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Glossary Biotechnology

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

S1 mapping  See S1 nuclease.

S1 nuclease  An enzyme that specifically degrades RNA or single-stranded DNA to 5´ mononucleotides. Purified from the filamentous fungus Aspergillus oryzae, S1 nuclease is used in assessing the extent of a hybridization reaction by removing unpaired regions. It is also used to remove the sticky ends of restriction fragments. In S1 mapping, the coding region of a gene is detected by performing mRNA-DNA hybridization and removing unpaired DNA with S1 nuclease.

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

saline resistance  See salt tolerance.

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

salt tolerance; saline resistance  The ability to withstand a concentration of sodium (Na+ ion), or of any other salt, in the soil (or in culture), which is damaging or lethal to other plants. Breeding and selection for increased tolerance and resistance in crop plants is of great current interest.

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

saprophyte  A vegetable organism that derives its nutriment from decaying organic matter.

satellite DNA  That portion of the DNA in plant and animal cells consisting of highly repetitious sequences (millions of copies) typically in the range from 5 to 500 bases. Thousands of copies occur tandemly (end-on-end) at each of many sites. It can be isolated from the rest of the DNA by density gradient centrifugation.

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

saturates  Noun: Oils containing saturated fatty acids.

SCA (single chain antigen)  Antibody-binding domains in which the two chains are produced by a gene and linked by a short peptide. See dabs.

scaffold  The central core structure of condensed 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 scale to a larger scale.

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

scarification  The chemical or physical treatment given to some seeds (where the seed coats are very hard or contain germination inhibitors) in order to break or weaken the seed coat sufficiently to permit germination.

scientific name  A unique identifier consisting of a genus and a species name (the specific epithet) in Latin, assigned to each recognized and described species of organism. Based on the Linnean system of classification. Susceptible to considerable blurring at the edges because, as Darwin came to realize, nature has not packaged living things into neatly discrete entities. cf cultivar; pathovar.

scion  The twig or bud to be grafted onto another plant, the root stock, in a budding or grafting operation.

scion-stock interaction The effect of a rootstock on a scion (and vice versa) in which a scion on one kind of rootstock performs differently than it would on its own roots or on a different rootstock.

sclerenchyma (Gr. skleros, hard + echyma, a suffix denoting tissue) A strengthening tissue in plants, composed of cells with heavily lignified cell walls.

SCP  See single-cell protein.

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

screen  To separate by exclusion or collection on the basis of a set of criteria (biochemical, anatomical, physiological, etc.). Screening is often applied to the process of selection for specific purposes, such as disease resistance or improved agronomic qualities in plants, improved performance in animals, specific enzyme properties in micro-organisms, etc.

SDS  Sodium dodecyl sulphate. See gel electrophoresis.

secondary antibody  In an ELISA or other immunological assay system, the antibody that binds to the primary antibody. The secondary antibody is often conjugated with an enzyme such as alkaline phosphatase.

secondary cell wall  The innermost layer of cell wall, with a highly organized microfibrillar structure, which is formed in certain cells after cell elongation has ceased. It gives rigidity to the cells.

secondary growth  Type of growth characterized by an increase in thickness of stem and root and resulting from 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. cf primary immune response.

secondary metabolite  A compound that is not necessary for growth or maintenance of cellular functions but is synthesized, generally, for the protection of a cell or micro-organism, during the stationary phase of the growth cycle.

secondary oocyte  See oocyte.

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

secondary plant products  Metabolic products not having a known functional or structural use in plant cells. They have been extracted from plant tissue cultures for pharmaceutical and food processing purposes (e.g., essential oils, food additives, flavours).

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 root  A branch or lateral root.

secondary spermatocyte  See spermatocyte.

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

secretion  The passage of a molecule from the inside of a cell through a membrane into the periplasmic space, or the extracellular medium.

