Detection of Genomic Variation

Glossary

Abbreviations and Definitions

Used in Molecular Studies

acetone powders preparations obtained by grinding tissues in ice-cold acetone and allowing the acetone to evaporate from the resultant solids.

additive distances a set of distances between pairs of sequences ot taxas that will precisely fit a unique, additive phylogenetic tree. Defined mathematically by satisying the four-point condition.

adenosine triphosphate (ATP) a polysaccharide extract that upon hydrolysis results in energy availability for processes such as muscle contraction and synthesis of macromolecules, including proteins and carbohydrates.

agarose the neutral gelling fraction of agar commonly used in gel electrophoresis.

alignment the juxtaposition of amino acids or nucleotides in homologous molecules that are assumed to contain residues that are all derived from a single common ancestral residue.

allele one of a series of possible alternative forms of a given gene differing in DNA sequence and affecting the structure and/or function of a single product (RNA and/or protein).

allopatric where populations, species, or taxa occupy separate geographic areas.

allozyme alternative (allelic) forms of proteins (enzymes) differentiated by net charge, and therefore detectable by electrophoretic separation and histochemical staining.

Alu family a short (300 bp), interspersed DNA sequence repeated about 500,000 times in the human genome, and characterized by containing a distinctive AluI restriction site.

amino acid the basic subunit of a protein, coded by triplets of bases in the DNA blueprint. There are twenty amino acids universally found in proteins.

aminoacyl-tRNA synthetase enzymes that covalently link amino acids to the 2' or 3' -OH position of tRNA.

amniotc fluid the fluid, containing fetal cells, surrounding the developing fetus.

AMP-FLP polymerase chain reaction amplified restriction fragment lengths consisting of variable number of tandem fetal defects

anode the positive electrode in an electrolytic cell (such as an electrophoresis chamber) toward which anions migrate.

antibody a large protein (immunoglobulin) made in response to a foreign antigen (generally a protein).

anticoagulant an agent, such as EDTA, used to prevent the clotting of whole blood.

anticodon three base sequence in a tRNA that bases pair wuth a specific triplet codon in mRNA.

antigen any molecule that provokes synthesis of an antibody (immunoglobulin).

antigenic site a region of five to ten amino acids on an antigen to which antibodies can be elicited.

antiparallel opposite polarities of two strands of a DNA double helix; one strand is 5'-3' top to bottom and the other strand is 3'-5'.

artiodactyl any order of hoofed mammals with an even number of toes on each foot.

assortative mating non-random mating during sexual reproduction involving a tendency for males of a particular kind to breed with females of a particular kind.

attenuation regulatory mechanism for controlling frequency of transcription of a gene that employs a nucleotide sequence that leads to premature transciption.

autoradiograph (autoradiogram) the resultant X-ray film after having been exposed to a radioactive source. A DNA probe tagged with a radioactive isotope such as 32P (radioactive phosphorus) will expose an X-ray film where the probe hybridizes to complementary sequences on the blot in contact with the film.

autozygosity homozygosity such that the two homologous genes are identical by descent.

auxotroph organism that requires one or more growth supplements in the culture medium.

background radiation radiation from a source other than the test sample specifically being analyzed.

bacterial stab a small container of agar with bacterial colonies suitable for storage or shipment.

bacteriophage virus that infects and reproduces in bacteria; often denoted as phage.

band shifting the phenomenon where DNA fragments in one lane of an eletrophoresis gel migrate across the gel more rapidly than identical fragments in a second lane.

base pair a pair of hydrogen-bonded nucleotides that join the two strands of a DNA double helix. In a double-stranded DNA molecule, adenine (A) forms a base pair with thymine (T), and guanine (G) pairs with cytosine (C).

Baye's theorem a statistical procedure to assess the relative probability of two alternative possibilities.

bidirectional replication DNA replication process that involves two replication forks moving in opposite directions.

blood group a classification of red blood cell surface antigens, for example, ABO.

bootstrapping a statistical method based on repeated random sampling with replacement from an original sample to provide a collection of new estimates of some parameter, from which confidence limits can be calculated.

bottleneck fluctuations in allelic frequencies when a large population passes through a contracted stage and then expands again with an altered genetic composition as a consequence of genetic drift.

buccal cells cells derived from the inner cheek lining. These cells are present in the saliva or can be gently scraped from the inner cheek surface.

buffy coat a thin layer of white blood cells that lies above the erythrocytes after vertebrate blood has been centrifuged.

C-bands dark bands on chromosomes produced by strong alkaline treatment at high temperature, followed by incubation in sodium citrate solution, followed by Giemsa staining. C-bands generally correspond to regions of constitutive heterochromatin.

C0t initial concentration of single-stranded DNA in a DNA reassociation experiment (in moles/liter) multiplied by time of incubation in seconds.

CAAT box a conserved nucleotide sequence located upstream of the transcription startpoints of most eukaryotic genes.

cap a G nucleotide (which is sometimes methylated that is added to the 5' end of eukaryotic mRNA after transcription.

CAP regulatory protein that is activated by cyclic AMP and is involved in transcription of the lac operon in E.coli.

carrier an individual with only one of two possible copies of an abnormal gene. The heterozygous state.

cassette film holder a light-proof holder, used in autoradiography for exposing X-ray film to radioactive blots.

catabolite repression reduced expression of bacterial genes, which results from growth of excess glucose.

cathode the negative electrode in an electrolytic cell (such as an electrophoresis chamber) toward which cations migrate.

cDNA complementary DNA, often refering to a cDNA library made with mRNA and the enzyme reverse transcriptase.

cDNA clone double-stranded DNA sequence that is complementary to a specific RNA and inserted in a cloning vector such as a plasmid.

cell division the process whereby a mother cell givcs rise to two identical daughter cells (see mitosis) or four gametes (see meiosis).

central branch the interior branch connecting the two internal nodes of a four taxa, unrooted phylogenetic tree.

central dogma the theory of DNA-RNA-protein transfer of genetic information.

chaotropic agent in DNA-DNA hybridization, an agent that reduces thermal stability of base pairing of DNA.

character compatibility a method of phylogenetic analysis that seeks the largest clique of a characters that can be fitted to a common tree so that each character state arises only once.

character a variable feature that in any given taxon or sequence takes one out of a set of two or more different states (e.g., eye color or the amino acid at position 12).

character polarity the inferred direction of change of a character in the phylogenetic tree; usually by reference to the character state in an outgroup.

character state the specific value taken by a character in a taxon or sequence (e.g., green eyes or glycine at position 12).

character-state tree a description of the transitions among the states of a multistates character, especially when the transitions do not define a linear series of states.

chi-square test. (c)2 a statistical test to determine how closely an observed set of data values correspond to the values expected.

chimera an individual comoposed of two different cell line originally derived from the union of different zygotes.

chloroplast a chlorophyll-containing plastid that functions as a plant photosynthetic site.

chorionic villi sample (CVS) a specimen of fetal tissue aspirated from the placenta at about 10 weeks gestation in the human.

chromatid the eukaryotic chromosome prior to replication, or one of the two longitudinal subunits of a chromosome after replication, joined by a centromere.

chromomere a region on a chromosome of densely packed chromatid fibers that produces a dark band (as on a polytene chromosome).

chromosome walk method for sequentially isolating overlapping segments of DNA, so that very large genes can be studied.

