Finding guide for terms in these glossaries Technologies map   Site Map

Ultimately, the new genomic and proteomics technologies are not just about generating reams of disparate bits of data, they aim to provide a unified view of complex biological systems. The first step in this process is generating gene networks from gene sequence and expression data. Such studies do not require new tools as much as sophisticated and comprehensive approaches to data compilation. Correspondingly, protein pathway studies pull together data about how changes in protein expression levels modulate the expression of other proteins in a cascade fashion. In our framework, integration at the protein level has been extended into systems biology, which can be described as the integration of genomic, proteomic and metabolic data.  CHI’s Drug Discovery and Development Map  http://www.healthtech.com/drugdiscoverymap.asp

AFM atomic force microscopy: A type of scanning probe microscopy in which a probe systematically rides across the surface of a sample being scanned in a raster pattern. The vertical position is recorded as a spring attached to the probe rises and falls in response to peaks and valleys on the surface. These deflections produce a topographic map of the sample. MeSH, 1995 Microscopy glossary

automation: Needed to industrialize processes, for higher throughput, greater reliability and often for cost- effectiveness. Related terms:  LIMS, robotics Drug discovery & development glossary

bioengineering: Rooted in physics, mathematics, chemistry, biology, and the life sciences. It is the application of a systematic, quantitative, and integrative way of thinking about and approaching the solutions of problems important to biology, medical research, clinical proactive, and population studies. The NIH Bioengineering Consortium agreed on the following definition for bioengineering research on biology, medicine, behavior, or health recognizing that no definition could completely eliminate overlap with other research disciplines or preclude variations in interpretation by different individuals and organizations.

Integrates physical, chemical, or mathematical sciences and engineering principles for the study of biology, medicine, behavior, or health. It advances fundamental concepts, creates knowledge for the molecular to the organ systems levels, and develops innovative biologics, materials, processes, implants, devices, and informatics approaches for the prevention, diagnosis, and treatment of disease, for patient rehabilitation, and for improving health. NIH, Bioengineering Consortium, 1997   http://www.becon.nih.gov/bioengineering_definition.htm   Bioengineering & Biomaterials glossary

biodefense:  The multiple independent efforts in biodefense need to be developed into a response network that can be implemented rapidly and effectively. This will require a detailed investigation into how to best prepare for and respond to a national incident or disaster. The infrastructure for generating and sharing information that can identify biodefense exposure and minimize consequences will prove to be an invaluable asset. An integrated database connecting disease centers that gives clinical conditions and potential exposure to disease is critical to this mission, as are biosensors that can give sensitive, real-time information that provide defense against large-scale exposure. This infrastructure in turn also needs to support a decision- making hierarchy so that information can be shared appropriately and resources can be mobilized. The introduction of state- of- the- art devices and technologies to enable this task needs to be integrated into this framework for readiness and response. Systems Integration in Biodefense, Aug. 21- 22, 2006, Washington DC   Bioengineering & Biomaterials glossary

biofuels: With First Generation Biofuels beginning to make a major contribution in addressing the US and the World’s need to transition from Fossil-Based Fuels to Renewables and Second Generation Biofuels beginning to create the promise of accelerating this transition without the food supply and other social and environmental costs associated with First Generation Biofuels, Biofuels Development is poised for tremendous growth over the next decade. Innovations in BioFuels (1st Annual) May 13-15, 2008 • Baltimore, Maryland

About Biofuels, Gevo, Industry Glossary http://www.gevo.com/glossary.php 35 plus terms defined. 

combinatorial chemistry:  Using a combinatorial process to prepare sets of  compounds from sets of  building blocks. [IUPAC Combinatorial Chemistry]  

Note that there is not enough matter in the universe to prepare all possible combinatorial variations. 

Related terms: combinatorial libraries, diversity, microtiter plates, molecular diversity, fully combinatorial, pool/ split Combinatorial libraries & synthesis glossary

disruptive technologies: Some technologies are improved in a linear fashion or incrementally.  Others truly change the paradigm.  Clayton Christensen writes about these in The Innovator's Dilemma. What is particularly interesting about Christensen's analysis (based on data from the disk drive industry) is that he found disruptive technologies tended to be much cheaper than existing technologies. Existing companies were quite capable of developing the technologies (and had). What they couldn't do was figure out how to market them and whether it made sense to devote sufficient resources to them (which in many cases would not have been the responsible thing to do.)  Related term nonlinear. Business of biopharmaceuticals glossary

emerging technologies: Are you ready to move your technology from the bench to the market?  CHI is offering a partnering program to immediately follow our conferences in Stem Cell Research, Tissue Modeling Technology and Mammalian Cell Culture.  This program is designed for biotechnology academic scientists and early-stage companies highly interested in partnering. PARTNERSHIPS MOVE EMERGING TECHNOLOGIES Partnering "Venture Ready" Stem Cell Research, Tissue Modeling Technology, and BioProcessing Developments, Aug. 17, 2006 Boston MA

enabling technologies:  InsightPharma Reports http://www.insightpharmareports.com/enabling.asp 

