A
- adoptive cell therapy - a form of cell immunotherapy where modified T cells are given to a patient to fight disease
- alignment - the process of lining up two or more sequences to assess their similarity. There are four alignment types in Benchling: consensus, global, local, and template.
- allogeneic cell therapy - the source of the material for a cell therapy coming from an unrelated donor
- amine group - an -NH2 functional group
- amino acid - the organic molecule that is the building block of proteins. Each amino acid contains an amino group and a carboxyl group that allows for peptide bond formation between amino acids in a peptide chain.
- animal models - a term used to describe non-human species used in research because it has been made, via genetic modification or otherwise, to mimic aspects of diseases found in humans.
- annotations - the process of identifying the location of and adding pertinent information to sequences regarding important sequence elements. The two annotation types in Benchling: functional and structural.
- antibiotic resistance marker - a gene that provides the cells expressing it with resistance to an antibiotic. It can be used to identify which cells are expressing a recombinant plasmid. Also referred to as a selectable marker.
- antibody - a protein produced by the immune system in response to foreign material to recognize and bind that specific foreign material. Also known as an antigen.
- antibody diagnostics - using antibodies to conduct diagnostic tests on various types of samples
- antibody-drug conjugate (ADC) - antibodies with small molecule therapeutic agents attached to allow for killing of diseased cells only while sparing healthy cells
- antibody therapeutics - using antibodies as treatment to fight cancer, infection, or autoimmune diseases
- antigen - the specific molecular structure of a pathogen that antibodies are created in response to
- antisense oligonucleotides (ASOs) - a single-stranded, short RNA therapeutic that targets and disrupts the activity of specific genes
- assembly - the process of putting two or more sequence fragments together into a longer sequence
- autologous cell therapy - the source of the material for a therapy coming from the patient being treated
B
- base pair editing guides - gRNAs that guide modified nucleases that promote the modification of cytosine to uracil to the target gene
- bioanalytical development - work done by multiple teams to support the processing and analysis of samples coming from preclinical and clinical studies
- bioconjugates - when used in reference to therapeutics it is a macromolecule drug that is chemically modified to carry other molecules. For example, chemotherapeutic drugs attached to an antibody
- biologics - a class of large molecule therapeutics that can include therapeutic peptides or whole proteins
- biomolecules - molecules present that are essential to one or more biological processes. The four major biomolecules are: carbohydrates, lipids, nucleic acids, and proteins
- bioprocess development - work done by multiple teams to support the production of a drug candidate
- bioreactor - a device where chemical processes can be carried out in and promotes growth of the input material
- binders - proteins or peptides whose main function is to bind other molecules
- binding affinity - the strength of the binding interaction between two molecules. In antibody research, the measured interaction would be between the antibody and its target
- bispecific antibody (BsAb) - an engineered antibody that can bind two different epitopes at the same time. The two epitopes can be on one antigen or two separate antigens, depending on the use case
- blunt ends - a DNA fragment with no single-stranded overhang
C
- carbohydrate - a biomolecule consisting of carbon, hydrogen, and oxygen that plays major roles in nutrient storage, energy production, and structural support. Also called a sugar.
- Cas nuclease - the nuclease enzyme used in CRISPR gene editing that makes double-stranded DNA breaks. Depending on the CRISPR use case, the Cas nuclease might be engineered to have other and/or additional functions. For example, dCas9 is an inactivated nuclease that does not form double-strand breaks but rests on top of the target site.
- cell - the most basic structural and functional unit bound in a membrane from which living organisms are made. Cells are the building blocks of tissues in multicellular organisms.
- cell immunotherapy - a treatment where immune cells are modified and given to a patient to help fight disease.
- cell sorting - a process that uses fluorescent antibodies to sort one cell type from other cells in a mixed sample
- cell therapy - a treatment where healthy or modified cells are injected, grafted, or implanted into a patient to treat a disease.
- central dogma - the principle describing the linear flow of genetic information from DNA to RNA to protein.
- chemically modified antibody - antibodies with small molecules chemically attached to them for therapeutic purposes.
- chromatin - the complex of DNA and protein that makes up chromosomes in eukaryotic cells.
