This page contains a glossary of some of the terms we use throughout the course. This page is constantly being updated with new terms and is currently in progress. Let us know if you think a terms should be on this page!

Jump to letter: # A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

#

2A Linker — A class of self-cleaving peptide linkers placed between two proteins. Used to express multiple proteins from a single transcription unit.

A

activator — a protein that binds DNA and promotes transcription of nearby DNA (often directionally, on one side of the binding site, but sometimes bidirectionally). An activator can do this by e.g. recruiting RNA polymerase, opening chromatin to allow access to the promoter region by RNAP (in eukaryotes), blocking a repressor from binding.

actuation — the process of making some change in some physical feature or quantity. For example, an genetic circuit could perform actuation by creating a fluorescent protein (its concentration in the cell changes to be larger than 0), a killer protein (again, the concentration changes and results in the death of the cell), or even make it move, changing the cells location.

aggregator — something that sums up inputs. For example, the $\sum$ operator is a mathematical aggregator, the OR gate is a logical aggregator with a limit (it can only sum up at most one input), the AND gate is a logical aggregator with a limit as well as a threshold (addition is performed only if all inputs are present, in which the output is still only 1). In the parts and compositors framework, the compositor works as an aggregator, summing up all the rates of change of some physical parameter due to various parts.

AHL — they are a class of homoserine lactones with an acyl group. These are small molecules that can diffuse between cells. They typically act as a quorum sensing signalling molecule as it can diffuse throughout a bacterial population such that the knowledge of the concentration of the AHL is shared between all bacteria. The bacteria can detect the AHL concentration by way of a transcription factor that can bind and be modulated by the AHL molecule. For example, the luxI gene produces an AHL that can then bind luxR, relieving its repressor on the corresponding promoter.

allosteric regulation — allosteric regulation happens when a conformational change (the allosteric part) affects the function of a protein or enzyme. For example, a small molecule may bind a transcription factor and cause a conformational change that removes the TFs ability to bind DNA, rendering it inactive.

alphavirus — small, spherical, enveloped viruses with a genome of a single positive sense RNA strand. Ahphaviruses have been engineered into self-replicating RNA and are commonly referred to as replicons.

AND gate — a digital logic element that produces a high output (1, true) if and only if all inputs (typically there are two) are high; otherwise, a low output (0, false) is produced

anneal — in the context of DNA assembly this means the coming together of complementary (or near-complementary, in some cases) sequences of DNA. This is often assisted by a change in temperature: two complementary sequences are often heated up (to say 95°C) and then allowed to cool down. The heating removes self-annealing, which causes secondary structures to form in the DNA, which might inhibit annealing to the other molecule. The cooling down allows the formation of hydrogen bonds between the two DNA strands. The opposite process to annealing is melting or denaturing of DNA, which happens at high temperatures.

antibiotic resistance gene — this gene creates a product that confers antibiotic resistance. For example, KanR confers resistance to the antibiotic kanamycin. This is useful for selection.

antibody — also known as an immunoglobulin (Ig), is a large, Y-shaped protein produced mainly by plasma cells that is used by the immune system to identify and neutralize pathogens such as bacteria and viruses.

antigen — any substance that causes an immune system to produce antibodies against it.

antisense — a sequence of nucleotides complementary to a coding sequence, which may be either the strand of a DNA that undergoes transcription, or a messenger RNA molecule.

aptamer — a sequence of RNA (or sometimes DNA) that folds into a particular 3D structure, enabling it to bind some molecule ligand, e.g. caffeine, with high specificity and strength. Binding of the ligand can sometimes induce a conformational change in the aptamer, which can be used as a signal for the binding event in aptamer-based circuits.

