Glossary

This glossary will cover the terms of Microbial Genetics

Acetylene-reduction assay: Procedure estimates nitrogenase activity by measuring the rate of acetylene reduced to ethylene.

Agarose Gel Electrophoresis: A method for separating nucleic acids (DNA or RNA) within a gel made of agarose in a suitable buffer under the influence of an electrical field. Suitable for separation of large fragments of nucleic acid, separation is based primarily upon the size of the nucleic acid. # A matrix composed of a highly purified form of agar that is used to separate larger DNA and RNA molecules ranging 20,000 nucleotides.

Ammonification: Liberation of ammonium (ammonia) from organic nitrogenous compounds by the action of microorganisms.

Ampicillin (beta-lactamase): An antibiotic derived from penicillin that prevents bacterial growth by interfering with cell wall synthesis.

Anneal: Generally synonymous with "hybridize". # The pairing of complementary DNA or RNA sequences, via hydrogen bonding, to form a double-stranded polynucleotide. Most often used to describe the binding of a short primer or probe.

Antagonist: Biological agent that reduces the number or disease-producing activities of a pathogen.

Antibiotic resistance: The ability of a microorganism to produce a protein that disables an antibiotic or prevents transport of the antibiotic into the cell. By using plasmids containing antibiotic resistance genes, the researcher can kill off all the bacteria which have not taken up his plasmid, thus ensuring that the plasmid will be propagated as the surviving cells divide.

Antibiotic: A class of natural and synthetic compounds that inhibit the growth of or kill other microorganisms.

Associative dinitrogen fixation: Close interaction between a free-living diazotrophic organism and a higher plant that results in an enhanced rate of dinitrogen fixation.

Base composition: Proportion of the total bases consisting of guanine plus cytosine or thymine plus adenine base pairs. Usually expressed as a guanine + cytosine (G + C) value, e.g. 60% G+C.

beta-Lactamase: Ampicillin resistance gene.

Biodiversity: The wide diversity and interrelatedness of earth organisms based on genetic and environmental factors.

Biomass: The total dry weight of all organisms in a particular sample, population, or area.

Biome: A grouping of plant ecosystems into a large distinct group occupying a major terrestrial region. They are created and maintained by climate.

Biotechnology: The scientific manipulation of living organisms, especially at the molecular genetic level, to produce useful products. Gene splicing and use of recombinant DNA (rDNA) are major techniques used.

Box: refers to a short nucleic acid consensus sequence or motif that is universal within kingdoms of organisms.

bp: Abbreviation for base pair(s). Double stranded DNA is usually measured in bp rather than nucleotides.

Buffer: A conjugate acid-base pair that is capable of resisting changes in pH when acid or base is added to the system. This tendency will be maximal when the conjugate forms are present in equal amounts.

Central dogma: Francis Crick's seminal concept that in nature genetic information generally flows from DNA to RNA to protein.

Chemoautotroph: Organism that obtains energy from the oxidation of reduced inorganic compounds or elements and obtains carbon from carbon dioxide.

Chemoheterotroph: Organism that obtains energy and carbon from the oxidation of organic compounds.

Chemolithotroph: Organism that obtains energy from the oxidation of inorganic compounds and uses inorganic compounds as electron donors.

Chemoorganotroph: Organism that obtains energy and electrons (reducing power) from the oxidation of organic compounds.

Chimeric DNA: Recombinant DNA whose components originate from two or more different sources.

Chromosome walking: The sequential isolation of clones carrying overlapping sequences of dna which span large regions of a chromosome. Overlapping regions of clones can be identified by hybridization.

Clade: A monophyletic taxon; a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. From the greek word "klados", meaning branch or twig.

Cladogram: A diagram, resulting from a cladistic analysis, which depicts a hypothetical branching sequence of lineages leading to the taxa under consideration. The points of branching within a cladogram are called nodes. All taxa occur at the endpoints of the cladogram.

Clone: An identical copy of an organism. Most plants, fungi, algae, and many other organisms naturally reproduce by making clones of themselves as a form of asexual reproduction.

Cohesive end: Also known as sticky end. Overhanging ends of a double-stranded DNA molecule that are capable of hybridizing with complementary ends.

Colony: A group of identical cells (clones) derived from a single progenitor cell.

Community: All organisms that occupy a common habitat and interact with one another.

