Technologies map    Finding guide to terms in these glossaries   Site Map   
Related glossaries include Applications Drug Discovery & Development,  
Technologies Assays & screening, Gene Amplification & PCR,  Molecular Imaging, Mass spectrometry, Microarrays & protein chips, Nanoscience & Miniaturization,  Sequencing,  Ultrasensitivity

actuator: A  peripheral [output] device which translates electrical signals into mechanical actions; e.g., a stepper motor which acts on an electrical signal received from a computer instructing it to turn its shaft a certain number of degrees or a certain number of rotations. See: servomechanism. FDA, US Glossary of Computerized System and Software Development Terminology 1998 http://www.fda.gov/ora/inspect_ref/igs/gloss.html  

An actuator, the reverse of a sensor, is a device that converts an electrical signal to an action. Actuators are further divided into three categories: simple actuators that move valves or beams using one simple physical law, micromotors, more complex in the design and the possibilities, and microrobots which are the latest release in microtechnology.  [National Textile Center, "MEMS: An Overview" 1998 http://www2.ncsu.edu/unity/lockers/project/ntcprojects/projects/F98-S12/memsovervie...

Narrower term: biosensor Broader term: sensors.

aliquot: Drug discovery & development glossary

amplification: See signal amplification, target amplification (and gene amplification).

assays: Assays & screening glossary

attomole: Ultrasensitivity glossary 

avidin: Protein found in raw egg white which binds to biotin (etymology is from its avidity to biotin).

bioluminescence: Luminescence produced by living systems. [IUPAC Photo]

biosensor: A device that uses specific biochemical reactions mediated by isolated enzymes, immunosystems, tissues, organelles or whole cells to detect chemical compounds, usually by electrical, thermal or optical signals. [IUPAC Bioinorganic] 

Narrower terms: electrochemical biosensor, spore based biosensor  Related term: sensor web

biotin: A vitamin of the B complex. It is a co-enzyme for various enzymes that catalyse the incorporation of carbon dioxide into various compounds. It is essential for the metabolism of fats. Biotin is attached to pyruvate carboxylase by a long, flexible chain like that of lipoamide in the pyruvate dehydrogenase complex. Adequate amounts are normally produced by the intestinal bacteria in animals. a.k.a. vitamin H (in USA). [FAO Glossary]

Narrower terms: biotin labelling, biotinylated- DNA, biotinylation Related term: streptavidin

biotin labelling  1. The attachment of biotin to another molecule. 2. The incorporation of a biotin- containing nucleotide into a DNA molecule.  [FAO Glossary]

biotinylated-DNA  A DNA molecule labelled with biotin by incorporation of biotinylated -dUTP into a DNA molecule. It is used as a non- radioactive probe in hybridization experiments, such as Southern transfer. The detection of the labelled DNA is achieved by complexing it with streptavidin (an antibiotic with a high affinity for biotin) to which is attached a colour- generating agent such as horseradish peroxidase that gives a fluorescent green colour upon reaction with various organic reagents. [FAO Glossary]

biotinylation: To label a probe with biotin.

blinking: See under green fluorescent protein

cantilevers: Nanoscience & miniaturization glossary

Catalyzed Reporter Deposition CARD: See Tyramide Signal Amplification TSA.

cell assays: Assays & screening glossary

chemiexcitation: Generation, by a chemical reaction, of electronically excited molecular entities from reactants in their ground electronic states. [IUPAC Photo]

chemiluminescence:  Emission of light as a result of a chemical reaction without an apparent change in temperature. MeSH, 1993

Luminescence arising from chemiexcitation. [IUPAC Photo]

chromophore, chromophore assisted inactivation: Pharmaceutical biology glossary

colorimetry: The methods used to measure color and to define the results of the measurements. [Photonics]

competitive hybridization: Gene amplification & PCR glossary

computational sensing: A rapidly emerging field that seamlessly integrates optics, electronics and signal processing. Computational sensors use multiplex methodologies to facilitate the sampling of signals, such as an optical spectrum or image, with maximum efficiency and fidelity. Centice, Technology computational sensors http://centice.com/technology/computational_sensors.htm 

dendrimers: Nanoscience & Miniaturization glossary

detection: The Oxford English Dictionary points out that detecting involves finding what is otherwise apt to elude notice, particularly that which is "artfully concealed".

