Biotech Glossary | Bioinformatics | Lab Protocol | Notes | Malaysia University |
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P1 Symbol for the parental generation or parents of a given individual.
pachynema (adj: pachytene) A mid-prophase stage in meiosis, immediately following zygonema and preceding diplonema. In microscopic preparations, the chromosomes are visible as long, paired threads. Rarely, four chromatids are detectable.
packaging cell line A cell line that is designed to produce viral particles that do not contain nucleic acid. After transfection of these cells with a full-size viral genome, fully infective viral particles are assembled and released.
packed cell volume (PCV) The volume of cells in a set volume of culture expressed as a percentage of that set volume after sedimentation (packing) by means of low speed centrifugation.
PAGE See polyacrylamide gel electrophoresis.
pairing; synapsis The pairing of homologous chromosomes during the prophase of the first meiotic division, when crossing over occurs.
pair-rule gene A gene that influences the formation of body segments in Drosophila.
palaeontology The study of the fossil record of past geological periods and of the phylogenetic relationships between extinct and contemporary plant and animal species.
palindrome (Gr. palindromos, running back again) Originally a word, sentence or verse that reads the same from right to left as it does from left to right. In biotechnology, the term is applied to a segment of DNA in which the base-pair sequence reads the same in both directions from a central point of symmetry. See the entry for inverted repeat for an example of a palindrome. See also palindromic sequence.
palindromic sequence A segment of duplex DNA whose 5´-to-3´ sequence is identical on each DNA strand. The sequence is the same when one strand is read left-to-right and the other strand is read right-to-left. Typically, recognition sites for type II restriction endonucleases are palindromes. See the entry for inverted repeat for an example of a palindrome.
palisade parenchyma Elongated cells found just beneath the upper epidermis of leaves, and containing many chloroplasts.
pAMP Ampicillin-resistant plasmid. See plasmid.
panicle (L. panicula, a tuft) An inflorescence, the main axis of which is branched; the branches bear loose racemose flower clusters.
panicle culture Aseptic culture of grain panicle segments to induce microspore germination and development.
panmictic population A population in which mating occurs at random.
panmixis Random mating in a population. cf apomixis.
paper raft technique See nurse culture.
PAR See photosynthetically active radiation.
paracentric inversion An inversion that is entirely within one arm of a chromosome and does not include the centromere.
paraffin [wax] A translucent, white, solid hydrocarbon with a low melting point. Paraffin is used as an embedding medium to support tissue for sectioning for light microscopy observation.
parallel evolution The development of different organisms along similar evolutionary paths due to similar selection pressures acting on them.
ParafilmTM A stretchable film based on paraffin wax; used to seal tubes and Petri dishes. ParafilmTM is a proprietary name which is applied colloquially to similar products.
parahormone A substance with hormone-like properties that is not a secretory product (e.g., ethylene; carbon dioxide).
parameter A value or constant pertaining to an entire population. cf statistic.
parasexual cycle A sexual cycle involving changes in chromosome number but differing in time and place from the usual sexual cycle; occurring in those fungi in which the normal cycle is suppressed or apparently absent.
parasexual hybridization See somatic hybridization.
parasite (Gr. parasites, one who eats at the table of another) An organism deriving its food from the living body of another organism.
parasitism The close association of two or more dissimilar organisms, where the association is harmful to at least one. cf commensalism; symbiosis.
parasporal crystal Tightly packaged insect pro-toxin molecules that are produced by strains of Bacillus thuringiensis during the formation of resting spores.
parenchyma 1. A plant tissue consisting of spherical, undifferentiated cells, frequently with air spaces between them.
2. Loose connective tissue formed of large cells.
parenchymatous Adjective used to describe spherical and undifferentiated cells with primary cell walls, capable of both cell division and differentiation.
par gene A gene found in bacterial and plant cells, and involved in partition of plasmids in cells.
parthenocarpy (Gr. parthenos, virgin + karpos, fruit) The development of fruit without fertilization.
parthenogenesis (Gr. parthenos, virgin + genesis, origin) Production of an embryo from an unfertilized egg. cf androgenesis; apomixis; gynogenesis.
partial digest Addition of a restriction enzyme to a DNA sample under particular conditions or for a limited period, such that only a proportion of the target sites in any individual molecule are cleaved. Partial digests are often performed to give an overlapping collection of DNA fragments for use in the construction of a gene bank. See complete digest; library.
particle radiation Refers to gamma (g) particles (positively charged) and beta (ß) particles (negatively charged), electrons, protons and neutrons. In plant tissue culture, these particles are used to produce mutant cells or organisms.
parts per million (ppm) Units of any given substance per one million equivalent units, such as the weight units of solute per million weight units of solution (i.e., 1 ppm = 1 mg/l).
parturition The process of giving birth.
passage The transfer or transplantation of cells from one culture vessel to another. cf sub-culture.
passage number The number of times the cells in the culture have been sub-cultured. In descriptions of this process, the dilution ratio of the cells should be stated so that the relative cultural "age" can be ascertained.
passage time Interval between successive sub-cultures.
passive immunity 1. Natural acquisition of antibodies by the foetus or neonate (newborn) from the mother.