AraC — araC gene and AraC protein, components of the L-arabinose operon in E. coli.

arabinose —  aldopentose commonly used in synthetic biology as a one-way or reversible switch for protein expression.

assemble, assembly — refering to synthesizing DNA in a laboratory, DNA cloning.

aTc — anhydrotetracycline, a tetracycline analog that binds the TetR protein better than tetracycline.

att-site — regions of DNA required for site-specific recombination.

attenuate, attenuation — to lessen or weaken the effect of something. For example, noise in a system can be attenuated with certain techniques, such as feedback, which can reduce the amount of noise or lessen its affect on the system.

attractor — a term from differential equations signifying a stable steady state of a system. Systems that are in a nearby state are attracted to this steady state and will evolve in a way to get closer to reaching the steady state.

authority over a property — the ability to affect it. For example, in a one-gene system with no regulation, the degradation rate of the protein has authority over the timing of the system (how long it takes to reach steady state). Changing the degradation rate changes the time constant related to reaching the steady state. The transcription rate in this system does not have authority over timing, but does have authority over the steady-state level.

autoregulation — self-regulation. For example, an electric heater could employ negative autoregulation in order to keep a steady temperature in the room. If it heats the room too much, the room gets hot; a temperature sensor can detect this and turn the heater off. Once the room cools down, the sensor can detect this event as well and turn the heater on. The heater regulates itself in this way. In this course we discuss the autoregulation of genes, where the gene product also regulates the expression of the gene (and thus itself).

AutoCAD — computer-aided design commercial software application.

B

backbone — term used in DNA cloning to refer to a DNA construct that serves as destination for other DNA parts.

band-pass — refers to the part of a signal transmitted through a band or range of the signal. In electrical engineering, a band-pass filter passes frequencies within a certain range and attenuates frequencies outside that range.

basal — baseline level. For example, there might be basal expression from a gene in the absence of activators or in the presence of repressors. This is the minimum amount of expression we can reach. The basal expression level can drastically affect the performance of systems, e.g. in positive autoregulation.

base — the basic building blocks of DNA and RNA. The primary nucleobases are cytosine (C), guanine (G), adenine (A), thymine (T) and uracil (U).

basepair — a pair formed between two bases.

BFP, EBFP — Blue fluorescent protein. "E" denotes newer enhanced version.

bifurcation point —

binding constant — constant associated with the binding and unbinding reaction of receptor and ligand molecules.

BioBrick —  DNA sequences which conform to a assembly standard that uses a specific restriction-enzyme-based protocol introduced at MIT in 2003.

BioCAD — information system that incorporates computer-aided design tools into synthetic biology.

BioCompiler — the concept of a computer software compiler applied to synthetic biology.

biomarker — a measurable indicator related to a particular state of a biological system.

bimodality — >a system with two modes of operation or behavior.

bistability — a system with two stable steady-states. The system must also have a third, metastable state due to the definition of stability.

bit — a single chunk of information. This information can be encoded in the state of something, e.g. the voltage level (high or low) of something, the concentration of something (high or low), the position of something (nucleus vs. cytosol, switch being flipped on vs. off).

Boolean — a variable with only two possible values: true or false.

BsaI — important restriction enzyme in DNA cloning protocols such as Golden Gate and MoClo.

C

CAG, pCAG — The CAG promoter is a strong promoter for expressing proteins in mammalian cells. It is composed of the cytolomegalovirus (CMV) promoter enhancer region, chicken ß-actin promoter and first intron/exon, and the rabbit ß-globin splice acceptor. Hence, CAG.

CRISPR/Cas9 — new tool based on the bacterial CRISPR-Cas system to target and/or edit genomes.

cascade — referring to having two or more sequential functional elements.

cassette — assembled part of DNA. Gene cassette or expression cassette.

ccdB — lethal gene that targets DNA gyrase. The lethal gene is useful for ensuring that the plasmid containing it cannot be propagated in standard E. coli strains.

CDS — from coding DNA sequence.