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

seed storage proteins  Proteins accumulated in large amounts in seeds not because of their enzymatic or structural properties but simply as a convenient source of amino acid for use when the seed germinates. They are of interest to biotechnologists:

    1. As a source of protein. Much of the world's food comes from plant seeds or fruits, and much of the protein in those seeds is storage protein. Thus a substantial amount of the world's food protein comes from plant storage protein. Any improvement of the nutritional content of those proteins could correspondingly improve human diet.

    2. As expression systems. Storage proteins are produced in very large amounts relative to other proteins, and are stored in stable, compact bodies in the plant seed. Several workers are seeking to make the plants produce other proteins in similarly large amounts and in as convenient a form, by splicing the gene for a desired protein into the middle of a plant storage protein gene.

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

segregant  A hybrid resulting from the crossing of two genetically unlike individuals.

segregation  The separation of the two members of a chromosome pair from each other at meiosis; the result is seen as the separation of alleles from each other in the gametes of heterozygotes; the occurrence of different phenotypes among offspring, resulting from chromosome or allele separation in their heterozygous parents. Mendel's first principle of inheritance (the Law of Segregation) predicts that heterozygotes will produce equal numbers of gametes containing each allele.

selectable  Having a gene product that, when present, enables a researcher to identify and preferentially propagate a particular organism or cell type. See reporter gene.

selectable marker  A gene whose expression allows the identification of:

    1. A specific trait or gene in an organism.

    2. Cells that have been transformed or transfected with a vector containing the marker gene. See b-lactamase, kanr.

selection  1. Differential survival and reproduction phenotypes.

    2. A system for either isolating or identifying specific organisms in a mixed culture.

selection coefficient, s  The proportion by which the fitness of a genotype is less than the fitness of a standard genotype, which is usually the genotype with the highest fitness. In general, relative fitness = 1 - s.

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, S  The difference between the mean of the individuals selected to be parents and the mean of the overall population.

selection pressure  The intensity of selection acting on a population of organisms or cells in culture. Its effectiveness is measured in terms of differential survival and reproduction, and consequently in change in the frequency of alleles 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 = heritability (narrow-sense) × selection differential.

selection unit  The minimum number of organisms or cells effective in the screening process.

selective agent  An environmental or chemical agent characterized by its lethal or sub-lethal stress on growing plants, or portion thereof in culture. A selective agent is mainly used when selection of resistant or tolerant individuals is the research aim. See single-cell line.

self-fertilization  The process by which pollen of a given plant fertilizes the ovules of the same plant. Plants fertilized in this way are said to have been selfed. An analogous process occurs in some animals, such as nematodes and molluscs.

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

self-pollination  Pollen of a plant is transferred to the female part of the same plant or another plant with the same genetic makeup. Opposite: cross-pollination.

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

self-sterility  See self-incompatibility.

SEM  See scanning electron microscope.

semen sexing  See sperm sexing.

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

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

semi-liquid  See semi-solid.

semi-permeable membrane  A cell or plasma membrane that is partially permeable; certain ions or molecules (water, solvents) can pass through it but others cannot (such as certain solutes).

semi-solid  Gelled but not firmly so; small amounts of a gelling agent are used to obtain a semi-solid medium; called also semi-liquid.

semi-sterility  A condition of only partial fertility in plant zygotes; usually associated with translocations.

senescence  The last stage in the post-embryonic development of multicellular organisms, during which loss of functions and degradation of biological components occur. A physiological ageing process in which cells and tissues deteriorate and finally die.

sense RNA  A primary transcript (RNA) that contains a coding region (contiguous sequence of codons) that is translated to produce a polypeptide.

sensitivity  For 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. cf aseptic; axenic; sterile.

septate (L. septum, fence)  Divided by cross walls into cells or compartments.

septum (L. septum, fence)  Any dividing wall or partition; frequently a cross wall in a fungal or algal filament.

sequence hypothesis  Francis Crick's seminal concept that genetic information exists as a linear DNA code; DNA and protein sequence are collinear.

sequence-tagged site (STS)  Short, unique DNA sequence (usually 200 to 500 bp) that, by being able to be amplified by PCR, is uniquely "tagged" to the site on the chromosome from which it was amplified.