CI a mixture of chloroform and isoamyl alcohol, used in DNA extraction protocols. Also an abbreviation for consistency index.

cladogram used in two ways by different authors: either a tree produced using the principle of parsimony, or a tree that depicts inferred historical relationships among entities. Generally, the branch lengths in a cladogram are arbitrary; only the branching order is significant. See phylogram.

clone 1.v. to insert a piece of DNA into a vector for subsequent amplification and isolation of that specific piece; 2.n. a piece of DNA composed of a vector and its insert.

cloning vector biological carriers such as plasmids, bacteriophage, or cosmids used to amplify an inserted DNA sequence.

cluster analysis a rapid method of hierarchically grouping taxa or sequences on the basis of similarity (or minimum distance).

coancestry coefficient the correlation of genes of different individuals in the same population; a measure of the relatedness of individuals within populations (symbolized by q or FST).

codon triplet of nucleotides in a gene that codes for a specific amino acid, or translation start-stop signal.

coefficient of inbreeding (F) see inbreeding coefficient. the proportion of homozygous loci in an individual; or, the probability that both alleles at corresponding loci were inherited from the same ancestor. Siblings oor parent and child: F = 0.25; grandparent and grandchild: F = 0.0625.

coefficient of relationship (r) the proportion of genes that two individuals have in common. It is the proportion of the genome that two individuals have inherited a specific gene orDNA fragment from a common ancestor. Siblings or parent and child: r = 0.25; first cousins: r = 0.125.

coefficient of variation (CV) a statistical measure of dispersion in relating the measure of dispersion (SD) to the average or mean (X). CV = SD + X * 100.

cold-induced constriction a chromosome-specific constriction induced in certain species with large chromosomes by prolonged treatment of the organism at 0.5-2.5oC in the presence of colchicine.

colony hybridizatrion method for detecting bacteria that carry a vector with a desired inserted sequence.

complementary sequence a sequence of nucleotides related by the base-pairing rules. For example, in DNA a sequence A-G-T in one strand is complementary to T-C-A in the other strand. A given sequence defines the complementary sequence.

complementation non-allelic gene functions in a double mutant organism to produce the necessary product for restoration of the wild type phenotype.

concerted evolution the maintenance of homogeneity among members of a family of DNA repeats within a species.

conditional lethal mutation kills the cell virus that harbors it, but only under certain (nonpermissive) conditions, such as elevated temperature.

confidence interval a statistical measure of confidence in a calculated value. A 95% confidence interval equates to the expectation that the value in question will lie within the range stated 95% if the time and ooutside the range 5%. A certain allele in a population may have a calculated frequencey of 1 in 500 people with confidence limits of 1 in 400 to 1 in 600 at the 99A% confidence interval.

confidence limits limits attached to a confidence interval. The 95% confidence limits, for example, when measurinf a 10-kb allele on a gel in certain laboratory may be 9.9 to 10.1-kb.

conformational isozymes multiple forms of a single gene product that differ in secondary or tertiary structure.

conjugation "mating" between two bacteria, which involves movement of genetic material from an F+ to and F- cell.

consensus sequence composite nucleotide sequence commonly believed to serve the same function in different genes (e.g., promoter sequences).

consistency index a measure of the amount of homoplasy exhibited by a set of characters or a tree, defined as the sum of the individual character ranges divided by the total length of the tree. If there is no homoplasy, these quantities will be equal, so that the consistency index achieves its maximum value of one.

constitutive hetrochromatin regions on chromosomes consisting mostly of highly repeated, noncoding sequences.

'control' region sequences of DNA usually near the beginningof a gene that regulate the transcription of the gene.

controls samples of predetermined concentration (known or unknown to the analyst) treated as unknowns in an assay. Controls are included as a part of quality control for each test run.

5',3' controls the beginning and end of a gene are called 5' and 3' relative to the direction of transcription. Control regions can be at either end.

copy number the number of copies of a given gene in a set of chromosomes, see multigene family.

core particle enzyme digestion product of nucleosome that contains histone octamer and approximately 150 bp of DNA.

cosmid plasmid vectors designed for cloning large fragments of eukaryotic DNA. The term signifies that the vector is a plasmid into which phage lambda cos sites (cohesive sites) have been inserted. As a result, the plasmid DNA can be packaged in a phage coat in vitro and used to infect a bacterium. Cosmid vectors can accept larger inserts than either plasmid or phage vectors.

covalent a strong chemical bond formed between atoms, for example, oxygen O=O, water H-O-H.

criterion in DNA-DNA hybridization, the stringency of reassociation of single-stranded DNA measured by the difference between the Tm of perfect duplexes in the incubation buffer and the temperature of incubation.

crossing-over the exchange of genetic material between chromosomes due to chromosome 'breakage' and reunion.

cross-hybridization the binding of a probe to a DNA sequence other than the intended target sequence. This occurs because of homology between the probe and the sequence and because low stringency hybridization wash coinditions are followed.

cryptic allele an undetected (by a particular technique) variant at a gene locus.

cryptic simplicity regions of DNA in which the frequency of given short DNA motifs (e.g., ATAG) is higher than expected by chance and in which several motifs are scrambled one with another, see slippage and pure simplicity.

cytoplasm collection of cell components that exist within the celll, but does not include nucleus.

D-loop (displacement loop) a region of the mitochondrial DNA in vertebrates that is often highly variable. Also known as the control region.

decant the process of pouring off the supernatant during separation from a pellet after a mixture has been centrifuged or left to settle.

degenerate genetic code the phenomenon of more than one DNA nucleotide triplet of bases coding for the same amino acid.

degenerate primers a pool of similar sequence primers shich differ at particular sites. These pools can be used as a universal type primer to amplify a sequence where the primer sites may be variable.

demographics the study of populations, especially growth rates and age structure.

denaturation for DNA or RNA, describes separation of double-stranded molecule to a single-stranded state, usually by heating; for protein, describes change in physical shape, which is usually renders it inactive.

depurination the process of partial DNA hydrolysis by acid at purine (adenine and guanine) sites, resulting in the cleavage of large DNA fragments into smaller pieces. This process of separating different improves Southern blotting.

dialysis the process of separating differnt size molecules in soution by means of their differential transfer across a porous membrane.

diploid the normal number of chromosomes (two copies of each - 2N) in virtually all eukaryotes.

direct repeats multiple identical (or closely related) nucleotide sequences in the same orientation in a DNA molecule.

discontinuous replication synthesis of DNA in many short (Okazaki) fragments that are later joined to form a single, contiuous strand.

discriminant function analysis a statistical method of assigning observations to groups based on previous observations from each group.

disequilibriun coefficient a term that desribes the difference between a joint frequency of two or more alleles and the product of the frequencies of the separate alleles.

dissimilarity a generic measure of the difference between two objects, usually measured on a scale of 0 to 1.

distance a measure of the difference between two objects, usually measured on a scale of 0 to1.

distance esrimates a phrase used to emphasize the potentially imperfect reflection of evolutionary history in distance values inferred from experimental or sequence data.

dizygotic twins produced from two separate zygotes. Also called fraternal twins. On average, one-half of their genomes are shared.

DNA (deoxyribonucleic acid) the molecular basis of heredity. DNA consists of a polysugar-phosphate backbone from which the bases (nucleotides) project. DNA forms a double helix that is held together by hydrogen bonds between specific pairs of bases (thymine to adenine, guanine to cytosine). Each strand in the double helix is complementary to its partner strand in terms of its base sequence.

DNA ligase enzyme that joins two double-stranded DNAs together, end to end, by catalyzing 3'OH and 5'P termini bond formation.

DNA polymerase an enzyme that catalyzes synthesis of DNA under direction of a single-stranded DNA template.

DNA reannealing double-stranded DNA separates into single strands when heated which reanneal back into double strands when temperature is lowered.

DNA turnover continual gain and loss of regions of DNA due to a variety of mechanisms of rearrangement; see gene conversion, unequal crossing-over, slippage, transposition.