- chromatography data system (CDS) - a software solution that manages chromatography data and methods
- chromosome - the condensed form of the linear DNA in eukaryotes. Chromatin is organized into chromosomes as it condenses preceding cell division.
- clinical development - a phase of the R&D lifecycle that tests lead candidates for safety and efficacy in human patients.
- (molecular) cloning - a set of methods used to assemble recombinant DNA for delivery and expression into a host organism.
- codon - a group of three consecutive nucleotides in mRNA that codes for a particular amino acid sequence.
- Codon Adaptation Index (CAI) - a calculation describing how codons are used in a gene. Can be applied during HR template design to preview what mutations to the sequence will result in silent mutations.
- cohort - the entire group of animals enrolled together in a study. Also called a study population.
- colony management - describes the day-to-day record keeping associated with maintaining all animals used by a specific company or laboratory.
- complementarity-determining regions (CDR) - the part of the antibody variable chain that allows the antibody to bind to the antigen.
- complementary DNA (cDNA) - the DNA synthesized from a single-strand RNA template by the reverse transcriptase enzyme.
- conjugation - in chemistry, it is the process of joining two or more chemical compounds
- consensus alignment - comparison of two or more sequences to calculate the order of the most frequent nucleotide or amino acid residues across a population
- constant domain - a sequence feature of both the heavy and light chains of antibodies and is responsible for determining the class (and thus mechanism of action) of an antibody
- constant region - the part of an antibody that can bind to cell receptors or other immune molecules to generate the appropriate immune response
- contig assembly - a means of assembling a whole genome from a set of reads. Software aligns overlapping reads (contigs) and assembles them into a single sequence
- covalent bond - a stable link between two atoms that share electrons
- chimeric antibody - monoclonal antibody molecules made up of domains from different species. In therapeutics, the host Fc region is generally replaced with a human Fc region while the host Fab remains
- Chimeric Antigen Receptor T cell therapy (CAR-T) - a cell therapy where killer T cells have been genetically engineered to express a chimeric protein that targets specific markers on malignant cells
- chimeric receptor - a receptor protein designed in a laboratory that joins two or more genes to create a protein with properties derived from each of the original genes
- Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) - a gene editing tool that works because a short RNA oligo identifies the target gene and directs a nuclease to that site to create double-strand breaks that can be repaired with random bases or with a template. There are a variety of ways CRISPR can be used outside of gene editing.
- CRISPR activation - use of a dCas nuclease modified with a transcription activator to promote expression of the target gene
- CRISPR interference - use of a dCas nuclease modified with a transcription repressor to prevent expression of the target gene
- CRISPR for epigenetic regulation - use of a dCas nuclease modified with an epigenetic editing effector to add or remove chemical modifications to individual bases or histone proteins
- CRISPR for nucleic acid visualization - use of a dCas nuclease modified with a fluorescent tag to visualize target nucleic acids
- cytokine - proteins that play a role in cell signaling and modulating the immune response
- cytotoxic - chemical compounds that kill cells
D
- deoxyribonucleotide triphosphate (dNTP) - a generic term for any four of the DNA nucleotides: dATP, dTTP, dCTP, dGTP
- dideoxynucleotide triphosphate (ddNTP) - chain forms of DNA nucleotides. ddNTP is the generic term for any of the four DNA nucleotides: ddATP, ddTTP, ddCTP, ddGTP
- differentiation - the maturation process cells undergo as they become specialized
- digest and ligate (assembly) - a plasmid assembly strategy associated with digesting both the insert and plasmid backbone with restriction enzymes to create complementary sticky ends that will facilitate the construction of a recombinant plasmid containing the digested insert
- discovery - a phase of the R&D lifecycle that conducts basic research to identify targets and screen drug candidates
- disulfide bond - a covalent bond that is formed specifically between thiol (-SH) groups to join two proteins together
- domain - a specific physical region of a protein structure that is associated with a particular function
E
- early development - a phase of the R&D lifecycle that further tests lead drug compounds in cell and animal models to determine if clinical trials are appropriate.
- efficacy studies - studies to determine the ability of a drug to produce the desired therapeutic effect.
- electronic lab notebook (ELN) - a software solution for storage of experimental procedures and data designed to replace paper lab notebooks.