Narrower terms: gated detection;  Ultrasensitivity: single molecule detection

detector technologies: Include direct detection, electrochemical, fluorescence, fluorescence polarization, colorimetry, mass spectrometry, luminescence, optical, primer extension and minisequencing. Michael Phillips, CHI Nucleic Acids Technologies conference, June 7-9, 2000

Detector instrumentation includes CCD cameras and lasers.

diagnostics: Molecular Medicine glossary

differential labeling: When comparing the proteomes of two cell states (e.g. diseased vs. normal), gel- to- gel variability in spot position and protein yield often places the results of such experiments in question. Differential labeling  enables one to analyze both states on a single gel, thus enabling direct comparison of protein levels. In this method, cells are treated with normal media, or media enriched in ¹⁵N. Corresponding proteins from each state will migrate to the same location on the gel, but analysis by mass spectrometry will distinguish the metabolically labeled peptides and thus quantify the two sets of proteins separately. This can have significant impact on reproducibility when comparing experiments. 

An analogous differential labeling technique uses Isotope Coded Affinity Tags (ICATs) that chemically modify peptide cysteines with a normal- or deuterium- labeled biotin reagent. Samples are pooled, purified by avidin chromatography and quantified as described above, but there is no need for metabolic labeling. Both differential labeling techniques permit combined samples to be pre- fractionated prior to separation, without losing information on their relative quantities. [CHI Summit Proteomics report]

direct detection: Labeling of the probe for Northern or Southern blotting is a very simple one- step process. The well- known dyes IRDye 700 and IRDye 800 contain a carbodiimide (CDI) active group that covalently binds to any single or double stranded nucleic acid. No enzymes are required: just incubate the CDI-IRDyes for 5 minutes at 70 °C and the labeling process is complete. The labeled nucleic acid can be used as probe to detect DNA or RNA.  [Westburg BV, Gel and blot imaging systems, 2001] http://www.westburg.nl/htm/products/gel_and_blot_imaging/odysseym...

direct detection: See also under reporter gene

dissociator assays: Proteomics glossary

dyes: Chemical substances that are used to stain and color other materials. The coloring may or may not be permanent. Dyes can also be used as therapeutic agents and test reagents in medicine and scientific research. [MeSH, 1963].

Related terms: labels, reagents Narrower term: spectroscopic dyes

ELISA: SEE Enzyme-Linked Immunosorbent Assay 

electrochemical biosensor: A self- contained integrated device, which is capable of providing specific quantitative or semi- quantitative analytical information using a biological recognition element (biochemical receptor) which is retained in direct spatial contact with an electrochemical transduction element. Because of their ability to be repeatedly calibrated, we recommend that a biosensor should be clearly distinguished from a bioanalytical system, which requires additional processing steps, such as reagent addition. A device which is both disposable after one measurement, i.e., single use, and unable to monitor the analyte concentration continuously or after rapid and reproducible regeneration should be designated a single use biosensor. [IUPAC Commission on Electroanalytical Chemistry, Electrochemical Biosensors: Recommended Definitions and Classification, 1999]  http://www.iupac.org/reports/1999/7112thevenot/  Broader term: biosensor

electrochemiluminescence: See Electrogenerated Luminescence ECL. [IUPAC Photo]

electrochemistry: The study of chemical changes resulting from electrical action and electrical activity resulting from chemical changes. MeSH, 1966

Related terms:  electrochemiluminescence, Electrogenerated Luminescence ECL, electroluminescence

Electrogenerated Luminescence ECL: Luminescence produced by electrode reactions. Also called electroluminescence or electrochemiluminescence. [IUPAC Photo]

electroluminescence: See electrogenerated chemiluminescence.  [IUPAC Photo]

electronic nose: An "electronic or artificial nose" is an instrument, which comprises a sampling system, an array of chemical gas sensors with differing selectivity, and a computer with an appropriate pattern- classification algorithm, capable of qualitative and/or quantitative analysis of simple or complex gases, vapors, or odors. Electrochemical Nose, Joseph R. Stetter and William R. Penrose, Electrochemistry Encyclopedia, 2001
http://electrochem.cwru.edu/ed/encycl/art-n01-nose.htm 

Standards, NOSE II Commission European Union, Call for participation in http://www.ipc.uni-tuebingen.de/weimar/research/maintopics/gassensors/nose/NOSEcall_standardisation.pdf 

electronic tongues:  For liquid analysis, based on the organizational principles of biological sensory systems, developed rapidly during the last decade. ... The exciting possibility of establishing a correlation between the output from an electronic tongue and human sensory assessment of food flavour, thereby enabling quantification of taste and flavour, is described. Application areas of electronic tongue systems including foodstuffs, clinical, industrial, and environmental analysis are discussed in depth. Y. Vlasov et. al., "Electronic tongues and their analytical application" Analytical Bioanalytical Chem. 2002 Jun;373 (3): 136- 146, June 2002 

