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Cell & tissue technologies glossary & taxonomy
Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions?  Mary Chitty
Last revised December 18, 2014
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aptamers: Technologies overview 

artificial cells: Artificial cells designed for specific applications combine properties of biological systems such as nanoscale efficiency, self- organization and adaptability at relatively low cost. Individual components needed for such structures have already been developed, and now the main challenge is to integrate them in functional microscopic compartments. Andrew Pohorille, "Artificial cells, prospects for biotechnology" Trends in Biotechnology, 20 (3): 123- 128, Mar. 2002

artificial chromosomes: DNA constructs that are composed of, at least, elements such as a REPLICATION ORIGIN; TELOMERE; and CENTROMERE, that are required for successful replication, propagation to and maintenance in progeny cells. In addition, they are constructed to carry other sequences for analysis or gene transfer. MeSH, 2001  Narrower terms: Bacterial artificial chromosome BACS, Yeast Artificial Chromosomes YACS 

Bacterial artificial chromosome BAC: A vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. Based on naturally occurring F-factor plasmid found in the bacterium E. coli. Compare cloning vector.  DOE

DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes. MeSH, 2002   Related term: BAC maps. Maps, genetic & genomic

biobanking: Today, biospecimen collections are used by multiple research groups for varying research aims, from basic research through clinical trials. A well- managed biobank is a critical prerequisite for high-quality biological research. The proper collection, processing, storage and tracking of biospecimens are critical components allowing researchers to better link molecular and clinical information.  Leaders in BioBanking Congress  July 14-16, 2015 • Toronto, ON Canada Program | Register | Download Brochure


biofabrication:  Biomaterials & bioengineering

biological specimen banks: Facilities that collect, store, and distribute tissues, e.g., cell lines, microorganisms, blood, sperm, milk, breast tissue, for use by others. Other uses may include transplantation and comparison of diseased tissues in the identification of cancer. MeSH 1993  

biopreservation: Wikipedia 

bioreactors: Bioprocessing & manufacturing

biorepository: An organization, place, room, or container (physical entity) where biospecimens are stored. In the context of the NCI Best Practices, only biorepositories containing human specimens collected with an intention to use them for research purposes (research biorepositories) are addressed. The physical structure, policies, and the biospecimens and data contained within it are defined collectively as a biospecimen resource, defined below (NCI Best Practices working definition). BioLINC Glossary, NHLBI   

Biorepositories (or biobanks) are "libraries" where biospecimens are stored and made available for scientists to study for clinical or research purposes. These biospecimens are commonly annotated with information about the patient from whom the biospecimen was taken, including data about their medical conditions and background. There are thousands of biorepositories in the United States, which vary widely by size, the type of biospecimens collected, and purpose. Office of Biorepositories and Biospecimen Research, National Cancer Institute What are biospecimens and biorepositories? 

biospecimen: A quantity of tissue, blood, urine, or other biologically derived material. The NHLBI Biologic Specimen Repository stores human biospecimens. Portions or aliquots of a biospecimen are referred to as samples (NCI Best Practices working definition). BioLINC Glossary, NHLBI   

Materials taken from the human body, such as tissue, blood, plasma, and urine that can be used for cancer diagnosis and analysis. When patients have a biopsy, surgery, or other procedure, often a small amount of the specimen removed can be stored and used for later research. Once these samples have been properly processed and stored they are known as human biospecimens. Doctors and researchers may analyze biospecimens to look for indications of disease in the donor. Biospecimens can confirm whether a disease is present or absent in a particular patient, but they also provide other information that may be useful to the physician or a researcher. Each sample may contain DNA, proteins, and other molecules important for understanding disease progression.  Office of Biorepositories and Biospecimen Research, National Cancer Institute What are biospecimens and biorepositories? 

cell assays: Assays & screening   Related term: high content screening
cell-based imaging: See Assays and Screening  high content analysis, high content screening Drug discovery & development cell-based drug discovery

Cell Chip TM System: Was a miniaturized automated platform that performs both High Throughput Screening and High Content Screening on microarrays of selectively localized living cells on chips. Cellomics, Inc. now owned by Thermo Scientific

cell chips:  The in vitro analysis of cell genomic activity has been revolutionized by a variety of chip technologies. Further important advances can be expected as high resolution analytical approaches are utilized to interrogate chips. [National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999] 

cell culture, cell culture techniques: Bioprocessing & manufacturing

cell fusion:
Fusion of somatic cells in vitro or in vivo, which results in somatic cell hybridization. MeSH  Broader term: fusion. Narrower term electroporation

cell microarrays: Cell assays performed on a microarray.   Related terms: tissue array, tissue biochips; Narrower term: Microarray categories frozen cell arrays

cell sorting: Cell sorters differ from cytometers in their ability to separate cells of interest from a complex mixture. Once a cell has been cytometrically characterized, the sorter uses a combination of electronic delays, electrostatic charging, and a static electromagnetic field to separate the chosen cell from the other cells in solution. Institute for Systems Biology, Seattle   Related terms: Molecular imaging  FACS, flow cytometry, flow sorting.  

cellular engineering: The Institute for Cell Engineering was created at The Johns Hopkins University School of Medicine in January 2001, its purpose to focus and strengthen research efforts whose goal at one time likely would have been described as science fiction. ICE supports and houses scientists working to understand how cells' fates are determined and to harness that information in order to select, modify and reprogram human cells. While basic research will be the hallmark of ICE science, the ultimate goal is to mold engineered human cells into therapeutic transplants for a wide range of currently devastating diseases, including Parkinson's disease, Lou Gehrig's disease or amyotrophic lateral sclerosis (ALS), diabetes and heart failure.  Johns Hopkins ICES 2006 

