarily of IgM antibodies, and generates immunologic memory. PRIMER: A short oligonucleotide that hybridizes with a template strand and provides a 3'-hydroxyl end for the initiation of nucleic acid synthesis. PRIMERWALKING: A method for sequencing long (>1 kb) cloned pieces of DNA. The initial sequencing reaction reveals the sequence of the first few hundred nucleotides of the cloned DNA. On the basis of these data, a primer that contains about 20 nucleotides and is complementary to a sequence near the end of sequenced DNA is synthesized and used for sequencing of the next few hundred nucleotides of the cloned DNA. This procedure is repeated until the complete nucleotide sequence of the cloned DNA is determined. PROKARYOTES: Organisms, usually bacteria, that have neither a membrane-bound nucleus enclosing their chromosomes nor functional organelles such as mitochondria and chloroplasts. PROMOTER. A region of DNA extending 150-300 bp upstream from the transcription start site that contains binding sites for RNA polymerase and a number of proteins that regulate the rate of transcription of the adjacent gene. PRONUCLEUS. Either of the two haploid gamete nuclei just prior to their fusion in the fertilized ovum. PROPHAGE: A repressed or inactive state of a bacteriophage genome that is maintained in a bacterial host cell as part of the chromosomal DNA. PROTEASE INHIBITOR: A protein that can form a tight complex with a protease and block its activity. PROTEASE: An enzyme that hydrolyzes peptide bond linkages and cleaves proteins into smaller peptides. PROTECTING GROUP: a group that is used to protect a functional group from unwanted reactions. After application the protecting group can be removed to reveal the original functional group. PROTEIN KINASE. An enzyme that adds phosphate groups to a protein molecule at serine, threonine, or tyrosine residues. PROTEINACEOUS INFECTIOUS PARTICLE (prion). A proposed pathogen composed only of protein with no detectable nucleic acid and which is responsible for Creutzfeldt-Jakob disease and kuru in humans and scrapie in sheep. PROTEOLYTIC. The ability to break down protein molecules. PROTO-ONCOGENES. Normal genes that are found in normal eukaryotic cells concerned with various aspects of cell division. If amplified, mutated, rearranged, or picked up by a retrovirus, they may give rise to oncogenes that can cause cancer. PROTOPLAST: A bacterial, yeast, or plant cell that has had its cell wall removed either chemically or enzymatically. PSEUDOAUTOSOMAL REGION. The distal tip of the Y chromosome short arm, which undergoes crossover with the distal tip of the X chromosome short arm during meiosis in the male. PSEUDOMONAS AERUGINOSA: One bacteria which can cause diarrhea or infection by action of it's toxin, which kills skin cells. Fluorescent. PSEUDOMONAS AERUGINOSA: One bacteria which can cause diarrhea or infection by action of it's toxin, which kills skin cells. Fluorescent. PSEUDOMONAS FLUORESCENS: Non-pathogenic and fluorescent. PSEUDOMONAS PUTIDA: Best known for growing on most any organic compound, especially aromatics. PSEUDOMONAS SACCHAROPHILA: A bacterium widely studied for metabolism and metabolic enzymes. PSEUDOMONAS SYRINGAE. The genetically engineered strain of this bacteria lacks a cell-surface protein that helps ice crystals to form. Spraying these bacteria on crops may prevent freezing-related damages. PSEUDOMONAS: Motile, non-spore forming, straight or curved rods (bacteria) which are heterotrophic aerobes (eat organics, and never ferment). PSEUDOTYPE FORMATION (PHENOTYPIC MIXING): The packaging of the genome of one virus in the envelope or capsid protein of another virus. PSYCHROPHILE: can grow at temperatures as low as 0' to 5'C. PT PORE. Permeability Transition pore; supposedly involved in the loss of the mitochondrial transmembrane potential and the release of cytochrome c into the cytosol. The PT pore includes VDAC, ANT and cyclophilin D. PTEN. PTEN is a tumor suppressor gene that codes for a phosphatase; it dephosphorylates phosphatidylinosyol-3,4,5-trisphosphate (PIP3) to PIP2. Thus PTEN activity controls the PIP3 pathway and by this downregulates the activity of involved kinases such as Akt/protein kinase B (PKB). PTEN knockout in mice results in embryonic lethality, whereas Pten heterozygous mice display hyperplastic/dysplastic features, features typical for autoimmune disorders and high tumor incidence. AICD and Fas-dependent apoptosis of peripheral T cells from Pten+/- mice is impaired due to the disregulation of the PI3-kinase/Akt dependent patheway PULSED FIELD ELECTROPHORESIS. An electrophoretic technique that allows the separation of relatively long (>5,000 kb) sequences of DNA. PURINE: Fusion of a pyrimidine and an imidazole ring, e.g., adenine or guanine. PYKNOSIS. Pyknosis describes the observation of condensed nuclei with clumped and condensed chromatin as a sign of cell death. Pyknosis is often accompanied by 'karyorrhexis'. A pyknosis inducing factor was identified as Acinus ('apoptotic chromatin condensation inducer in the nucleus'), which is the precursor of an active chromatin condensating factor. Acinus is cleaved by caspase-3 PYRIMIDINE: A nitrogen-containing, single-ring, basic compound that occurs in nucleic acids. The pyrimidines in DNA are cytosine and thymine; in RNA, cytosine and uracil. PYROGEN: causes fever Q-BANDING. The pattern of bright and dim fluorescent crossbands seen on chromosomes under ultraviolet light after quinacrine mustard staining. QUASIDOMINANCE. The pattern of inheritance produced by the mating of an affected homozygote with an individual heterozygous for the same recessive trait so that homozygous affected members appear in 2 or more successive generations. QUENCHER: The portion of a molecule that can quench fluorescence. R,S CONVENTION: a formal non-ambiguous, nomenclature system for the assignment of absolute configuration of structure to chiral atoms, using the Cahn, Ingold and Prelog priority rules. R-BANDING. A chromosome banding technique in which chromosomes are heated in a phosphate buffer; produces dark and light bands in patterns that are the reverse of those produced by G-banding. RACEMIC MIXTURE, RACEMATE: an equimolar mixture of the two enantiomeric isomers of a compound. [As a consequence of the equal numbers of laevo- and dextro-rotatory molecules present in a racemate, there is no net rotation of plane polarized light.] RADICAL: a term applied to an atom or molecule having one or more free valencies. RADIOALLERGOSORBENT TEST (RAST). A solid-phase radioimmunoassay for detecting IgE antibody specific for a particular allergen. RADIOIMMUNOASSAY (RIA). A widely used technique for measurement of primary antigen-antibody interactions, and for the determination of the level of important biological substances in mixed