DNAase deoxyribonuclease; enzyme that cleaves phosphodiester bonds in DNA, to break the molecule into pieces.

dominant trait phenotypically expressed when an abnormal gene is present in the heterozygous or homozygous state.

dot (slot)-blot a DNA analysis system where sample DNA is directly pipetted onto a mambrane, as opposed to the Southern blot procedure of enzymatic digestion, electrophoresis, and Southern transfer.

double-stranded helix three-dimensional shape exhibited by two complementary base-paired DNA strands.

downstream direction away from transcription start site in DNA and towards the last section of the coding region to be transcribed.

editing system of enzymes that monitors each nucleotide to ensure that it is correctly base paired during DNA replication.

electrodecantation the settling of proteins of high molecular weight toward the bottom of a horizontal gel during electrophoresis.

electroendosmosis movement of ionized buffer solution through a gel caused by gel charge groups.

electromorph an electrophoretically indistinguishable class of isozymes. Electromorphs represent alleles if all differences between variants result in changes in eletrophoretic migration rate.

electrophoresis the separation of macromolecules in the presence of an electric current. Electrophoresis is routinely used to separate both proteins and DNA fragments; allozymes are separated based on differences in net charge, whereas DNA fragments are separated based on differences in size.

elongation factors regulatory proteins that associate with ribosomes to promote either the tRNA binding or the translocation step in the elongation phase of translation.

endonuclease enzyme that cleaves phosphodiester bonds within a nucleic acid.

endoplasmic reticulum (ER) folded membrane sheets to which polysomes (sites of protein synthesis) are anchored.

enhancer nucleotide sequence that increases the utilization of eukaryotic promoters; it can function in either an upstream or downstream location relative to the promoter.

enzyme proteins that act as catalysts in metabolic reactions. Enzymes act in a very specific way on particular target molecules and allow the manipulation of DNA and hence, the detection of DNA polymorphism.

epigenetic all processes relating to the expression and interaction of genes.

Escherichia coli (E. coli) intestinal bacterium widely used because it can be conveniently cultured for prokaryotic genetics studies.

eukaryote a multicellular organism having true membrane-bound nuclei containing chromosomes that undergo mitosis.

evolutionary distance an idealized measure of the evolutionary separation of sequences or taxa, such as the total number of fixed mutational events. They are defined so that the values are additive and hence will precisely fit an additional evolutionary trree.

excision-repair an enzyme system that removes a short, single-stranded sequence of double-stranded DNA, containing mispaired or damaged bases, and replaces it by synthesizing a sequence complementary to the remaining strand.

exon that portion of a DNA strand within a gene that codes for a protein. Coding regions that are broken up into two or more segments within a gene, are separated by regions of non-coding DNA called introns.

exonuclease enzyme that cleaves nucleotides one at a time off the end of a DNA or RNA molecule.

extra chromosomal inheritance (extra nuclear inheritance). Cytoplasmic inheritance of DNA via organelles, such as mitochondria (or plasmids), in female gametes. The human egg, for example, transmits approximately 10,000 mitochondria.

extranuclear DNA DNA located in organelles such as mitochondria and plastids. This material is also referred to as cytoplasmic DNA and its inheritance as maternal or cytoplasmic since the organelles are transmitted only from the male via gamete cytoplasm.

F factor bacterial plasmid that functions to generate sex or fertility characteristics.

F plasmid fertility plasmid in E.coli, which permits a donor bacterial cell to conjugate (mate) with a recipient bacterial cell.

F-statistics a set of coefficients that describe how genetic variation is partitioned within and among populations and individuals (see coancestry coefficient and inbreeding coefficient).

F1 generation progeny of a cross between two parental types that differ in one of more genes.

filter hybridization method for nucleic acid hybridization performed by soaking a denatured DNA preparation, immobilized on a nitrocellulose filter, in a solution of radioactively labeled RNA or DNA.

fingerprinting separation of the DNA of an individual into defined fragments the lengths of which are determined by the spacing of given restriction of enzyme sites. Numbers and lengths of fragments form a unique 'DNA fingerprint' for an individual.

fixation index the frequency of homozygosity for a particular allele at a given locus. See inbreeding coefficient.

fluorometric assay the process of molecules absorbing light of one wavelength and emitting at a different (higher) wavelength.

frameshift mutation inserion or deletion of either one or two nucleotide bases in an exon such that the genetic code is read in a different frame, resulting in an altered downstream amino acid sequence.

G-bands dark bands on chromosomes produced by Giemsa staining. G-bands occur primarily in AT-rich regions.

G-test a log-linear version of the chi-squared statistical test for goodness of fit.

gamma rays (g rays) a type of radiation from certain radioactive sources, for example, 125I.

gaps editing symbols that are inserted into sequences in the process of alignment in order to compensate for presumptive insertion and deletion events.

gene a sequence of DNA that functions as a unit (e.g., coding for a specific protein).

gene conversion the ability of one allele of a gene (or one member gene of a gene family) to alter the sequence of another allele (or another member gene) to its own sequence. Usually occurs during meiotic recombination. For example Aa can become AA or aa. If conversion is biased there is a preference for A or a.

gene conversion domain a stretch of DNA involved in gene conversion whicn can vary from a few to thousands of base pairs in length.

gene family set of very similar genes derived by duplication of an ancestral gene and subsequent minor alteration in each gene in the family.

genetic code set of 64 codons (triplets) in DNA and the amino acids they represent.

genetic distance a measure of the number of allelic substitutions per gene that have occurred during the separate evolution of two populations or species.

genetic marker mutant gene usually recognizable by a restriction enzyme that is useful in genetic mapping studies for locating sites of other genes.

genome the sum total of all the DNA on a haploid set of chromosomes in the nucleus of an individual, including both coding and non-coding sequences.

genomic library a random collection of cloned DNA fragments (usually in viral or cosmid vectors) that together represent virtually all of an organism's DNA. Partial or subgenomic libraries contain only restriction fragments of a certain size range.

gyrase topoisomerase (enzyme) that can introduce negative supercoils into DNA.

half-life (t1/2) the time required for a radioisotope to decrease to one-half-life of its original quantity, (the t1/2 for 32P is 14 days).

HAP hydroxyapatite. HAP is used in columns to separate single-stranded DNA from double-stranded DNA.

haplodiploid alternating chromosome number due to the cyclical nature of the organism's life cycle.

haplotype a set of alleles of closely-linked genes that tend to be inherited together, uniquely identifying a chromosome.

Hardy-Weinberg equilibrium an equilibrium of genotypes achieved in populations of infinite size (in which there is no immigration, emigration, selection, or mutation) after at least a generation of panmictic mating. With two alleles A and B of frequency p and q, respectively, the Hardy-Weinberg equilibrium frequencies of the genotypes AA, AB, and BB are p2, 2pq, and q2 respectively.

helicase enzyme that unwinds DNA double helix during DNA replication at the replication fork.

hemoglobin the oxygen carrying pigment of red blood cells composed of two a-chains, two b-chains, and heme groups.

heterochromatin chromosomal segments or whole chromosomes that generally exhibit a condensed state throughout interphase and late replication.

heteroduplex formed when one strand of one DNA duplex invades and displaces one strand of another DNA duplex without correct A-T and G-C pairing all along its length; a hybrid DNA-DNA molecule formed from tracer and driver from different individuals or (usually) species.

heterogametic sex the sex that produces gametes each with either an X or Y chromosome. In mammals, the Y-bearing sperm are male determinant and the X female.

heterogeneous nuclear (hn) RNA trancripts of varying size synthesized by RNA polymerase II.

heteroplasmy individuals carrying more than one type of mitochondrial or chloroplast DNA.

heterozygosity the condition of having a pair of dissimilar alleles at a locus.

Hfr strain of E.coli that exhibits an unusually high frequency of recombinations.

histones class of approximately five small, basic DNA binding proteins of eukaryotes that together with DNA and RNA comprise chromatin.