Broader term: sensors

excitation: Narrower terms: chemiexcitation, photoexcitation Related terms: quencher, quenching, scintillation

FISH Fluorescence In Situ Hybridization: Gene Amplification & PCR

femtomole: Ultrasensitivity glossary 

fluorescence polarization: First described in 1926 (Perrin) and has been a powerful tool in the study of  molecular interactions. When fluorescent molecules are excited with plane polarized light, they emit light in  the same polarized plane, provided that the molecule remains stationary throughout the excited state (4  nanoseconds in the case of fluorescein). However, if the excited molecule rotates or tumbles out of the  plane  of polarized light during the excited state, then light is emitted in a different plane from that of the initial  excitation. If vertically polarized light is used to excite the fluorophore, the emission light intensity can be  monitored in both the original vertical plane and also the horizontal plane. The degree to which the emission  intensity moves from the vertical to horizontal plane is related to the mobility of the fluorescently labeled  molecule. If fluorescently labeled molecules are very large, they move very little during the excited state  interval, and the emitted light remains highly polarized with respect to the excitation plane. If fluorescently  labeled molecules are small, they rotate or tumble faster, and the resulting emitted light is depolarized  relative to the excitation plane. PanVera [now part of Invitrogen] website http://www.panvera.com/ls/fpabout.html

Based on the observation that emission signals from small fluorescent molecules are relatively depolarized, while binding to a larger molecule reduces the tumbling rate of the fluorescer, resulting in a relatively polarized emission signal.

Fluorescence Recovery After Photobleaching FRAP: A method used to study the lateral movement of MEMBRANE PROTEINS and LIPIDS. A small area of a cell membrane is bleached by laser light and the amount of time necessary for unbleached fluorescent marker- tagged proteins to diffuse back into the bleached site is a measurement of the cell membrane's fluidity. The diffusion coefficient of a protein or lipid in the membrane can be calculated from the data. (From Segen, Current Med Talk, 1995). MeSH 2003

Based on the principal of observing the rate of recovery of fluorescence due to the movement of a fluorescent marker into an area of the membrane which contains this same marker but which has been rendered non- fluorescent via an intense photobleaching pulse of laser light. The two- dimensional diffusion coefficient (D) of the fluorophore is related to both its rate and extent of recovery. FRAP has proved to be a popular means to assess the structure of artificial and biological membranes. [Cell & Developmental Biology, Univ. of North Carolina Chapel Hill School of Medicine] http://www-cellbio.med.unc.edu/facilities/frap.htm

fluorescence: Luminescence which occurs essentially only during the irradiation of a substance by electromagnetic radiation. [IUPAC Compendium]

The property of emitting radiation while being irradiated. The radiation emitted is usually of longer wavelength than that incident or absorbed, e.g., a substance can be irradiated with invisible radiation and emit visible light. X-ray fluorescence is used in diagnosis. MeSH

Narrower terms: FISH Fluorescence In Situ Hybridization, Fluorescence Resonance Energy Transfer FRET, green fluorescent protein GFP;  FRAP Fluorescence Recovery After Photobleaching, fluorescence polarization, LIF Laser Induced Fluorescence Related terms: fluorophore

Fluorescence In Situ Hybridization: See Gene Amplification & PCR FISH 

Fluorescence Resonance Energy Transfer FRET: A type of FLUORESCENCE SPECTROSCOPY using two FLUORESCENT DYES with overlapping emission and absorption spectra, which is used to indicate proximity of labeled molecules. This technique is useful for studying interactions of molecules and PROTEIN FOLDING. MeSH 2003

A distance- dependent interaction between the electronic excited states of two dye molecules in which excitation is transferred from a donor molecule to an acceptor molecule without emission of a photon. FRET is dependent on the inverse sixth power of the intermolecular separation, making it useful over distances comparable with the dimensions of biological macromolecules. Thus, FRET is an important technique for investigating a variety of biological phenomena that produce changes in molecular proximity. [Molecular Probes website, Handbook, 2001] http://www.probes.com/handbook/sections/0002.html

Has been used for many years to make spectroscopic distance measurements on ensembles of molecules. Recent advances in new fluorescent dyes and optical methods have increased the spatial resolution, distance range, and sensitivity of this method so that it continues to be one of the few tools available for measuring nanometer- scale distances in biological molecules. In FRET, energy is transferred from a donor fluorophore to an acceptor fluorophore over a range of 20-100 Å. ... Dynamic events, such as the relative motion between donor and acceptor molecules, however, cannot be detected by conventional FRET methods due to the lack of synchronized events in a population of molecules.  NIGMS,  Single Molecule Detection and Manipulation Workshop "Single Molecule Fluorescence of Biomolecules and Complexes Protein Folding April 17-18, 2000 http://www.nigms.nih.gov/news/reports/single_molecules.html#examples  