Competency: An ephemeral state, induced by treatment with cold cations, during which bacterial cells are capable of uptaking foreign DNA.

Competent: bacterial cells which are capable of accepting foreign extra-chromosomal dna. There are a variety of processes by which cells may be made competent.

Complementary (copy) DNA (cDNA): Single-stranded DNA produced from an RNA template (usually mRNA) by reverse transcriptase in vitro. It lacks the introns present in corresponding genomic DNA. It is most commonly made to use in PCR to amplify RNA.

Consensus sequence: The nucleotides or amino acids most commonly found at each positions of the sequences of related molecules.

Cosmid: A genetically-engineered plasmid containing bacteriophage lambda packaging signals and potentially very large pieces of inserted foreign dna (up to 50 kb) which can be replicated in bacterial cells.

De novo: Literally, ‘from new’ as opposed to inherited.

Denaturation: with respect to nucleic acids, refers to the conversion from double-stranded to the single-stranded state, often achieved by heating or alkaline conditions. This is also called "melting" DNA. With respect to proteins, refers to the disruption of tertiary and secondary structure, often achieved by heat, detergents, chaotropes, and sulfhydryl-reducing agents.

Denaturing gel: an agarose or acrylamide gel run under conditions which destroy secondary or tertiary protein or RNA structure. For protein, this usually means the inclusion of 2-me (which reduces disulfide bonds between cysteine residues) and sds and/or urea in an acrylamide gel. For rna, this usually means the inclusion of formaldehyde or glyoxal to destroy higher ordered rna structures. In dna sequencing gels, urea is included to denature dsdna to ssdna strands. In denaturing gels, macromolecules tend to be separated on the basis of size and (to some extent) charge, while shape and oligomerization of molecules are not important. Contrast with native gel.

Denitrification: Reduction of nitrate or nitrite to molecular nitrogen or nitrogen oxides by microbial activity (dissimilatory nitrate reduction) or by chemical reactions involving nitrite (chemical denitrification).

Developmental biology: The field of biology which deals with the process of the growth and differentiation of an organism.

DGGE: Identification of mutations by electrophoresis of double-stranded DNA samples through a denaturing gradient, such as urea. Certain mutations affect the migration pattern by changing the point in the gel at which the DNA denatures; mutant sequences can be distinguished from wild-type sequences by comparing the electrophoretic pattern.

Diazotroph: Organism that can use dinitrogen as its sole nitrogen source, i.e. capable of N2 fixation.

Dideoxy sequencing: enzymatic determination of DNA or RNA sequence by the method of sanger and colleagues, based on the incorporation of chain terminating dideoxynucleotides in a growing nucleic acid strand copied by dna polymerase or reverse transcriptase from a DNA or RNA template. Separate reactions include dideoxynucleotides containing A, C, G or T bases. The reaction products represent a collection of new.

DNase: Deoxyribonuclease, a class of enzymes which digest DNA. The most common is DNase I, an endonuclease which digests both single and double-stranded DNA.

dNTP: deoxyribonucleoside triphosphate.

E. coli: A common Gram-negative bacterium useful for cloning experiments. Present in human intestinal tract. Hundreds of strains of E. coli exist. One strain, K-12, has been completely sequenced.

Ecogenetics: The branch of genetics that studies how (inherited or acquired) genetic factors influence human susceptibility to environmental health risks. It studies the genetic basis of environmental toxicity to develop methods for the detection, prevention and control of environment-related disease. Ecogenetics interacts with ecology, molecular genetics, toxicology, public health medicine and environmental epidemiology.

Ecological genetics: The analysis of genetics of natural populations and of the adaptations of them to the environment.

Ecology: The study of the interrelationships among living organisms and their environment. Human ecology means the study of human groups as influenced by environmental factors, including social and behavioral ones.

Ecosystem: All the organisms in a particular region and the environment in which they live. The elements of an ecosystem interact with each other in some way, and so depend on each other either directly or indirectly.

Electrophoresis: Method of separating closely-related proteins by differences in size and electrical charge. The technique of separating charged molecules in a matrix to which is applied an electrical field.

Electroporation: A method for introducing foreign nucleic acid into bacterial or eukaryotic cells that uses a brief, high voltage dc charge which renders the cells permeable to the nucleic acid. Also useful for introducing synthetic peptides into eucaryotic cells.

