Q - Z

q Denotes the longer of the two chromosome arms, e.g. human 10q is the long arm of human chromosome 10.

q-beta replicase A viral RNA polymerase secreted by a bacteriophage that infects E. coli. It has the property of being able to copy RNA sequences at a rapid rate.

QSAR Abbreviation for quantitative structure-activity relationship.

QTL Abbreviation for quantitative trait locus.

quadrivalent A chromosome configuration visible in late prophase and metaphase of the first meiotic division, where four chromosomes are linked by chiasmata. Can occur in autotetraploids when four homologous chromosomes pair, or in diploids as a result of heterozygosity for a reciprocal translocation between two non-homologous chromosomes.

quadruplex The inheritance of alleles in autotetraploids. A genotype AAAa will produce gametes AA, Aa in the ratio 3:1.

qualitative trait A trait that shows discontinuous variation - i.e. individuals can be assigned to one of a small number of discrete classes.

quantitative genetics The area of genetics concerned with the inheritance of quantitative traits that show continuous variation, as opposed to qualitative traits. Since many of the critical targets in both plant and animal breeding are of this type, most practical improvement programs involve the application of quantitative genetics.

quantitative inheritance Inheritance of measurable traits that depend on the cumulative action of many genes and/or involve a significant proportion of non-genetic determination.

quantitative structure-activity relationship (Abbreviation QSAR). A computer modelling technique that enables the prediction of the likely activity of a molecule before it is synthesized. QSAR analysis relies on recognizing associations of molecular structures and activity from historical data.

quantitative trait A measurable trait that shows continuous variation (e.g. height, weight, colour intensity, etc.) - i.e. the population cannot be classified into a few discrete classes.

quantitative trait locus (Abbreviation: QTL). A locus where allelic variation is associated with variation in a quantitative trait. The presence of a QTL is inferred from genetic mapping, where the total variation is partitioned into components linked to a number of discrete chromosome regions.

quantum speciation The rapid formation of new species, primarily by genetic drift.

quarantine Isolation for a period after arrival in a new location, to allow any pre-existing disease symptoms to appear. Used in the context of regulations restricting the sale or shipment of living organisms, usually to prevent disease or pest invasion of an area.

quaternary structure A level of protein structure where several individual molecules assemble together and form a functional cluster. A classic example is haemoglobin, a complex of four myoglobin-like units. See: tertiary structure.

quiescent A temporary suspension or reduction in the rate of activity or growth, while retaining the potential to resume prior activity. Applies particularly to cell division. See: dormancy.

R genes A class of plant genes conferring resistance to a specific strain (or group of strains) of a particular pathogen. Their primary function is to sense the presence of the pathogen and to trigger the defence pathways in the plant. R genes have been cloned from a number of plant species.

R₁ The first-generation offspring of a recombinant (genetically modified) organism. Not standard terminology. See: T₀, T₁, and T₂.

race A distinguishable group of organisms of a particular species. Criteria for distinctness can be one or a combination of geographic, ecological, physiological, morphological, genetic and karyotypic factors.

raceme An inflorescence in which the main axis is elongated but the flowers are borne on pedicels that are about equal in length.

rachilla Shortened axis of a spikelet.

rachis Main axis of a spike; axis of fern leaf (frond) from which pinnae arise; in compound leaves, the extension of the petiole corresponding to the midrib of an entire leaf.

radiation hybrid cell panel (Abbreviation: RH). A somatic cell hybrid panel in which the chromosomes from the species of interest have been fragmented by irradiation prior to cell fusion. The resultant small fragments of chromosomes greatly increase the power of physical mapping in the species of interest.

radicle The portion of the plant embryo which develops into the primary root.

radioimmunoassay (Abbreviation: RIA). An assay based on the use of a radioactively labelled antibody, where the amount of radiation detected indicates the amount of target substance present in the sample.

radioisotope An unstable isotope that emits ionizing radiation. Synonym: radioactive isotope.

raft culture See: nurse culture.

ramet An individual member of a clone, descended from the ortet.

random amplified polymorphic DNA (Abbreviation: RAPD). A PCR-based genotyping technique in which genomic template is amplified with single, short (usually 10-mer) randomly chosen primers. Typical patterns consist of a small number of amplified products of up to 2 kbp in length, which are separated by electrophoresis.

random genetic drift See: genetic drift.

random mutagenesis A non-directed change of one or more nucleotide pairs in a DNA molecule.

random primer method A method for labelling DNA probes, mainly for Southern hybridization experiments. A mixture of short oligonucleotides is hybridized to a single-stranded DNA probe. In the presence of DNA polymerase and deoxyribonucleotides - one of which is labelled - DNA synthesis then generates labelled copies of probe DNA.

RAPD Abbreviation for random amplified polymorphic DNA.

rate-limiting enzyme The enzyme whose activity controls the output of final product from a multi-enzyme metabolic pathway.

rational drug design A systematic method of creating compounds by analysing their structure, function and stereochemical interactions.

reading frame The reading frame defines which sets of three nucleotides are read as triplets, and hence as codons, in DNA transcription. The start point is usually determined by the initiation codon, AUG. Thus the sequence AUGGCAAAA would be read as AUG/GCA/AAA not as A/UGC/CAA/AA. See: open reading frame.

read-through Transcription or translation that proceeds beyond the normal stopping point because of the absence of the usual transcription or translation termination signal of a gene.

recA A protein, found in most bacteria, that is essential for DNA repair and DNA recombination.

recalcitrant Of seeds, unable to survive drying and subsequent storage at low temperature. See: field gene bank.

receptacle Enlarged end of the pedicel or peduncle, to which other flower parts are attached.

receptor A trans-membrane protein located in the plasma membrane that can bind with a ligand on the extracellular surface, as a result of which it induces a change in activity on the cytoplasmic surface. More generally, a site in a molecule that allows the binding of a ligand.

receptor-binding screening A biotechnology-based method for drug discovery, which relies on the fact that many drugs act by binding to specific receptors on or in cells. Since receptors in vivo bind to hormones or to other cells, and thereby control the cell's behaviour, a receptor bound with a drug will likely affect the normal activity of the cell.

recessive Describing an allele whose effect with respect to a particular trait is not evident in heterozygotes. Opposite: dominant.

recessive allele Allelic state of a gene, where homozygosity is required for the expression of the relevant phenotype. Opposite: dominant allele.

recessive 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. Synonym: anti-oncogene recessive-acting oncogene. See: oncogene.

recessive-acting oncogene See: recessive oncogene.

reciprocating shaker A platform shaker used for agitating culture flasks, with a back and forth action at variable speeds.

recognition sequence Synonym of recognition site.

recognition site A nucleotide sequence, typically 4-8bp long and often palindromic, that is recognized by, and at which a restriction endonuclease binds to the DNA. For some restriction endonucleases, the presence of a methylated residue within the recognition site abolishes recognition. Synonym: recognition sequence; restriction site.

recombinant A term used in both classical and molecular genetics. 1. In classical genetics: An organism or cell that is the result of meiotic recombination. 2. In molecular genetics: A hybrid molecule made up of DNA obtained from different organisms. Typically used as an adjective, e.g. recombinant DNA.

recombinant DNA The result of combining DNA fragments from different sources.

recombinant DNA technology A set of techniques for manipulating DNA, including: the identification and cloning of genes; the study of the expression of cloned genes; and the production of large quantities of gene product.

recombinant human (Abbreviation rh). A prefix denoting molecules made through the use of recombinant DNA technology.

recombinant protein A protein encoded by a cloned gene. Synonym: heterologous protein.

recombinant RNA RNA molecules joined in vitro by T4 RNA ligase.

recombinant toxin A single multifunctional toxic protein encoded by a recombinant gene.

recombinant vaccine A vaccine produced from a cloned gene.

recombinase A class of enzymes that are able to alter the arrangement of DNA sequences in a site-specific way.

recombination The production of a DNA molecule with segments derived from more than one parent DNA molecule. In eukaryotes, this is achieved by the reciprocal exchange of DNA between non-sister chromatids within an homologous pair of chromosomes during prophase of the first meiotic division.

recombination fraction The proportion of recombinant (with respect to two loci) gametes arising from meiosis. Linkage maps are based on estimates of recombination fraction between all pair-wise combinations of loci. See: map distance. Synonyms: recombination frequency, crossing-over unit.

recombination frequency Synonym: recombination fraction

recombinational hot spot A chromosomal region where recombination appears to occur more frequently than expected.

reconstructed cell A viable transformed cell resulting from genetic engineering.

reduction division The first division of meiosis in which the chromosome number is reduced from the somatic to the gametic number.

refugium (pl.: refugia) An area set aside to provide protection/escape from ecological consequences occurring elsewhere.

regeneration The growth of new tissues or organs to replace those injured or lost. In plant tissue culture, regeneration refers to the development of organs or plantlets from an explant. See: conversion; micropropagation; organogenesis.

regulator Substance regulating growth and development of cells, organs, etc.

regulatory gene A gene with the primary function of controlling the rate of synthesis of the products of one or several other genes or pathways.

regulatory sequence A DNA sequence involved in regulating the expression of a gene, e.g. a promoter or operator region (in the DNA molecule).

rejuvenation 1. Reversion from adult to juvenile stage. 2. The process of regular reproduction of seed stocks or collections in gene banks, in order to ensure continued viability.

relaxed circle See: nicked circle.

relaxed circle plasmid See: plasmid.

relaxed plasmid A plasmid that replicates independently of the bacterial chromosome and is present in 10-500 copies per cell.

release factor 1. A soluble protein that recognizes termination codons in mRNAs and terminates translation in response to these codons. 2. A hormone, produced by the hypothalamus, which stimulates the release of a hormone from the anterior pituitary gland into the bloodstream.

remediation The cleanup or containment of a hazardous waste disposal site to the satisfaction of the applicable regulatory agency. This can sometimes be accomplished with naturally occurring or engineered micro-organisms or plants. See: bioremediation.

renaturation Of DNA, the reforming of two complementary molecules into a double-stranded structure, following heat or chemical induction of dissociation (denaturation). Of protein, the resumption of three-dimensional conformation, allowing the molecule to function normally. Denaturation of many proteins is irreversible, but denatured DNA molecules will renature readily under appropriate chemical and physical conditions.

rennin An enzyme, secreted by cells lining the stomach in mammals, responsible for the clotting of milk. Used in the manufacture of certain dairy products.

repeat unit A sequence of nucleotides that occurs repeatedly, often in a head-to-tail arrangement (tandemly).

repetitive DNA DNA sequences that are present in a genome in many copies, some of it originating from retrotransposon activity. A substantial proportion of all eukaryotic genomes is composed of this class of DNA, whose biological function is uncertain. Sometimes referred to as 'junk DNA'.

replacement The addition of a cloned corrected copy of a defective gene. See: homogenotization.

replacement therapy The administration of metabolites, co-factors or hormones that are deficient as the result of a genetic disease.

replica plating Duplicating a population of bacterial colonies growing on agar medium in one Petri plate to agar medium in another Petri plate.

replicase A viral enzyme necessary for the replication of the virus in the host cell.

replication The in vivo synthesis of double-stranded DNA by copying from a single-stranded template.

replication fork Y shaped structure associated with DNA replication. It represents the point at which the strands of double-stranded DNA are separated so that replication can proceed.

replicative form (Abbreviation: RF). The molecular configuration of viral nucleic acid that is the template for replication in the host cell.

replicon The portion of a DNA molecule which can be replicated from a single origin of replication. Plasmids and the chromosomes of bacteria, phages and other viruses usually have a single origin of replication so that their entire genome constitutes a single replicon. Eukaryotic chromosomes have multiple origins of replication, so comprise several replicons. Also used to describe a DNA molecule capable of independent replication.