samples. It takes advantage of the specificity of the antigen-antibody interaction and the sensitivity that derives from measurement of radioactively labelled materials. RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD): A diagnostic procedure in which chromosomal DNA (usually from plants but sometimes from microorganisms or animals) is characterized by the DNA fragments that are synthesized when PCR is initiated after the addition of a single primer to the reaction mixture. RANDOM PRIMER METHOD: A protocol for labeling DNA in vitro. A sample of random oligonucleotides containing all possible combinations of nucleotide sequences is hybridized to a DNA probe. Then, in the presence of a DNA polymerase and the four deoxyribonucleotides (one of which is labeled), the 3'-hydroxyl ends of the hybridized oligonucleotides provide initiation sites for DNA synthesis that uses the separated strands of the probe DNA as a template. This reaction produces labeled copies of portions of the probe DNA. RAPID AMPLIFICATION OF cDNA ENDS (RACE): PCR used to generate double-stranded DNA (cDNA) from the 3' end (3'RACE) or the 5' end (5'RACE) of a specific mRNA. READ-THROUGH: Transcription or translation that proceeds beyond the normal stopping point because the transcription or translation termination signal of a gene is absent or mutated. READING FRAME. A series of triplet codons beginning from a specific nucleotide. Depending on where one begins, each DNA strand contains three different reading frames. REAGIN. Allergist's term for IgE antibodies. REC-A: recA catalyzes pairing of ssDNA with complementary dsDNA (recombinase),forms D loop , requires ATP hydrolysis, helical filament of recA around ssDNA, 6 recA monomers per turn, ssDNA is 50% more stretched out than regular beta-DNA,; filament has POLARITY, allows movement in 1 direction on dsDNA, movement requires ATP hydrolysis, 2 sites in recA, one binds ssDNA, other binds complementary strand. recA also a key part of the SOS response: DNA damage triggers an emergency response, group of >15 genes turned on following DNA damage expression kept low by lexA repressor (binds to promoter of each gene), when DNA damage occurs, get ssDNA, recA binds to it; ssDNA::recA filament binds lexA molecules, bound lexA is induced to degrade itself and other lexA molecules, reduces [lexA], can't bind to promoters of the SOS genes, expression of SOS genes now goes ahead. The RecA protein, a molecule of 38,000 Mr (125,126), is a multifunctional polypeptide directing a number of activities, none of which is completely understood in detail. It's central role in homologous recombination and DNA-damage repair has created considerable interest. Widespread distribution and evolutionary conservation of recA. RECBCD: recBCD generates ssDNA needed for recombination, 325kd complex which has nuclease + helicase activity, unwinding requires ATP, unwinding faster than rewinding, so makes a loop behind recBCD; cleavage at chi sequence, 8bp sequence, one chi every ~4.5kb on E. coli chromosome, makes single-strand cut next to chi site, continues to unwind, topo I, ruvABC involved in branch migration, ruvC is "resolvase", cleaves Holliday intermediate. RECESSIVE GENE: An allele that does not demonstrably contribute to the phenotype in a heterozygote. RECESSIVE(-acting) ONCOGENE, (anti-oncogene). A single copy of this gene is sufficient to suppress cell proliferation; the loss of both copies of the gene contributes to cancer formation. RECOGNITION SEQUENCE (site). A nucleotide sequence--composed typically of 4, 6, or 8 nucleotides--that is recognized by a restriction endonuclease. Type II enzyrnes cut (and their corresponding modification enzymes methylate) within or very near the recognition sequence. RECOMBINANT DNA. Hybrid DNA produced in a test tube by joining segments of DNA from natural or synthetic sources. These segments can then be inserted into the genetic material of an organism to introduce a novel function. RECOMBINATION FRACTION. In linkage analysis, the fraction of meiotic events that show a recombination between 2 loci. RECOMBINATION FREQUENCY. The frequency at which crossing over occurs between two chromosomal loci--the probability that two loci will become unlinked during meiosis. REDUCTION: chemical processes in which the proportion of more electronegative substituents is decreased, or the charge is made more negative, or the oxidation number is lowered. REGULATORY GENE. A gene whose protein controls the activity of other genes or metabolic pathways. REGULATORY PROTEIN: A protein that plays a role in either turning on or turning off transcription. REL PROTEINS. Family of structurally Related proteins which are the subunits of the NF-kB transcription factor. Five different Rel proteins (also called Rel/NF-kB proteins) have been identified so far: p50, p52, p65, Rel-B, and cRel. All those Rel proteins contain a conserved N-terminal region, called the Rel Homology Domain (RHD). RELAXED PLASMID. A plasmid that replicates independently of the main bacterial chromosome and is present in 10-500 copies per cell. RENATURE. The reannealing (hydrogen bonding) of single-stranded DNA and/or RNA to form a duplex molecule. REOVIRUS. The human reovirus is a double-stranded RNA virus. Since reovirus infections are in general asymptomatic and reovirus replication depends on an activated Ras signalling pathway it may be useful in tumor therapy since many tumors display increased ras activity. Indeed, reovirus was shown to selectively infect ras overexpressing tumor cells and suppress tumor growth REPLICA PLATING: The transfer of cells from bacterial colonies on one petri plate to another petri plate; the locations of the colonies that grow on the second plate correspond to those on the original (master) petri plate. REPLICATION FORK. The unwound region of the DNA double helix in which replication takes place. REPLICATION SEGREGATION. Refers to changes in the proportions of mitochondrial DNA alleles as the mitochondria reproduce. REPLICON. A unit of genetic material which behaves autonomously during replication of DNA. In bacterias, a whole chromosome is a replicon. In eukaryotes, chromosomes are divided into hundreds of replicons. Each replicon contains a segment beginning with a binding site for RNA polymerase. REPRESSOR. A DNA-binding protein in prokaryotes that blocks gene transcription by binding to the operator. REPRODUCTIVE IMMUNOPHENOTYPE. This checks for the presence of Natural Killer Cells. In most cases, Natural Killer Cells are good because they reduce the likelihood of developing cancer. In some cases excessive NK activity can kill the embryo or interfere with the endocrine system that produces hormones essential for pregnancy. At high Natural Killer Cell levels IVIg is prescribed. IVIg is made from pooled