dabs (single-domain antibodies) Antibodies with only one (instead of two) protein chain derived from only one of the domains of the antibody structure. Dabs exploit the finding that, for some antibodies, half of the antibody molecule binds to its target antigen almost as well as the whole molecule. The potential advantages of dabs are that they can be made easily by bacteria or yeasts, and offer a way to clone antibody-like molecules into bacteria, and hence to be able to easily screen millions of antibodies. Related ideas are single-chain antigen binding technology (SCA), biosynthetic antibody binding sites (BABS), minimum recognition units (MRUs), and complementary determining regions (CDRs).
DAD See domestic animal diversity.
dA - dT tailing See complementary homopolymeric tailing.
dalton (symbol: Da) A unit of atomic mass roughly equivalent to the mass of a hydrogen atom. 1.67 × 10-24 g. Named after the famous nineteenth-century chemist, John Dalton (1766-1844)). Used in shorthand expressions of molecular weight, especially as kilo- (kDa) or megadaltons (MDa), which are equal to respectively to 1 × 103 and 1 × 106 daltons.
Darwinian cloning Selection of a clone from a large number of essentially random starting points, rather than isolating a natural gene or making a carefully designed artificial one. Molecules which are more similar to those needed are selected, mutated to generate new variants, and re-selected. The cycle proceeds until the required molecule is found. The advantage of the system is that the selection is from a vast number of possibilities.
ddNTP See di-deoxynucleotide.
death phase The final growth phase, during which nutrients have been depleted and cell number decreases. See growth phases.
deceleration phase The phase of declining growth rate, following the linear phase and preceding the stationary phase in most batch-suspension cultures. See growth phases.
de-differentiation The process by which cells lose their specialization and proliferate by cell division to form a mass of cells which, in response to appropriate stimuli, may later differentiate again to form either the same cell type or a different one. De-differentiation occurs in response to wounding and in tissue cultures. See re-differentiation.
deficiency Insufficiency or absence of one or more usable forms of enzymatic, nutritional or environmental requirements, so that development, growth or physiological functions are affected.
defined 1. Fixed conditions of medium, environment and protocol for growth.
2. Precisely known and stated elements of a tissue culture medium. cf undefined.
degeneracy (of the genetic code) The specification of one amino acid by more than one codon. It arises from the inevitable redundancy resulting from 64 triplets in a triplet code (4 x 4 x 4 = 64) encoding only 20 amino acids.
degeneration 1. Changes in cells, tissues or organs due to disease.
2. The reduction in size or complete loss of organs during evolution.
dehalogenation The removal of halogen atoms (chlorine, iodine, bromine, fluorine) from molecules, usually during biodegradation.
dehiscence The spontaneous and often violent opening of a fruit, seed pod or anther to release and disperse the seeds or pollen.
dehydrogenase An enzyme that catalyses the remove of hydrogen atoms in biological reactions.
dehydrogenation A chemical reaction in which hydrogen is removed from a compound.
de-ionized water Water which is free of most inorganic (not completely free, since Na is present in ample quantities) and most organic compounds.
deletion A mutation involving the removal of one or more base pairs in DNA sequence. Large deletions are visible as the lack of chromosomal segments.
deliberate release Putting something into the outside world; in biotechnology it means putting a genetically modified organism (GMO) into field trials.
deme A group of organisms in the same taxon.
de-mineralize To remove the mineral content (salts, ions) from a substance, especially water. Removal methods include distillation and electrodialysis. The process is de-mineralization.
denaturated DNA Duplex DNA that has been converted to single strands by breaking the hydrogen bonds of complementary nucleotide pairs. Usually achieved by heating.
denaturation Loss of native configuration of a macro-molecule (protein or nucleic acid) by physical or chemical means, usually accompanied by loss of biological activity. Denatured proteins often unfold their polypeptide chains and express changed properties of solubility. The separation of duplex nucleic acid molecules into single strands. Most commonly used by genetic engineers to describe the destruction of hydrogen bonds maintaining the double-stranded nature of all or part of a DNA molecule.