2. The artificial introduction of specific antibodies by the injection of serum from an immune animal.
In both cases, temporary protection is conferred on the recipient.
patent A government-issued document that assigns the holder the exclusive right - for a defined period of time - to manufacture, use or sell an invention.
paternal Pertaining to the father.
pathogen (Gr. pathos, suffering + genesis, beginning) An organism that causes a disease in another organism.
pathogen-free Freedom from disease-causing organisms (bacteria, fungi, viruses, etc.).
pathotoxin Very dilute substance synthesized and released by some pathogen, and which interacts with the host metabolism.
pathovar In plant pathology, strains of bacteria causing disease in specific plant cultivars.
pBR322 One of the first plasmid vectors widely used; especially used for cloning DNA in E. coli. See plasmid.
PCR See polymerase chain reaction.
PCV See packed cell volume.
pectin (Gr. pektos, congealed) A white amorphous substance which, when combined with acid and sugar, yields a jelly substance cementing cells together (the middle lamella).
pectinase (Gr. pektos, congealed) Enzyme catalysing the hydrolysis of pectins.
pedicel (L. pediculus, a little foot) Stalk or stem of the individual flowers of an inflorescence.
pedigree A table, chart or diagram recording the ancestry of an individual.
peduncle (L. pedunculus, a late form of pediculus, a little foot) Stalk or stem of a flower that is born singly; the main stem of an inflorescence.
PEG See polyethylene glycol.
penetrance The percentage of individuals in population that show a particular phenotype among those capable of showing it, i.e., among those that have the genotype normally associated with that phenotype.
peptide A sequence of amino acids linked by peptide bonds; a breakdown or build-up unit in protein metabolism.
peptide bond A chemical bond holding amino acid sub-units together in proteins.
peptide vaccine A short chain of amino acids that can induce antibodies against a specific infectious agent.
peptidyl-tRNA binding site; P-site The site on a ribosome that hosts the tRNA to which an amino acid for the growing polypeptide chain is attached.
peptidyl transferase An enzyme bound tightly to the large sub-unit of the ribosome that catalyses the formation of peptide bonds between amino acids during translation.
perennial (L. perennis, lasting years) A plant that grows more or less indefinitely from year to year and, once mature, usually produces seed each year.
pericentric inversion An inversion that includes the centromere, hence involving both arms of a chromosome.
periclinal The plane of cell wall orientation or cell division parallel to the surface of the organ. cf anticlinal.
periclinal chimera Genotypically or cytoplasmically different tissues arranged in concentric layers.
pericycle (Gr. peri, around + kyklos, circle) Region of the plant bounded externally by the endodermis and internally by the phloem. Most roots originate from the pericycle.
periplasm The space (periplasmic space) between the cell (cytoplasmic) membrane of a bacterium or fungus and the outer membrane or cell wall.
permanent wilting point (PWP) The moisture content of soil at which plants wilt to such an extent that they fail to recover even when placed in a humid atmosphere.
permeable (L. permeabilis, that which can be penetrated) Used of a membrane, cell or cell system through which substances may diffuse.
persistence Ability of an organism to remain in a particular setting for a period of time after it is introduced.
persistent 1. Continues to exist or to remain attached.
2. Chemicals with a long inactivation time, such as some pesticides, which may accumulate in the food chain.
PERV See porcine endogenous retrovirus.
pesticide A toxic chemical product that kills harmful organisms (e.g., insecticides, fungicide, weedicides, rodenticides).
petal One of the parts of the flower that make up the corolla.
petiole (L. petiolus, a little foot or leg) Stalk of leaf. See pedicel; peduncle.
petite mutant A respiration-deficient yeast mutant that produces small colonies when grown on glucose-containing medium.
Petri dish Flat round dish with a matching lid, made of glass or plastic material, and used for culturing organisms. a.k.a. plates, hence the term to "plate" (q.v.) a culture.
PFGE See pulsed-field [gel] electrophoresis.
pH A measure of acidity and alkalinity. Equal to the log of the reciprocal of the hydrogen ion concentration of a solution, expressed in grams per litre. A reading of 7 is neutral (e.g., pure water), whereas below 7 is acid and above 7 is alkaline.
phage See bacteriophage.
phagemids Cloning vectors that contain components derived from both phage chromosomes and plasmids.
phagocytes Immune system cells that ingest and destroy viruses, bacteria, fungi and other foreign substances or cells.
phagocytosis The process by which minute food particles or foreign particles invading the body are engulfed and broken down by certain animal cells.
pharmaceutical agent See therapeutic agent.
phase state The coupling or repulsion of two linked genes.
pH-electrode-based sensor Sensor in which a standard electrochemical pH electrode is coated with a biological material. Many biological processes raise or lower pH, and the changes can be detected by the pH electrode.
phenocopy An organism whose phenotype (but not genotype) has been changed by the environment to resemble the phenotype usually associated with a mutant organism.
phenolic oxidation Many plant species contain phenolic compounds that blacken through oxidation. The process is initiated after plants are wounded. Phenolic oxidation may lead to growth inhibition or, in severe cases, to tissue necrosis and death. Antioxidants are incorporated into the sterilizing solution or isolation medium to prevent or reduce oxidative browning. cf activated charcoal.