HLA human leukocyte antigen; antigens located on the surface of most cells, excluding red blood cells and sperm. These antigens are closely associated with transplant rejection.

homeobox nucleotide sequence, found in many genes, that codes for a polypeptide with DNA-binding properties.

homeric isozyme an enzyme composed of multiple identical polypeptide chains.

homogametic sex the sex that produces gametes with only one type of sex chromosome. In mammals, each egg carries one X chromosome. Sperm carry an X or a Y chromosome.

homogenization the process, arising as a consequence of DNA turnover, which ensures that most member genes of a multigene family are very similar in sequence; see molecular drive.

homologous chromosomes that pair during meiosis and contain the same linear arrangement of genes. The human has 22 homologous pairs of autosomes (non-sex chromosomes) plus two sex chromosomes per nucleus. The members of each pair have an identical sequence of genes; however, the alleles at corresponding homologous loci may be identical (homozygous) or different (heterozygous).

homologous reaction in immunological studies, a reaction in which antibodies are reacted with the same antigen to which the antibodies were produced.

homology common ancestry of two or more genes or gene products (or portions thereof).

homoplasmy individuals carrying only one type of mitochondrial or chloroplast DNA.

homoplasy a collection of phenomena that leads to similarities in character states for reasons other than inheritance from a common ancestor. These include convergence, parallelism, and reversal.

homozygous the presence of identical alleles at acorresponding homologous chromosome loci.

hotspot region in DNA where mutations occur at exceptionally high frequency.

hybridization formation of a double-stranded nucleic acid molecule from complementary single-stranded molecules.

hybridization stringencies the fidelity with which single strands of DNA reanneal depends on the stringency of hybridization determined by temperature and ionic conditions.

hybridize to induce the pairing of complementary DNA strands, often from different individuals or species, to form a DNA-DNA hybrid molecule.

hybrizymes alleles found in hybrid zones that are rare or absent in populations of the parental (nonhybrid) species.

hydrogen bond a relatively weak bond between a hydrogen(H) atom, covalently bound to a nitrogen (N) or oxygen (O) atom, and another atom. These bonds bind complimentary DNA strands. THey acan be broken by increasing temperature.

hydrophilic describes molecules (e.g., some amino acids) that prefer to be in contact with water.

hydrophobic describes molecules that prefer to avoid direct contact with water.

hypervariability extreme genetic variations between individuals in certain genomic sequences, see fingerprinting.

hypervariable region a segment of a chromosome characterized by considerable variation in the number of tandem repeats at one or more loci.

immunbiological distance (ID) a measure that estimates the number of amino acid replacements (AAR) between two homologous proteins. For microcomplement fixation with albumin , one ID unit is approximately equal to one AAR.

immunodiffusion an immunological assay that monitors reaction of antibody and antigen in agar gels.

immunoelectrophoresis an immological assay in which antigens are first separated based on charge in an electric field and then exposed to antibodies to one or more antigens. Immunoelectrophoresis is used to identify antigens that two species have in common and test the purity of an antiserum.

immunogenic a substance that is capable of eliciting the production of antibodies.

in situ hybridization the annealing of a mobile, labeled nucleic acid probe to a stationary nucleic acid target (usually whole chromosomes) to form base-paired duplexes.

in vitro means "in glass" and refers to a biological process carried out in the laboratory separate from an organism.

inbreeding coefficient the correlation of genes within individuals (symbolized by F or FIT; this is the overall inbreeding coefficeint), or the correlation of genes within populations (symbolized by f or FIS; this is the the within-population inbreeding coefficieint). FIS is also known as the fixation index. Both FIS ahd FIT are measures of deviation from expected Hardy-Weinberg proportions; positive values indicate a deficiency of heterozygotes while negative values indicate an excess of heterozygotes.

inducer small molecule (e.g., galactose) that causes the operon to be expressed.

induction expression of specific genes in response to the presence of substrates for the proteins (enzymes), coded by the induced genes.

ingroup an assumed monophyletic group, usually comprising the taxa of primary interest.

initiation factors regulatory proteins that associate with the small subunit of the ribosome to facilitate initiation of translation of the mRNA.

inosine (I) nucleotide containing the base hyporanthine, which base pairs with cytosine (C).

insert the DNA of interest that has been cloned, or inserted, into a vector.

insertion placemment of additional nucleotide pairs in a specific site in DNA.

insertion sequence (IS) DNA sequence in bacteria capable of relocating itself to a new location in the genome, using transposase included in its nucleotide sequence.

intergenic spacer (IGS) a region of DNA separating classes of ribosomal RNA genes in tandem arrays.

interior branches branches in a phylogentic tree that do not connect to a tip of the tree.

interlocus variance differences between genes in the number and frequency of alleles in a population.

internal nodes the branch points in a phylogenetic tree . If the tree is rooted, the root node is also an internal node.

interspersed repetitive DNA short segments of DNA that have been found in hundreds of thousands of copies interspersed throughout the genome, rather than being serially repeated like satellite DNAs.

intralocus variance the frequency distribution of alleles of a gene in a population.

intron the non-coding sequence in a gene between the exons that is transcribed, but eventually removed from the mRNA by specific splicing enzymes. Because introns never become part of a protein, there is little functional constraint on the majority of their sequence, and thus, these regions tend to evolve rapidly.

inverted repeats symmetrical nucleotide sequence of DNA that is repeated in opposite orientations on same molecule.

isochizomer restriction endonuclease with the same recogniton sequence as another restriction endonuclease.

isoelectric point the pH at which the positive and negative charges of a protein are equal.

isoloci two or more loci of a multilocus enzyme system that produce products of the same electrophoretic mobility.

isology sequence similarity of aligned nucleic acids or polypeptides; the similarity may be due to homology or convergence.

isozyme alternative forms of a compound enzyme which is composed of polypeptides coded by different genes. They differ from one another in either catalytic or physical properties.

jackknifing a statistical method of numerical sampling based on n samples of size n-1 used to calculate the variance of an estimate from an original sample of size n.

joining region (J) short segment of an antibody gene that is joined to a larger segment to constitute a complete variable region of an immunoglobulin gene.

Klenow fragment the portion of bacterial DNA polymerase I lacking 5' to 3' exonuclease activity.

label to chemically "tag" a piece of DNA so that it can be visualized in some manner. Most commonly, DNA is labeled with a radioactive element, enabling detection of its presence using x-ray film. Labeling may also be achieved by colorimetric methods or by chemiluminesence. Visualization of larger amounts of DNA requires less sensitivity and is often possible using stains such as ethidium bromide.

Lac operon collection of genes in some bacteria that produce enzymes for metabolizing the milk sugar lactose.

lagging strand (DNA) replication of DNA employing short segments (Okazaki fragments).

lambda (l) bacteriophage a virus of the bacteium E. coli that is widely used as a cloning vector in molecular biology. It is a double-stranded DNA virus approximately 50 kb in length, with single-stranded complementary ends that allow the virus to circularize after entering its bacterial host. The DNA is packaged into a protein coat in the mature virus.

lampbrush chromosome a bivalent at diplotene stage in a female meiotic cell; found in the oocytes of most animals.

leader (sequence) nontranslated sequence of mRNA, upstream of the initiation codon.

library collection of cloned fragments in a vector (plasmid or phage); usually "cDNA" or "genomic."

ligase an enzyme that covalently joins two single stranded DNA molecules when annealed end to end on a DNA template.

ligation enzymatically catalyzed formation of a phosphodiester bond that links two DNA molecules.

linearly ordered character a multistate character frequencies in which the allowed transitions between states form a linear chain.

linkage a measure of association between loci. Loci on different chromosomes are nonlinked. Those close together on the same chromosme are closely linked and are usually inherited together.

linkage disequilibrium non-random association of genes in the gametes of a population: the tendency of certain alleles of one locus to occur with certain alleles of another locus with frequencies greater than expected by chance.

linker (DNA) DNA contained in a nucleosome that is not directly complexed with histones.

lipid bilayer model for cell membranes in which hydrophobic portions of two layers of lipid molecules face inward and hydrophilic portions face outward.

long-terminal repeats (LTR) nucleotide sequence that is repeated at the end of a DNA molecule.

looping (of DNA) double-stranded DNA bends back on itself, usually when in contact with proteins.

lysis the last step in the bacteriophage life cycle, which involves bursting of the bacterial cell membrane and release of multiple phage progeny.

lysogenic cycle a cycle of phage growth in which the phage become a stable prophage component of the bacterial genome.

lytic cycle a cycle of phage growth in which the phage are replicated many times, resulting in eventual destruction of the host bacterial cell and release of the progeny phage.