Narrower term: single-pair FRET spFRET

fluorescent proteins:  From fluorescent probes to novel techniques to cellular imaging -- FRET, BRET, Photoswitchable Fluorescent Proteins, Functional Imaging, Fluorescent Probes for in vitro and in vivo, Multicolor Fluorescent Proteins, Cellular Imaging, Imaging Technologies, Bioluminescence/ Fluorescence, Protein Tagging, Quantum Dots, Life Cell Imaging, Optical Imaging  In Vitro Molecular Imaging, Nov 27-28, 2007, San Diego CA 

Narrower terms: green fluorescent proteins. Fluorescent proteins can also be yellow and cyan.
Related term: Fluorescence Resonance Energy Transfer  FRET

fluorophore: The categories of greatest need [in single molecule studies] are improving the photophysical properties of fluorophores used for single molecule spectroscopy There is a need for synthesis of probes with desirable spectral and luminescent characteristics, such as small size, high quantum yield, high extinction, reduced photobleaching, blinking, and photoisomerization. The best probes will be compatible with conditions inside the cell and will move freely in the cell. Emerging technologies have made use of silicon and lanthanide nanocrystals (Quantum dots), which emit enough photons to be detected at very low concentrations, plasmon and Raman probes, and G/C/Y/R- fluorescent proteins, but there is still much to be done to optimize these probes. High throughput screening and combinatorial approaches need to be applied to this problem.   [NIGMS, Single Molecule Detection and Manipulation Workshop "Single Molecule Fluorescence of Biomolecules and Complexes Protein Folding April 17-18, 2000] http://www.nigms.nih.gov/news/reports/single_molecules.html#examples

May refer to either the fluorescent label or marker, or to the atoms which make the label fluorescent.

green fluorescent protein GFP: As a label for reporting cellular events in situ has been explored by a large number of laboratories. GFP and its mutants offer a powerful advantage as clonable markers for use in living tissue. However, photoisomerization and flickering of the emission signal ('blinking') create a challenge in single molecule experiments for both types of probe. Studies are in progress by W.E. Moerner and others (for example, see 6,7) to understand the basis for the long- lived dark states that lead to fluctuations in the emission spectra from these molecules, and to develop improved probes with reduced photoisomerization and blinking. [NIGMS  Single Molecule Detection and Manipulation Workshop" Single Molecule Fluorescence of Biomolecules and Complexes Protein Folding April 17-18, 2000] http://www.nigms.nih.gov/news/reports/single_molecules.html#examples 

Broader term: fluorescent proteins

High Throughput Screening HTS:  Assays & screening glossary

haptenylation reagents: A prerequisite for multicolor applications such as fluorescence in situ hybridization is the availability of multiple hapten molecules, along with their complementary binding proteins. The avidin– biotin system can provide only single- color detection, whereas antibody– hapten methods can generate a number of unique signals, limited only by the specificity of the antibody– hapten detection and the ability to distinguish the signals from different antibodies. The characteristics of a suitable hapten include a unique chemical structure that is not commonly found in cells, a high degree of antigenicity so as to elicit good antibody production, and a means for incorporating the hapten into the detection system.   Molecular Probes,  Handbook of Fluorescent Probes, Section 2.4  Biotinylation and haptenylation reagents, 2002 http://www.probes.com/handbook/sections/0402.html

Isotope Coded Affinity Tags (ICAT): See under differential labeling

ISH: See in situ hybridization.

immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents. MeSH, 1988

Immunohistochemistry involves using antibodies (typically visualized via an enzyme- linked antibody assay) that specifically bind to proteins of interest. This method allows one not only to assess levels of a protein but also to localize the protein within cells in the tissue sample.

IHCWorld: Immunohistochemistry methods & techniques http://ihcworld.com/ 

Related terms: Biomarkers glossary biomarkers Cell biology glossary gene localization, subcellular localization;  Gene definitions localization; Proteins protein localization

in situ hybridization ISH: Gene amplification & PCR

indirect detection: See under reporter gene

isothermal: Isothermal conditions are important in immunoassays, immunohistochemistry, in situ amplification and in cell- based assays, in which one wants to retain the morphology and viability of the cells. The relative simplicity of an isothermal reaction also indicates greater utility for point of care diagnostic applications. [CHI Summit Proteomics report]

Having a constant temperature.