blood and is processed and washed so that it is free of HIV and other blood-borne illnesses (it comes out clear after processing). At lower levels of Natural Killer Cells, some doctors use prednisone, a steroid. These tests measure the following CD (Cell Designation) levels: CD-3 (normal 63-86); CD-4 (normal 31-53); CD-8 (normal 17-35); CD-19 (normal 3-8); C56 (normal 3-12) these are the Natural Killer Cells; CD3/IL2-R (normal 0-5); CD19/CD5 (normal 0-30), high numbers in this category interfere with the reproductive hormones necessary for pregnancy. REPULSION (TRANS CONFIGURATION): The phase state in which a dominant version and a recessive version of two different genes occur on the same chromosome. RESOLUTION: the separation of a racemate into its two enantiomers by means of some chiral agency. RESONANCE: the representation of a compound by two or more canonical structures in which the valence electrons are rearranged to give structures of similar probability. [The actual structure is considered to be a hybrid or the resonance forms.] RESPIRATORY BURST. Oxygen dependent increase in metabolic activity within phagocytic cells stimulated by bacteria or parasites, to be microbicidal. RESTRICTION DIGEST. The process in which DNA is exposed to restriction enzymes (restriction endonuclease), causing it to be cleaved into fragments of DNA called restriction fragments. RESTRICTION ENDONUCLEASE (enzyme). A class of endonucleases that cleaves DNA after recognizing a specific sequence, such as BamH1 (GGATCC), EcoRI (GAATTC), and HindIII (AAGCTT). Type I. Cuts nonspecifically a distance greater than 1000 bp from its recognition sequence and contains both restriction and methylation activities. Type II. Cuts at or near a short, and often symmetrical, recognition sequence. A separate enzyme methylates the same recognition sequence. Type III. Cuts 24-26 bp downstream from a short, asymmetrical recognition sequence. Requires ATP and contains both restriction and methylation activities. RESTRICTION ENZYMES. Bacterial enzymes that cleave DNA at very specific locations. RESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP): The occurrence of variations in the lengths of certain DNA fragments that are produced after cleavage with a type II restriction endonuclease. The differences in DNA lengths are due to the presence or absence of a specific restriction endonuclease recognition site(s) and are detected by DNA hybridization with DNA probes after separation by gel electrophoresis. RESTRICTION MAP: The linear array of restriction endonuclease sites on a DNA molecule. RESTRICTION SITE: The sequence of nucleoticle pairs in duplex DNA that is recognized by a type II restriction endonuclease. Sometimes called restriction enzyme site, restriction endonuclease site, or recognition site. RETICULOENDOTHELIAL SYSTEM. A network of phagocytic cells. RETROVIRUS. A member of a class of RNA viruses that utilizes the enzyme reverse transcriptase to reverse copy its genome into a DNA intermediate, which integrates into the hostcell chromosome. Many naturally occurring cancers of vertebrate animals are caused by retroviruses. REVERSE TRANSCRIPTASE: An RNA-dependent DNA polymerase that uses an RNA molecule as a template for the synthesis of a complementary DNA strand. REVERSE TRANSCRIPTION-POLYMERASE CHAIN REACTION (RT-PCR): A two-step protocol for synthesizing cDNA molecules. First, cDNA strands are synthesized in vitro by reverse transcriptase with oligo(dT) as a primer and mRNA as the template. Second, a specific cDNA strand is amplified by the polyrnerase chain reaction (PCR), with one primer directed to a sequence of the first cDNA strand and the other to a sequence of the complementary cDNA strand (second strand) that is synthesized during the first PCR cycle. REVERSIBLE PROCESS: a process in which the forward reaction can reach an equilibrium with the reverse reaction. RGD TRIPEPTIDE. Arginine-glycine-aspartate tripeptide motif which can be found in proteins of the extracellular matrix. Integrins link the intracellular cytoskeleton of cells with the extracellular matrix by recognizing this RGD motif. Without attachment to the extracellular matrix, cells normally undergo apoptosis ('anoikis'). Soluble RGD peptides induce apoptosis and might be used as drugs against angiogenesis, inflammation and cancer mestastasis. RHD. Rel Homology Domain (RHD), the conserved N-terminal domain of Rel/NF-kB proteins. It contains the DNA-binding and dimerization domains and the nuclear localization signal. RHIZOBIA. Bacteria in a symbiotic relationship with leguminous plants that results in nitrogen fixation. RHODOSPIRILLUM RUBRUM: This bacterial strain is studied for metabolism - it makes hydrogen when growing on light (it's a phototroph) with organic and amino acids as C- and N-sources. RHOGAM. The immunoglobulin, very similar to IVIg, that is given to Rh negative women carrying Rh positive infants to prevent her body from developing an immunity against the babies red blood cells. RIBOSE: The 5-carbon sugar component of RNA. RIBOSOMAL BINDING SITE (SHINE-DALGARNO SEQUENCE): Sequence of nucleotides near the F-phosphate end of a bacterial mRNA that facilitates the binding of the mRNA to the small ribosomal subunit. RIBOSOMAL RNA (rRNA). The RNA component of the ribosome. RIBOSOME-BINDING SITE. The region of an mRNA molecule that binds the ribosome to initiate translation. RIBOSOMES. Cytoplasmic organelles composed of ribosomal RNA and protein, on which polypeptide synthesis from messenger RNA occurs. RIBOZYME: An RNA molecule that has catalytic activity. RIBULOSE BISPHOSPHATE CARBOXYLASE (Rubisco): Most abundant enzyme in the world, it is found in all green plants and is responsible for the fixation of carbon dioxide in photosynthesis. RING CHROMOSOME. A structurally abnormal chromosome in which the end of each chromosome arm has been deleted and the broken arms have reunited to form a ring. RNA (RIBONUCLEIC ACID): polynucleotide that has ribose as its pentose sugar and uracil as one of its pyrimidines. RNA POLYMERASE: An enzyme that links an incoming ribonucleotide, which is determined by complementarity to a base in a template DNA strand, with a phosphodiester bond to the 3'-hydroxyl group of the last incorporated ribonucleotide of the growing RNA strand during transcription. ROLLING CIRCLE: A mode of DNA replication that produces concaterneric duplex DNA. ROTAMERS: isomers formed by restricted rotation. [See also conformational isomers.] S1 NUCLEASE: An enzyme that specifically degrades single-stranded DNA. SACCHARIFACTION: Hydrolysis of polysaccharides, after liquefaction, by glucoamylase to maltose and glucose. SACCHAROMYCES: These are yeasts which feed on sugars. SALMONELLA TYPHIMURIUM: Causes salmonella, but is not especially virulent, and therefore is nice