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).

biotin labelling 1. The attachment of biotin to another molecule. 2. The incorporation of a biotin- containing nucleotide into a DNA molecule. b

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.

biotinylation: To label a probe with biotin.

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

chemiluminescence: Emission of light as a result of a chemical reaction without an apparent change in temperature. Luminescence arising from chemiexcitation.

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

detection: The Oxford English Dictionary points out that detecting involves finding what is otherwise apt to elude notice, particularly that which is "artfully concealed".
The drive of genomic and proteomic research and diagnostics towards greater performance is resulting in demands for improved approaches to labels and other methods for detection of biological molecules. Achieving greater speed, sensitivity and accuracy are being pushed to the limits, all while moving towards greater automation and lower costs. Innovative techniques, including nanolabels, extended multiplexing and direct detection, are being used to achieve some of these goals. Challenging applications, such as assays of living cells or single molecule detection, help push technology - which can also be beneficial for many other applications.

detector technologies: Include direct detection, electrochemical, fluorescence, fluorescence polarization, colorimetry, mass spectrometry, luminescence, optical, primer extension and minisequencing.

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.

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.

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.

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.

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

electronic nose: An emerging technology with potential application across a wide range of application areas, including bacteriological and environmental monitoring, explosive detection, process monitoring and control, product quality control, and fraud detection. … An instrument which comprises an array of electronic chemical sensors with partial specificity and an appropriate pattern recognition system, capable of recognising simple or complex odours (and other gaseous mixtures)1. The ability of an electronic nose to rapidly discriminate between slight variations in complex mixtures makes the techniques ideal for on- line process diagnostics and screening across a wide range of application areas.

fluorescence polarization: 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. 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.

Fluorescence Recovery After Photobleaching FRAP: 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.

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

Fluorescence Resonance Energy Transfer FRET: 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. 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.

fluorescent perturbation: Active microelectronic array devices have been developed for a number of different applications in DNA diagnostics and pharmacogenomics research. A new technique called fluorescent perturbation now allows a fluorescent DNA probe to be used in ways that can provide further information and advantages to the assay. Fluorescent perturbation involves using a pulsed DC electric field to "perturb" the fluorophore on a DNA probe bound to the target molecule. This perturbation leads to modulation of the fluorescent signal that immediately distinguishes single base mismatches in the target sequence. The new technique has potential advantages for single nucleotide polymorphism (SNP) analysis in that it is extremely rapid and requires only one probe for the analysis.

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.

gold nanoparticles: Have a number of unique physical properties, including high extinction and scattering coefficients, catalytic activity, and fluorescence quenching, that make them extremely flexible labels for DNA detection schemes. As a result, we have developed DNA array protocols whereby target hybridization to array elements can be determined by electrical conductivity, scattered light, or even absorption visible to the naked eye. These technologies have offered a great deal of promise for simple and inexpensive, yet selective and sensitive, analysis of gene expression and mutation. However, the thiol chemistry that is commonly used to connect oligonucleotides to gold surfaces is sometimes not strong enough to survive molecular biology protocols (such as PCR). This has limited the direct impact of gold nanoparticle labels on the practice of DNA arrays. We have recently developed universal ligands that permit more stable conjugates between gold nanoparticles and biomolecules. These ligands allow enzyme reactions to be conducted directly on gold nanoparticle- bound DNA, and will further enable the labels’ direct use in biological and clinical DNA sequence analysis.

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.

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

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.

LDC Labelling During Cleavage: Recent progress in nucleic acids detection for diagnostic purposes has clearly established the importance of labeling strategy to reach high sensitivity and specificity. A new strategy called "Labeling During Cleavage (LDC)", which is a chemical labeling procedure, has been developed in our laboratory for labeling amplified RNA targets without affecting the amplification efficiency and fidelity. LDC is a universal labeling technology which is able to achieve the two functions in one step : labeling and fragmentation of RNA molecules prior to their hybridization and detection on DNA- chip. Labeling results on high density DNA chip demonstrated the robustness and the sensitivity of this chemistry which doesn't affect the specificity during the hybridization step.