LDC Labelling During Cleavage: 

LIF Laser Induced Fluorescence: The optical emission from molecules that have been excited to higher energy levels by absorption of electromagnetic radiation. The main advantage of fluorescence detection compared to absorption measurements is the greater sensitivity achievable because the fluorescence signal has a very low background. For molecules that can be resonant excitated, LIF provides selective excitation of the analyte to avoid interferences. LIF is useful to study the electronic structure of molecules and to make quantitative measurements of analyte concentrations. Analytical applications include monitoring gas-phase concentrations in the atmosphere, flames, and plasmas; and remote sensing using light detection and ranging (LIDAR). [Brian Tissue, "LIF" Chemistry Hypermedia Project, Chemistry Dept. Virginia Tech, Virginia Polytechnic Institute, US, 2000 ] http://www.chem.vt.edu/chem-ed/spec/laser/lif.html

Related term: Molecular imaging glossary  fluorescence spectroscopy- single molecule

label: A marker, tag or indicator distinguishable by the observer but not by the system and used to identify a tracer. [IUPAC Radioanalytical, Pure & Applied Chemistry: 2514- 2576, 1994]

There is a need to develop better methods for inserting site- specific labels in the samples for detection, as well as mechanical handles for manipulation. Site- directed mutagenesis, approaches using chimeras, clonable tags, reporter genes, protection/ deprotection protocols, and protein modification using derivatized amines and thiols, such as His tags, are currently used, but flexibility in the placement of chemical handles in the sample remains a limitation. [NIGMS, Single Molecule Detection and Manipulation Workshop "Single Molecule Fluorescence of Biomolecules and Complexes Protein Folding, April 17-18, 2000] http://www.nigms.nih.gov/news/reports/single_molecules.html#examples 

Labels & stains for tissues and cells, Apr 24-25, 2006 Boston MA

Narrower terms: nanolabels, biotin, differential labelling, ICAT, optical tagging, streptavidin, target labelling  Related terms: assays, dyes, reagents, staining and labeling, target labelling, tracer; Ultrasensitivity glossary

label free detection: Label-free detection of biomolecules is currently receiving intense attention due to the clear advantages it offers over fluorescent methods. These researchers are pursuing a label-free protein detection method based upon field-effect detection-a technique that has been used for DNA, but not yet for proteins. If they are successful, they will develop arrays of sensors for the purpose of high-throughput parallel detection, and examine the generality of their findings for various diverse proteins. Label Free Electrical Detection of Proteins, Deshpande Center for Technological Innovation, MIT http://web.mit.edu/deshpandecenter/proj_manalis.html 

lasers: Molecular Imaging glossary

luminescence: The property of giving off light without emitting a corresponding degree of heat. It includes the luminescence of inorganic matter or the bioluminescence of human matter, invertebrates and other living organisms. [MeSH]

Spontaneous emission of radiation from an electronically or vibrationally excited species not in thermal equilibrium with its environment. [IUPAC Compendium]

Narrower terms:  bioluminescence, chemiluminescence, electrochemiluminescence, Electrogenerated Luminescence ECL. 

luminometer: Light measuring instrument.

microcantilevers: See under label free detection

microsequencing: Sequencing glossary  

minisequencing: Sequencing glossary  

mole: Ultrasensitivity glossary

molecular biosensors: Devices of molecular size that are designed for sensing different analytes on the basis of biospecific recognition. They should provide two coupled functions - the recognition (specific binding) of the target and the transduction of information about the recognition event into a measurable signal. Fluorescence sensing of intermolecular interactions and development of direct molecular biosensors Danièle Altschuh ^{1 *}, Sule Oncul ², Alexander P. Demchenko ² Journal of Molecular Recognition: `9 (6): 459-477 published online 6 Nov 2006 http://www3.interscience.wiley.com/cgi-bin/abstract/113445627/ABSTRACT?CRETRY=1&SRETRY=0 .

molecular combing: A method ... which can straighten and align molecules of genomic DNA on a solid surface. The technology also includes a battery of novel statistical methods developed for analyzing the large amounts of data obtained from FISH analyses made on individual DNA molecules.