M13 a filamentous bacteriophage of the bacterium E. coli that is widely used for cloning and sequencing. The genome of M13 is circular and approximately 6500 bp in length. M13 occurs in both a double-stranded replicative form (used for cloning small fragments) and a single-stranded form (used for Sanger dideoxy sequencing).

maximum parsimony a method of phylogenetic tree inference based on the principle of minimizing the amount of evolutionary change needed to explain the data.

mean (arithmetic) a statistical measure of central tendencey equeating to an arithmentic average of a group pf values. The mean of 10+20+50+5+15=100 /5=20.

median a statistical measure of central tendency equating to the mid value in a ranked series. The median of the series 5, 10, 15, 20, 50 is 15.

meiosis the process whereby a sex cell nucleus, after chromosomal replication, divides twice to form four nuclei each with one-half the original chromosome number.

melt the process of disrupting the hydrogen bonds linking complementary DNA strands.

melting temperature (Tm) midpoint of the heat denaturation curve for double-stranded DNA.

membrane for eukaryotic cell, a lipid bilayer that contains various proteins and surrounds the cytoplasm.

Mendel's laws 1) Segregation: during meiosis only one member of each homologous chromosome pair is transferred to a specific gamete. 2) Independent assortment: during meiosis the members of the different homologous pairs assort independently when transferred to a specific gamete, for example, AA' and BB' homologoous chromosome pairs could give rise to AB, AB' A'B or A'B' possible gametes.

messenger RNA (mRNA)single-stranded template RNA that contains information for amino acid sequence of the protein.

methylation (me) one form of methylation, the most common in mammals, invloves the conversion of cytosine to 5-methyl cytosine. Methylation can prevent cleavage of DNA at a restriction enzyme recognition site, for example, Hpa II cleaves at CCGG but not at CmeCGG.

microcomplement fixation a quantitive immunological assay that estimates amino acid replacements between homologous proteins by measuring the fixation of complement in an antigen-antibody reaction.

microfuge a high speed (usually 10,000+ rpm) centrifuge for centrifugation of small (usually < 2 mL) specimens.

microsatellite a class of repetitive DNA. Microsatellites are simple sequence repeats two to eight nucleotides in length. For example the repeat unit can be simply "CA", and might exist in a tandem array (CACACACACA...) be highly polymorphic.

minisatellite tandem array of from 10 to 50 copies of a non-coding length (typically 10 to 100 nucleotides) of DNA. Arrays on different chromosomes are usually with different numbers of repeated copies giving rise to unique individual DNA fingerprints.

mismatch bases that do not match in "complementary" DNA strands. Depending in the blot wash stringency conditions, some mismatch can be tolerated between hybridized sample and probe DNA complementary regions, for example,

missense mutation change in DNA nucleotide sequence that leads to substitution of one amino acid for another in the protein.

mitochondrion a DNA-containing cytoplasmic organelle of eukaryotes. Mitochondria are referred to as the powerhouse of the cell because they are sites of ATP production.

mitochondrial DNA (mtDNA) the DNA contained within the mitochondria of a cell, separate from the DNA in the nucleus. The mtDNA is a circular DNA molecule, generally between 16,000 and 20,000 base pairs long.

mobile elements lengths of DNA that can move from one position to another in the genome.

molecular clock hypothesis the hypothesis that molecules evolve in direct proportion to time, so that differences between orthologous molecules in two different species used to estimate the time elapsed since the two species last shared a common ancestor.

molecular drive a process which spreads mutant genes through a multigene family (homogenization) and through a sexual population (fixation) as a consequence of a variety of non-Mendelian DNA turnover mechanisms in eukaryotic nuclear genomes.

molecular systematics the detection, description, and explanation of molecular biological diversity, both within and among species.

monoclonal antibody a single antibody produced in quantity by cultured lines of hybridoma cells.

monomorphic bands DNA fragments of specific sizes found in most indiviuals. Each different size monomorphic fragment os detected by cleaving genomic DNA with a specific rrestrction enzyme and hybridizing with a specific monomorphic probe. These fragments provide excelletn markers for use in quality control especially as related to band shifts.

monomorphic loci genes represented by a single fixed allele in a population.

monophyletic a group that contains all of the descendants of the most recent common ancestor of the constituent species.

mosaic an individual composed of two genetically different cell lines originally derived from the same zygote.

most parsimonious reconstruction any assignment of ancestral states to characters on a tree so that the change of each character is minimized (subject to any constraints being enforced).

multiallele refers to a number of different possible allelas at a specific locus. See allele.

multigene family a collection of identical or near identical genes in the genome. The numbers of gene copies and their distribution amongst chromosomes varies widely between species depending on the gene family in question.

multilocus refers to a number of different loci or positions in the genome. See locus.

negative supercoiling twisting of double-stranded DNA in the opposite direction of the natural double helix twist.

neutral allele a mutation in a gene that has little or no effect on the reproductive success of the individual carrying the allele.

neutral mutation any change in the sequence of genomic DNA that does nopt affect the physical make-up of the individual.

nick gap in one strand of DNA of a double helix, caused by breakage of a phosphodiester bond.

nick translation method for radioactive labeling double-stranded DNA; DNA polymerase begins at a nick and replaces the original strand with a new one.

non-genic sequence the bulk of sequnces in nuclear genomes which do not code for polypeptides.

non-Mendelian segregation frequencies of genetic variants amongst the gametes of an individual which are not in accordance with predictions based on Mendel's laws of inheritance. All mechanisms of DNA turnover lead to patterns of non-Mendelian segregation.

non-synonymous substitution a nucleotide substitution, usually in the first or second position of a codon, that causes a replacement of an amino acid in a polypeptide chain.

nonsense codon a DNA triplet of bases that does not code for an amino acid but serves as a termination signal during protein translation.

NPH normalized percentage of hybridization. Defined as the extent of hybridization in a heteroduplex comparison divided by that for the homoduplex control, expressed as a percentage.

nuclear genome the portion of the genome contained in the nucleus of eukaryotes, i.e., the chromosomes.

nucleolar organizer region a region on a chromosome that contains the ribosomal RNA genes and associarted spacers.

nucleosome chromatin subunit that consists of DNA and a set of eight histone proteins.

nucleotide one of the monomeric units from which DNA molecules are constructed, consisting of a purine or pyrimidine base, a pentose sugar, and a phosphoric acid group. The nucleotides of DNA are deoxyadenylic acid, thymidylic acid, deoxygualinic acid, and deoxycytidylic acid. The nucleotides are often referred to interchangeably with their corresponding nitrogenous base, i.e., the nucleotide deoxyadenylic acid is often referred to as adenine (represented in a sequence by "A").

nucleus the genome-containing (membrane-bound) structure of eukaryotic organisms.

null allele an allele that produces either no protein or a nonfunctional protein product.

objective function a function that defines the relative quality of any given phylogenetic tree in terms of a set of data.

OD optical density, as measured in a spectrophotomenter. Used to estimate concentration and purity of DNA solutions.