phenols; phenolics Compounds with hydroxyl group(s) attached to the benzene ring, forming esters, ethers and salts. Phenolic substances are produced from newly explanted tissues, oxidizing to form coloured compounds visible in nutrient media.
phenotype (Gr. phaneros, showing + type) The visible appearance or set of traits of an organism resulting from the combined action of genotype and environment. cf genotype.
phenylalanine See amino acid.
pheromone A hormone-like substance that is secreted by an organism into the environment as a specific signal to another organism, usually of the same species.
phloem (Gr. phloos, bark) Food-conducting tissue in plants, consisting of sieve tubes, companion cells, phloem parenchyma and fibres.
phosphatase An enzyme that hydrolyses esters of phosphoric acid, removing a phosphate group from an organic compound.
phospho-diester bond A bond in which a phosphate group joins adjacent carbons through ester linkages. A condensation reaction between adjacent nucleotides results in a phospho-diester bond between 3´ and 5´ carbons in DNA and RNA.
phospholipase A2 An enzyme which degrades type A2 phospholipids.
phospholipid A class of lipid molecules in which a phosphate group is linked to glycerol and two fatty acyl groups. A major component of biological membranes. See inositol lipid.
phosphorolysis The cleavage of a bond by orthophosphate; analogous to hydrolysis referring to cleavage by water.
phosphorylation The addition of a phosphate group to a compound.
photoautotroph See autotroph; heterotroph.
photo-bioreactor Bioreactor dependent on sunlight, which is taken up by its content of plant material, usually algae.
photoheterotroph See heterotroph.
photon A quantum of light; the energy of a photon is proportional to its frequency; E = hv, where E is energy; h is Planck's constant, 6.62 × 10-27 erg-second; and v is the frequency.
photoperiod (Gr. photos, light + period) The length of day or period of daily illumination provided or required by plants for reaching the reproductive stage.
photoperiodism The response of an organism to changes in day length.
photophosphorylation The formation of ATP from ADP and inorganic phosphate using light energy in photosynthesis.
photoreactivation A DNA repair process that is light dependent.
photosynthate The carbohydrates and other compounds produced in photosynthesis.
photosynthesis A chemical process by which green plants synthesize organic compounds from carbon dioxide and water in the presence of sunlight.
photosynthetic Able to use sunlight energy to convert atmospheric carbon dioxide into organic compounds. Nearly all plants, most algae and some bacteria are photosynthetic.
photosynthetic efficiency Efficiency of converting light energy into organic compounds.
photosynthetically active radiation (PAR) Radiant energy captured by the photosynthetic system in the light reactions, usually taken to be the wavelengths between 400 and 700 nm.
phototropism (Gr. photos, light + tropos, turning) A growth curvature in which light is the stimulus.
phylogeny A diagram illustrating the deduced evolutionary history of populations of related organisms.
physical map A map showing physical locations on a DNA sequence, such as restriction sites and sequence-tagged sites. Also a diagram of a chromosome or a karyotype, showing the location of loci (genes and markers) See mapping.
phytochrome A reversible pigment system of a protein nature, found in the cytoplasm of green plants. Phytochrome is associated with the absorption of light that affects growth, development and differentiation of a plant, independent of photosynthesis, e.g., in the photoperiodic response.
phytohormone A substance that stimulates growth or other processes in plants. They include auxins, abscissic acid, cytokinins, gibberellins and ethylene. Phytohormones are chemical messengers that may pass through cells, tissues and organs and stimulate biochemical, physiological and morphological responses.
phytokinin See cytokinin.
phytoparasite (adj: phytoparasitic) Parasite on plants.
phytopathogen An organism that causes disease in plants.
phytosanitary Plant health, including quarantine.
phytostat The name adopted by Tulecke in 1965 for an apparatus designed for the semi-continuous chemostat culture of plant cells.
pigments Molecules that are coloured by the light they absorb. Some plant pigments are water soluble and are found mainly in the cell vacuole.
pinocytosis The process by which a living cell engulfs a minute droplet of liquid.
pipette A slender graduated tube into which small amounts of liquids are taken up by suction, for measuring and transferring.
pistil (L. pistillum, a pestle) Central organ of the flower, typically consisting of ovary, style and stigma. The pistil is usually referred to as the female part of a perfect flower.
plantlet A small rooted shoot developed from seed or from cultured cells either by embryogenesis or organogenesis.
plant cell culture Growth of plant cells or roots of plants in bioreactors.
plant cell immobilization Entrapment of plant cells in gel matrices; the cells are suspended in small drops of the material, which then is set or allowed to harden to make little carriers. Materials such as alginates, agar or polyacrylamide can be used.
plant genetic resources (PGR) Defined in the International Undertaking on Plant Genetic Resources (FAO, 1983) to mean the reproductive or vegetative propagating material of the following categories of plants:
(i) cultivated varieties (cultivars) in current use and newly developed varieties;
(ii) obsolete cultivars;
(iii) primitive cultivars (landraces);
(iv) wild and weed species, near relatives of cultivated varieties; and
(v) special genetic stocks (including elite and current breeder's lines and mutants).
plaque A clear spot on an otherwise opaque culture plate of bacteria or cultured bacteria cells, showing where cells have been lysed by viral infection.
plasma cells Antibody-producing white blood cells derived from B lymphocytes.
plasma membrane See cell membrane; plasmalemma.
plasmalemma (Gr. plasma, anything formed + lema, a husk or shell of a fruit) A delicate cytoplasmic double membrane found on the outside of the protoplast, adjacent to the cell wall. See cell membrane.