CFP — Cyan fluorescent protein.

chaperone —  proteins that assist the covalent folding or unfolding and the assembly or disassembly of other macromolecular structures.

characterization, characterizable — referring to a system or element that can be measured and analyzed to understand its function.

chassis — the conceptual extension of the living cell in synthetic biology.

chromophore —   part of a molecule responsible for its color.

circuit —  formed by individual interconnected components in a biological system for a specific function.

cistron, poly-cistronic — a cistron is a gene.

classifier —  system with the ability to classify a particular biological state.

cloning, molecular cloning — the assembly and replication of new DNA constructs from existing pieces of DNA

CMV — strong viral promoter commonly used in mammalian synthetic biology.

codon — a triplet of ribonucleotides in mRNA that encodes for an amino acid.

coherent FFL —  a feed-forward loop (FFL) is defined as coherent if the signs of the direct and indirect pathways onto the last node are the same, or incoherent if they are the opposite

combinational logic — logic functions and circuitry that do not have a state, i.e. the output is determined completely by the input. The presence of state would indicate a memory element, which are not allowed in combinational logic. The simple logic gates, e.g. AND, OR, NOT, NAND, NOR, are all combinational devices.

combinatorial library —  comprised of different possible combinations that compose a functional element or elements.

competitive inhibitor, competitive inhibition — inhibitor that competes with another molecule or molecules in the inhibition process.

composability — design principle with the objective of creating elements that can be assembled in various combinations to satisfy specific system requirements

compositor —

constitutive — produced or active in relatively constant amounts. A constitutive promoter is constantly active.

construct — an assembled part of DNA.

context — the setting in which something occurs.

cooperativity — the ability for binding events to promote additional binding events. E.g. the binding of the first oxygen molecule to hemoglobin makes the binding of the second molecule much more likely, which in turn makes the binding of the third molecule much more likely, which in turn makes the binding of the fourth molecule much more likely. We often want to use repressors that exhibit cooperativity, as they exhibit a non-linear response useful for creating devices that can be analyzed with the digital abstraction.

coupling — connecting or pairing.

Crick strand — a less-often-used nomenclature for the anti-sense DNA strand

cross-talk — interaction between two or more elements generally not meant to interact.

D

de novo — from scratch. E.g. de novo DNA synthesis is the synthesis of DNA from basic building blocks like nucleotides or oligonucleotides, instead of creating a new molecule of DNA that's a copy of an existing molecule of DNA (templated synthesis).

decomposition — conceptual breakdown of a system into elemental parts.

derivative — represents the rate of change of a function.

differentiation — action or process of differentiating into another biological state.

digestion — the process of treating a substance (e.g. DNA) with enzymes to promote decomposition into essential components.

digital — expressed in discrete quantities, such as 0 and 1.

dissociation constant — inverse of the association constant.

DNA — is a molecule that carries most of the genetic instructions used in the development, functioning and reproduction of all known living organisms and many viruses.

DNA assembly — the process of putting together pieces of DNA into larger DNA constructs, e.g. plasmids.

downstream — refers to an element, reactive or location at a later stage in a series of elements or events.

dox, doxycycline — an inducer molecule for TetR. Also see aTc.

ds — double-stranded, e.g. dsDNA or dsRNA, indicating that there are two complementary strands that are annealed together

dual use — a technology is dual use if it can be used for immense good as well as terribly bad things. A classic example is nuclear fusion, which could be used to create sustainable energy or destructive bombs. Synthetic biology is often considered dual use, as it can further many fields, e.g. medicine, for the better, but could also theoretically be used to cause harm.

E

E. coli, Escherichia coli — a family of bacteria. The strains based on the K-12 strain cannot colonize the human gut and can thus be safely (in biosafety level 1 containment, the lowest level) used as organisms in the field of synthetic biology. Some strains of E. coli, however, can be pathogenic to humans. They have a small, ~4.6 megabasepair circular genome, are easily transformed, and replicate fast (cell replication can be made to be limited by the DNA replication only by the use of proper growth conditions). For these reasons, the K-12 based strains are heavily used by laboratories across the world.