- electrophoresis - a group of experimental methods for separating macromolecules on the basis of their size and charge. Molecular biologists most commonly use gel electrophoresis where a polymer gel acts as the matrix to separate samples by size.
- enzyme-linked immunosorbent assay (ELISA) - a type of test that uses enzyme linked antibodies to detect the presence of specific proteins within a sample.
- endogenous - material delivered to a cell or organism originating from within the cell or organism. Generally refers to DNA or RNA, and sometimes proteins.
- engineered nucleases - a class of gene editing techniques that use specifically engineered enzymes to generate a double-strand break at a target gene. Examples include Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) which both require the fusion of a DNA-binding domain to the nuclease. CRISPR is another example of an engineered nuclease gene editing platform.
- enhancers - a regulatory DNA sequence that serves as a binding site for proteins that regulate the rate of transcription for a particular gene.
- enzyme - a protein that acts as a catalyst for a specific biochemical reaction.
- epigenetic modification - chemical modifications to histone proteins or nucleotides that regulate whether genes are expressed or silenced.
- epigenetic regulation - the process in which gene expression is controlled by chemical modifications of bases or histone proteins that alter chromatin structure.
- epitope - the specific sequence of an antigen that an antibody recognizes and binds to.
- error prone PCR - a variation of traditional PCR that uses a polymerase with no proofreading capabilities to generate random mutations of template DNA
- eukaryote - a category of cells distinguished by having a distinct nucleus and membrane bound organelles in the cytoplasm.
- exogenous - material delivered to a cell or organism that was derived outside of the cell or organism.
- exon - the portions of DNA that code for proteins.
F
- fragment, antigen, binding region (Fab region) - region on an antibody composed of one constant and one variable domain from each heavy and light chain of the antibody. Another way to refer to the variable region of an antibody.
- fragment crystallizable region (Fc region) - tail region of an antibody that interacts with cell surface receptors and some proteins of the complement system, allowing antibodies to activate the immune system. Another way to refer to the constant region of an antibody.
- functional annotations - these identify regions of a sequence that contribute to specific functions. For example, motifs and domains.
- functional group - a defined group of atoms within a molecule that are responsible for the characteristic(s) of the molecule.
- fusion protein - proteins designed in a laboratory that join two or more genes to create a protein with properties derived from each of the original genes. Sometimes referred to as chimeric proteins.
G
- GC clamp - the presence of a guanine (G) or cytosine (C) nucleotide within the last five bases of a primer. Serves to improve the specificity of a primer binding to its complementary sequence.
- gene - a unit of heredity in DNA that's sequence contains information directing the production of a protein via an mRNA molecule.
- gene editing - a group of technologies that allow scientists to change the DNA within a cell. There are a variety of mechanisms that scientists use to change DNA.
- genotype - an organism's complete set of genetic material.
- gene therapy - the addition or transplantation of normal genes into cells to replace missing or defective genes for therapeutic purposes.
- gene addition - a technique that involves the insertion of a functional copy of a gene into a person’s cells.
- gene replacement - a technique that replaces a faulty gene at it’s endogenous location in the genome.
- gene reprogramming - a technique used to activate or add specific gene(s) to change the characteristic of specific cells.
- gene inhibition - a technique that can be used to remove a gene or introduce mutations to prevent gene expression.
- Gibbs free energy (ΔG) - the energy required for a substance to spontaneously react. For PCR, it refers to the amount of energy needed for a primer to form secondary structures.
- Gibson (assembly) - a plasmid assembly strategy that utilizes homologous overhangs on the insert and plasmid backbone to construct a recombinant plasmid
- global alignment - an alignment classification that aligns two or more similar sequences from beginning to end, aligning each letter in each sequence only once. It is generally used to identify mutated residues or regions.
- glycosylation - the modification of a protein by the addition of a carbohydrate
- Golden Gate (assembly) - a plasmid assembly strategy that uses Type IIS enzymes to create overhangs on the insert and plasmid backbone to allow quick construction of a recombinant plasmid
- guide RNA (gRNA) - a short (16-24 base pair) RNA oligo used in CRISPR gene editing that identifies the gene of interest and recruits the Cas nuclease to that location.