for research. SALMONELLA: named after D. E. Salmon. Inhabitants of the intestinal tract of warm-blooded animals, grow on a wide variety of carbon and energy sources, cause diseases (pathogens). SARA. Smad Anchor for Receptor Activation, an anchor protein that recruits Smad2 and Smad3 to the TGF-beta receptor. SATELLITE DNA. A portion of the DNA that differs enough in base composition so that it forms a distinct band on cesium chloride gradient centrifugation; usually contains highly repetitive DNA sequences. SATELLITE RNA (viroids). A small, self-splicing RNA molecule that accompanies several plant viruses, including tobacco ringspot virus. SATURATED: the term given to organic molecules which contain no multiple bonds. SAWHORSE PROJECTION: the sideways projection of a carbon-carbon single bond and the attached substituents. SCAFFOLD. The nuclear structure observed when histones are experimentally removed from chromosomes. Thought to represent a structural component of the nucleus and of chromosome. SDS-PAGE: Sodium dodecyl sulfate-polyacrylamide gel electrophoresis. SECRETORY COMPONENT. A surface receptor on epithelial cells lining mucosal surfaces which binds dimeric IgA and transports it through the cell into mucosal secretions. SEGREGATION. The separation of allelic genes at meiosis. Because allelic genes occupy the same locus on homologous chromosomes, they pass to different gametes. SELECTABLE MARKER. A gene whose expression allows one to identify cells that have been transforrned or transfected with a vector containing the marker gene. SEMICONSERVATIVE REPLICATION. During DNA duplication, each strand of a parent DNA molecule is a template for the synthesis of its new complementary strand. Thus, one half of a preexisting DNA molecule is conserved during each round of replication. SENESCENCE (AGING): The last stage in the postembryonic development of multicellular organisms, during which loss of functions and degradation of biological components occur. SENSE MUTATION. A mutation that changes a termination (stop) codon into one that codes for an amino acid. Such a mutation results in an elongated protein. SEQUENCE HYPOTHESIS. Francis Crick's seminal concept that genetic information exists as a linear DNA code; DNA and protein sequence are colinear. SEQUENCE TAGGED SITE (STS): A short (200- to 500-bp) DNA sequence that occurs once in the genome and is identified by PCR amplification. SEQUENCE TAGGED SITE CONTENT MAPPING: Markers that are based on unique polymerase chain reaction primers that are used to determine shared sites among clones of a library, which in turn facilitates the assembly of a contig. SEROTYPE: Classification of an organism or protein on the basis of its interaction with antibodies. SERPINS. A family of serine protease inhibitors. SHEAR: The sliding of one layer across another, with deformation and fracturing in the direction parallel to the movement. SHIGELLA: named for K. Shiga, who isolated a species which causes dysentery. Just like Eschericia, they inhabit the intestinal tract of warm-blooded animals, grow on a wide variety of carbon and energy sources, but they are commonly pathogens. SHORT TANDEM REPEAT (STR) : DNA sequence with a sequential repeating set of two (di-), three (tri-), or four (tetra-) nucleotide pairs. SHORT TANDEM REPEAT POLYMORPHISM (STRP): Two or more short tandem repeats that differ from each other by the number of repeated nucleoticle units with each allelic DNA sequence occurring at a frequency of 1% or more in a large population. The difference in the lengths of allelic short tandem repeats is detected by gel electrophoresis following the polymerase chain reaction with primers that are complementary to unique DNA sequences that flank a short tandem repeat. SHORT TEMPLATE: A DNA strand that is synthesized during the polymerase chain reaction and has a primer sequence at one end and a sequence complementary to the second primer at the other end. SHUTTLE (BIFUNCTIONAL) VECTOR: A plasmid cloning vehicle, usually a plasmid, that can replicate in two different organisms because it carries two different origins of replication. SIDEROPHORE: A low-molecular-weight substance that binds very tightly to iron. SIGMA FACTOR: An accessory bacterial protein(s) that directs the binding of RNA polymerase to specific promoters. SIGNAL SEQUENCE (LEADER PEPTIDE): Segment of about 15 to 30 amino acids at the N terminus of a protein that enables the protein to be secreted (pass through a cell membrane). The signal sequence is removed as the protein is secreted. SIGNAL TRANSDUCTION. The biochemical events that conduct the signal of a hormone or growth factor from the cell exterior, through the cell membrane, and into the cytoplasm. This involves a number of molecules, including receptors, proteins, and messengers. SILENCER. The cis regulatory element that reduces transcription of a gene. SINGLE-STRAND CONFORMATION ANALYSIS/POLYMORPHISM (SSCA,SSCP): A mutation detection assay that is based on the conformation of single strands of DNA (ssDNA). If there is a nucleotide difference between the DNA molecules from two different sources, then following denaturation and gel electrophoresis the locations of the single strands in the two lanes of the gel will be different. SIX-CUTTER: A type II restriction endonuclease that binds and cleaves DNA at sites that contain six nucleotide pairs. SIZE MARKERS: A set of macromolecules of known relative molecular masses that are used to calculate the relative molecular masses of electrophoretically fractionated macromolecules. SKEWED X-INACTIVATION. A nonrandom pattern of inactivation of 1 of the X chromosomes in a female that can arise through a variety of mechanisms. When this occurs, the active X chromosome may bear the mutant allele and the female will show signs and symptoms of the disease. The female is called a manifesting heterozygote or a carrier. SLE. Systemic Lupus Erythematosus; autoimmune disease, antinuclear antibodies against blood cells and other tissues lead to the formation of soluble immune complexes which cause vascular inflammations. SLOW-REACTING SUBSTANCE OF ANAPHYLAXIS (SRS-A). A group of leukotrienes released by mast cells during anaphylaxis which induces a prolonged constriction of smooth muscle. This prolonged constriction is not reversible by treatment with antihistamines. SMAD/DPC4. Smads are pivotal to intracellular signalling by members of the TGF-beta family. Smad2 and Smad3 are receptor-regulated Smads that interact with, and become phosphorylated by, activated type-I receptor kinases. The phosphorylated Smad then binds Smad4, and this heteromeric complex is translocated to the nucleus where it controls the transcription of target genes which are leading to inhibition of proliferation in most normal cells. Smad was reported to induce