2mm plasmid A naturally occurring, double-stranded, circular DNA plasmid (6 318 bp) found in the nuclei of yeast. Many yeast plasmid vectors are derived from the 2mm plasmid. a.k.a. 2mm circle; 2 m-plasmid; 2-micron plasmid.
plasmid An extrachromosomal, autonomous circular DNA molecule found in certain bacteria, capable of autonomous replication. Plasmids can transfer genes between bacteria and are important tools of transformation in genetic engineering. They exist in an autonomous state and are transferred independently of chromosomes. See nicked circle; pAMP; relaxed plasmid; stringent plasmid; supercoiled plasmid.
plasmodesma (Gr. plasma, something formed + demos, a bond, a band; pl: plasmodesmata) Fine protoplasmic thread passing through the plant cell wall that separates two protoplasts.
plasmolysis (Gr. plasma, something formed + lysis, a loosening) Separation of the cytoplasm from the cell wall, due to removal of water from the protoplast.
plastid (Gr. plastis, a builder) A cytoplasmic body found in the cells of plants and some protozoa. Chloroplastids, for example, produce chlorophyll that is involved in photosynthesis.
plastoquinone A quinone which is one of a group of compounds involved in the transport of electrons in photosynthesis in chloroplasts.
plate 1. Verb: To distribute a thin film of something. Hence micro-organisms or plant cells are plated onto nutrient agar.
2. Noun: Refers to the two segments of a Petri dish or a similar-shaped item.
platform shaker See shaker.
plating efficiency The percentage of inoculated cells which give rise to cell colonies when seeded into culture vessels.
pleiotropy (adj: pleiotropic) The situation in which a particular gene has an effect on several different traits.
ploidy The number of sets of chromosomes per cell, e.g., haploid, diploid, polyploid.
plumule (L. plumula, a small feather) The first bud of an embryo or that portion of the young shoot above the cotyledons.
pluripotent See totipotent.
pneumatic reactor See airlift fermenter.
point mutation A change in DNA at a specific site in a chromosome. Includes nucleotide substitutions and the insertion or deletion of one or a few nucleotide pairs. See mutation.
polar bodies In female animals, the products of a meiotic division that do not develop into an ovum. The first polar body comprises one of the two products of meiosis I, and it may not go through meiosis II. The second polar body comprises one of the two products of meiosis II.
polar mutation A mutation that influences the functioning of genes that are downstream in the same transcription unit.
polar nuclei Two centrally located nuclei in the embryo sac that unite with a second sperm cell in a triple fusion. In certain seeds, the product of this fusion develops into the endosperm.
polar transport The directed movement within plants of compounds (usually endogenous plant growth regulators) mostly in one direction; polar transport overcomes the tendency for diffusion in all directions.
polarity (Gr. pol, an axis) The observed differentiation of an organism, tissue or cell into parts having opposed or contrasted properties or form.
pole cells A group of cells in the posterior of Drosophila embryos that are precursors to the adult germ line.
pollen (L. pollen, fine flour) The mass of germinated microspores or partially developed male gametophytes of seed plants.
pollen culture The in vitro culture and germination of pollen grains. Callus cultures thus obtained will form shoots or embryoids which develop into monoploid plants. See anther culture; microspore culture.
pollen grain A microspore produced in the pollen sac of angiosperms or the microsporangium of gymnosperms. Unicellular, with variable shape and size, and usually ovoid from 25 to 250mm.
pollination Transfer of pollen from anther to stigma in the process of fertilization in angiosperms; transfer of pollen from male to female cone in the process of fertilization in gymnosperms.
poly (A) polymerase Enzyme that catalyses the addition of adenine residues to the 3´ end of pre-mRNAs to form the poly-(A) tail. See polyadenylation; polymerase.
poly-(A) tail See polyadenylation.
polyacrylamide gel electrophoresis (PAGE) A method for separating nucleic acid or protein molecules according to their molecular size. The molecules migrate through the inert gel matrix under the influence of an electric field. In the case of protein PAGE, detergents such as sodium dodecyl sulphate (SDS) are often added to ensure that all molecules have a uniform charge. Secondary structure can often lead to the anomalous migration of molecules. Therefore it is common to denature protein samples by boiling them prior to PAGE. In the case of nucleic acids, denaturing agents such as formamide, urea or methyl mercuric hydroxide are often incorporated into the gel itself, which may also be run at high temperature. PAGE is used to separate the products of DNA-sequencing reactions and the gels employed are highly denaturing, since molecules differing in size by a single nucleotide must be resolved.
polyacrylamide gels Often referred to incorrectly as acrylamide gels. These gels are made by cross-linking acrylamide with N,N'-methylene-bis-acrylamide. Polyacrylamide gels are used for the electrophoretic separation of proteins, DNA and RNA molecules. Polyacrylamide beads are also used as molecular sieves in gel chromatography, marketed as Bio-gelTM.
