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
https://en.wikipedia.org/wiki/Aptamer
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 |
DOI: https://doi.org/10.1351/PAC-REP-09-08-16
https://www.degruyter.com/view/j/pac.2010.82.issue-5/pac-rep-09-08-16/pac-rep-09-08-16.xml
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 http://www.wired.co.uk/news/archive/2013-05/28/electroceuticals
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 http://www.becon.nih.gov/bioengineering_definition.htm
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 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
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
http://users.erinet.com/3277/Mnemosyne%20Mnews%20Jan%2001.pdf 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, complex. Genomics
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
https://www.techopedia.com/definition/3411/platform
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
http://www.pharmtech.com/platform-technologies
Don’t build products build platforms,
Inc. 2012
https://www.inc.com/phil-simon/why-your-company-should-build-platform.html
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, http://semiconductorglossary.com/
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 http://www.altitudeinc.com/five-ways-to-make-any-piece-of-tech-sexy/
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 http://grants.nih.gov/grants/guide/pa-files/PA-01-049.html
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
https://en.wikipedia.org/wiki/Surface_plasmon_resonance
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
https://en.wikipedia.org/wiki/Glossary_of_robotics Glossary of Machine
Vision, Wikipedia
https://en.wikipedia.org/wiki/Glossary_of_machine_vision HSTAT Health
Services Technologies Assessment Text, National Library of Medicine
https://www.ncbi.nlm.nih.gov/books/NBK16710/
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. http://goldbook.iupac.org/
Technologies Conferences
http://www.healthtech.com/conferences/upcoming.aspx?s=TCH
BioIT World Expo http://www.bio-itworldexpo.com/
Technologies Short courses http://www.healthtech.com/Conferences_Upcoming_ShortCourses.aspx?s=TCH
Keeping
up with emerging technologies
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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