- good "x" practices (GxP) - a collection of quality guidelines and regulations to ensure the safety of pharmaceutical products where "x" stands for the various disciplines within the industry. The ones used most often by Benchling are:
- good clinical laboratory practices (GCLP) - standards for managing samples from clinical studies
- good laboratory practices (GLP) - standards for managing samples from preclinical studies
- good manufacturing practices (GMP) - standards for the manufacturing of pharmaceutical products
H
- hairpin (loop) - an unpaired loop of essential RNA that is created when an mRNA strand folds, then forms base pairs with another section of the same strand. The resulting loop structure resembles a U-shape, or hairpin
- (immunoglobulin) heavy chain - the heavier molecular weight subunit of a multimeric protein. In an antibody, the constant domains of the heavy chain help determine the mechanism of action
- HELM notation - the hierarchical editing language for macromolecules (HELM) that describes the structure and composition of complex biological molecules
- helper T cell - a subset of T cells that coordinate killer T cell response
- histone - a group of proteins that DNA wraps around to facilitate chromatin formation
- hit - a molecule that shows the desired type of activity in a screening assay, or a compound confirmed to have binding activity to the target
- homology arms - the sequences flanking either side of the edited region in the donor DNA used for HR repair. These regions on the donor DNA are complementary to the genomic DNA and help establish the donor DNA as the template to be used to repair the strand break
- homology repair (HR) - a DNA repair pathway that repairs double-stranded DNA breaks using donor DNA as a template
- housekeeping RNA - a constitutively expressed gene that is required for the basic functioning of cells
- homologous recombination template (HR template) - a synthesized DNA sequence with homologous regions (homology arms) surrounding an edited target sequence that is used during homology-directed repair to repair double-strand DNA breaks and introduce mutations
- human pluripotent stem cell therapy (hPSC) - a category of self-renewing cells that maintain the ability to differentiate into nearly any cell type. hPSCs include both human embryonic stem cells and human induced pluripotent stem cells
- humanized antibody - monoclonal antibody molecules where most of the host Fc and Fab regions are replaced with human sequences
- hybridoma - a culture of hybrid cells created by fusing B cells and immortalized myeloma cells. A successful fusion creates a cell line that can be expanded and continually produce a large amount of a single monoclonal antibody
- hybridoma technology - a technology used to produce large numbers of monoclonal antibodies
- hydrocarbon - an organic molecule made up of carbon and hydrogen
- hydrogen bond - a weak, noncovalent interaction between a positively charged hydrogen atom and a negatively charged atom, often nitrogen, oxygen, or fluorine
I
- immunoassay - a biochemical test that uses antibodies to detect or measure the presence of specific proteins in other substances. When used in a diagnostic setting, these tests are often called immunodiagnostics
- immunogenicity - an immune response against a drug or other therapeutic agent
- immunoglobulins - another term for antibody
- indel - insertion or deletion of nucleotides in DNA
- induced pluripotent stem cell therapy (iPSC) - de-programming adult stem cells so they can be re-programmed to take on the characteristics of any cell needed for therapy
- innate immune response - a form of nonspecific immunity that protects against all antigens. Innate immune responses contrast with the adaptive immune response which uses antibodies to target specific antigens
- insert - a piece of DNA that codes for a specific gene of interest that is inserted into a larger DNA vector, generally a plasmid backbone, for expression in a host organism
- in silico - a step(s) in an experiment that are performed on the computer or via computational simulation
- Internet of Things (IoT) - a network of physical objects that connect and exchange data with devices and systems via the internet
- intron - a noncoding sequence within a eukaryotic gene that is excised from an RNA molecule after transcription during splicing
- in vitro - a term that refers to experiments carried out in models of a living organism, but not in the organism itself. For example, cell culture or screening purified proteins for activity
- in vivo - a term that refers to experiments carried out in a living organism. For example, animal models or human clinical trials
- Investigational New Drug (IND) - a request from a company to obtain FDA authorization to begin clinical studies in humans
K
- killer T cells - a subset of T cells that destroy cells
- kilobase (kb) - a unit of measure for DNA and RNA that describes 1,000 base pairs
- (gene) knock-in - describes the targeted insertion of an exogenous gene at a specific locus in the genome. Generating a desired insertion often requires the use of homology repair mechanisms
- (gene) knockout - describes the removal or inactivation of a specific gene
L
- laboratory information management system (LIMS) - a software solution that allows researchers to manage both samples and data and supports laboratory operations