Endonuclease: Cleaves bonds within a nucleic acid chain; they may b especific for rna or for single-stranded or doublestranded dna. A restriction enzyme is a type of endonuclease

Endophyte: An organism that lives inside another.

Endosymbiosis: When one organism takes up permanent residence within another, such that the two become a single functional organism. Mitochondria and plastids are believed to have resulted from endosymbiosis.

Ethidium bromide: A fluorescent dye used to stain DNA and RNA. The dye fluoresces when exposed to UV light. # Intercalates within the structure of nucleic acids in such a way that they fluoresce under uv light. Ethidium bromide staining is commonly used to visualize rna or dna in agarose gels placed on uv light boxes. Proper precautions are required, because the ethidium bromide is highly mutagenic and the uv light damaging to the eyes. Ethidium bromide is also included in cesium chloride gradients during ultracentrifugation, to separate supercoiled circular dna from linear and relaxed circular dna.

Evolution: Darwin's definition: descent with modification. The term has been variously used and abused since darwin to include everything from the origin of man to the origin of life. The long-term process through which a population of organisms accumulats genetic changes that enable its members to successfully adapt to environmental conditions and to better exploit food resources.

Evolutionary tree: A diagram which depicts the hypothetical phylogeny of the taxa under consideration. The points at which lineages split represent ancestor taxa to the descendant taxa appearing at the terminal points of the cladogram.

Exonuclease: An enzyme which hydroylzes dna beginning at one end of a strand, releasing nucleotides one at a time (thus, there are 3' or 5' exonucleases).

Expression vector: A plasmid or phage designed for production of a polypeptide from inserted foreign DNA under specific controls.

Fingerprinting: The use of RFLPs or repeat sequence DNA to establish a unique individual-specific pattern of DNA fragments.

Galactosidase The presence of betagalactosidase activity in the cytoplasm of transfected cells can be readily detected by its ability to convert a colorless substrate (Xgal) to a blue-colored product.

Gel electrophoresis: A method to analyze the size of DNA (or RNA) fragments. In the presence of an electric field, larger fragments of DNA move through a gel slower than smaller ones. If a sample contains fragments at four different discrete sizes, those four size classes will, when subjected to electrophoresis, all migrate in groups, producing four migrating "bands". Usually, these are visualized by soaking the gel in a dye (ethidium bromide) which makes the DNA fluoresce under UV light.

GEM: A genetically engineered microorganism.

Gene cloning: The process of synthesizing multiple copies of a particular DNA sequence using a bacteria cell or another organism as a host.

Gene expression: The process of producing a protein from its DNA- and mRNA-coding sequences.

Gene mapping: Procedures used to determine the linear sequence of genetic loci on a chromosome.

Gene: A locus on a chromosome that encodes a specific protein or several related proteins. It is considered the functional unit of heredity.

Genetic distance: A measurement of genetic relatedness of populations. The estimate is based on the number of allelic substitutions per locus that have occurred during the separate evolution of two populations. Link to a lecture on Estimating Genetic Distance and GeneDist: Online Calculator of Genetic Distance. The software Arlequin, PHYLIP, GDA, PopGene, Populations and SGS are suitable to calculate population-topopulation genetic distance from allele frequencies. GenAlEx can be used to calculate genetic distance on Excel.

Genetic engineering: The manipulation of an organism's genetic endowment by introducing or eliminating specific genes through modern molecular biology techniques. A broad definition of genetic engineering also includes selective breeding and other means of artificial selection.

Genetic marker: A gene or group of genes used to "mark" or track the action of microbes.

Genomic DNA: The DNA contained in the chromosomes of a cell.

Genomic library: A DNA library which contains dna fragments hopefully representing each region of the genome of an organism, virus, etc, cloned into individual vector molecules for subsequent selection and amplification.

Genotype: The genetic constitution of an individual with respect to a specified locus or loci

GMO: Genetically modified organism.

Host strain (bacterial): The bacterium used to harbor a plasmid. Typical host strains include HB101 (general purpose E. coli strain), DH5H (ditto), JM101 and JM109 (suitable for growing M13 phages), XL1-Blue (general-purpose, good for blue/white lacZ screening). Note that the host strain is available in a form with no plasmids (hence you can put one of your own into it), or it may have plasmids present (especially if you put them there). Hundreds, perhaps thousands, of host strains are available.