Okazaki fragments short run of nucleotide's synthesized lagging strand during DNA replication.

OLA (oligonucleotide ligation assay) a method of genetic typing that typically assays biallelic variation resulting from single base substitutions. Uses one oligonucleotide (oligo) probe for each allelic variant at a specific site and a second oligonucleotide as a reporter. If the allele specific oligo is a perfect match with the target sequence to be assayed, it will be ligated or joined to the reporter oligo which contains a colored label. Otherwise the reporter is washed out of the well and no color results. Two separate reactions, one for each allele specific oligo, detect the presence/absence of each allele.

oligo-dT a polymer of deoxyribothymidylate used in the purification of mRNA.

oligonucleotide short DNA fragment typically of 15 or more nucleotides. Generally refers to single stranded, synthetic DNA molecules used as probes or primers.

oncogenes genes that when expressed transform cells into a tumor-like state, characterized by rapid growth.

operator nucleotide sequence that binds repressor protein and prevents transcription of adjacent gene.

operon set of genes in bacteria that is coordinately regulated and contributes to a single cellular function.

ordered character a multistate character for which the changes between states are constrained; not all states can be reached directly from any other.

ORF open reading frame; start and stop codons are present around a DNA sequence.

organellar genome the DNA contained in cytoplasmic organelles (i.e., mtDNA and cpDNA).

outgroup comparison a method that can be used for assigning the direction of change to ordered characters by examining the state in lineages outside of the group of primary interest.

overdominance heterozygote advantage. The situation in which the heterozygote genotype (Aa) is more fit that either the homozygous recessive (aa) or homozygous dominant (AA) genotypes.

palindrome DNA sequence consisting of adjacent inverted repeats that read the same in left direction on one strand as in right direction on the other strand. For example, 5'- GAATTC-3', 3' CTTAAG-5'.

paracentric inversion an inversion of a chromosome that does not include the centromere.

parapatric adjacent but nonoverlappimg distributions (see allopatric, sympatric).

partially ordered character a multistate character that is ordered, but for which the permitted state transitions do not form a linear series.

PCI a mixture of phenol, chloroform, and isoamyl alcohol, used in DNA extraction protocols.

pellet the button of particulate material formed afgter a suspension has been centrifuged.

peptide polymer synthesized by forming a covalent bond between the X-amino group of one amino acid and the X-carboxyl group of another amino acid.

pericentric inversion an inversion of a region of a chromosome that includes the centromere.

peripheral branches the branches on a phylogenetic tree that connect to a terminal taxon or sequence.

permissive condition circumstance, usually an environmental condition, that allows a conditional, lethal mutant organism to live.

phenogram a branching diagram that links entities by estimates of overall similarity. Usually constructed using UPGMA cluster analysis.

phenotype the physical make-up of an individual as define by genetic and nongenetic factors.

phylogram a tree that depicts inferred historical relationships among entities. Differs from cladogram in that the branches are drawn proportional to the amount of inferred character change.

phylopatry when offspring share their home-range with their parents; non dispersal.

plaque a clear spot on a bacterial lawn (in a petri plate) that results from lysis of the resident bacteria by bacteriophage.

plasmid a self-replicating extrachromosomal genetic element found in a variety of bacterial species that generally confers some advantage to the host cell (i.e., resistance to antibiotics, etc.). Plasmids are double-stranded, circular DNA molecules ranging in size from 1 to 200 thousand base pairs commonly used as vectors for cloning.

plastid a plant cytoplasmic DNA-containing organelle such as a chloroplast. Each, as with mitochondria, contains chromosomes whose genes together wioth those of nuclear DNA control the organelle function.

polyadenylation (poly A)addition to the 3' end of a eukaryotic RNA sequence of adenylic acids.

poly A-tail the adenine nucleotide polymer attached to the 3' end of pre-mRNA.

polycistronic mRNA mRNA that contains coding sequences of more than one gene.

polymerase an enzyme that assembles the subunits of macromolecules. DNA polymerases have the ability to synthesize the complementary strand of a single stranded DNA template. Synthesis only extends from existing double-stranded sequence across single-stranded template; thus synthesis can be controlled in reactions such as PCR or sequencing using oligonucleotide primers that will anneal to form short double stranded sections contiguous to specific regions of interest.

polymerase chain reaction (PCR) a series of thermal cycles of denaturation, annealing of primers, and primer extension catalyzed by a thermostable DNA polymerase, in which a target DNA fragment is amplified exponentially; primers that have nucleotide sequences complementary to the DNA that flanks the target region are added to sample DNA along with a heat-stable DNA polymerase. The DNA is heated to separate the complementary strands and then cooled to let the primers bind to the flanking sequences. The polymerase initiates synthesis of complementary DNA. The reaction is allowed to proceed for a series of replication cycles. Twenty cycles will yield a millionfold amplification; thirty cycles will yield an amplification factor of one billion.

polymorphism intraspecific variation. On the DNA level, this refers to differences in base pair sequence between two individuals.

polyphyletic group a group of species that are classified together, some of which are descended from different ancestral groups.

polyploid an organism, or individual, with a higher than usual multiple of the fundamental number of chromosomes.

polyribosome (polysome) mRNA and ribosome complex that is engaged in synthesis of a protein.

polytene chromosome a somatic chromosome that has undergone many rounds of endoreplicaton such that each chromosomal element consists of hundreds to thousands of unseparated chromatids.

positional homolgy the property of residues in a set of sequences that are derived from the same ancestral residue, with or without intervening substitutions.

positive supercoiling twisting of double-stranded DNA in the same direction as the natural double helix twist.

posttranslation modification any process that modifies a polypeptide after its translation from RNA.

PPS a solution of phenoxyethanol-phosphate-sucrose, used to preserve proteins.

prehybridization the process of incubating a DNA blot with a hybridization solution to, in part, block cross-reactive sites. This precedes the addition of labeled probe.

primary structure the sequence of subunits, such as amino acids or nucleotides, in a polymer.

primary transcript the full length, unmodified RNA synthesized from a single gene.

primer-dimer partial homology of two primers or palindrome region of a single primer that allows them to anneal.

primers short pieces of single stranded DNA (10-30 bp) annealed to the 5' end of a DNA template used to initiate synthesis of the complementary strand of the template piece of DNA. Primers can be designed so that they will bind only to a very specific region of the DNA, and will thus initiate synthesis of a targeted sequence (as in PCR or DNA sequencing).

probe in molecular biology, any biochemical molecule that can be used to distinguish a specific molecule of interest apart from others of its kind. A DNA probe is a segment of DNA with a sequence homologous to the DNA of interest. If the probe is labeled, the sequence can be visualized independently from the rest of the DNA in the sample.

prokaryote a unicellular organism lacking a membrane-bound nucleus, for example, bacteria. Prokaryotes do not undergo mitosis.

promoter the DNA sequence that binds RNA polymerase and serves as a starting point for transcription.

protein one or more polypeptides chains composed of amino acid subunits folded together to make a structural element or metabolic enzyme.

proteinase K a hydrolytic enzyme used in the digestion of proteins to amino acids.

pulse chase experiment in which cells are briefly exposed to radioactive precursors and analyzed to determine fate of initial radioactiove precursor.

purine a heterocyclic ring molecule with various side chains. (Adenine and guanine are purines found in DNA and RNA.)

pyrimidine a heterocyclic ring molecuule with six carbons and various side chains. (Cytosine abd uracil are pyrimidines found inRNA, while cytosine and thymine are found in DNA.)

Q-bands fluorescent (under UV light) bands on chromosomes produced by quinacrine staining. Q-bands are brightest in AT-rich regions.