The Human Genome Project taught that evolutionary improvement in existing technologies (e.g., DNA sequencing) can have a revolutionary impact on science. The systems approach taken by the Genomes to Life program dictates that existing technologies must evolve to a high-throughput capability. In addition, revolutionary technologies need to be developed, incorporating new modes of robotics and automation as well as advanced information and computing technologies. Enabling Technologies, DOE Genomes to Life, US http://www.doegenomestolife.org/technology/index.html

Frequently cited examples of enabling technologies for drug discovery and development are combinatorial chemistry, high-throughput screening, microarrays, bioinformatics and computational biology, nanotechnologies, and imaging (including biosensors and biomarkers) Business of biopharmaceuticals glossary

gene manipulation: The use of in vitro techniques to produce DNA molecules containing novel combinations of genes or altered sequences, and the insertion of these into vectors that can be used for their incorporation into host organisms or cells in which they are capable of continued propagation of the modified genes. [IUPAC Biotech] Genetic Manipulation & Disruption glossary

genetic engineering: Directed modification of the gene complement of a living organism by such techniques as altering the DNA, substituting genetic material by means of a virus, transplanting whole nuclei, transplanting cell hybrids, etc. [MeSH, 1989] Related term: recombinant DNA technology. [IUPAC Compendium] Bioengineering & Biomaterials glossary

genomic arrays: Allow toxicologists to look at cellular behavior in a completely new light. In a sense, recording individual gene responses to powerful insults such as alkylating agents was akin to studying the effects of poverty by monitoring a person's bank account - the complete picture is much larger than what is actually being measured. But genomic arrays simultaneously report indicators of multiple dimensions of the cellular response to stimuli. Now, in addition to gaining insight into basic cellular mechanisms of repair, researchers looking at a variety of indicators and responses of toxicity may gain some predictive power regarding individual compounds - and individual humans. Both academic and private laboratories have already begun work on finding genes that induce protection or sensitivity to toxicants in individual cells and people. [NIEHS News "Arrays cast toxicology in a new light" Environmental Health Perspectives 09 (1), Jan. 2001] http://ehpnet1.niehs.nih.gov/docs/2001/109-1/niehsnews.html Microarray categories

genomic technologies: One of the primary reasons for the success of the Human Genome Project has been the development and use of high- throughput strategies for data generation, and the placement of the data immediately in the public domain. Most of the sequence data, the underlying maps and the sequence assemblies were generated through the use of large- scale automated processes. Now, methods such as sequence analysis of whole genomes, DNA microarray technology and mass spectrometry have been or are being developed as high- throughput approaches for additional types of genomic analyses, such as determining the parameters of gene expression or the location of gene products by the thousands at a time instead of individually. High- throughput methods to determine the location of cis- regulatory elements and, to a lesser extent, other sequence elements, are also beginning to be developed. However, at present, there is no single approach or compilation of approaches that can accurately and efficiently identify every sequence feature in genomic DNA. Determination of all Functional Elements in Human DNA,  Release date, NHGRI,  February 21, 2003 RFA: HG-03-003 http://grants1.nih.gov/grants/guide/rfa-files/RFA-HG-03-003.html  Genomics glossary

hyphenated techniques: Usually involves a combination of chromatography and/ or mass spectrometry, NMR or other spectroscopy  technologies.

Laser Capture Microdissection LCM: The laser capture microscope is a relatively new tool that allows procurement of DNA, RNA and proteins of small and pure populations of cells. Traditionally used for separation of tumor cells, many additional applications of this technology, e.g. for developmental biology, or in vitro fertilization, have evolved. In addition, the combination of laser capture microscopy with other high sensitivity, high-throughput technologies such as microarrays offers exciting new possibilities for scientists in research and clinic. Laser Capture Microscopy, April 25-26, 2006, Boston MA    Cell biology glossary

mass spectrometry: Mass Spectrometry for Protein Biomarker Discovery will provide an in-depth update on the state- of- the- art technologies and experimental design when using MS for protein biomarker discovery and profiling. The meeting addresses all aspects of proteomics applications of MS, including sample preparation, experimental design, MS profiling, and data analysis and interpretation. The meeting also provides a review of the latest MS technologies to achieve better throughput, dynamic range, and sensitivity. Mass Spectrometry for Protein Biomarker Discovery, Sept 11, 2006,  Philadelphia, PA

