Glossary of Terms

A-F     G-L     M-Q      R-Z

Amino acid The chemical building blocks from which proteins are made. Instructions for the production of amino acids are coded in DNA (or in some viruses, RNA), and the sequence of codes along a length of DNA (or RNA) determines which protein is made.
Amplicon A PCR product that is a copy of the original DNA or RNA target region.
Amplification The process of producing many DNA copies from one original DNA or RNA target region. PCR is a nucleic acid amplification technique.
Anneal The biochemical process of hybridising, or binding, two segments of complementary nucleic acid (RNA or DNA) at an optimal temperature of 40-65�C.
Antimicrobial A drug that inhibits or kills a microorganism (e.g., virus, bacteria or fungus).
Bacterium A one-celled organism, smaller than a human cell, whose genetic material is not confined within a nucleus.
Bases The components of DNA which pair to make the ‘rungs’ of the DNA ladder. There are four types of bases in DNA which bond in complementary pairs: Adenine to Thymine and Cytosine to Guanine. In RNA, the base Uracil replaces Thymine.
Baseline
Measurement		 A baseline viral load measurement is calculated from two tests performed one to two weeks apart.
Buffer A general term used when referring to a solution or reagent that can resist a change in pH upon the addition of either acidic or alkaline material.
CD4 cell count   HIV attaches itself to an antigen, CD4, on the surface of certain lymphocytes (CD4 cells), which have an important role in the body’s immune system. Cells infected with HIV are destroyed by other lymphocytes (see cytotoxicity) so the CD4 cell count is low in untreated PWA's infected with HIV. In PWA's on antiviral therapy the CD4 cell count shows how effective treatment is in destroying the virus.
cDNA Complementary DNA. The product of reverse transcription of RNA.
Combination therapy Treatment with more than one drug simultaneously. In HIV combination therapy is more effective than monotherapy in preventing the development of drug resistance.
Co-receptor A receptor that acts together with another receptor.
Cross-resistance Resistance of a virus to more than one drug of the same group: e.g. resistance to certain protease inhibitors may result in a PWA being unable to benefit from other protease inhibitors.
Cytoplasm Cell contents other than the nucleus.
Cytotoxicity Cell killing. Some lymphocytes are cytotoxic, and their function is to destroy cells infected with a pathogen such as HIV.
Denature The process of separating double stranded DNA into single strands by breaking the hydrogen bonds between bases. This is most often accomplished by heating the DNA solution to temperatures greater than 90�C or by treating it with strong alkali.
DNA Deoxyribonucleic acid. A long molecule that in most organisms carries the genetic information in the form of a code. (See Gene).
DNA Polymerase An enzyme that can synthesize new complementary DNA strands using a DNA template and primer. Several of these enzymes are commercially available, including Taq DNA Polymerase and rTth DNA Polymerase.
Double helix Refers to the structure of DNA which consists of two antiparallel polynucleotide chains held together by hydrogen bonds. They are twisted around each other in a helical formation.
Enzyme A protein that initiates and controls a chemical reaction in the body or in a cell without itself becoming changed during the reaction.
Extension Refers to the elongation of the DNA chain that is being synthesized using the parent DNA strand as the template for synthesis of that daughter strand. This is a natural process that occurs during DNA replication. Extension occurs during the PCR process with DNA Polymerases (Taq or rTth).
Fitness The advantage that a particular strain of an organism has over other strains in the same population. The fittest strain of HIV, e.g. a drug-resistant one in an environment in which drug is present, will replicate faster than less fit strains and become the dominant one.
Gene The basic unit of inheritance, consisting of DNA or (in some viruses such as HIV) RNA. Carries coded instructions for cells to produce proteins essential to life.
Genetic barrier The need for multiple mutations to make a virus resistant to the various drugs used in combination therapy.
Genotype The total genetic make-up of an organism (e.g. virus or human). The HIV genotype can include genes that make the virus resistant to drug treatments.
