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Map 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 various
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. Thus, by necessity, biobanking is both a science and a business.
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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 http://en.wikipedia.org/wiki/Biopreservation 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 https://biolincc.nhlbi.nih.gov/glossary/ 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? http://biospecimens.cancer.gov/patientcorner/ 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 https://biolincc.nhlbi.nih.gov/glossary/ 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? http://biospecimens.cancer.gov/patientcorner/ cell assays: Assays & screening
Related term: high content screening 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 http://www.cellomics.com 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] Google = about 1,570 Sept. 16, 2003; about 10,800 June 21, 2004
cell culture, cell culture techniques: Bioprocessing
& manufacturing cell microarrays: Cell assays performed on a microarray. Google "cell microarrays" = about 91 July 10, 2002; about 426 Sept. 16, 2003; about 653 June 21, 2004 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 http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Generation/Cell_Sorting
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 http://www.hopkins-ice.org/about/index.html 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 http://www.ruf.rice.edu/~bioewhit/courses/bioe321/home.html
cellular imaging: NIGMS supports research that will lead to a better understanding of cell structure, function and regulation at the most basic level. A growing number of imaging strategies and techniques enable fundamental breakthroughs at cellular and subcellular levels. NIGMS funds projects applying and developing a wide range of imaging applications and technology, including optical/fluorescence microscopy for cellular imaging, electron microscopy, single molecule spectroscopy, live cell imaging and the development of probes and sensors. National Institute of General Medical Sciences, NIH http://www.nigms.nih.gov/Initiatives/CellImaging/Overview.htm 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 http://www.lbl.gov/tt/techs/lbnl2538.html 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 http://www.sciencedaily.com/releases/2008/12/081218141720.htm Google = about 21,800 Nov 12, 200, about 20, 700 March 30 2009 cellular resolution: See Expression molecular profiling MP 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?" http://www.genome.gov/10000204
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 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 http://www.cancer.gov/cancertopics/understandingcancer/genomewideprofiling/page5 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 http://authors.elsevier.com/JournalDetail.html?PubID=622814&Precis=&popup=
Google = about 34,000 Sept. 23, 2004; about 375,000 Nov 12, 2007 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 http://www.eurekalert.org/pub_releases/2002-12/aaft-tt121202.php
Related term: electron tomography dielectrophoresis: http://en.wikipedia.org/wiki/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 http://en.wikipedia.org/wiki/Diffusion_tensor_imaging 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 http://www.fei.com/applications/life-sciences/structural-biology/electron-tomography.aspx electrorotation: http://en.wikipedia.org/wiki/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 http://research4.dfci.harvard.edu/nfcr-ctae/research/tech_glossary.php
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 http://www.ornl.gov/hgmis/publicat/primer/intro.html
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 http://commonfund.nih.gov/GTEx/
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 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 http://web.mit.edu/solab/Research/ImageCytometry.html 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 in vivo molecular imaging: An essential tool in drug discovery and
development, translational approaches in in vivo molecular imaging research,
utilization in therapeutic areas
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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 http://www.celanphy.science.ru.nl/Bruce%20web/scanning%20microscopy.htm
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 Google = about 2,640 Aug. 8, 2002; about 4,170 June 23, 2004 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 http://commonfund.nih.gov/LINCS/overview.aspx 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 http://lymphochip.nih.gov/current.html 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 http://www3.interscience.wiley.com/cgi-bin/abstract/63002751/START 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 http://grants.nih.gov/grants/guide/pa-files/PA-09-062.html 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 http://newscenter.lbl.gov/press-releases/2009/03/05/3-d-microtissues/
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 http://www.sciencedaily.com/releases/2009/05/090504094426.htm
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: http://grants1.nih.gov/grants/guide/pa-files/PA-02-125.html 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 http://en.wikipedia.org/wiki/Nuclear_transfer See also under enucleated nucleome: -Omes & -omics optical mapping: http://en.wikipedia.org/wiki/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 Google = about 2,330 Aug. 8, 2002; about 7,000 June 23, 2004 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 http://www.nist.gov/public_affairs/taglance/tag97win/tag97win.htm Google = about 5,230 Aug. 8, 2002; about 16,600 June 23, 2004 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 http://jp.physoc.org/cgi/content/full/550/1/135 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 http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=10087620&form=6&db=b... 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
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
Related terms: cloning, enucleated, nuclear transfer
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 http://www.rockefeller.edu/lectures/cohen102700.html 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 http://www.the-scientist.com/yr2000/aug/amber_p1_000821.html
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 http://grants.nih.gov/grants/guide/rfa-files/RFA-RR-99-003.html
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 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 http://mutamorphosis.wordpress.com/2009/03/02/sonic-eukaryotes-sonocytology-cytoplasmic-milieu-and-the-temps-interieur/ 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 http://www.chidb.com/newsarticles/issue15_2.asp 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 http://www.chidb.com/newsarticles/issue15_2.asp surface plasmon resonance: Microscopy synthetic
biology: 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
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 http://ccr.cancer.gov/tech_initiatives/tarp/ 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 http://www.dfhcc.harvard.edu/visitorcenter/tissue-banking/
Related terms: biobanking, biospecimens tissue chips: See also
tissue microarrays Google = "tissue
arrays" about 1040 July 10, 2002 "tissue chips" about 77 Sept.
16, 2003 tissue arrays about 3,170 tissue chips about 213 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 (http://www.astm.org/1) 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 http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/Standards/ucm135369.htm 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 http://www.nsf.gov/od/lpa/nsf50/nsfoutreach/htm/n50_z2/pages_z3/45_pg.htm 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 http://tissuearray.org/yale/tisarray.html
Google= about 1071 July 10, 2002; about 5,360 Sept. 16, 2003 Related
term lymphochip 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: Compared to traditional cell-based assay
monolayers, three-dimensional (3D) models more closely mimic native tissues. 3D
tissue models provide a means for systematic, repetitive, and quantitative
investigation of drugs, serving as platforms for screening of drugs as well as
pharmacokinetic and pharmacodynamic analysis of drugs.
Predictive Functional
Tissue Models: Moving into the Third Dimension of Drug Discovery and Development
November 17-18, 2011 • Boston, MA Program
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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 http://www.europabio.org/white_biotech.htm 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 http://www.cpha.ca/en/activities/xeno/glossary.aspx 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, http://www.cpha.ca/en/activities/xeno/glossary.aspx
Related term:
heterologous transplantation Bibliography
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