- 2D-PAGE
- This gel separates proteins on a two-dimensional sheet of gel, first in one direction based on the isoelectric point, then in the other direction based on the molecular weight of the proteins under investigation.
- ADMET
- absorption, distribution, metabolism, elimination, toxicology
- Allele
- Short for "allelomorph"; different forms of a gene that can exist at a single locus; the alleles might differ in DNA sequence and also affect the functioning of a single product.
- Allele frequency
- Describes the commonness of an allele in a given population, i.e. the percentage of all alleles at a given locus in a population gene pool represented by a particular allele.
- Amino acid
- Building block of proteins; around 20 amino acids are present in proteins: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine.
- Amplicon
- A stretch of DNA that has been specifically amplified by PCR
- Antibody
- An inducible immunoglobulin protein that is produced by the B lymphocytes of the immune system. It recognizes and binds to a specific antigen molecule of a foreign substance introduced into the organism. Upon binding to corresponding antigens, the antibodies set in motion a process to eliminate the antigens.
- Antigen
- Any foreign substance (self - non-self discrimination), such as virus, bacterium, or protein. After introduction into an organism, the antigenic substances elicit an immune response by stimulating the production of specific antibodies.
- Aptamer
- DNA or RNA molecule which has been artificially manipulated to allow binding with other molecules and viruses.
- Array technology
- In a broader context, array technology refers to computer science, engineering and also telecomminications. The technology may involve 2D gel electrophoresis, CCDs, detection technologies, fiber optics, imaging, ink jetting, mass spectrometry, photolithography, phosphorimagers, piezoelectric, semiconductors and spotting robots.
- Arrayer
- Robot for making microarrays. The robot transfers clones from microwell plates to microscope slides.
- Association Study
- Study that compares DNA samples from populations of individuals with and without a specific clinical trait
- BAC
- Stands for Bacterial Artificial Chromosome, a cloning and sequencing vector derived form a bacterial chromosome into which a 100,000 bp fragment or more can be inserted.
- BioChip
- Miniaturised substrates onto which a large number of biomolecules are attached with high density and in a defined microarray.
- Bioinformatics
- Science dealing with the classification, storage, retrieval and analysis of genomic and proteomic information; molecular modelling.
- Biosensor
- Device in which recognition systems of biological chemicals are coupled to microelectronics to allow the low-level detection of substances such as proteins etc. in body fluids or pollutants in water.
- Biotinylation
- DNA probes are labelled with biotin. Biotinylated triphosphates are incorporated into the molecule by enzyme-dependent labelling reactions such as e.g. nick translation or random primed labelling. Afterwards, the probe is hybridised to the target. The location of biotin is visualised by complexing it with a streptavidin molecule that is attached to a colour-generating agent.
- BLAST
- Heuristic homology search algorithm
- Bootstrap
- Recalculation of results with randomly rearranged datasets to exclude the possibility of artefacts in data clustering.
- cDNA
- Complementary DNA; DNA which is synthesised from a messenger RNA template which is complementary to the coding strand of genomic DNA.
- cDNA arrays
- Developed at Stanford University; the microarrays are glass slides on which cDNA has been deposited by high-speed robotic printing and suited for expression analysis of up to 10,000 cDNA clones per array from EST sequencing projects. The microarray measurements are carried out as differential hybridisations, namely mRNA from two different sources is labelled with two different fluorescent dyes, then passed over the array at the same time. The fluorescence signal from each mRNA population is evaluated independently to calculate the treated or control expression ratio.
- Cell array
- High-throughput characterisation of gene function using cell arrays.
High-density ordered array involving either living cells (microwells) or printed microarrays (slides). The latter involve full-length open reading frames of the genes in expression vectors that are printed at high density on a slide along with a transfection reagent. The slide is then placed in a cell culture plate and the microarray of DNA constructs is covered with adherent cells. Cells grow on top of the DNA spots, are transfected, and drive the expression of specific proteins.
- Chromosome
- Threadlike component in the cell which contains DNA and proteins. Humans have 23 pairs of chromosomes --> 46 chromosomes
- Clone
- A group of genes, cells or organisms that are derived from a common ancestor. Genetic material is not combined and the members of the clone therefore all genetically identical to the parent.