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).

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. 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.

label free detection: Micro cantilevers with piezoresistive readout used as a sensitive biochemical sensors is a highly interesting technology, since it offers a label detection of molecules. Basically, a biochemical reaction at the cantilever surface can be monitored as a bending of the cantilever due to a change in the surface stress. The change in surface stress is then transformed into a change in the integrated piezoresistor, which is easily monitored by simple instrumentation. Since a very small bending of a cantilever can be measured, this detection method has proven to be very sensitive. Due to the simple readout technique, this technology is ideal for de-central analysis where limited sample preparation and instrumentation is necessary. An array of cantilevers is placed in a microliquid handling system, and the cantilevers are coated with a 'detector film' that reacts with the biomolecules of interest in a test sample. By coating each cantilever in the array with different 'detector films', a multiple of different biomolecules can be detected simultaneously. The change in surface stress on the cantilever surface is related to the change of Gibbs' free energy during the molecular interaction between the biomolecules of interest and the 'detector film', and the microcantilevers can therefore be used for detection of a wide variety of molecules like DNA, proteins, antibody, etc. Microcantilever based sensors offer a platform for highly sensitive, label free molecular recognition on small sample volumes, which could be interesting for point of care diagnostic.

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

microtransponders: Used in a novel DNA detection system that is capable of accurately detecting and differentiating a large number of unique DNA sequences in a single assay. Microtransponders are cube- shaped, miniature, radio- frequency transmitters, only hundreds of micrometers on each side. The presence of complementary DNA sequences in a biological specimen is determined by reacting fluorophore- labeled specimen nucleic acid with transponders, each derivatized with a different oligonucleotide probe. A scanner then detects and measures the fluorescent signal generated by the labeled specimen nucleic acid hybridized to the probe on the transponder and identifies the nucleic acid sequence involved by means of laser activation of the transponder's memory. The technology is ideal for assays in which screening for many genes, gene fragments, or mutations is necessary.

molecular biosensors: Quantification of trace elements in complex biological matrices remains a formidable task in analytical chemistry requiring both high sensitivity and selectivity. One way to solve these problems is to apply the selectivity and avidity of proteins in molecular biosensors. The properties of these proteins can then be further enhanced for use as molecular biosensors by combining the tools of molecular and structural biology. We have been developing biosensors for metal ions and anions using carbonic anhydrase and periplasmic binding proteins, respectively, as the receptor molecule. For the metal ion sensors, we are using site- directed and random mutagenesis to vary the metal affinity, metal specificity, metal binding dynamics, fluorescence signal transduction, and immobilization procedures to optimize properties of the sensor. We have recently completed a field test where this sensor was used to measure copper concentrations in seawater.

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.

nanobarcodes particles: Nanobarcodes™ particles, comprise freestanding, cylindrically- shaped metal nanoparticles that are self- encoded with sub- micron stripes. Nanobarcodes particles are prepared by electrochemical reduction of metal ions into the cylindrical pores of metallized templates, followed by release from the template. Intrinsic differences in reflectivity between adjacent metal stripes (e.g. gold and silver) allow individual particles to be identified by conventional optical microscopy. By varying the physical dimensions (length and width), the composition (number/type of metals) and striping pattern (number/ width/ order of stripes), libraries of thousands of uniquely identifiable particle types ("flavors") can be prepared. Nanobarcodes particles are thus the nanoscale equivalent of conventional bar codes. For biological applications, the level of multiplexing is equal to the number of distinct flavors.

nanodots: Utilizing simple photochemical transformations, we have produced highly fluorescent silver nanodots from otherwise nonfluorescent silver oxide nanoparticles. Readily observable on a single molecule level, these novel nanomaterials can be written with a wide array of emission colors spanning the visible spectrum. Once controlled, these materials offer promise to optically label different species with different colors and follow ensuing dynamics.