replisome The complete replication apparatus, present at a replication fork, that carries out the replication of DNA.

reporter gene A gene that encodes a product that can be readily assayed. Used as a marker to confirm the incorporation of a transgene into a cell, organ or tissue, and as a means of testing the efficiency of specific promoters.

repressible enzyme An enzyme whose activity can be diminished by the presence of a regulatory molecule.

repressible gene A gene whose expression can be diminished or extinguished by the presence of a regulatory molecule.

repression Inhibition of transcription by preventing RNA polymerase from binding to the transcription initiation site.

repressor A protein which binds to a specific DNA sequence upstream from the transcription initiation site of a gene and prevents RNA polymerase from commencing mRNA synthesis.

reproduction 1. Sexual reproduction: the regular alteRNAtion of meiosis and fertilization which provides for the production of offspring. The main biological significance of sexual reproduction lies in the phenomenon of recombination. 2. Asexual or agamic reproduction: the development of a new individual from a single cell or group of cells in the absence of meiosis. See: apomixis.

repulsion A double heterozygote in which the dominant (or wild-type) allele at one locus and the recessive (or mutant) allele at a second linked locus occur on the same chromosome (genetic constitution Ab/aB). Synonym: trans configuration. Opposite: coupling, cis configuration.

residue 1. See: polymer. 2. Materials remaining after degradation and/or attempted removal, e.g. pesticide residues in food.

resistance The ability to withstand abiotic (high temperature, drought etc.) or biotic (disease) stress, or a toxic substance. Often in the context of genetic determination of resistance.

resistance factor A plasmid that confers antibiotic resistance to a bacterium.

rest period A physiological condition of viable seeds, buds or bulbs that prevents growth even in the presence of otherwise favourable environmental conditions. Synonym: dormancy.

restitution nucleus A single nucleus arising from a failure of nuclear division, either during meiosis, in which a gamete is formed with the unreduced chromosome number; or at mitosis to give a cell with a doubled chromosome number.

restriction endonuclease A class of enzymes that cut DNA after recognizing a specific sequence. The three types of restriction endonuclease are: I. Where the cut occurs within a random sequence at sites >1kbp from the recognition sequence, and has both restriction and methylation activities. II: Cuts within, or near a short, usually palindromic recognition sequence. A separate enzyme methylates the same recognition sequence. III: Cuts 24-26bp downstream from a short, asymmetrical recognition sequence, requires ATP and has both restriction and methylation activities. Type II enzymes are the class used for most molecular biology applications.

restriction enzyme Synonym of restriction endonuclease.

restriction exonuclease A class of enzymes that degrade DNA or RNA, starting from either the 5'- or the 3'-end.

restriction fragment A shortened DNA molecule generated by the cleavage of a larger molecule by one or more restriction endonucleases.

restriction fragment length polymorphism (Abbreviation: RFLP). A class of genetic marker based on the detection of variation in the length of restriction fragments generated when DNA is treated with restriction endonucleases. Differences in fragment lengths arise due to genetic variation with respect to the presence or absence of specific recognition site(s). RFLPs were initially detected by Southern hybridization but are now detected by electrophoresis of digested PCR product.

restriction map The linear arrangement of restriction endonuclease recognition sites along a DNA molecule.

restriction site Synonym of recognition site.

reticulocyte A slightly immature red blood cell.

retro-element Any of the integrated retroviruses or the transposable elements that resemble them.

retroposon A transposable element that moves via reverse transcription but lacks the long terminal repeat sequences necessary for autonomous transposition. Much of the repetitive DNA that makes up a large proportion of eukaryotic genomes consists of silenced (i.e. inactive) retroposons. Synonym: retro-transposon.

retroviral vectors Gene transfer systems based on viruses that have RNA as their genetic material.

retrovirus A class of eukaryotic RNA viruses that, by using reverse transcription, can form double-stranded DNA copies of their genomes, which can integrate into the chromosomes of an infected cell. Pathogenic retroviruses include HIV and the causative agents of many vertebrate animal cancers.

reversal transfer Transfer of a culture from a callus-supporting medium to a shoot-inducing medium.

reverse genetics See: positional cloning.

reverse mutation See: reversion.

reverse transcriptase An enzyme that uses an RNA molecule as a template for the synthesis of a complementary DNA strand. Synonym: RNA-dependent DNA polymerase.

reverse transcription The synthesis of DNA from a template of RNA, accomplished by reverse transcriptase.

reversion Restitution of a mutant gene to the wild-type condition, or at least to a form that gives the wild-type phenotype; more generally, the appearance of a trait expressed by a remote ancestor. Synonym: reverse mutation.

RF Abbreviation for replicative form.

RFLP Abbreviation for restriction fragment length polymorphism.

rh Abbreviation for recombinant human.

rhizobacterium A micro-organism whose natural habitat is near, on, or in, plant roots.

Rhizobium (pl.: Rhizobia) Prokaryotic species which are able to establish a symbiotic relationship with leguminous plants, as a result of which elemental nitrogen is fixed or converted to ammonia. See: nitrogen fixation.

rhizosphere The soil region in the immediate vicinity of growing plant roots.

Ri plasmid A class of large conjugative plasmids found in the soil bacterium Agrobacterium rhizogenes, which can infect certain plants and cause hairy root disease. Like Ti plasmids, Ri plasmids include sequences that are transferred to plant cells and inserted into the plant's DNA as part of the infection process.

RIA Abbreviation for radioimmunoassay.

ribonuclease (Abbreviation: RNAse). Any enzyme that catalyses the hydrolysis of RNA.

ribonucleic acid (Abbreviation: RNA). An organic acid polymer composed of adenosine, guanosine, cytidine and uridine ribonucleotides. The genetic material of some viruses, but more generally is the molecule, derived from DNA by transcription, that either carries information (messenger RNA), provides sub-cellular structure (ribosomal RNA), transports amino acids (transfer RNA), or facilitates the biochemical modification of itself or other RNA molecules.

ribonucleoside See: nucleoside.

ribonucleotide See: nucleotide.

ribose A monosaccharide found in all ribonucleosides, ribonucleotides and RNA. Its close analogue, 2-deoxyribose, is similarly found in all deoxyribonucleosides, deoxyribonucleotides and DNA.

ribosomal binding site A sequence of nucleotides near the 5' end of a bacterial mRNA molecule that facilitates the binding of the mRNA to the small ribosomal sub-unit. Also called the Shine-Delgarno sequence.

ribosomal DNA The coding locus for ribosomal RNA. This is generally a large and complex locus, typically composed of a large number of repeat units, separated from one another by the intergenic spacer. A repeat unit comprises a gene copy for each individual ribosomal RNA component, separated from one another by the internal transcribed spacer.

ribosomal RNA (Abbreviation: rRNA). The RNA molecules that are essential structural and functional components of ribosomes, where protein synthesis occurs. Different classes of rRNA molecule are identified by their sedimentation (S) values. E. coli ribosomes contain one 16S rRNA molecule (1541 nucleotides long) in one (small) ribosomal sub-unit, and a 23S rRNA (2904 nucleotides) and a 5S rRNA (120 nucleotides) in the other (large) sub-unit. These three rRNA molecules are synthesized as part of a large precursor molecule which also contains the sequences of a number of tRNAs. Special processing enzymes cleave this large precursor to generate the functional molecules. Constitutes about 80% of total cellular RNA.

ribosome The sub-cellular structure that contains both RNA and protein molecules and is the site for the translation of mRNA into protein. Ribosomes comprise large and small sub-units.

ribosome-inactivating protein (Abbreviation: RIP). A class of plant proteins that inhibit normal ribosome function, and are thus highly toxic. Type 1 RIPs consist of single polypeptide chain proteins; type 2 (e.g. ricin) consist of two proteins linked by a disulphide bridge, one the toxin and the other a lectin that attaches to recognition sites on a target cell.

ribozyme An RNA molecule that can catalyse chemical cleavage of itself or of other RNAs. Synonyms: catalytic RNA, gene shears.

ribulose A keto-pentose sugar (C₅H₁₁O₅) involved in the carbon dioxide fixation pathway of photosynthesis.

ribulose biphosphate (Abbreviation: RuBP). A five-carbon sugar combined with carbon dioxide to form a six-carbon intermediate in the first stage of the dark reaction of photosynthesis.

rinderpest Cattle plague; a viral infection of cattle, sheep and goats.

RIP Abbreviation for ribosome-inactivating protein.

risk analysis A process consisting of three components: risk assessment, risk management and risk communication performed to understand the nature of unwanted, negative consequences to human and animal health, or the environment.

risk assessment a scientifically based process consisting of the following steps: i) hazard identification; ii) hazard characterization; iii) exposure assessment; and iv) risk characterization.

risk communication The interactive exchange of information and opinions throughout the risk analysis process concerning hazards and risks, risk-related factors and risk perceptions, among risk assessors, risk managers, consumers, industry, the academic community and other interested parties, including the explanation of risk assessment findings and the basis of risk management decisions.

risk management The process, distinct from risk assessment, of weighing policy alternatives, in consultation with all interested parties, considering risk assessment and other factors relevant for the health protection of consumers and for the promotion of fair trade practices, and, if needed, selecting appropriate prevention and control options.

R-loops Single-stranded DNA regions in RNA-DNA hybrids formed in vitro under conditions where RNA-DNA duplexes are more stable than DNA-DNA duplexes.

RNA Abbreviation for ribonucleic acid.

RNA editing Post-transcriptional processes that alter the information encoded in RNAs.

RNA polymerase A polymerase enzyme that catalyses the synthesis of RNA from a DNA template.

RNAase Abbreviation for ribonuclease.

RNA-dependent DNA polymerase See: reverse transcriptase.

RNase Abbreviation for ribonuclease.

rol genes A family of genes, present on the Ri plasmid of Agrobacterium rhizogenes, that when transferred to a plant upon infection by the bacterium, induce the formation of roots. Used as a means of root induction on different species and cultivars of micropropagated fruit trees.

root The descending axis of a plant, normally below ground, which serves to anchor the plant and to absorb and conduct water and mineral nutrients.

root apex The apical meristem of a root; very similar to the shoot apical meristem in that it forms the three meristematic areas: the protoderm (develops into the epidermis); the procambium (the stele); and the growth meristem (the cortex).

root cap A mass of reinforced cells covering and protecting the apical meristem of a root.

root culture The culture of isolated apical or lateral root tips to produce in vitro root systems with indeterminate growth habits. Used to study mycorrhizal, symbiotic and plant-parasitic relationships.

root cutting Cutting made from sections of roots alone.

root hairs Outgrowths from epidermal cell walls of the root, specialized for water and nutrient absorption.

root nodule A small round mass of cells attached to the roots of leguminous plants, containing symbiotic nitrogen-fixing bacteroids, particularly Rhizobium spp.

root tuber Thickened root that stores carbohydrates.

root zone The volume of soil or growing medium containing the roots of a plant. In soil science, the depth of the soil profile in which roots are normally found.

rootstock The trunk or root material to which buds or scions are inserted in grafting. See: stock.

rotary shaker Rotating apparatus with a platform on which liquid media or cultures can be continuously shaken.

Roundup-readyä Describing transgenic crop varieties that carry the bacterial gene which detoxifies the herbicide glyphosate, thereby making them resistant to its application.

rRNA Abbreviation for ribosomal RNA.

RuBP Abbreviation for ribulose biphosphate.

ruminant Animal having a rumen - a large digestive sac in which fibrous plant material is fermented by commensal microbes, prior to its digestion in a "true" stomach (the abomasum). Common farm ruminants are cattle and sheep.

runner A lateral stem that grows horizontally along the ground surface and gives rise to new plants either from axillary or terminal buds. Synonym: stolon.

rust A generic descriptor for various serious fungal plant pathogens, which infect the leaves and stems of crops. The appearance of spores is reminiscent of metallic rust, although the colour varies, according to species, from yellow to reddish-brown.

