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Evolving Terminologies for Emerging Technologies
Suggestions? Comments? Questions?
Mary Chitty 
Last revised July 03, 2019 


Technologies term index   Cell & tissue technologies       Genomic Technologies       Protein technologies

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  

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

aliquot: (analytical chemistry) A known amount of a homogeneous material, assumed to be taken with negligible sampling error The term is usually applied to fluids. The term "aliquot" is usually used when the fractional part is an exact divisor of the whole; the term "aliquant' has been used when the fractional part is not an exact divisor of the whole. When a laboratory sample or test sample is 'aliquoted' or otherwise subdivided, the portions have been called split samples.  IUPAC Compendium  Related term: sample preparation

aptamer: Oligonucleotide which displays specific binding to a protein or other target, often selected by an iterative cycle of affinity- based enrichment.

A synthetic, specially- designed oligonucleotide with the ability to recognize and bind a protein ligand molecule or molecules with high affinity and specificity.   
Narrower terms: photoaptamers,  Functional genomics  Protein technologies peptide aptamer;  Genomic technologies SELEX, spielgemers

Aptamers are included in the IUPAC, Electrochemical nucleic acid based biosensors  

automation: Automating processes is often a critical part of industrializing processes developed in the research lab.  Higher throughput, quality control and better reproducibility are part of this process.. Automation may be cheaper, particularly in the long run.  Related terms:  Bioprocessing  LIMS, robotics

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    Bioengineering & Biomaterials 

After many years of service to the NIH Bioengineering community, the NIH Bioengineering Consortium (BECON) has completed its mission. Bioengineering has now become an important activity supported at nearly every NIH institute and center, and much of what BECON had done has now been well integrated across the NIH.  Many of the bioengineering funding announcements and technical reports at the BECON website have migrated to the National Institute of Biomedical Imaging and Bioengineering -

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

directed evolution
a method used in protein engineering that mimics the process of natural selection to evolve proteins or nucleic acids toward a user-defined goal.[1] It consists of subjecting a gene to iterative rounds of mutagenesis (creating a library of variants), selection (expressing the variants and isolating members with the desired function), and amplification (generating a template for the next round). It can be performed in vivo (in living cells), or in vitro (free in solution or microdroplet). Directed evolution is used both for protein engineering as an alternative to rationally designing modified proteins, as well as studies of fundamental evolutionary principles in a controlled, laboratory environment. Wikipedia accessed 2018 Sept 3

directed protein evolution: Systematic approaches to directed evolution of proteins have been documented since the 1970s. The ability to recruit new protein functions arises from the considerable substrate ambiguity of many proteins. The substrate ambiguity of a protein can be interpreted as the evolutionary potential that allows a protein to acquire new specificities through mutation or to regain function via mutations that differ from the original protein sequence. All organisms have evolutionarily exploited this substrate ambiguity. When exploited in a laboratory under controlled mutagenesis and selection, it enables a protein to “evolve” in desired directions. One of the most effective strategies in directed protein evolution is to gradually accumulate mutations, either sequentially or by recombination, while applying selective pressure. This is typically achieved by the generation of libraries of mutants followed by efficient screening of these libraries for targeted functions and subsequent repetition of the process using improved mutants from the previous screening. Here we review some of the successful strategies in creating protein diversity Yuan L, Kurek I, English J, Keenan R. Laboratory-Directed Protein Evolution. Microbiology and Molecular Biology Reviews. 2005;69(3):373-392. doi:10.1128/MMBR.69.3.373-392.2005.

display technologies: New classes of compounds and synthetic biologics are being translated by display to a biologically active drug. There are a number of success stories where display methodologies have been used to generate drug candidates that are currently in the clinic.  See also antibody display, cDNA display, phage display, peptide display, ribosome display  

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

enabling technologies:  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).  

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

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

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   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  Genomics

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

Laser Capture Microdissection LCM:  Cell biology

mass spectrometry: 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

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

Roger Brent has compared microarrays to the telescope or microscope because they enable the observer to see what was previously unobservable.   Microarrays & protein chips   

Micro-and Nanofluidics in Diagnostics and Life Sciences DVD April 25, 2010 •

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

molecular evolution: The aims and scope statement of the Journal of Molecular Evolution states that topics addressed cover "experimental and theoretical work aimed at deciphering features of molecular evolution and the processes bearing on these features, from the initial formation of macromolecular systems onward, includ[ing] the evolution of informational macromolecules and their relation to more complex levels of biological organization, up to populations and taxa. This coverage accommodates well such subfields as comparative structural and functional genomics, population genetics, the molecular evolution of development, the evolution of gene regulation and  gene interaction networks, and in vitro evolution of DNA and RNA. Aims and Scope, Journal of Molecular Evolution, Springer