- Codon
- Sequence of three nucleotide bases that specifies a certain amino acid or a stop or start codon.
- Combinatorial chemistry
- A robotic system methodically synthesising large numbers of compounds, each having a composition slightly different from the previous one.
- DNA
- Deoxyribonucleic acid consists of a polysugar-phosphate backbone from which the purines and pyrimidines project. The backbone is formed by bonds between the phosphate molecule and carbon 3 and 5 of the adjacent deoxyribose molecules. The nitrogenous base extends from carbon 1 of each sugar. It forms a double helix hold together by hydrogen bonds between specific pairs of bases (Watson-Crick model) and each strand in the double helix is complementary to its partner with regard to its base sequence.
See also: DNA array, DNA chip, DNA microarray
- DNA array
- DNA arrays consist of large numbers of DNA molecules spotted in a systematic order on a solid substrate. Depending on the spotting technique used, the number of spots can range from hundreds to thousands.
See also: DNA, DNA chip, DNA microarray
- DNA chip
- These chips are also referred to as DNA arrays, or microarrays. Approx. 10,000 cDNAs can be spotted onto a microscope slide and subsequently be hybridised with a double-labelled probe.
See also: DNA, DNA array, DNA microarray
- DNA microarray
- This kind of microarray consists of a set of regular arranged spots of DNA recognition elements (e.g. oligos) positioned on a rigid support. The diameters of the spots range between 20 and 200 micrometers. Usually 50 to 80,000 spots cover an area of approximately 1 square centimetre.
The technology is based on the selective recognition of gene sequences by hybridisation, namely the base-pairing of the 4 nucleotides. Upon hybridisation with e.g. a fluorescently-labelled sample (oligo, cDNA, mRNA, PCR product) the signals can be analysed.
See also: DNA, DNA array, DNA chip
- Drug lead
- Compound that has shown evidence of pharmacological activity on a drug target serving as a leading structure.
- Drug target
- A gene or protein that plays a role in a disease process and is the intended site of drug activity.
- EST
- Expressed sequence tags: Short (300-500 bp) single-pass sequences from mRNA (cDNA). They represent a snapshot of genes that are expressed at a given developmental stage and/or in a given tissue.
- Gene
- Hereditary unit that occupies a specific locus within the genome or chromosome and which can have one or more specific effects on the phenotype of the organism. A gene can be present in various allelic forms.
- Gene expression
- The degree to which a gene is active in a certain tissue of the body, measured by the amount of mRNA in the tissue. General: transcription and translation of a gene into a protein recombinant.
- Gene signature
- The genes that are consistently expressed in samples of a given tissue type.
- Gene targeting
- Technique for specifically inserting genetic loci modified in desired ways into e.g. laboratory mice.
- Genetic engineering
- Technology used to alter the genetic material of living cells in a way that the cells are capable of producing new substances or performing new functions.
- Genetic map
- Map of the positions of gene loci on a chromosome
- Genetic mapping
- The position of a gene on the chromosome is determined by means of recombination frequencies, and other solely genetic means.
- Genetic marker
- A piece of DNA or a gene whose properties (and sometimes also their position on the chromosomes) are known and can be used to identify particular cells or organisms; they might also be used as a reference point in a genetic mapping experiment.
- Genome
- The term describes the total genetic information of a specific unit of inheritance such as e.g., the nucleus or the mitochondria.
- Genomic microarray
- Technology that allows the assessment of multiple gene targets for the identification of gene amplifications or deletions in a different samples.
- Genomics
- The systematic and comprehensive analysis of the structure and function of the genome with the aim to identify and understand the role of genes.
- Genotype
- Genetic constitution of an organism.
- GMO
- Genetically modified organism
- HLA
- Human leukocyte antigen; the HLA system is very complex and characterised by extreme polymorphism. There are many websites dealing with HLA or Mhc (Major histocompatiblity complex), among them http://syfpeithi.de where you will also find references to further interesting links to HLA.
- HTS
- High throughput screening
- Hybridisation
- Binding of two single stranded nucleic acid strands by complementary base pairing.