sequencing  The determination of the order of nucleotides in a DNA or RNA molecule, or that of amino acids in a polypeptide chain. See DNA sequencing.

serial divisions  Splitting at about monthly intervals of excised shoot-tip material growing on culture medium, in order to induce additional plantlets.

serial float culture  A technique of floating anthers on liquid medium developed by Sunderland. Anther dehiscence, pollen release and development occur at intervals of several days, and in different nutrient media.

serology (adj: serological)  The study of serum reactions between an antigen and its antibody. Serology is mainly used to identify and distinguish between antigens, such as those specific to micro-organisms or viruses. Serology is also employed as an indicator technique to assay plants suspected of being virus-infected.

serum albumin  A globular protein obtained from blood and body fluids.

sewage treatment  Sewage treatment is one of the most widespread biotechnological processes in Western societies, to deal with the huge amounts of human and animal waste that such societies produce. Sewage treatment methods vary widely, but all have a biological basis to break down the organic material in sewage and convert it into something that can be safely discharged into the environment (usually rivers or seas).

sex chromosomes  Chromosomes that are connected with the determination of sex: X and Y chromosomes in mammals; W and Z chromosomes in birds.

sex determination  The method by which the distinction between males and females is established in a species.

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

sex linkage  The location of a gene on a sex chromosome, typically on the X chromosome.

sex mosaic  See gynandromorph.

sexed embryos  Embryos separated according to sex.

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.

sex-influenced dominance  The tendency for the type of gene action to vary between the sexes within a species. Thus the presence of horns in some breeds of sheep appears to be dominant in males and 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 where two cells (gametes) fuse to form one fertilized cell or zygote. cf asexual reproduction; gamete; hybrid.

shake culture  An agitated suspension in culture providing adequate aeration for cells in the liquid medium. Usually an Erlenmeyer flask containing the culture is attached to a horizontal or platform shaker, or agitated with a magnetic stirrer.

shaker; platform shaker  A platform fitted with clips for grasping Erlenmeyer flasks, with set or variable speed control. Shaking speed must be adjusted for gentle and even agitation of suspension cultures. cf reciprocating shaker.

shear  1. The sliding of one layer across another, with deformation and fracturing in the direction parallel to the movement. This term usually refers to the forces that cells are subjected to in a bioreactor or a mechanical device used for cell breakage.

    2. To fragment DNA molecules into smaller pieces. DNA, as a very long and fairly stiff molecule, is very susceptible to hydrodynamic shear forces. Forcing a DNA solution through a hypodermic needle will fragment it into small pieces. The size of the fragments obtained is inversely proportional to the diameter of the needle's bore. The actual sites at which the shear force breaks a DNA molecule are approximately random. Therefore DNA fragments may be generated by random shear and then cloned (by either tailing their ends or using linkers) so as to create a complete gene library of an organism. This method is little used now, having been replaced by the use of partial digests with four-base-pair cutters, such as Sau3A, as a means of generating random DNA fragments.

Shine-Dalgarno sequence  A conserved sequence in 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  A young branch that grows out from the main stock of a tree, or the young main portion of a plant growing above ground.

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

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

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

short template  A DNA strand that is synthesized during the polymerase chain reaction and has a primer sequence at one end and a sequence complementary to the second primer at the other end.

short-day plant  Plant that requires a night (or dark period) longer than its critical dark period to induce flower formation.

shuttle vector; bifunctional 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 'shuttle' genes from one to the other. For example, the YEp, pJDB219, is a shuttle vector able to replicate in E. coli from its pMB9 origin and in Saccaromyces cerevisiae from its 2 µm-plasmid origin.

Sib-mating  Crossing of siblings. Matings involving two individuals of the same parentage; brother-sister matings.

siderophore  A low molecular weight substance 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  In vascular plants, a long and slender sieve element with relatively unspecialized sieve areas and with tapering end walls that lack sieve plates.

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

sievert (symbol: Sv)  The SI unit of ionizing radiation.