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 single-stranded polynucleotides, or altering the secondary and tertiary structure of a protein, destroying its activity.
denitrification A chemical process in which nitrates in the soil are reduced to molecular nitrogen, which is released to the atmosphere.
de novo (L. "from the beginning, anew") Arising, anew, afresh, once more. Also ex novo.
density gradient centrifugation High-speed centrifugation in which molecules "float" at a point where their density equals that in a gradient of caesium chloride or sucrose. The density gradient may either be formed before centrifugation by mixing two solutions of different density (as in sucrose density gradients) or it can be formed by the process of centrifugation itself (as in CsCl and Cs2SO4 density gradients). See centrifugation.
deoxyribonucleic acid See DNA.
deoxyribonuclease (DNase). Any enzyme that hydrolyses DNA.
de-repression The process of "turning on" the expression of a gene or set of genes whose expression has been repressed (turned off). Displacement of a repressor protein from a promoter region of DNA. When attached to the DNA, the repressor protein prevents RNA polymerase from initiating transcription. The "turning on" of a gene.
derivative 1. Resulting from or derived from.
2. Term used to identify a variant during meristematic cell division.
desiccant Any compound used to remove moisture or water.
desiccate To dry, exhaust or deprive of water or moisture. Any chemical used for this purpose is called a desiccant. An apparatus for drying and preventing hygroscopic samples from rehydrating is a desiccator. The process is desiccation.
dessicator Apparatus for drying or depriving of moisture.
desoxyribonucleic acid Obsolete spelling of deoxyribonucleic acid (DNA).
desulphurization (USA: desulfurization) Technology for removing sulphur from oil and coal by use of bacteria. Sulphur residues in fuels end up as sulphur dioxide when the fuel is burned, resulting in acid rain. Bacteria may oxidize sulphites (insoluble) into sulphates (soluble), which can be washed away with the bacteria.
detergent Substance which lowers the surface tension of a solution, improving its cleaning properties (e.g., Tween-20TM, a surfactant and wetting agent). See surfactant; wetting agent.
determinate growth Growth determined and limited in time, as in most floral meristems and leaves. The differentiation process is irreversibly established. Determinate growth contrasts with the usual culture growth, which is infinite and indeterminate.
determination Process by which undifferentiated cells in an embryo become committed to develop into specific cell types, such as neurons, fibroblasts or muscle cells.
determined Describing embryonic tissue at a stage when it can develop only as a certain kind of tissue.
development The sum total of events that contribute to the progressive elaboration of an organism. The two major aspects of development are growth and differentiation.
deviation 1. In statistics: the difference between an actual observation and the mean of all observations.
2. An alteration from the typical form, function or behaviour. Mutation or stress are the common reasons behind deviation.
dextrin An intermediate polysaccharide compound resulting from the hydrolysis of starch to maltose by amylase enzymes.
dextrose See glucose.
dG - dC tailing See complementary homopolymeric tailing.
diabetes A disease associated with the absence or reduced levels of insulin, which is a hormone essential for the transport of glucose to cells.
diagnostic procedure A test or assay used to determine the presence of an organism, substance or nucleic acid sequence alteration.
diakinesis A stage of meiosis just before metaphase I, in which the separation of homologous chromosomes is almost completed.
diazotroph An organism that can fix atmospheric nitrogen.
dicentric chromosome A chromosome having two centromeres.
dichogamy The condition in which the male and the female reproductive organs of a flower mature at different times, thereby making self-fertilization improbable or impossible.
dicot See dicotyledon.
dicotyledon (Gr. dis, twice + kotyledon, a cup-shaped hollow) A plant with two cotyledons, or seed leaves. One of the two classes of plants in the Angiosperms (the other class is the monocotyledons). Colloquially called a dicot. Examples include many crop plants (potato, pea, beans), ornamentals (rose, ivy) and timber trees (oak, beech, lime).
di-deoxynucleotide (ddNTP) A deoxynucleotide that lacks a 3´- hydroxyl group, and is thus unable to form the 3´-5´ phospho-diester bond necessary for chain elongation. Di-deoxynucleotides are used in DNA sequencing and the treatment of viral diseases. Also sometimes referred to as didN. See nucleotide.
didN See di-deoxynucleotide (ddNTP).
differential centrifugation A method of separating sub-cellular particles according to their sedimentation coefficients, which are roughly proportional to their size. Cell extracts are subjected to a succession of centrifuge runs at progressively faster rotation speeds. Large particles, such as nuclei or mitochondria, will be precipitated at relatively slow speeds; higher G forces will be required to sediment small particles, such as ribosomes.