S phase The phase in the cell cycle during which DNA synthesis occurs.

S₁ mapping A method to characterise post-transcriptional modifications in RNA (removal of introns etc.) by hybridizing RNA with single-stranded DNA and treating with S₁ nuclease.

S₁ nuclease An enzyme obtained from the filamentous fungus Aspergillus oryzae which specifically degrades RNA or single-stranded DNA into its constituent mononucleotides, and cleaves nicked double-stranded DNA at the nick.

saccharifaction Following liquefaction, the hydrolysis of polysaccharides by glucoamylase to maltose and glucose.

saline resistance Synonym for salt tolerance.

Salmonella A genus of rod-shaped, Gram-negative bacteria that are a common cause of food poisoning.

salt tolerance The ability of a plant in soil or in culture to withstand a concentration of common salt (sodium chloride) which is damaging or lethal to most other plants. Breeding and selection for increased tolerance and resistance in crop plants is of great current interest. Synonym: saline resistance. An organism with extreme salt tolerance is a halophyte.

sap Fluid content of the xylem and phloem cells of plants. Fluid content of the vacuole generally referred to as cell sap.

saprophyte An organism (generally a fungus) that depends on dead plant or animal tissue for its source of nutrition and metabolic energy.

satellite DNA Highly repetitive DNA in plant and animal genomes, consisting of millions of copies of sequences typically in the range 5-500 bp long. Thousands of copies occur tandemly (head-to-tail) at each of many sites. It can be isolated from the rest of the genomic DNA by density gradient centrifugation.

satellite RNA A small, self-splicing RNA molecule that accompanies several plant viruses, including tobacco ringspot virus. Synonym: viroid.

SC Abbreviation for synaptonemal complex.

SCA Abbreviation for specific combining ability.

scaffold The central proteinaceous core structure of condensed eukaryotic chromosomes. The scaffold is composed of non-histone chromosomal proteins.

scale up Conversion of a process, such as fermentation of a micro-organism, from a small laboratory scale to a larger industrial scale.

scanning electron microscope (Abbreviation: SEM). An electron-beam-based microscope used to examine, in a three dimensional screen image, the surface structure of prepared specimens.

SCAR Abbreviation for sequence characterized amplified region.

scarification The chemical or physical treatment given to certain seeds having hard, impermeable seed coats in order to puncture or weaken the seed coat sufficiently to permit water uptake and germination.

SCE Abbreviation for sister chromatid exchange.

scion A twig or bud used for grafting onto another plant or rootstock.

scion-stock interaction The effect of a rootstock on a scion (and vice versa) in which a particular scion grafted onto a specific s performs differently than it would either on its own roots or on a different rootstock.

sclerenchyma A strengthening tissue in plants, composed of cells with heavily lignified cell walls.

SCP Abbreviation for single-cell protein.

scrapie A spongiform encephalopathy disease of sheep. See: proteinaceous infectious particle.

screen Preliminary characterization of a sample collection on the basis of a set of simple established criteria (biochemical, anatomical, physiological, etc.). Often applied to the process of selection for specific purposes, such as for disease resistance or for improved agronomic performance in crop plants.

SDS Abbreviation for sodium dodecyl sulphate.

SDS-PAGE Abbreviation for sodium dodecyl sulphate polyacrylamide gel electrophoresis.

secondary antibody In an ELISA or other immunological assay system, the antibody designed to bind to the primary antibody, and to which a label is generally attached.

secondary cell wall The innermost layer of cell wall, giving rigidity to the cells. Characterized by its highly organized microfibrillar structure, and only formed in certain cells after cell elongation has ceased.

secondary growth Type of growth characterized by an increase in the thickness of stem and root, and resulting from the formation of secondary vascular tissues by the vascular cambium.

secondary immune response The rapid immune response that occurs during the second (and subsequent) encounters of the immune system of a mammal with a specific antigen. See: primary immune response.

secondary messenger A chemical compound within a cell that is responsible for initiating the response to a signal from a chemical messenger (such as a hormone) that cannot enter the target cell itself.

secondary metabolism The production by living organisms of substances not essential for primary metabolic functions or physiology. Their role is associated with interaction with the environment, for example for defence, as elicitors or as attractants. Some of these have useful pharmacological or nutritional properties, while others are toxic.

secondary metabolite Product of secondary metabolism.

secondary oocyte See: oocyte.

secondary phloem Phloem tissue formed by the vascular cambium during secondary growth in a vascular plant.

secondary plant product See: secondary metabolite.

secondary root A branch or lateral root.

secondary spermatocyte See: spermatocyte.

secondary structure Localized three dimensional conformations adopted by macromolecules, in particular nucleic acids and polypeptides. These arise as a result of the action of non-covalent forces generated by interactions between residues which are brought into close contact with one another. Examples are alpha-helix regions and beta-pleated sheets in proteins, and hairpin loops in nucleic acids. See: primary structure, tertiary structure, quaternary structure.

secondary thickening Deposition of secondary cell wall materials which result in an increase in thickness in stems and roots.

secondary vascular tissue Vascular tissue (xylem and phloem) formed by the vascular cambium during secondary growth in a vascular plant.

secondary xylem See: secondary vascular tissue.

secretion The transport of a molecule from the inside of a cell through the cell membrane.

seed Botanically, the matured ovule without accessory parts. Colloquially, anything which may be sown; i.e. seed potatoes (which are vegetative tubers); seed of wheat (karyopses) etc.

seed storage proteins Proteins accumulated in large amounts in protein bodies within seeds. They act as a source of amino acids during germination. Of interest in biotechnology: 1. As a major source of human and animal nutritional protein. 2. As a model expression system. Since they are produced in large amounts relative to other proteins, and are stored in stable, compact bodies in the plant seed, it may be possible to engineer transgenes which are expressed in the same way as seed storage proteins - i.e. in large amounts and in a convenient form.

segment-polarity gene A gene that functions to define the anterior and posterior components of body segments in Drosophila.

segregant An individual derived from a cross between two unlike parents.

segregation For genes, the separation of allele pairs from one another and their resulting assortment into different cells at meiosis. For chromosomes, the separation and re-assortment of the two homologues in anaphase of the first meiotic division. For individuals, the occurrence of different genotypes and/or phenotypes among offspring, resulting from chromosome or allele separation in their heterozygous parents.

selectable Having a gene product that, when present, enables the identification and preferential propagation of a particular genotype. See: reporter gene.

selectable marker A gene whose expression allows the identification of a specific trait or gene in an organism.

selection 1. Differential survival and reproduction of phenotypes. 2. A system for either isolating or identifying specific genotypes in a mixed population.

selection coefficient A measure of the intensity of selection at a locus, commonly abbreviated as s. It represents the proportionate reduction in the gametic contribution of a particular genotype, compared with the (generally most favoured) standard genotype.

selection culture A selection based on difference(s) in environmental conditions or in culture medium composition, such that preferred variant cells or cell lines (presumptive or putative mutants) are favoured over other variants or the wild type.

selection differential The difference between the mean of the individuals selected to be parents and the mean of the overall population; it represents the average superiority of the selected parents; commonly abbreviated as S.

selection pressure The intensity of selection acting on a population of organisms or on cells in culture. Its effectiveness is measured in terms of differential survival and reproduction, and consequently in changes in allele frequency in a population.

selection response The difference between the mean of the individuals selected to be parents and the mean of their offspring. Predicted response is calculated as the product of narrow-sense heritability and selection differential.

self-incompatibility In plants, the inability of the pollen to fertilize ovules (female gametes) of the same plant.

self-replicating elements Extrachromosomal DNA elements that have origins of replication for the initiation of their own DNA synthesis.

self-sterility Synonym of self-incompatibility.

SEM Abbreviation for scanning electron microscope.

semen sexing Synonym of sperm sexing.

semi-conservative replication During DNA duplication, each strand of a parent DNA molecule acts as a template for the synthesis of a new complementary strand. Thus, one half of a pre-existing DNA molecule is conserved during each round of replication.

semi-continuous culture Cells in an actively dividing state which are maintained in culture by periodically draining off the medium and replenishing it with fresh medium.

semi-permeable membrane A natural or synthetic material which selectively allows the passage of certain ions or molecules.

semi-sterility The condition of partial fertility. Often associated with chromosomal aberrations or the result of mutagenesis.

senescence A late stage in the development of multicellular organisms, during which irreversible loss of function and degradation of biological components occur. The physiological ageing process in which cells and tissues deteriorate and finally die.

sense RNA The RNA transcript of the coding strand DNA (often represented as the (+)-strand). Opposite: antisense RNA. When both sense and antisense transcripts of a gene are present simultaneously, gene silencing is often the result.

sensitivity In diagnostic tests, the smallest amount of the target molecule that the assay can detect.

sepsis Destruction of tissue by pathogenic micro-organisms or their toxins, especially through infection of a wound.

septate (adj.) See: septum.

septum A dividing wall or partition, which splits a structure into separate cells or compartments.

sequence The linear order of nucleotides along a DNA or RNA molecule, and the process of obtaining this. Genome sequencing aims to generate the linear order of all nucleotides present in the nuclear DNA of an organism.

sequence characterized amplified region (Abbreviation: SCAR). A molecular marker obtained by the conversion to a sequence-tagged site of a single random amplified polymorphic DNA product.

sequence divergence The percent difference in the nucleotide sequence between related nucleic acid sequences, or in the amino acid sequence in a comparison between related proteins.

sequence hypothesis The concept that genetic information exists as a linear DNA code, and that DNA and gene product sequence are collinear.

sequence tandem repeat (Abbreviation: STR). See: tandem repeat.

sequence-tagged site (Abbreviation: STS). Short unique DNA sequence (200-500 bp long) that can be amplified by PCR and is thus tagged to the site on the chromosome from which it was amplified.

serial division Splitting of excised shoot-tip material growing in vitro, in order to induce the development of greater numbers of plantlets.

serial float culture A technique whereby immature anthers are floated on a liquid medium, and continue their development through to the release of pollen.

serology The study of serum reactions between an antigen and its antibody. Mainly used to identify and distinguish between antigens, such as those specific to particular micro-organisms or viruses.

serum Blood plasma that has had its clotting factor removed.

serum albumin A globular protein obtained from blood and body fluids. Bovine and human serum albumins are abbreviated BSA and HSA respectively.

sewage treatment A widespread biotechnological processes in developed economies. Methods vary widely, but all are designed for the biological break-down of human and animal waste in order to allow safe discharge into the environment.

sex chromosome Differentiated chromosome which is responsible for the determination of sex of the individual. For all mammals, a small number of flowering plants and many insects, female individuals carry a pair of X chromosomes, and males carry one X and one Y. For birds, reptiles and most amphibians, male individuals carry a pair of W chromosomes, and females carry one W and one Z. In some insects there is only one sex chromosome, X, and sex is determined by the number of these present. Synonym: allosome. Opposite: autosome.

sex determination Any method by which the distinction between males and females is established in a species, particularly at an early stage of foetal development.

sex duction The incorporation of bacterial genes into F factors and their subsequent transfer, by conjugation, to a recipient cell.

sex factor A bacterial episome (e.g. the F plasmid in E. coli) that enables the cell to be a donor of genetic material. The sex factor may be propagated in the cytoplasm, or it may be integrated into the bacterial chromosome.

sex hormones Steroid hormones that control sexual development in animals.

sex linkage Referring to genes present on one of the sex chromosomes, thus genetically linked to the sex of the individual.

sex mosaic Synonym of gynandromorph.

sexed embryos Embryos separated according to sex.

sex-influenced dominance The tendency for gene action to vary between the sexes within a species. For example, the presence of horns in some breeds of sheep appears to be dominant in males but recessive in females.

sex-limited Expression of a trait in only one sex; e.g. milk production in mammals; egg production in chickens.

sexual reproduction The process whereby two gametes fuse to form one fertilized cell (zygote).

shake culture An agitated suspension in culture providing adequate aeration for cells in the liquid medium. Usually achieved using platform shakers, or by constant stirring with a magnetic stirrer.

shaker A platform, with set or variable speed control, used to agitate vessels containing liquid cell cultures. Also described as a platform shaker.

shear Literally the sliding of one layer across another, with deformation and fracturing in the direction parallel to the movement. In the present context, used to describe 1. the forces that cells are subjected to in a bioreactor or a mechanical device used for cell breakage. 2. the intentional or unintentional fragmentation of large DNA molecules, achieved commonly by passing a concentrated DNA solution through a hypodermic needle. This treatment generates random breaks in the DNA, and the average size of fragments can be manipulated by varying the bore of the needle.