p21waf1 expression. Smad/DPC4 is a tumor suppressor gene which is deleted or mutated in about 50% of pancreatic adenocarcinomas. SMALL NUCLEAR RNA (snRNA). Short RNA transcripts of 100-300 bp that associate with proteins to form small nuclear ribonucleoprotein particles (snRNPs), which participate in RNA processing. SODD. The Silencer of Death Domains (SODD) was isolated as a protein that prevents constitutive activation of TNF-R1. It interacts with the Death Domains of TNF-R1 and DR3 but not with those of Death Domain Receptors (DDRs) such as TNF-R2, Fas, DR4, or DR5. It was demonstrated that SODD interacts with a region of TNF-R1 that also interacts with TRADD. SODD and TNF-R1 are pre-associated in non-stimulated cells, and upon TNF treatment this SODD-TNF-R1 complex is rapidly disrupted. Overexpresion of SODD prevents TNF-induced cell death and activation of NF-kB SODIUM DODECYL SULFATE: An anionic detergent that denatures proteins. SOMATIC CELL HYBRID PANEL: A set of derived chromosome-specific hybrid cell lines that each carry a different portion of a particular chromosome. The members of such a panel have chromosomal deletions and, in some cases, carry translocated chromosomes that retain a segment of a particular chromosome. Ideally, the retained portions of the cell lines of a panel cover the entire chromosome. Also called somatic cell hybrid mapping panel, somatic cell deletion panel. SOUTHERN BLOTTING: A technique for transferring denatured DNA molecules that have been separated electrophoretically from a gel to a matrix (such as a nitrocellulose or nylon membrane) on which a hybridization assay can be performed. SPARGER: A device that introduces air into a bioreactor in the form of separate, fine streams. SPLICE SITE: The nucleotides at (1) the end of an exon and the beginning of an intron and (2) the end of an intron and the beginning of the next exon that are required for the joining of two exons and removal of an intron during the processing of a primary transcript to a functional mRNA. SPORE. a haploid cell formed following meiosis which then undergoes mitosis and gives rise to a haploid individual, such as the gametophyte in green algae or plants. In fungi, a haploid spore gives rise to a new mycelium. SSCP. Abbreviation for single-strand conformation polymorphism. SSOP. Sequence-specific oligonucleotide probe. Together with PCR-SSP, commonly used to type classical MHC genes following amplification by PCR reaction (see also serological typing). SSP. Sequence-specific primer. PCR-SSP is a common method to type classical MHC genes. STABILITY CONSTANT: when a complex is formed between a metal ion and an a ligand in solution, the equilibrium may be expressed by a constant which is related to the free energy change for the process: For: M + A = MA : - deltaG = RTlnK STANDARD METABOLIC RATE (SMR). the number of kilocalories an ectotherm requires to maintain minimum function at a defined environmental temperature. STAPHYLOCOCCUS: named for their appearance, like a bunch of grapes (Greek, staphyl). They're Gram-positive, non-motile, non-spore-forming and aerobic (but will ferment). STATIONARY PHASE. The plateau of the growth curve after log growth, during which cell number remains constant. New cells are produced at the same rate as older cells die. The assymptotic maximum of the hyperbolic tangent. STEADY STATE: In continuous fermentation, when the number of cells that are removed with the outflow is exactly balanced by the number of newly synthesized cells. STEREOSPECIFIC REACTIONS: reactions in which bonds are broken and made at a particular carbon atom and which lead to a single stereoisomer. If the configuration is altered in the process the reaction is said to involve inversion of configuration; if the configuration remains the same the transformation occurs with retention of configuration. STERIC HINDRANCE: the phenomenon of physical blockage of a particular site within a molecule by the presence of local atoms or groups of atoms. [As a consequence of steric hindrance, a reaction at a particular site will be impeded.] STICKY END. aka COHESIVE END. Overhanging ends of a double-stranded DNA molecule that are capable of hybridizing with complementary ends. STR. Abbreviation for short tandem repeat. These often serve as polymorphic markers. STREPTOCOCCUS PNEUMONIAE: Naturally found benignly in the respiratory system, but quite willing to turn pathogenic if your defenses are down, causing all sorts of problems, but especially pneumonia (Streptococcal pneumonia is often lethal). STREPTOCOCCUS: Some of the bad-boy bacteria in this genus cause various diseases, while some of the altar boy-bacteria are involved in making buttermilk and other fermented foods [link to fermented foods]. They are Gram-positive, non-motile, non-spore-forming and aerobic (but will ferment, producing lactic acid.) STREPTOCOCCUS: streptos is Greek for 'twisted', coccus is Greek for 'grain'. Some of the bad-boy bacteria in this genus cause various diseases, while some of the altar boy-bacteria are involved in making buttermilk and other fermented foods [link to fermented foods]. For the boring: they're Gram-positive, non-motile, non-spore-forming and aerobic (but will ferment, producing lactic acid.) STREPTOMYCES: streptos is Greek for 'twisted', myces is Latin for 'fungus'. Not a bit related to Streptococcus! Form branching filaments as they reproduce, and mostly noted for making antibiotics (Current favorites: Chloramphenicol, Erythromycin, Neomycin, Nystatin, Streptomycin, Tetracycline). STRINGENCY. Reaction conditions--notably temperature, salt, and pH--that dictate the annealing of single-stranded DNA/DNA, DNA/RNA, and RNA/RNA hybrids. At high stringency, duplexes form only between strands with perfect one-to-one complementarity; lower stringency allows annealing between strands with some degree of mismatch between bases. STRINGENT PLASMID. A plasmid that only replicates along with the main bacterial chromosome and is present as a single copy, or at most several copies, per cell. STRP. short tandem repeat polymorphism. STRUCTURAL ISOMERISM: isomers which differ in the order of bonding of the constituent atoms. SUBSTITUTION REACTIONS: reactions in which one atom or group of atoms is replaced by another atom or group of atoms. [See electrophilic substitutions and nucleophilic substitutions.] SUBTILISIN: A proteolytic enzyme usually found in Bacillus subtilis. SUCROSE DENSITY GRADIENT CENTRIFUGATION: A procedure used to fractionate mRNAs or DNA fragments on the basis of size. SUPERCOILED PLASMID. The predominant in vivo form of plasmid, in which the plasmid is coiled around histone-like proteins. Supporting proteins are stripped away during extraction from the bacterial cell, causing the plasmid molecule to supercoil around itself in