Humic acid: Dark-colored organic material extracted from soil by various reagents (e.g., dilute alkali) and that is precipitated by acid (pH 1 to 2).

In situ: Refers to performing assays or manipulations with intact tissues.

In vitro: Literally, ‘in glass’ meaning in the laboratory.

In vivo: Refers to biological processes that take place within a living organism or cell. # Literally, ‘in the living organism’.

Inducer: A small molecule, such as iptg, that triggers gene transcription by binding to a regulator protein, such as lacz.

Insert: In a complete plasmid clone, there are two types of DNA - the "vector" sequences and the "insert". The vector sequences are those regions necessary for propagation, antibiotic resistance, and all those mundane functions necessary for useful cloning. In contrast, however, the insert is the piece of DNA in which you are really interested.

Intergenic regions: DNA sequences located between genes that comprise a large percentage of the human genome with no known function.

Intergenic: Between two genes; e.g. intergenic DNA is the DNA found between two genes. The term is often used to mean non-functional DNA.

Kb: 'kilobase" unit of 1000 nucleotide bases, either RNA or DNA.

Labeled DNA strands of varying lengths, all terminating with a dideoxynucleotide at the 3' end (at the site of a complementary base in the template nucleic acid), and are separated in a polyacrylamide/urea gel to generate a sequence "ladder". This method is more commonly used than "maxam-gilbert" (chemical) sequencing. Dideoxynucleotide chain termination sequencing Also termed Sanger sequencing.

Library: A set of cloned fragments together representing with some degree of redundancy the entire genetic complement of an organism.

Ligase (DNA ligase): An enzyme that catalyzes a condensation reaction that links two DNA molecules via the formation of a phosphodiester bond between the 3' hydroxyl and 5' phosphate of adjacent nucleotides.

Lysis: The destruction of the cell membrane.# Cell rupture caused by physical or chemical means, or by phage infection and propagation leading to the release of the cell content; also the death of microorganisms after the stationary phase of a batch fermentation.

Marker: A gene which, on expression, allows easy identification of cells which carry it. Normally used to describe genes carried by a vector which are used to detect vector presence or state in a host cell.

Maxam-Gilbert sequencing: A method to determine the sequence of a stretch of DNA based on its differential cleavage pattern in the presence of different chemical exposures. A nucleic acid chain can be cleaved following G, A, C, or C and T by exposure of ³²P-labeled DNA to neutral dimethylsulfate, dimethylsulfate-acid, hydrazine-NaCl-piperidine or hydrazinepiperidine alone, respectively.

Melting temperature: The temperature at which the two strands of a double-stranded DNA molecule come apart. A short (<18 nucleotides) oligonucleotides Tm value (°C) is estimated by the formula: Tm = (number of A + T)x2 + (number of G + C)x4.

Metagenome: Metagenome referenced the collection of genes sequenced from the environment could be analyzed in a way analogous to the study of a single genome.

Metagenomic DNA: The community total DNA extracted from an environmental system.

Microbial mats (biofilms): Layered groups or communities of microbial populations.

Miltiplex PCR: Multiplex PCR is the term used when more than one pair of primers is used in a PCR. The goal of multiplex PCR is to amplify several segments of target DNA simultaneously and thereby to conserve template DNA, save time, and minimize expense. It is a PCR strategy that enables the amplification of multiple DNA targets in one run.

Molecular cloning: The biological amplification of a specific DNA sequence through mitotic division of a host cell into which it has been transformed or transfected.

Molecular genetics: The study of the flow and regulation of genetic information between DNA, RNA, and protein molecules.

Multicopy plasmids: Present in bacteria at amounts greater than one per chromosome. Vectors for cloning dna are usually multicopy; there are sometimes advantages in using a single copy plasmid.

Multiple cloning site: An artificially constructed region within a vector molecule which contains a number of closely spaced recognition sequences for restriction endonucleases. This serves as a convenient site into which foreign dna may be inserted.

Mycorrhizae: Symbiotic association between a fungus and the roots or rhizoids of a plant. # symbiotic association between a fungus and the roots or rhizoids of a plant. # Fungi that form symbiotic relationships with roots of more developed plants.

Native gel: An electrophoresis gel run under conditions which do not denature proteins (i.e., In the absence of SDS, urea, 2-mercaptoethanol).