EDA —

EECS — electrical engineering and computer science.

effector — an organ or cell that acts in response to a stimulus.

eigenvalue — scalar for which a differential equation has a nonzero solution under given conditions.

eigenvector — a special vector associated with a linear system of equations and eigenvalues of the system.

elongation — a stage in translation where amino acids are added by the formation of peptide bonds.

endogenous — present in the cell naturally.

endonuclease — a nuclease that cuts within a sequence (compared to an exonuclease which cuts at the end of the sequence)

enhancer — enhances transcription.

entry vector — part of the Gatewat DNA cloning system.

equilibrium — state at which opposing reactions in a biological system are balanced.

eukaryote, eukaryotic — organisms with membrane-bound organelles, especially the nucleus, which contains the genetic material, and is enclosed by the nuclear envelope.

exonuclease — a nuclease that cuts at the end of a sequence, base by base (compared to an endonuclease which cuts in the middle of a sequence)

expression vector — DNA vector that expresses a gene.

F

FACS — type of  flow cytometry for sorting a mixture of cells into two or more containers, one cell at a time, based upon the fluorescent characteristics of each cell.

feedback — occurs when outputs of a system are routed back as inputs as part of a chain

FFL, feed-forward loop — describing an element or pathway within a system that passes a controlling signal from a source to a load downstream of the source.

fixed point —

flow cytometry — laser-based  technology employed in cell counting, cell sorting, and biomarker detection by suspending cells in a stream of fluid and passing them by an electronic detection apparatus.

fluorescent marker, fluorescent protein — the use of a protein that fluoresces as a biomarker.

flux — the action or process of flowing in a biological system.

fusion protein — a single protein composed of two or more proteins that originally acted separately.

G

gal, galactosidase —  part of an assay frequently used in genetics, molecular biology, and other life sciences. An active enzyme may be detected using X-gal, which forms an intense blue product after cleavage by β-galactosidase, and is easy to identify and quantify.

Gal4 — A DNA binding protein derived from yeast. Commonly fused with trans-activation domains such as VP16

gate — see logic gate

Gateway — DNA cloning method that enables transfer of DNA-fragments between plasmids using a proprietary set of recombination sequences.

Gaussian — another term for normal distribution.

gel, gel electrophoresis, DNA gel — a DNA gel is a matrix used to separate pieces of DNA by size using gel electrophoresis where in the presence of an electric field pieces of DNA move through the matrix at different speeds determined by their size, shape, and charge

gene —  region of DNA that encodes a functional RNA or protein product, and is the molecular unit of heredity.

GFP, EGFP — Green fluorescent protein. "E" denotes newer enhanced version.

Gibson — DNA cloning method which allows for the joining of multiple DNA fragments in a single, isothermal reaction.

Gillespie algorithm

GOI — gene of interest

Golden Gate — DNA cloning method to simultaneously assemble multiple DNA fragments into a single piece using Type IIs restriction enzymes and T4 DNA ligase.

GRN, gene-regulatory network — collection of regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins.

GRO —

H

hairpin — a loop structure formed in both DNA or RNA. Common type of secondary structure in RNA molecules.

hazard — undesired output of a genetic circuit generally caused by different delays in different branches of the circuit.

hBax — human gene involved in the regulation of apoptosis.

HeLa — commonly used cell line used in scientific research derived from the cervical cancer cells of Henrietta Lacks.

heterodimer — formed by two different macromolecules.

hierarchical composition — composition arranged in order or rank of hierarchy.

Hill term — see Hill function

Hill function — the (bound) Hill function has the general form $\frac{[X]^n}{K^n + [X]^n} = \frac{([X]/K)^n}{1 + ([X]/K)^n}$ and shows the fraction of $Y$ bound by $X$ at equilibrium. The unbound Hill function is the fraction of $Y$ not bound by $X$, 1 minus the bound Hill function, or $\frac{K^n}{K^n + [X]^n} = \frac{1}{1 + ([X]/K)^n}$. $[X]$ is the concentration of $X$, $K$ is the dissociation constant for binding, $n$ is the Hill coefficient indicating the degree of cooperativity. If multiple binding configurations are possible, say $Y$ can also be bound by $Z$, list the "states" that you are interested in at the top of the fraction in the numerator and all possible states in the denominator. Each state is of the form $([X]/K)^n$; the state with nothing bound is thus $1$ and the state bound by both $X$ and $Z$ is $([X]/K_X)^{n_X} ([Z]/K_Z)^{n_Z}$

holoenzyme — active form of an enzyme that requires a cofactor to be active.