Half-life The time taken for the amount of drug in the body (or its concentration in plasma) to be reduced by 50% as a result of metabolism and excretion.
HIV Human immunodeficiency virus. In an untreated infected person suppresses the immune system, leading to severe infections and AIDS.
Host An organism (e.g. human) in which another organism (e.g. HIV) lives and reproduces.
Integrase A viral enzyme that integrates the viral genetic code into the host cell’s DNA.
Intracellular Inside the cell.
Intercellular Outside the cell.
Logs Short for logarithm. The number of times ten must be multiplied with itself to equal a number. For example, 100,000 is 5 logs (10 x 10 x 10 x 10 x 10). Logs are used to express viral load results and changes in viral load.
Lymphocyte White blood cells.
Master Mix Chemical solution which contains everything needed for reagent PCR. This solution includes nucleotides, enzyme cofactors, Taq or rTth DNA Polymerase, AmpErase�, buffers and primers.
Membrane A thin pliable covering or lining. The plasma membrane that surrounds an animal cells consists of a double layer of fat (lipid) molecules, which protects the cell contents from the external environment. The viral membrane that surrounds a virus is part of the host plasma membrane. The virus sheds this membrane when it enters a new host cell, and collects a new membrane as it leaves the host to infect other cells.
Monotherapy Treatment with a single drug. (See also Combination therapy).
Mutant A gene, cell or organism in which a mutation has occurred.
Mutation A sudden change in a gene. In HIV some mutations make the virus resistant to one or more antiviral drugs.
Nadir See viralogical nadir.
Nucleotide A sub-unit of DNA or RNA, consisting of a base (purine or pyrimidine), a sugar and a phosphate. The sequence of bases in adjacent nucleotides within a gene determines which protein is encoded by the gene.
Nucleus A discrete part of the cell containing the genes and separated from the surrounding cytoplasm by a membrane.
PCR Polymerase Chain Reaction. The process of target amplification used in the AMPLICOR� Microwell Plate Tests and COBAS AMPLICOR™ Analyser Automated PCR Tests.
Phenotype The outward appearance or behaviour of an organism (e.g. virus or human). The phenotype depends partly on the organism’s genotype and partly on the environment (e.g. nutrients, temperature). Drug resistance in HIV is the phenotypic expression of resistance genes.
Pol gene A gene found in HIV and other retroviruses. It encodes reverse transcriptase and other essential enzymes essential to retroviral replication inside the host cell. Several pol mutations are known to be associated with resistance to different antiviral drugs.
Polymerase An enzyme that is capable of synthesizing new strands of DNA from a single stranded template and free deoxynucleotides under appropriate reaction conditions. During PCR, Roche systems use Taq DNA Polymerase to make DNA amplicon using the DNA strand as a template. rTth DNA Polymerase is used to perform reverse transcription (synthesizing cDNA from RNA) and which then, through PCR, produces DNA amplicon.
Polymerase chain reaction A method that increases the sensitivity of DNA testing (e.g. to detect HIV) by making multiple copies of the DNA sequence in question.
Primers A small synthetic segment of DNA used to initiate or "prime" the new DNA synthesis. In PCR, primers are small segments of DNA of a defined length and sequence that are used to initiate DNA synthesis by DNA Polymerase (Taq or rTth).
Probe A small piece of DNA that is used to isolate or detect complementary target in the reaction mixture.
Protease An enzyme that breaks up proteins.
Protein A molecule consisting of a chain of amino acids. A major source of the building materials for tissues (e.g. muscle, blood), enzymes, receptors and many other body components.
Purines The name that classifies the bases with a 2 ring structure, Adenine and Guanine. Purine bases will only bond with pyrimidine bases.
Pyrimidines The name that classifies the bases with 1 ring structures: Thymine, Cytosine and Uracil. Pyrimidine bases will only bond with purine bases.
Receptor A protein located on or in a cell, which recognises and binds to a specific type of molecule.
