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Technologies overview
Evolving Terminologies for Emerging Technologies
Suggestions? Comments? Questions?
Mary Chitty MSLS
Last revised January 09, 2020 

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     Finding guide for terms in these glossaries Technologies term index   

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

aptamers: (from the Latin aptus – fit, and Greek meros – part)  are oligonucleotide or peptide molecules that bind to a specific target molecule. Aptamers are usually created by selecting them from a large random sequence pool, but natural aptamers also exist in riboswitches. Aptamers can be used for both basic research and clinical purposes as macromolecular drugs. Aptamers can be combined with ribozymes to self-cleave in the presence of their target molecule. These compound molecules have additional research, industrial and clinical applications.  Wikipedia accessed 2018 Feb 16  

The term “aptamer” should be clearly distinguished from other terms such as “ribozyme”, “DNAzyme”, and “aptazyme”, which are defined as follows. Ribozymes are catalytic RNAs; some ribozymes have been found in Nature and mediate phospho diester bond cleavage and peptide bond formation. In vitro selection has been used to generate RNA enzymes with novel structures and catalytic functions (i.e., Diels–Alder reactions, biphenyl isomerization, C–S bond by Michael reaction, etc.). DNAzymes are DNA-based catalysts that have not been found in Nature and are generated only by in vitro selection. The ligand-binding and catalytic features of NA can be combined to generate allosteric ribozymes or “aptazymes”. When ligands bind to an aptazyme, conformational changes in the ligand-binding domain are transduced to a change in the catalytic core and a concomitant modulation of catalytic activity. The term “aptamer” has been recently used also to denominate a new class of peptidic bioreceptors. To avoid misunderstanding in this report with the term, aptamers are only considered NA-based aptamers. Note: In vitro selection is an iterative method.  Electrochemical nucleic acid-based biosensors: Concepts, terms, and methodology (IUPAC Technical Report), Pure and Applied Chemistry, IUPAC Technical report
 Published Online: 2010-04-20 | 

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

bioelectronics: the field of developing medicines that use electrical impulses to modulate the body's neural circuits. Virtually all of the body's organs and functions are regulated through circuits of neurons communicating through electrical impulses. The theory is that if you can accurately map the neural signatures of certain diseases, you could then stimulate or inhibit the malfunctioning pathways with tiny electrodes in order to restore health, without having to flood the system with molecular medicines. Electroceuticals swapping drugs for devices, Wired 28 May 2013  Related term: electroceuticals  Bioengineering & Biomaterials

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

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

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).  

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.

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   

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

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: 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   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 technologies: A platform is a group of technologies that are used as a base upon which other applications, processes or technologies are developed. What does platform mean? Technopedia

in bioprocessing It is not easier to develop platforms for either upstream or downstream, it is just different. The main difference in developing platform processes for either is that, in most cases, one develops upstream processes for the cell line and the expression system, while downstream processes are tailored to the molecule itself. If the molecules are of a similar type, then the downstream process becomes easy to develop. In terms of difficulty, the cell lines and expression systems are inherently variable, and clone-to-clone variability adds to the complexity. Scale factors are also more difficult to control in cell culture and fermentation. In general, upstream therefore probably poses a slightly greater challenge assuming that the molecules are in a given class or category. Platform Technologies, Pharmaceutical Technology 2012  
Don’t build products build platforms
, Inc. 2012

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  RNA

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

semiconductor: Material whose conductivity, due to charges of both signs, is normally in the range between that of metals and insulators and in which the electric charge carrier density can be changed by external means. IUPAC Compendium
Semiconductor glossary, Jerzy Ruzyllo,

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 smartphones, GitHub, Google  robotics, nanotechnology, , Java,  and wearables 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
5 Ways to Make Sexy Technology,
Altitude   Suggestions include 1. Define yourself around customers' business problems 2. Make it simple but allow for complexity, 3. Don't forget emotion 4. Connect, connect, connect 5. Explore new business models. 

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

Surface Plasmon Resonance:.  A biosensing technique in which biomolecules capable of binding to specific analytes or ligands are first immobilized on one side of a metallic film. Light is then focused on the opposite side of the film to excite the surface plasmons, that is, the oscillations of free electrons propagating along the film's surface. The refractive index of light reflecting off this surface is measured. When the immobilized biomolecules are bound by their ligands, an alteration in surface plasmons on the opposite side of the film is created which is directly proportional to the change in bound, or adsorbed, mass. Binding is measured by changes in the refractive index. The technique is used to study biomolecular interactions, such as antigen - antibody binding.  MeSH, 1999 

SPR is the resonant oscillation of conduction electrons at the interface between negative and positive permittivity material stimulated by incident light. SPR is the basis of many standard tools for measuring adsorption of material onto planar metal (typically gold or silver) surfaces or onto the surface of metal nanoparticles. It is the fundamental principle behind many color-based biosensor applications, different lab-on-a-chip sensors and diatom photosynthesis.  Wikipedia accessed 2018 Sept 29  Related term: biosensors

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  

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.  Bioengineering & Biomaterials

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

Technologies resources
Glossary of Robotics, Wikipedia
Glossary of Machine Vision, Wikipedia
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.  

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

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