Can be used to both measure and analyze molecules under study. It involves introducing enough energy into a target molecule to cause its ionization and disintegration. The resulting fragments are then analyzed, based on the mass/ charge ratio to produce a "molecular fingerprint."   A significant force behind progress in proteomics .Mass Spectrometry glossary

microarray: Tool for studying how large numbers of genes interact with each other and how a cell’s regulatory networks control vast batteries of genes simultaneously. Uses a robot to precisely apply tiny droplets containing functional DNA to glass slides. Researchers then attach fluorescent labels to DNA from the cell they are studying. The labeled probes are allowed to bind to cDNA strands on the slides. The slides are put into a scanning microscope to measure … how much of a specific DNA fragment is present. [NHGRI]  

Microarrays build bridges on which biologists and clinicians can meet to understand, diagnose, and treat diseases. Microarray based technologies allow for rapid access to molecular pathways, more precise diagnosis and prognosis of disease, better understanding of drug action, and the ability to better define therapeutic strategies. That, coupled with the FDA’s growing interest in the use of microarrays as diagnostic devices, holds a bright future for both researchers developing pharmaceuticals and clinicians improving diagnostics. Microarrays in Medicine, April 26 - 27, 2006,  Boston MA    Roger Brent has compared microarrays to the telescope or microscope because they enable the observer to see what was previously unobservable.   Microarrays & protein chips glossary   

miniaturization: Desirable for many technologies for overall cost reduction (including reduction in the amount of reagents and analytes). Important to remember that building space is often the least available and most expensive component of a laboratory budget. Nanoscience & Miniaturization glossary

molecular imaging: Sessions include Imaging Probe Design, Technology Innovations, Pre-Clinical Imaging, Clinical Applications In Vivo Molecular Imaging, Nov. 16-17, 2005 - La Jolla, CA  In Vivo Molecular Imaging, November 14-15, 2006, La Jolla CA

multiplex: A sequencing approach that uses several pooled samples, greatly increasing sequencing speed. [DOE] Originally a 19th century telecommunications (telegraph) term. Gene amplification & PCR glossary

NMR Nuclear Magnetic Resonance: A technology for protein structure determination. NMR generally gives a lower- resolution structure than X-ray crystallography does, but it does not require crystallization. NMR & X-ray crystallography glossary

nanodelivery: Targeted therapy offers the promise of creating drugs that by the specificity of their design and delivery make them both more effective and less toxic. Multifunctional devices offer novel capabilities, including the possibility of delivering a detection, imaging agent, and drug in one vehicle. This creates the unique advantage of being able to give distribution data and traceability through the use of one agent, that can in tandem detect, address, and monitor disease. This functionality can be leveraged to deliver multiple combinations of drugs by extended release. Nanotechnology promises to create a break-through class of imaging agents that offer distinct advantages and can be used for the early detection and diagnosis of disease. Diagnostic molecules have the potential to act as biomarkers in drug development and diagnostics, and can be used in the imaging of cancer in living subjects. Targeted Nanodelivery for therapeutics and molecular imaging, Oct. 11-12, 2006, Baltimore MD     Nanoscience & miniaturization glossary

nanoscience: Nanoscience is primarily the extension of existing sciences into the realms of the extremely small (nanomaterials, nanochemistry, nanobio, nanophysics, etc.) while nanoengineering represents the extension of the engineering fields into the nano- scale realm (nanofabrication, nanodevices, etc.). [Mnemosyne Mnews 21 (3) January 2001 " The Nanotechnology Initiative and Future Electronics" Presentation by Gail J. Brown, Air Force Research Laboratory, Wright-Patterson Air Force Base, Nov.16, 2000]  http://users.erinet.com/3277/Mnemosyne%20Mnews%20Jan%2001.pdf   Nanoscience & miniaturization glossary

nonlinear: Advances in genomic technologies are a mix of incremental improvements to existing technologies (linear) and occasionally, a truly new paradigm or breakthrough.  Related terms: disruptive technologies, emerging technologies, complex. Genomics glossary

PCR Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double- stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult to isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships. MeSH, 1991

Demand for genomic and gene expression analysis continues. However, nucleic acid isolation and purification is one of the most technically challenging and labor-intensive procedures performed in any laboratory, whether for biodefense, drug discovery, or diagnostics. Whatever technology is selected, success depends on a balanced combination of good experimental design, sample preparation, primer/probe design, amplification, detection, and analysis, as well as the selection of equipment and reagents. Nucleic Acid-Based Technologies June 26-28, 2006 • Arlington VA   Gene amplification & PCR glossary