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

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

signal peptide  See signal sequence.

signal sequence  A segment of about 15 to 30 amino acids at the N terminus of a protein, that enables the protein to be secreted (pass through a cell membrane). The signal sequence is removed as the protein is secreted. Also called 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 compared to the response level when no specific stimulus (activity) is present.

silencer  A DNA sequence that helps to reduce or shut off the expression of a nearby gene.

simple sequence repeat (SSR)  See microsatellite.

simplicity  For diagnostic tests, the ease with which an assay can be implemented.

SINEs  Short interspersed nuclear elements. Families of short (150 to 300 bp), moderately repetitive elements of eukaryotes, occurring about 100,000 times in a genome. SINES appear to be DNA copies of certain tRNA molecules, created presumably by the unintended action of reverse transcriptase during retroviral infection.

single-cell line; cell strain  A culture initiated from a single cell, usually from suspension cultures of single cells or small aggregates plated on solidified medium. The latter may incorporate a selective agent, from which tolerant or resistant individual cell lines or cell clones can be selected. See selective agent.

single-cell protein (SCP)  Protein produced by micro-organisms. The dried mass of a pure sample of a protein-rich-micro-organism, which may be used either as feed (for animals) or as a food (for humans).

single-chain antigen  See SCA.

single copy  A gene or DNA sequence which occurs only once per (haploid) genome. Most structural genes, those encoding functional proteins, are single-copy genes.

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

single-nucleotide polymorphism (SNP; pronounced "snip")  A polymorphism (q.v.) at a particular base site in a coding sequence, e.g., at base 306 in a particular gene, one individual could be heterozygous for A and G: the maternal allele could have an A at this site, while the paternal allele has a G at this site. This type of polymorphism is extensive throughout the genome, and has the great advantage of being detectable without the need for gel electrophoresis, which opens the way for large-scale automation of genotyping.

single-strand-DNA-binding protein  A protein that coats DNA single strands, keeping them in an extended state.

single-stranded  A term used to describe nucleic acid molecules consisting of only one polynucleotide chain. The genomes of certain phages, e.g., MI3, are single-stranded DNA molecules; rRNA, mRNA and tRNA are all single-stranded nucleic acids, but they all contain double-stranded regions formed by the intra-strand base-pairing of self-complementary sequences.

sires  Male animals used for breeding.

site-directed mutagenesis  The introduction of base changes - mutations - into a piece of DNA at a specific site, using recombinant DNA methods.

site-specific  A term used to describe any process or enzyme which acts at a defined sequence within a DNA or RNA molecule. Type II restriction enzymes are site-specific endonucleases and the recombination systems encoded by some transposons are site-specific, such as is the integration of phage into the E. coli chromosome.

site-specific mutagenesis  A technique to change one or more specific nucleotides within a cloned gene in order to create an altered form of a protein with one or more specific amino acid changes. a.k.a. oligonucleotide-directed mutagenesis; oligonucleotide-directed site-specific mutagenesis.

six-base cutter  A type II restriction endonuclease that binds (and subsequently cleaves) DNA at sites that contain a sequence of six nucleotide pairs that is uniquely recognized by that enzyme. Because any sequence of six bases occurs less frequently by chance than any sequence of four bases, six-base cutters cleave less frequently than do four-base cutters. Thus, six-base cutters create larger fragments than four-base cutters.

small nuclear ribonucleoprotein (snRNP; pronounced snurp(s))  A compound comprising small nuclear RNA (q.v.) and nuclear protein, that is heavily involved in the post-transcriptional processing of mRNA, especially the removal of introns. snRNPs are a major component of spliceosomes (q.v.).

small nuclear RNA (snRNA)  Short RNA transcripts of 100-300 bp that associate with proteins to form small nuclear ribonucleoprotein particles (snRNPs) (q.v.); most snRNAs are components of the spliceosomes (q.v.) that excise introns from pre-mRNAs in RNA processing. See RNA.