Wikipedia   Narrower terms: applied molecular evolution; Proteomics  directed protein evolution   Related term: gene shuffling

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

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

nanoscience: The study of phenomena and manipulation of materials at atomic, molecular and macromolecular scales, where properties differ significantly from those at a larger scale. Draft definitions, Royal Society, Royal Academy of Engineering  Nanotechnology and Nanoscience, 2003   Nanoscience & miniaturization

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, complexGenomics

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.   Gene amplification & PCR

platform companies: The pharmaceutical industry faces a crisis of productivity in R&D, and hundreds of new companies have been founded based on tools that can aid in improving drug development. There is a growing consensus, however, that the business model of a tool provider faces enormous challenges, compounded by being out of favor by the investment community. In order to obtain new, or additional funding, many technology companies are remaking themselves into drug discovery companies, employing their proprietary technology not as a service for others, but for the in-house discovery of therapeutics.  Also referred to as "technology platform companies", the ones developing and marketing the instrumentation and informatics needed to make use of genomic data - the 21st century equivalent of the pick and shovel manufacturers of the 19th century Gold Rush.

platform technology:  A technique or tool that enables a range of scientific investigations. Examples include combinatorial chemistry for producing novel compounds, high- throughput screening for in vitro chemical screening, and in vivo biophotonic imaging for disease detection and chemical testing in living animals. Xenogen Glossary, 2001

Related terms  FIPCO, target technologies, tool technologies

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  Genomic Technologies

RNAi RNA interference:  A gene silencing phenomenon whereby specific dsRNAs ( RNA, DOUBLE- STRANDED) trigger the degradation of homologous mRNA ( RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA- INDUCED SILENCING COMPLEX (RISC). DNA METHYLATION may also be triggered during this process. MeSH 2003 

Nature Reviews Focus on RNAi 

robot: The word 'robot' was coined by the Czech playwright Karel Capek (pronounced "chop'ek") from the Czech word for forced labor or serf. ...The use of the word Robot was introduced into his play R.U.R. (Rossum's Universal Robots) which opened in Prague in January 1921. The play was an enormous success and productions soon opened throughout Europe and the US. R.U.R's theme, in part, was the dehumanization of man in a technological civilization. You may find it surprising that the robots were not mechanical in nature but were created through chemical means. Comp-AI Robotics FAQ 

robotic system: Automated device where materials are transferred by the physical movement of a delivery device relative to the ultimate receptacle, or vice versa. See also fluidic system. IUPAC Combinatorial Chemistry

robotics:  "A reprogrammable, multifunctional manipulator designed to move material, parts, tools, or specialized devices through various programmed motions for the performance of a variety of tasks" Robot Institute of America, 1979  Obviously, this was a committee-written definition. It's rather dry and uninspiring. Better ones for 'robotics' might include: Force through intelligence. Where AI meet the real world. ...refers to the study and use of robots. The term was coined and first used by the Russian- born American scientist and writer Isaac Asimov (born Jan. 2, 1920, died Apr. 6, 1992). Comp- AI Robotics FAQ 

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

sample: 1. In statistics, a group of individuals often taken at random from a population for research purposes 2. One or more items taken from a population or a process and intended to provide information on the population or process. 3. Portion of material selected from a larger quantity in some manner chosen so that the portion is representative of the whole. [IUPAC Tox] Related terms: aliquot, autosampler  See also Microarrays sample

sample prep, sample preparation:  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.  Related terms: LIMS Laboratory Information Management Systems,  aliquot, microtiter plate, solid phase extraction, split sample;  Labels, signaling & development :Ultrasensitivity single cell detection, single molecule detection;    Proteins  depletion, pre- fractionation; Cell biology LCM Laser Capture Microdissection, subcellular fractionation; others?

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

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

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  Ultrasensitivity

standards:   Bioinformatics , Microarrays

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 Drug targets

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.  

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

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HSTAT Health Services Technologies Assessment Text,  National Library of Medicine 
IUPAC  International Union of Pure and Applied Chemistry, Compendium of Chemical Terminology: Recommendations, compiled by Alan D. McNaught and Andrew Wilkinson, Blackwell Science, 1997. "Gold Book" 6500+ definitions.  

How to look for other unfamiliar  terms

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

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