Glossary

This glossary has been taken from Bacterial Fundamental Genetics  by Nancy Trun and Janine Trempy and Basic Virology  by Edward K Wagner & Martinez J. Hewlett. Our thanks go to the authors of these two books for compiling these extensive glossaries. 

For a .pdf of the glossary please click here (228kb) 

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3' overhang  Restriction enzymes that cleave the DNA asymmet­rically leaving single-stranded bases. If the single-stranded bases end with a 3' hydroxyl, the enzyme is said to leave a 3' overhang. 

5' overhang  Restriction enzymes that cleave the DNA asymmet­rically leaving single-stranded bases. If the single-stranded bases end with a 5' phosphate, the enzyme is said to leave a 5' overhang. 

- 10 site  A part of the promoter that is ~10 base pairs upstream of the +1 site. The -10 and the -35 site constitute the sites to which RNA polymerase binds. 

- 35 site  A part of the promoter that is ~35 base pairs upstream of the +1 site. 

- 1 site  The base at which RNA polymerase starts polymerizing RNA. 

3' to 5' exonuclease  A subunit of all DNA polymerases capable of removing nucleotides from an exposed 3' end. This is the editing (proofreading) function used to ensure that the correct nucleotide was added by DNA polymerase III to a growing DNA chain. 

a fragment  The ?rst ~60 amino acids of ß-galactosidase that can combine with the last ~960 amino acids of ß-galactosidase (the w fragment) to form an active enzyme. 

f fragment  The last ~960 amino acids of ß-galactosidase that can be combined with the a fragment of ß-galactosidase to form an active enzyme. 

abortive infection:  Infection of a cell where there is no net increase in the production of infectious virus. 

abortive transformation:  See transitory (transient or abortive) transformation  . 

acid blob activator:  A regulatory protein that acts in trans  to alter gene expression and whose activity depends on a region of an amino acid sequence containing acidic or phosphorylated residues. 

acquired immune deficiency syndrome (AIDS):  A disease characterized by loss of cell-mediated and humoral immunity as the result of infection with human immunodeficiency virus (HIV). 

activation  (of a gene, operon, or regulon) A mechanism of gene regulation that requires the induction of the expression of the genes. Frequently, activation involves a regulatory factor binding to the promoter region and activating the promoter. 

acute infection:  An infection marked by a sudden onset of detectable symptoms usually followed by complete or apparent recovery. 

adaptive immunity (acquired immunity):  See immunity  . 

adjuvant:  Something added to a drug to increase the effectiveness of that drug. With respect to the immune system, an adjuvant increases the response of the system to a particular antigen. 

agnogene:  A region of a genome that contains an open reading frame of unknown function; originally used to describe a 67- to 71-amino acid product from the late region of SV40. 

AIDS:  See acquired immune deficiency syndrome  . 

aliquot:  One of a number of replicate samples of known size. 

alkylating agent  Mutagenic chemicals that attach an alkyl group (methyl or ethyl) to a base and change the base's hydrogen-bonding capabilities. Guanine is the most sensitive to alkylating agents. 

allele  A unique form of a given gene. For example, the wild-type copy of a gene is one allele and a mutant copy of the same gene is also an allele of that gene. Allele is a genetic term used to describe the form of the gene present in the cells. 

allele number  A unique number or letter given to each mutation. Different mutations are distinguished by their allele numbers. 

a -TIF:  The alpha trans  -inducing factor protein of HSV; a structural (virion) protein that functions as an acid blob transcriptional activator. Its specificity requires interaction with certain host cellular proteins (such as Oct1) that bind to immediate-early promoter enhancers. 

ambisense genome:  An RNA genome that contains sequence information in both the positive and negative senses. The S genomic segment of the Arenaviridae and of certain genera of the Bunyaviridae have this characteristic. 

amorphous:  Without definite shape or form. 

anabolic  The process or the enzymes that build (i.e. synthesize) a substrate rather than break down a substrate. An example is the amino acid tryptophan, whose synthesis requires the action of four different enzymes encoded by ?ve different genes. 

aneuploid:  A eukaryotic cell with an ill-defined number of fragmented chromosomes, as a result of long periods of continuous passage in culture. 

animal model for a (specific) disease:  An experimental system using a specific laboratory animal to investigate aspects of pathogenesis of an infectious disease not usually occurring in that animal. 

annotated sequence  The sequence of a piece of DNA that lists, in addition to the order of the bases, other features of the DNA includ­ing promoters, mRNA start sites, open reading frames, transcription and translation regulation sites, and other unusual sequences. These features can be either predictions or biologically determined entities. 

antibodies:  Glycoprotein molecules secreted by B lymphocytes with a defined structure consisting of an N-terminal region of variable amino acid sequence (the Fab region), which combines with specific antigenic determinants, and a C-terminal region of constant amino acid sequence (the Fc region), which serves as a biological marker identifying the molecule as part of the immune response. 

antibiotic resistance determinant  A gene whose protein prod­uct confers resistance to a speci?c antibiotic. The mechanism of re­sistance differs for each antibiotic. Some antibiotics are inactivated by cleaving them, some by modifying them, and some by simply pumping them out of the cell as fast as they come into the cell. The most commonly used antibiotic resistant determinants for E. coli  are ampicillin, kanamycin, tetracycline, and chloramphenicol resistance. 

antigen:  Usually a macromolecule that induces an immune response by virtue of small regions that combine with antigen-combining sites on immune cells. 

antigen-presenting cell (APC):  A cell in which an antigen is processed, followed by expression of epitopes on the surface in conjunction with major histocompatibility antigens. See also dendritic cells  . 

antigen processing:  Partial degradation of an antigen within an antigen-presenting cell (APC) followed by its expression at the surface of the APC in the presence of a major histocompatibility protein. 

antigenic drift:  The slow change in structure of an antigen over time due to accumulated mutational changes in the sequence of the gene encoding the antigen. 

antigenic shift:  An abrupt change in an antigen associated with a pathogen due to the acquisition of a novel gene substituting for the original one. 

antiparallel  A description for the opposite polarities of the two strands of a DNA molecule. One strand is orientated 5' to 3' and the other strand is 3' to 5'. 

antisense oligonucleotide:  A short oligonucleotide with a sequence complementary to a specific sequence of nucleotides on a nucleic acid molecule; under investigation as a potential highspecificity target for binding and, thus, inactivating viral genes or mRNA. 

antiserum:  The plasma fraction containing antibody molecules of the blood of a subject mounting an immune response to the protein or other molecule against which the antibody is directed. 

antiviral drug:  Any drug that specifically inhibits some process in the replication of a virus without undue toxicity to the host in which the virus is replicating. 

antiviral effector molecule (AVEM):  One of a number of cellular proteins that function to limit virus replication when activated by the presence of dsRNA in a cell activated by interferon. 

antiviral state:  A state induced by interferon in a susceptible cell. The cell is partially refractory to virus replication in this state. 

AP endonuclease  An enzyme that catalyzes the breakage of phos­phodiester bonds within a DNA molecule at a site upstream and downstream of an apurinic or apyrimidinic site. 

apathogenic:  Not pathogenic. 

APC:  See antigen-presenting cell  . 

apical surface:  The surface of epithelial cells that face the exterior or an extracellular compartment of the organism. This surface contains specific membrane-associated proteins mediating specific functions; this surface is distinct from the basolateral regions that communicate with adjoining cells. 

apoptosis:  Programmed cell death; a specific linked set of cellular responses to specific stimuli, such as loss of replication control, that leads to a specific course of changes resulting in cell death. 

apurinic site  A site in the DNA where a purine has been removed from the DNA phosphatesugar backbone. The bond affected is the N-glycosidic bond. 

apyrimidinic site  A site in the DNA where a pyrimidine has been removed from the DNA phosphatesugar backbone. The bond affected is the N-glycosidic bond. 

arboviruses:  Arthropod-borne viruses. 

arti?cial chromosome  A cloning vector designed to accept 401000 kilobases of cloned DNA. These vectors rely on the features that make up a chromosome for their replication and partitioning into daughter cells. 

ascites:  An accumulation of fluid in the peritoneal cavity of the body. 

aseptic meningitis:  An infection of the CNS's surface tissue from which no bacteria or metazoan pathogen can be cultured; therefore, by elimination, a viral infection. 

assay:  A measurement or test. 

assimilation  The part of the homologous recombination process where the RecAssDNA ?lament binds to and unwinds another dsDNA, promoting base pairing of the complementary nucleotides. 

asymptomatic:  Without detectable symptoms. 

atomic force microscopy (AFM):  A technique for displaying surface features of a sample by recording the deflection of a microscopic probe as it passes over the sample. Resolution with this technique can be on the order of the diameter of a DNA molecule (2.0 nm). 

ATPase  An enzyme that degrades ATP. Frequently, the ATPase pro­vides the energy released from the degradation of ATP to other pro­teins that require energy to carry out their function. 

attenuate:  Losing virulence due to an accumulation of mutations in virus-encoded proteins mediating pathogenesis during continued passage of a virus in a natural population or in the laboratory. 

attenuation  A regulatory mechanism of some anabolic operons (i.e. trp  operon) that controls the ef?ciency of transcription after transcription has initiated, but before mRNA synthesis of the oper-on's genes takes place. 

autoimmune disease:  A disease characterized by the subject's immune system attacking and destroying ostensibly normal host tissue. 

autophosphorylation  The ability of an enzyme to phosphory­late itself. The addition of phosphate groups to an enzyme often re­sults in the activation of the enzyme's function. 

AVEM:  See antiviral effector molecule  . 

avirulent:  A genetic variant of a virulent pathogen that does not cause the disease usually associated with the agent. 

B lymphocytes:  The immune cells that secrete soluble antibodies. 

back mutation:  A change in the genome of an organism or virus that returns the genotype to the wild type or original strain. 

bacterial plasmid:  An extrachromosomal circular genetic element with the capacity to replicate as an episome in bacteria. This plasmid often may confer antibiotic resistance on its host. It frequently is utilized for maintaining cloned fragments of DNA. 

bacterial restriction:  A set of endonuclease-mediated responses to foreign DNA sequences encoded by bacterial genes designed to destroy the genomes of invading bacteriophages and plasmids. 

bacteriophage  A virus that infects bacteria. Bacteriophage (or phage for short) are usually speci?c for a single bacterial species. 

bacteriocidal  Any compound or physical treatment that kills the bacteria. 

bacteriostatic  Any compound or treatment that prevents bacte­ria from growing but does not kill them. 

baltimore scheme:  A scheme of virus classification stressing the mechanism for expression of viral mRNA and the way that information is encoded in the viral genome as primary criteria; formalized by David Baltimore. 

basal level of transcription  Refers to the amount of transcrip­tion that originates at a given promoter when the promoter is func­tioning at its lowest level. For a promoter that is activated by a protein, it is the amount of transcription in the absence of the acti­vator protein. For a promoter that is repressed by a protein, it is the amount of transcription in the presence of the repressor protein. 

base analogs  Chemicals with similar properties to the natural oc­curring bases (A, T, G, C, U). DNA polymerase III will incorporate base analogs into a growing DNA strand as if they were the naturally occurring nucleotide. 

base modi?ers  Chemicals that modify the structure of bases so that they no longer base pair in a predictable manner (A with T and G with C). 

base plate:  Complex portion of a tailed bacteriophage's capsid that contains projecting protein pins mediating the noncovalent interactions between the phage and host cell that lead to injection of the viral genome. 

base substitution mutations  A mutation where one base has been substituted for another. Base substitutions are also another name for point mutations. 

basolateral surface:  The interior surface of epithelial cells that face other epithelial cells of this and adjoining tissue. The region is distinct from the apical surface that contacts the exterior. 

benign tumor:  A group of cells forming a discrete mass resulting from limited alterations in cellular growth properties; distinguished from a malignant tumor or cancer in that the cells do not metastasize throughout the body. 

bidirectional DNA synthesis  DNA replication proceeding out­ward from the origin in both directions at the same time. The conse­quences of this are that the leading and the lagging strands are synthesized at the same time. 

bioinformatics  De?ned as the study of information content and information ?ow in biological systems and processes. Bioinformat­ics bridges the biological sciences with the computer sciences. 

biopanning  The process of screening a library of clones for a clone with a useful characteristic. Biopanning frequently refers to screen­ing a phage display library for a phage with a useful or interesting insert. 

bioterrorism:  The threat to use or the actual deployment of an infectious agent (fungal, bacterial, or viral) to inflict harm and/or engender fear, especially in a civilian population. 

bloodbrain barrier:  The physical and biochemical parameters creating the relative physical and physiological isolation and physical separation of the CNS from the circulatory system and any pathogens that may be present in it. 

bp:  Abbreviation for a base pair. 

blue/white screen  The visual screen that is used to tell when a plasmid has a cloned insert. The blue color results from an a fragment of ß-galactosidase combining with an f fragment of ß-galactosidase to form an active ß-galactosidase molecule. When the a fragment is inactivated by a cloned insert, no active ß-galactosidase is made. 

blunt ends  A double-stranded DNA end where both strands end at the same base. Some restriction enzymes cleave symmetrically in their recognition sequence. There are no single-stranded bases after the enzyme has cut the DNA. These enzymes are said to leave blunt ends. 

broad host range plasmids  Plasmids that can be stably main­tained in more than one species. They must contain an origin that functions in different species or more than one origin. 

building blocks  A group of small molecules that are used to build macromolecules. For example, the four bases and the phosphate sugars used for the backbone are the building blocks of DNA. Amino acids are the building blocks for proteins. 

buoyant density:  The density at which a macromolecule or virus floats in a gradient under conditions of equilibrium in a centrifugal field. 

burst size:  Amount of (usually infectious) virus produced from a single infected cell. 

bypass suppressors  Suppressor mutations that bypass the need for the gene containing the primary mutation. Bypass suppressors also work with deletions in the gene containing the primary mutation. 

cAMP:  3',5'-cyclic adenosine monophosphate. 

cancer:  A disease of multicellular organisms characterized by genetic modifications to specific cells that result in the formation of malignant tumors composed of cells without the ability to respond to normal growth-control signals limiting their replication and spread in the body. 

cancer cell:  A cell isolated from a malignant tumor and displaying the altered growth and other properties associated with the tumor. 

cap:  The methylated guanosine residue at the 5' end of eukaryotic mRNA molecules that is added posttranscriptionally as a 5'-5'-phosphodiester. 

cap site:  The location of initiation of transcription of a specific eukaryotic mRNA. 

cap snatching or stealing:  The endonucleolytic removal of the 5'-methylated cap region of nascent eukaryotic mRNAs and transfer to a nascent viral mRNA. The process occurs during the replication of orthomyxoviruses and bunyaviruses. 

capillary electrophoresis:  The separation of charged particles in an applied electric field (10 to 30kV) across a capillary tube of small (20 to 100µm) diameter. The technique has the advantage over conventional electrophoresis in that it produces quantitatively reproducible separation in a very short (less than one hour) time, using small sample sizes. 

capsid:  The viral protein shell surrounding the virion core and its nucleic acid genome. 

capsomer (capsomere):  One of a group of identical protein subunits making up a viral capsid. 

capsule  or capsular polysaccharide  The thick slime layer com­posed of polysaccharides that surrounds the cell and protects it from dehydration and the immune system. A given bacterial species can produce more than one type of capsule. 

carbohydrates  Composed of simple sugars and used as a source of energy for the cell as well as a component of several cell structures. 

carcinogen:  A chemical substance that induces a cancer. 

