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Glossary

Synthetic Biology Terms and Definitions

A

Active Pharmaceutical Ingredient (API): Often referred to as bulk pharmaceuticals. The FDA defines API as any substance or mixture of substances intended to be used in the manufacture of a drug product and that, when used in the production of a drug, becomes an active ingredient in the drug product.

Artemisinin: A drug also known as qinghaosu, used to treat malaria, derived from the sweet wormwood plant, Artemisia annua. The artemisinin metabolic pathway was engineered into yeast to produce a precursor and its subsequent chemical conversion into artemisinin provided a cheaper source of the drug than conventional chemical synthesis.

Antibody: A glycoprotein produced and released by a B-lymphocyte (B-cell) in response to a foreign antigen. The antibody can recognize and bind the antigen. An antibody drug is the drug which eliminates target or inhibits function of target protein taking advantage of specific binding property.

Antigen: A compound that induces the formation of a specific antibody.

Autoimmune Disease: When the immune System mistakenly identifies its own tissues as foreign, and attacks them, causing tissue damage and inflammation.


B

Biobricks: Standardised DNA Sequences that can be used as modular building blocks to rapidly create more complex sequences.

Biohacking: DIY synthetic biology carried out by individuals and small groups, often as part of a community, rather than large research institutions.

Biofuel: A fuel that is produced through biological processes, such as agriculture and anaerobic digestion, rather than a fuel produced by geological processes such as those involved in the formation of fossil fuels. Biofuels can be derived directly from plants, or indirectly from agricultural, commercial, domestic, and/or industrial wastes.

Biologic: A regulatory term that refers to any virus, therapeutic serum, toxin, antitoxin, vaccine, blood, blood derivative, blood component, monoclonal antibody, somatic cell gene therapy product or allergenic product used to prevent, treat or cure injuries or diseases in humans.

Biopharmaceutical: A term commonly used to refer to a drug product, such as insulin, that is manufactured using genetically modified organisms as a product system.

Bioreactor: A vessel capable of supporting cell culture, typically at large-scale.

Bioeconomy: Economic activity derived from scientific and research activity focused on biotechnology.

Biological Engineering: The application of engineering principles to biology.

Biomedical Engineering: The application of biological and other sciences toward medical innovations.

Biotechnology: Technology based on biology - biotechnology is any technological application that uses biological systems or organisms to make or modify products for specific uses.

Biosensor: A biological sensor, made up of a transducer and a biological element that may be an enzyme, an antibody or a nucleic acid. The bioelement interacts with the substance being tested and the biological response is converted into an electrical signal by the transducer.


C

Carlson Curve: Term used to describe the biotechnology equivalent of Moore’s law and is named after Rob Carlson, who predicted that the doubling time of DNA sequencing technologies (measured by cost and performance) would be at least as fast as Moore's law. The Carlson Curves illustrate the rapid decreases in cost, and increases in performance, of a variety of technologies, including DNA sequencing, DNA synthesis and a range of physical and computational tools.

CAR-T Cell: A white blood cell with an artificial receptor, allowing one to define which antigen the T-cell targets.

Chassis: The under lying biology in which a device or system is implemented. This can be a living organism (host) or an in vitro system for transcription and translation.

Cell-free systems: In vitro tools that can be used to study biological reactions that usually take place within a cell, without having to worry about complex intracellular interactions.

C1 Fermenter: Gas-fermenting microbes able to grow on C1 compounds, such as carbon monoxide (CO), carbon dioxide (CO2) and methane (CH4), derived from non-food sources such as waste gases from industry (steel manufacture, oil refining, coal and natural/shale gas) as well as synthesis gas (or short syngas) (CO/CO2 and H2 mixtures) produced from sustainable resources, such as biomass and domestic/agricultural wastes

Codon: A sequence of 3 nucleotides within DNA or RNA that encodes a specific amino acid.

Copy Number: DNA sequences often repeat. The number of repeats is the copy number. Variation in the copy number of certain sequences can cause genetic diseases.

CRISPR-Cas9: A technique that uses a bacterial enzyme to edit DNA sequences. It is considered significantly more versatile and accurate than previous methods of genetic manipulation.

Cell Therapy: Cell Therapy refers to the treatment of disease by administering living cells to patient. The use of stem cells to treat injury is an example of cell therapy.

Cell Culture: The growth of cells as independent units, usually in suspension. The cells are not organized in tissues.

Cell Line: Cells originating from sub-culture of a primary cell culture. The term may be prefixed with ‘continuous’ to indicate the potential for further sub-culture.

Cell Strain: Cell derived from a cell line or primary cell culture by selection of a specific property or marker, which is maintained through subsequent sub-cultures.

Clone: A cell/organism is genetically identical to the cell/organism it is derived from.

Clinical Trial: A clinical trial is conducted for the evaluation of the safety and efficacy of a drug in humans.

Commodity Chemical: A class of chemicals, which are manufactured on a very large scale for global trade and industry.

Computer aided design (CAD): The use of computer software in the creation of a design. In Synthetic Biology it can be used to design DNA sequences.