R-bands bands on chromosomes that exhibit the reverse pattern of Q- or G- bands.

radioimmunoassay (RIA)a immunological assay that recognizes major antigenic sites and can be used to study minute quantities of proteins (including proteins recovered from recent fossils).

radionuclide a radioactive element. = 32P (radioactive phosphorous) is a high energy b-nuclide.

random mating any male mating with any female without preference, see assortative mating.

RAPD (random amplified polymorphic DNA) An analysis of PCR products produced by short non-specific primers. High levels of polymorphism are often observed using this technique.

rDNA ribosomal DNA; the genes for several classes of ribosomal RNA molecules that go into the construction of ribosomes, usually in long tandem arrays in the chromosomes.

reading frame the nucleotide sequence of an mRNA as it is translated into a polypeptide, begining with the AUG initiation codon.

Rec A E. coli DNA repair gene capable of exchanging single-stranded DNA segments.

recessive a trait phenotypically expressed only when an abnormal gene is present in the homozygous state.

recessive allele form of a gene that normally does not contribute to the phenotype unless present in two copies in homozygous recessive individuals.

reciprocity the degree to which reciprocal measures of divergence (e.g., A to B versus B to A) agree.

recombinant DNA DNA formed by the union of two heterozygous DNA molecules, for example, the lgiation of a human growth hormone gene into a plasmid.

recombinant DNA techniques techniques capable of locating, cloning, and genetically manipulating genes and other DNA sequences.

recombination the occurrence of progeny with gene combinations other than those found in their parents, caused by the independent assortment of chromosomes and gametes in a sexual species or by crossing-over between chromosomes.

regulation control of the activity of a gene or enzyme by mechanisms which increase or decrease that activity.

regulatory gene gene that codes for an DNA or protein used to control the expression of other separate genes.

renaturation process of a macromolecule returning to its native three-dimensional structure. For DNA this involves the two strands b ase pairing; for protein, it involves folding to its active configuration.

repetitive DNA nucleotide sequences occurring repeatedly in chromosomal DNA. Repetitive DNA can belong to the highly repetitive or middle repetitive categories. The highly repetitive fraction contains sequences of several nucleotides repeated millions of times. Middle repetitive DNA consists of segments 1 to 500 base pairs in length repeated 100 to 10,000 times each.

replication fork the Y-shaped region of DNA, which serves as the site of synthesis of new strands.

repressor protein a regulatory protein that binds to the operator locus on DNA and blocks transcription oif the adjacent gene.

resolvase enzyme that carries out recombination between two repeated transposons.

restriction enzyme (endonuclease) an enzyme that cleaves double-stranded DNA. Type I restriction endonucleases are not sequence-specific; type II restriction endonucleases cleave DNA at particular recognition sequences (typically 4-6 bp palindromes).The enzymes are named by an acronym that indicates the bacterial species from which they were isolated, followed by a Roman numeral that gives the chronological order of discovery when more than one enzyme came from the same source. DNA fragments produced by certain enzymes, such as EcoRI, can anneal with any other fragment produced by that enzyme. This property allows splicing of foreign genes into E. coli plasmids or bacteriophage vectors.

restriction fragment length polymorphism (RFLP) a polymorphism in an individual, population, or species defined by restriction fragments of a distinctive length. Usually caused by gain or loss of a restriction site, but may result from an insertion or deletion of a fragment of DNA between two conserved restriction sites.

restriction map linear representation of DNA sequence that illustrates sites cut by specific restriction enzymes.

restriction sites short motifs of DNA capable of being recognized by a restriction enzyme leading to the cutting of the DNA molecule into separate fragments. Each restriction enzyme has a unique cutting site.

reverse dot-blot a number of oligonucleotide probes are immobilized on membrane and the labeled target DNA (often PCR amplified) is then added, permits testing a number of specific alleles at one time

reverse transcriptase enzyme that synthesizes DNA from an RNA template,used in direct RNA sequencing.

reversiblity the ability of a character state to change back to its original state.

reversion change in nucleotide sequence of DNA that reverses the effects of the original mutation.

Rho factor E. coli protein that recognizes specific nucleotide sequences and causes RNA polymerase to terminate transcription.

ribosome component of protein synthesis machinery comprised of RNA and protein; it provides structural support for mRNA.

RNA polymerase enzyme that synthesizes RNA from ribonucleotide triphosphates; it requires a DNA template.

RNA splicing process that removes segments of RNA (usually "introns") from a long RNA molecule and joinsremaining segments (usually "exons").

Robertsonian translocation fission or fusion of chromosomes at their centromeres.

rolling circle replication process for replicating double-stranded circular DNA.

rRNA ribosomal RNA, the nucleic acid component of ribosomes, which functions in translation of proteins from mRNA.

satellite DNA long tandem arrays of repeated sequences that band apart from most nuclear DNA in CsCl ultracentrifugation. Usually in millions of copies, generally located at centromeres and telomeres of chromosomes. Generally thought to be generated by unequal crossing-over.

secondary structure the folding pattern of proteins or nucleic acids, which results from interaction of subunits.

sequential electrophoresis the use of a series of different electrophoretic conditions to uncover hidden heterogeneity in isozyme electrophoresis.

sex plasmid plasmid which is capable of initiating conjugation (mating) between two bacteria.

Shine-Dalgarno sequence the AGGAGG purine sequence on bacterial mRNA, which facilitates binding of the mRNA to a ribosome.

sibship genetic relationships between members of a familial pedigree (e.g. cousins, siblings, etc.).

Sigma factor subunit of RNA polymerase that facilitates binding to promoter sites on DNA.

similarity a generic measure of the resemblance between two objects, usually on a scale from 1 to 0.

single copy DNA usually refers to sequences that appear only once in the entire genome. Specific genes or sequences that are single copy are much more difficult to isolate because they represent such a small percentage of the total DNA of an organism.

single-copy gene genes for which only two alleles exist (one from each parent) in a diploid cell.

size marker DNA fragments of known molecular weight and base pair length, such as l-phage digested with the restriction enzyme Hind III, run on electrophoresis gels for the determination of DNA sample fragment sizes.

slippage a mechanism of DNA turnover by which gains-and losses occur of short motifs (usually less than 10 nucleotides) in DNA helix leading to pure and cryptic DNA simplicity.

Southern blot a membrane onto which DNA has been transferred directly from an electrophoretic gel.

specific activity (SA) a measure of the incorporation of radiolabeled nucleotide into a probe, for example, counts per minute (cpm) per microgram of probe.

specificity the degree to which antibodies react with multiple antigenic sites. Initially antibodies are monospecific, but with longer periods of immunization they become more cross reactive (react with more antigenic sites).

spliced mRNA mRNA after removal of the intron coding regions from the premessenger and linking of the exon coding portions.

splicing process which removes introns from RNA and joins exons (coding sequences) to form "translatable" mRNA.

SSRBC sensitized sheep red blood cells used for assays in microcomplement fixation.

stacking (of bases) the tight packing of purine and pyrimide base-pairs in double-stranded DNA, favored by the energy of interaction.

state set a mathematical set of character states used during a parsimony analysis to keep track of the states that are consisitent with the minimum amount of change.

STE a buffer used in many DNA procedures; contains sodium chloride, Tris, and EDTA.

STES a buffer with sodium chloride, Tris, EDTA, and sucrose used in DNA isolation.

strip removal, by melting of hydrogen bonds, of hybridized probe from DNA blots

stringency in DNA-DNA hybridization or DNA-RNA hybridization, the conditions of the hybridization (such as temperature and concentration of chemical additives) that determine the degree of similarity that will result in formation of hybrid molecules.

subbands nonallelic bands in isozyme electrophoresis that represent the electrophoretic location of conformational isozymes.

subclone a fragment of DNA that is taken from an existing clone and subsequently cloned again. When the DNA of interest represents only a fraction of the originally cloned insert, subcloning is often done to facilitate handling of the clones as smaller clones are often less cumbersome to work with.

subrepeat a tandem array of repeats within a larger repeating unit, usually also in tandem array (eg. subrepeats within the intergenic spacers of rDNA- see above).

sugar/phosphate backbone the ribose (deoxyribose) sugar and phosphate groups that compose the structural backbone of a DNA molecule.

supercoiling coiling of a large, circular, double-stranded DNA molecule back around itself.

suppressor a mutation which acts to restore the original nucleotide sequence.

synonymous substitutionmutations in a codon, usually at the third position, which do not lead to a change in amino-acid at the polypeptide level.