Nested PCR: A very sensitive method for amplfication of dna, which takes part of the product of a single pcr reaction (after 30-35 cycles), and subjects it to a new round of PCR using a different set of PCR primers which are nested within the region flanked by the original primer pair.

Nested PCR: It is a conventional PCR with a second round of amplification using a different set of primers. This second set of primers is specific to a sequence found within the DNA of the initial conventional PCR amplicon. The use of a second amplification step with the "nested" primer set results in a reduced background from products amplified during the initial PCR due to the nested primers’ additional specificity to the region. The amount of amplicon produced is increased as a result of the second round of amplification and due to a reduction in any inhibitor concentrations.

Niche: The portion of the environment which a species occupies. A niche is defined in terms of the conditions under which an organism can survive, and may be affected by the presence of other competing organisms.

Nicked circle (relaxed circle): During extraction of plasmid DNA from the bacterial cell, one strand of the DNA becomes nicked. This relaxes the torsional strain needed to maintain supercoiling, producing the familiar form of plasmid.

Nitrification: Oxidation of ammonium to nitrate through the combined action of two chemoautotrophic organisms, one forming nitrite from ammonium and the other oxidizing nitrite to nitrate.

Nitrogen fixation: The conversion of gaseous nitrogen into a form usable by plants. Ususally by bacteria.

Nodule: The enlargement or swelling on roots of nitrogen fixing plants. The nodules contain symbitic nitrogen-fixing bacteria.

Nucleotide: A nucleic acid building block consisting of a purine or pyrimidine base, a sugar (deoxyribose in DNA and ribose in RNA) and a phosphate group

Oligonucleotide: A short nucleic acid molecule; normally refers to molecules between 5 and 200 nucleotide residues (bases) long. # A DNA polymer composed of only a few nucleotides.

Operon: A complete unit of bacterial gene expression and regulation, including the structural gene or genes, regulator gene(s), and control elements in dna recognized by regulator gene products(s).

Ori: The origin of replication in prokaryotes.

Origin of replication (ori ): Section of DNA sequence which is recognised by a cell's DNA replication proteins, allowing initiation of new DNA synthesis. DNA molecules which do not carry an ori recognised by the host cell will be eventually lost from a growing population unless they are incorporated into the cell's genome

Outgroup: In a cladistic analysis, any taxon used to help resolve the polarity of characters, and which is hypothesized to be less closely related to each of the taxa under consideration than any are to each other.

Palindrome: A word or DNA sequence that reads the same forward and backward. With DNA, the sequence reads the same going forward in the one strand and backward in the other strand of the double helix.

Parsimony: Refers to a rule used to choose among possible cladograms, which states that the cladogram implying the least number of changes in character states is the best.

Phagemid: A type of plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, the phagemid is replicated along with the phage DNA and packaged into phage capsids.

Phylogenetics: Field of biology that deals with the relationships between organisms. It includes the discovery of these relationships, and the study of the causes behind this pattern. # Study of reconstructing evolutionary genealogical ties between taxa and line of descent of species or higher taxon.

Phylogeny: The evolutionary relationships among organisms; the patterns of lineage branching produced by the true evolutionary history of the organisms being considered. # An evolutionary tree showing the inferred relationships of descent and common ancestry of any given taxa.

Physical map: A map showing physical locations on a DNA molecule, such as restriction sites, and sequence-tagged sites.

Plasmid: An extrachromosomal, usually circular, double stranded DNA which is capable of replication within a cell, and which usually contains and expresses genes encoding resistance to antibiotics. By strict definition, a plasmid is not essential to the life of the cell. # A circular DNA molecule, capable of autonomous replication, which typically carries one or more genes encoding antibiotic resistance proteins. Plasmids can transfer genes between bacteria and are important tools of transformation for genetic engineers.

Polyacrylamide gel (PAGE): Used to separate proteins and smaller dna fragments and oligonucleotides by electrophoresis. When run under conditions which denature proteins (i.e., In the presence of 2-mercaptoethanol, sds, and possibly urea), molecules are separated primarily on the basis of size. #. Electrophoresis through a matrix composed of a synthetic polymer, used to separate proteins, small DNA, or RNA molecules of up to 1000 nucleotides. Used in DNA sequencing.

Polymerase (DNA): Synthesizes a double-stranded DNA molecule using a primer and DNA as a template.