differentially permeable Referring to a membrane, through which different substances diffuse at different rates; some substances may be unable to diffuse through such a membrane.
differentiation (L. differre, to carry different ways) A process in which unspecialized cells develop structures and functions characteristic of a particular type of cell. Development from one cell to many cells, accompanied by a modification of the new cells for the performance of particular functions. In tissue culture, the term is used to describe the formation of different cell types.
diffusion (L. diffusus, spread out) The movement of molecules from a region of higher concentration to a region of lower concentration.
digest To cut DNA molecules with one or more restriction endonucleases. See cleave.
dihaploid An individual which arises from a doubled haploid.
dihybrid An individual that is heterozygous for two pairs of alleles; the progeny of a cross between homozygous parents differing at two loci.
dimer Association of two molecules.
dimethyl sulphoxide; dimethyl sulfoxide (C2H6OS; m.w. 78.13) A highly hygroscopic liquid and powerful solvent with little odour or colour. It is an organic co-solvent used in small quantities to dissolve neutral organic substances in tissue culture media preparation. DMSO also has uses as a cryoprotectant.
dimorphism The existence of two distinctly different types of individuals within a species. An obvious example is the sexual dimorphism in certain animals.
diplochromosome See endoreduplication.
diploid (Gr. diploos, double + oides, like) 1. The status of having two complete sets of chromosomes, most commonly one set of paternal origin and the other of maternal origin.
2. An organism or cell with a double set (2n) of chromosomes (most commonly one of paternal origin, and the other of maternal origin), or referring to an individual containing a double set of chromosomes per cell. Somatic tissues of higher plants and animals are ordinarily diploid in chromosome constitution, in contrast with the haploid gametes.
diploid cell A cell which contains two sets of chromosomes. cf haploid cell.
diplonema (adj: diplotene) Stage in prophase of meiosis I following the pachytene stage, but preceding diakinesis, in which one pair of sister chromatids begin to separate from the other pair, i.e., the centromeres begin to disjoin.
diplophase Phase with 2n chromosomes.
direct embryogenesis Embryoids form directly in culture, without an intervening callus phase, on the surface of zygotic or somatic embryos or on explant tissues (leaf section, root tip, etc.).
direct organogenesis Formation of organs directly on the surface of cultured intact explants. The process does not involve callus formation.
direct repeat Two or more stretches of DNA within a single molecule which have the same nucleotide sequence in the same orientation. Direct repeats may be either adjacent to one another or far apart on the same molecule. For example
directed mutagenesis The process of generation of nucleotide changes in cloned genes by any one of several procedures, including site-specific and random mutagenesis. Also called in vitro mutagenesis.
directional cloning The technique by which DNA insert and vector molecules are digested with two different restriction enzymes to create non-complementary sticky ends at either end of each restriction fragment, so allowing the insert to be ligated to the vector in a specific orientation and preventing the vector from re-circularizing. See cloning.
disarm To delete from a plasmid or virus genes that are cytotoxic or tumour inducing.
discontinuous variation Phenotypic variation involving distinct classes, such as red versus white, tall versus dwarf. See continuous variation.
discordant Members of a pair showing different, rather than similar, characteristics.
disease (L. dis, a prefix signifying the opposite + M.E. aise, comfort) The opposite of ease. Any alteration from the state of metabolism necessary for the normal development and functioning of an organism, usually associated with infection by a pathogen or the malfunction or absence of one or more genes.
disease resistance The ability to remain healthy by resisting disease or the disease agent. Disease resistance or tolerance is a subject of intense interest in biotechnology.
disease-free A plant or animal certified through specific tests as being free of specified pathogens. Disease-free should be interpreted to mean "free from any known diseases" as "new" diseases may yet be discovered to be present. cf disease indexing.
disease-indexing Disease-indexed organisms have been assayed for the presence of known diseases according to standard testing procedures. cf disease-free.
disinfectation Full elimination of internal micro-organisms from a culture; disinfectation is rarely obtained. cf disinfestation.
disinfestation The elimination or inhibition of the activity of surface-adhering micro-organisms. cf disinfection.