CAT:  Chloramphenicol acetyl transferase. This bacterial enzyme transfers one or two acetyl groups to the structure of the drug, chloramphenicol, making it refractive to uptake by the cell. CAT is a prokaryotic gene and is therefore well-suited for use as a reporter gene in eukaryotic cells (see also reporter gene  ). 

catabolic  The process or enzymes that break down a sub­strate rather than build a substrate. An example is the enzyme b-galactosidase, which breaks lactose into glucose and galactose. 

catabolite repression:  A control mechanism for metabolite use in bacteria mediated by levels of cAMP. It ensures that glucose or other energy sources not requiring expression of inducible metabolic enzymes are utilized first. 

catabolite repression  Cells growing in medium containing glu­cose do not express, at high levels, certain sugar metabolizing oper­ons (i.e. lac  ) even if the inducers of those operons are present. Catabolite repression relies on the levels of cAMP and CAP protein to relay information on the sugars that are present. 

CBP1 (cap-binding protein):  A eukaryotic ribosome-associated protein involved in the initiation of translation. It functions by binding the 5'-cap structure of eukaryotic mRNA. 

CCR5:  A cellular chemokine (growth factor) receptor that is used for attachment during HIV infection of macrophage cells. 

CD4, CD8:  Specific protein antigenic markers found on the surface of different functional classes of T lymphocytes. 

cDNA:  Complementary DNA; produced by the reverse transcription of an RNA molecule. 

cell-mediated immunity (CMI):  The portion of the immune response that requires specific recognition between receptors on individual T lymphocytes and antigenic determinants on the surface of antigen-presenting cells. 

centrifugation:  Subjection of a sample to an artificial gravity field resulting from rapid rotation. 

chain initiation, chain elongation, and chain termination  The steps needed to produce RNA molecules. RNA polymerase must bind to a promoter, initiate RNA chain formation, elongate the RNA chain, and then terminate it at the appropriate place. 

chemokine:  An extracellular signaling molecule capable of activating a target cell with appropriate receptors for its recognition. 

chemotaxis  The movement of a bacterial cell towards a favorable environment and away from a harmful environment. The rotation of the ?agella is used to move the cell. 

chicken pox:  A childhood disease marked by a distinctive rash and caused by the herpesvirus varicella-zoster virus. 

chi site  The speci?c DNA sequence used in the homologous re­combination process. The sequence of chi is 5' GCTGGTGG 3'. Once RecBCD passes the chi site in the correct orientation, its 3' to 5' ex­onuclease activity is inhibited. This generates ssDNA for RecA to bind and assimilate. 

Chlorella  virus:  A DNA virus of the green algae Chlorella  . 

chorioallantoic membrane:  The membrane located between the shell and chicken embryo in an embryonated egg; used as a location for growth of certain viruses such as poxvirus. 

circular permutation  The genomes of some bacteriophage al­ways contain the same genes but they are not always present on the infecting phage in the same order. For example, one phage may have the order ABCDEFG, another may have CDEFGAB, and another may have DEFGABC. These different phage genomes are circularly per­muted with respect to each other. 

cirrhosis:  Liver damage characterized by tissue hardening and loss of function and circulation. 

cis  -acting genetic element:  A genetic element that functions only in the contiguous piece of DNA or RNA in which it is present. 

CJD:  See Creutzfeldt-Jakob disease  . 

clinical trial:  A formal process for testing the effectiveness of a drug or vaccine on human subjects in a clinical setting. 

clonal selection:  The selective stimulation of subsets of immune cells reactive with a single antigenic determinant that results in the proliferation of cells specifically responding to that antigen. 

clones:  Genetically identical biological entities derived from a single parental entity. 

cloning  The process of putting a piece of chromosomal or other DNA into a vector using in vitro manipulations of the DNA. 

CMI:  See cell-mediated immunity  . 

CNS:  Central nervous system. 

coding strand  The strand in a dsDNA molecule that matches the base sequence of the RNA that is made from it. 

coinheritance  The ability to inherit two genes in a single genetic cross. 

cointegrate  A structure that contains two copies of a transposon in a single DNA molecule. The transposons are arranged as direct repeats. 

cold sensitive  A secondary phenotype caused by some muta­tions. The gene product containing the mutation is not functional at low temperatures. 

cold virus:  One of a number of RNA genome-containing viruses known to be causative agents of mild infections of the upper respiratory tract and nasopharynx. 

colony  The group of cells that are formed when bacteria are plated on a solid growth media and incubated for a period of time. If the cell concentration is low enough, each colony is formed from one bac­terium. For E. coli  , the average colony contains approximately one million cells. 

colony blotting  A version of Southern blotting where colonies on an agar plate are transferred to a ?lter and lysed in situ. The DNA from the colonies is attached to the ?lter. The ?lter is exposed to a tagged probe the same as for a standard Southern blot. Colony blots are used to ?sh speci?c genes out of libraries of clones. 

competence  A transient physiological state in which the bacteria can take up naked DNA and transport it into their cytoplasm. 

competent  Cells that are in the physiological state where they can take up naked DNA. 

competence factors  Small peptides that act to induce the ex­pression of the genes needed to make the cell able to take up naked DNA. Some competency factors bind to surface receptors and initi­ate a relay of information across the membrane and into the cyto­plasm. Other competency factors are transported into the cell to effect a change in regulation. 

complement:  A group of serum proteins that bind to an antibody-antigen complex on the surface of a cell, and sequentially undergo a complex maturation process resulting in cell lysis. 

complementary strands of nucleic acid:  Strands of single-stranded nucleic acid whose sequence is determined by the Watson-Crick base-pairing rules relative to a reference strand. 

complementation:  The growth of two replication-deficient mutant organisms or viruses that have mutations in different trans  -acting genes so that each can supply the deficient gene product of the other. 

composite transposons  Composed of modular units. They have insertion elements on either end. The central piece of DNA can en­code many different functions. 

concatamer  A long DNA molecule that contains multiple copies of the same DNA sequences linked end to end. Concatomers are fre­quently the result of rolling circle replication. An example is a phage genome that is arranged in a head-to-tail manner (i.e. if the genes in the phage DNA are arranged ABC, then in a concatomer the genes would be ABCABCABCABC). 

conditional lethal mutations:  Genetic alterations in a specific protein or genetic element that lead to a replication deficiency under controlled laboratory conditions such as high temperature. 

confocal microscopy:  Technique using a computer-enhanced microscope equipped with laser illumination optics that allow a very small focal plane to be visualized with various wavelengths of light. 

conformational epitopes:  Antigenic determinants that are only present when the antigen is in a specific (usually native) conformation. 

conjugation  The process of moving DNA from one cell to an­other through cell-to-cell contact and using a specialized plasmid that encodes an F pilus such as an F factor or an R factor. The proteins needed for conjugation are encoded by a plasmid. 

consensus sequence  A base sequence generated from closely re­lated sequences with similar functions. For example, many operons are controlled by campCAP binding to their promoter regions. The DNA sequence that campCAP binds to is not identical in every operon. If all of the sequences are aligned, a most probable binding site or consensus sequence can be derived. 

constitutive  The synthesis of a gene product continuously. 

contact inhibition:  The cessation of cell replication or movement when the cell is in contact with other cells of the same type. 

construct  The molecule that is made by rearranging DNA se­quences in vitro using cloning techniques. 

contigs  A group of clones whose inserts contain DNA sequences that overlap with each other. Contigs are used to reconstruct the se­quence of a genome in the computer. 

continuous cell line:  A clonal cell line that has been maintained in culture for a large number of passages and is essentially immortal. 

control regions  The sequences that are used in controlling the expression of a gene or genes. 

core RNA polymerase  The core subunits, ßß'a 2 , of RNA polymerase that synthesizes RNA by adding ribonucleotides to a growing mRNA chain. Core RNA polymerase does not need a primer to begin synthesis. It does not speci?cally recognize promoters and begins RNA synthesis randomly. 

cos  The name describing ?'s cohesive end sites. cos  sites are used to circularize the ? genome after it is injected into the cytoplasm of a cell. 

counterselection  A counterselection prevents cells of a speci?c genotype from growing. It is used in genetic crosses to ensure that the parental cells cannot grow and only the recombinants grow. 

coupled transcription/translation:  The linked process (often in prokaryotic cells) where synthesis of protein encoded by an mRNA molecule commences during ongoing transcription of the mRNA. 

CPE:  See cytopathic effect  and cytopathology  . 

creutzfeldt-Jakob disease (CJD):  A slow, noninflammatory infection of the human CNS caused by a prion. 

cryo-electron microscopy:  The preparation of a specimen by embedding it in vitreous (noncrystalline) ice in the absence of stain and its visualization using an electron beam of low intensity. This method preserves much structural integrity of the virion, especially in enveloped viruses. 

cryptic ORFs:  Open translational reading frames in a eukaryotic mRNA downstream of an efficiently translated one and, thus, one usually not recognized by eukaryotic ribosomes. 

cut-and-paste transposition  Another name for non-replicative transposition. 

CXCR4:  A cellular chemokine (growth factor) receptor used by HIV for attachment during infection of T cells. 

cytochalasin B:  One of a number of compounds that interfere with formation of the actin-fiber cytoskeleton that anchors the nucleus inside the cell. 

cytokine:  One of a group of proteins (usually glycosylated) secreted by cells that have a specific effect on the growth and behavior of target cells. Examples include the interferons. 

cytolysis:  Cell lysis. 

cytopathic effect (CPE):  See cytopathology  . 

cytopathology:  Observable changes to the appearance, metabolic processes, growth, and other properties of a cell induced by a virus infection. 

cytoplasm  The aqueous compartment surrounded by the inner membrane. It contains the chromosome, ribosomes, and many en­zymes used to degrade or build molecules. The cytoplasm is also the location for transcription and translation. 

deamination  The loss of exocyclic amino groups from cytosine, adenine, or guanine. 

defective interfering particles:  Defective virus particles that reduce the efficiency of infection by normal virus particles in the same stock. 

defective virus particles:  Virus particles that are normal or apparently normal in appearance but cannot initiate a productive replication cycle. 

deletion  The loss of one or many base pairs from the DNA. 

de novo protein synthesis  New protein synthesis needed for certain cellular processes. For example, many chromosomes need newly synthesized proteins to initiate DNA replication. This implies that a protein is used only once and then inactivated or degraded. The next time that the protein is needed, it must be newly synthesized. 

denature:  To disrupt the higher-order structure of a protein or nucleic acid-containing 

macromolecule. 

denaturation temperature:  The temperature at which a biological macromolecule loses its functional higher-order structure by virtue of thermal disruption of hydrogen bonding and other forces contributing to its stability. In the case of double-stranded nucleic acids, this is the temperature where the two complementary strands can no longer associate (also the melting temperature or Tm). 

dendritic cells:  Cells derived from bone marrow that play a major role in presenting processed antigen to T cells. 

density labeling  A way of tagging speci?c cellular components by using a heavy isotope of one of the naturally occurring element, for example 15 N instead of 14 N. 

deoxyribonucleoside  Also called, deoxynucleoside or nucleo­side for short. This is the nomenclature used to describe a base at­tached to a sugar (adenosine, guanosine, thymidine, cytidine, uridine) 

deoxyribonucleotide  Also called deoxynucleotide, or nu­cleotide for short. This is the nomenclature used to describe a base at­tached to a sugar containing a phosphate group (nucleoside 5' monophosphate: AMP, GMP, TMP, CMP, UMP). 

dephosphorylation  The removal of a phosphate from a mole­cule. Some proteins are activated or inactivated by the additional or removal of a speci?c phosphate. 

depurination  The removal of a purine from the DNA backbone, leaving an unpaired base on one strand of the DNA. 

desiccation:  The act of drying out. 

differential display analysis:  A method for comparing the population of cellular transcripts in a population of cells before and after an induced metabolic change, such as infection with a virus or stimulation with a cytokine. 

differential polyadenylation site usage:  The termination of eukaryotic transcription employing alternate polyadenylation signals. The process generates overlapping mRNAs with different 3' terminal regions. 

dilution endpoint:  The dilution in a quantal assay at which the agent being tested cannot evoke a positive response. 

diploid  A cell containing two complete copies of the chromo­some. Diploidy is the state of a cell that contains two complete chromosomes. 

direct repeats  DNA sequences that are repeated in a head-to-tail fashion. If the sequence is ATTGCC then it will be repeated ATTGCCATTGCCATTGCC. 

disease-based classification scheme:  One of a number of classification schemes for viruses based on the disease caused. 

DNA  Deoxyribonucleic acid. The molecule that is passed from generation to generation and speci?es the physical characteristics of the cell that contains it. DNA is composed of a sugarphosphate backbone and the four bases: thymine, adenine, guanine, and cytosine. 