Replication Viral reproduction. Viruses do not reproduce sexually; instead they multiply inside the host cell by budding, making perhaps millions of copies of themselves each day in the lymphocytes of an infected person.
Resistance The ability of a virus to resist the effects of antiviral drugs intended to stop its replication.
Retrovirus A virus whose genes are carried as RNA and which converts RNA to DNA to enable it to integrate with the host cell DNA.
Reverse The process of making cDNA (complementary DNA) transcription using an RNA template. An essential step in PCR for retroviruses, eg HIV.
Reverse transcriptase A retrovirus enzyme that synthesises DNA from RNA.
Reverse transcription Synthesis of DNA from RNA. Occurs naturally in retroviruses. In other organisms RNA is synthesised from DNA.
RNA Ribonucleic acid. In most organisms, the molecule that 'translates' the information coded by DNA into proteins. In some viruses, such as HIV, the codes (genes) themselves are carried in RNA.
rTth DNA
Polymerase		 Recombinant thermostable DNA Polymerase originally isolated from the bacterium Thermus thermophilus. rTth has optimal activity at 70-80�C and survives the denaturation steps of PCR. In addition to DNA Polymerase activity, it has efficient reverse transcriptase activity in the presence of manganese.
Selective pressure An environmental force (e.g. for HIV the presence of an antiviral drug) that allows a strain with a certain gene (e.g. a resistance mutation) to survive and multiply at the expense of other strains.
Sensitivity The susceptibility of an organism (e.g. HIV) to inactivation or death by a drug.
Strain A variety of organism defined by the genes it contains. A population of an organism may consist of several different strains.
Taq DNA
Polymerase		 Thermostable DNA Polymerase originally isolated from the bacterium Thermus aquaticus. Taq has optimal activity at 70-80�C and is not degraded during the high heat denaturation steps of PCR.
Target Sequence A nucleotide sequence of DNA or RNA within the organism genome that is known, conserved and characteristic for the intended test.
Template An RNA or DNA strand that provides the pattern for synthesis of a complementary strand. In most organisms DNA is the template for RNA; in HIV and other retroviruses RNA is the template for DNA.
Thermal Cycler A programmable temperature block that rapidly changes the temperatures among those needed to accomplish the Polymerase Chain Reaction (PCR). A typical PCR method may have to cycle at 94�C then 55�C and then 72�C and repeat this cycle for as many as 30 to 40 cycles. This process is automated by the COBAS AMPLICOR™ Analyser.
T lymphocyte A white blood cell that recognises foreign proteins (e.g., bacteria, transplanted tissue) and mobilises other cells to destroy the invading organism or foreign tissue. HIV infects certain T lymphocytes (CD4 lymphocytes), thereby causing immunodeficiency.
Transcription The process of making RNA from DNA.
Viral load The number of copies of viral RNA per ml of plasma. An undetectable (i.e. very low) viral load appears to be associated with a more durable response to treatment and is thus an aim of antiviral therapy.
Virological nadir Point a which an individual’s viral load is at its lowest, as established by sequential viral load testing.
Virus A minute parasitic organism, much smaller than a bacterium, which can replicate only inside the cells of its host. Consists of a core of DNA or RNA surrounded by a protein coat. Viral genes are integrated into the host's genes and instruct the host cell to make viral protein.
Wild type The natural (non-mutant) form of a gene.


References:
Dr Nick Cammack, Roche Discovery, UK.
Dr Graeme Moyle, Chelsea & Westminster Hospital, UK - personal discussion.
Dictionary of Genetic Engineering. SG Oliver and JM Ward. Cambridge University Press.
Encyclopaedia of Molecular Biology. Edited by John Kendrew. Blackwell, 1994
Glossary of molecular genetics. Drug Ther Bull 1996; 34: 15-16
Greene WC. The molecular biology of human immunodeficiency virus type 1 infection. N Engl Med J. 1991; 324:308-17

 
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