nanolabels: DNA ‘barcodes’, nanoscopic data molecules on the basis of DNA with a storage capacity of at least 32bit. They can be used as invisible markers for labeling of industrial products like paints, oils, lubricants etc., paper- based materials and documents, ink, pharmaceuticals, medical samples and organic materials. The molecules can even be used for labeling of single genes, thus, for the first time, allow labeling of genetically engineered products and food. Also, for the first time, the molecules can be encrypted to guarantee full fake- security of the labeled products.

nanoparticles: Both synthetic (bottom- up) and transformative (top- down) fabrication rely on the availability of building block materials and artifacts such as quantum dots, nanotubes and nanofibers, ultrathin films and nanocrystals. These also include their assemblies in coatings, dispersions, colloids, aerogels and nanoporous structures, as well as organic dendrimers, block copolymers and nanocomposites, and also biomolecules such as proteins, nucleic acids etc. Despite the multitude of nanoparticles that have been generated in the laboratory, there is a need for fabrication and proliferation of a much larger variety of such nanomaterials. ... Serial direct structuring methods include robotic nanoassembly by the atomic force microscope (AFM) and strain- directed assembly, while parallel soft lithography techniques comprise various nanoimprinting, molding, embossing processes, as well as DNA- directed assembly etc. Alternatives to such technologies are offered by miniaturization of hard microlithography, including X-ray (LIGA), electron or ion lithography, and molecular beam epitaxy (MBE). Other processes address 3-D templating and growth of aerogels, sol- gel methods, laser or plasma vaporization and condensation, laser- guided particle transport and electrophoretic techniques. ... To improve throughput and efficiency, parallel probe arrays, distributed/ scanned beams and lab- on- a- chip MEMS, including chemical and biological array sensors and actuators, must be developed as robust, miniaturized alternatives to serial, large-scaled instrumentation. Integration of equipment across multiple scales, exemplified by a chain of a manipulator with a MEMS micro- manipulator as the end effector, to process nano- electro- mechanical structures (NEMS) is necessary to process multi- scale nanostructured parts. Instrumentation research must also strive to improve resolution and bandwidth, commensurate to the scale and dynamics of nanostructure interaction phenomena that must be monitored and regulated. Last, teleoperation of large and costly equipment for telecharacterization and telefabrication via the internet is desirable for collaborative and shared use. Nanoparticles, including nano- clusters, [nano]- layers, [nano]- tubes, and two- and three- dimensional structures in the size range between the dimensions of molecules and 50 nm (or in a broader sense, submicron sizes as a function of materials and targeted phenomena), are seen as tailored precursors for building up functional nanostructures.

nanosensors: Nanosensors with antibody probes have recently been developed for the detection of biological species or xenobiotic chemical compounds in a single cell. Combining the exquisite specificity of biological recognition probes and the excellent sensitivity of laser- based optical detection, these nanosensors are capable of detecting and differentiating biochemical constituents of complex systems in order to provide unambiguous identification and accurate quantitation in a single cell. The development of nanosensors opens new horizons to biomolecular research at the single- cell level, and permits the ability to probe the intact cellular architecture for biomedical applications.

neurally inspired sensor: A variety of neurotransmitters and neuronal messengers, such as dopamine and Nitric Oxide, respectively, influence the electrical excitability of neurons. A neurally inspired sensor would transduce the association of the neurochemical and produce a small electrical current. The neurally inspired interface would transduce the electrical current and produce a suitable output in the form of a voltage, digital data stream or even a spike pattern. To meet this objective, we have proposed and developed a neurochemical sensor and a and a very large scale integrated (VLSI) circuit chip circuit interface.

phage derived probes: Filamentous phage can serve as a scaffold, able to form on its surface an indefinite number of potential antigen- binding sites by displaying random peptides fused to major coat protein pVIII. We constructed libraries with random peptides fused to pVIII in various formats (landscape libraries) and selected phages that act as substitute antibodies specific for a panel of test antigens and threat agents. We demonstrated that page-derived probes bind biological agents and, as a part of analytical platforms, generate a detectable signal. Phages are prospective probes in a new generation of sensors for food safety control and environmental in a real- time monitoring. As elements of field- use detectors, they are superior to monoclonal antibodies, since they are inexpensive, highly specific, and strong binders, resistant to unfavorable environmental conditions.

photobleaching: 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.

photoexcitation: Luminescence arising from photoexcitation.