A new field that addresses issues related to understanding and manipulating cell structure-function relationships. This course is intended to be a bridge between cell biologists and engineers, to understand quantitatively cell biological aspects. Cellular engineering is intrinsically connected to the new field of tissue engineering. Rice University BIOE 321Cellular Engineering course, 2003  

cellular imaging: NIGMS supports research that will lead to a better understanding of cell structure, function and regulation at the most basic level. Such visualization at the cellular and subcellular level will lead to fundamental breakthroughs in understanding cell structure and function and how they are dynamically regulated. National Institute of General Medical Sciences, NIH  

cellular models 3D: 3D Cellular Models  June 11-12, 2015 • Boston, MA Program | Register | Download Brochure
3D Cellular Models

cellular protein complexes:  Scientists at Berkeley Laboratory and the University of California, San Francisco have invented a high-throughput method for purifying and identifying protein complexes in wild-type cells without the use of affinity tags and genetic manipulation. This “tagless” strategy detects polypeptides in endogenous protein complexes and then identifies the polypeptides by mass spectrometry.  The invention overcomes the limitations of target affinity purification—the most commonly used method for identifying protein complexes. Target affinity purification can only be applied to biological systems that are amenable to genetic manipulations; may destabilize or alter the protein-protein interactions being studied, causing false positive and false negative results; and requires that a separate genetic strain be constructed, cultured, and analyzed for each polypeptide. Lawrence Berkeley National Lab, Available Technologies: High Throughput Purification and Identification of Cellular Protein Complexes 2009  

cellular reprogramming: "made-to-order" cell lines by reprogramming cells from ill patients. These cell lines, and the techniques for producing them, offer long-sought tools for understanding -- and hopefully someday curing -- difficult-to-study diseases such as Parkinson's disease and type 1 diabetes. Science's Breakthrough of the Year: Cellular Reprogramming 2008   

cellular resolution: See Expression molecular profiling MP

chemical cytometry:
The use of high- sensitivity chemical analysis techniques to study single cells. Sergey N. Krylov, Zheru Zhang, Nora W.C. Chan, Edgar Arriaga, Monica M. Palcic, Norman J. Dovichi, Correlating cell cycle with metabolism in single cells: Combination of image and metabolic cytometry, Cytometry 37 (1): 14- 20, 17 Aug, 1999  Related terms: metabolic cytometry;  flow cytometry

Chinese Hamster Ovary CHO cells: Cell line derived from the ovary of the Chinese hamster, Cricetulus griseus. The species is a favorite for cytogenetic studies because of its small chromosome number. The cell line has provided model systems  for the study of genetic alterations in cultured mammalian cells.  MeSH, 1992

chromosome microdissection: A technique that physically removes a large section of DNA from a complete chromosome. The smallest portion of DNA that can be isolated using this method comprises 10 million base pairs - hundreds or thousands of individual genes. … Cytogeneticists. are able to identify each chromosome based on its unique pattern of dark and light bands. Certain abnormalities, however, cause chromosomes to have unusual banding patterns. …Some chromosomal aberrations have been linked to cancer and inherited genetic disorders, and the chromosomes of many tumor cells exhibit irregular bands. To understand more about what causes these conditions, scientists hope to determine which genes and DNA sequences are located near these unusual bands. Chromosome microdissection is a specialized way of isolating these regions by removing the DNA from the band and making that DNA available for further study. NHGRI "What is chromosome microdissection?"

chromosome painting: A technique for visualizing CHROMOSOME ABERRATIONS using fluorescently labeled DNA probes which are hybridized to chromosomal DNA. Multiple fluorochromes may be attached to the probes. Upon hybridization, this produces a multicolored, or painted, effect with a unique color at each site of hybridization. This technique may also be used to identify cross-species homology by labeling probes from one species for hybridization with chromosomes from another species. MeSH, 1999  Broader term: FISH

comparative genomic hybridization:
This fast growing technique for analyzing genomic information by focusing on the differences in the number of sequence copies is firmly established in basic research and is making swift inroads into the clinic. CGH will eventually play a significant role in the $10 billion molecular diagnostics market, not least in tracking the pathogenesis of, and detecting and monitoring cancer. Insight Pharma Reports: Comparative Genomic Hybridization: Current State and Future Directions, 2006

A method that allows researchers to detect large-scale changes in chromosomes. They can visualize where there is extra genetic material (repeating copies), deleted material, or regions where large portions of genetic material exchange between chromosomes. Many cancers exhibit these types of chromosomal abnormalities. Genome Wide Profiling Comparative Genomic Hybridization, National Cancer Institute   Related terms: in situ hybridization

cryobiology: Cryobiology: International Journal of Low Temperature Biology and Medicine publishes research articles on all aspects of low temperature biology and medicine. Research Areas include: Cryoprotective additives and their pharmacological actions, Cryosurgery, Freeze-drying, Freezing, Frost hardiness in plants, Hibernation, Hypothermia, Medical applications of reduced temperature, Perfusion of organs. Cryobiology, Elsevier   Related terms: antifreeze proteins: Protein categories;  cryomedicine, cryotherapy: Molecular Medicine; cryoelectron tomography: Molecular Imaging; cryoelectron microscopy: Microscopy; cryogenic probe NMR & X-ray crystallography     

cryoelectron microscopy:  Microscopy in which the samples are first stained immunocytochemically and then examined using an electron microscope. Immunoelectron microscopy is used extensively in diagnostic virology as part of very sensitive immunoassays. MeSH 1999 [accessed prior to 2004] 