DNA-dependent DNA polymerase I or DNA Pol I  An enzyme that uses a DNA template to polymerize nucleotides onto a free 3' OH of an existing RNA oligonucleotide (primer). DNA Pol I has a 3' to 5' exonuclease activity that is called an editing or proofreading ac­tivity. It also has a 5' to 3' exonuclease activity that removes nu­cleotides from a double-stranded DNA molecule's exposed 5' end. The polymerizing activity is used to ?ll in small gaps in a DNA mole­cule that have arisen due to the removal of mismatched base pairs and the removal of RNA primers during the editing process. 

DNA-dependent DNA polymerase II or DNA Pol II  An enzyme that uses a DNA template to polymerize nucleotides onto a free 3' OH of an existing RNA (primer). DNA Pol II has a 3' to 5' exonuclease activity that is called an editing or proofreading activity. This poly­merase is primarily involved in DNA repair processes. 

DNA-dependent DNA polymerase III or DNA Pol III  An enzyme that uses a DNA template to polymerize nucleotides onto a free 3' OH of an existing RNA oligonucleotide (primer). DNA Pol III has a 3' to 5' exonuclease activity that is called an editing or proofreading activity. It also has a 5' to 3' exonuclease activity that can remove nucleotides from single-stranded DNA. DNA Pol III is the major replicating enzyme in E. coli  . 

DNA end problem:  A dilemma in the replication of a linear DNA molecule that results from the constraint that the polymerase must synthesize in the 5' to 3' direction from a primer. The result is the loss of bases from the end of such a linear molecule, such as occurs in replication of the telomeric regions of eukaryotic DNA. 

DNA gyrase  A topoisomerase that can introduce negative supercoils. 

DNA ligase:  One of a class of enzymes involved in DNA replication and repair that join two fragments of DNA together by forming a phosphodiester bond. 

DNA polymerase:  One of a class of enzymes of complex structure that catalyze the synthesis of a new strand of DNA complementary to the template strand in a primer-dependent reaction. 

DNA vaccine:  A vaccine comprising a DNA molecule containing the gene for one or more antigenic proteins that can be expressed to elicit immunity when the DNA is injected into a test subject. 

DnaA box  A speci?c base pair sequence, 5' TTATCCACA 3' present four times in the oriC  . Ten to 12 molecules of DnaA protein bind the DnaA boxes to form a complex (primosome) needed for the initia­tion of DNA replication. 

DnaA  Ten to 12 molecules of DnaA bind the DnaA boxes to force the hydrogen bonds of the AT rich region in the oriC  to dissociate, thus opening the double-stranded DNA molecule for access by other initiator proteins (i.e. DnaB, DnaC) of the primosome. 

DnaB  A helicase that is loaded onto the primosome. Its activity is used to further dissociate (unwind) the double strands of the DNA so that replication can be initiated by DnaG primase. 

DnaC  An enzyme that adds DnaB helicase to the primosome. 

DnaG  A DNA-dependent RNA primase that synthesizes the short ribonucleotide primer (511 ribonucleotides in length). This short RNA primer provides a free 3' OH group for DNA poly­merase III to use for adding on deoxyribonucleotides during replication. 

dominant mutation  A mutation that still exhibits a phenotype when it is in the presence of a wild-type copy of the same gene. 

donor cell  In a bacterial genetic cross, the cell that is donating the DNA to the other cell (the recipient cell). For example, in an Hfr cross, the Hfr is in the donor cell and gets transferred into the recipi­ent cell. 

dsRNA:  Double-stranded RNA. 

dsRNA-dependent protein kinase (PKR):  The enzyme induced by interferon action on a target cell that phosphorylates eIF-2 in the presence of dsRNA, thus resulting in inhibition of protein synthesis; part of the interferon-induced antiviral state. 

duplication  A mutation resulting from a stretch of bases being re­peated in the DNA sequence. 

early genes  Phage genes that are expressed ?rst after the injection of phage DNA into a bacterium. 

EBV:  See Epstein-Barr virus  . 

eclipse period:  The time during the replication cycle of a virus when no infectious virus can be isolated, i.e., between virus adsorption and genome penetration and the appearance of newly synthesized infectious virus. 

ED50:  Median effective dose; in a quantal assay, the dilution of a pathogen sufficient to ensure that 50% of standard aliquots of that dilution will contain the infectious agent. 

editing  Some DNA polymerases contain 3' to 5' exonuclease aci­tivity that can be used to monitor if the correct base has been in­serted into the growing DNA chain. If the wrong base is polymerized into the chain, the 3' to 5' exonuclease activity removes it giving DNA polymerase a second chance to get it right. 

effector T cells:  Cells of the immune system that act on antigen-bearing cells as part of the immune response. Two major classes include the helper T cells (TH cells), which interact with antigenpresenting cells in the stimulation of reactive B lymphocytes, and cytotoxic or killer T cells (TC), which act on antigen-bearing cells to destroy them. 

efficiency of plating (EOP)  The efficiency with which a phage forms plaques on different host strains. Restriction and modi?ca­tion enzymes were discovered because the EOP of phage grown on different strains of E. coli  was altered by up to four logs, depending on the last strain the phage was plated on. 

electron microscope:  An instrument for viewing biological specimens at a resolution greater than the wavelength of light, using electrons accelerated to a high energy and, thus, short wavelength. 

electroporation  The process of putting DNA into cells using a large jolt of electricity. Electroporation can be used for bacterial, yeast, and mammalian cells. 

ELISA:  See enzyme-linked immunosorbent assay  . 

encephalitis:  An inflammation of the brain or tissues of the upper CNS. 

encephalopathy:  A noninflammatory disease of the brain. 

endocytosis:  The process of incorporation of viruses or large molecules into a cell by formation of a specific vesicle at the cell surface that engulfs the material and transports it into the cell's interior. 

endonuclease:  A nuclease that initiates hydrolysis of a nucleic acid by attack at an interior phosphodiester bond. 

endoplasmic reticulum:  The complex membrane system in eukaryotic cells that is continuous with the nucleus. It is the site of lipid and membrane synthesis as well as the synthesis of proteins destined to be secreted or remain membrane associated in the cell. 

enhancers: Cis  -acting control sequences in eukaryotic DNA that facilitate transcription from a promoter located a relatively long distance from them. 

enteroviruses:  A group of RNA viruses replicating in the vertebrate gut and causing mild to severe enteric disease. 

env:  The gene encoding the polyprotein translation product that contains the envelope glycoproteins of a retrovirus. 

envelope (membrane):  The lipid bilayer with associated proteins that encompasses a cell or a virus. 

environment suppressors  Suppressor mutations that alter the cell environment and allow the gene product containing the pri­mary mutation to function at some noticeable level. 

enzyme-linked immunosorbent assay (ELISA):  An enzymatic method for measuring an immune reaction by binding an enzyme to the Fc region of an antibody molecule and using the activity of this enzyme to indicate the presence of the antibody to which it is bound. 

epidemiology:  The study of the spread and control of infectious disease in human populations. 

epidermis:  The outer surface of the skin. 

episome:  An extrachromosomal (usually circular) genetic element able to replicate in concert with chromosomes of the cell in which it resides. 

epitopes:  Small regions of (usually) hydrophilic amino acids making up specific antigenic determinants in protein antigens. 

epizoology:  The study of the spread and control of infectious disease in nonhuman populations. 

Epstein-Barr virus (EBV):  A human herpesvirus. 

error frequency:  The rate of introduction of errors during the replication of a DNA or RNA genome. 

etiology:  The cause of a disease or pathologic condition. 

eukaryotic translation initiation factors (CBP1, eIF-2, eIF-3, eIF-4A, eIF-4B, eIF-4C, eIF-4F, eIF-5, eIF-6):  Ribosome-associated proteins that function in the initiation of translation of an open reading frame on eukaryotic mRNA. 

exconjugants  Cell that have undergone conjugation and ex­changed DNA. 

exocytotic (exocytic) vesicles:  Membrane vesicles within a cell that carry acromolecules or viruses for release at the cell surface. 

exons:  The portions of RNA that remain as mature mRNA after the removal of introns by splicing. 

exonuclease  An enzyme that catalyzes the breakage of phospho-diester bonds, affecting the nucleotides at the very end of a DNA molecule. Exonucleases are described as having a 3' to 5' or a 5' to 3' nuclease activity. This describes which end of the DNA strand will have its nucleotides removed ?rst. 

explant:  The removal of intact tissue from an organism followed by maintenance in culture medium. 

expression vectors  Plasmid vectors that are designed to tran­scribe and translate a cloned gene. 

exponential growth  A phase in the growth of bacteria where the number of cells doubles in a set amount of time for a number of gen­erations. Exponential growth requires an excess of nutrients. Once the doubling time is no longer constant, then exponential growth is over. 

extragenic suppressors  Suppressor mutations that occur outside the gene containing the primary mutation. 

extremophile:  An organism that can grow at extreme limits of environmental conditions, such as high temperature (thermophile) or high salt (halophile). 

F  + A strain containing an F factor. The F factor is located extrachro­mosomally and contains only F DNA. 

F factor  The plasmid that is capable of moving DNA from one cell to another. The F factor encodes all of the proteins necessary for transfer of the DNA. 

F pilus  The hair-like structure that is located on the surface of a strain carrying an F factor. The F pilus is used to bring the two cells in close contact so that DNA can be transferred between them. The F pilus is 23 microns in length and F-containing cells have between one to three of them. 

F prime (F')  An F factor that is located extrachromosomally but carries chromosomal DNA in addition to F factor DNA F pilus:  See sex pilus  . 

fab region:  The N-terminal half of an antibody molecule that has both regions of constant and variable sequences. The antigen-combining sites are in the regions of variable sequence. 

Fc region:  The C-terminal half of an antibody molecule that shares the same sequence as all other antibodies of that class. 

feeder layer:  A layer of cultured cells included with explanted tissue to provide optimal conditions for survival of the tissue. 

feline panleukopenia:  A (generally) fatal viral disease of cats, characterized by extreme reduction in circulating leukocytes (white blood cells). 

female cells  Cells that do not contain an F factor, an Hfr, or an F'. 

filamentous phage  Phage whose infectious particles are long ?l­aments of nucleic acid that are coated by protein. 

fimbriae  Hair-like projections that are attached to the outer sur­face of the outer membrane of certain bacteria. Fimbriae are made of protein and help bacterial cells adhere to animal cells. 

flagella  Flagella are long whip-like structures that are embedded in the membranes. At the base of each ?agella in the inner mem­brane is a motor that rotates the ?agella and propels the cell. Flagella can rotate both clockwise and counterclockwise, resulting in the bacteria moving in different directions. 

flu:  See influenza  . 

flush ends  The ends of a linear dsDNA that do not contain any single-stranded bases. Also known as blunt ends. 

focus of infection:  Identification of areas cells that have been infected with virus on a tissue culture plate. The areas are recognized by the cytopathology  produced by the virus in question. Such areas may be observable microscopically or, in some cases, macroscopically. Foci of infection may be used quantitatively for the enumeration of biologically active virus particles. 

forward mutation  Mutations that change the wild-type nu­cleotide sequence. 

frame shift:  A mutation that affects the sequence of the encoded protein by altering the translational reading frame. 

frameshift mutations  The addition or deletion of one or two bases to a nucleotide sequence that results in the original genetic code being read out of frame during translation. 

fulminant infection:  A severe, sudden, often fatal infection characterized by rapid invasive spread of the infectious agent; often refers to a particularly severe form of hepatitis. 

fusion (membrane fusion):  The process in which the membrane envelope of a virus combines with a cell membrane or vesicle in the process of virus entry. 

gag  :  The gene encoding the polyprotein translation product that contains the capsid proteins of a retrovirus; the group-specific antigens of a retrovirus. 

gain of function mutation  A mutation that has acquired or ex­aggerated a speci?c phenotype. Gain of function mutations are fre­quently dominant. 

gel electrophoresis  The technique of separating molecules in a gel matrix in an electric ?eld. Gels are frequently made of agarose or polyacrylamide. 

gene  A region of the DNA that speci?es a protein, a tRNA, or a rRNA. 

gene conversion  In a recombinational cross, both alleles in the cross are usually recovered. In a gene conversion event, one allele is recovered twice and one allele is lost. Gene conversion is caused when the mismatched base pairs in the heteroduplex DNA created during recombination are repaired to the mutant base pairs. 

gene linkage  Tendency of genes located close together on a chro­mosome to be inherited together in a recombinational cross. The higher the frequency of being inherited together, the closer the two genes are. 

gene product  The protein product that is translated from mRNA. If the RNA is not translated (tRNA, rRNA, or stable RNA), then the RNA is the gene product. 

gene regulation  The mechanism(s) used to control the expres­sion of a gene into its corresponding gene product. Gene regulation can occur transcriptionally, translationally, post-transcriptionally, and/or post-translationally. 

generalized transducing phage  A phage that can incorporate chromosomal DNA into its phage particle in place of phage DNA. Many different segments of the chromosome can be incorporated into different phage particles. 

generalized transduction  Movement of any piece of chromoso­mal DNA from one bacterium to another using a bacteriophage to carry the DNA. 

genetic marker:  A genetic characteristic that can be screened or selected for. 

genetic recombination:  The creation of new genotypic arrangements by the breakage and rejoining of chromosomes. 

genome:  The nucleic acid molecule that encodes the genetic information of an organism. 

genotype  The information in the DNA that speci?es the charac­teristics of a cell. g erman measles (rubella):  A usually mild rash and fever caused by an RNA virus, characterized by severe neurological damage to a fetus in the first trimester of gestation glycoproteins:  Proteins that have sugar residues covalently linked to specific amino acids. Such proteins are often secreted from cells or associated with membranes in such a way that the major portion projects through the membrane. 

glycosylation:  The process of adding sugar residues onto membrane and excreted glycoproteins in the Golgi apparatus. 

golgi apparatus:  Vesicles in the eukaryotic cell that receive newly synthesized lipids and proteins from the endoplasmic reticulum and transport them to the correct location in the cell. Specific chemical modifications to the proteins and lipids transported take place in the Golgi apparatus. 

green ?uorescent protein (GFP)  A protein isolated from jelly­?sh that absorbs light at a speci?c wavelength and emits it at a differ­ent wavelength. The emitted light can be seen in living cells using low-light photography. Fusing GFP to a protein of interest allows the movement of the protein of interest to be monitored in vivo. 

growth factors:  Complex macromolecules that function to signal specific cells to replicate. 