T50H the interpolated temperature along a heteroduplex DNA melting curve at which 50%of the DNA is double-stranded in comparison to the homoduplex control. T50H differs from Tm when all DNA in DNA-DNA hybridization reaction does not form duplexes. The difference inT50H nbetween homoduplex and heteroduplex curves is DT50H.

tag a tracer linked into a molecule, for example, 32P labeling of a DNAprobe.

tandem array multiple copies of a sequence of DNA that are arranged one after another in series. Repeat units can be short nucleotide sequences or entire sets of genes.

Taq polymerase a thermostable DNA polymerase from Thermus aquaticus, thermophilic bacterium. Used for amplification via the polymerase chain reaction.

TATA box an A-T-rich sequence, usually consisiting of 7 or 8 nucleotides, located approximately 25 base-pairs upstream of the transcription start site. It serves as a binding site for RNA polymerase.

TEACL tetraethylammonium chloride, a chaotrophic agent used to eliminate the effect of base composition on hybrid melting temperature in DNA-DNA hybridization.

template the single-stranded DNA blueprintfor complementary strand assembly or the productionof pre-mRNA.

terminal nodes tips of a phylogenetic tree at which contemporary sequences or taxa are placed.

tertiary structure the native three-dimensional configuration of a macromolecule, which results after its subunit interactions are complete.

thermal cycler a computerized incubator capable of rapid temperature changes over a broad range. Typically used for amplifying discrete DNA sequences by the polymerase chain reaction (PCR).

thymine dimer adjacent thymine residues in DNA that have been chemically linked, usually by the action of ultraviolet irradiation.

titer the concentration of a substance as determined by the amount of a known reagent required to bring about a given effect in a test solution. In microcomplement fixation, the concentration of antibody that gives 75% complement fixation under standard conditions.

TLD thermoluminescent dosimeter; a film-badge type monitor used to record radiation exposure from a radioactive source.

Tm the interpolated temperature along a DNA melting curve at which 50% of the duplex DNA formed in a DNA-DNA hybridization reaction is double-stranded. The difference in Tm between homoduplex and heteroduplex curves is DTm.

Tmode the interpolated temperature of the peak of a differential plot of a DNA melting curve. The difference inTmode between homoduplex curves is DTmode.

topoisomerase enzyme that alters amount of supercoiling in large, double-stranded DNA molecules.

tracer radioactively labeled, usually fractionated single-copy DNA used in DNA-DNA hybridization experiments.

trailer (sequence) nucleotide sequence at the 3' end of a mRNA that is not translated into part of the protein.

transduction transfer of bacterial gene from one bacterium to another by a bacteriophage.

transfer RNA (tRNA) small RNA that transfers amino acids to the mRNA template for protein synthesis.

transition a nucleotide substitiution that changes one purine into the other purine, or that changes one pyrimidine to the other pyrimidine.

translocation change in the position of a chromosome segment within a genome.

transposable element a genomic element that can move from site to site in the genome of an organism, either through direct DNA copying (at least in prokaryotes) or reverse transcription from an RNA intermediate (probably the usual mechanism in eukaryotes).

transposase enzyme that functions to insert a transposon into a new site in DNA.

transposition see mobile elements. Duplicative transposition occurs when a given DNA region replicates and the extra copy moves to another position in the genome. Non-duplicative transposition occurs when the DNA region moves from one position to another: no extra copies are involved.

transposon a segment of DNA flanked by transposable elements that is capable of moving its location in the genome.

transversion a nucleotide substitution that changes a purine to a pyrimidine, or vice versa.

tree length the total amount of change in a maximum parsimony tree, or the sum of the branch lengths in a minimum distance tree.

triplet code a series of three successive DNA or RNA nucleotide bases that codes for a specific amino acid, for example, AUG coders for methionine.

ultrametric distances pairwise distance values that precisely fit a rooted tree with a constant molecular clock. Defined mathematically by satisfying the three-point condition.

unequal crossing-over crossing-over at a time when two chromatids or two chromosomes are not fully aligned leading to the gain of DNA on one chromatid (chromosome) with an equivalent loss in the other. A process of gain and loss which can generate multigene families and maintain their homogeneity; see DNA turnover, molecular drive.

unequal rate effect a misnomer for the tendency of homoplasy in long branches of a phylogenetic tree to artifactually group these branches together during tree inference.

unordered character a character for which any state can change directly to any other state.

unrooted tree a phylogenetic tree in which the location of the most recent common ancestor of the taxa is unknown (or not indicated).

UPGMA unweighed pair group method using arithmetic average. A cluster analysis technique.

upstream direction ahead of the start site for transcription or translation.

uracil pyrimidine base in RNA that appears in place of the thymine found in DNA.

UV transilluminator a source of ultraviolet (UV) light used to detect ethidium bromide stained DNA.

van der Waals forces weak attractive forces that result from transitory fluctuations in electron-charged densitites in neighboring atoms.

variable number tandem repeat loci (VNTR loci) loci containing variable numbers of shory tandemly repeated sequences, resulting in a high frequency of length variation that can be revealed with an appropiate restriction endonuclease.

vector a self-replicating DNA molecule that exists with, but is separate from the genome of the host cell. Many different vectors have been identified and genetically engineered for use in molecular biology. DNA inserted into a vector will be replicated along with the vector. In this manner, DNA of interest can be obtained in large quantities i.e., cloned. For example, the human insulin gene can be cloned into the plasmid vector pBr 322 which in turn will replicate in E. coli cultures.

wash the process of removing nonbound or loosely bound probe from blots after hybridization. This process reduces background interference.

Watson-Crick model refers to the DNA molecu;e that forms a double helix ladder with the complementary strands held by hydrogen bonds between specific base pairs.

wobble hypothesis explanation for ability of certain tRNAs to exhibit unusual base-pairing with more than one triplet codon.

WPGMA weighted pair group method using arithmetic average. A cluster analysis technique.

X-chromosome a chromosome responsible for sex determination. Two copies are present in the genome of the homogametic sex and one copy in the heterogametic sex. The human female has two X-chromosomes and the male one X.

xenology homology that arises via lateral gene transfer between unrelated species (e.g., by retroviruses).Y-chromosome a chromosome responsible for sex determination in the heterogametic sex. This ocurs in male (XY) mammals and female (ZW) birds.

Y-chromosome a chromosome responsible for sex determination in the heterogametic sex. This ocurs in male (XY) mammals and female (ZW) birds.

zygosity twin development from one or two zygotes. If one, the twins are identical (monozygotic); if two, they are fraternal (dizygotic).

zygote the diploid cell resulting from the union of a haploid egg and sperm.

zymogram the pattern on an allozyme electrophoresis gel visualized by histochemical staining.

Freifelder, D. and Malacinski, G.M. 1993. Essentials of Molecular Biology 2nd Ed. Jones and Bartlett, Boston, Massacusetts.

Hillis, D.M. and Morits, C. 1990. Molecular Systematics. Sinauer, Sunderland, Massachusetts.

Hoelzel, A.R. and Dover, G.A. 1991. Molecular Genetic Ecology. Oxord University Press, New York. D. Rickwood, ed.

Kirby, L.T. 1990. DNA fingerprinting- An introduction. Stockton Press, New York.