disjunction Separation of homologous chromosomes during anaphase I of meiosis; separation of sister chromatids during anaphase of mitosis and anaphase II of meiosis. As soon as the sister chromatids have separated, they are each called a chromosome. See non-disjunction.
disomy (adj: disomic) The presence of a pair of specific chromosome. This is the normal condition, and abnormal occurrences are monosomy (q.v.), trisomy (q.v.) and nullisomy (with respectively one chromosome of a pair, three or none). There are also abnormal disomic conditions, such as when both chromosomes of the pair were inherited from the same parent.
dispense Portion out a nutrient medium into containers, such as test tubes, jars, Erlenmeyer flasks, Petri dishes, etc.
disaccharide A carbohydrate consisting of two linked sugar units.
dissecting microscope A microscope with a low magnifying power of about 50×, used to examine or excise small plant or animal parts.
dissection (L. dissectio, a dissecting or being dissected) Separation of a tissue by cutting for analysis or observation.
dissolve Pass chemicals into solution.
distillation (L. distillatio, a distilling process) The process of heating a mixture to separate the more volatile from the less volatile parts, and then cooling and condensing the resulting vapour so as to produce a more nearly pure or refined substance.
di-sulphide bond A chemical bond that stabilizes the three-dimensional structure of proteins, and hence the protein's normal function. They form between cysteine residues in the same or different peptide molecules. a.k.a. di-sulphide bridge.
di-sulphide bridge See di-sulphide bond.
ditype In fungi, a tetrad that contains two kinds of meiotic products (spores), e.g., 2AB and 2ab. See tetrad (1).
diurnal Term describing the occurrence of an event at least once every 24 hours. cf circadian.
divergent evolution See adaptive radiation.
dizygotic twins Two-egg twins, i.e., a pair of individuals that shared the same uterus at the same time, but which arose from separate and independent fertilization of two ova.
DMSO See dimethyl sulphoxide.
DNA (deoxyribonucleic acid; formerly spelt desoxyribonucleic acid) The long chain of molecules in most cells that carries the genetic message and controls all cellular functions in most forms of life. The information-carrying genetic material that comprises the genes. DNA is a macro-molecule composed of a long chain of deoxyribonucleotides joined by phospho-diester linkages. Each deoxyribonucleotide contains a phosphate group, the five-carbon sugar 2-deoxribose, and a nitrogen-containing base. The genetic material of most organisms and organelles so far examined is double-stranded DNA; a number of viral genomes consist of single-stranded DNA or single-or double-stranded RNA. In double-stranded DNA, the two strands run in opposite (anti-parallel) directions and are coiled round one another in a double helix. Purine bases on one strand specifically hydrogen bond with pyrimidine bases on the other strand, according to the Watson-Crick rules (A pairs with T; G pairs with C). Hence a constant width for the double helix of 20 Å (2.0 nm) is maintained. In the B-form, DNA adopts a right-handed helical conformation, with each chain making a complete turn every 34 Å (3.4 nm), or once every ten bases. See also mtDNA.
DNA amplification Multiplication of a piece of DNA in a test-tube into many thousands of millions of copies. The most commonly used process is the polymerase chain reaction (PCR) system, but other systems are being developed, including ligase chain reaction (LCR), nucleic acids sequence-dependent amplification, and the Q-b system.
DNase (deoxyribonuclease) An enzyme that catalyses the cleavage of DNA. DNase I is a digestive enzyme secreted by the pancreas, that degrades DNA into shorter nucleotide fragments. Many other endonucleases and exonucleases are involved in DNA repair and replication. cf nuclease.
DNA bank In AnGR: Storage of DNA, which may or may not be the complete genome, but should always be accompanied by inventory information. (Note: at the present time, animals cannot be re-established from DNA alone.) (Source: FAO, 1999)
DNA chip See DNA micro-array.
DNA cloning See gene cloning.
DNA construct A DNA molecule inserted into a cloning vector, usually a plasmid.
DNA diagnosis The use of DNA polymorphisms to detect the presence of a specific allele (often associated with a disease or syndrome) or DNA sequence.
DNA fingerprint The unique pattern of DNA fragments identified originally by Southern hybridization (using a probe that binds to a polymorphic region of DNA) or now by polymerase chain reaction (PCR) (using primers flanking the polymorphic region). See genetic fingerprinting.