GST-fusion protein  GST is glutathione S-transferase, a protein that binds glutathione. GST, when fused to a protein of interest al­lows the fusion protein to be puri?ed in a single step. 

HAART:  Highly active antiretroviral therapy. The use of four or five different antiviral drugs in an attempt to dramatically reduce the viral load of a patient infected with HIV. 

haploid  A cell that contains only a single copy of the chromo­some. Haploidy is the state of a cell that contains only one chromosome. 

HCCs:  See hepatocellular carcinomas  . 

head-full packaging  Inserting (packaging) DNA into phage heads until the head is completely full of DNA and no more DNA will ?t inside. 

helicase  An enzyme that unwinds (i.e. separates) the strands of a DNA molecule by disassociating the hydrogen bonds between the paired bases. This enzymatic activity would be found at a replication fork when the two parental strands need to be separated so that they may be used as templates by the replication machinery. 

helix:  A spiral. 

helper virus:  A virus in a mixed infection (usually in cultured cells) that provides a complementing function so that a co-infecting defective virus can replicate. 

hemagglutination (hemadsorption):  The ability of a virus membrane or a virus-infected cell to stick to red blood cells, caused by the action of one or several specific viral glycoproteins. 

hepatitis virus:  One of a group of viruses (many unrelated) that target the liver. 

hepatocellular carcinomas (HCCs):  Malignant tumors derived from cells of the liver. 

herd immunity:  A qualitative state in a population exposed to an infectious disease where the existence of a sufficient number of recovered and immune individuals restricts the spread of the disease. 

herpes simplex virus (HSV):  One of two closely related neurotropic human viruses containing a DNA genome and characterized by the ability to form latent infections. HSV type 1 (HSV-1) normally infects facial tissue while HSV-2 infects genital tissue. 

herpes zoster virus (HZV):  The causative agent of chicken pox. 

herpesvirus:  One of a large group of related viruses containing large DNA genomes and possessing a similar structure whose infection is characterized by establishment of a latent infection. 

heteroduplex DNA  A segment on a double-stranded DNA mole­cule in which the two DNA strands are of different origin and thus do not have perfectly complementary nucleotide sequences. 

Hfr  A strain containing an F factor that has integrated into the chromosome of a bacterium. 

high copy number plasmids  Plasmids that are present in the cell in greater than approximately 20 to 30 copies per cell. 

histidine tag  At least six histidine residues in a row that can be added to a protein of interest. The histidines bind to metal ions such as nickel or zinc ions. This allows fusion proteins that contain the his-tag to be puri?ed in a single step. 

histology:  Microscopic study of cellular structure and organization. 

HIV:  See human immunodeficiency virus  . 

holoenyzme  A term used to describe an enzyme containing all of its subunits (both catalytic and regulatory). An example would be RNA polymerase, when this enzyme contains both its core catalytic subunits (ßß'a 2 ) and its regulatory subunit (sigma factor). 

homologous recombination  Recombination between two DNA molecules that have identical or nearly identical DNA sequences. 

homology  In the recombination process, homology refers to DNA sequences that are identical or nearly identical. 

host range:  The organism or group of organisms that a virus can infect. 

hotspots  Sites in the DNA where a given event occurs more fre­quently than is predicted for a random event. For example, some transposons insert preferentially at speci?c sites. Some transposons have hotspots, others do not. A hotspot for one transposon will not necessarily be a hotspot for a different transposon. 

housekeeping genes  Those genes whose products are required at some level for the cells to grow. Housekeeping genes are always ex­pressed. 

HSV:  See herpes simplex virus  . 

HTLV:  See human T-cell leukemia virus  . 

human immunodeficiency virus (HIV):  A human retrovirus; the causative agent of AIDS. 

human T-cell leukemia virus (HTLV):  A human retrovirus that is a causative agent of some forms of leukemia. 

humoral immunity:  Immunity due to antibody molecules circulating in the blood and lymphatic system. 

hybrid (nucleic acid hybrid):  A double-stranded nucleic acid molecule formed by Watson-Crick base pairing of a given sequence with its complementary sequence, which can be either RNA or DNA. 

hybridoma cell:  A cell derived by the fusion of an antibody-secreting B cell and a myeloma cell. Hybridomas are clonal and immortal, and secrete the antibody that was secreted by the parental B cell. 

hydrophilic:  Used to describe a molecule or portion thereof that is hydrated in solution due to energetically favorable interactions with water molecules. 

hydrophobic:  Used to describe a molecule or portion thereof whose interaction with water molecules is energetically unfavorable. 

HZV:  See herpes zoster virus  . 

ICAM:  See intercellular adhesion molecule  . 

icosahedron:  A regular solid polygon made up of 12 vertices and 20 faces. 

ID50:  Median infectious dose; in a quantal assay, the dilution at which half the tested aliquots are able to initiate an infection, i.e., contain infectious virus. 

identical sequences  When comparing two or more sequences, the same base or amino acid is found in all sequences at a given place. Identical sequences can be either DNA or protein sequences. 

IFN:  See interferon  . 

illegitimate recombination  Recombination that does not rely on homologous sequences to occur. 

incompatibility  The inability to maintain in the same cell two plasmids that utilize the same origin of replication. An example of this is the inability of closely related F factors and R factors to be maintained in the same cell. 

inducer  A small molecule that can cause an operon to express its genes. An example of an inducer is allolactose. The addition of allo­lactose results in the inactivation of the Lac repressor and the induc­tion of the operon thus allowing the lac  genes to be expressed. 

immunity:  The ability to resist or defend against a pathogen by innate immune responses or acquired immune responses to particular antigens by clonal selection of reactive lymphocytes. 

immunofluorescence:  A method of detecting and localizing an antibody bound to its cognate antigen by use of a fluorescent dye attached to the Fc region of the antibody molecule. This allows microscopic observation using ultraviolet illumination. 

immunologically naive:  Refers to a subject that has never been infected with the infectious agent in question. 

in situ hybridization:  One of a number of methods for localizing a specific nucleic acid sequence or species within a cell, accomplished by fixing the cell, making it permeable, and hybridizing an appropriate probe under conditions where cellular structure is maintained. 

inapparent infection:  An infection not characterized by overt symptoms of disease, but in which there is active replication of the pathogen. 

incubation period:  The time between initial infection and the onset of notable symptoms of a disease. 

inducible genes:  Genes whose expression can be induced under appropriate conditions. 

influenza (flu):  A generally mild infectious disease of the upper respiratory tract caused by a group of viruses with segmented RNA genomes and characterized by rapid genetic change. 

informational suppressors  Suppressors that affect a general cel­lular process such as transcription, translation, or DNA replication to ?x the primary mutation. 

informed consent:  Permission given for an experimental medical or research procedure only after a full disclosure of the possible dangers to the individual and the benefit to medical knowledge. 

initiator tRNA: N  -formylmethionine-tRNA (fMet tRNA), which initiates the first amino acid in translation of bacterial proteins. In eukaryotic cells, the initiator tRNA is Met-tRNA with no formylation. 

inner membrane  The inner-most membrane of E. coli  . It forms the major barrier between the cytoplasm and the outside of the cell. 

inoculation:  Process of introducing a substance into an organism. 

insertion  Mutations that are the result of addition of base pairs to the genome. 

insertion elements  The simplest type of transposon. They are small (~750 to ~2000 base pairs) and encode only transposase, the protein needed to move them. 

int  :  The retrovirus gene encoding the enzymatic function that catalyzes the integration of proviral cDNA into the host chromosome. 

integral membrane protein:  A cell membrane-associated protein within but not extending appreciably beyond the membrane envelope. 

interactive suppressors  Suppressors that compensate for the de­fect in the gene containing the primary mutation by mutating an­other gene whose product interacts with the primary gene product. 

intercalation  Certain chemicals that are large ?at molecules are capable of slipping between the base pairs of the DNA helix. This mode of interacting with DNA is known as intercalation. 

intercellular adhesion molecule (ICAM):  One of a large family of glycoproteins projecting through the cellular envelope that mediate the association between cells and between cells and surfaces; used by some viruses (notably poliovirus) as a receptor for entry. 

interference:  In a mixed virus infection, a phenomenon where some function encoded by the interfering virus reduces the efficiency of replication of the wild-type virus. See defective interfering particles  . 

interferon (IFN):  A group of proteins (cytokines) secreted by virus-infected and certain other cells that act to induce a specific set of cellular antiviral and antitumor responses in other cells. 

interleukin:  A cytokine secreted by an effector cell of the immune system that functions to stimulate other immune cells. 

intermolecular  Events or processes that happen between two dis­tinct molecules. 

internal ribosome entry site (IRES):  A feature in the secondary structure near the 5' end of a picornaviral RNA genome that allows eukaryotic ribosomes to bind and begin translation without binding to a 5' capped end. 

intracellular trafficking proteins:  Intracellular proteins whose main function is to recognize specific molecules and guide them to the appropriate subcellular location. 

intragenic suppressors  Suppressor mutations that occur in the same gene as the primary mutation. 

intramolecular  Events or processes that happen within the same molecule. 

introns:  The portions of a eukaryotic RNA removed by splicing. 

inversion  A mutation that results from a ?ipping of several base pairs in the DNA sequence. 

inverted repeats  DNA sequences that are arranged such that the sequence is inverted and repeated within the same molecule. If the sequence is ATTGCC then it will be repeated CCGTTA in the same molecule. 

in vitro  Reactions that take place in a test-tube and not inside a cell. 

iontophoresis:  Movement of a positively charged compound in an electric field. 

IRES:  See internal ribosomal entry site  . 

isoform:  One of different structural forms of a protein. Isoforms may differ in their activity.

jackpot  A mutation that occurs early in the growth of a culture. Jackpots affect the mutation frequency but not the mutation rate. 

jennerian vaccine:  A live-virus vaccine that elicits an immune response to a related pathogenic virus infecting another species. 

kb:  Abbreviation for kilobases (thousand bases); used in designating the size of DNA and RNA. If the molecules are double stranded, the appropriate unit is kilobase pairs (kbp). 

keratinized tissue:  Tissue marked by a large amount of keratin, such as at the surface of the skin, the cornea, and hair. 

killed-virus vaccine:  A vaccine made up of a virus suspension that has been chemically treated so that it is no longer able to cause a productive infection. 

kinase  An enzyme that adds phosphates to a speci?c molecule or substrate. 

Koch's rules:  A set of criteria that must be met to demonstrate that a specific microorganism is the causative agent of an infectious disease; named for Robert Koch, the nineteenth-century German microbiologist who first formulated them. 

kozak sequence:  The sequence ANNAUGG, which was identified by Marilyn Kozak as being a favored sequence for the initiation of protein translation on eukaryotic mRNA. 

kuru:  A human encephalopathy caused by a prion and associated with ritualized funeral cannibalism. 

lagging strand  During DNA replication, the lagging strand of DNA is synthesized in a discontinuous fashion using short DNA segments ( Okazaki fragments) and relying on many initiating events. 

Last Universal Common Ancestor (LUCA):  In an evolutionary cladogram, the (usually theoretical) common ancestral form or forms that precede the development of further diverging forms. For instance, the ancestral cell or cells that led to the development of both prokaryotes and eukaryotes. 

late genes  Genes that are expressed from phage DNA late in an infection. These usually include the genes that encode capsid and tail proteins. 

latency-associated transcripts (LATs):  Transcripts expressed by many neurotropic herpesviruses during the latent phase of infection. 

latent infection:  Usually refers to a period following acute herpesvirus infection in which the viral genome is present in specific cells, but in which genes encoding the replication genes are not expressed and viral replication does not take place. 

LATs:  See latency-associated transcripts  . 

LD50:  Median lethal dose; in a quantal assay, the dilution at which half the tested aliquots are able to initiate a lethal infection, i.e., contain sufficient infectious virus to kill the test subject. 

leader sequence  A short sequence of mRNA that is used to regu­late speci?c operons. For example in the trp  operon, the leader se­quence contains two trp  codons that are used to monitor tryptophan levels in the cell. 

leading strand  During DNA replication, the leading strand of DNA is synthesized in a continuous fashion, relying on only one ini­tiation event. 

leaky mutations Mutations that cause only a partial loss of func  ­tion of the gene product. 

lentivirus:  A group of retroviruses, such as HIV and visna virus, characterized by a slow, progressive pathogenic course. 

lesions  A term used to describe types of DNA damage. 

lethal selection  A selection where the cells that do not grow are actively killed by the selective agent. Most antibiotics can be used as lethal selection agents. 

leucine zipper:  A protein motif that involves the hydrophobic interaction between two amphipathic helices in which one side of each helix contains an alignment of leucine residues. 

leviviridae:  A family of positive-sense, single-stranded RNA bacteriophages, including MS2. 

library  A population of clones (usually tens of thousands) that each has one random pieces of chromosomal DNA cloned into a vec­tor. Within the population, every piece of the chromosome can be found on at least one vector. The population is known a library. Libraries can be made for any large piece of DNA such as mouse, yeast, bacterial, or human chromosomes. 

linkage  A measure of how close two genes are on the chromosome. 

lipids  Molecules composed of long chains of carbons. Their major property is that they are greasy, hydrophobic molecules. One type of lipid, known as a fatty acid, is the major component of all membranes. 

Lipopolysaccharides (LPS)  Specialized lipids that contain large carbohydrate side chains. They are embedded in the outer lea?et of the outer membrane of certain bacteria. LPS is very densely packed and helps protect bacteria from toxic compounds. 

live-virus vaccine:  A vaccine made up of a virus that has been specifically attenuated, usually by serial passage in a nonhuman host cell. 

localized mutagenesis  A technique used to limit mutagenesis to a speci?c and small region of the chromosome. For example, cells are mutagenized, P1 is grown on the cells, and a speci?c region of the chromosome is selected in a transductional cross. Only the region of DNA that was incorporated into the transducing particle was mutagenized. 

long terminal repeat (LTR):  The 5' and 3' terminal regions of the proviral-integrated DNA of a retrovirus that contains control regions for viral RNA transcription. 

loss of function mutation  A mutation that results in the inabili­ty of a gene product to carry out the same functions as the wild-type gene product. 

low copy number plasmids  Plasmids that are maintained in cells in approximately 1 to 10 copies. Low copy number plasmids re­quire an active partition system to ensure that they are transmitted from mother to daughter cells. 