polyadenylation Post-transcriptional addition of a polyadenylic acid tail to the 3´ end of eukaryotic mRNAs. Also called poly-(A) tailing. The adenine-rich 3´ terminal segments is called a poly (A) tail.
polyclonal antibody A serum sample that contains a mixture of immunoglobulin molecules secreted against a specific antigen, each recognizing a different epitope, some antibodies of which bind to different antigenic determinants of one antigen.
polycloning site See polylinker.
polyembryony In the ordinary course of events, one embryo is formed in each ovule and is derived from the fertilization of the ovum in the solitary embryo sac. However, two or more embryos could start development even though only one may reach maturity.
polyethylene glycol (PEG); carbowax A polymer having the general formula: HOCH2(CH2OCH2)XCH2OH and available in a range of molecular weights from ca 1000 to ca 6000. PEG 4000 and PEG 6000 are commonly used to promote cell or protoplast fusion, and to facilitate DNA uptake in the transformation of organisms such as yeast. PEG is also used to concentrate solutions by withdrawing water from them.
polygene One of many genes of small effect influencing the development of a quantitative trait; results in continuous variation and in quantitative inheritance. See gene.
polygenic Controlled by many genes of small effect.
polylinker A segment of DNA that contains a number of different restriction endonuclease sites. a.k.a. multiple cloning site (MCS).
polymer A compound composed of many identical smaller sub-units; resulting from the process of polymerization.
polymerase chain reaction (PCR) A procedure that amplifies a particular DNA sequence. It involves multiple cycles of denaturation, annealing to oligonucleotide primers, and extension (polynucleotide synthesis), using a thermostable DNA polymerase, deoxyribonucleotides, and primer sequences in multiple cycles of denaturation-renaturation-DNA synthesis. See polymerase.
polymerase An enzyme that catalyses the formation of polymeric molecules from monomers. A DNA polymerase synthesizes DNA from deoxynucleoside triphosphates using a complementary DNA strand and a primer. An RNA polymerase synthesizes RNA from monoribonucleoside triphosphates and a complementary DNA strand. See poly-(A) polymerase; polymerase chain reaction; RNA polymerase; taq polymerase.
polymerization Chemical union of two or more molecules of the same kind such as glucose or nucleotides to form a new compound (starch or nucleic acid) having the same elements in the same proportions but a higher molecular weight and different physical properties.
polymery The phenomenon whereby a number of genes at different loci (which may be polygenes) can act together to produce a single effect.
polymorphism The occurrence of two or more alleles at a locus in a population. a.k.a. genetic polymorphism.
polynucleotide A chain of nucleotides in which each nucleotide is linked by a single phospho-diester bond to the next nucleotide in the chain. They can be double- or single-stranded. The term is used to describe DNA or RNA. See nucleotide.
polypeptide A linear molecule composed of two or more amino acids linked by covalent (peptide) bonds. They are called dipeptides, tripeptides and so forth, according to the number of amino acids present.
polyploid (Gr. polys, many + ploid, fold) Tissue or cells with more than two complete sets of chromosomes, that results from chromosome replication without nuclear division or from union of gametes with different number of chromosome sets, hence triploid (3x), tetraploid (4x), pentaploid (5x), hexaploid (6x), heptaploid (7x), octoploid (8x)).
polysaccharide (Gr. polys, many + Gr. sakcharon, sugar) Long-chain molecules, such as starch and cellulose, composed of multiple units of a monosaccharide.
polysaccharide capsules Carbohydrate coverings with antigenic specificity that are present on some types of bacteria.
polytene chromosomes Giant chromosomes produced by interphase replication without division, and consisting of many identical chromatids arranged side by side in a cablelike pattern.
polyunsaturates Oils containing polyunsaturated fatty acids.
polyspermy The entry of several sperm into the egg during fertilization, although only one sperm nucleus actually fuses with the egg nucleus.
polyvalent vaccine A recombinant organism into which antigenic determinants have been cloned from a number of different disease-causing organisms, and used as a vaccine. See vaccine.
polyvinylpyrrolidone (PVP) (C6H9NO)n) An occasional constituent of plant tissue culture isolation media. PVP is of variable molecular weight and has antioxidant properties, so is used to prevent oxidative browning of explanted tissues. PVP is less frequently used as an osmoticum in culture media.
population density Number of cells or individuals per unit. The unit could be an area or volume of medium.
population genetics The branch of genetics that deals with frequencies of alleles and genotypes in breeding populations. cf. quantitative genetics.
population A local group of organisms belonging to the same species and interbreeding.
porcine endogenous retrovirus (PERV) The provirus (q.v.) of a porcine retrovirus. With the increasing interest in the use of pig organs for xenotransplantation to humans, there has been concern that PERVs could be activated after transplantation, creating an infection in the human recipient.
positional candidate gene A gene known to be located in the same region as a DNA marker that has been shown to be linked to a single-locus trait or to a quantitative trait locus (QTL) (q.v.) and whose function suggests that it could be the source of genetic variation in the trait in question.
positional cloning The process that commences with searching for markers linked to a particular inherited trait, then using those markers to identify the approximate location of the gene responsible for the trait, and then using various cloning strategies (including chromosome walking, q.v.) to identify, isolate and characterize the gene. Originally, the strategy was called reverse genetics, a term that some consider to be a misnomer and misleading.
position effect The situation in which a change in phenotype results from the change of the position of a gene or group of genes.
positive control system A mechanism in which the regulatory protein(s) is required to turn on gene expression.
positive selectable marker See dominant marker selection.
positive selection 1. See dominant marker selection.