Molecular combing relies on the action of a receding air/ water interface, or meniscus, to uniformly straighten and align DNA molecules on a solid surface. The advantages of this approach reside in the reproducibility of the results, their precision (1 to 4 kb resolution) and the relative ease of analysis afforded by the ability to visualize the molecules directly. Beyond its obvious applications to genomic studies and genetic diseases, it creates new experimental possibilities for research into cancer. Indeed, as a tool, molecular combing is a versatile approach to a wide range of subjects and questions of fundamental interest. This is especially true for the multifaceted domain of DNA replication in eukaryotes. [Aaron Bensimon et. al. "Detection of Genomic Alteration by Molecular Combing" NCI Innovative Molecular Analysis Technologies Programs, July 6-8, 2000, Chantilly VA]  http://otir.nci.nih.gov/cgi-bin/imat_search.cgi?ABSTRACTID=IMAT-00-007

molecular distillation: Molecular Imaging glossary

molecular probe techniques: See under PCR glossary probes

nanocrystals: Nanoscience & Miniaturization glossary Broader term: labels

nanodetector: Molecular imaging glossary

nanodots: See Nanoscience & miniaturization glossary 

nanolabel: A novel double-codified nanolabel (DC-AuNP) based on gold nanoparticle (AuNP) modified with anti-human IgG peroxidase (HRP)-conjugated antibody is reported. It represents a simple assay that allows enhanced spectrophotometric and electrochemical detection of antigen human IgG as a model protein. Ambrosi A, Castañeda MT, Killard AJ, Smyth MR, Alegret S, Merkoçi A. Double-codified gold nanolabels for enhanced immunoanalysis,  Analytical Chemistry 2007 Jul 15;79 (14): 5232- 5240. Epub 2007 Jun 19. http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17579481&ordinalpos=1&itoo...  

nanomole: Ultrasensitivity glossary

nanoparticles: Nanoscience & miniaturization glossary 

Optical tagging OT: See under LIF Laser Induced Fluorescence.

phosphorimagers: Microarrays glossary

photobleaching:  Light-induced change in a chromophore, resulting in the loss of its absorption of light of a particular wave length. The photon energy causes a conformational change in the photoreceptor proteins affecting PHOTOTRANSDUCTION. This occurs naturally in the retina ( ADAPTATION, OCULAR) on long exposure to bright light. Photobleaching presents problems when occurring in PHOTODYNAMIC THERAPY, and in FLUORESCENCE MICROSCOPY. On the other hand, this phenomenon is exploited in the technique, FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING, allowing measurement of the movements of proteins and LIPIDS in the CELL MEMBRANE. [MeSH 2003]

Cell biologists have used photobleaching to investigate the lateral mobility of fluorophores on the cell surface since the 1970s. Fusions of green fluorescent protein (GFP) to specific proteins extend photobleaching techniques to the investigation of protein dynamics within the cell, leading to renewed interest in photobleaching experiments. J. White, E. Stelzer "Photobleaching GFP reveals protein dynamics inside live cells " Trends in Cell Biology 9 (2): 61- 65, Feb. 1999 http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=10087620&form=6&db=b...

photoexcitation: Luminescence arising from photoexcitation. [IUPAC Photo]

photon, photonics: Molecular Imaging glossary

picomole: Ultrasensitivity glossary 

primed in situ labeling: A technique that labels specific sequences in whole chromosomes by in situ DNA chain elongation or PCR (polymerase chain reaction). [MeSH, 1999]

primer:  Gene Amplification & PCR

probes:  Gene Amplification & PCR

quantum dot: Nanoscience & Miniaturization glossary

quencher: A molecular entity that deactivates (quenches) an excited state of another molecular entity, either by energy transfer, electron transfer, or by a chemical mechanism. [IUPAC Photo]

quenching: 1. Arresting the course of a chemical reaction by chemical or physical means. (in photochemistry) 2. The deactivation of an excited molecular entity intermolecularly by an external environmental influence (such as a quencher) or intramolecularly by a substituent through a nonradiative process. 3. (in radiation chemistry) The process of inhibiting continuous or multiple discharges following a single event in certain types of radiation detectors. [IUPAC Compendium]

reactant: A  substance that is consumed in the course of a chemical reaction.  It is sometimes known, especially in the older literature, as a reagent, but this term is better used in a more specialized sense as a test substance that is added to a system in order to bring about a reaction or to see whether a reaction occurs (e.g. an analytical reagent). [IUPAC Compendium] 

Related term: reagents

reagents:  Substances used for the detection, identification, analysis, etc. of chemical, biological, or pathologic processes or conditions. .. Reagents are substances used for the detection or determination of another substance by chemical or microscopical means, especially analysis. Types of reagents are precipitants, solvents, oxidizers, reducers, fluxes, and colorimetric reagents.     MeSH ‘indicators and reagents’

Related term: reactant

reporter gene: Reporter Gene detection has become invaluable in the study of gene function and related cellular events. In these studies, the reporter gene acts as a surrogate for the coding region of the gene under study. Upon transfection of the reporter construct, expression of the reporter gene may be monitored by direct (e.g. enzymatic) or indirect (e.g. immunochemical) assay of the reporter protein. Localized expression of the reporter protein can be detected via immunochemistry using antibodies specific for the expressed reporter protein. Reporter gene products, Cortex Biochem, US http://www.cortex-biochem.com/F/ 