SNP  See single nucleotide polymorphism.

snRNA  See small nuclear RNA.

snRNP  See small nuclear ribonucleoprotein.

sodium dodecyl sulphate (SDS)  See gel electrophoresis.

soil amelioration  The improvement of poor soils, usually using bacteria or fungi. This contrasts with bioremediation, which is the cleaning up of toxins, usually in soils. Amelioration includes breaking down organic matter; forming humus; by solubilizing them, making minerals - such as phosphates - in the soil available to plants; fixing nitrogen; and sometimes an element of bioremediation as well.

soilless culture; soil-free culture  Tissue culture and hydroponics. Growing plants in nutrient solution without soil.

solid media  Nutrient media that has been solidified, such as by addition of agar.

somaclonal variation  Epigenetic or genetic changes, sometimes expressed as a new trait, resulting from in vitro culture of higher plants.

somatic  Referring to vegetative or non-sexual stages of a life-cycle.

somatic cell  Any cell of a multicellular organism that composes the body of that organism but does not produce gametes. cf gamete; somatic cell gene therapy.

somatic cell embryogenesis  Embryos are produced either from somatic cells of explants (direct embryogenesis) or by induction on callus formed by explants (indirect embryogenesis). a.k.a. asexual embryogenesis.

somatic cell gene therapy  The delivery of a gene or genes to a tissue other than reproductive cells of an individual, with the aim of correcting a genetic defect. cf somatic cell.

somatic cell variant  A somatic cell with unique characters not present in the other cells, such as might be selected for in a screening trial that following a mutation event.

somatic embryo; somatic embryoid  An organized embryonic structure morphologically similar to a zygotic embryo but initiated from somatic (non-zygotic) cells. Under in vitro conditions, somatic embryos go through developmental processes similar to embryos of zygotic origin.

somatic hybridization  1. Asexual fusion of protoplasts from somatic cells of genetically different parents.

    2. Hybridization by induced fusion of cells (protoplasts) from two contrasting genotypes for production of hybrids or cybrids which contain various mixtures of nuclear and/or cytoplasmic genomes, respectively.

    a.k.a. parasexual hybridization.

somatic hypermutation  A high frequency of mutation that occurs in the gene segments encoding the variable regions of antibodies 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 calluses by artificial means.

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

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

somatotrophin; somatotropin  See growth hormone.

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

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

source DNA  The DNA from an organism that contains a target gene; this DNA is used as 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 cellulose or nylon membrane to which DNA fragments previously separated by gel electrophoresis have been transferred by capillary action. Named after Ed Southern.

Southern blotting  A technique for transferring denatured DNA molecules that have been separated electrophoretically, from a gel to a matrix (such as a nitrocellulose membrane) on which a hybridization assay can be performed.

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

Southern transfer  See Southern blotting.

speciation  The development of one or more species from an existing species.

sparger  A device that introduces into a bioreactor air in the form of separate fine streams.

specialized  Anatomically or physiologically adapted for particular functions or habitats.

species (L. species, appearance, form, kind)  A class of potentially interbreeding individuals that are 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.

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

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

sperm  Abbreviation of spermatozoon, q.v.

spermatid  One of the four cells formed by the meiotic divisions in spermatogenesis. Spermatids become mature spermatozoa (sperm).

spermatocyte  Sperm mother cell. The cell that undergoes two meiotic divisions (spermatogenesis) to form four spermatids; the primary spermatocyte before completion of the first meiotic division; the secondary spermatocyte after completion of the first meiotic division.

spermatogenesis  The series of cell divisions in the testis by which maturation of the gametes (sperm) of the male takes place.

spermatogonium (pl: spermatogonia)  Primordial male germ cell that may divide by mitosis to produce more spermatogonia. A spermatogonium may enter a growth phase and give rise to a primary spermatocyte.

spermatozoon (pl: spermatozoa; abbr: sperm)  The mature, mobile reproductive cell of male animals, produced by the testis.

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

sperm sexing  The separation of 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. Achieved by means of inactivation of X-bearing or Y-bearing sperm via antibodies directed against sex-specific peptides on the surface of sperm cells, or fluorescence-activated cell sorting (FACS) (q.v.), in which sperm that have been pre-treated with a fluorescent dye that binds to DNA are separated according to the quantity of fluorescence detected by a laser beam, based on the principle that X-bearing sperm contain more DNA than Y-bearing sperm.