2. A method by which cells that carry a DNA insert integrated at a specific chromosomal location are selected.
post-replication repair A recombination-dependent mechanism for repairing damaged DNA.
post-translational modification The specific addition of phosphate groups, sugars (glycosylation), or other molecules to a protein after it has been synthesized.
potentiometric See enzyme electrode.
ppm See parts per million.
precocious germination Premature germination of the embryo, prior to completion of embryogenesis.
pre-filter A coarse filter used to screen out large particles before air is forced through a much finer filter. See HEPA filter; laminar air-flow cabinet.
pre-mRNA See primary transcript.
pressure potential The pressure generated within a cell; it is the difference between the osmotic potential within the cell and the water potential of the external environment, provided the cell volume is constant.
pre-transplant Stage III in tissue culture micropropagation; the rooting, hardening stage prior to transfer to soil. See micropropagation.
preventive immunization; vaccination Infection with an antigen to elicit an antibody response that will protect the organism against future infections.
Pribnow box Consensus sequence near the mRNA start-point of prokaryotic genes. See TATA box.
primary (L. primus, first) First in order of time or development.
primary antibody In an ELISA or other immunological assay, the antibody that binds to the target molecule.
primary cell A cell or cell line taken directly from a living organism, which is not immortalized.
primary cell wall The cell wall layer formed during cell expansion. Plant cells possessing only primary walls may divide or undergo differentiation.
primary culture A culture started from cells, tissues or organs taken directly from organisms. A primary culture may be regarded as such until it is sub-cultured for the first time. It then becomes a cell line.
primary germ layers See germ layers.
primary growth 1. Refers to apical meristem-derived growth; the tissues of a young plant.
2. Refers to explant growth during the initial culture period; such as primary callus growth.
primary immune response The immune response that occurs during the first encounter of a mammal with a given antigen. cf secondary immune response.
primary meristem Meristem of the shoot or root tip giving rise to the primary plant body.
primary tissue A tissue that has differentiated from a primary meristem.
primary transcript The RNA molecule produced by transcription prior to any post-transcriptional modifications; also called a pre-mRNA in eukaryotes.
primer A short DNA or RNA fragment annealed to a template of single-stranded DNA, providing a 3´ hydroxyl end from which DNA polymerase extends a new DNA strand to produce a duplex molecule.
primer DNA polymerase DNA polymerase that provides primers for the DNA polymerization. Unlike RNA polymerase, DNA polymerase is unable to initiate the de novo synthesis of a polynucleotide chain. DNA polymerase can only add nucleotides to a free 3´ hydroxyl group at the end of a pre-existing chain. A short oligonucleotide, known as a primer, is therefore needed to supply such a hydroxyl group for the initiation of DNA synthesis.
primer walking A method for sequencing long (>1 kb) cloned pieces of DNA. The initial sequencing reaction reveals the sequence of the first few hundred nucleotides of the cloned DNA. On the basis of these data, a primer containing about 20 nucleotides and complementary to a sequence near the end of sequenced DNA is synthesized, and is then used for sequencing the next few hundred nucleotides of the cloned DNA. This procedure is repeated until the complete nucleotide sequence of the cloned DNA is determined.
primordium A group of cells which gives rise to an organ.
primosome A protein-replication complex that catalyses the initiation of synthesis of Okazaki fragments during discontinuous replication of DNA. It involves DNA primase and DNA helicase activities.
prion See proteinaceous infectious particle.
probability Statistics: The frequency of occurrence of an event.
proband The individual in a family in whom an inherited trait is first identified.
probe 1. For diagnostic tests, the agent that is used to detect the presence of a molecule in a sample.
2. A DNA or RNA sequence labelled or marked with a radioactive isotope or that is used to detect the presence of a complementary sequence by hybridization with a nucleic acid sample.
probe DNA A labelled DNA molecule used to detect complementary-sequence nucleic acid molecules by molecular hybridization. To localize the probe DNA sequence and reveal the complementary hybridization sequence, autoradiography or fluorescence is used. See multilocus probe; nucleotide.
procambium (L. pro, before + cambium) A primary meristem that gives rise to primary vascular tissues and, in most woody plants, to the vascular cambium.
procaryote; procaryotic See prokaryote; prokaryotic.
processed pseudo-gene A copy of a functional gene which has no promoter, no introns and which, consequently, is not itself transcribed. Pseudo-genes are thought to originate from the integration into the genome of cDNA copies synthesized from mRNA molecules by reverse transcriptase. Pseudo-genes therefore have a poly (dA) sequence at their 5´ ends. Because they are not subject to any evolutionary pressure to maintain their coding potential, pseudo-genes accumulate mutations and often have stop codons in all three reading frames.