LTR:  See long terminal repeat  . 

lymph nodes:  Small bodies of lymphatic tissue within the lymphatic system to which antigenic material is transported by antigen-presenting cells. 

lyophilize:  Freeze-dry. 

lysate  After a cell has been broken open, the content of the cell is referred to as a cell lysate. The cell lysate is the starting material for puri?cation of individual cell components. 

lysogeny:  Ability of certain bacteriophages (notably, bacteriophage ?) to integrate its genome into that of the host bacteria and remain associated as a genetic passenger as the bacteria replicate. 

lysogen  A bacterium that contains a stable, silent phage genome. The phage genome is inherited by the daughter cells of the bacterium. 

lysogenization  The process by which a phage DNA is incor­porated stably into the bacterial cell and replicated and inherited by daughter cells. 

lysozyme  An enzyme, usually isolated from egg whites, that is ca­pable of degrading the peptidoglycan cell wall of Gram-negative bacteria. 

lytic  The growth phase of phage that is designed to produce many offspring as quickly as possible. 

mAbs:  See monoclonal antibodies  . 

macrolesions  Mutations that involve more than one base pair. 

macromolecules  Large chemical structures in cells that are com­posed of smaller molecules known as building blocks. For example, DNA is a macromolecule that is composed of a sugarphosphate backbone and the bases A, T, C, and G. Proteins are macromolecules that are composed of amino acids. 

macrophage:  The primary antigen-presenting cell of the lymphatic system. Male cells  Cells that contain an F + , F', or Hfr. 

major histocompatibility antigen:  A complex set of membrane glycoproteins encoded by the major histocompatibility complex (MHC). These antigens are on the surface of an antigenpresenting cell and determine whether or not an immune cell recognizes the presenting cell as self. This is a necessary step in mounting an immune response. 

male-specific phage:  A bacteriophage that uses the sex pilus of the host cell as a receptor. 

malignant tumor:  See cancer  . 

maltose binding protein (MBP)  An E. coli  protein that binds to maltose. The gene encoding MBP can be fused to another gene so that a fusion protein is made. The fusion protein will bind to maltose, allowing puri?cation of the fusion protein in a single step. 

MCSs:  See multiple cloning sites  . 

meningitis:  An infection of the lining of the brain and brain stem. 

merodiploid  A cell that contains two copies of some chromoso­mal DNA but not two complete chromosomes. 

messenger RNA (mRNA)  The RNA that is made by transcribing speci?c parts of the DNA molecule. mRNA encodes protein(s). 

metastasis:  The process by which a cancer (malignant) cell breaks away from the tumor in which it originated, spreads to a new location in the body, and establishes a new tumor. 

methyl-directed mismatch repair  A mechanism that identi?es and corrects mismatched base pairs in a hemimethylated DNA molecule (the newly synthesized daughter strand is not methylated whereas the parental template strand is). The enzymes involved in this repair, MutHLS, identify the mismatched base pair and excise the improperly placed base from the nonmethylated daughter strand. DNA polymerase I ?lls in the gap spanning the area that used to contain the mismatched base pair. 

methyltransferases  DNA repair enzymes with the capability of removing methyl groups from a base, such as guanine. 

microarray  A small solid support that carries DNA oligonu­cleotides representing every gene in a speci?c cell's genome. Mi­croarrays can be used to monitor expression of all of the genes under a given condition. 

microarrays:  An ordered series of small (<200 micron) spots of material (nucleic acid or protein) immobilized on a solid surface (see also microchip) such that their interaction with a target molecule in solution can be observed. Microarrays usually contain thousands of such sample spots. 

microchip:  A small glass surface containing thousands of immobilized samples to be used in a microarray analysis. If the samples are DNA, it may be called a DNA chip or a genome chip. 

microglial cells:  Cells of the CNS that function as immune cells. 

microhomology  Small regions of homology that can be used to make duplications and inversions. 

microlesions  Mutations that involve only one base pair. 

middle genes  The genes that are expressed from the phage genome between the early and late genes. 

mismatched base pair  A pair of nucleotides that do not hydro­gen bond correctly and thus are not complementary. 

missense mutation  A base pair substitution that changes the nu­cleotide sequence encoding a polypeptide and also changes the cor­responding amino acid sequence of the protein. 

mixed infection:  A (viral) infection in which two or more distinct genotypes are able to infect the same cell or individual at the same time. 

MOI:  See multiplicity of infection  . 

mobilizable plasmids  Plasmids that do not contain all of the genes necessary for moving themselves from one cell to another but which can be moved from cell to cell using another plasmid's conju­gation system. 

mobilization  The process of moving a plasmid from one cell to another using plasmid-encoded proteins. 

modi?cation  The process of modifying speci?c sites in the DNA to prevent restriction enzymes from digesting the DNA. If a bacteria contains a restriction enzyme it must contain a modi?cation enzyme to protect its DNA. 

modi?cation enzyme  The enzyme that modi?es the site that a restriction enzyme cuts. Modi?cation enzymes prevent restriction enzymes from digesting the DNA. 

molecular mimicry  The immunological resemblance between two unrelated proteins, for instance, a viral protein and a cellular protein. The resemblance usually involves part of the protein structure. Such mimicry can lead to immunological consequences for the host during a viral infection, such as precipitation of autoimmune phenomena. 

monoclonal antibodies (mAbs):  Antibodies produced by a single clone of identical B cells or hybridoma cells. 

monopartite genome:  A viral genome made up of a single segment. 

monospecific:  An antibody or antiserum preparation that reacts only with the antigen of interest. 

mosaicism:  Refers to organized tissue in which there is more than one distinct genotype intermixed with another. 

Mu  A bacteriophage that uses transposition as an integral part of its lifestyle. 

mucosa:  The epithelial layer lining the digestive, respiratory, or urogenital tract. 

multipartite genome:  A viral genome comprising two or more fragments. 

multiple cloning sites (MCSs):  Sequences of closely spaced restriction enzyme cleavage sites constructed into a cloning vector to make available several possible points of insertion for DNA. 

multiple cloning site cassettes (MCS)  A sequence of DNA usu­ally 50 to 75 base pairs in length that specify the recognition sites for restriction endonucleases. 

multiple sclerosis:  A neurodegenerative, autoimmune disease of the CNS. There is good evidence that at least some forms result from a complication caused by the persistence of an infectious agent (probably a virus) from an acute infection that occurred many years previously. 

multiplicity of infection (MOI):  Average ratio of infectious virus particles to target cells in a given infection. 

muropeptides  Strands of peptidoglycan that are added to a grow­ing cell to build the cell wall. 

mutagens  Chemicals or physical treatments that alter DNA and increase the mutation rate. 

mutation:  An inheritable change in the base sequence of the nucleic acid genome of an organism. 

mutation frequency  A simple but potentially inaccurate way to measure mutagenic potential. The frequency is how many muta­tions occurred in a given culture. 

mutation rate An accurate way to measure mutagenic potential. The mutation rate is the probability that a speci?c gene will be mu  ­tated in one generation. 

Mx:  One of a family of proteins induced by interferon action on a target cell. Many of these proteins have unknown functions, but MxA specifically interferes with the initial infection of cells by influenza and vesicular stomatitis virus. 

myelitis:  Inflammation of the spinal cord. 

myeloma cells:  Immortal tumor cells derived from lymphocytes. Such cells are useful in creating hybridomas to produce monoclonal antibodies, but they do not produce normal antibodies themselves. 

myxoma virus:  A poxvirus that normally infects South American hares. It was introduced (with mixed success) into Australia in an attempt to control the devastating increase in the population of European rabbits introduced by English settlers. 

negative regulation  A scheme for controlling the amount of a gene product that is made. This scheme relies on limiting produc­tion of a gene product by inhibiting its expression. Frequently, a pro­tein (the negative regulator) binds to the promoter of the gene and prevents expression of the gene. 

negative-sense RNA:  An RNA molecule whose sense is opposite that of mRNA. 

negative-sense RNA virus:  A single-stranded RNA virus whose genome is the opposite sense of mRNA. The viral genome must be transcribed into mRNA by a virion-associated enzyme as the first step in virus gene expression. 

negative strand:  See negative sense  . 

neoplasm:  A tumor or localized group of proliferating cells that have become independent of the normal control of cell replication. 

neurotropic virus:  A virus targeting cells of the nervous system. 

neutral mutations  Mutations that have no phenotype. 

nitrosoguanidine  A powerful mutagen that tends to produce mainly transition mutations. 

non-composite transposons  Complex transposons that are not formed from modular units. They do not have IS elements at their ends. 

non-lethal selection  Selections where the cells that do not grow are not actively killed. 

nonpermissive cell:  A cell that will not support the (efficient) replication of a specific virus. 

nonpermissive temperature:  The temperature at which a conditionally lethal, temperaturesensitive mutant will be nonfunctional. 

nonproductive infection:  An infection in which the virus interacts with the host cells so that its infectivity is lost, but no progeny virus are produced. 

non-replicative transposition  A mechanism for transposition where the transposon is cleaved from its original site and ligated into a new site. A minimal amount of DNA synthesis is carried out by mis­match repair enzymes to restore the duplex DNA. Nonsense mutation  A base pair substitution, in which the nu­cleotide sequence of a codon encoding an amino acid has been changed to a codon encoding one of three termination codons (UGA, UAA, UAG). 

nonstructural protein:  In a virus infection, a protein expressed by the virus that does not function or is not  found in the infectious virus particle. See structural protein  . 

nucleic acids  Macromolecules composed of a sugarphosphate backbone and four nucleotide bases. The two types of nucleic acids in living systems are DNA and RNA. DNA contains the bases ade­nine, cytosine, guanine, and thymine. RNA contains the bases ade­nine, cytosine, guanine, and uracil. 

nucleoprotein:  A proteinnucleic acid complex. 

nucleoside 5' triphosphate  The precursor to the nucleotide, it consists of a base, sugar, and three phosphate groups (ATP, GTP, TTP, CTP, UTP). 

nucleotide excision repair  A DNA repair process that uses nucle­ase activity to remove damaged or mismatched nucleotides. 

null  A mutation that results in a nonfunctional gene product. When a transposon inserts into a gene, it disrupts the genes and no functional gene product can be made from that insertion, except in very rare instances. 

Oct1:  The cellular octamer-binding protein that binds to eight nucleotides in double-stranded DNA with the nominal sequence TATGARAT (R is any purine). This protein serves as an adapter for the binding of the HSV a-TIF transcriptional activator to enhancers of immediate-early promoters. 

okazaki fragments:  Short fragments of nascent DNA synthesized using an RNA primer that is an early intermediate of DNA chain growth on the discontinuous (lagging) strand. 

2  ' ,5  ' -oligoadenylate synthetase (2  ' ,5  ' -AS):  The enzyme that polymerizes ATP into 2',5'-oligoadenylate; activated by double-stranded RNA and induced by interferon activation of a target cell. 

oligonucleotide  A short stretch of DNA, usually less than 100 base pairs. Oligonucleotides are short enough to be synthesized in vitro. 

oncogenes (c-onc, v-onc):  Genes encoding the proteins originally identified as the transforming agents of oncogenic viruses, some of which were shown to be normal components of cells; v-onc is the viral version of an oncogene while c-onc is the cellular version of the same gene. 

open translational reading frame (ORF):  A sequence of bases read three at a time between a translation initiator signal (AUG) and a translational termination signal (UAA, UAG, or UGA) in an mRNA or in the DNA encoding that mRNA. Each triplet of bases specifies a specific amino acid in the protein encoded by the ORF. 

operator  The original nomenclature to describe a regulatory re­gion in front of a group of coordinately regulated structural genes that interacts with a speci?c repressor protein to control the tran­scription of these genes. 

operon:  A set of regulated genes in bacteria expressed as a single transcript modulated by the activity of a nearby regulatory gene. 

operon fusions  A fusion of a gene of interest to a reporter gene in which the transcriptional signals come from the gene of interest and the translational signals come from the reporter gene. 

opposite polarity:  The orientation of a strand of nucleic acid whose phosphodiester backbone is in the opposite 5' to 3' direction relative to another strand. 

optical density  The measurement used to monitor the growth of a culture of cells. Light at a speci?c wavelength is passed through the culture. The amount of light that is scattered by the culture is recorded. Light scatter is proportional to the number of particles or cells. 

ORF  . See open translational reading frame  . 

ori:  See origin of replication  . 

origin-binding protein:  A protein involved in initiating rounds of DNA (or RNA) replication by binding to the specific origin sequence. 

origin for DNA replication (ori)  A DNA sequence that must be present in cis for replication of a DNA molecule to take place. The se­quence is usually the binding site for a number of proteins that are required for DNA replication. 

origin of replication (ori):  Specific site in a DNA or RNA genome at which a round of replication is initiated. 

origin of transfer (oriT)  The place in the F factor where transfer of DNA to the recipient strain is initiated. 

outer membrane  The outer membrane is composed of a lipid bi­layer, proteins, and lipopolysaccharides. It is the outer-most barrier of Gram-negative cells and acts to protect them from toxic substances. 

overproduction suppressors  Suppressor mutations that in­crease the expression of either the mutant gene product or the rate-limiting component of the affected pathway. 

oxidative stress response regulon  A group of operons whose genes are coordinately regulated in response to oxidative stress. 

pac  site  A site on the phage DNA where proteins bind and begin inserting the phage DNA into the phage head. 

packaging signal:  A specific sequence of bases within the genome of a virus that functions in the association and insertion of the genome into the procapsid. 

palindromic sequence:  A sequence of nucleotides in a double-stranded molecule that is selfcomplementary and, thus, has the same 5' to 3' sequence on both complementary strands; for example, GATATC. 

palliative treatment:  A treatment of a disease or condition designed to minimize discomfort. 

papillomaviruses:  A large group of viruses with DNA genomes that are classified as papovaviruses and cause warts. 

parameters (of an experiment):  Measurable characteristics of an experiment. 

particle to PFU ratio:  Ratio of total virus particles to infectious particles in a specific virus stock. 

parvovirus:  One of a group of viruses with small, single-stranded DNA genomes. 

passage (serial passage):  In virology, the sequential infection, harvest, and reinfection of a virus into a host or cell culture. 

pathogen:  A disease-causing organism or entity. 

pathogenesis:  The mechanism of causing a disease. 

pathogenic (pathogenicity)  The ability of an organism to cause damage or death to its host. 