Electron microscopy involving rapid freezing of the samples. The imaging of frozen-hydrated molecules and organelles permits the best possible resolution closest to the living state, free of chemical fixatives or stains. MeSH, accessed Sept. 2004

cryoelectron tomography:  A technology for taking three- dimensional pictures of a cell overcame key technical obstacles in 2002, providing insights into how the cell's machinery carries out some of the basic processes of life. "Cryoelectron tomography" works essentially like a doctor's CT scan; a computer constructs a 3-D image of a flash- frozen cell from a series of image "slices" created by penetrating electron beams.  "Science's Top 10" AAAS, 19 Dec. 2002  Related term: electron tomography
cryonics: Wikipedia

dielectrophoresis:  Can be used to separate cells. Many medical applications. Related term: electrorotation  

diffusion tensor imaging: Determination of axonal pathways provides an invaluable means to study the connectivity of the human brain and its functional network. Diffusion tensor imaging (DTI) is unique in its ability to capture the restricted diffusion of water molecules which can be used to infer the directionality of tissue components. In this paper, we introduce a white matter tractography method based on anisotropic wavefront propagation in diffusion tensor images. A front propagates in the white matter with a speed profile governed by the isocontour of the diffusion tensor ellipsoid. By using the ellipsoid, we avoid possible misclassification of the principal eigenvector in oblate regions. Jackowski M, Kao CY, Qiu M, Constable RT, Staib LH. White matter tractography by anisotropic wavefront evolution and diffusion tensor imaging Med Image Anal 9(5): 427- 440, Oct 2005  Broader term: MRI Magnetic Resonance Imaging  Related term: tractography   Wikipedia 

electron tomography: Electron tomography studies proteins and cells with imaging technologies based on advanced transmission electron microscopy (TEM). Researchers confront a stubborn, multidimensional gap in which technological deficiencies along at least three different axes coincide: ... Electron tomography bridges the gaps ... Its resolution at the nanometer level falls between the sub-Ångström resolution of XRD and NMR and the sub-micrometer scale of light microscopy. It is sufficient to resolve the tertiary and quaternary structure of proteins, protein complexes and cellular structures.  FEI 

electrorotation: Related term: dielectrophoresis

enucleated: Cell from which the nucleus has been removed, used for nuclear transfer to produce a cloned animal from differentiated cells. Related terms: cloning, nuclear transfer, quiescence

expression microdissection: A new tissue microdissection method ... that permits array target to be efficiently prepared from cells that express a particular protein. The technique is performed using a specially designed polymer tethered to an antibody for cell targeting and to an enzyme (reverse transcriptase) for subsequent labeling of cDNA in the marked cells (or, alternatively, to a dye- generating enzyme for activation of LCM Laser Capture Microdissection] film for subsequent recovery of the targeted cells).  RF Chauaqui et. al. Nature Genetics 32 Suppl:509- 514, Dec. 2002  Related terms: layered expression scanning; Laser Capture Microdissection LCM

FACS: Fluorescence Activated Cell Sorting, also known as flow cytometry. FACS is a powerful technique for analyzing and characterizing cells that are marked with a fluorescent label (s) and is used widely in both basic research and clinical diagnostic applications. As the individual suspension cell passes through the sensing region of the FACS machine, fluorescent signals are acquired, analyzed, and stored in a computer. The size of cells as well as the expression of interested molecules (such as proteins) within a single cell can be determined. Specific cells can be further separated, sorted, and collected for further analysis.  NFCR Center for Therapeutic Antibody Engineering Glossary  Related terms: cell sorting, flow cytometry, flow sorting

flow cytometry: Technique for characterizing or separating particles such as beads or cells, usually on the basis of their relative fluorescence. IUPAC Combinatorial Chemistry

Technique using an instrument system for making, processing, and displaying one or more measurements on individual cells obtained from a cell suspension. Cells are usually stained with one or more fluorescent dyes specific to cell components of interest, e.g., DNA, and fluorescence of each cell is measured as it rapidly transverses the excitation beam (laser or mercury arc lamp). Fluorescence provides a quantitative measure of various biochemical and biophysical properties of the cell, as well as a basis for cell sorting. Other measurable optical parameters include light absorption and light scattering, the latter being applicable to the measurement of cell size, shape, density, granularity, and stain uptake. MeSH, 1982  Related terms: cell sorting, FACS, flow sorting; Labels, signaling & detection: fluorescence, dyes Narrower term: metabolic cytometry

flow sorting: Employs flow cytometry to separate, according to size, chromosomes isolated  from cells during cell division when they are condensed and stable. As the chromosomes flow singly past a laser beam, they are differentiated by analyzing the amount of DNA present, and individual chromosomes are directed to specific collection tubes. Primer on Molecular Genetics, ORNL, US   Related terms: cell sorting, FACS, flow cytometry

genotype tissue expression: The Common Fund's Genotype-Tissue Expression (GTEx) program aims to study human gene expression and regulation in multiple tissues, providing valuable insights into the mechanisms of gene regulation and, in the future, its disease-related perturbations. Genetic variation between individuals will be examined for correlation with differences in gene expression level to identify regions of the genome that influence whether and how much a gene is expressed. The GTEx project includes the following initiatives: Novel Statistical Methods for Human Gene Expression Quantitative Trait Loci (eQTL) Analysis  Laboratory, Data Analysis, and Coordinating Center (LDACC) caHUB Acquisition of Normal Tissues in Support of the GTEx Project. NIH Common Fund