production environment In AnGR: All input-output relationships, over time, at a particular location. The relationships will include biological, climatic, economic, social, cultural and political factors, which combine to determine the productive potential of a particular livestock enterprise. (Source: FAO, 1999)
· high-input production environment A production environment where all rate-limiting inputs to animal production can be managed to ensure high levels of survival, reproduction and output. Output and production risks are constrained primarily by managerial decisions. (Source: FAO, 1999)
· medium-input production environment A production environment where management of the available resources has the scope to overcome the negative effects of the environment on animal production, although it is common for one or more factors to limit output, survival or reproduction in a serious fashion. (Source: FAO, 1999)
· low-input production environment A production environment where one or more rate-limiting inputs impose continuous or variable severe pressure on livestock, resulting in low survival, reproductive rate or output. Output and production risks are exposed to major influences which may go beyond human management capacity. (Source: FAO, 1999)
production traits In AnGR: Characteristics of animals, such as the quantity or quality of the milk, meat, fibre, eggs, draught, etc., they (or their progeny) produce, which contribute directly to the value of the animals for the farmer, and that are identifiable or measurable at the individual level. Production traits of farm animals ate generally quantitatively inherited, i.e., they are influenced by many genes whose expression in a particular animal also reflects environmental influences. (Source: FAO, 1999)
productivity The amount of product that is produced within a given period of time from a specified quantity of resource.
pro-embryo (L. pro, before + embryon, embryo) A group of cells arising from the division of the fertilized egg cell or somatic embryo before those cells which are to become the embryo are recognizable.
progeny See offspring.
progeny testing For a single locus: the practice of ascertaining the genotype of an individual from its offspring, such as by mating it to other individuals and examining the progeny. For a quantitative trait: the collection and use of progeny performance as a clue to the breeding value of the parent of those progeny.
progesterone A hormone produced primarily by the corpus luteum of the ovary, but also by the placenta, that prepares the inner lining of the uterus for implantation of a fertilized egg cell.
prokaryote (L. pro, before + Gr. karyon, a nut, referring in modern biology to the nucleus). A member of a large group of organisms, including bacteria and blue-green algae, which do not have the DNA separated from the cytoplasm by a membrane in their cells. The DNA is usually in one long strand. Prokaryotes do not undergo meiosis and do not have functional organelles such as mitochondria and chloroplasts. cf eukaryote.
prolactin A hormone, produced by the anterior pituitary gland, that stimulates and controls lactation in mammals.
proliferation (L. proles, offspring + ferre, to bear) Increase by frequent and repeated reproduction; growth by cell division.
pro-meristem The embryonic meristem that is the source of organ initials or foundation cells.
promoter 1. A nucleotide sequence of DNA to which RNA polymerase binds and initiates transcription. It usually lies upstream of (5´ to) a coding sequence. A promoter sequence aligns the RNA polymerase so that transcription will initiate at a specific site.
2. A chemical substance that enhances the transformation of benign cells into cancerous cells. See constitutive promoter.
promoter sequence A regulatory DNA sequence that initiates the expression of a gene.
pro-nuclear micro-injection The initial method of transgenesis in animals, involving injecting many copies of a particular gene into one of the two pro-nuclei of a fertilized ova. Characterised by a very low success rate. As animal cloning (q.v.) becomes more common, pro-nuclear micro-injection will be replaced by micro-injection of cloned genes into a culture of cloned embryos produced by nuclear transfer, which can be tested for expression of the transgene before transfer to recipient females. See transgenesis.
pro-nucleus Either of the two haploid gamete nuclei just prior to their fusion in the fertilized ovum.
proofreading The enzymatic scanning of newly-synthesized DNA for structural defects, such as mis-matched base pairs. It is effected by DNA polymerase.
propagation (L. propagare, to propagate) The multiplication of plants by numerous types of vegetative material; an ancient practice dating from the dawn of agriculture, carried out in a nursery or directly in the field (vegetative propagation), and now in in vitro culture (micropropagation).
propagule Any structure capable of giving rise to a new plant by asexual or sexual reproduction, including bulbils, leafbuds, etc.
pro-phage The genome of a temperate bacteriophage integrated into the chromosome of a lysogenic bacterium and replicated along with the host chromosome.
prophase (Gr. pro, before + phasis, appearance) An early stage in nuclear division, characterized by the shortening and thickening of the chromosomes and their movement to the metaphase plate. It occurs between interphase and metaphase. During this phase, the centriole divides and the two daughter centrioles move apart. Each sister DNA strand from interphase replication becomes coiled, and the chromosome is longitudinally double except in the region of the centromere. Each partially separated chromosome is called a chromatid. The two chromatids of a chromosome are sister chromatids.
protamines Small basic proteins that replace the histones in the chromosomes of some sperm cells.
protease An enzyme that hydrolyzes proteins, cleaving the peptide bonds that link amino acids in protein molecules.
protein (Gr. proteios, of the first rank) A macromolecule composed of one to several polypeptides. Each polypeptide consists of a chain of amino acids linked together by covalent (peptide) bonds. They are naturally-occurring complex organic substances (egg albumen, meat) composed essentially of carbon, hydrogen, oxygen and nitrogen, plus sulphur or phosphorus, which are so associated as to form sub-microscopic chains, spirals or plates and to which are attached other atoms and groups of atoms in a variety of ways. The word was coined by Jöns J. Berzelius (1838) to emphasize the importance of this group of molecules. See polypeptide.