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

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

spike (L. spica, an ear of grain)  An inflorescence in which the main axis is elongated and the flowers are sessile.

spikelet (L. spica, an ear of grain + diminutive ending -let)  The unit of inflorescence in grasses; a small group of grass flowers.

spindle (A.S. spinel, a tool for spinning thread by hand)  In mitosis and meiosis, refers to the spindle-shaped intracellular structure in which the chromosomes move.

spine  Hard, sharp structure on the surface of a plant; usually a modified leaf.

spliceosomes  Organelles responsible for the removal of introns from mRNA by means of splicing (q.v.).

splicing  During the maturation of eukaryotic mRNA, the process that eliminates intervening intron sequences and covalently joins exon sequences of RNA. cf split gene; exon; guide sequence. In recombinant DNA technology, the term refers to the latter of the two processes just described, namely joining fragments of DNA together. See gene splicing.

split genes  In eukaryotes, structural genes are typically divided up (split) by a number of non-coding regions called introns. cf exon; guide sequence; splicing.

spore  1. A reproductive cell that develops into an individual without union with other cells; some spores such as meiospores occur at a critical stage in the sexual cycle, but others are asexual in nature.

    2. A small, protected reproductive form of a micro-organism, often synthesized when nutrient levels are low.

spririllum  A rigid, spiral-shaped bacterium.

spirochaete  A non-rigid, corkscrew-shaped bacterium that moves by means of muscular flexions of the cell.

spore mother cell  See sporocyte.

sporocyte  A diploid cell that gives rise to four haploid spores by meiosis.

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

sport  An individual or portion thereof distinguished by a spontaneous mutation. Sports are sometimes of great agricultural worth, but alternatively, they may be disadvantageous and may be rogued during agricultural production.

SSR  simple sequence repeat. See microsatellite.

stages of culture (I-IV)  See micropropagation.

staggered cuts  Symmetrically cleaved phospho-diester bonds that lie on both strands of duplex DNA but are not opposite one another.

stamen (L. stamen, the standing-up things or a tuft of thready things) Flower structure made up of an anther (pollen-bearing portion) and a stalk or filament. The stamen is the male part of the flower.

standard deviation  A statistical measure of variability in a population of individuals or in a set of data; the square root of the variance.

standard error  A statistical measure of variation in a population of means, used to indicate how well sample estimates represent population parameters.

starch (M.E. strechen, to stiffen)  A complex insoluble carbohydrate, consisting of various proportions of two glucose polymers, amylose and amylopectin; the chief food storage substance of plants, which is composed of several hundred hexose sugar units and which easily breaks down on hydrolysis into these separate units.

sporophyll  A leaf that bears spore producing structures (sporangia).

start codon; initiator codon  The set of three nucleotides in an mRNA molecule with which the ribosome starts the process of translation. The start codon sets the reading frame for translation. The most commonly used start codon is AUG, which is decoded as methionine in eukaryotes and as N-formylmethionine in prokaryotes. AUG appears to be the only start codon used by eukaryotes, while in bacteria, GUG (valine) may sometimes be employed. See initiation codon; initiator.

stationary culture  A culture maintained in the growth chamber with no agitation movement. The antonym is shake culture.

stationary phase  The plateau of the growth curve after log growth, during which cell number remains constant. New cells are produced at the same rate as older cells die. See growth phases.

statistic  An estimate based on a sample or samples of a population, providing an indication of the true population parameter.

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

stele (Gr. stele, a post)  The central cylinder, inside the cortex, of roots and stems of vascular plants. See meristele.

stem (O.F. stemn)  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 active somatic cell that undergoes division and gives rise to other stem cells or to cells that differentiate to form specialized cells.

sterile  1. Medium or object with no perceptible or viable micro-organisms.