heterologous transplantation:  Transplantation between animals of different species. MeSH 1965  Related term: xenotransplantation

host: A cell whose metabolism is used for growth and reproduction of a virus, plasmid, or other form of foreign DNA.  IUPAC Biotech

host-vector system: A compatible combination of host (e.g. bacteria) and vector (e.g. plasmid) that allows propagation of DNA. IUPAC Biotech

human tissue engineering No universally agreed definition exists. But a Commission working hypothesis suggests a human tissue engineered product means any autologous (emanating from the patient himself) or allogeneic (coming from another human being) product which: contains, consists of, or results in engineered human cells or tissues; and has properties for, or is presented as having properties for, the regeneration, repair or replacement of tissue, where the new tissue or cells, in whole or in part, are structurally and functionally analogous to the original tissue that is being regenerated, repaired or replaced. European Commission: Enterprise Europe, Facing the Future: Human Tissue Engineering, No. 15, April- June 2004  Broader term: tissue engineering 

hybridoma: A hybrid cell line resulting from the fusion of a specific antibody- producing spleen cell (lymphocyte) with a myeloma cell, which has the growth characteristics of the myeloma component and the antibody- secreting characteristics of the lymphocyte, and will multiply to become a source of pure monoclonal antibody. IUPAC Biotech

Cells artificially created by fusion of activated lymphocytes with neoplastic cells. The resulting hybrid cells are cloned and produce pure or "monoclonal" antibodies or T-cell products, identical to those produced by the immunologically competent parent, and continually grow and divide as the neoplastic parent. MeSH, 1982

image analysis/image processing:  Assays & screening  [in context of high -content screening]

image cytometry: A technique encompassing morphometry, densitometry, neural networks, and expert systems that has numerous clinical and research applications and is particularly useful in anatomic pathology for the study of malignant lesions. The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. MeSH, 1996  

an image-based study or measurement of cells. How image cytometry differs from normal microscopic studies of cells is that very large populations of cells (typically on the order of 104 to 108 cells) are imaged. To make this technically feasible on the two-photon microscope, high-speed imaging techniques are required. ... one of the main strengths of TPM is its ability to image thick tissues specimens ... An important avenue that we are also pursing is the visualization and image analysis tools necessary to study these types of datasets. A typical dataset can generate tens of gigabytes of data, far too much for a human operator to manually classify. It becomes necessary to use automated segmentation procedures to classify the cell population into various sub-populations of biological interest.  So Lab, MIT 

immortalizing oncogene  A gene that upon transfection enables a primary cell to grow indefinitely in culture. FAO glossary

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. Related terms: Biomarkers  biomarkers Cell biology  gene localization, subcellular localization;  Gene definitions localization; Proteins protein localization
IHCWorld: Immunohistochemistry methods & techniques 

in vivo molecular imaging: An essential tool in drug discovery and development, translational approaches in in vivo molecular imaging research, utilization in therapeutic areas  In Vivo Molecular Imaging June 8-9, 2011 • Philadelphia, PA Program | Register | Download Brochure  
In Vivo Molecular Imaging

Laser Capture Microdissection LCM:
One of the most exciting new developments in biomedical research is laser capture microdissection, a technique which allows for the isolation of single cells or populations of cells from human or animal tissue sections.  This technique enables the researcher to investigate DNA and proteins from specific cells or groups of cells free of adjacent tissue or contact contaminants.  Such cutting-edge technologies as DNA microarrays and proteomics depend upon the isolation of single cells or pure populations of cells with specific phenotypes for meaningful results. East Carolina University, LCM Core Laboratory 2010   

Can be used to help isolate low- abundance proteins.
Laser Capture Microdissection Wikipedia   
Related terms: Expression expression microdissection, layered expression scanning, molecular profiling

laser scanning cytometry LSC: There are two major forms of laser scanning microscopy, namely confocal laser scanning microscopy (CLSM) and multiphoton laser scanning microscopy (MPLSM). he two forms are very similar at the illumination side (as opposed to the detection side of the methodology).  Bruce Jenks, Cellular Animal Physiology, Univ. of Nijmegen Netherlands  Broader terms: cytometry, Molecular imaging  lasers  

laser tweezers: Laser tweezers  and related approaches are important for manipulation and isolation of subcellular organelles and structural components. National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999  Related terms: optical trapping, optical tweezers; Broader term: micromanipulation

Library of Integrated Network-Based Cellular Signatures LINCS: The basic components of biological systems – genes, proteins, metabolites and other molecules – work together in a highly orchestrated manner within cells to promote normal development and sustain health. Understanding how these interconnected components of biological pathways and networks are maintained in health, and how they become perturbed by genetic and environmental stressors and cause disease, is challenging but essential to developing new and better therapies to return perturbed networks to their normal state.  To achieve this goal, the Library of Integrated Network-based Cellular Signatures (LINCS) program aims to develop a “library” of molecular signatures, based on gene expression and other cellular changes that describe the response that different types of cells elicit when exposed to various perturbing agents, including siRNAs and small bioactive molecules. High-throughput screening approaches will be used to interrogate the cells and mathematical approaches will be used to describe the molecular changes and patterns of response. The data will be collected in a standardized, integrated, and coordinated manner to promote consistency and comparison across different cell types. LINCS NIH Common Fund 