Shine-Dalgarno sequence A conserved sequence of prokaryotic mRNAs that is complementary to a sequence near the 5' terminus of the 16S ribosomal RNA and is involved in the initiation of translation. See: ribosomal binding site.

shoot apex See: shoot tip.

shoot differentiation The development of growing points, leaf primordia and finally shoots from a shoot tip, axial bud, or callus surface.

shoot tip The terminal bud (0.1 - 1.0 mm) of a plant, which consists of the apical meristem (0.05 - 0.1 mm) and the immediately surrounding leaf primordia and developing leaves, and adjacent stem tissue. Synonym: shoot apex.

shoot-tip graft A shoot tip or meristem tip grafted onto a prepared seedling or micropropagated rootstock in culture. Meristem tip grafting is mainly used for in vitro virus elimination from Citrus spp. and other plants. Synonym: micrograft.

short interspersed nuclear element (Abbreviation: SINE). Families of short (150-300 bp), moderately repetitive DNA elements of eukaryotic genomes. They appear to be DNA copies of certain tRNA molecules, created presumably by the unintended action of reverse transcriptase during retroviral infection.

short-day plant A plant which will not flower until triggered to do so by exposure to one or a number of dark periods equal to or longer than its critical period. Other plant species are long-day and some are daylength neutral. Genetic variation for daylength sensitivity is present in many crop species.

shotgun genome sequencing A strategy for sequencing a whole genome, in which the genomic DNA is initially fragmented into pieces small enough to be sequenced. Specialized computer software is then used to piece together the individual sequences to create long contiguous tracts of sequenced DNA.

shuttle vector A plasmid capable of replicating in two different host organisms because it carries two different origins of replication and can therefore be used to transfer genes from one to the other. Synonym: bifunctional vector.

sib-mating The deliberate crossing of siblings. Generally done where self-incompatibility prevents the production of self-fertilized progeny.

siderophore A low molecular weight entity that binds very tightly to iron. Siderophores are synthesized by a variety of soil micro-organisms to ensure that the organism is able to obtain sufficient amounts of iron from the environment.

sieve cell A long and slender sieve element in vascular plants, characterized by relatively unspecialized sieve areas and tapering end walls that lack sieve plates.

sieve element The phloem cell concerned with longitudinal conduction of food materials.

sieve plate Perforated wall area in a sieve tube element, through which strands connecting sieve tube protoplasts can pass.

sieve tube A tube within the phloem tissue of a plant, composed of joined sieve elements.

sigma factor The sub-unit of prokaryotic RNA polymerases responsible for the initiation of transcription at specific initiation sequences.

signal peptide See: signal sequence.

signal sequence A stretch of 15-30 amino acid residues at the N terminus of a protein, which is thought to enable the protein to be secreted (pass through a cell membrane). The signal sequence is removed as the protein is secreted. Synonyms: signal peptide, leader peptide.

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, ligands and messengers.

signal-to-noise ratio A specifically produced response (signal) compared to the response level (noise) when no specific stimulus (activity) is present.

silencing Loss of gene expression either through an alteration in the DNA sequence of a structural gene, or its regulatory region; or because of interactions between its transcript and other mRNAs present in the cell (see: antisense RNA).

silent mutation See: mutation.

simple sequence repeat (Abbreviation: SSR). See: microsatellite.

SINE Abbreviation for short interspersed nuclear element.

single-cell line See: cell strain.

single-cell protein (Abbreviation: SCP). Protein produced by micro-organisms, particularly yeast. Used as either a feed or a food additive.

single copy A gene or DNA sequence which occurs only once per (haploid) genome. Many structural genes are single copy.

single domain antibody See: dAb.

single node culture Culture of separate lateral buds, each carrying a piece of stem tissue.

single nucleotide polymorphism (Abbreviation: SNP). A genetic marker resulting from variation in sequence at a particular position within a DNA sequence. SNPs are commonly the result of transition changes (A for G, T for C), but also transversions (G or A for T or C) and single base deletions. Such variation is extensive throughout all genomes, and offers the particular advantage of being detectable without the need for gel electrophoresis.

single primer amplification reaction (Abbreviation: SPAR). A PCR-based genotyping technique in which genomic template is amplified with a single primer.

single-strand conformational polymorphism (Abbreviation: SSCP). A technique for detection of mutations in a defined DNA sequence. Single-stranded polynucleotides are electrophoretically separated on non-denaturing gels. Intrachain base pairing results in a limited number of conformers stabilized by intrachain loops, and mutated DNA shows on electrophoresis an altered assortment of such conformers.

single-strand DNA binding protein A protein that coats single-stranded DNA, preventing renaturation and so maintaining the DNA in an extended state.

single-stranded DNA (Abbreviation: ssDNA). DNA molecules separated from their complementary strand, either by its absence or following denaturation.

single-stranded nucleic acid Nucleic acid molecules consisting of only one polynucleotide chain. The genomes of many viruses are single-stranded DNA molecules, as are most biologically effective RNAs. Many RNA molecules do include double-stranded regions formed by the intra-strand base-pairing of self-complementary sequences, and these determine the 3-dimensional shape (conformation) that they adopt in vivo.

sire Male animal chosen for breeding.

sister chromatid exchange (Abbreviation: SCE). Reciprocal interchanges of the two chromatid arms within a single chromosome.

site-specific A term used to describe any process or enzyme which acts at a defined sequence within a DNA or RNA molecule.

site-specific mutagenesis The induction of mutations, by molecular biology techniques, in one or more specific nucleotides within a defined coding sequence in order to create altered forms of the gene product. Used to define the active sites of proteins and for protein engineering.

sitosterol See: phytosterol.

six-base cutter Type II restriction endonucleases whose recognition site and cleavage site consist of a characteristic sequence of six nucleotide pairs. See: four-base cutter.

small nuclear ribonucleoprotein (Abbreviation: snRNP). A complex of small nuclear RNA and nuclear protein, heavily involved in the post-transcriptional processing of mRNA, especially the removal of introns. snRNPs are a major component of spliceosomes.

small nuclear RNA (Abbreviation: snRNA). RNA transcripts of 100-300 bp that associate with proteins to form small nuclear ribonucleoprotein particles. Most snRNAs are components of the spliceosomes.

SNP Abbreviation for single nucleotide polymorphism.

snRNA Abbreviation for small nuclear RNA.

snRNP Abbreviation for small nuclear ribonucleoprotein.

sodium dodecyl sulphate (Abbreviation: SDS). A detergent used to solubilize protein and DNA from biological materials. Specific use in sodium dodecyl sulphate polyacrylamide gel electrophoresis.

sodium dodecyl sulphate polyacrylamide gel electrophoresis (Abbreviation: SDS-PAGE). A widely employed electrophoretic method for the separation of proteins from biological samples. The sodium dodecyl sulphate gives a uniform charge density to the surface of proteins or nucleic acids, so that their rate of migration through the gel is determined largely by their molecular weight.

soil amelioration The improvement of poor soils. Includes the fungal and bacterial break down of plant organic matter, to form humus; the release of minerals - such as phosphates - to the soil, making them available to plants; the fixation of nitrogen. Can sometimes include an element of bioremediation.

soil-less culture Growing plants in nutrient solution without soil. Synonym: hydroponics.

solid medium Nutrient medium solidified by the addition of a gelling agent, commonly agar.

somaclonal variation Epigenetic or genetic changes induced during the callus phase of plant cells cultured in vitro. Sometimes visible as changed phenotype in plants regenerated from culture.

somatic Referring to cell types, structures and processes other than those associated with the germ line.

somatic cell Cells not involved in sexual reproduction, i.e. not germ cells.

somatic cell embryogenesis The process of differentiation of somatic embryos either from explant cells (direct embryogenesis), or from callus generated from explants (indirect embryogenesis). Synonym: asexual embryogenesis.

somatic cell gene therapy The delivery of a transgene(s) to a somatic tissue in order to correct a physiological defect.

somatic cell hybrid panel A panel of cells created by cell fusion, typically involving a reference species (e.g. hamster) and the species of interest (e.g. sheep) with each member of the panel containing a different mixture of chromosomes from the two species. By relating the presence or absence of cloned fragments (via in situ hybridization) or PCR products to the presence or absence of particular chromosomes from the species of interest, such panels can be used for physical mapping.

somatic cell variant A somatic cell with unique characters not present in the other cells, and which could be selected for by an appropriate screen.

somatic embryo An organized embryo-like structure. Although morphologically similar to a zygotic embryo it is initiated from somatic plant cells. Under in vitro conditions, somatic embryos go through developmental processes similar to embryos of zygotic origin. Each somatic embryo is potentially capable of developing into a normal plantlet.

somatic hybridization Naturally occurring or induced fusion of somatic protoplasts or cells of two genetically different parents. The difference may be as wide as interspecific. Wide synthetic hybrids formed in this way (i.e. not via gametic fusion) are known as cybrids. Not all cybrids contain the full genetic information (nuclear and non-nuclear) of both parents.

somatic hypermutation The high frequency of mutation that occurs in the gene segments encoding the variable regions of immunoglobulins during the differentiation of B lymphocytes into antibody producing plasma cells.

somatic reduction Halving of the chromosomal number of somatic cells; a possible method of producing "haploids" from somatic cells and calli by artificial means.

somatocrinin Growth hormone-releasing hormone. See: growth hormone.

somatostatin Growth hormone-inhibiting hormone. See: growth hormone.

somatotropin See: growth hormone.

sonication Disruption of cells or DNA molecules by high frequency sound waves.

SOS response The synthesis of a whole set of DNA repair, recombination and replication proteins in bacteria suffering severe DNA damage (e.g. following exposure to UV light).

source DNA The DNA from an organism that contains a target gene, and used as the starting material in a cloning experiment.

source organism A bacterium, plant or animal from which DNA is purified and used in a cloning experiment.

Southern blot A nitrocellulose or nylon membrane to which DNA fragments previously separated by gel electrophoresis, have been transferred by capillary action. See: blot.

Southern hybridization A procedure in which a cloned, labelled segment of DNA is hybridized to DNA restriction fragments on a Southern blot.

spacer sequence A DNA sequence separating neighbouring genes; spacer sequences are not usually transcribed.