Polymerase Chain Reaction (PCR): PCR is the basis for a number of extremely important methods in molecular biology. It can be used to detect and measure vanishingly small amounts of DNA and to create customized pieces of DNA. It has been applied to clinical diagnosis and therapy, to forensics and to vast numbers of research applications. It would be difficult to overstate the importance of PCR to science.

Primer extension: Referred to the reaction during PCR, after annealing the primer on ssDNA, new corresponding complementary oligonucleotide will be added by Taq Polymerase. This leads to synthesis of complementary DNA will takes place during this step.

Primer: An oligonucleotide which is complementary to a specific region within a DNA or RNA molecule, and which is used to prime (initiate) synthesis of a new strand of complementary DNA at that specific site, in a reaction or series of reactions catalyzed by a dna polymerase. The newly synthesized DNA strand will contain the primer at its 5' end. Typically, primers are chemically synthesized oligonucleotides 15-50 nucleotides in length, selected on the basis of a known sequence. However, "random primers" (shorter oligonucleotides, about 6 nucleotides in length, and comprising all possible sequences) may be used to prime DNA synthesis from DNA or RNA of unknown sequence completely known, but probably serves to enhance stability of the RNA.

Probe: Usually refers to a DNA or RNA molecule which has been labeled with ³²P or with biotin, to facilitate its detection after it has specifically hybridized with a target DNA or RNA sequence. However, the term may also refer to antibody probes used in western blots.

Promoter: A specific sequence within a double-stranded DNA molecule that is recognized by an RNA polymerase, which binds to it and uses it to begin transcribing the DNA template into a new RNA.

Proofreading: In DNA synthesis, the ability of DNA polymerase to recognize mismatched bases. DNA polymerase corrects mistakes with its exonuclease activity.

Protease: An enzyme that cleaves peptide bonds that link amino acids in protein molecules.

RAPD: Random amplification of polymorphic DNA. A method for identifying differences between genomes of different individuals by PCR with a single short (usually 10-base) primer, which will anneal with complementary sequence at undetermined positions in the genome. The products form a type of "genetic fingerprint".

Real-time PCR: During PCR, a fluorogenic probe, consisting of an oligodeoxynucleotide with both reporter and quencher dyes attached, anneals between the two standard PCR primers. When the probe is cleaved during the next PCR cycle, the reporter is separated from the quencher so that the fluorescence at the end of PCR is a direct measure of the amplicons generated throughout the reaction. Such a system is amenable to automation and gives precise quantitative information.

Recombinant DNA: The process of cutting and recombining DNA fragments from different sources as a means to isolate genes or to alter their structure and function.

Recombinant: An arrangement of alleles unlike that in either parent, resulting from either independent assortment or from crossing-over.

Renature: The reannealing (hydrogen bonding) of single stranded DNA and/or RNA to form a duplex molecule.

Reporter Gene: The use of a functional enzyme, such as betagalactosidase, luciferase, or chloramphenicol acetyltransderase, downstream of a gene, promoter, or translational control element of interest, to more easily identify successful introduction of the gene into a host and to measure transcription and/or translation.

Restriction endonuclease (enzyme): A class of endonucleases that cleaves DNA after recognizing a specific sequence, such as BamH1 (GGATCC), EcoRI (GAATTC), and HindIII (AAGCTT). Type I. Cuts nonspecifically a distance greater than 1000 bp from its recognition sequence and contains bothrestriction and methylation activities.

Restriction fragment: The piece of DNA released after restriction digestion of plasmids or genomic DNA.

RFLP (restriction fragment length polymorphism): Genetic polymorphism as revealed by the sizes of fragments generated with a particular restriction endonuclease enzyme (such as EcoRI, PstI, BglII). # Restriction fragment length polymorphism. A difference in restriction fragment length between individuals due to loss or gain of a restriction enzyme site due to point mutation, or insertion or deletion between consecutive sites. Normally detected by Southern blotting and probing. Used in detection of genetic disease alleles etc.

RNase: Ribonuclease; an enzyme which degrades RNA. It is ubiquitous in living organisms and is exceptionally stable. The prevention of RNase activity is the primary problem in handling RNA.

rRNA: Ribosomal RNA (four sizes in eukaryotes: 5S, 5.8S, 18S, and 28S; Three for prokaryotes, 6S, 16S and 23S); RNA component of the ribosome, which may play catalytic roles in translation. # Any of several RNAs which become part of the ribosome, and thus are involved in translating mRNA and synthesizing proteins. They are the most abundant RNA in the cell (on a mass basis).