    2. Incapable of fertilizing or being infertile.

sterile room  Operation room for performing inoculations under aseptic conditions; usually now replaced by use of laminar air-flow cabinets, in which filtered air is blown from the inside to the outside. See laminar air-flow cabinet.

sterility  Inability to produce offspring.

sterilize  1. The process of elimination of micro-organisms, such as by chemicals, heat, irradiation or filtration.

    2. The operation of making an animal incapable of producing offspring.

sterilization  The act of sterilizing.

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

sticky ends; cohesive ends  The single-stranded nucleotide sequence left on a restriction fragment by type II restriction enzymes that cut each strand at a separate location. These unpaired regions are available for hybridization with complementary ends on other fragments during the creation of recombinant DNA. a.k.a. protruding end; overhang; cohesive end. See cohesive ends.

stigma (L. stigma, a prick, a spot, a mark)  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 made. Stock plants are usually maintained carefully in an optimum state for (sometimes prolonged) explant use. Preferably they are certified-pathogen-free plants.

stock solutions  Pre-prepared solutions of individual components and used to prepare many different types of media. Certain substances, including Ca and Mg sulphates and phosphates must not be combined until actual medium preparation because insoluble combinations are formed and precipitate.

stolon (L. stolo, a shoot)  A lateral stem that grows horizontally along the ground surface. The runners of white clover, strawberry and bermuda grass are examples of stolons. cf runner.

stoma  (Gr. stoma, mouth; pl: stomata)  1. Any of various small openings or pores in an animal body, especially an opening resembling a mouth in various invertebrates.

    2. Botany: A minute pore in the epidermis of the leaf or stem of a plant, forming a slit of variable width between two specialized cells (guard-cells), which allows movement of gases, including water vapour, to and from the intercellular spaces. Also, the whole pore with its associated guard-cells.

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

stomatal index  = (number of stomata per mm2 × 100)/(number of stomata per mm2 + number of epidermal cells per mm2). This value has been found useful in comparing leaves of different sizes. Relative humidity and light intensity during leaf development affect the value of stomata index.

stop codon; termination codon  A set of three nulecotides 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 found: UAA (ochre), UAG (amber) and UGA (opal). Mutations which generate any of these three codons in a position which normally contains a codon specifying an amino acid are known as nonsense mutations. Stop codons can also be called nonsense codons. See chain terminator; nonsense mutation; suppressor.

strain  A group of individuals from a common origin within a species.

strain isolation  Isolation of any bacterium, animal or plant from the outside world.

stratification  Treatment of moist seeds at low temperature (+2° - +4°C) to break dormancy.

stress  See water stress.

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

stringent plasmid  A plasmid that only replicates along with the main bacterial chromosome and is present as a single copy, or at most several copies, per cell. See plasmid.

stroma  Tissue that forms the framework of an organ.

structural gene  A DNA sequence that forms the blueprint for the synthesis of a polypeptide.

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  See sequence-tagged site.

style (Gr. stylos, a column)  Slender column of tissue that arises from the top of the ovary and through which the pollen tube grows.

sub-clone  A method in which smaller DNA fragments are cloned from a large insert which has already been cloned in a vector.

sub-cloning  1. Splicing part of a cloned DNA molecule into a different cloning vector.

    2. The process of transferring a cloned DNA fragment from one vector to another. See cloning.

sub-culture  Division and transfer of a portion or inoculum of a culture to fresh medium. Sometimes used to denote the adding of fresh liquid to a suspension culture. cf inoculum; passage.

sub-culture interval  The time between subsequent sub-cultures of cells. Sub-culture interval has no relationship to the term cell generation time.

sub-culture number  The number of times cells, etc., have been sub-cultured, i.e., transplanted by inoculation from one culture vessel to another.

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 isolating a single cell or groups of cells having properties or markers not shared by all cells of the strain.

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 disease-causing organism or produced from a cloned gene. A vaccine composed of a purified antigenic determinant that is separated from the virulent organism. cf vaccine; enzyme.

sucker  A shoot that arises from an underground root or stem and grows at the expense of the parent plant. cf turion.