SPAR Abbreviation for single primer amplification reaction.

sparger A device that introduces, into a bioreactor, air in the form of fine bubbles.

spatial autocorrelation statistics A set of statistical parameters aimed to depict the spatial (geographical) pattern of genetic diversity in a population.

speciation The evolutionary differentiation of a pre-existing species into one or more distinct species.

species A class of individuals capable of interbreeding, but which is reproductively isolated from other such groups having many characteristics in common. A somewhat arbitrary and sometimes blurred classification; but still quite useful in many situations.

specific combining ability (Abbreviation: SCA). A component of genetic variance calculable where a number of genotypes are intercrossed in all possible combinations. The SCA measures the deviation of the performance of a particular cross from the average general combining ability of its two parents.

specificity For diagnostic tests, the ability of a probe to react precisely and uniquely with its target molecule.

spent medium After sub-culture, medium which is discarded because it has been depleted of nutrients, dehydrated, or accumulated toxic metabolic products.

sperm Abbreviation for spermatozoon.

sperm competition Competition between different spermatozoa to fertilize the egg cell of a single female.

sperm sexing The separation of mammalian sperm into those bearing an X chromosome and those bearing a Y chromosome, in order to be able to produce, via artificial insemination or in vitro fertilization, animals of a specified sex. Methods for achieving this include the inactivation of X-bearing or Y-bearing sperm by antibodies recognizing sex-specific sperm surface peptides, and fluorescence-activated cell sorting.

spermatid Immature spermatozoon. One of the four cells formed at the end of the second meiotic division in spermatogenesis.

spermatocyte The premeiotic parental cell of the spermatids; the primary spermatocyte before the initiation of the first meiotic division; the secondary spermatocyte after completion of the first meiotic division, but before the initiation of the second division. Synonym: sperm mother cell.

spermatogenesis The series of cell divisions in the testis as a result of which the formation and the maturation of the male gametes (i.e. sperm) are achieved.

spermatogonium (pl.: spermatogonia) Primordial male germ cell. These can either divide by mitosis to produce daughter cells, or enter a growth phase and differentiate into a primary spermatocyte.

spermatozoon (Abbreviation: sperm). (pl.: spermatozoa) The mature, mobile gametic cell of male animals, produced in the testis.

spharoblast Nodule of wood which can give rise to adventitious shoots with juvenile characteristics.

spheroplast (AlteRNAtive spelling: sphaeroplast). A microbial or plant cell from which most of the cell wall has been removed, usually by enzymatic treatment. Strictly, in a spheroplast, some of the cell wall remains, while in a protoplast the cell wall has been completely removed. In practice, the two words are often used interchangeably.

spike 1. An inflorescence in which the main axis is elongated and the flowers are sessile. 2. The deliberate addition of a known quantity of a known substance to an analytical sample, used to validate the analytical technique.

spikelet The unit of inflorescence in grasses, made up of a small group of florets.

spindle An intracellular fibrous structure, involved in the control of chromosome movement in mitosis and meiosis.

spliceosome A complex of small nuclear ribonucleoproteins and other proteins that assemble on an immature mRNA and catalyse the excision of an intron. See: splicing.

splicing 1. During the maturation of eukaryotic mRNA, the process that removes intron sequences and covalently joins exon sequences. Synonym: editing. 2. In recombinant DNA technology, the term refers to the ligation of two fragments of DNA together.

splicing junction The DNA sequence immediately surrounding the boundary between an exon and an intron. There is a degree of sequence conservation in these regions, allowing the identification of introns in newly sequenced genes.

split gene In eukaryotes, the encoding DNA of many structural genes is made up of exons and introns. This commonly found pattern of interruption in the coding sequence is referred to as a 'split gene'.

spontaneous mutation A mutation occurring in the absence of any known mutagen.

sporangium (pl.: sporangia) A reproductive structure in plants that produces spores. A megasporangium produces megaspores, which give rise to the female gametophyte; in seed plants it is represented by the ovule. A microsporangium produces microspores, which give rise to the male gametophyte; it is represented in seed plants by the pollen sac.

spore 1. A reproductive cell that develops into an individual without union with other cells; some spores such as meiospores are the product of the germ line, but others are asexual in nature. 2. A small, protected resting body, often synthesized by micro-organisms when nutrient levels are low.

spore mother cell Synonym of sporocyte.

sporocyte A diploid germ line cell that is the parent of the four haploid spores generated by meiosis.

sporophyll A leaf that bears sporangia.

sporophyte The diploid generation in the life cycle of a plant, and that produces haploid spores by meiosis.

sport An individual plant, or portion thereof, showing a recognizably different phenotype from the parent, presumably as a result of spontaneous mutation. Novel traits displayed by some sports can become of great agricultural worth, but generally they are disadvantageous.

ssDNA Abbreviation for single-stranded DNA.

SSR Abbreviation for simple sequence repeat. See: microsatellite.

stacked genes Refers to the insertion of two or more genes into the genome of an organism. An example would be a plant carrying a Bt transgene giving insect resistance, and a bar transgene giving resistance to a specific herbicide.

stages of culture (I-IV) See: micropropagation.

staggered cuts Symmetrically cleaved phosphodiester bonds that lie on both strands of double-stranded DNA, but are not opposite one another.

stamen Floral structure made up of an anther and a filament. The stamen is the male organ of a flower.

standard deviation A statistical measure of variability in a population of individuals or in a set of data.

standard error A statistical measure that indicates the predictive accuracy over all individuals of a mean value derived from a sample population.

starch The major plant carbohydrate storage substance, particularly but not exclusively found in seeds, and used both as food and feed source and for various industrial processes. A large water-insoluble heterogenous group of polysaccharides, consisting of various proportions of the two glucose polymers, amylose and amylopectin. Starch is broken down into simple metabolisable sugars in vivo by the action of amylases.

start codon The codon which specifies the first amino acid of a polypeptide chain and at which the ribosome starts the process of translation. In bacteria, this is either AUG (translated as n-formyl methionine) or, rarely, GUG (valine). In eukaryotes, it is always AUG and is translated as methionine. The start codon sets the reading frame for translation. Synonym: initiation codon.

starter culture Micro-organisms that are deliberately added to foods to alter flavour, colour, texture, smell, or taste.

stationary culture A culture maintained without agitation.

stationary phase The plateau of the growth curve, during which cell number remains relatively constant, following the logarithmic phase. See: growth phases.

steady state In a continuous fermentation process, the condition under which the number of cells removed with the outflow is exactly balanced by the number of newly synthesized cells.

stele The central vascular cylinder, inside the cortex, of roots and stems of higher plants.

stem The main body of the above-ground portion of a tree, shrub, herb or other plant; the ascending axis, whether above or below ground, of a plant.

stem cell An undifferentiated somatic cell that is capable of either division to give rise to daughter stem cells, or differentiating into any specialized cell type given the appropriate signals. Cultured stem cells are critical to the concept of therapeutic cloning.

sterile 1. Medium or object free of viable micro-organisms (see: disinfect). 2. Incapable of producing viable gametes.

sterile room Dedicated space for the carrying out of activities that require sterile conditions. Can usually be achieved more economically with a laminar air-flow cabinet.

sterility Complete or partial failure of an individual to produce functional gametes or viable zygotes under a given set of environmental conditions.

sterilize 1. The elimination of micro-organisms, using heat, irradiation, filtration or chemicals. 2. The operation of making an animal incapable of producing offspring.

Steward bottle Flask developed for the growth of cells and tissues in a liquid medium, in which they can be periodically submerged during rotation.

sticky end See: extension.

stigma Receptive portion of the style, to which pollen adheres.

stirred-tank fermenter A growth vessel in which cells or micro-organisms are mixed by mechanically-driven impellers.

stock The lower portion of a graft. See: rootstock.

stock plant The source plant from which cuttings or explants are obtained. Stock plants should be well maintained to optimize explant and cutting quality.

stock solution Pre-prepared solution of commonly used reagents.

stolon A lateral stem that grows horizontally along the ground surface. Used by some plant species as a mechanism for dispersal, since stolon nodes can differentiate into normal stems and roots, giving rise to a daughter plant removed from the parent.

stoma (pl.: stomata) 1. Any of various small openings or pores in an animal body, especially an opening resembling a mouth in various invertebrates. 2. A pore in the epidermis of the leaf or stem of a plant, which allows the exchange of gases, including water vapour, to and from the intercellular spaces. Sometimes used loosely to refer to the pore along with its associated pair of guard cells. Synonym: stomate. See: stomatal complex.

stomatal complex Includes the stoma, together with its guard cells and, when present, any related subsidiary cells.

stomatal index A measurement of the surface density of stomata. This parameter has been found useful in comparing leaves of different sizes. Relative humidity and light intensity during leaf development affect the value of stomatal index.

stop codon A set of three nucleotides for which there is no corresponding tRNA molecule to insert an amino acid into the polypeptide chain. Protein synthesis is hence terminated and the completed polypeptide released from the ribosome. Three stop codons are known: UAA (ochre), UAG (amber) and UGA (opal). Synonyms: chain terminator; nonsense codon, termination codon.

STR Abbreviation for sequence tandem repeat. See: tandem repeat.

strain A group of individuals derived by descent from a single individual within a species.

stratification Subjection of moist seeds to a period of low temperature (+2 to +4 °C) to break dormancy.

streptavidin A microbial protein with a high affinity for the B complex vitamin biotin. The specific interaction of these two molecules has been exploited in labelling technology and in applications where a specific molecule needs to be captured or purified.

stress Non-optimal conditions for growth. Stresses may be imposed by biotic (pathogens, pests) or abiotic (environment, such as heat, drought etc.) factors.

stress protein See: heat shock protein.

stringency Reaction conditions (notably temperature, salt concentration and pH) that affect the annealing process of single-stranded DNA or RNA to make double-stranded DNA or RNA, or DNA/RNA hybrids. At high stringency, duplexes form only between strands with perfect complementarity; lower stringency allows the annealing of strands with some degree of mismatch.

stringent plasmid A plasmid that can only replicate at the same time as does the main bacterial chromosome, and is present as a single or, at most, several copies per cell.

stroma The supporting connective tissue of an organ or plastid.

structural gene A gene that encodes a polypeptide, with either enzymatic or structural functions, and that is required for the normal metabolism and growth of a cell or organism.

structure-functionalism The scientific tradition that stresses the relationship between a physical structure and its function, e.g. the related disciplines of anatomy and physiology.

STS Abbreviation for sequence-tagged site.

style Slender column of tissue that arises from the top of the ovary and terminates in the stigma, and through which the pollen tube must grow to achieve fertilization.

sub-clone A procedure in which a large cloned DNA molecule is divided into smaller fragments, each one of which is then separately cloned.

sub-culture Division and transfer of a portion of a culture to fresh medium. Sometimes used to denote the adding of fresh liquid to a suspension culture. Synonym: passage.

sub-culture interval The time between consecutive sub-cultures of cells.

sub-culture number The number of times cells, etc., have been sub-cultured..

subgenomic promoter A promoter added to a virus for a specific heterologous gene, resulting in the formation of mRNA for that gene alone.

subspecies Population(s) of organisms sharing certain characteristics that are not present in other populations of the same species.

sub-strain Derived from a strain by the isolation of an individual or group of individuals having properties or markers not shared by the strain as a whole.

substrate 1. A compound that is altered by an enzyme. 2. Food source for growing cells or micro-organisms. 3. Material on which a sedentary organism lives and grows.

sub-unit vaccine One or more immunogenic proteins, either purified from the pathogen itself or produced from a cloned pathogen gene. A vaccine composed of a purified antigenic determinant that is separated from the virulent organism.

sucker A shoot that arises from an underground root or stem. Of particular significance to grafted plants, since the sucker will be genotypically rootstock, rather than scion.

suckering Type of vegetative propagation where lateral buds grow out to produce an individual that is a clone of the parent.

sucrose density gradient centrifugation A procedure used to fractionate nucleic acids on the basis of their size.

superbug Jargon for a particular engineered strain of Pseudomonas, in which various hydrocarbon-degrading genes, derived from different plasmids, were combined into one genotype. This provided the basis for the precedent-setting legal decision that declared that genetically engineered organisms were patentable. See: Chakrabarty decision

supercoil The conformation of a double-stranded DNA molecule placed under torsional stress as a result of interactions with proteins. The stress is accommodated by a twist imposed on the duplex. A left-handed supercoil favours unwinding of the double helix; a right-handed supercoil favours tighter winding.