vitro. SUPERCOILED/SUPERTWISTED DNA. A closed circular DNA molecule in which the DNA molecule is further twisted on itself to form a more compact molecule. Left-handed (negative) supercoiling leads to a loosening of the strands of the double helix (underwinding). Positive supercoiling is not seen in vivo. (gamma-DNA) SUPERGENE. A group of neighboring genes on a chromosome that tend to be inherited together and sometimes are functionally related. SUPERNATANT. The soluble liquid of a sample after centrifugation or precipitation of insoluble solids. SUPPRESSION. A mechanism for producing a specific state of immunologic unresponsiveness by the induction of suppressor T cells. This type of unresponsiveness is passively transferable by suppressor T cells or their soluble products. SURVIVIN. Survivin is a member of the human IAPs. Elevated survivin expression was reported in most human tumors. In HeLa cells, survivin was found to be expressed in the G2/M phase of the cell cycle in a cycle regulated manner and to associate with the microtubuli of the mitotic spindle in a specific and saturable reaction. Disruption of survivin-microtubuli interactions resulted in loss of anti-apoptotic activity of survivin and increased caspase-3 activation. Survivin may be required to counteract a constitutive pathway that induces apoptosis during mitosis SV40 T. The Simian virus large T antigen is a single dual purpose protein able to block both Rb and p53. SYMPORT. a membrane-bound carrier molecule which simultaneously transports two different solutes, such as a proton and sucrose or proton and auxin SYNAPSIS. The pairing of homologous chromosome pairs during prophase of the first meiotic division, when crossing over occurs. SYNCYTIOTROPHOBLAST. This is a specialized cell of the placenta (also a trophoblast) which acts like a dialysis membrane between the mothers blood and the babies blood, feeding the baby as well as removing waste products from the babies blood. SYNGENEIC. Refers to genetically identical members of the same species. T lymphocytes (T cells). White blood cells, produced in the bone marrow, that aid B cells in making antibodies to fight bacterial infections. They also are instrumental in rejection of foreign tissue, and may be important in the body's defense against cancer. Undergoes a developmental stage in the thymus. T-DNA (t-DNA, transfer DNA, tumor-DNA). The transforming region of DNA in the Ti plasmid of Agrobacterium tumefaciens. T-RNA (t-RNA, transfer RNA). The class of small RNA molecules that transfer amino acids to the ribosome during protein synthesis. See Transfer RNA. T-dependent antigen. An immunogen that is able to induce antibody synthesis only in the presence of lymphokines released by helper T cells. T-independent antigen. An immunogen which induces antibody synthesis in the absence of lymphokines released by T cells; the antibodies are generally only of the IgM isotype. T4 DNA LIGASE: An enzyme from bacteriophage T4-infected cells that catalyzes the joining of duplex DNA molecules and repairs nicks in DNA molecules. The enzyme joins a 5'-phosphate group to a 3'-hydroxyl group. T4 DNA POLYMERASE END LABELING: DNA that has been cut with a restriction endonuclease(s) is mixed with T4 DNA polymerase and one labeled deoxyribonucleotide, The 3' exonuclease activity of the T4 DNA polymerase removes deoxyribonucleotides from the 3' ends of the DNA fragments. Immediately after a deoxyribonucleotide that is the same as the deoxyribonucleotide in the reaction mixture is cleaved off, the T4 DNA polymerase activity incorporates a labeled deoxyribonucleotide from the reaction mixture. No further incorporation of deoxyribonucleotides occurs because there is only one kind of deoxyribonucleotide in the reaction mixture. TAP1. Transporter Associated with antigen Processing 1 (is induced by NF-kB). TAP belongs to the ABC family of ATP-dependent transporters. It transports peptides (which have been processed in the cytoplasm by the proteasome) into the ER, where the peptides are assembled into ternary complexes wit the alpha and beta2-m chains of the MHC1 for antigen presentation TAQ POLYMERASE. A heat-stable DNA polymerase isolated from the bacterium Therrnus aquaticus, used in PCR. Originally patented despite occuring naturally in hot springs. TATA BOX: The DNA sequence, to which RNA polymerase binds, that lies upstream from the site of initiation of transcription and ensures that transcription starts at a specified nucleotide. Also called a Pribnow box in prokaryotes and a Hogness box in eukaryotes after the researchers who discovered the function of the TATA box in prokaryotes and eukaryotes, respectively. TAUTOMERISM: a form of structural isomerism where the two structures are interconvertible by means of the migration of a proton. TCA CYCLE. The tricarboxylic acid cycle (also known as the Krebs cycle). A major metabolic pathway involved in aerobic cellular respiration (energy production) which takes place in the mitochondria of animal and plant cells. Pyruvic acid produced during glycolysis is converted to acetyl CoA which is then oxidized to CO2. The reducing power of the end products NADH and FADH2 are used in the synthesis of ATP by oxidative phosphorylation. TELOMERE. The end of a chromosome. TEMPLATE STRAND: The polynucleotide strand that a polymerase uses for determining the sequence of nucleofides during the synthesis of a new nucleic acid strand. TEMPLATE. An RNA or single-stranded DNA molecule upon which a complementary nucleotide strand is synthesized. TERMINATION CODON (TRANSLATIONAL STOP SIGNAL): A naturally occurring codon that does not base pair with the anticodon of any tRNA. Generally, the three codons in this class (UAA, UAG, and UGA) are used to terminate translation, although in some rare instances one of these codons does code for an amino acid. TGF-BETA SUPERFAMILY. Members of the Transforming Growth Factor beta family are cytokines that regulate the proliferation of cells; often they inhibit the cellular proliferation of normal cells. TH1 and TH2. Helper T cells; T cells that induce B cells to make antibody responses to antigens. Activated helper T cells express glycoprotein g39 which is a ligand for CD40 expressed on B cells: interaction of g39 with CD40 results in B cell activation, what is enhanced by cytokines and lymphokines expressed by T helper cells (IL-2, IL-4, IL-5 ...). Th1 cells enhance microbicidal action of monocytes and macrophages on intracellular microorganisms while Th2 cells diminish the potency of the cellular immune response initiated by Th1 cells. Th1 cells diminish, to some extent, the priming of naive T cells to develop into IL-4 producers. THERMOPHILE: A microorganism that grows optimally at high temperatures, usually above 50'C. Some thermophiles can grow at temperatures of 