- in vitro
- Experiment performed in a test tube/laboratory apparatus
- in vivo
- in a living organism
- Lab-on-the-chip
- Microfabricated system for performing biochemical assays such as e.g. capillary electrophoresis, probe preparation, PCR reactions (microfluidics-based chips)
- LCM
- Laser Capture Microdissection conceived and first developed as a prototype research tool at the National Institute of Child Health and Human Development (NICHD) and the National Cancer Institute (NCI) of the National Institutes of Health (NIH). LCM was developed into a commercial laboratory instrument by Arcturus Engineering, Inc. and the NIH.
- Linkage
- Tendency for some parental alleles to be inherited together (opp. Mendel's law).
- Linkage disequilibrium
- Describes a condition in which certain alleles at two linked loci are nonrandomly associated with each other. This might be either because of very close physical proximity or because the combination is under some kind of selective pressure.
- LNA
- Locked nucleic acid; a novel class of nucleic acid analogues. LNA monomers are bicyclic compounds that are structurally similar to RNA nucleosides; the term LNA refers to the observation that the furanose ring conformation is restricted in LNA by a methylene linker that connects the 2'O position to the 4'-C position. Therefore, all nucleic acids that contain one or more LNA modifications are called LNA. Duplexes formed with either DNA or RNA have a very high thermal stability (approximately 3°C to 8°C per modified base higher).
- Locus
- Position on a chromosome that is occupied by a particular gene
- MAGE
- MAGE antigens are a family of closely related proteins, which are typical of human melanoma cells and are used for cancer immunotherapy treatment. They can be used for the simultaneous identification of the presence or absence of MAGE's antigens.
- MAML
- Microarray Markup Language - adopted from "XML, Extensible Markup Language" - that provides a framework for describing experiments done on all kinds of DNA arrays. For more information please refer to http://www.mged.org, which is the homepage of the Microarray Gene Expression Data Society. The MGED is an international organisation for facilitating the sharing of microarray data. Standards for microarray data annotation and representation are to be established.
- Manual spotting system
- Microarrays can also be produced by manually spotting biomolecules onto glass slides. The total number of samples is however smaller than that spotted by an automated system. In addition, the pitch between adjacent features is greater than in an automated array (usual pitch 0.5 - 1.0 mm)
- Map distance
- The distance between genes expressed as map units or centiMorgans (cM).
- Marker
- Marker can refer to
a gene with a known location on a chromosome and a clear-cut phenotype, that can be used as a point of reference when mapping a new mutant or antigenic markers that serve to distinguish cell types
- Mass spectrometry
- Technique uesed to measure and analyse a substance in terms of the ratios of mass to charge of its components.
- MEMS
- MicroElectroMechanical Systems. Today, it usually relates to a microsystem that is integrated in a chip. Originally, MEMS technology was mainly used in the semiconductor industry.
- Methylation
- Methylation of cytosine (usually in CG stretches) --> sign for transcription factors to activate the gene and thus produce a protein. It is generally understood that genes that are available for transcription are sometimes less heavily methylated than the same genes in cells in which they are never expressed. It also refers to the addition of a methyl group to a chemical compound or macromolecule.
- microarray
- Arrangement of miniaturised test sites on a small surface; spot sizes are usually less than 250µm. Many tests can be performed simulatenously or in parallel.
- Microfluidics
- Handling of volumes of liquids as small as 0.1 nanoliter.
- Microfluidics chips
- The chips contain very tiny channels in which the movement of fluids can be controlled. They allow the intergration and miniaturisation of many laboratory processes. Due to the tiny size, only low quantities of chemicals and test materials are required.
- Microtransponder
- Cube-shaped (~100µm), miniature radio-frequency transmitters out of silicon. The transponder has a memory and emits characteristic radiofrequencies upon activation (in this case by a laser).
- Molecular imprinting
- Process by which functinal monomers can self-assemble around a template molecule. Afterwards they are cross-linked into place. The template molecule can be removed under defined conditions. A cavity is thus left behind which is complementary in shape and functionality. Molecules can be bound which are identical to the template.
- mRNA
- messenger RNA; RNA molecule that functions during translation to specify the sequence of amino acids in a nascent polypeptide. In eukaryotes, mRNA is formed in the nucleus from premessenger RNA molecules.
- Multifactorial disease
- Polygenic disease, i.e. disease determined by the action of several independent genes.