live cell assays: Assays  

lymphochip: A specialized DNA microarray, termed the "Lymphochip", that is enriched in genes which are selectively expressed in lymphocytes and genes which regulate lymphocyte function (1). Since the majority of human lymphomas appear to represent malignant transformation of the germinal center B lymphocyte, a cDNA library was created from germinal center B lymphocytes that were purified by flow sorting from human tonsils. Louis Staudt Lab "Current Projects" NCI, NIH  Related terms: Cancer genomics

metabolic cytometry:: A form of chemical cytometry that monitors a cascade of biosynthetic and biodegradation products generated in a single cell. Sergey N. Krylov, Zheru Zhang, Nora W.C. Chan, Edgar Arriaga, Monica M. Palcic, Norman J. Dovichi, Correlating cell cycle with metabolism in single cells: Combination of image and metabolic cytometry, Cytometry 37 (1): 14- 20, 17 Aug, 1999  

micellar nanocontainers: Block copolymer micelles are water- soluble biocompatible nanocontainers with great potential for delivering hydrophobic drugs. An understanding of their cellular distribution is essential to achieving selective delivery of drugs at the subcellular level. R. Savic, L. Luo, A. Eisenberg, D. Maysinger, Micellar nanocontainers distribute to defined cytoplasmic organelles Science 300 (5619): 615- 618, Apr. 25, 2003  Broader term: nanocontainers

microimaging: An emerging area of scientific opportunity is the design and use of probes to study structure and function at the molecular and subcellular level in living cells. Approaches and tools such as labels that attach to specific peptide or nucleotide moieties, Fluorescent Resonance Energy Transfer, Green Fluorescent Protein (and mutant color variants), and genetically-engineered voltage or ion-sensitive fluorophores are making it possible to begin to visualize not only the distribution of molecular species in cells, but the manner in which they interact. Research and development of these, and other such technologies, hold the promise of providing scientists the capabilities to track the ebb and flow of signal transduction cascades, protein-protein interactions, protein-nucleotide interactions, movement of subcellular elements within cells, and other dynamic events. And, it appears that as such tools are elaborated and further studied, they will permit such observations to be quantitative and made in real time. Finally, bioengineering individual probes that are detectable by multiple modalities, (e.g., electron microscopy, fluorescent microscopy and fluorescent spectroscopy, magnetic resonance imaging) would add great value by allowing independent lines of scientific inquiry to converge on the same cellular process and/or structure as indicated by the multimodal probe. This area of science and technology is poised for major advances, and these advances would bring new levels of understanding of the molecular physiology of nervous system cells, as well as the manner in which this physiology is affected by disease, pharmacologic agents, development, etc. Probes for Micro- Imaging the Nervous System, SBIR, 2008  

micro-PET: Molecular Imaging

microspectrophotometry: Analytical technique for studying substances present at enzyme concentrations in single cells, in situ, by measuring light absorption. Light from a tungsten strip lamp or xenon arc dispersed by a grating monochromator illuminates the optical system of a microscope. The absorbance of light is measured (in nanometers) by comparing the difference between the image of the sample and a reference image. MeSH 1990

microtissues: Scientists at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory can now control how cells connect with one another in vitro and assemble themselves into three-dimensional, multicellular microtissues. The researchers demonstrated their method by constructing a tailor-made artificial cell-signaling system, analogous to natural cell systems that communicate via growth factors.  A new way to assemble cells into 3D microtissues, Lawrence Berkeley National Lab, 2009

microdissection: See Laser Capture Microdissection, tissue microdissection  

models biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment. MeSH 1973

multiprotein complexes:  Most cellular processes are carried out by molecular machines that consist of many interacting proteins. These protein complexes lie at the heart of life science research, but they are notoriously hard to study. Their abundance is often too low to extract them directly from cells and generating them with recombinant methods has been a daunting task. A new technology to produce multiprotein complexes, developed by researchers at the European Molecular Biology Laboratory [EMBL] in Grenoble, France, and the Paul Scherrer Institute [PSI] in Villigen, Switzerland, now makes the biologist's life easier. First Fully Automated Pipeline For Multiprotein Complex Production Science Daily May 7, 2009

nanoimaging: Real-time subcellular imaging of structure, function, properties and metabolism has the potential to make enormous contributions to solving biomedical problems. Trans- NIH Bioengineering Nanotechnology Initiative, SBIR, PA Number 02- 125:  

nano-PET: Molecular Imaging

Near InfraRed spectroscopy NIR: A noninvasive technique that uses the differential absorption properties of hemoglobin and myoglobin to evaluate tissue oxygenation and indirectly can measure regional hemodynamics and blood flow. Near- infrared light (NIR) can propagate through tissues and at particular wavelengths is differentially  absorbed by oxgenated vs. deoxygenated forms of hemoglobin and myoglobin. illumination of intact tissue with NIR allows qualitative assessment of changes in the tissue concentration of these molecules. The analysis is also used to determine body composition. MeSH, 1997

nuclear transfer: Wikipedia  See also under enucleated

nucleome: -Omes & -omics

optical mapping:  Uses DNA from lysed cells.