RNAi RNA interference:  The Nobel Prize in Physiology & Medicine for 2006 was awarded to two excellent researchers for their discovery of RNA interference. This illustrates just how far gene silencing by double-stranded RNA has come in a relatively short amount of time. RNA-based silencing has created an enormously powerful tool for validation of drug targets. Even more recently RNAi therapeutic development has raced ahead at great speed with much excitement. In vivo delivery, tissue specificity and toxicity are among the challenges to developing successful therapeutic agents. Dealing with off-target effects in siRNA screening is still a challenge and recent research points to similar findings with shRNA. Approaches such as use of multiple siRNA’s per gene and other controls will be discussed as well as a look at knockdown validation studies. Developing lentivirus-based systems will be explored with case studies using primary cell lines and some discussion of the microRNA space will be included. Beyond Genome: RNAi, June 19-20, 2007, San Francisco CA  Genetic manipulation & disruption glossary

recombinant DNA technology: A body of techniques for cutting apart and splicing together different pieces of DNA. When segments of foreign DNA are transferred into another cell or organism, the substance for which they code may be produced along with substances coded for by the native genetic material of the cell or organism. Thus, these cells become "factories" for the production of the protein coded for by the inserted DNA.  [NIGMS] Related terms:  biotechnology, gene manipulation, genetic engineering Genetic Manipulation & Disruption glossary

robust:  A process which is relatively insensitive to human foibles and variables in the way (for example, an assay) is carried out, a statistical term.  Algorithms glossary

sample prep:  Extracting, creating and keeping samples and templates of highest quality are the key factors for producing high-throughput data of optimal quality. For successful data output, state of the art information on the rapidly emerging integration of technologies is necessary. Proteomic  and Genomic Sample Prep, May 19-21, 2008, Boston MA  Drug discovery & development glossary  Bioprocessing glossary

sequencing: (proteins, nucleic acids) Analytical procedures for the determination of the order of amino acids in a polypeptide chain or of nucleotides in a DNA or RNA molecule. [IUPAC Compendium] Sequencing glossary

sexy technologies:  What makes technologies sexy?  It seems to be a combination of being new, innovative, challenging, affording clever people a chance to learn new skills (and demonstrate how competitive and bright they are) and expensive (or otherwise unavailable to everyone). A quick search of the web identifies high- speed computers, robotics, nanotechnology, HDTV, Java,  wireless communications and biomaterials as "sexy" by some criteria.  I'd be interested to hear other interpretations and nuances of this class of technologies. Are there significant differences in what are sexy technologies to biologists, businesspeople, chemists, computer scientists and others?  Business of biopharmaceuticals glossary

single molecule detection: Recent advances in optical imaging and biomechanical techniques have demonstrated that it is possible to make observations on the dynamic behavior of single molecules, to determine mechanisms of action at the level of an individual molecule, and to explore heterogeneity among different molecules within a population. These studies have the potential to provide fundamentally new information about biological processes and are critical for a better understanding of cellular function. ...  Single molecule methods are likely to lead to significant advances in understanding molecular movement, dynamics, and function. NIGMS, NICDC, NHGRI, Single Molecule Detection and Manipulation, Feb. 12, 2001  http://grants.nih.gov/grants/guide/pa-files/PA-01-049.html  Ultrasensitivity glossary

standards: Bioinformatics glossary, Microarrays glossary

synchrotrons: Devices for accelerating protons or electrons in closed orbits where the accelerating voltage and magnetic field strength varies (the accelerating voltage is held constant for electrons) in order to keep the orbit radius constant. MeSH, 1993  NMR & X-ray crystallography  

target validation technologies: A number of technologies including downregulation of gene expression (gene knockdown, antisense, ribozymes and zinc finger proteins), protein inhibition (phage libraries and antibodies), cellular assays, chemical genetics, and combinatorial biology are linked with target validation. The integration of various technologies is another challenge Targets glossary

technology platforms: Includes technology platform launches, proof-of-concept studies, comparative evaluations, major deals, and new internal initiatives. PharmaWeek http://www.pharmaweek.com/pharmaweek.asp 

technology validation:  This Center offers technology validation services to a broad range of Commercial Investigators, from emerging Biotechs to large Pharma and Instrument Manufacturers. In the TVC, technology validation is defined as confirmation of the appropriateness, effectiveness, robustness, accuracy, and reproducibility of a particular technology when applied to a specific task. Successful validation is defined by technical and statistical parameters established in advance by INCAPS in consultation with the customer. Indiana Centers for Applied Protein Sciences,  http://www.indianacaps.com/about/centers.shtml 

tissue models:   Cells, tissues, and organs function in a 3-D environment. Utilization of 3-D in vitro tissue models can help validate functionally new targets and pre- selected hits more efficiently then immediate in vivo testing.  Tissue Models for Therapeutic Development, Aug. 15-16, 2006, Boston MA  Bioengineering & Biomaterials glossary

zeptomole: 10^–21 mole. One- sextillionth. Ultrasensitivity glossary

Bibliography
HSTAT Health Services Technologies Assessment Text,  National Library of Medicine http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=hstat 

Alpha glossary index

How to look for other unfamiliar  terms

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