DNA helicase (gyrase) An enzyme that catalyses the unwinding of the complementary strands of a DNA double helix.
DNA hybridization The pairing of two DNA molecules, often from different sources, by hydrogen bonding between complementary nucleotides. This technique is frequently used to detect the presence of a specific nucleotide sequence in a DNA sample.
DNA ligase An enzyme that catalyses a reaction that links two DNA molecules via the formation of a phospho-diester bond between the 3´ hydroxyl and 5´ phosphate of adjacent nucleotides. It plays an important role in DNA repair and replication. DNA ligase is one of the essential tools of recombinant DNA technology, enabling (among other things) the incorporation of foreign DNA into vectors. The ligase enzyme encoded by phage T4 is commonly used in gene-cloning experiments. It requires ATP as a co-factor. T4 is used in vitro to join the vector and insert DNAs.
DNA micro-array A small glass surface to which has been fixed an array of DNA fragments, each with a defined location. A typical DNA chip would contain 10 000 discrete spots (each containing a different DNA fragment) in an area of just a few square centimetres. When a solution of fluorescently labelled DNA fragments is hybridized to the chip, spots to which hybridization occurs are visible as fluorescence. If the spots on the chip are genes (expressed sequence tags, q.v.), hybridization with cDNA from a particular tissue shows which genes are expressed in that tissue. If the spots are short, synthesized oligonucleotides (approximately 25 bases) corresponding to that part of a gene containing a single nucleotide polymorphisms (SNP)(q.v.), with a separate spot for each of the 4 possible bases at that site, hybridization with genomic DNA from an individual plant or animal enables that individual to be genotyped at as many SNP loci as are represented on the chip. The big advantage of DNA chips is the extent to which the process of genotyping can be automated, thereby enabling huge numbers of plants or animals to be genotyped for a huge number of loci.
DNA polymerase An enzyme that catalyses the synthesis of double-stranded DNA, using single-stranded DNA as a template. See polymerase.
DNA polymorphism The existence of two or more alternative forms (alleles) of a chromosomal locus that differ in nucleotide sequence or have variable numbers of repeated nucleotide units. See allele.
DNA primase An enzyme that catalyses the synthesis of short strands of RNA that initiate the synthesis of DNA strands.
DNA probe A labelled (tagged) segment of DNA that is able, after a DNA hybridization reaction, to detect a specific DNA sequence in a mixture of sequences. If the tagged sequence is complementary to any one in the mixture, the two sequences will form a double helix. This will be identified thanks to its label (either by radioactivity or fluorescence).
DNA repair A variety of mechanisms that repair errors that occur during DNA replication.
DNA repair enzymes Enzymes that catalyse the repair of DNA.
DNA replication The process whereby DNA makes exact copies itself, under the action of and control of DNA polymerase.
DNAase See DNase.
DNA sequencing Procedures for determining the nucleotide sequence of a DNA fragment. There are two common methods for doing this:
· the Maxam and Gilbert technique (chemical degradation), that uses different chemicals to break the DNA into fragments at specific bases; or
· the Sanger technique (called the di-deoxy or chain-terminating method) uses DNA polymerase to make new DNA chains, with di-deoxy nucleotides (chain terminators) to stop the chain randomly as it grows.
In both cases, the DNA fragments are separated according to length by polyacrylamide gel electrophoresis, enabling the sequence to be read directly from the gel.
DNA topo-isomerase An enzyme that catalyses the introduction or removal of supercoils in DNA.
DNA transformation See transfection; transformation.
DNA delivery system A generic term for any procedure that transports DNA into a recipient cell.
Dolly The [name of the] first mammal to be created by cloning a cell from an adult animal. In this particular case, the cell came from the mammary tissue of an adult ewe. The creation of Dolly showed that the process of differentiation into adult tissue is not, as previously thought, irreversible. The result was achieved by nuclear transfer (q.v.). Dolly's birth was announced in 1997. Since then, cattle and mice have also been cloned from adult cells.
domain A segment of a protein that has a discrete function or conformation. At the protein level, a domain can be as small as a few amino acid residues or as large as half of the entire protein.
domestic animal diversity (DAD) In AnGR: The spectrum of genetic differences within each breed, and across all breeds within each domestic animal species, together with the species differences; all of which are available for the sustainable intensification of food and agriculture production.