optical trapping:  Optical trapping of small particles by forces exerted by laser radiation pressure has recently been introduced into the study of biological systems. The single- beam gradient trap (optical tweezers) employs a single strongly focused laser beam. In this case, particle size is much less than and the laser light exerts a force pulling the particle toward the high focus part of the beam. Such manipulation of micron- sized (particle size larger than ) particles is also feasible. Manipulations of cells and intracellular organelles have extended to laser cutting (scissors) and to use of two- photon systems. National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999      Relate/synonymous? terms: laser tweezers, optical tweezers 

optical tweezers: Developed at Bell Labs in the 1980s ... The method relies on the fact that light waves exert minute forces as well as transmitting energy. If an object is small enough -  in this case about 5 micrometers across -- it can be "trapped" or held still by a focused beam of laser light. When the laser's position changes, the trapped object moves too ... The new technique allows researchers to make measurements not possible with conventional methods and should make it easier to judge the effectiveness of inhibitors and other medicines at a variety of concentrations. "Optical tweezers measure stickiness" NIST Technology at a glance, Winter 1997    Related terms: laser tweezers; optical traps (How similar are these to optical tweezers?)  Broader term: micromanipulation

organotypic: Despite their wide use, the physiological relevance of organotypic slices remains controversial. Such cultures are prepared at 5 days postnatal. Although some local circuitry remains intact, they develop subsequently in isolation from the animal and hence without plasticity due to experience. Development of synaptic connectivity and morphology might be expected to proceed differently under these conditions than in a behaving animal. deSimoni, Anna et. al, Development of rat CAI Neurones, Journal of Physiology 550 (1) : 135-147, 2003 

organotypic models:  Carcinoma cell invasion is traditionally studied in three-dimensional organotypic models composed of type I collagen and fibroblasts. However, carcinoma cell behavior is affected by the various cell types and the extracellular matrix (ECM) in the tumor microenvironment. In this study, a novel organotypic model based on human uterine leiomyoma tissue was established and characterized to create a more authentic environment for carcinoma cells. A novel organotypic model mimics the tumor microenvironment. Nurmenniemi S, Sinikumpu T, Alahuhta I, Salo S, Sutinen M, Santala M, Risteli J, Nyberg P, Salo T  Am J Pathol. 2009 Sep;175(3):1281-91. Epub 2009 Aug 13. .

patch clamping: A technique for studying the electrical currents involved in the movement of ions across cell membranes. With this technique, an electrode is affixed to the membrane so that a small patch of membrane is electrically isolated, allowing currents through it can be determined. Patch clamping is a high-resolution technique, meaning that movements through one ion channel can be recorded. Patch clamping can also involve the use of very fine pipette to measure what is going on in or on an individual cell.  

patch clamp pipettes: Ultrasensitivity Related terms: single cell transcriptome, proteome, and metabolome

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

Useful for determining cellular structure.

physiological proteomics:  Proteomics relying on two- dimensional (2-D) gel electrophoresis of proteins followed by spot identification with mass spectrometry is an excellent experimental tool for physiological studies opening a new perspective for understanding overall cell physiology. This is the intriguing outcome of a method introduced by Klose and O'Farrell independently 25 years ago. Physiological proteomics requires a 2-D reference map on which most of the main proteins were identified. ...  A big challenge for future studies is to provide an experimental protocol covering the fraction of intrinsic membrane proteins that almost totally escaped detection by the experimental procedure used in this study. K. Buttner et. al. A comprehensive two- dimensional map of cytosolic proteins of Bacillus subtilis Electrophoresis. 22(14):2908-2935, 2001 Aug.

plasmid, plasmids: Extrachromosomal genetic element consisting generally of circular double- stranded DNA, which can replicate independently of chromosomal DNA.  Used as vectors for cloning DNA in bacteria or yeast host cells. IUPAC Bioinorganic 

Autonomously replicating, extrachromosomal circular DNA molecules, distinct from the normal bacterial genome and nonessential for cell survival under nonselective conditions. Some plasmids are capable of integrating into the host genome. A number of artificially constructed plasmids are used as cloning vectors. DOE

Any extrachromosomal hereditary determinant. Plasmids are self- replicating circular molecules of DNA that are found in a variety of bacterial, archaeal, fungal, algal, and plant species. MeSH, 1978  

Positron Emission Tomography PET: Molecular Imaging

quiescence:  This is the state in which all but the most basic functions of a cell or group of cells has stopped. This is usually a response to an unfavourable environment, such as one in which the food supply is low or absent. The cell becomes dormant until its surroundings are more favourable. In this state the genes that define the specialist function of a cell "switch off" making the cell suitable for nuclear transfer.  Cloning & nuclear transfer: A short glossary, Mike McKeen,  Roslin Institute Online, Scotland, 1999

Related terms: cloning, enucleated, nuclear transfer rDNA: See recombinant DNA  

reverse genomics: A genetic approach that has proved useful in discovering and characterizing mammalian genes that regulate cell proliferation and suppress tumorigenesis. In reverse genomics, scientists use "reporter genes," whose expression is controlled by DNA sequences linked to them, to investigate genetic regulatory mechanisms in both simple and higher organisms. Researchers can now directly isolate genes that specify functions of particular interest using reporter- gene- containing cassettes that can manipulate, as well as monitor, the expression of genes in mammalian chromosomes. Stanley N. Cohen, Stanford Univ. "Manipulative Reporter Genes and "Reverse Genomics"  Joshua Lederberg Distinguished Lecture in Molecular Genetics, Rockefeller Univ. Oct. 27, 2000   Related term: Genomic technologies reverse genetics

single cell detection and manipulation: [Viola Vogel, director of the Center of Nanotechnology at the University of Washington] indicated that single cell detection is even more nascent. "If you want to make a single molecule measurement in a cell system, you need to develop a lot of the technology that does not exist today," remarked Jay Trautman, CEO of Praelux Inc., Lawrenceville, N.J. That technology should allow researchers to target individual molecules within the cell, track where they are going, and record changes--all without significantly interfering with cellular physiology. Dave Amber " Researchers Seek Basics Of Nano Scale" Scientist 14 (16): 1, Aug. 21, 2000