- Multiplex
- This word is mainly used as 'multiplexing', thus referring to a method by which many parameters are simultaneously tested and processed.
- Mutation
- Change in the structure of DNA, thus leading to a change in the characterstics of an organism or indivudal cell as a result of altered protein or RNA content specified by the mutated DNA. One can differentiate for example between silent mutations, point mutations, back mutations, or somatic mutations.
- Nick translation
- Refers to the in vitro procedure used to radioactively label DNA uniformly to a high specific activity. Nicks are introduced into the unlabelled DNA by an endonuclease, thus creating 3' hydroxyl termini. E. coli DNA polymerase then adds radioactive residues to the 3' hydroxy terminus of the nick; nucleotides are removed from the 5' side. This procedure leads to an identical DNA molecule with the nick located further along the duplex.
- Nucleotide
- Monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose, and a phosphoric acid group. The nucleotides of DNA are deoxyadenylic acid, thymidylic acid, deoxyguanilic acid, and deoxycytidylic acid. Those of RNA are adenylic acid, uridylic acid, guanylic acid and cytidylic acid.
- Oligonucleotide chips
- Oligonucleotide chips consist of small glass plates with thousands of short 20-mer oligonucleotide probes attached to their surface. The oligos are synthesized directly onto the surface using a combination of semiconductor-based photolithography and light-directed chemical synthesis. Very large numbers can be probed; at present chips contain over 65,000 probes.
- Operon
- A unit that consists of one of more cistrons which function coordinateley under the control of an operator gene.
- ORF
- Open Reading Frame; a reading frame refers to a nucleotide sequence that starts with an initiation codon, partitions the subsequent nucleotides into amino-acid-encoding triplets and ends with a termination codon. The interval between the start and stop codons is referred to as the open reading frame.
- PCR
- Polymerase chain reaction. This is an in vitro technique for the selective amplification of defined nucleic acid regions in a DNA mixture by copying the complementary strands of a target DNA molecule simultaneously for a series of cycles until the desired amount is obtained.
The principle:
Primers are synthesised which have nucleotide sequences complementary to the DNA that flanks the target region. Then, the DNA is heated to separate the complementary DNA strands and cooled to allow the primers to bind to the flanking sequences. Heat-stable DNA (Taq) is added and the reaction allowed to proceed for a series of replication cyles. Twenty cycles will render an approximately millionfold amplification of the soruce DNA.
- Penetrance
- Defined as the ratio of individuals who have a disease-causing allele and manifest the disease versus those who have this disease causing allele but do not manifest the associated disease. Diseases are usually associated with either high penetrance or low penetrance alleles.
- Peptide
- Two or more amino acids are joined by a so-called peptide-bond.
- Phenotype
- Observable properties of an organism produced by the genotype in conjunction with the environment.
- Photolithography
- Selective masking generates light patterns that direct chemical transformations to specific areas of photosensitive surfaces. Photolithography usually requires expensive equipment and particular knowledge; the technology is protected by patents
- Physical map
- Map of the linear order of genes on a chromosome with units that indicate their distances determined by methods other than genetic recombination. These include e.g. nucleotide sequencing, electon micrographs of heteroduplex DNAs, etc.)
- Piezoelectric
- Becoming electrically polarised when subject to the mechanical stress; quartz for example produces an electric charge when squeezed.
- Plasmid
- Small circular DNA replicating independently of the chromosome in bacteria and unicellular eukaryotes (e.g. yeasts). Plasmids usually carry genes for e.g. antibiotic resistance, colicin production and are widely used in genetic engineering as vectors. Vectors are vehicles into which foreign genes are inserted for subsequent cloning or expression in bacterial cells.
- Point mutation
- In molecular genetics, a point mutation is caused by the substitution of one nucleotide for another. In classical genetics, point mutation refers to any mutation that is not associated with a cytologically detectable chromosomal aberration or one that has no effect on crossing over.
- Polygeny
- Most diseases are polygenic, i.e. caused by the interplay of several genes.
- Polymorphism
- In classical population genetics, polymorphism refers to the coexistance of different alleles in a population/species at significant frequencies (the most frequent allele should be less than 95%%). However, the term polymorphism is frequently used simply to indicate that genetic variation occurs within a certain part of the genome. In extreme, polymorphism can refer to just one nucleotide, e.g., SNP.