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 mRNAs or DNA fragments on the basis of size.

substitution  A point mutation in which one base pair in the DNA sequence is replaced by another.

superbug  Jargon for the bacterial strain of Pseudomonas developed by Chakrabarty, who combined hydrocarbon-degrading genes carried on different plasmids into one organism. Although this genetically engineered micro-organism is neither "super" nor a "bug", it represents a landmark example because it showed how genetically modified microbial strains could be used in a novel way and because it was the basis for the precedent-setting legal decision that declared that genetically engineered organisms were patentable.

supercoil  A DNA molecule that contains extra twists as a result of overwinding (positive supercoils) or underwinding (negative supercoils).

supercoiled plasmid  The predominant in vivo form of plasmid, in which the plasmid is coiled around histone-like proteins. Supporting proteins are stripped away during extraction from the bacterial cell, causing the plasmid molecule to supercoil around itself in vitro. See Plasmid.

supergene  A group of neighbouring genes on a chromosome and that tend to be inherited together and sometimes are functionally related.

supernatant  The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids.

suppressor  Mutations in suppressor genes are able to overcome (suppress) the effects of mutations in other, unlinked, genes. A common, and very useful, kind of suppressor mutation occurs within the gene encoding a tRNA molecule and results in a change in the tRNA's anticodon. Such a mutant tRNA can reverse the effect of chain-terminating mutations, such as amber or ochre, in protein-encoding genes. See stop codon; nonsense mutation.

suppressor mutation  A mutation that partially or completely cancels the phenotypic effect of another mutation.

suppressor-sensitive mutant  An organism that can grow when a second genetic factor - a suppressor - is present, but not in the absence of this factor.

surfactant  A surface-active agent or wetting agent, such as Tween 20TM or Tween 80TM, TeepolTM, Lissapol FTM, AlconoxTM, etc. Surfactants act by lowering the surface tension and are common addenda to solutions used to surface sterilize materials prior to aseptic excision of explants. See detergent; wetting agent.

susceptible  The characteristic of a host organism such that it is incapable of suppressing or retarding an injurious pathogen or other factor.

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

sustainable intensification of animal production systems  In AnGR: The manipulation of inputs to, and outputs from, livestock production systems aimed at increasing production and/or productivity and/or changing product quality, while maintaining the long-term integrity of the systems and their surrounding environment, so as to meet the needs of both present and future human generations. (Source: FAO, 1999)

    Sustainable agricultural intensification respects the needs and aspirations of local and indigenous people, takes into account the roles and values of their locally adapted genetic resources, and considers the need to achieve long-term environmental sustainability within and beyond the agro-ecosystem. (Source: FAO, 1999)

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

symbiosis (Gr. syn, with + bios, life)  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. An example is the association of the mycelium of mycorrhizal fungi with roots of seed plants. See commensalism; parasitism.

symbiotic association  An intimate partnership between two organisms, in which the mutual advantages normally outweigh the disadvantages.

sympatric speciation  The formation 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 to either its abortion or its development into a flower or an inflorescence, and the uppermost lateral bud takes over the further axial growth of the stem.

symplast  The system of protoplasts in plants, that are interconnected by plasmodesmata.

synapsis  See pairing.

synaptonemal complex  A ribbonlike protein structure formed between synapsed homologues at the end of the first meiotic prophase, binding the chromatids along their length and facilitating chromatid exchange.

synchronous culture  A culture in which the majority of the cells are dividing at the same time or are at a specific phase of the cell cycle.

syncytium  A group of cells in which cytoplasmic continuity is maintained. cf acellular.

syndrome  A group of symptoms that occur together and represent a particular disease.

syngamy  Fertilization.

synergids  The two nuclei within the embryo sac at the upper end in the ovule of the flower, which, with the third (the egg), constitute the egg apparatus.

synkaryon  A nucleus formed by the fusion of nuclei from two different somatic cells during somatic-cell hybridization. See hybrid cell.

synteny  The occurrence of two or more loci on the same chromosome, without regard to the distance between them.

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