supercoiled plasmid The predominant in vivo form of most plasmids, in which the DNA is coiled around histone-like proteins. When supporting proteins are stripped away during DNA extraction from the bacterial cell, the plasmid molecule also tends to supercoil around itself in vitro.

supergene A group of tightly linked genes that are co-inherited, and may be functionally related.

supernatant The liquid phase remaining after insoluble materials are pelleted by centrifugation or precipitation.

suppressor mutation A mutation that reverses the effect of an earlier mutation, e.g. a mutation in a gene for a tRNA that permits it to read and override an amber mutation.

suppressor-sensitive mutant An organism that can grow in the presence, but not in the absence of a second genetic factor (the suppressor).

susceptible Inability to withstand injury due to biotic or abiotic stress. Opposite: resistance, tolerance.

suspension culture A type of culture in which cells and/or clumps of cells grow and multiply while suspended in a liquid medium.

symbiont An organism living in symbiosis with another, dissimilar organism.

symbiosis The close association of two different kinds of living organisms where there is benefit to both or where both receive an advantage from the association. A prominent example is the colonization of Rhizobium spp. inside the roots of leguminous plants.

sympatric speciation The evolution of new species by populations that inhabit the same or overlapping geographic regions.

sympodial A type of plant development in which the terminal bud of the stem stops growing due either to its abortion, or to its differentiation into a floral meristem. Frequently, the uppermost lateral bud then takes over the further axial growth of the stem.

synapsis Synonym of chromosome pairing.

synaptonemal complex (Abbreviation: SC). A ribbon-like proteinaceous structure formed between paired homologous chromosomes at the end of the first meiotic prophase. The SC binds the chromatids along their length, and facilitates crossing over.

synchronous culture A culture in which the cell cycle is synchronized for the majority of the cells present. Synchrony can be induced by the addition of drugs which arrest the cell cycle at specific stages.

syncytium A group of cells in which cytoplasmic continuity is maintained; the effect is of a multinucleate cell.

syndrome A group of specific characters that occur together, and are characteristic of a particular disease or genetic condition (e.g. Down's syndrome).

synergid One of the two haploid nuclei at the micropylar end of the embryo sac of higher plants. The third nucleus is the egg.

synergism An interaction between two organisms (e.g. Rhizobium and legumes) in which the growth of one is helped by the other. Opposite: antagonism.

syngamy Synonym of fertilization.

synkaryon The initial hybrid nucleus of the zygote, formed by the fusion of the gametic nuclei upon fertilization. A hybrid nucleus formed by the fusion of two different somatic cells during somatic cell hybridization is called a heterokaryon.

synteny The occurrence of two or more loci on the same chromosome, without regard to their genetic linkage. Increasingly used to describe the conservation of gene order between related species.

T Abbreviation for thymine.

T cell Lymphocytes which pass through the thymus gland during maturation. Different kinds of T cells play important roles in the immune response. Synonym: T lymphocyte. See: T-cell-mediated (cellular) immune response.

T cell receptor An antigen-binding protein, located on the surface of mammalian killer T cells, which mediates the cellular immune response. T cell antigen encoding genes are assembled from gene segments by somatic recombination processes that occur during lymphocyte differentiation.

T lymphocyte See: T cell.

T₀, T₁ and T₂ Successive generations of plants following a transformation event. The parent transformed plant is T₀, its immediate progeny is T₁, and the progeny of the T₁ are T₂ plants etc. Of particular interest is the stability of transgene expression from T₀ to T₂, and beyond.

T4 DNA ligase An enzyme, present in bacteria infected with bacteriophage T4, which catalyses the joining (ligation) of, and repairs nicks in, duplex DNA molecules. Ligation activity requires that one DNA molecule has a 5'-phosphate group, and that the other has a free 3'-hydroxyl group.

tag See: label.

tailing The in vitro addition, to the 3'-hydroxyl ends of a double-stranded DNA molecule, of multiple copies of a single nucleotide by the enzyme terminal transferase. Synonym: homopolymeric tailing.

tandem array See: tandem repeat.

tandem repeat Two (or more) contiguous identical DNA sequences. The orientation can be either head-to-tail, or head-to-head. Synonyms: tandem array, sequence tandem repeat.

tank bioreactor A fermentation vessel designed to grow large scale quantities of a micro-organism (bacteria, yeast or fungi). Most tank bioreactors are designed to be stirred mechanically, since this allows effective distribution throughout the culture of gas and nutrients. Alternative bioreactors use fibre or membrane surfaces to immobilize the cultured cells.

tap root Root system in which the primary root has a much larger diameter than any lateral roots (e.g. carrot). Opposite: fibrous root.

Taq polymerase A heat-stable DNA polymerase isolated from the thermophilic bacterium Thermus aquaticus, widely used in PCR.

target In diagnostic tests, the molecule or nucleic acid sequence assayed in a sample. In mutagenesis, the gene sequence that needs to be altered to generate the desired change in phenotype.

target site duplication A short sequence of DNA duplicated when a transposable element inserts at a new locus; usually found at each end of the insertion.

targeted drug delivery A method of delivering the activated form of a drug molecule to the site in the body where it is needed, rather than allowing it reach the target by uncontrolled diffusion.

targeting vector A cloning vector carrying a DNA sequence capable of participating in a recombinational event at a specified chromosomal location in the host cell.

TATA box A widely conserved adenine- and thymine-rich DNA sequence found 25-30 bp upstream of the transcription initiation point of many eukaryotic genes. The TATA box is implicated in the promotion of gene transcription as it acts as a binding site for RNA polymerase. Analogous to the Pribnow box in prokaryotic promoters. Synonym: Hogness box.

tautomeric shift The transfer of a hydrogen atom from one position in an organic molecule to another position. Tautomers can have widely different biological activities, as the shift can induce a significant change in the conformation of the molecule.

tautomerism A type of isomerism in which the two isomers arising from a tautomeric shift are in equilibrium.

T-cell-mediated (cellular) immune response The synthesis of antigen-specific T cell receptors and the development of killer T cells in response to an encounter of immune system cells with an unrecognized immunogenic molecule.

T-DNA The DNA segment of the Ti plasmid, present in pathogenic Agrobacterium tumefaciens, that is transferred to plant cells and inserted into the plant's DNA as part of the infection process. Wild type T-DNA encodes enzymes that induce the plant to synthesize specific opines that are required for bacterial growth. In engineered T-DNAs, these genes are replaced by a transgene(s).

telomerase An enzyme that maintains the structure of the telomere by adding the required repetitive sequences to the ends of eukaryotic chromosomes.

telomere The structure found at the end of eukaryotic chromosomes containing specialized repetitive (and widely conserved across species) DNA sequences, which are necessary to assure the completion of a cycle of DNA replication.

telophase The last stage in each mitotic or meiotic division, in which the chromosomes coalesce at each pole of the dividing cell.

temperate phage A phage (virus) that invades but does not normally destroy (lyse) the host bacterial cell. Under specific circumstances, the lytic cycle is induced, resulting in the release of infective phage particles.

temperature-sensitive mutant An organism that can grow at one temperature but not at another.

temperature-sensitive protein A protein that is functional at one temperature but loses function at another (usually higher) temperature.

template An RNA or single-stranded DNA molecule, used by polymerases to generate a complementary nucleotide strand.

template strand See: anticoding strand.

terminal bud A branch tip, an undeveloped shoot containing rudimentary floral buds or leaves, enclosed within protective bud scales.

terminal transferase An enzyme that catalyses the addition of nucleotides to the 3' end of a DNA molecule.

terminalization Repelling movement of the centromeres of bivalents in the diplotene stage of the meiotic prophase, that appears to move visible chiasmata toward the ends of the bivalents.

termination codon See: stop codon.

termination signal In transcription, a nucleotide sequence that specifies RNA chain termination.

terminator 1. A DNA sequence just downstream of the coding segment of a gene, which is recognized by RNA polymerase as a signal to stop synthesizing mRNA. 2. A term used in GMO technology for a transgenic method which genetically sterilizes the progeny of the planted seed, thereby preventing the use of farm-saved seed.

terminator codon See: stop codon.

terminator gene A specific variety-level genetic use restriction technology. A patented technique.

terminator region A DNA sequence that signals the end of transcription.

tertiary structure The three-dimensional conformation taken up by complete macromolecules as a result of intramolecular interactions, such as hydrogen-bonding. See: primary structure, secondary structure, quaternary structure.

testcross A cross between a genetically unknown individual and a recessive tester to determine whether the individual in question is heterozygous or homozygous for a certain allele. It can also used as a method to test for linkage, i.e. to estimate recombination fraction.

testis (pl.: testes) Male sex organ where spermatozoa mature and are stored.

testosterone Male hormone, synthesized in the testis of mammals; used to induce sex reversal in fish.

test-tube fertilization See: in vitro fertilization.

tetracycline An antibiotic that interferes with protein synthesis in prokaryotes. A gene encoding resistance to tetracycline has been widely used as a marker to distinguish between transformed and non-transformed cells in the production of transgenic plants.

tetrad The four haploid cells formed after the second meiotic division in plants (pollen tetrads) or fungi (ascospores).

tetraploid An organism, or a tissue whose cells contain four haploid sets of chromosomes.

tetrasomic (Noun: tetrasome). Pertaining to a nucleus or an organism with four members of one of its chromosomes, whereas the remainder of its chromosome complement is diploid. Chromosome formula: 2n + 2.

tetratype In fungi, a tetrad of spores that contains four different types; e.g. AB, aB, Ab and ab.

TGGE Abbreviation for thermal gel gradient electrophoresis.

thallus Plant body without true roots, stems, or leaves.

therapeutic agent A compound used for the treatment of a disease or for improving the well-being of an organism. Synonyms: pharmaceutical agent, drug.

therapeutic cloning The potential use of stem cells to grow, in vitro, tissue or organs for use in transplantation. Because these cells would be obtained from, and would therefore be genetically identical to the patient's own cells, problems of transplant rejection would be overcome. The technique would also remove the difficulty of identifying an organ donor.

thermal gel gradient electrophoresis (Abbreviation: TGGE). A method for separating DNA fragments according to their mobility under increasingly denaturing conditions imposed by heat.

thermal shock Exposure to reduced or increased temperature for a significant period.

thermolabile Not resistant to heat, often in the context of a molecule which is unstable upon heating. Opposite: thermostable.

thermophile An organism which is adapted to high temperatures, such as in hot springs and geysers, smoker vents on the sea floor, and domestic hot water pipes. A wide range of bacteria, fungi and simple plants and animals can grow at temperature up to 50 °C; thermophiles grow and reproduce at above 50 °C. They can be classified, according to their optimal growth temperature, into simple thermophiles (50-65 °C); thermophiles (65-85 °C), and extreme thermophiles (>85 °C). See: mesophile, psychrophile.

thermosensitivity Loss of biological activity of a molecule at high temperature.

thermostable A molecule which retains its biological activity at some specified higher temperature. Opposite: thermolabile.

thermotherapy Exposure to elevated temperatures, a technique mainly used for virus or mycoplasma elimination, taking advantage of the higher thermostability of the host over its pathogen. Synonym: heat therapy.

thinning 1. Removal of older stems to promote new growth. 2. Removal of excess fruits to improve the size and quality of the remaining fruits. 3. Removal of seedlings spaced too closely for optimum growth.

thymidine The deoxyribonucleoside resulting from the combination of the base thymine (T) and the sugar 2-deoxy-D-ribose. See: TTP.

thymidine kinase (Abbreviation: 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.

thymidine triphosphate Abbreviation: TTP; dTTP is strictly correct but rarely used.

thymidylic acid (Abbreviation: TMP or dTMP). Synonym for thymidine 5'-monophosphate, a deoxyribonucleotide containing the nucleoside thymidine.

thymine (Abbreviation: T). One the bases found in DNA. See: thymidine.