90' to 100'C. THIOBACILLUS DENITRIFICANS: Grows on carbon dioxide, using sulfur as an electron donor, and nitrate as an electron acceptor (i.e. S goes to SO4 while NO3 goes to NH3.) A very frugal organism. THIOBACILLUS: named for sulfur. These bacteria oxidize sulfur (elemental), sulfides (H2S, and similar) and thiosulfate (S2O3) for energy. THIOREDOXIN: A small protein that acts as an electron carrier. THYMIDINE KINASE (tk). An enzyme that allows a cell to utilize an alternate metabolic pathway for incorporating thymidine into DNA. Used as a selectable marker to identify transfected eukaryotic cells. THYMIDYLATE SYNTHASE: An enzyme that catalyzes the methylation of the uracil moiety in dUMP to convert it to dTMP. TI (Ti) PLASMID: A large extrachromosomal element that is found in strains of Agrobacterium and is responsible for crown gall formation. TISSUE PLASMINOGEN ACTIVATOR (tPA): biotechnology thrombolytic TITRE. The reciprocal of the last dilution of a titration giving a measurable effect; e.g. if the last dilution giving significant agglutination is 1:128, the titre is 128. TNFR FAMILY. Tumor Necrosis Factor Receptor family is important in mediating inflammation and cytotoxicity. Members of the TNFR family are the Death Receptors on the cell surface which mediate apoptosis upon stimulation by specific ligands. TOLERANCE. Diminished or absent capacity to make a specific response to an antigen, usually produced as a result of contact with that antigen under nonimmunizing conditions. TOSYLATION: a reaction which introduces the toluene-4-sulphonyl group into a molecule. [Generally by reaction of an alcohol with tosyl chloride to give the tosylate ester.] TOTIPOTENT (PLURIPOTENT): When a cell is able to respond to any one of a number of different stimuli and, subsequently, to develop into any one of a number of differentiated cell types. TOXOID. A nontoxic derivative of a toxin used as an immunogen for the induction of antibodies capable of cross-reacting with the toxin. TPL-2 KINASE. TPL-2 kinase is homologous to NIK. TPL-2 interacts with the C-terminus of NF-kB p105 and mediates phosphorylation of NF-kB p105 (probably not directly but by a downstream kinase). Upon phosphorylation, NF-kB p105 is either totally degraded or only partially degraded from its C-terminus by the proteasome to yield the NF-kB p50 subunit; while the p105 levels are clearly decreased by TPL-2 activity, the p50 levels remain quite constant. The degradation of p105 presumably generates active NF-kB by releasing associated NF-kB/Rel subunits from p105 which can translocate into the nucleus TRAFs. TNFR-associated factors TRANSCAPSIDATION. The partial of full coating of the nucleic acid of one virus with a coat protein of a differing virus. TRANSCRIBED TRIPLET: A set of three contiguous nucleotides of the transcribed DNA strand of the coding region of a structural gene that determines a codon in the mRNA. TRANSCRIPT MAPPING: Assigning gene transcripts, in the form of cDNA clones or expressed sequence tags, to specific chromosome regions by fluorescence in situ hybridization, hybridization, polyrnerase chain reaction (PCR), analysis of somatic cell hybrid mapping panels, or other strategies. TRANSCRIPTION factor: A protein that facilitates RNA synthesis by binding to a specific DNA sequence or another transcription factor that is bound to a specific DNA sequence. TRANSCRIPTION. The synthesis of mRNA using a DNA template. TRANSDUCTION: The transfer of nonviral DNA by a virus to a cell. TRANSFECTION. The uptake and expression of a foreign DNA sequence by cultured eukaryotic cells. (eg after "punching" holes in cell wall with LiAc - Lithium Acetate) TRANSFORMATION. In prokaryotes, the natural or induced uptake and expression of a foreign DNA sequence--typically a recombinant plasmid in experimental systems. In higher eukaryotes, the conversion of cultured cells to a malignant phenotype--typically through infection by a tumor virus or transfection with an oncogene. TRANSFORMING ONCOGENE. A gene that upon transfection converts a previously immortalized cell to the malignant phenotype. TRANSFORMING RETROVIRUS. A retrovirus carrying an additional DNA sequence (often an oncogene) that confers the ability to transform infected cells to malignant phenotype. TRANSGENE: A gene from one source that has been incorporated into the genome of another organism. TRANSITION-STATE INTERMEDIATE. In a chemical reaction, an unstable and high-energy configuration assumed by reactants on the way to making products. Enzymes are thought to bind and stabilize the transition state, thus lowering the energy of activation needed to drive the reaction to completion. TRANSLATION: The process of protein (polypeptide) synthesis in which the amino acid sequence of a protein is determined by mRNA mediated by tRNA molecules, and carried out on ribosomes. TRANSLOCATION: (1) The movement of peptidyl-tRNA and mRNA from the aminoacyl site to the peptidyl site on the ribosome during the elongation phase of translation; this movement opens the aminoacyl site for the next codon. (2) The transfer of chromosome material from one chromosome to another. (3) The movement of compounds through a plant. TRANSPOSASE: An enzyme that is encoded by a transposon gene and that facilitates the insertion of the transposon into a new chromosomal site and excision from a site. TRANSPOSON (TRANSPOSABLE ELEMENT): A DNA sequence (mobile genetic element) that can insert randomly into a chromosome, exit the site, and relocate at another chromosomal site. TRANSPOSON. A mobile genetic element that can move from one location in the gene and reinsert at another site. TRANSVAGINAL ULTRASOUND ASPIRATION. An ultrasound-guided technique for egg retrieval. A long, thin needle is passed through the vagina into the ovary. When the follicle is entered, suction is applied to retrieve the eggs. It is also known as ultrasound-guided egg aspiration and transvaginal egg retrieval. TRANSVERSION. A mutation in which purine is substituted for pyrimidine or vice versa. TRIBRID PROTEIN: A fusion protein that has three segments, each encoded by parts of different genes. TRICHLOROETHYLENE: An organic compound, used as a solvent and degreasing agent, that often persists in the environment. TRICHODERMA: A fungus, most of which feed on plant pathogens. TRIPARTITE MATING: A process in which conjugation is used to transfer a plasmid vector to a target cell when the plasmid vector is not self-mobilizable. When (1) cells that have a plasmid with conjugative and mobilizing functions are mixed with (2) cells that carry the plasmid vector and (3) target cells, mobilizing plasmids enter the cells with the plasmid vector and mobilize the plasmid vector to enter into the target cells. Following tripartite mating, the target cells with the plasmid vector are