- laboratory execution system (LES) - a software solution that drives quality and compliance and allows for management of lab, and process procedural-centric workflows
- large molecule - molecules with high molecular weight (therapeutics)
- leads - compounds that might be therapeutically useful but require more testing and optimization
- ligation - the process of joining DNA fragments in a reaction catalyzed by an enzyme called ligase
- light chain - peptide sequences that bind to heavy chains and make up the Fab fragment of an antibody
- lipid - a biomolecule made up of long hydrocarbon chains or rings and is water insoluble
- lipid nanoparticles (LNPs) - nanoparticles composed of lipids that serve as a vehicle for drug delivery
- local alignment - matching one or more sequences over a specific region of another sequence
- long non-coding RNA - a class of RNA that has more than 200 nucleotides and does not encode proteins
M
- macromolecule - a polymer built from covalently linked monomeric subunits. Includes carbohydrates (polysaccharides), lipids, nucleic acids, and proteins
- major histocompatibility complex (MHC) - proteins found on cell surfaces that help the immune system recognize foreign material. MHC compatibility plays a large role in identifying matches for organ and bone marrow donations
- mass spectrometry - a technique that can be used to sequence protein samples
- mesenchymal stem cell therapy (MSCT) - a type of therapy frequently used in regenerative medicine for neurological and cardiac disorders as well as in bone and cartilage diseases. Mesenchymal stem cells are multipotent, which means they are cells that can differentiate into more than one type of cell, but are more limited than pluripotent cells
- metastatis - cancer that spreads from where it started to a distant part of the body. Cancer cells that break away from the original (primary) tumor, travel through the blood or lymph system, and form a new tumor in other organs or tissues of the body.
- mets - short for metastasis. Can also refer to tumors resulting from metastasis
- modified nucleic acid - a category of DNA or RNA therapeutics that incorporate nucleic acid monomers into a sequence
- modified peptide - a category of therapeutics that incorporate modified, unnatural, or other synthetic amino acids into a peptide sequence
- molecular biology - a field of study that focuses on understanding how the structure and function of biomolecules and macromolecules are regulated
- monoclonal antibodies (mAbs) - the identical antibodies produced from a single B cell
- motif - short, recurring patterns in DNA, RNA, and protein sequences that have well-defined biological functions. Multiple motifs may combine to form a domain
- mRNA therapy - therapeutics that deliver protein coding mRNA to a cell or organism to promote the generation of a specific protein
- multiple cloning site (MCS) - a short stretch of DNA engineered into plasmid backbones containing many restriction sites
- multiplex bead assays - an assay that uses antibody-coated latex beads to detect the presence of an antigen in a sample
N
- natural killer cell therapy (NK) - a form of cell therapy that uses natural killer cells and the innate immune response to target cancer and other diseased cells
- next generation sequencing (NGS) - a wide category of high throughput sequencing techniques
- nitrogenous base - a molecule made of a nitrogen-containing ring that is most often found attached to a pentose sugar in nucleic acids
- non-homologous end joining (NHEJ) - a DNA repair pathway that repairs double-stranded DNA breaks by randomly adding or deleting small sequences of nucleotides
- non-polar molecule - molecules that lack accumulation of positive or negative charges which usually makes the molecule water insoluble
- nucleotide - a biomolecule made up of a nitrogenous base connected to a pentose sugar with a 5’ phosphate. Nucleotides serve as the building blocks of nucleic acids, like DNA and RNA
- nucleus – the structure in a eukaryotic cell that contains its genetic material
O
- oligonucleotide (oligo) - short, single strands of synthetic DNA or RNA
- open reading frame (ORF) - sequences of nucleotides that contain no stop codon and indicate potential protein-coding sequences in DNA
- organelle - a discrete structure within the cytoplasm of a eukaryotic cell that carries out a specialized function
- organic - describes chemical compounds that contain carbon and hydrogen
- organism - a living being that has an organized structure, can react to stimuli, reproduce, grow, adapt, and maintain homeostasis. Organisms can be unicellular or multicellular
- origin of replication (Ori) - a sequence of DNA where the initiation of replication occurs on plasmids
P
- payload - the small molecule cargo carried by an anti-body drug conjugate (ADC)
- peptide - short chains of amino acids. When multiple peptides are joined together they form a protein
- peptide bond - a chemical bond joining two amino acids together via the carboxyl group of one amino acid and the amine group of the second amino acid
- pharmacokinetics - the study of the behavior of drugs in the body, generally focused around drug absorption, metabolism, distribution, and excretion (ADME)
- pharmacology studies - a series of studies investigating the biological effects of a drug in a complex living organism that informs decision making during drug development. Examples include pharmacokinetics (PK), pharmacodynamics (PD), and pharmacogenomics.