protein crystallization Making crystals of a protein, as a key part of most methods used for determining a protein's three-dimensional structure.
protein drug See therapeutic agent.
protein engineering Generating proteins with modified structures that confer properties such as higher catalytic specificity or thermal stability.
protein kinase An enzyme that adds phosphate groups to a protein molecule at the sites of serine, threonine or tyrosine residues.
protein metabolic step One step in the chain of reactions that take place in an organism and dictate the composition of that organism.
protein sequencing The process of determining the amino-acid sequence of a protein or its component polypeptides.
protein synthesis The creation of proteins from their constituent amino acids, in accordance with the genetic information carried in the DNA of the chromosomes.
proteinaceous infectious particle; prion An abnormal form of a normal cell protein, with no detectable nucleic acid, found in the brain of mammals and believed to be the agent responsible for the class of diseases called spongiform encephalopathies, including scrapie in sheep and bovine spongiform encephalopathy (BSE; mad cow disease) in cattle.
proteolysis Enzymatic degradation of a protein.
proteolytic The ability to break down protein molecules.
protoclone Regenerated plant derived from protoplast culture or a single colony derived from protoplasts in culture.
protocol (Gr. protokollon, first leaf glued to a manuscript and describing the contents) The step-by-step experiments proposed to describe or solve a scientific problem, or the defined steps of a specific procedure.
protocorm In orchids, seeds contain an unorganized embryo comprising only a few hundred cells. During seed germination this embryo forms a tuberous structure, called a protocorm, from which develops a complete plant. In cultures, vegetative parts of several orchids form round, smooth protocorms which may be multiplied indefinitely or induced to regenerate a whole plant.
protoderm (Gr. protos, first + derma, skin) A primary meristem tissue that gives rise to epidermis.
protogyny The condition in which the female reproductive organs (carpels) of a flower mature before the male ones (stamens), thereby ensuring that self-fertilization does not occur.
protomeristem See promeristem.
proto-oncogene A normal cellular gene that can be changed to an oncogene by mutation or by being incorporated into a retrovirus and then being transcribed at inappropriate times and/or in inappropriate tissues. See cellular oncogene; oncogene.
protoplasm The essential, complex living substance of cells, upon which all vital functions of nutrition, secretion, growth and reproduction depend.
protoplast (Gr. protoplastos, formed first) A bacterial or plant cell for which the relatively rigid wall has been removed either chemically or enzymatically, leaving its cytoplasm enveloped by only a delicate peripheral membrane. Protoplasts are spherical and smaller than the elongate, angular shaped and often vacuolated cells from which they have been released.
protoplast culture The isolation and culture of plant protoplasts by mechanical means or by enzymatic digestion of plant tissues or organs, or cultures derived from these. Protoplasts are utilized for selection or hybridization at the cellular level and for a variety of other purposes.
protoplast fusion The coalescence of the plasmalemma and cytoplasm of two or more protoplasts in contact with one another. Initial adhesion of two protoplasts is a random process but coalescence can be induced.
prototroph An organism such as a bacterium that will grow on a minimal medium.
protozoan (pl: protozoa) A microscopic, single-cell organism.
pro-toxin A latent, non-active precursor form of a toxin.
protruding end See extension.
provirus A retrovirus in which the single RNA strand has been converted into a double-strand DNA, which has been integrated into a host genome.
pseudo-affinity chromatography See affinity chromatography.
pseudo-autosomal region A section at one end of the X and Y chromosomes for which there is sufficient homology that there is pairing (synapsis) during meiosis I.
pseudo-gene A copy (duplicate) of a functional gene that, as a result of mutation following duplication, can no longer function.
pseudocarp; false fruit A fruit that incorporates, in addition to the ovary wall, other parts of the flower, such as the receptacle (e.g., strawberry).
Pseudomonas spp. A common Gram-negative bacterial genus that is widely distributed. Many of the soil forms produce a pigment that fluoresces under ultraviolet light, hence the descriptive term fluorescent pseudomonas.
P-site See peptidyl-tRNA site.
psychrophile A micro-organism that can grow at temperatures below 30°C and as low as 0°C.
PUC A widely used expression plasmid, containing a galactosidase gene. See plasmid.
pulsed-field gel electrophoresis (PFGE) A procedure used to separate very large DNA molecules by alternating the direction of electric current in a pulsed manner across a semisolid gel.
punctuated equilibrium The occurrence of speciation events in bursts, separated by long intervals of species stability.
pure culture Axenic culture.
pure line A strain in which all members have descended by self-fertilization or close inbreeding . A pure line is genetically uniform.
purification tag See affinity tag.
purine A double-ring, nitrogen-containing base present in nucleic acids; adenine (A) and guanine (G) are the two purines present in most DNA and RNA molecules.
PVP See polyvinylpyrrolidone.
PWP See permanent wilting point.
pyrethrins Active constituents of pyrethrum (Tanacetum cinerariifolium) flowers, used as insecticides.
pyrimidine A single-ring, nitrogen-containing base present in nucleic acids; cytosine (C) and thymine (T) are commonly present in DNA, whereas uracil usually replaces thymine in RNA.
pyrogen Bacterial substance that causes fever in mammals.