separated from the other cell types in the mixture by various selection procedures. TRIPLET. A sequence of 3 nucleotides comprising a codon of a nucleic acid and representing the code for an amino acid (triplet code, codon). TRIPLOBLASTIC. Possessing three germ layers: the endoderm, mesoderm, and ectoderm. Most eumetazoa are triploblastic. TROPHOBLAST. These are the cells of the embryo that become the placenta and attach the baby to the mother's uterus. These cells provide an armor of protection completely around the baby in the uterus. They also serve to nourish the baby carrying food from the mother's blood to the babies blood. These are the cells that are biopsied during a chorionic villus biopsy (CVS) to determine if the baby is genetically normal. TRYPSIN. A proteolytic enzyme that hydrolyzes peptide bonds on the carboxyl side of the amino acids arginine and lysine. Released in the pancreatic juice which digests protein in the small intestine TUMOR SUPPRESSOR PROTEINS. Tumor suppressor proteins protect cells from uncontrolled proliferation and transformation into tumor cells. They affect several cellular pathways, such as those controlling proliferation, apoptosis, differentiation and genomic identity. The common definition of a tumor suppressor gene requires the demonstration of mutations of both copies of a candidate gene in tumors (Knudson's two-mutation criterion). P53 is an example of a tumor-suppresser gene. TUNEL. Terminal deoxyNucleotidyl (dUTP) transferase-mediated End Labeling. In vivo apoptose assay for the detection of DNA fragmentation in cells. UBIQUITIN. A small protein that becomes covalently linked to a protein targeted for degradation. UNEQUAL CROSSING OVER. Crossing over between similar DNA sequences that are misaligned, resulting in sequences with deletion or duplication of DNA segments. A cause of a number of genetic variants, e.g., -thalassemia and Lepore hemoglobin. UPSTREAM: In molecular biology, the stretch of DNA base pairs that lie in the 5' direction from the site of initiation of transcription. Usually, the first transcribed base is designated +1 and the upstream nucleofides are indicated with minus signs, e.g., - 1, - 10. Also, to the 5' side of a particular gene or sequence of nucleotides. VALENCE ISOMERISATION: the isomerisation of molecules which involve structural changes resulting only from a relocation of single and double bonds. If a dynamic equilibrium is established between the two isomers it is also referred to as valence tautomerism. An example is the valence tautomerism of cyclo-octa-1,3,5-triene.] VARIABLE SURFACE GLYCOPROTEIN (VSG). One of a battery of antigenic determinants expressed by a microorganism to elude immune detection. VDAC. The Voltage-Dependent Anion Channel is involved in the mechanism of cytochrome c release from the mitochondrial intermembrane space into the cytosol. VDAC was shown to interact with Bcl-XL, Bax and Bax. Bcl-XL decreased the conductivity of VDAC, whereas Bax and Bak increased the conducticity of VDAC. Bax and Bak also induced VDAC to be permeable for cytochrome c. Moreover, mitochondria from VDAC-deficient yeast did not release cyto c in presence of Bax, but mitochondria from VDAC-deficient yeast reconstituted with the human vdac gene released cyto c in presence of Bax VDAC might also interact with ANT or other components of the PT pore. VECTOR. The agent used to carry new DNA into a cell. Viruses or plasmids are often used as vectors. VINYL GROUP: the ethenyl group, -CH=CH2. VIR GENES: A set of genes on a Ti plasmid that prepare the T-DNA segment for transfer into a plant cell. VIRION. a complete virus particle that consists of an RNA or DNA core with a protein coat, sometimes with external envelopes. It is the extracellular infective form of a virus. VIROID. A plant pathogen that consists of a naked RNA molecule of approximately 250-350 nucleotides, whose extensive base pairing results in a nearly correct double helix. VIRUS. An infectious particle composed of a protein capsule and a nucleic acid core, which is dependent on a host organism for replication. A double-stranded DNA copy of an RNA virus genome that is integrated into the host chromosome during lysogenic infection. W, Z CHROMOSOMES. Sex chromosomes in species (like snakes, birds, moths) where the female is the heterogametic sex (WZ). WALDEN INVERSION: a Walden inversion occurs at a tetrahedral carbon atom during an SN2 reaction when the entry of the reagent and the departure of the leaving group are synchronous. The result is an inversion of configuration at the centre under attack. WALKER'S A and B-BOX CONSENSUS SEQUENCES. Those sequences are nucleotide binding sites, e.g. in Apaf-1. WD-repeats. Loosely conserved set of sequences which is found in many regulatory proteins, including beta-subunits of heterotrimeric G proteins, the SREBP cleavage-activating protein, but also in Apaf-1. WESTERN BLOTTING: Transfer of protein from a gel to a membrane. Wild type A genetic term that denotes the most commonly observed phenotype, or the normal state, in contrast to a mutant condition. WILD TYPE. The term used to indicate the normal allele (often symbolized as +) or the normal phenotype. X-AUTOSOME TRANSLOCATION. The reciprocal translocation between the X chromosome and 1 of the autosomes. X-LINKED DOMINANT. A trait that is manifested in the heterozygous female as well as in the male who has the mutant allele on 1 of the X chromosomes. X-LINKED RECESSIVE. A disorder manifested exclusively in a male who is a heterozygote or a homozygous female when the abnormal gene is carried on the X chromosome. A female is usually a carrier if she is heterozygous and transmits the disease to the son. XENOPUS. An amphibian (frog) who shared a common ancestor with mammals about 350 million years ago. The oldest species in which all three regions of the MHC are known to be linked. XYLOSE: A 5-carbon sugar that is a major constituent of hemicellulose. YEAST ARTIFICIAL CHROMOSOMES (YAC). An artificial chromosome created from DNA, centromere and telomere of yeast chromosomes. Heavily used as vector in cloning of very large (>1Mb) genomic fragments. YEAST: A single-celled, usually rounded fungus. Z-DNA. A region of DNA that is "flipped" into a lefthanded helix, characterized by alternating purines and pyrimidines, and which may be the target of a DNA-binding protein. ZINC FINGER PROTEINS. Transcription-activator proteins containing finger-like structures containing zinc atoms. ZOO BLOT. A Southern blot containing conserved DNA sequences from related genes of different species. It is taken as evidence that the sequences are coding sequences from a specific gene. Hybridization of a cloned human DNA sequence to DNA from various vertebrate organisms to determine whether the cloned DNA is evolutionarily conserved.