D

Device: A collection of parts (pieces of DNA, see: Part) that perform a higher order function.

Drug Delivery: Drug delivery refers to effective transport of pharmaceutical compounds to the location of the body where the therapeutic effects are needed.

DNA: Deoxyribonucleic acid. The molecule that encodes the instructions for making amino acids and proteins, required for almost all biological functions and processes within living organisms.

DNA Synthesis: The creation of DNA. This is done naturally within living organisms, but can also be done artificially

Drug Product: A dosage form, such as tablet or solution, intended for use in the diagnosis, treatment or prevention of disease in humans or animals.

Downstream Processing: The process of extracting and purifying a product from cell culture.

Design of Experiments (DoE): A systematic method for evaluating how specific processes involved in an experiment affect the outcome of that experiment.


E

Expression (genetics): The process in which the product coded for by a gene is made. Genes are expressed and proteins are synthesized.


F

Feedstock: Raw, unprocessed materials used in manufacturing or industrial processes.

Fermentation (biotechnology): A process by which a product is produced by mass culture of microorganisms under controlled conditions.

Fermentor: A vessel in which microorganisms or cells are grown under controlled conditions of temperature, nutrient levels, aeration, pH and mixing.

Food and Drug Administration (FDA): The US federal agency empowered by Congress to regulate the production of cosmetics, electronic products, food, medical devices, diagnostic devices and prescription and over-the-counter pharmaceuticals for human and veterinary use.

Foundry (Synbio): A facility that can carry out every step of the process of creating a new synthetic biological system, using CAD and robotics.

Freedom to operate: Being able to carry out a particular action without infringing on another's intellectual property.


G

Gene Drive: Altering the likelihood that a gene will be inherited in order to effect change at a population level.

Gene Expression: The process by which gene information recorded in DNA exerts its function. Gene information is transcribed into messenger RNA and delivered to ribosome where functional proteins, such as enzymes, are synthesized; the function of the gene is executed by the action of such proteins.

Gene Therapy: Replacing a gene that is missing or correcting a function of a faulty gene, in order to treat or cure an illness.

Genome: The complete set of genes in an organism.

Glycosylation: The process of adding carbohydrate groups on to a protein immediately after synthesis, prior to secretion from eukaryotic cells.

Genetic Engineering: A term commonly referring to methods that allow a gene from one organism to be transferred to another, either of the same or different species.

Genetically Modified Organism (GMO): A cell or organism into which a gene from one organism has been transferred.


H

Hackathon: An event, originally in computer programming, where individuals gather for a few days of intensive collaboration on a shared project.


I

iGEM: International Genetically Engineered Machine. A competition for synthetic biology students in which multidisciplinary teams use biobricks to build novel genetically engineered systems.

Investigational New Drug (IND): The data package showing safety and efficacy of the drug for the application of commencement of clinical trials.

Immunotherapy: Manipulating the body's immune response to treat a disease, either by causing, enhancing, or suppressing its effects.

International Gene Synthesis Consortium (IGSC): Consortium of the leading gene synthesis companies formed to co-ordinate best practices in risk reduction. Representing more than 80% of the worldwide gene synthesis capacity, the IGSC applies a common screening protocol to promote biosecurity in the gene synthesis industry. By screening the sequences of synthetic gene orders and the customers who place them, the companies aim to support government efforts to prevent the misuse of gene synthesis technology.

In vitro: Carrying out experiments with microorganisms or biological molecules in a controlled environment, for example in a petri dish.

In vivo: Carrying out experiments within whole living organisms or within their natural environment.


K

Kozak Sequence: A sequence of mRNA that acts as a ribosome binding site (see below) in eukaryotic organisms.


L

Lean LaunchPad: An intensive 11 week course to provide the business skills needed to develop ideas for a product or service into viable start-up company.

Library (DNA): A collection of fragmented DNA sequences cloned into host microorganisms so that researchers can further study the DNA.

Lead compound: A lead compound in the drug discovery process is a compound that has expected biological activity found in the early discovery stage. Drug seeds are developed later from the lead compound by the chemical modification to improve the potency and down-regulate the side effects, which is called lead optimization step.


M

Metabolite: A metabolite is any substance produced during metabolism (digestion or other bodily chemical processes).

A primary metabolite is a metabolite directly involved in normal growth, development, and reproduction. It usually performs a physiological function in the organism. E.g. ethanol, lactic acid and amino acids. A secondary metabolite is a molecule not required for growth, but offering some survival value to the organism. E.g. alkaloids, antibiotics, naphthalenes, nucleosides, phenazines, quinlolines, terpenoids, peptides and growth factors.

Mutant: A phenotypic variant of a cell resulting from an altered gene.

Medical Device: Items that are not drugs or biologics but which are used in the diagnosis or treatment of diseases or injury.

Mass Spectrometry: An analytical technique that can be used to identify the chemical elements within a compound.

Molecular targeted drug: Molecular targeted drugs refer to drugs that target specific molecules (proteins, and etc.) to exhibit efficacy. For example, cancer growth is suppressed by the inhibition of the molecules needed for the cancer cell proliferation. Molecular targeted drugs are expected to have lower side effects since they specifically bind to target molecules but not to the molecules which may cause unwanted effects.