single cell NMR imaging:  Spatial and temporal molecular species maps of intact single cells will be needed by biologists in the future. The development of single cell NMR imaging is thus particularly important for characterization of non- protein signaling elements within the cell. National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999

single cell studies: Recent developments in optical imaging, particularly quantitative fluorescence microscopy; ultra- small volume sampling and analysis; incorporation of optically useful probes, [Labels, signaling & detection] such as green fluorescent protein into cellular constituents; combinations of photobleaching and imaging; and optical approaches to determining the rates and equilibria of intracellular processes clearly indicate the enormous potential of in vivo single cell studies for our understanding of cell physiology, as well as the remaining substantial difficulties. Biologists need tools capable of analyzing the genomic and proteomic information of the living single cell. The quantitation, localization, and identification of proteins within the cell, as well as full characterization of intracellular interactions involving proteins in their structural, catalytic, and control roles, will be essential for development of a comprehensive and integrative view of cell physiology. Furthermore, development of highly specific drugs must ultimately involve screening against in vivo cellular processes. Thus, the envisioned technology development will enable the application of profoundly powerful combinatorial approaches to understanding and regulating the interior world of the cell, as well as characterizing the cell- physiological consequences of rare phenotypes - particularly those associated with disease. NCRR, NHGRI, NIGMS Integrated Genomics Technologies Request for Applications, Dec. 23, 1998

site-directed mutagenesis: The substitution or modification of a single amino acid at a defined location in a protein is performed by changing one or more base pairs in the DNA using recombinant DNA technology. IUPAC Bioinorganic

Mutagenesis where the mutation is caused by in vitro induction directed at a specific site in a DNA molecule. The most common method involves use of a chemically synthesized oligonucleotide mutant which can hybridize with the DNA target molecule. The resulting mismatch - carrying DNA duplex may then be transfected into a bacterial cell line and the mutant strands recovered. MeSH, 1991 

somatic cell hybrids: culture lines that contain the entire complement of the mouse genome and a few human chromosomes. These culture lines are developed by mixing human and mouse cells in the presence of the Sendai virus. The virus facilitates the fusing of the two cell types to form a hybrid cell. For a reason that is not entirely known, most, but not all, human chromosomes are lost from the hybrid cell

Somatic Cell Nuclear transfer (SCNT)A technique that combines an enucleated egg and the nucleus of a somatic cell to make an embryo. SCNT can be used for therapeutic or reproductive purposes, but the initial stage that combines an enucleated egg and a somatic cell nucleus is the same. See also therapeutic cloning and reproductive cloning.

sonocytology:  Sonocytology, a recently developed technique within nanotechnology research, uses a scanning probe microscope to record the vibrational movements of cell walls and amplifies those vibrations so that humans can hear them. ...In this paper, I will address how raw cellular vibrations are converted into cellular sounds that scientists can interpret as conveying meaningful information regarding the dynamism of cellular interiors. Further, I will examine the conditions that enable scientists to describe cells as actors capable of ‘speaking’ or ‘screaming,’ and how listening to cellular sounds may eventually change how scientists think about cells—as subjects that are dynamic, environmentally situated, and experiential. SONIC EUKARYOTES: SONOCYTOLOGY, CYTOPLASMIC MILIEU AND THE TEMPS INTERIEUR 2 03 2009 SOPHIA ROOSTH  MutaMorphosis  

subcellular localization:  A variety of approaches—including tagging and fluorescence technologies, cellular isolation methods, gels, and mass spectrometry—are being used in these studies, which aim to track the location and/or movement of proteins or protein complexes in subcellular compartments.  "Protein Localization Studies provide key insights into protein function" CHI's GenomeLink 15.2 

subcellular issue-specific localization: A major methodology is an immunohistochemistry approach that uses 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 a tissue sample.  "Protein Localization Studies provide key insights into protein function" CHI's GenomeLink 

surface plasmon resonance: Microscopy 

synthetic biology: This exciting field is evolving so rapidly that no widely accepted definitions exist. Common to many explanations is the idea of synthetic biology as the application of engineering principles to the fundamental components of biology. … More recent advances however, have enabled scientists to make new sequences of DNA from scratch. By combining these advances with the principles of modern engineering, scientists can now use computers and laboratory chemicals to design organisms that do new things—like produce biofuels or excrete the precursors of medical drugs. To many people, this is the essence of synthetic biology.    What is synthetic biology: Defining the concept, Synthetic Biology Project

Synthetic biology is the name given to an emerging field of research that combines elements of biology, engineering, genetics, chemistry, and computer science. Synthetic biology – called ``synbio’’ for short – joins the knowledge and techniques of biology with the practical principles and techniques of engineering. Achievements in synthetic biology rely on artificially created DNA to create new biochemical systems or organisms with novel or enhanced characteristics. President's Council on Bioethics Synthetic BIology FAQ 2010

Synthetic biology: planning for a secure future, American Institute of Biological Sciences

President's Council on Bioethics Synthetic BIology report 2010
Synthetic Biology FAQ 

synthetic lethal screening: Second- site mutations that are not lethal themselves, but in combination with the primary defect cause lethality. Used in yeast genetics, but can be generalized to model organisms other than yeast. The rationale is that many mutations commonly found in tumors that result in instability of the genome are loss- of- function mutations, and it is difficult to replace the function of missing or altered proteins with a small- molecule drug. The idea of screening for second- site mutations is to identify targets that when inhibited by a specific novel drug may specifically result in the death of cells that have such a loss- of- function mutation, but that will be nontoxic to normal cells. 