SPR Surface Plasmon Resonance: A biosensing technique in which biomolecules capable of binding to specific analytes or ligands are first immobilized on one side of a metallic film. Light is then focused on the opposite side of the film to excite the surface plasmons, that is, the oscillations of free electrons propagating along the film's surface. The refractive index of light reflecting off this surface is measured. When the immobilized biomolecules are bound by their ligands, an alteration in surface plasmons on the opposite side of the film is created which is directly proportional to the change in bound, or adsorbed, mass. Binding is measured by changes in the refractive index. The technique is used to study biomolecular interactions, such as antigen - antibody binding.  MeSH, 1999

Narrower term: Surface Plasmon Resonance microscopy Imaging glossary

sample, sample prep, sample preparation: Drug discovery & development glossary

scanning technology: Molecular Imaging glossary

screening: Assays & screening glossary

scintillation: Burst of luminescence of short duration caused by an individual energetic particle. [IUPAC Radioanalytical]

selectivity: The extent to which a compound hits the intended drug target. [CHI Breaking Bottlenecks report] See also IUPAC note Molecular Medicine glossary  about selectivity and specificity often being used interchangeably.

sensitivity: 100% sensitivity = 100% true positives, 0% false positives.

sensor model language SensorML:  Sensor Model Language (SensorML) for In-situ and Remote Sensors. Edited by Mike Botts (University of Alabama in Huntsville). Open GIS Discussion Paper [not an adopted standard]. Open GIS Consortium Inc. Issued by the OGC Natural Resources and Environment (NRE) Working Group. Publication Date: 2002-12-20. Reference number: OGC 02-026r4. Version 0.7. 118 pages. With associated XML Schemas. http://xml.coverpages.org/ni2003-01-31-b.html With definitions of sensors.

sensor web: An independent network of wireless, intra- communicating sensor pods, deployed to monitor and explore a limitless range of environments. This adaptable instrument can be tailored to whatever conditions it is sent to observe. [Jet Propulsion Lab, NASA "Sensor Web Project"]  http://sensorwebs.jpl.nasa.gov/

sensors: An equipment which detects, and may indicate, and/or record objects and activities by means of energy or particles emitted, reflected, or modified by objects. [Dept. of Defense US, Dictionary of Military Terms] http://www.dtic.mil/doctrine/jel/doddict/   

Related terms: actuators, labels, nanoparticles, sensor model language, transducers 
Narrower terms:  biosensor, electrochemical biosensors, electronic biosensor, electronic nose, electronic tongues, molecular biosensors, nanosensors,  neurally inspired sensor, spore based biosensors 

signal amplification: Gene amplification & PCR

signal to noise: Ratio which can interfere with detection. Can also refer to data analysis. Biological data is often very "noisy". This is particularly seen when trying to look at low abundance biomolecules.

signals: Produced by dyes, fluorescence or radioactivity. (Non- radioactive materials, because of disposal and other problems, and improvements in other technologies) are increasingly in demand.

Related terms: detection, reagents, actuators

single cell, single molecule: Ultrasensitivity glossary

single-pair FRET spFRET: Designed to overcome the averaging effects of ensemble studies because measurements are made on single molecules freely diffusing in solution. This method limits the observation period to the diffusion time of each molecule through the focal spot of a laser on the order of a few hundred milliseconds, but it permits the rapid gathering of data at single- molecule resolution on a large number of molecules in a short time period. SpFRET can be used to study intramolecular conformational changes by placing the donor and acceptor fluorescent tags on two different sites of the same macromolecule, or alternatively, intermolecular interactions can be studied by attaching the donor and acceptor tags to two different macromolecules.  NIGMS, Single Molecule Detection and Manipulation Workshop "Single Molecule Fluorescence of Biomolecules and Complexes Protein Folding April 17- 18, 2000 http://www.nigms.nih.gov/news/reports/single_molecules.html#examples 

solution arrays: Functionalized particle sets for multiplexed bioanalysis in solution. [Michael Natan, SurroMed, Inc.  personal communication Dec. 2001]