Ti plasmid Tumour-inducing plasmid. A large plasmid present in pathogenic Agrobacterium tumefaciens, responsible for the induction of tumours in plant with crown gall disease. Engineered forms of this plasmid are central to the production of transgenics in many crop species. See: T-DNA.

tissue A group of cells of similar structure which sometimes performs a special function.

tissue culture The in vitro culture of cells, tissues or organs in a nutrient medium under sterile conditions.

titre 1. The concentration of infectious virus particles present in a suspension. 2. A measure of antibody concentration, given by the highest dilution of the sample that results either in a useable immunoassay, or in the formation of visible precipitate when challenged by the appropriate antigen.

tk Abbreviation for thymidine kinase.

TMP Abbreviation for the deoxyribonucleotide thymidine 5'-monophosphate. See: thymidylic acid.

tolerance Incomplete resistance to a given biotic or abiotic stress. Tolerant genotypes are less inhibited by the stress, but are not immune.

tonoplast The cytoplasmic membrane bordering the vacuole of plant cells. It plays a prominent role in regulating the osmotic pressure exerted by the cell sap.

topo-isomerase See: DNA topo-isomerase.

totipotency The ability of a cell or tissue to be induced to regenerate into a complete organism.

totipotent (adj.) See: totipotency.

toxicity The extent to which a toxic compound negatively affects a given trait.

toxin A compound produced by one organism, which is deleterious to the growth and/or survival of another organism of the same or different species.

tracer A substance (typically a radioactive isotope or a fluorescent dye) that can be detected by physical means, and which is used to analyse the progress of a chemical reaction or a biological process.

tracheid An elongated, tapering xylem cell, with lignified pitted walls, adapted for solute conduction and physical support. Found in conifers, ferns and related plants.

trait One of the many characteristics that define an organism. The phenotype is a description of one or more traits. Synonym: character.

trans configuration See: repulsion.

trans heterozygote A double heterozygote that contains two mutations arranged in the trans configuration.

trans test See: complementation test.

trans-acting 1. A term describing substances that are diffusable and that can affect spatially separated entities within cells. 2. A genetic element (e.g. a promoter sequence) that is effective only when present in the trans configuration.

trans-acting factor Any of the multiple ancillary DNA-binding proteins that interact with the cis-regulatory DNA sequences to control gene expression.

transcapsidation The partial or full coating of the nucleic acid of a virus particle with the coat protein of a different virus.

transcript An RNA molecule that has been synthesized from a specific DNA template. In eukaryotes, the primary transcript produced by RNA polymerase is often processed or modified in order to form functional mRNA, rRNA or tRNA. See: splicing.

transcription Synthesis of RNA from a DNA template via RNA polymerase.

transcription factor A protein that regulates the transcription of genes.

transcription unit A segment of DNA that contains signals for the initiation and termination of transcription, and is transcribed into one RNA molecule.

transcriptional anti-terminator A protein that prevents RNA polymerase from terminating transcription at specific transcription termination sequences.

transcriptional roadblock A DNA-binding protein which affects the rate at which RNA polymerases transcribe genes. The protein/DNA complex interferes with the passage of the elongation complex. In some cases these obstacles are readily bypassed, but in others a significant level of pausing or termination occurs, and this can then act as a control point for gene expression.

transducing phage See: transduction.

transduction 1. Genetic: the transfer by means of a viral vector of a DNA sequence from one cell to another. 2. Signal: any process that helps to produce biological responses to events in the environment (e.g. transduction of hormone binding into cellular events by hormone receptors).

transfection The infection of a cell with isolated viral DNA (or RNA), resulting in the production of intact viral particles.

transfer RNA See: tRNA.

transferase A class of enzymes that catalyses the transfer of a group of atoms from one molecule to another.

transformant A cell or organism that has been genetically altered through the integration of a transgene(s). Primary: the first generation following the transformation event. Secondary: progeny of the primary transformant.

transformation 1. The uptake and integration of DNA in a cell, in which the introduced DNA is intended to change the phenotype of the recipient organism in a predictable manner. 2. The conversion, by various means, of cultured animal cells from controlled to uncontrolled cell growth, typically through infection with a tumour virus or transfection with an oncogene.

transformation efficiency or frequency The fraction of a cell population that takes up and integrates the introduced transgene; expressed as the number of transformed cells recovered divided by the total number of cells in a population.

transforming oncogene A gene that, upon transfection, converts a previously immortalized cell to the malignant phenotype.

transgene An isolated gene sequence used to transform an organism. Often, but not always, the transgene has been derived from a different species than that of the recipient.

transgenesis The introduction of a gene or genes into animal or plant cells, which leads to the transmission of the input gene (transgene) to successive generations.

transgenic An individual in which a transgene has been integrated into its genome. In transgenic eukaryotes, the transgene must be transmitted through meiosis to allow its inheritance by the offspring.

transgressive variation The appearance, in a segregating generation, of individuals showing expression of a trait outside the extremes defined by the parent of the cross that was used to generate the population.

transient expression Short-term activity of a transgene following its introduction into target tissue. Transient expression usually implies non-integration of the transgene into the host genome.

transition The substitution in DNA or RNA of one purine by another purine, or of one pyrimidine by another pyrimidine. See: transversion, base substitution.

transition stage The period between juvenile and reproductive stages of growth.

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 polypeptide synthesis in which the amino acid sequence is determined by mRNA, mediated by tRNA molecules, and carried out on ribosomes.

translational initiation signal See: initiation codon.

translational start codon See: initiation codon.

translational stop signal See: termination codon.

translocation 1. The movement of nutrients or products of metabolism from one location to another. 2. Change in position of a segment of a chromosome to another, non-homologous chromosome.

transposable (genetic) element A DNA element that can move from one location in the genome to another. Synonym: transposon.

transposase An enzyme encoded by a transposon gene that catalyses the movement of a DNA sequence to a different site in a DNA molecule.

transposition The process whereby a transposon or insertion sequence inserts itself into a new site on the same or another DNA molecule. The exact mechanism is not fully understood and different transposons may transpose by different mechanisms. Transposition in bacteria does not require extensive DNA homology between the transposon and the target DNA.

transposon Synonym of transposable genetic element.

transposon tagging A method of gene isolation that exploits the disruption of normal gene expression that is the result of an insertion of a transposon within, or close to the target. Since the sequence of the transposon is known, this can be used as a DNA probe to define the DNA fragment containing the target gene. Large-scale experiments to generate populations of gene mutations are colloquially referred to as gene machines.

transversion The substitution in DNA or RNA of one purine by a pyrimidine or vice versa. See: transition, base substitution.

tribrid protein A fusion protein that has three segments, each encoded by parts of different genes.

trichome A short filament of cells, resulting in a hair-like structure.

tri-hybrid The hybrid offspring of a cross between parents carrying contrasting alleles at three loci.

trinucleotide repeat Tandem repeats of three nucleotides that are present in many genes. Commonly trinucleotide repeats have undergone variable expansion in copy number, forming the basis of microsatellite markers, and occasionally resulting in the formation of alleles giving rise to genetic disease.

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.

triplet A sequential group of three nucleotides in DNA or RNA. See: codon.

triploid A cell, tissue or organism containing three times the haploid number of chromosomes.

trisomic (adj.) See: trisomy.

trisomy The presence in a diploid cell or organism of an extra chromosome of one homologue (chromosome formula: 2n + 1). See: disomy; monosomic.

triticale The hybrid man-made species formed by the crossing of tetraploid or hexaploid wheat with diploid rye.

tRNA Abbreviation for transfer RNA. Small RNA molecules that transfer amino acids to the ribosome during protein synthesis. Each tRNA binds just one species of amino acid and recognizes a specific codon in the mRNA, thus implementing the genetic code.

tropism Plant response to an external stimulus, resulting in the bending/turning of stem or root growth. Typical tropisms are phototropism (light), geotropism (gravity) or hydrotropism (water).

true-to-type Conforming to the phenotype of the breed/variety.

trypsin A proteolytic enzyme used in vivo for the digestion of peptides. It acts by hydrolysing peptide bonds on the carboxyl side of the amino acids arginine and lysine.

trypsin inhibitor Substances inactivating trypsin, typically found in seed tissue of certain plants, where they are thought to have evolved as anti-feedant agents against insect predators.

TTP Abbreviation for thymidine 5'-triphosphate. TTP is required for DNA synthesis since it is a direct precursor molecule. See: thymidine, thymidylic acid.

tubulin The major protein component of the microtubules of eukaryotic cells.

tumble tube A glass tube mainly used in vitro to agitate and consequently aerate suspension cultures. The tube, which is commonly attached to a slowly revolving platform, is closed at both ends, with a side-neck opening.

tumor-suppressor gene A gene that regulates cell growth. If such a gene becomes dysfunctional, and potentiating damage occurs to the cell, then uncontrolled growth and a cancer may result. See: p53 gene, oncogene.

tumour virus A virus capable of transforming a cell to a malignant phenotype.

tumour-inducing plasmid See: Ti plasmid.

tunica The outer one- to four-cell layer region of the apical meristem, where cell division is anticlinal, i.e. perpendicular to the surface. See: apical meristem.

turbidostat An open continuous culture in which a pre-selected biomass density is uniformly maintained by automatic removal of excess cells. The fresh medium flows in response to an increase in the turbidity (usually corresponding to cell density) of the culture.

turgid Swollen, distended; referring to a cell that is extended as a result of adequate water uptake. Loss of turgidity in plant cells is a sign of water deficit.

turgor potential See: pressure potential.

turgor pressure The pressure within a cell resulting from the absorption of water into the vacuole and the imbibition of water by the protoplasm.

turion An underground bud or shoot from which an aerial stem arises. See: sucker.

twin One of two individuals originating from the same zygote.

U Abbreviation for uracil.

ubiquitin A small protein, present in all eukaryotic cells, which plays an important role in tagging proteins destined for proteolytic cleavage (because they are damaged or no longer needed).

ultrasonication See: sonication.

UMP Abbreviation for the (ribo)nucleotide uridine 5'-monophosphate. See: uridylic acid.

understock Host plant for a grafted scion, a branch or shoot from another plant; an understock may be a fully grown tree or a stump with a living root system.

undifferentiated Undifferentiated cells are those which have not been committed to become part of a specialized tissue.

unencapsidated A virus not enclosed by a coat protein or capsid.

unequal crossing over Abnormal meiotic event, in which one chromatid contains a duplication and the other a deletion. Often arises in a region containing repeated DNA sequences, which can pair out of register.

unicellular Tissues, organs or organisms consisting of a single cell.

uniparental inheritance The inheritance of genes exclusively from one parent, e.g. chloroplast DNA is inherited either maternally (many angiosperms) or paternally (most gymnosperms).

unisexual Higher organisms (animals or plants) possessing either male or female reproductive organs, but not both.

univalent An unpaired chromosome at the first division of meiosis.

universal donor cell Cells that, after introduction into a recipient, will not induce an immune response that leads to their rejection.

universality Referring to the genetic code, the triplet codons are translated to the same amino acid, with minor exceptions, in virtually all species.

unorganized growth In vitro formation of tissues with few differentiated cell types and no recognizable structure; typical structure of calli formed in tissue culture. Opposite: organized growth.

upstream 1. The stretch of DNA lying in the 5' direction from the site being considered. Where the reference point is the initiation of transcription, the first transcribed base is designated +1 and upstream nucleotides are marked with minus signs, e.g. -1, -10; 2. In chemical engineering, those phases of a manufacturing process that precede the biotransformation step. Refers to the preparation of raw materials for a fermentation process. Also called upstream processing.

upstream processing See: upstream (2).

uracil (Abbreviation: U). One the bases found in RNA. See: uridine.

uridine The (ribo)nucleoside resulting from the combination of the base uracil (U) and the sugar D-ribose. See: uridylic acid, uridine triphosphate.

uridine triphosphate (uridine 5'-triphosphate) (Abbreviation: UTP). Required for RNA synthesis since it is a direct precursor molecule. See: uridylic acid.

uridylic acid Synonym for uridine 5'-monophosphate (abbreviation: UMP), a (ribo)nucleotide containing the base uracil. See: uridine triphosphate.

utilization of farm animal genetic resources The use and development of animal genetic resources for the production of food in a sustainable system of agriculture.