- Primer walking
- Sequencing method in which the sequence data of the sequenced section are exploited to synthesize the following primer. Starting from the first priming site this continues until the DNA template has been sequenced completely.
- Principal component analysis
- Visual and numerical analysis of collinearity among variables. Allows for the mapping of high-dimensional data to a lower dimension for visualisation, analysis and modelling.
- Probe
- In general, probe refers to any biochemical/nucleic acid/oligo etc. labelled with radioactive isotopes or tagged in other ways for identification. A probe is used to identify or isolate a gene, its product, or a protein. In microarrays, the probe is immobilised in regular arrangement on the substrate.
- Protein arrays
- Arrays consisting of proteins themselves or of probes used for capturing proteins.
- Pseudogene
- Stretch of DNA related in sequence to a funtional gene; it is however inactive as a result of the changes it has accumulated during evolution.
- Radioimmunoassay
- = RIA: very sensitive diagnostic test using radioactively labeled specific antibodies or antigens to detect trace amounts of substances.
- Reader
- Synonym for microarray scanner; after fluorescent labelling and hybridisation, the reader scans the microarrays into a computer for subsequent analysis.
- Regulatory sequence
- A DNA sequence involved in regulating the expression of structural genes in the common operon. These stretches of DNA might be attenuators, operators, or promoters.
- RT-PCR
- Reverse Transcriptase Polymerase Chain Reaction: The mRNA is first reverse-transcribed into cDNA, and the cDNA is then amplified to measurable levels using PCR. PCR primers for all genes of interest are required.
- SAGE
- Technique for measuring mRNA levels that is different from that of RT-PCR, oligonucleotide chips and cDNA microarrays. Double stranded cDNA is created from the mRNA and a "sequence tag" (10 bp) is cut from a specific location in each cDNA. Subsequently, the sequence tags are concatenated into a long double stranded DNA which is afterwards amplified and sequenced. The advantages are that it is not necessary to know the mRNA sequence beforehand (also unknown genes can therefore be detected) and it relies on sequencing equipment that is usually present in most laboratories. The method does, however, require a large amount of sequencing.
- Scanner
- Also referred to as "reader"; after fluorescent labelling and hybridisation, the scanner or reader scans the microarrays into a computer for subsequent analysis.
- SELDI
- Surface-Enhanced Laser Desorption/Ionisation invented by T. William Hutchens
- Sequencing
- Determination of a DNA sequence by either of two methods: The chemical cleavage method, developed by Maxam and Gilbert, is today hardly used, or the controlled interruption of enzymatic replication (Sanger et al.). It can also be determined by various automated methods developed from these two methods.
- Shotgun library
- Library of transformed plasmid clones, containing size-selected DNA inserts such as e.g. plasmids, cosmids, PCR fragments or whole genomes. The original DNA is nonspecifically fragmented by shering and then subcloned in a suitable vector.
- SNP
- Single nucleotide polymorphism; a site on the DNA strand at which the base sequence differs among individuals (Pronounce "snip").
See also: SNP chips, SNPs
- SNP chips
- Microarrays that are used for the genome wide genotyping of SNPs (single nucleotide polymorphisms)
See also: SNP
- SNPs
-
See also: SNP
- Substrate
- Substance on which an enzyme acts in biochemical reactions; or, in hybridisation arrays, the particular material onto which the biomolecules are deposited. These surfaces include glass, nylon, silicon or ceramic.
- Target
- Free nucleic acid sample/protein/etc. whose identity and abundance is to be detected.
- Telomere
- Refers to the end of each chromosome arm distal to the centromere. It consists of special DNA elements (repeats) that are replicated by a special mechanism to help avoid shortening the chromosome ends. The enzyme responsible for this feature is called "telomerase".
- Trait
- The same as "character"; refers to any detectable phenotypic property of an organism.
- Vector
- A vector is a self-replicating DNA molecule (DNA vector, lambda cloning vector, plasmid cloning vector) that transfers a DNA segment between host cells; sometimes it is also called a "vehicle". It might also be an organism that transfers a parasite from one host to another.
- YAC
- Microarrays that are used for the genome wide genotyping of SNPs (single nucleotide polymorphisms)