tissue array analysis: The simultaneous analysis of multiple samples of TISSUES or CELLS from BIOPSY or in vitro culture that have been arranged in an array format on slides or microchips. MeSH 2005  Tissue Array Research Program, National Cancer Institute   

tissue banking:  When remaining or extra tissue that has been removed during a medical procedure such as an operation, biopsy, or blood test is collected and stored. This extra tissue, not needed for your diagnosis or treatment, is used by scientists to study disease and find better ways to diagnose, prevent, and treat cancer in the future.  Dana Farber Cancer Institute   Related terms: biobanking, biospecimens
Tissue Banks & Repositories Tools, NCI 
Tissue Biospecimen Banking & Technology Tools Knowledge Center, NCI  

tissue chips: See also tissue microarrays 

Tissue Engineered Medical Products Standards TEMPS:  The standards process for tissue engineered medical products is underway within the American Society for Testing and Materials International (ASTM) Committee F-04, Division IV Tissue Engineered Medical Products ( of Committee F04 on Medical and Surgical Materials and Devices. Information describing the process and progress will be presented at this FDA site. Updated information and current draft documents can be viewed at (http://www.astm.org2). Additional information on Tissue Engineering may be obtained at the Pittsburgh Tissue Engineering Initiative3 site.  FDA, Center for Devices & Radiologic Health, US, Tissue Engineered Medical Products Standards TEMPS, 2009 

tissue engineering:  Generating tissue in vitro for clinical applications, such as replacing wounded tissues or impaired organs. A cell culture facility is required for cell harvest and expansion. MeSH, 2002

The term "tissue engineering" was coined at an NSF [National Science Foundation] -sponsored meeting in 1987. At a later NSF- sponsored workshop, tissue engineering was defined as "...the application of principles and methods of engineering and life sciences toward fundamental understanding ...and development of biological substitutes to restore, maintain and improve [human] tissue functions." This definition is intended to include procedures where the biological substitutes are cells or combinations of different cells that may be implanted on a scaffold such as natural collagen or as synthetic, biocompatible polymers to form a tissue. "Tissue Engineering" National Science Foundation  Narrower term: human tissue engineering Related term: Cell biology  cell patterning

tissue microarrays: Tissue microarrays are produced by a method of re-locating tissue from conventional histologic paraffin blocks such that tissue from multiple patients or blocks can be seen on the same slide. This is done by using a needle to biopsy a standard histologic sections and placing the core into an array on a recipient paraffin block. This technique, originally described by in 1987 by Wan, Fortuna and Furmanski in Journal of Immunological Methods. They published a modification of Battifora's "sausage" block technique whereby tissue cores were placed in specific spatially fixed positions in a block. The technique was popularized by Kononen and colleagues in the laboratory of Ollie Kallioneimi after a publication in Nature Medicine in 1998. This technology should not be confused with DNA microarrays where each tiny spot represents a unique cloned cDNA or oligonucleotide. In tissue microarrays, the spots are larger and contain small histologic sections from unique tissues or tumors. What are tissue microarrays?, Tissue Microarray Facility, Yale University School of Medicine, US    Related term  lymphochip
Tissue Microarray Pro
gram, NCI NIH US 

tissue microdissection: A laboratory method that is used to procure specific cells or cell populations from a histology slide under direct microscopic visualization. The recovered cells can be studied with a variety of DNA, messenger RNA, and protein analysis methods, including new high- throughput gene expression and proteomics technologies. This approach is permitting investigators to comprehensively examine the molecular anatomy of cells in tissue sections for the first time. JW Gillespie, The role of tissue microdissection in cancer research. Cancer Journal 2001 Jan-Feb;7(1): 32- 39, Jan- Feb 2001  

tissue models:  Related term: organotypic

vector: 1. A DNA molecule (plasmid, virus, bacteriophage, artificial or cut DNA molecule) capable of being replicated and bearing cloning sites for the introduction of foreign DNA, used to introduce this DNA into host cells. 2. Any organism that transmits a disease between two hosts. IUPAC Biotechnology 

An agent, such as a virus or a small piece of DNA called a plasmid, that carries a modified or foreign gene. When used in gene therapy, a vector delivers the desired gene to a target cell. NHGRI 

The two different senses of the IUPAC definitions should be clear from context.  The organisms transmitting pathogens can be insects or small animals. Vectors used in gene therapy are not pathogenic.  Narrower terms: BAC Bacterial Artificial Chromosome, cloning vector, genetic vector, plasmids    Vector databases see Databases & software directory 

white biotechnology:  An emerging field within modern biotechnology that serves industry. It uses living cells like moulds, yeasts or bacteria, as well as enzymes to produce goods and services. Living cells can be used as they are or improved to work as "cell factories" to produce enzymes for industry.  EuropaBio "What is white biotechnology?", 2004

xenografts: The living animal material that is transplanted into humans in xenotransplantation.. Health Canada, Therapeutic Products Programme,  Scientific Issues Raised by Xenotransplantation, Canadian Public Health Association, 2000 

xenotransplantation:  The term usually meant to describe the transfer of living cells, tissues and organs from non- human animals into humans for medical purposes. Public Consultation on Xenotransplantation glossary, Canadian Public Health Association,   Related term: heterologous transplantation
, CBER, FDA   

Yeast Artificial Chromosomes YACS: Chromosomes in which fragments of exogenous DNA ranging in length up to several hundred kilobase pairs have been cloned into yeast through ligation to vector sequences. These artificial chromosomes are used extensively in molecular biology for the construction of comprehensive genomic libraries of higher organisms. MeSH, 2002

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

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