SCAR ( Sequence characterized amplified region): A locus representing a single RAPD fragment which has been sequenced. Primers specific to the locus can be designed and used in PCR amplification.

Secondary Structure: Local structure within a protein which is conferred by the nature of the side chains of adjacent amino acids (e.g., alpha helix, beta sheet, random coil); local structure within an RNA molecule which is conferred by base pairing of nucleotides which are relatively closely positioned within the sequence (e.g., hairpins, stem-loop structures).

Selectable marker: A gene which is usually constitutively expressed and allows the selection of cells which carry it through growth on a selective medium. The most common example is the use of the ß-lactamase gene in plasmid vectors to confer ampicillin resistance on the host cell. # A gene whose expression allows one to identify cells that have been transformed or transfected with a vector containing the marker gene.

Soil microbial biomass: Total mass of microorganism alive in a given volume or mass of soil.

SSCP: It is a simple procedure where denatured PCR products are electrophoresed through a non-denaturing polyacrylamide gel. The single strands adopt primary conformations that are dependent on their nucleotide sequence and this determines the rate at which they migrate through the gel matrix. Each PCR product with a different sequence therefore, will be theoretically represented by two bands corresponding to the two strands of the amplified molecule

Sticky End: The terminus of a DNA molecule which has either a 3' or 5' overhang, and which typically results from a cut by a restriction endonuclease. Such termini are capable of specific ligation reactions with other termini which have complementary overhangs. A sticky end can be "blunt ended" either by the removal of an overhang, or a "filling in" reaction which adds additional nucleotides complementary to the overhang

Subcloning: The process of transferring a cloned DNA fragment from one vector to another. (See Cloning.) # If you have a cloned piece of DNA (say, inserted into a plasmid) and you need unlimited copies of only a part of it, you might "sub-clone" it. This involves starting with several million copies of the original plasmid, cutting with restriction enzymes, and purifying the desired fragment out of the mixture. That fragment can then be inserted into a new plasmid for replication. It has now been subcloned.

Supercoil: Double-stranded circular DNA which is twisted about itself. Commonly observed with plasmids and circular viral DNA genomes (such as that of hepatitis B virus). A nick in one strand of the plasmid may remove the twist, resulting in a relaxed, circular DNA molecule. A complete break in the DNA puts the plasmid in a linear form. Supercoils, relaxed circular DNA, and linear DNA all have different migration properties in agarose gels, even though they contain the same number of base pairs.

Swedberg unit: the rate at which a given solute molecule suspended in a less dense solvent sediments in a field of centrifugal force.

taq Polymerase: A DNA polymerase which is very stable at high temperatures, isolated from the thermophilic bacterium Thermus aquaticus. Very useful in PCR reactions which must cycle repetitively through high temperatures during the denaturation step.

Temperate: An RNA or single-stranded DNA molecule upon which a complementary nucleotide strand is synthesized.

Template DNA: A DNA strand that serves as blueprint during DNA replication and transcription.

Terminator: A sequence downstream from the 3' end of an open reading frame that serves to halt transcription by the RNA polymerase. In bacteria these are commonly sequences that are palindromic and thus capable of forming hairpins. Sometimes termination requires the action of a protein, such as Rho factor in E. coli.

Thermostabile polymerases: The prototype polymerase, Taq, and newer versions such as Vent and Tth polymerase are derived from microorganisms that normally reside at high temperature. Consequently, their DNA polymerase enzymes are quite stable to heat denaturation, making them ideal enzymes for use in the polymerase chain reaction.

Tm: The midpoint of the temperature range over which DNA is melted or denatured by heat; the temperature at which a duplex nucleic acid molecule is 50% melted into single strands, it is dependent upon the number and proportion of G-C base pairs as well as the ionic conditions. Often referred to as a measure of the thermal stability of a nucleic acid probe:target sequence hybrid.

Transformation (with respect to bacteria): The process by which a bacterium acquires a plasmid and becomes antibiotic resistant. This term most commonly refers to a bench procedure performed by the investigator which introduces experimental plasmids into bacteria.