- phosphodiester bond - a strong covalent bond between the 3’ carbon of one nucleotide and the 5’ carbon of another. These bonds form the backbone of DNA and RNA macromolecules
- plasmid - self-replicating, circularized DNA found in prokaryotic organisms
- plasmid assembly - a set of methods used to assemble recombinant DNA for delivery and expression into a host organism. Can also be referred to as cloning
- plasmid backbone - genetically engineered plasmid templates that can be more easily manipulated during cloning
- plasmid map - a graphical representation of a plasmid that shows the locations of major elements of the plasmid
- polymerase - an enzyme which brings about the formation of a particular polymer, especially DNA or RNA, from a template strand
- post translational modifications (PTMs)–a chemical modification that occurs to one or more amino acids of a protein after translation
- polymerase chain reaction (PCR) - a protocol that researchers use to amplify DNA. There are several different types of PCR reaction that are variations of traditional PCR amplification
- preclinical development - toxicity and efficacy studies on lead candidates in cell lines, tissue samples, and animal models
- primers - short single-stranded sequences of DNA or RNA that can bind to a complementary template to recruit other enzymes, usually polymerase, to the site
- primer dimers – two primer molecules that have attached to each other because of complementary bases in each primer
- procedures - used in early development to describe conducting experiments with validated processes under regulatory conditions
- process development - the design of methods to scale up production of lead candidate compounds
- processes - used in early development to describe the validated steps being executed in a procedure
- prokaryote - a category of cells that are distinguished by the absence of a nucleus and membrane bound organelles
- promoter - a DNA sequence element that is recognized by RNA polymerase and initiates gene transcription
- protein engineering - a process for developing, modifying, and optimizing protein sequences to achieve a protein that is suitable for specific applications
- proteome - refers to the entire set of proteins expressed by a cell, tissue, or organism
Q
- quantitative polymerase chain reaction (qPCR) - sometimes referred to as real-time PCR and allows researchers to detect the concentration of template DNA via fluorescence during each round of amplification
- quantitative reverse transcription polymerase chain reaction (qRT-PCR) - used to detect concentration of template RNA via fluorescence during each round of amplification. It combines aspects of qPCR and RT-PCR
R
- radiolabeled antibody - an antibody with radioisotopes attached for diagnostic and/or therapeutic purposes
- recombinant DNA - a plasmid that is modified to include genes from multiple sources
- recombinant enzyme - an enzyme produced by bringing together genetic material from multiple sources to express in a host organism
- restriction digestion - a process where a nuclease enzyme, also known as a restriction enzyme, cuts DNA at specific sequences
- restriction sites - specific sequences of DNA recognized by restriction enzymes as the site to make a double-strand break
- reverse transcription polymerase chain reaction (RT-PCR) - a protocol researchers use to amplify DNA used to run PCR amplification reactions on RNA samples
- ribosome - a large macromolecular complex that translates mRNA into protein and is composed of ribosomal RNA and ribosomal proteins
- RNA aptamers - RNA molecules that target and bind proteins to modulate their activity
- RNA interference (RNAi) - a post-transcriptional process mediated by double-stranded RNA in eukaryotes that leads to targeted gene silencing and degradation of mRNA.