specificity: In the five disciplines that eventually contributed to the formation of molecular biology, ideas of specificity had widely different standing and character. In microbiology, the relevance of specificity in the present day sense awaited resolution of the long, piecemeal shift of opinions about what sort of creatures micro- organisms were....[Oswald Avery, Chargaff, Lwoff, Luria Delbruck, Jacques Monod, Alice Audureau]  Mendelian genetics itself had always been highly specific, of course, and from very early the genetic specificity - the map - was understood to form a strictly linear array  [Thomas Hunt Morgan, Boris Ephrussi, George Beadle, Edward Tatum]... In physical chemistry, specificity was not abstract and not linear, but concretely physical and three- dimensional [Pauling] ... Crystallography, in its way, was also permeated with specificity [Edward Tyson Reichert, Amos Peaslee Brown, Felix Haurowitz] ... Specificity in the present- day sense of unique molecular structures was never a surprise to the crystallographers ... The fifth discipline in the synthesis that formed molecular biology was biochemistry. Yet the standard view of the rise of molecular biology has somewhat taken for granted, for example, the radical sharpening of ideas of specificity represented by Fritz Lipmann's elucidation of the way energy is supplied to the steps of cellular reactions.  And it grievously undervalues the work of the two biochemists who proved decisive in changing the way people thought about specificity.  The man who released the present day understanding of molecular specificity in living processes was Frederick Sanger ... the most general and profound [result of his methods] was that proteins are entirely and uniquely specified.  [Horace Freeman Judson Eighth Day if Creation, Cold Spring Harbor Laboratory Press, 1996 pp. 583- 585]

100% specificity = 100% true negatives, 0% false negatives. See also Molecular Medicine glossary (analytical and clinical sensitivity and specificity).

spectroscopic dyes: These dyes—in particular, nanoparticles — are emerging as alternatives to fluorescent dyes. Because the emission spectra of nanoparticles vary according to these particles’ specific size and shape, these nanostructures can be used in multicolor detection formats, potentially offering much greater multiplexing than is currently achievable. The fact that chemists have been able to create a great variety of structures (and properties) in nanoparticles suggests that these particles might be more "finely tunable" than organic dyes, allowing better results from biological assays CHI High- Content Analysis Market Outlook report, 2004  

staining and labeling: The marking of biological material with a dye or other reagent for the purpose of identifying and quantitating components of tissues, cells or their extracts. MeSH, 2001

Related terms: label, tags

Stokes shift: Microarrays glossary

streptavidin:  A 60 kD extracellular protein of Streptomyces avidinii with four high-affinity biotin binding sites. Unlike AVIDIN,  streptavidin has a near neutral isoelectric point and is free of carbohydrate side chains. [MeSH, 1998]

TSA Tyramide Signal Amplification: Was developed by NEN (now a part of PerkinElmer Corporation) and licensed to Molecular Probes for in- cell and in-tissue applications, permits significant amplification of the detectability of targets by a horseradish peroxidase (HRP)– mediated scheme. In the TSA method, the labeled tyramide becomes covalently linked to tyrosine residues in or near the target. Molecular Probes,  Handbook of Fluorescent Probes, Section 2.4  Biotinylation and haptenylation reagents, 2002 http://www.probes.com/handbook/sections/0402.html

TSA - also known as Catalyzed Reporter Deposition (CARD) - is a signal- amplification technology designed to enhance detection sensitivity in DNA arrays, in situ hybridization (ISH) assays, and other applications.  [Kerstens HM, Poddighe PJ, Hanselaar AG. "A novel in situ hybridization signal amplification method based on the deposition of biotinylated tyramine." Journal of Histochemistry & Cytochemistry. 1995. 43:347-352.]

tag: See label, capture tag, Isotope Coded Affinity Tags ICAT, optical tagging. This is different from tagging for information retrieval

target amplification: Gene amplification & PCR

target labelling: Targets glossary 

tracer: Labelled members of a population used to measure certain properties of that population.  [IUPAC Radioanalytical]  

transducer: A device that transforms one form of signal or energy into another form. Therefore, the term transducer can be used to include both sensors and actuators [14] and is the most generic and widely used term for micromachines. [National Textile Center, "MEMS: An Overview" 1998] http://www2.ncsu.edu/unity/lockers/project/ntcprojects/projects/F98-S12/mems...

Transducers, Wikipedia http://en.wikipedia.org/wiki/Transducers 

tunable lasers: Molecular Imaging glossary

yoctomole, zeptomole:  Ultrasensitivity glossary  

Bibliography
Electrochemistry Dictionary, maintained by Zoltan Nagy, hosted by Ernest B. Yeager Center for Electrochemical Sciences (YCES) and the Chemical Engineering Department, Case Western Reserve University,  US,  800 + terms, 2005 http://electrochem.cwru.edu/ed/dict.htm 

Alpha glossary index

How to look for other unfamiliar  terms

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.