(Source: FAO, 1999)
dominance The type of gene action exhibited by a dominant allele (q.v.).
dominant 1. Describing an allele whose effect with respect to a particular trait is the same in heterozygotes as in homozygotes. The opposite is recessive.
2. Describing the most conspicuously abundant and characteristic species of a community.
3. Describing an animal that is allowed priority in access to food, mates, etc., by others of its species because of its success in previous aggressive encounters.
dominant marker selection Selection of cells via a gene encoding a product that enables only the cells that carry the gene to grow under particular conditions. For example, plant and animal cells that express the introduced Neor gene are resistant to the compound G418, while cells that do not carry the Neor gene are killed by G418. a.k.a. positive selection; see also positive selectable marker.
dominant selectable marker gene A gene that allows the host cell to survive under conditions where it would otherwise die.
dominant(-acting) oncogene A gene that stimulates cell proliferation and contributes to oncogenesis when present in a single copy. See oncogene.
donor plant (mother plant) An explant, graft or cutting used as a source of plant material for micro-propagation purposes. a.k.a. ortet. cf explant.
dormancy (F. dormir, from L. dormire, to sleep) An inactive period in the life of an animal or plant during which growth slows or completely ceases. Physiological changes associated with dormancy help the organism survive adverse environmental conditions. Annual plants survive the winter as dormant seeds, while many perennial plants survive as dormant tubers, rhizomes, or bulbs. Hibernation and aestivation in animals help them survive extremes of cold and heat, respectively. cf rest period.
dosage compensation A phenomenon whereby inactivation of all but one of the X chromosomes in female mammals results in males and females producing the same quantity of peptide from X-linked genes.
double crossing-over Two simultaneous reciprocal breakage and reunion events between the same two chromatids.
double helix Describes the coiling of the antiparallel strands of the DNA molecule, resembling a spiral staircase in which the paired bases form the steps and the sugar-phosphate backbones form the rails.
double fertilization A process, unique to flowering plants, in which two male nuclei, which have travelled down the pollen tube, separately fuse with different female nuclei in the embryo sac. The first male nucleus fuses with the egg cell to form the zygote; the second male nucleus fuses with the two polar nuclei to form a triploid nucleus that develops into the endosperm.
double recessive An organism homozygous for a recessive allele at each of two loci.
double-stranded complementary DNA (dscDNA) A double-strand DNA molecule created from a cDNA template.
doubling time See generation time.
downstream 1. In molecular biology, the stretch of nucleotides of DNA that lie in the 3´ direction from the site of initiation of transcription, which is designated as +1 (remembering the convention that the sequence of a DNA molecule is written from the 5´ end to the 3´ end). Downstream nucleotides are marked with plus signs, e.g., +2, +10. Also, to the 3´ side of a particular gene or sequence of nucleotides.
2. In chemical engineering, those phases of a manufacturing process that follow the biotransformation stage. Usually refers to the recovery and purification of the product of a fermentation process. See downstream processing.
downstream processing A general term for all the things which happen in a biotechnological process after the biology, be it fermentation of a micro-organism or growth of a plant. It is particularly relevant to fermentation processes, which produce a large quantity of a dilute mixture of substances, products and micro-organisms. These must be separated, and the product must be concentrated and purified, and converted into a form which is useful. See downstream.
drift See genetic drift.
drug See therapeutic agent.
drug delivery Method by which a therapeutic agent is delivered to its site of action. For traditional therapeutic agents this is another name for formulation. However, biotechnology has allowed the development of a range of new therapeutic-agent delivery systems, such as liposomes and other encapsulation techniques, and a range of mechanisms that target a therapeutic agent to a particular cell or tissue. See therapeutic agent.
dry weight The moisture-free weight of tissue obtained by drying at high (oven-drying) or low (freeze-drying) temperatures for an interval sufficient to remove all water.
dscDNA See double-stranded complementary DNA.
dsDNA Double-stranded DNA.
dual culture A culture made of a plant tissue and one organism (such as a nematode) or an obligate parasite/micro-organism (such as a fungus). Dual culture techniques are used for a variety of purposes, including assessing host-parasite interactions and the production of axenic cultures.
duplex DNA Double-stranded DNA.
duplication The occurrence of a segment more than once in the same chromosome or genome.