PCR:  See polymerase chain reaction  . 

peptidoglycan  The macromolecule that is used to build the rigid structure that surrounds the cell and maintains the cell's shape. Peptidoglycan is composed of several repeating sugar molecules. 

periplasm or periplasmic space  The aqueous compartment be­tween the inner and outer membranes of E. coli  . It contains proteins that transport nutrients into the cell, waste out of the cell, sense the environment, and convey this information to the cytoplasm. The periplasm resembles the outside of the cell in osmolarity and solute concentration. 

permissive temperature  The temperature at which a cold-sensitive or a temperature-sensitive mutation is able to function. 

Peyer's patches (gut-associated lymphatic tissue):  Lymphatic tissues in the gut that allow antigenic proteins and pathogens to interact directly with the immune system. 

Phage or bacteriophage  Viruses that infect bacteria. 

phage particles  Phage infect bacteria and can produce offspring. The offspring produced from an infection are called phage particles. Most of the phage particles are infective and can go on to produce more offspring. Sometimes something will be wrong with a phage particle and it will not produce offspring. While all phage are infec­tive, not all phage particles are infective. 

phage genome  The nucleic acid enclosed in the phage particle that speci?es the production of more phage. 

phenotypes  The physical characteristics of a cell that are speci?ed by that cell's DNA. 

phosphatase  An enzyme that removes phosphates from a specif­ic molecule or substrate. 

phosphodiester bond  A covalent bond between a free 5' phos­phate of one nucleotide and a free 3' hydroxyl group of an adjacent nucleotide, formed by the catalytic activity of ligase. This type of bond links nucleotides together to form the phosphatesugar back­bone of DNA. 

phosphorylation  The addition of phosphates to a molecule or substrate. 

photoreactivation  A DNA repair process that reverses the effects of ultraviolet light through the use of visible light. 

photolyase  The enzyme used in photoreactivation to split apart pyrimidine dimers formed by exposure to ultraviolet light. The en­zyme consists of two subunits and requires visible light to be active. 

picornavirus:  Small viruses with RNA genomes. Poliovirus is an example. 

pilot protein:  A protein associated with the genome of tailed bacteriophages that functions to begin the process of genome injection into the host cell once the cell wall has been breached through the association with the base plate. 

pilus  A ?lamentous (hair-like) structure attached to the surface of the bacterial cell (singular: pilus; plural: pili). 

placebo:  An inert or innocuous substance used as a negative control for testing a drug in clinical trials. 

plaques  Circular clear areas in a lawn of bacteria growing on an agar plate. Plaques contain phage but have few or no bacteria grow­ing in them. 

plaque-forming unit (PFU):  A unit of infectious virus determined by the ability of the virus to form a plaque or area of lysed cells on a lawn of susceptible cells. 

plasmid  A piece of DNA that exists outside the chromosome. Plas­mids must contain an origin of DNA replication ( ori  ) so that they can be replicated and inherited by daughter cells. 

plasmid-like replication:  The replication of an extrachromosomal DNA element, especially a circular molecule such as the genome of SV40 or polyomavirus. 

plasmodesmata:  The cytoplasmic connections between plant cells. 

point mutation  A microlesion involving the addition, deletion, or substitution of one base pair. 

Poisson analysis:  The statistical analysis of the probability of a given event happening after a small number of trials. 

polar mutation  A mutation that affects the expression of down­stream genes that are in the same operon. 

polarity:  For a nucleic acid, the direction in which the sequence is read, i.e., 5' to 3' or vice versa. 

polyA polymerase:  The enzyme that adds the polyA tail at the 3' end of eukaryotic mRNA molecules. 

polyadenylation signals:  A specific sequence (AAUAAA) in a nascent eukaryotic mRNA that specifies the site for endonucleolytic cleavage of the transcript and addition of the polyA tail. 

polycistronic mRNA:  An mRNA molecule that contains multiple open reading frames, usually found in prokaryotic mRNAs. 

polyclonal:  Refers to an antiserum containing a number of different types of antibody molecules directed against various determinants on an antigen. These antibodies are secreted by various B cells, each derived from a distinct precursor by clonal selection. 

polydnavirus:  A DNA virus replicating in the ovaries of certain parasitic wasps that can suppress the immune response of the caterpillar prey to the developing wasp embryo. 

polymerase chain reaction  A technique for amplifying any spe­ci?c segment of DNA in vitro. A piece of DNA is used as the template. Speci?c DNA primers, one for each strand, are used to initiate DNA synthesis and DNA polymerase from a bacterium that grows at 70°C. The DNA is synthesized by cycling the reaction through three tem­peratures. 94°C is used to denature double-stranded DNA, a temper­ature between 40°C and 55°C is used to anneal the primers to the template, and 70°C is used for DNA synthesis. This cycle can be re­peated 20 to 30 times so that a signi?cant quantity of DNA can be synthesized. 

polypeptide or protein  A string of amino acids each linked to­gether by a peptide bond. 

positive-sense RNA:  RNA whose sequence is the sense of mRNA. 

positive-sense RNA virus:  A single-stranded RNA virus whose genome is the same sense as mRNA. 

positive strand:  See positive sense  . 

post-replicative repair (PRR)  A repair mechanism that does not repair damaged DNA, but rather tolerates the lesions so that the damaged DNA can still be replicated. PRR uses homologous recom­bination to ?ll in gaps that form when DNA Pol III hits a lesion in the template and does not ?ll in a nucleotide, but rather skips ahead. PRR is RecA dependent. 

post-ranscriptional modifications:  Cellular enzymatic modifications to the primary structure of a transcript following synthesis from the DNA (or RNA) template; include polyadenylation, capping, and splicing. 

post-transcriptional regulation  Regulation of the gene product at any step after the RNA has been transcribed. 

post-translational regulation  Regulation of the protein's activi­ty after it has been translated. 

pre-initiation complex:  The assembly of transcription factors and RNA polymerase II at 

the TATA box and cap site of a eukaryotic transcript that forms just prior to the initiation of transcription. 

pre-biotic  Referring to the time in the history of the earth before the existence of cellular forms of life, or before the existence of living structures, such as self-replicating molecules. 

Pribnow box:  An AT-rich sequence 10 to 12 base pairs upstream of the start site of prokaryotic transcription that serves as an association site for RNA polymerase; analogous to the TATA box of eukaryotic mRNA. 

primary cells:  Cells isolated directly from the tissue of origin that display all the histological and growth properties of cells in the tissue of origin. 

primary mutation  The mutation that leads to the defect that is re­versed by a suppressor or pseudorevertant. 

primer  A small stretch of linked nucleotides. In the case of DNA synthesis, this small stretch consists of ribonucleotides that DNA polymerase can attach deoxyribonucleotides to. 

primosome  The initiator complex consisting of DnaA, DnaB, and DnaC, whose activities at oriC  (speci?cally at the DnaA boxes of oriC  ) result in the separation of the double-stranded DNA molecule so that DnaG can prime DNA replication. 

prion:  An infectious agent spread by ingestion that does not appear to contain any genetic material. It is thought to be a host cell protein that is folded in such a way as to lead to neurological degeneration and can induce similar conformational changes in identical proteins originally folded in a benign manner in the infected individual. 

probe  A molecule that is tagged in some manner so that it can be easily detected and is used to identify a molecule of interest. For ex­ample, a gene of interest can be tagged and used in a colony blot to detect the plasmids that carry the gene of interest. Probes can be tagged with radioactivity, ?uorescent dyes, or enzymes, to name a few. 

procapsid:  A precursor to a mature viral capsid. 

prodromal period:  A time prior to the onset of full symptoms of a disease when specific physiological responses resulting from it can be discerned by a practiced observer. 

productive infection:  A virus infection of cells in which more infectious virus is produced than was present to initiate the infection. 

professional antigen presenting cells  Cells of the immune system whose function is to 

take up antigens by endocytosis, degrade them into fragments, and display the fragments 

on their surface in complex with class II MHC. Such cells include macrophage and Blymphocytes. 

programmed cell death:  See apoptosis  . 

promoters  A sequence of DNA found adjacent to the coding re­gion of a gene that RNA polymerase containing a sigma factor recog­nizes and binds to, subsequently initiating mRNA transcription. The promoter sequence contains two highly conserved motifs at -10 and -35. 

promoter recognition  The ?rst step in the synthesis of RNA. RNA polymerase recognizes the promoter and binds to it. 

proofreading  DNA polymerases contain enzymatic activities that allow them to recognize a mispaired nucleotide and remove it before moving on and adding more bases. See editing. 

propagate:  Spread by replication. 

prophage  The phage DNA that is maintained in a silent state inside a bacterium. 

prophylactic:  Preventative. 

prot  ( protease  ):  The gene expressed by a number of viruses, especially retroviruses, that catalyzes the proteolytic maturation of polyproteins into specific virus proteins. 

protease  An enzyme that degrades proteins by catalyzing the breakage of a peptide bond between the amino (NH 2 ) group of one amino acid and the carboxyl (COOH) group of another amino acid. 

protein or polypeptide  Macromolecules composed of a chain of amino acids that are used for many different purposes in the cell. The amino acid sequence of a protein is speci?ed by the cell's DNA. Pro­teins are used for building and tearing down molecules, transporting nutrients into the cell, all major processes such as transcription and translation, and generating energy. 

protein fusion  Fusion of a gene of interest to a reporter gene such that all signals needed for transcription and translation come from the gene of interest. The protein that is produced contains a stretch of amino acids from the gene of interest linked to a stretch of amino acids from the reporter gene. 

proteome  All the proteins present in a cell at any given time or under some speci?c condition. 

proteomics  The study of which of the proteins in a cell are, at what time, and under what condition. proteosome  A complex structure within eukaryotic cells that is the site of protein degradation. Proteins destined for turnover at the proteosome have been tagged by the addition of ubiquitin  . 

prototrophy:  The ability of bacteria to grow and replicate with only an energy and carbon source (usually a sugar) and inorganic sources of nitrogen, sulfur, and phosphorus. 

provirus:  The double-stranded cDNA produced by reverse transcriptase as the first step in infection by a retrovirus. 

pseudo- pac  sites  Sites in the chromosomal DNA molecule that are used to package chromosomal DNA into the heads of generalized transducing phage. 

pseudorevertant  A mutation that reverses the phenotype of an­other mutation. pulse:  As applied to a virus infection or other molecular and biochemical applications, a short time interval in which an experimental modification of conditions such as the addition of a radioactive precursor is carried out. 

pulse-chase experiment:  An experimental protocol in which a radioactive precursor is provided to a system for a defined, usually short, amount of time, which is then followed by the addition of a large excess of unlabeled precursor (chase) to dilute the pool of material; used to follow the fate of material synthesized during the pulse period. 

p yrimidine dimer  A type of lesion that forms when the DNA mol­ecule is exposed to ultraviolet light. Examples of dimers include 64 pyrimidine-pyrimidone and cyclobutane dipyrimidine. Pyrimidine dimers can be repaired by photoreactivation, UvrABC endonuclease excision repair, or tolerated by post-replicative repair. 

quantal assay:  A statistical assay of infectious virus based on dilution endpoints. 

quasi-species swarm:  A population of RNA viruses in which, by random errors made during genome replication, a large number of possible variants are represented, for instance, any population of HIV particles. 

quorum-sensing system  A system that detects a change in the number of cells in a given volume and relays this information to the inside of the cell. Once the signal has been internalized, it affects the regulation of genes whose products allow the cell to adapt to the environment. 

R-loop mapping:  A method of visualizing genes using electron microscopy to detect the looping out of DNA from an RNADNA duplex formed by the hybridization of mRNA and the double-stranded DNA gene encoding it. 

R factors  Plasmids that can carry many antibiotic resistance genes as well as the genes needed for conjugation. 

random reassortment:  The random mixing of genomic segments following mixed infection with a virus with a segmented genome; an important mechanism for generating genetic diversity in reoviruses and influenza viruses. 

rate zonal centrifugation:  A technique of subjecting a macromolecule, organelle, or virus particle to a high centrifugal field so that its rate of sedimentation allows it to be separated from other materials that have different sedimentation rates. 

raw sequence  The base sequence of a piece of DNA that simply lists the order of the As, Cs, Gs, and Ts. 

reactivation (recrudescence):  Periodic reappearance of an infectious agent following a period of latency; a hallmark of herpesvirus infections. 

reanneal:  To allow the two complementary strands of a double-stranded nucleic acid that have been separated (denatured) by chemical or thermal denaturation to re-form the original duplex. 

rearrangements  Mutations that result from the scrambling of DNA bases without loss of any base pairs. 

receptor:  A specific macromolecule (usually a protein) on the surface of a cell that interacts with one or several specific proteins present in the exterior medium. In the case of a virus infection, the cellular receptor interacts with a specific viral structural protein or proteins to initiate infection. 

recessive  A mutation that does not exhibit any phenotypes when it is placed in a cell with a wild-type copy of the same gene. 

recipient cells  Cells in a genetic cross that are receiving the DNA from the donor cell. For example, in a transduction, the transducing phage is grown on the donor and used to infect the recipient cells. 

reciprocal  In homologous recombination, DNA is exchanged be­tween two DNA sequences. In a reciprocal cross, the information from one DNA sequence is moved to a second DNA sequence con­comitantly with the DNA sequences from the second molecule being moved to the ?rst DNA sequence. No DNA sequences are lost in a reciprocal cross, they are simply rearranged. 

recombinant:  See genetic recombination  . 

recombinase  The enzyme responsible for the exchange of DNA in a site-speci?c recombination event. 

regulatory protein  A protein whose function is to regulate or control expression of genes. Expression can be controlled negatively through the repression of gene expression or positively through the activation of gene expression. 

regulon A group of operons or a subset of genes in a group of oper  ­ons whose expression is coordinately regulated by a global regulato­ry mechanism. 

reovirus:  Viruses with a segmented, dsRNA genome. 

replica plate:  A method of replicating an organism or virus on a solid or semisolid surface so that the spatial relationship between individual clones is maintained for screening or selection. 