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

propidium iodide: A stain used in fluorescence microscopy that stains inactive (dead) cells and fluoresces red

quantum dot: An important strategy for nonisotopic labeling of single molecules is the use of highly luminescent semiconductor nanocrystals, or 'quantum dots,' that can be covalently linked to biological molecules. Quantum dots offer several advantages over organic dyes, including increased brightness, stability against photobleaching, a broad continuous excitation spectrum, and a narrow, tunable, symmetric emission spectrum. Because quantum dots are nontoxic and can be made to dissolve in water, efforts are underway to explore their use in labeling single molecules in living cells.

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.

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.

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).

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.

Resonance Light Scattering (RLS) particles: Sensitive labels that have been implemented for a wide variety of analytical bioassays. Spherical gold and silver RLS particles™ of uniform dimension (between 40- 120 nm diameter) generate highly intense monochromatic light when illuminated with configured white light. The colored light signal generated by a single RLS Particle is 104 to 106 times greater than the signal obtained for the most sensitive fluorescent molecule. The intensity and color of scattered light generated by individual RLS particles is stable and dependent upon particle composition and diameter according to predictive algorithms. The surface of RLS particles can be derivatized with a variety of biomolecules to affect specific binding in analytical bioassays. Sensitive RLS reagent and instrumentation systems for microarrays, immunocytology/ histology, in situ hybridization, microtiter well assays, and microfluidics have been developed.

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.

scintillation: Burst of luminescence of short duration caused by an individual energetic particle.

selectivity: The extent to which a compound hits the intended drug target. [CHI Breaking Bottlenecks report] See also IUPAC note Clinical genomics glossary about selectivity and specificity often being used interchangeably. sensitivity: 100% sensitivity = 100% true positives, 0% false positives.

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.

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. A device that provides a usable electrical output signal in response to a signal.

Narrower terms: biosensor, electronic biosensor, electronic nose, neurally inspired sensor

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.

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.

solution arrays: Functionalized particle sets for multiplexed bioanalysis in solution.

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. 100% specificity = 100% true negatives, 0% false negatives. See also Clinical genomics 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 Screening report, 2002] .

spore-based biosensor: A real-time biosensing system has been developed that uses microbial spores as nanodetectors responding to proximal bacterial cells by emitting fluorescent light signals.1 As compared to other cells, spores have unique levels of functionality particularly suited for biosensing, i.e., they are extremely rugged cells without detectable metabolic activity (dormant), but still capable of responding to specific external stimuli (germinants) by rapidly reactivating normal- cell functions... A real- time bacteriologic biosensor would have a critical impact in public health and other major industries now relying on culture- based testing that usually requires 16- 48 hours for completion. Potential applications of the technology include: clinical diagnostics; bioterrorism defense, testing blood products intended for transfusion; screening food and beverages; environmental monitoring; and sterility testing.

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.

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.

TSA Tyramide Signal Amplification: 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. It is being commercialized by NEN Life Science Products. With TSA, the enzyme horseradish peroxidase is used to activate and deposit a reactive tyramide- labeled tag (e.g., biotin or fluorescent dyes). This amplifies the signal, which can then be detected by routine means. NEN reports that in some applications, TSA increases detection limits up to 100-fold, enabling very low levels of nucleic acids or target proteins to be discerned. Researchers in the Netherlands used biotinylated tyramine- based CARD to amplify ISH signals and reported that the detection limit was "highly increased" and that CARD is especially suitable for visualizing very weak ISH signals.

tag: See label, capture tag, Isotope Coded Affinity Tags ICAT, optical tagging

tracer: Labelled members of a population used to measure certain properties of that population.

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.

Up-converting Phosphors (UPT): A new class of reporter particles. These pre- ceramic materials up- convert infrared to visible light in any biologic matrix. Therefore, once labeled with probes or proteins they allow the detection of attomolar concentrations of target analyte.