UTP See: uridine triphosphate.

V region Variable region in antibodies. See: CDR.

v/v Abbreviation for volume per volume. The relative proportion of each liquid in a mixture.

vaccination See: preventive immunization.

vaccine A preparation of dead or attenuated (weakened) pathogens, or of derived antigenic determinants, that can induce the formation of antibodies in a host, and thereby produce host immunity against the pathogen. See: sub-unit vaccine, viral vaccine, DNA vaccine, inoculum.

Vaccinia The cowpox virus used to vaccinate against smallpox and, experimentally, as a carrier of genes for antigenic determinants cloned from other disease organisms.

vacuole A fluid-filled membrane-bound cavity inside many plant cells, in which various plant products and by-products are stored.

variable domain Regions of antibody molecules that have different amino acid sequences in different antibody molecules. These regions are responsible for the antigen-binding specificity of the antibody.

variable expressivity Variation in the phenotype caused by different alleles of the same gene and/or by the action of other genes and/or by the action of non-genetic factors.

variable number tandem repeat (Abbreviation: VNTR). A DNA sequence, present as tandem repeats, for which the number of copies varies greatly between unrelated genotypes.

variable surface glycoprotein (Abbreviation: VSG). One of a battery of antigenic determinants expressed by a micro-organism to elude immune detection.

variance A statistical term representing a measure of the dispersion of data from the overall mean. Used to quantify the variability of a population.

variant An individual that is genetically distinct from others in the population.

variation Differences between individuals within a population or among populations.

variegation The occurrence, within a single tissue, organ or organism, of mosaicism. Usually referring to plants showing either both green and albino colouration in a leaf, or flecks of contrasting colour in a flower. The origin of variegation can be through viral infection, nutritional deficiency, or genetic instability caused by transposon activity. See also: chimera

variety 1. A naturally occurring subdivision of a species, with distinct morphological characters. 2. A defined strain of a crop plant, selected on the basis of phenotypic (sometimes genotypic) homogeneity.

vascular Plant tissue specialized for the conduction of water or nutrients

vascular bundle A strand of tissue containing primary xylem and primary phloem (and procambium if present) and frequently enclosed by a bundle sheath of parenchyma or fibres.

vascular cambium In biennials and perennials, cambium giving rise to secondary phloem and secondary xylem.

vascular plant Plant species possessing organized vascular tissues.

vascular system 1. A specialized network of vessels for the circulation of fluids throughout the body tissue of an animal. 2. The system of vascular tissue in plants.

vector 1. An organism, usually an insect, that carries and transmits pathogens. 2. A small DNA molecule (plasmid, virus, bacteriophage, artificial or cut DNA molecule) that can be used to deliver DNA into a cell. Vectors must be capable of being replicated and contain cloning sites for the introduction of foreign DNA.

vegetative propagation See: asexual propagation.

velocity density gradient centrifugation A procedure used to separate macromolecules based on their rate of movement through a density gradient.

velogenetics The combined use of marker-assisted selection and embryo technologies such as OPU, IVM and IVF, in order to increase the rate of genetic improvement in animal populations.

vermiculite Material made from expanded mica used as a rooting medium and as a soil additive.

vernalization Chilling juvenile plants for a minimum period in order to induce flowering. Some plants require veRNAlization to flower, but others have no such requirement.

vessel A series of xylem elements whose function is to conduct water and nutrients in plants.

vessel element A type of cell occurring within the xylem of flowering plants. Many are water-conducting vessels.

viability The capability to live and develop normally.

viability test Assay of the number or percent of living cells or plants in a population following a specific treatment. Often used to describe quality of seed following long-term storage.

viable Capable of normal completion of life cycle.

vibrio Comma-shaped bacterium.

vir genes A set of genes on a Ti plasmid that prepare the T-DNA segment for transfer into a plant cell.

viral coat protein A protein present in the layer surrounding the nucleic acid core of a virus.

viral oncogene A viral gene that promotes tumour development in a host.

viral pathogen A disease-causing virus.

viral vaccine Vaccine consisting of live viruses, genetically engineered to avoid causing the disease itself.

virion A complete infectious virus particle.

viroid A plant pathogenic agent, composed of an infectious single-stranded low molecular weight RNA, and no coat protein.

virulence The degree of ability of an organism to cause disease. The relative infectiousness of a bacterium or virus, or its ability to overcome the resistance of the host metabolism.

virulent phage A phage that destroys its host bacterium.

viruliferous A vector (usually insect) organism that carries virions and spreads the virus from host to host by mechanical means.

virus An infectious particle composed of a protein capsule and a nucleic acid core (DNA or RNA), which is dependent on a host organism for replication.

virus-free Plant, animal, cell, tissue or meristem which exhibits no viral symptoms or contains no identifiable virus particles.

virus-tested Description of a organism or a cell stock certified as being free of certain specified viruses following recognized procedures of virus diagnosis.

vitamin Naturally occurring organic substance required by living organisms in small amounts to maintain normal health.

vitrified Cultured tissue having leaves and sometimes stems with a glassy, transparent or wet and often swollen appearance. The process of vitrification is a general term for a variety of physiological disorders that lead to shoot tip and leaf necrosis. Synonym: water soaked.

viviparous (adj.) See: vivipary.

vivipary 1. A form of reproduction in animals in which the developing embryo obtains its nourishment directly from the mother via a placenta or by other means. 2. A form of asexual reproduction in certain plants, in which the flower develops into a bud-like structure that forms a new plant when detached from the parent. 3. The development of young plants in the inflorescence of the parent plant.

V_max The maximal rate of an enzyme-catalysed reaction. V_max is the product of E_o (the total amount of enzyme) and K_cat (the catalytic rate constant).

VNTR Abbreviation for variable number tandem repeat.

volatilization The conversion of a solid or liquid into a gas or vapour.

VSG Abbreviation for variable surface glycoprotein.

w/v Abbreviation for weight per volume. The relative proportions of solid and liquid in a solution.

walking See: chromosome walking; primer walking.

wall pressure Pressure that a cell wall exerts against the turgor of the cell contents. Wall pressure is equal and opposite to the turgor potential.

wash-out The loss of the slower growing micro-organism when two organisms are being grown together.

water potential The pressure gradient that induces the flow of water, particularly with reference to plant water uptake from the soil, comprising the net effects of suction, solutes and matric forces.

water soaked See: vitrified.

water stress Occurs when plants are unable to absorb enough water to replace that lost by transpiration. Short-term water stress leads to turgor loss (wilting). Prolonged stress leads to cessation of growth, and eventually plant death.

wax Water-insoluble esters of long-chain acids with long-chain alcohols. Waxes form protective waterproof layers on leaves, stems, fruits, animal fur and integuments of insects.

weed A plant growing where it is not wanted. Generally used to describe plants which colonize readily, and can compete for resources with a planted crop.

weediness The ability of a plant to colonize a disturbed habitat and compete with cultivated species.

western blot A technique whereby a complex mixture of size-separated proteins is fixed to a solid support, and then probed with a labelled antibody. Useful, for example, for the measurement of levels of production of a specific protein in a particular tissue or at particular developmental stage.

wet weight See: fresh weight.

wetting agent A substance (usually a detergent) that improves the contact of a liquid to a solid surface by reducing its surface tension.

wild type The most frequent allele or genotype found in nature, or a specified organism against which mutants are defined.

wilt Drooping of stems and foliage due to loss of cell turgor. May be caused by water stress or by disease.

wilting point The moisture content of soil at which plants start to wilt, but not to the extent that they fail to recover when placed in a humid atmosphere. See: permanent wilting point.

wobble hypothesis An explanation of how one tRNA may recognize more than one codon. The first two bases of the mRNA codon and anticodon pair properly, but the third base in the anticodon has some flexibility that permits it to pair with either the expected base or an alternative.

x The basic number of chromosomes in a polyploid series, monoploid/haploid = x; diploid = 2x; triploid = 3x; etc.

xanthophyll A yellow oxygen-containing carotenoid, present in chloroplasts.

X-chromosome See: sex chromosome.

xenia The immediate effect of pollen on some characters of the endosperm.

xenobiotic A chemical compound that is not produced by, and often cannot be degraded by, living organisms.

xenogeneic Refers to organs, genetically engineered ("humanized") todecrease the chance of rejection, that have been grown in an animal of another species for potential transplant to humans.

xenotransplantation The transplantation of tissue or organs from one species to another species, typically from pigs to humans. Zoonoses are an important issue.

xerophyte A plant very resistant to drought, typically adapted to extremely dry environments.

X-linked The presence of a gene on the X-chromosome.

X-linked disease A genetic disease caused by an allele at a locus on the X-chromosome.

xylem A complex tissue specialized for the conduction of water and mineral nutrients in solution. Xylem may also function as a supporting tissue, particularly secondary xylem.

YAC Abbreviation for yeast artificial chromosome.

Y-chromosome See: sex chromosome.

yeast A unicellular ascomycete fungus, commonly found as a contaminant in plant tissue culture.

yeast artificial chromosome (Abbreviation: YAC). A vector which can be propagated in budding yeast (Saccharamyces pombe), consisting of the minimal elements required for a chromosome to replicate, and allowing for the cloning of large DNA fragments (hundreds of kilobase pairs).

yeast episomal vector (Abbreviation: YEp). A cloning plasmid vector for the yeast Saccharomyces cerevisiae maintained as an extrachromosomal nuclear DNA molecule.

yeast extract A mixture of substances from yeast. See: organic complex..

Z-DNA A form of DNA, in which the double helix is wound in a left-hand, instead of a right-hand, manner. DNA adopts the Z conformation when purines and pyrimidines alternate on each strand, e.g. 5'CGCGCGCG 3' or 3'GCGCGCGC5'. Synonym: zig-zag DNA.

zig-zag DNA See: Z-DNA.

zinc finger A DNA-binding protein motif, characterized by two closely spaced cysteine and two histidine residues that serve as ligands for a single Zn²⁺ ion. When bound, the structure takes on a conformation in which amino acid side chains protrude in a way that allows interaction with the DNA major groove.

zone of elongation The section of the young root or shoot just behind the apical meristem, in which the cells are enlarging and elongating rapidly.

zoo blot Hybridization of cloned DNA from one species to DNA from a range of other organisms to determine the extent to which the cloned DNA is evolutionarily conserved.

zoo FISH Fluorescence in situ hybridization technique, probing metaphase chromosomes of one species with DNA from another species. The technique allows inferences to be made regarding the evolutionary relationships between species. See: Fluorescence in situ hybridization.

zoonosis A disease that is communicable from animals to humans.

zoospore A spore that possesses flagella and is therefore motile.

zygonema Stage of meiotic prophase during which chromosome synapsis occurs.

zygospore A thick-walled resistant spore developing from a zygote resulting from the fusion of gametes in the course of isogamy.

zygote The diploid cell formed by the fusion of two haploid gametes during fertilization in eukaryotic organisms with sexual reproduction.

zygotene (adj.) See: zygonema.

zymogen Inactive enzyme precursor that after secretion is chemically altered to the active form of the enzyme.