replication fork  The region in a replicating molecule where the replication machinery is adding nucleotides to a growing DNA chain. 

replicative intermediate (RI):  The replicating structure, consisting of a template strand and multiple complementary progeny strands, found in cells infected with a single-stranded RNA virus. There are two forms: RI-1 is the complex synthesizing complementary strands using virion (genomic) or virion-sense RNA as a template; RI-2 contains RNA complementary to genomic RNA as the template and genomic-sense RNA as the product strands. 

replicative transposition  A mechanism for transposition where one strand of the transposon is cleaved and ligated to one strand of the new insertion site. Extensive DNA replication across the entire transposon by DNA replication enzymes restores the duplex DNA. 

replicon  An independently replicating DNA molecule that is sta­bly maintained in a population of cells. Plasmids are referred to as replicons. 

reporter gene  A gene not normally found within a eukaryotic cell whose expression can be used as a measure of gene expression in that cell. Chloramphenicol acetyl transferase (CAT) is a bacterial enzyme that can be used in this way for the study of gene expression in eukaryotes. 

repression  Control of gene expression by preventing a gene from being expressed. 

repressor:  A regulatory protein that blocks the expression of a gene by binding to a specific regulatory sequence in the DNA encoding it. 

reservoir:  The source of an infectious agent. 

resolvase:  An enzyme that can convert DNA recombination intermediates, such as the Holliday structure, to separate molecules by endonucleolytic scission and rejoining. 

response regulator protein  One of two proteins that make up a two-component regulatory system. The response regulator protein is activated, usually by phosphorylation, in response to signals re­ceived from a membrane-bound sensor kinase protein (the second component of this system). A response regulator protein is often a transcriptional activator, whose ability to activate gene expression is controlled by the signals it receives from the corresponding sensor kinase protein. 

restriction  The process by which DNA is cut at a speci?c sequence by an enzyme known as a restriction endonuclease. 

restriction endonucleases  or restriction enzymes  Proteins produced by many different species of bacteria that recognize for­eign DNA sequences and cleave the foreign DNA on both strands at a DNA sequence speci?c for each restriction enzyme. Bacterial restric­tion systems are a primitive immune system in that they protect bac­teria from foreign DNA coming into the cytoplasm. There are three types of restriction enzymes (Type I, II, and III). The three categories are based on the number of proteins that make up the enzyme, the cofactor requirements, if the proteins form a complex- and the na­ture of the sequence that is recognized by the enzyme. Commer­cially useful restriction endonucleases (Type II) recognize and cleave the short, speci?c sequence of DNA. 

restriction enzyme:  A DNA endonuclease that is expressed in bacterial cells in order to degrade foreign DNA. The recognition sites are often palindromic, and various specific restriction endonucleases recognize exact double-stranded DNA sequences of 4 to 8 bases. The ability to cleave large pieces of DNA into specific fragments with such enzymes is an important basic tool in molecular cloning methods. 

restriction site  The site in the DNA that is cleaved by a restriction enzyme. 

retroelements:  Regions of genomic DNA that contain structures such as long terminal repeats and genes for expressing reverse transcriptase and other enzymatic functions seen in retroviruses. Retrotransposons are one type of retroelement. 

reverse transcriptase (Pol):  An enzyme, originally discovered in retroviruses, that uses singlestranded RNA as a template for the synthesis of a cDNA sequence; can also use DNA as a template, and can degrade RNA from a DNARNA hybrid. This latter activity is termed RNase H activity. 

reversion  The process of reversing the phenotype of a mutant bacterium. 

revertant  A mutant cell that regains its wild-type phenotype by a second mutation. Revertants can be either a reversal of the mutant base pair back to the wild-type base pair (true revertant) or a second mutation that compensated for the ?rst mutation (pseudorevertant or suppressor). 

RI-1 (RI-2):  See replicative intermediate  . 

ribonucleoprotein:  A complex of RNA and protein; see nucleoprotein  . 

ribosomal RNA  RNA molecules that are used to build a ribosome. Ribosomes are the large complex of RNA and proteins that translate mRNA into proteins. 

ribosome binding site  or ShineDalgarno sequence  The bases in the mRNA where the ribosome binds to begin translating the mRNA into protein. 

ribozyme:  An enzymatic activity of certain RNA molecules, such as the self-splicing of plant viroid RNA. 

RNA  Ribonucleic acid is a macromolecule that is composed of a sugarphosphate backbone and the four bases: uracil, adenine, thymine, and guanine. 

RNA-dependent transcriptase:  An enzyme synthesizing RNA (usually mRNA) using Watson-Crick base-pairing rules and RNA as a template. 

RNA editing:  An enzymatic change in the sequence of RNA by directly changing one of the bases. The process occurs in the replication of hepatitis delta virus as well as in the biogenesis of plant mitochondrial mRNA. 

RNA polymerase  The enzymes responsible for transcribing DNA into RNA. The holoenzyme consists of the subunits: ßß'a 2 s, with the s factor acting as the speci?city factor, directing RNA polymerase to initiate transcription from speci?c promoter sequences. 

RNase H:  A ribonucleolytic activity of the reverse transcriptase enzyme that degrades the RNA portion of an RNADNA hybrid. 

RNase L:  A ribonucleolytic activity that degrades mRNA when induced by 2',5'-oligoadenylate in the presence of dsRNA; part of the antiviral state induced by interferon. 

R:U  5 :(PB):leader region:  The 5' terminal region of a retrovirus genome, containing a sequence also present on the 3' end (R), a sequence unique to the 5' end (U5), a binding site for the tRNA primer of replication (PB), and an untranslated region between PB and the first open reading frame (leader). 

rolling circle replication  The process by which phage make one long piece of DNA that contains multiple phage genomes. Phage use rolling circle replication to make DNA molecules that they can pack­age into phage heads. 

rubella:  German measles. 

s value:  A numerical measure of the sedimentation rate of a macromolecule, organelle, or virus when the material is subjected to high centrifugal fields under defined conditions. 

same-sense or silent mutation  A base pair substitution that changes the nucleotide sequence encoding a polypeptide but fails to result in a change in the amino acid sequence. 

sarcoma:  A malignant solid tumor of mesodermal cells, such as muscle. 

SARS:  severe acute respiratory syndrome. A disease caused by a coronavirus (SARS-CoV) with significant pathology and mortality. The first SARS cases were identified in China and Singapore in early 2003. 

scaffolding proteins:  Proteins that are involved in the assembly of a viral capsid but are not part of the mature virion. 

SCID mouse:  Severe combined immune-deficient mouse. These animals are useful in experimental models and have been specifically bred so that they lack both T-cell and B-cell immunity. 

scrapie:  A slow, progressive, prion-caused neurological disease of sheep that leads to paralysis and death. 

screen:  To isolate manually or automatically a desired mutant or cell line using observable differences between the desired phenotype and the background. 

segmented genome:  A viral genome existing as two or more separate segments of nucleic acid; for example, the genome of influenza viruses. 

select:  To isolate a desired genotype by incubating it and other genotypes under conditions where only the desired entity can replicate efficiently. 

selectable marker  A gene in a vector that makes a gene product that confers a positive or selectable phenotype on cells that contain the vector. The selectable marker is used to select out of a mixed population cells that contain the vector. 

selection  The environmental conditions used to allow only some cells in a population to grow. 

selective agar  Growth media used to identify speci?c cells and exclude the growth of other cells. For example, selective agar is used to select transductants from a mixture of bacteria and transducing phage particles. 

selfish genes:  Genes whose only function is to replicate themselves, providing no advantage to the entity carrying them; originally defined by Francis Crick to explain the existence of certain self-replicating genetic elements. 

semiconservative replication  During DNA replication, both strands of the DNA molecule serve as templates for the synthesis of new complementary strands. The newly synthesized complementa­ry strand (also called daughter strand) will hydrogen bond with its corresponding template strand (also called parental strand). Thus, each DNA molecule will consist of a parental and a daughter strand. 

senesce:  To age to infirmity; in the case of normal cells in culture, the gradual loss of the ability to divide after multiple serial passages. 

Sensor-kinase protein  One of two proteins that make up a two-component regulatory system. The sensor protein is a membrane-bound kinase that autophosphorylates in response to a speci?c environmental signal. It transfers this phosphoryl group to a re­sponse regulator protein so that the regulator may activate or repress express of the appropriate genes. 

septum  The structure that is built between two dividing cells to wall them off from each other. The septum is mainly composed of membranes and peptidoglycan. 

sequela:  The long-term consequence of a disease. 

serotype:  An organism or microbe with a distinct immunological signature. 

sex pilus:  One of the projecting portions of the bacterial cell wall that can instigate mating with a bacterial cell of another sex; used as a receptor by male-specific bacteriophages. 

Shine-Dalgarno sequence:  A sequence element in prokaryotic mRNA, discovered by John Shine and Lynn Dalgarno, that binds to 16s rRNA and signals the site of initiation of translation at the nearest AUG downstream. 

short patch repair  Repair of a uv light induced dimer by excision of the dimer from the DNA by UvrABC and synthesis across the gap by DNA polymerase I. 

short sequence repeats (SSR)  Repeated DNA sequences that can be used for illegitimate recombination. The SSR can be as short as 38 base pairs. 

shuttle vectors  Vectors that can replicate and be maintained in two different species. One of the species is usually E. coli  , where it is easy to manipulate DNA, and the other can be from bacteria, yeast, or even mammals. 

siblings  Cells in a culture that are derived from each other and all contain the same mutation(s). 

sigma factor  The speci?city determinant of RNA polymerase. 

This subunit directs core RNA polymerase to promoters during ini­tiation of transcription. Signal transduction  The mechanism by which two-component regulatory systems (sensorregulator pairs) function. It involves the transferring of signals, usually in the form of phosphoryl groups so that environmental signals outside the cell can in?uence gene ex­pression inside the cell. 

silent mutation  A mutation that does not confer a phenotype on the cell that carries it. s imilar sequences  When comparing two or more sequences, sim­ilar amino acids are found at a given position. Similarity usually refers to amino acid sequences because some amino acids have simi­lar properties and are interchangeable. For example, valine and ala­nine both have hydrophobic characteristics. 

site-speci?c recombination  Recombination between two spe­ci?c sequences in DNA that requires a unique set of proteins to carry out the cleavage and joining reactions. For example, recombination between attP  in ? and attB  in the chromosome is a site-speci?c re­combination reaction. 

smallpox (variola):  The first human viral disease to be eradicated from the population; caused by a cytoplasmic DNA virus. The disease had two forms caused by different viral serotypes: variola major was the most severe form while variola minor was a form characterized by a lower death rate and generally milder symptoms. 

snRNA:  One of a class of small nuclear RNAs of eukaryotic cells involved in splicing; functions with cognate proteins to form a nuclear organelle termed a small nuclear ribonucleoprotein particle  or snRNP. 

SOS mutagenic repair  A DNA repair regulon that responds to ex­tensive DNA damage. SOS genes are repressed by the transcriptional repressor, LexA. Upon extensive DNA damage, LexA is cleaved, fully activating the expression of the SOS genes whose gene products are needed to repair the damaged DNA. 

southern blotting  A techniques ?rst described by E.M. Southern to detect homologies between two DNA molecules when the se­quence of the two DNA molecules is not known. One of the DNAs is electrophoresed on a gel and transferred to a ?lter. The DNA strands are separated after the DNA has been transferred on the ?lter. The second sequence is tagged and incubated with the ?lter. The tagged DNA will bind to the ?lter only where a homologous DNA sequence has been attached to the ?lter. 

specialized transducing phage  A phage that can carry a speci?c segment of chromosomal DNA as part of its genome. The segment of chromosomal DNA is the same in every phage particle. 

specialized transduction  Movement of a speci?c fragment of chromosomal DNA from one bacterium to another. The fragment of DNA is usually incorporated and replicated as part of bacteriophage DNA. Because of this, the speci?c fragment of chromosomal DNA can be ampli?ed by growing a large number of the phage. 

spliceosomes:  The nuclear organelles made up of snRNA, unspliced pre-mRNA, and specific proteins that are formed as the first step in the splicing reaction of eukaryotic mRNA. 

splicing:  The process of removing interior segments (introns) of eukaryotic pre-mRNA as part of posttranscriptional modification. 

spore  The storage form of some bacteria that are made in the de­velopmental pathway called sporulation. Spores contain a bacterial genome surrounded by a tough protective coating. In some species, spores can survive for decades. 

sporulation  A process that results in the formation of a dormant spore that is resistant to chemicals, heat, and physical agents, and which contains an entire copy of the bacterial chromosome. Only some bacteria are capable of sporulation. 

ssDNA-binding protein:  A protein involved in DNA replication that prevents reannealing of the two denatured strands at the replication point by binding to the single-stranded DNA in a sequence-independent manner. 

SSPE:  See subacute sclerosing panencephalitis  . 

stem loop structures  Found in nucleic acid molecules when single-stranded regions ?nd intramolecular complementary bases to pair with to form regions of double strandedness. Also called hair­pin structures or secondary structures. The base pairing that forms is a result of noncovalent, hydrogen bonding between complementa­ry nucleotides within the same single-stranded molecule. Stem loop structures can be found at the ends of genes to signal where tran­scription stops. 

sticky ends or staggered ends  The linear ends of a dsDNA mole­cule that contain a few single-stranded nucleotides. Restriction en­zymes that cleave the DNA asymmetrically at their recognition site produce sticky ends on the DNA. The sticky end can have either a 5' overhang or a 3' overhang. 

stimulation index:  A quantitative measure of T-cell proliferation in response to stimulation by a recognized antigen. 

stochastic:  Random. 

strong stop:  A step in the transcription of a retroviral genome into cDNA by reverse transcriptase; occurs after synthesis of cDNA from the tRNA primer to the 5' end of the genome and is a result of translocation of the newly synthesized cDNA strand to the other end of the RNA template. 

structural protein:  A viral protein that is normally found specifically associated with the infectious virus particle. 

subacute sclerosing panencephalitis (SSPE):  A rare autoimmune disease caused by the host immune system destroying neural tissue in which noninfectious measles virus is maintained following recovery from the acute phase of infection; usually occurs within 5 years of the initial infection. 

subcutaneous:  Under the skin. 

subgenomic mRNA:  An RNA transcript of an RNA viral genome that contains only part of the sequence present in the entire genome. 

subunit vaccine:  A vaccine preparation that contains only a viral antigenic protein. 

suicide vectors  Phage vectors that can infect a speci?c bacterium but not replicate or produce offspring. 

supercoiling   DNA that is highly twisted and compacted. 

superinfection  The process of a phage infecting a cell that is already lysogenic for the phage. In most cases, the incoming phage cannot replicate. 

suppression:  Change in the phenotype of a mutant by the effect of a mutation in a different gene, negating the effect of the original mutant. 

suppressor  A mutation that reverses the phenotype of another mutation. 

surface exclusion  The process of a cell containing an F prevent­ing mating with another cell that contains an F. Cells that contain an F produce at least two proteins to indicate the presence of the F. TraS inhibits DNA transfer and TraT inhibits mating pair formation. 

symmetry:  Arrangement of repeating subunits in a structure; refers to the arrangement of virus capsomers within the virion. 

symptoms:  Diagnostic features of a disease. 

syncytia:  Cells whose cytoplasm has fused; one type of cytopathology induced by infection with some viruses. 

syndrome:  A set of symptoms characteristic of a specific disease. This term is often used to describe a long-lasting condition. 