- RNAi therapies - therapies that use RNA interference techniques to disrupt gene expression. There are a variety of RNAi therapies that target different cellular machinery to regulate gene expression
- RNA sequencing - a technique that leverages NGS techniques to sequence all of the RNA being expressed in a cell
- RNA therapeutics - a broad category of therapeutics that use RNA as a platform to modulate gene expression
- ribonucleoprotein (RNP) - a complex that contains both protein and RNA. Often used to describe Cas9 protein bound to guide RNA (gRNA)
- runs - used in early development to describe multiple sets of conducted procedures
S
- Sanger sequencing - conventional DNA sequencing where one fragment of DNA is sequenced at a time
- scientific data management system (SDMS) - a software solution that allows for managing lab instrument data workflows, methods, and data archiving
- sequence assembly - refers to the process of aligning sequenced fragments of DNA to reconstruct the original sequence
- sequence homology - two or more DNA, RNA, or protein sequences that have the same sequence between two given points
- sequencing - a set of techniques used by molecular biologists to determine the order of biomolecules in a sample. Most sequencing used by molecular biologists is for DNA, RNA, or protein samples
- short regulatory RNA - a variety of different types of non-coding RNA molecules that play a role regulating gene expression by either activating or inhibiting gene expression
- short hairpin RNA (shRNA) therapeutic - a short RNA sequence that folds into a hairpin structure and is processed into a single strand in the cell in order to degrade mRNA in a highly specific, targeted manner
- shotgun assembly - a method of sequencing a genome by sequencing small DNA fragments individually, then assembling these sequencing reads into one large sequence
- silencer - a DNA sequence element capable of binding proteins that repress expression
- simplified molecular-input line-entry system (SMILES) strings - a notation for describing the structure of chemical compounds
- single-chain variable fragment (scFv) - a fusion protein consisting of the heavy chain and light chain variable regions of an antibody. These are the regions of an antibody that are responsible for binding antigens
- single nucleotide polymorphism (SNP) - the substitution of a single nucleotide at a specific position in a DNA sequence
- site-directed mutagenesis - an experimental protocol where specific mutations are introduced to a target sequence by primers that are not a 100% match
- small interfering RNA (siRNA) therapeutic - a short, double-stranded RNA therapeutic that is processed into a single strand in the cell in order to degrade mRNA in a highly specific, targeted manner
- small molecules - chemical compounds with low molecular weight (therapeutics)
- specificity - the measure of how well an antibody can distinguish target antigens from other proteins
- splicing - the post-transcriptional processing of RNA to remove non-coding introns and join coding regions (exons) to generate mRNA
- sticky ends - the short single-stranded overhang of a DNA fragment that results from restriction digestion. These fragments easily re-attach to other ends that are complementary to it
- structural annotations - notations identifying regions of a sequence that encode for specific features. For example, ORFs and regulatory regions
- substructure - a substructure refers to specific chemical features within a larger chemical structure, often with a specific property or activity
- synthetic peptide - chemically synthesized amino acid chains
T
- T cell - a type of white blood cell that plays a large role in the adaptive immune response
- T Cell Receptor therapy (TCR) - a cell therapy where killer T cells are engineered to express new T cell receptors that target certain MHCs expressed on malignant cells
- template alignment - aligns one or more sequences against a specific template sequence to examine locations of sequence differences compared to the template
- toxicology study - a systematic investigation to determine the harmful effects or metabolites that might result from using a specific drug
- transcription - the process by which DNA is used as a template to synthesize RNA
- transgene - refers to a gene that has been artificially introduced to an organism
- translation - the process by which mRNA is used to direct the incorporation of amino acids into a protein
- treatment group - groups of animals that receive the same treatment during a study
- Tumor Infiltrating Lymphocyte therapy (TIL) - a cell therapy where T cells are removed from within a patient’s solid tumor, activated and expanded, then transplanted back into the patient
V
- variable domain - a sequence feature of both the heavy and light chains of antibodies and is responsible for antigen binding
- variable region - the part of the antibody that recognizes and binds the antigen and determines binding specificity
- viral vectors - viruses modified to be non-pathogenic to carry and deliver genetic material into cells. Viral vectors themselves can be used as a gene therapy platform or to package and deliver engineered nuclease therapies
- virus - an infectious particle made up of a protein coat enclosing genetic material (DNA or RNA) that can replicate within a host cell and spread from host cell to host cell
W
- whole exon sequencing (WES) - a technique that sequences all the coding regions in a genome, requiring the use of NGS