N

Nucleic Acids: Nucleic acids, such as DNA or RNA, contain an organism's genetic information. DNA encodes genetic information and RNA interprets the genetic information, translating it for protein synthesis.

NMR Spectropscopy: Nuclear magnetic resonance spectroscopy. An analytic technique that uses the magnetic properties of certain atoms to determine the properties and structure of atoms or molecules.


O

Oligonucleotide: An Oligonucleotide is the polymer of 2-20 nucleotides.

Operon: A collection of genes all controlled by a single promoter region, meaning they will be transcribed into a single piece of mRNA, which can then be split or translated into multiple proteins at the same time.

Origin of Replication: The sequence in a genome where DNA replication begins.

Open Source: The principle of sharing designs and information openly and at no cost.


P

Part: A piece of DNA that encodes a biological function. Eg promoter, RBS

Point of Care: The point at which clinicians deliver treatment or other healthcare services to patients.

Pre-Clinical Studies: Is the stage of research that begins before testing in humans (clinical trials) can begin, and during which important feasibility, iterative testing and drug safety data is collected.

Phase 1 Clinical Trials: Studies of potential pharmaceuticals performed on healthy human volunteers to determine the safety of potential products and their metabolic, pharmacological and toxicological properties.

Phase 2 Clinical Trials: Studies of potential pharmaceuticals performed on a small number of diseased patients to determine the product’s potential effectiveness and potential side effects.

Phase 3 Clinical Trials: Studies of potential pharmaceuticals performed on a population of hundreds to thousands of patients to establish therapeutic effects, side effects and recommended dose levels.

Primary Culture: A culture starting from cells taken directly from tissues from an animal. The culture is no longer primary after sub-cultured.

Process Analytical Technology (PAT): A regulatory mechanism for designing, analysing and controlling manufacturing processes to ensure that pharmaceutical products meet required standards.

Promoter: A sequence of DNA to which RNA polymerase can attach, allowing transcription of DNA into mRNA during protein synthesis.

Protein Synthesis (Expression): During protein synthesis, DNA is transcribed into mRNA, which can then be read by a ribosome, translating the sequence of base pairs in the mRNA into a sequence of amino acids, assembled by the ribosome into a protein.


Q

Quality by Design: A business concept where the features of a product are specifically designed to met the needs of the target audience.

Quorum Sensing: Systems whereby organisms will behave differently according local population size. This can range from bacteria expressing different proteins, to social insects such as ants making complex, colony-wide decisions.


R

Recombinant DNA: DNA that contains sequences of DNA from different sources that were brought together by techniques of molecular biology and not by traditional breeding methods.

Responsible innovation: A commitment to carrying out research responsibly and to high ethical and legal standards, reflecting fully on possible economic, environmental and social implications of research.

Recombinant Protein: A protein produced from a foreign DNA sequence introduced into a cell.

Ribosome Binding Site (RBS): A section of mRNA that a ribosome can attach to, beginning the process of translating the mRNA code into a protein (see: Nucleic Acids).


S

Scale-up: The transition between producing small amounts of product to production of large quantities for commercial sale.

SynbiCITE (Syn-bee-city): Innovation and Knowledge Centre for Synthetic Biology, the UKs national centre for the innovation of commercialization of synthetic biology.

SynGas: Short for Synthesis Gas. A Mixture of hydrogen, carbon monoxide and carbon dioxide used as an intermediate in the creation of synthetic natural gas and other chemicals.

Synthetic Biology: Synthetic biology aims to design and engineer biologically based parts, novel devices and systems as well as redesigning existing, natural biological systems.

Suspension Culture: A culture consisting of cells suspended in a liquid culture medium.

Second-generation sequencing: DNA sequencing techniques developed in the 1990s that are significantly faster and more cost effective than the previously used Sanger sequencing.

Scar: A region of DNA, formed where 2 separate DNA sequences are joined together, that cannot be cut by the enzymes which originally cut the 2 joined sequences.

System: a collection of DNA devices (see: Device) that lead to a desired (usually useful) behaviour.


T

Transfection: The transfer of genetic material into animal cells.

Transformation: The transfer of genetic material into bacterial cells.

Transgenic: An organism that has been implanted with genes from another species.


U

Upstream Processing: A strategy for manipulating cells so that they achieve high specific productivity for a required product.

Unmet Medical Need: Unmet medical needs refer to diseases without effective therapies.


V

Vector: Plasmid or modified virus, into which a DNA fragment of interest is integrated, and which carries the DNA of interest into the host cell


X

X-Ray Crystallography: A method for analysing the atomic and molecular structure of a crystalline substance using X-rays.


Z

Zika Virus: A virus spread by female mosquitos of the genus Aedes which causes Zika fever. Zika fever causes either no or mild symptoms in most people. However, it is linked to significant birth defects in the children of women who are infected whilst pregnant. Synthetic Biologists are currently trialling the use of synthetic biology techniques to control mosquito populations and therefore the spread of the disease.