T (large T) antigen:  The autoregulatory multifunctional early protein expressed by papovaviruses that functions to initiate rounds of viral DNA replication, inactivate cellular tumor suppressor genes, and activate late transcription. 

t (small t) antigen:  The early protein colinear with the N-terminal portion of T antigen expressed during infection with polyomaviruses. Its function is dispensable for virus replication in cultured cells. 

T lymphocytes:  Immune cells that react with other cells bearing foreign antigens on their surface due to viral infection or genetic alteration. 

TAP: T  ransporter associated with a  ntigen p  rocessing. Transport proteins responsible for moving fragments of antigens into the Golgi prior to presentation in complex with MHC I. 

target DNA  The DNA that the transposon is moving into. 

target immunity  The inability of a transposon to transpose near a copy of itself. Only some transposons have this property. Immuni­ty can extend over at least 175 kilobases for some transposons. 

target tissue (organ):  The tissue or organ of an individual infected with a pathogen that, when infected, is responsible for the appearance of the characteristic symptoms of the disease. 

TATA box:  The AT-rich region (canonical sequence TATAA) about 25 base pairs upstream of the cap site of eukaryotic transcripts that serves as the nucleation point for the assembly of the pre-initiation transcription complex. 

TATGARAT sequence:  The nominal 8-base sequence in double-stranded DNA to which the Oct1 and related proteins bind. In HSV-1 these elements occur in the enhancers for the immediate- early gene promoters, and the binding of Oct1 leads to subsequent association with the a-TIF protein and transcriptional activation. 

tautomer  An alternative form (a structural isomer) of a base in which a spontaneous transient rearrangement of bonds results in the electrons being distributed differently among the atoms. 

TCID  50 :  Median tissue culture infectious dose; in a quantal assay, the dilution at which half the tested aliquots are able to initiate an infection in a test culture of cells, i.e., contain an infectious virus particle or PFU. 

T-DNA  The piece of the Ti plasmid that is moved into the plant cells. The T-DNA enters the plant nucleus where it is integrated into the plant nuclear genome. 

tegument:  The matrix of proteins and other material between the capsid and envelope of a herpesvirus virion. 

telomere:  A structural element at the end of a eukaryotic chromosome that contains multiple repeated DNA sequences and a closed end. 

temperate phage  A phage that is capable of both lytic and lyso­genic growth. 

template  A chain of nucleotides that is used in a polymerization reaction to produce a complementary DNA or RNA strand. 

temperature sensitive  A secondary phenotype of a mutation that causes the mutant gene product to not function at increased temperatures. 

temperature-sensitive (ts) mutation:  A conditional lethal mutation where an altered protein cannot assume its correct folding and structure at a high (nonpermissive) temperature and, thus, cannot function. At a lower (permissive) temperature, the protein can assume its correct structure and function normally. 

termination factor (  r factor):  A protein that is involved in the termination of transcription of one class of prokaryotic mRNA molecules. 

terminal redundancy  The ends of the DNA of certain phage genomes that have overlapping sequence homology. If the sequence of the genes is ABCDE, terminally redundant molecules would have the sequence ABCDEAB. The overlapping sequence homology, or terminal redundancy, allows the ends of the phage DNA to circular­ize by homologous recombination. 

terminator  The sequence at the end of a gene that instructs RNA polymerase to stop transcribing. Terminators have step loop structures. 

therapeutic index:  A numerical measure of the effectiveness of a drug or therapeutic method. It is most simply the ratio of some numerical measure of the effectiveness against the disease or infectious agent to a measure of undesirable side effects. 

theta replication  The bidirectional replication of a circular DNA molecule where initiation of replication starts at a single ori  . Struc­tures that look like the Greek letter theta are produced. 

three-factor crosses  Examining the behavior of three genes in a single genetic cross. 

thymidine kinase (TK):  An enzyme involved in the salvage of pyrimidines within the cell; encoded by a number of herpesviruses and some other large DNA viruses. 

Ti plasmids  Plasmids that are found in Agrobacterium tumifaciens  and are responsible for the formation of crown gall tumors in plants. There are many different versions of the Ti plasmid, each having subtle differences. All are capable of inducing tumors in plants. 

titer:  Quantitative measure of the amount of a medically important substance or entity. 

topoisomerase  An enzyme that eliminates or introduces either underwinding or overwinding of a double-stranded DNA molecule. It catalyzes single (type I) and double (type II) strand breaks chang­ing the relative positions of the DNA strands, and then ligating the breaks. It differs from a nuclease in the way it creates these breaks or reseals them. Topoisomerses use the process of transesteri?cation, rather than hydrolysis, to break or reseal a phosphodiester bond be­tween two nucleotides. 

trans  -acting genetic elements:  Genetic elements, transcripts, or proteins functioning throughout the cell in which it is expressed; the converse of a cis  -acting element, which only functions on elements within the contiguous genome in which it occurs. 

transcription:  The enzymatic synthesis of RNA from either a complementary DNA or RNA template. 

transcription factors:  A group of nuclear proteins of eukaryotes involved with RNA polymerase in the transcription of RNA from a DNA template. Many transcription factors are able to bind to specific sequences within the promoters and other regulatory regions of transcripts. 

transcription fusion or operon fusion  A fusion of the DNA from a promoter that is under study to a reporter gene. The signals needed for transcription come from the promoter under study and the signals needed for translation are provided by the reporter gene. 

transdimer synthesis  A tolerating mechanism used to replicate damaged DNA. The speci?city of the polymerizing DNA polymerase III is relaxed so that any nucleotide can be placed across from a lesion in the template strand. 

transcription-termination/polyadenylation signal (cleavage/polyadenylation signal):  A sequence of bases that occur over 25 to 100 base pairs at the 3' end of the gene encoding a specific transcript that signals the point at which the RNA polymerase disassociates from the template. A major feature of this region is the presence of one or more sequences that are templates for polyadenylation signals in the transcript. 

transducing particles  Bacteriophage particles that contain bac­terial chromosomal DNA instead of (generalized transducing phage) or in addition to (specialized transducing phage) phage DNA. 

transductants  Bacteria that have received a piece of chromoso­mal DNA from a transducing phage. 

transduction  The process of using a bacteriophage to move pieces of chromosomal DNA from one bacterial cell to another. 

transfection:  The process of introduction of nucleic acid into a cell by nonspecific chemical means. 

transfer RNA (tRNA)  A macromolecule that is used in the process of translating a messenger RNA into a protein. tRNA serves as a bridge between the mRNA and the amino acid speci?ed by the tRNA. 

transformants  Bacterial cells that have taken up free DNA. The transformed DNA, if it contains an origin of replication ( ori  ), can exist independently from the chromosome. If it does not have an ori  , yet contains sequences homologous with the chromosome, it can undergo homologous recombination. 

transformasome  A membrane-enclosed compartment that con­tains a 3050 kilobase dsDNA fragment. Transformasomes are used by some bacteria to move free DNA from the environment into the cytoplasm. 

transformation  A process by which bacterial cells acquire free (naked) DNA from their environment. Some bacteria are naturally competent and others can be physically manipulated to take up free DNA. 

transient expression:  The temporary expression of genetic information in a cell after the insertion of genome sequences into that cell by some artificial means (e.g., transfection  ). In this case, the new information is not stably incorporated into the genetic material of the cell, but is expressed temporarily during the lifetime of the cell. 

transition  A base substitution mutation where a purine replaces a purine (an A for a G or vice versa) or a pyrimidine replaces a pyrimi­dine (a C for a T or vice versa). 

transitory (transient or abortive) transformation:  The change of a cell's growth characteristics by the temporary expression of a transforming gene product without a genotypic change in that cell; a temporary state of transformation, such as with a nonintegrating plasmid. 

translation  The synthesis of protein from an mRNA template. 

translational fusion or protein fusion  A fusion of the DNA from a promoter that is under study to a reporter gene. The signals needed for both transcription and translation are provided by the promoter under study. 

translational regulation  Regulation of transcription of an mRNA into a protein. 

translocation  A mutation that results from base pairs being moved to a new site on the chromosome. 

transposable element  Another name for a transposon. 

transposase  A protein encoded by a transposon that is required for movement of the transposon. Transposase actually breaks the DNA backbone at the donor site between the transposon and the adjacent DNA and joins it to the DNA at the new insertion site. 

transposon  A segment of DNA that is capable of moving itself from one piece of DNA to another piece of DNA. 

transversion  A base substitution mutation where a purine re­places a pyrimidine (a G for a T) or a pyrimidine replaces a purine (C for a G). 

tropism:  The tendency of a virus or other pathogen to favor replication in a specific set of tissues or site in the body. 

true revertant  A reversal of the phenotypes of a mutation by changing the mutated base back to the wild-type base. 

tumor antigen (T antigen):  Generally, an antigen found on or in a tumor but not a normal cell; specifically an early multifunctional protein expressed by polyomavirus and SV40. 

tumor suppressor genes:  Cellular genes whose function is to block uncontrolled cell replication. 

two-component signal transduction  A process that consists of at least two proteins, the sensor kinase and the response regulator protein. The sensor kinase senses speci?c changes in the environ­ment and then communicates the change biochemically (usually in the form of a phosphate) to the response regulator. The response regulator alters the expression of the genes whose products respond to the environmental change. 

two-factor crosses  Examining the behavior of two genes in a sin­gle genetic cross. 

  ubiquitin  A small (76 amino acid) protein in eukaryotic cells that is covalently linked to proteins destined for degradation at the proteosome  . 

uptake signal sequence (USS)  A short and speci?c sequence of nucleotides that must be present in free DNA in order for it to be taken up by certain bacteria during natural transformation. 

unidirectional DNA synthesis  DNA synthesis from the origin that proceeds in only one direction at a time. 

VA RNA:  One of two small (about 160 nucleotides) transcripts transcribed early from the adenovirus genome by host RNA polymerase III; responsible for inhibiting the effects of interferon-a and interferon-ß. 

vaccination:  The process of using an inactivated or attenuated pathogen (or portion thereof ) to induce an immune response in an individual prior to his or her exposure to the pathogen. 

variola:  See smallpox  . 

variolation:  The practice of injecting dried exudate from recovering smallpox patients into an immunologically naive individual in order to generate protective immunity. 

vector:  The agent or means by which an infectious agent is spread from one individual to another; also refers to an engineered plasmid or virus designed to transfer genes into an organism. 

vegetative DNA replication:  Exponential viral genome replication. 

very short patch repair  A repair mechanism that recognizes and repairs TG mismatched bases in a speci?c sequence. VSP is a three-step process by which Vsr endonuclease recognizes the mismatch and cleaves the phosphodiester backbone next to the mismatch and removes the mismatch. DNA Pol I adds back the correct base. 

vesicle:  A membrane-bound cellular compartment; also a fluid-filled blister or pouch that contains the infectious agent during an infectious disease. 

viable cell count  A way to measure the number of cells in a cul­ture. The culture is diluted and a known amount of it is plated on solid growth media known as an agar plate. The agar plate is incu­bated until colonies are formed and the number of colonies are counted. Each colony represents one cell in the original culture. 

viremia:  The presence of a virus in the blood and circulatory system. 

virion:  A virus particle that appears structurally complete when viewed in the electron microscope. 

viroid:  A plant pathogen that is the smallest known nucleic acid-based agent of infectious disease. Each is a 250- to 350-base circular RNA molecule that encodes no protein and is not encapsidated. Hepatitis delta virus shares some features of viroids, including a highly structured circular RNA genome. 

virulence:  A measure of the severity of the disease-causing potential of a pathogen. 

virulence factors  Factors that allow pathogenic (disease-causing) bacteria to invade or colonize other, usually eukaryotic, cells. 

virus  A protein-coated nucleic acid molecule that can infect sensi­tive cells, transporting the nucleic acid into the cytoplasm. Once there, the nucleic acid is used to make more of the virus. The proge­ny viruses leave the cell and go on to infect other cells. Viruses that infect bacteria are called bacteriophage. 

virus passage:  Transmission and generation of virus stocks by multiple rounds of virus replication, usually in the laboratory. 

Watson-Crick base-pairing rules:  The basic rules that describe how one strand of a doublestranded nucleic acid can specify the sequence of the complementary strand; named for the two scientists who formally proposed them based on chemical and x-ray crystallographic data of double-stranded DNA. Most simply stated: 1) A pairs with T (or U in RNA), G pairs with C; and 2) the two strands are antiparallel. 

wild type  Refers to a gene or a protein sequence that contains no known mutations and is present in most members of a species. 

XGal  (5-bromo-4-chloro-3-indoyl-ß-D-galactoside)A chemically synthesized derivative of lactose that can be used to indicate when cells are producing active ß-galactosidase. When intact XGal is col­orless and when cleaved by ß-galactosidase, a blue-colored indigo dye is produced. 

x-ray crystallography:  The determination of structure at the atomic level by the analysis of x-rays that are reflected from the planes of a crystal prepared from a macromolecule or virus particle. 

zoonosis:  A virus disease of another animal species that can cause a human disease. 

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