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Technologies
map Finding guide to terms in these glossaries Site
Map
Related glossaries include Drug
Discovery & Development, Molecular
Diagnostics
Technologies Assays & screening, Cell
& tissue technologies 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, Glossary of Computerized System and
Software Development Terminology last updated 2009 http://www.fda.gov/iceci/inspections/inspectionguides/ucm074875.htm
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.
amplification: See signal amplification, target amplification (and gene
amplification).
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
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]
co-localization:
During the examination and digital recording of multiply labeled
fluorescent specimens, two or more of the emission signals can often overlap in
the final image due to their close proximity within the microscopic structure.
This effect is known as colocalization and usually occurs when fluorescently
labeled molecules bind to targets that lie in very close or identical spatial
positions. The application of highly specific modern synthetic fluorophores and
classical immunofluorescence techniques, coupled with the precision optical
sections and digital image processing horsepower afforded by confocal and
multiphoton microscopy, has dramatically improved the ability to detect
colocalization in biological specimens. Colocalization of Fluorophores in
Confocal Microscopy, Olympus 2004-2009 http://www.olympusfluoview.com/applications/colocalization.html
Wikipedia http://en.wikipedia.org/wiki/Colocalization
colorimetry:
The methods used to measure color and to define
the results of the measurements. [Photonics]
competitive hybridization: Gene
amplification & PCR glossary
computational
sensing: emerging scientific and engineering field that can be defined as
process of extraction, analysis and use of knowledge about the instrumented
environment and sensed phenomena. Examples include event and anomaly detection,
trends tracking, reverse engineering of environment and physical, chemical, and
biological laws, identification of actual and virtual sources of excitation,
hypothesis checking-driven deployment, causality identification, and
generalization of knowledge obtain in multiple environments. Sensing is not just
the ultimate objective of embedded sensor networks, but also powerful enabler
and facilitator for many sensor network tasks such as deployment and sampling
rate determination. Center for Embedded Network Sensing, UCLA http://research.cens.ucla.edu/about/
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.
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...
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
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
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
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
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
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.
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
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
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.
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
single-molecule technology that enables the direct visualization of multiple
whole genomes and the detection of large genome changes. Genomic Vision’s
Molecular Combing Technology is Set to Innovate Facio-scapulo-humeral Dystrophy
(FSHD) Diagnosis, Paris France 2010 press release http://www.genomicvision.com/media/press%20release%20FSHD%20-FINAL%20-%2016-2.10.pdf
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.
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...
photoexcitation:
Luminescence arising from photoexcitation. [IUPAC Photo]
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]
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/
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. 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
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
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 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...
Wikipedia http://en.wikipedia.org/wiki/Transducers
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.
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