homeostasis — the property of remaining stable in the face of changing external conditions. For example, maintaining a stable population of pancreatic β cells even though the immune system is killing these cells in Type I diabetes would require an artificial homeostasis system as seen in lecture 3.

homodimer — formed by two macromolecules of the same kind.

homogeneous —  same or similar kind or nature.

homolog — refers to the similarity in DNA sequences of different DNA fragments or regions.

host — organism that receives and hosts another.

I

IFP — Input fluorescent protein. A fluorescent reporter for a circuit's input.

in vitro — used to refer to experiments conducted outside of a living animal (e.g. cell culture).

in vivo — used to refer to experiments conducted in a living animal (e.g. mice).

incoherent FFL —a feed-forward loop (FFL) is defined as coherent if the signs of the direct and indirect pathways onto the last node are the same, or incoherent if they are the opposite

inducer, induction, inducible — a system that can be induced by another molecule is an inducible system. Induction is the process of inducing the system.

inhibitor, inhibition — a molecule that can cause inhibition of a reaction or activity is called an inhibitor.

initiation — initial part of protein translation.

insulator — genetic boundary element that blocks interaction on a region of DNA.

integrase — enzyme that catalyzes the integration of a fragment of DNA into another part of DNA.

integration —  the event of a DNA fragment incorporating into another part of DNA.

interconnect — connected to each other.

interface — part where two systems or parts interact.

inverter — part that inverts the current state of a signal or system.

IPTG — an inducer molecule for LacI. Mimics allolactose, a product from the metabolism of lactose (i.e. a metabolite).

IRES — an internal ribosome entry site.

isogenic — organisms that have the same or closely similar genotype.

JBEI

K

KanR — gene which confers resistance to kanamycin.

Karnaugh-map, K-map — matrix system used to simplify boolean algebra expressions.

kinase — an enzyme that adds a phosphate group to some chemical moiety. For enzymes, the resulting change in phosphorylation state can change the activity of the enzyme (reduce or increase it, change the substrate affinity, or change the reaction being catalyzed). For DNA, a phosphate on the 5' end of a piece of DNA is required for it to be ligated to another piece of DNA.

kilobase, kb — a thousand DNA bases

knockout — the removal of a gene. A knockout (KO) organism is lacking some gene.

L

LacI — gene encoding for the lac repressor. In the absence of lactose, the lac repressor halts production of the enzymes encoded by the lac operon.

LacZ —  gene that encodes for β-galactosidase, which cleaves lactose into glucose and galactose.

Langevin equation — a stochastic differential equation describing the time evolution of a subset of the degrees of freedom.

LasI — part of the Las quorum sensing system, which consists. It binds to LasR to regulate several genes.

latch — a circuit used to store information.

leakiness — condition of permitting licky gene expression.

library of parts — library of DNA elements with the purpose of making DNA assembly more efficient.

ligand — a molecule (often small) that binds something (often much larger than the ligand) in a specific way. For example, an inducer molecule that binds a transcription factor is a ligand and caffeine is a ligand for a caffeine-specific RNA aptamer.

ligase, ligation — a ligase is an enzyme that catalyzes the formation of a covalent bond between large molecules, e.g. DNA or RNA, for which it catalyzes the formation of the phosphodiester bond in the backbone of the nucleic acid polymer. Ligases can use single-stranded or double-stranded (more commonly used) DNA (or even RNA) as the substrate, but are often specific to the type of substrate, while not being sequence-specific. All commonly used ligases require a 5' phosphate group on the substrate, which is absent from most synthetic oligonucleotides and thus have to be specifically ordered as such or enzymatically phosphorylated with a poly-nucleotide kinase (PNK).

linker — a linker sequence is inserted between two proteins in a translational fusion in order to allow the two proteins to fold independently. This sequence is typically made of glycines and/or lysines, which are relatively flexible residues, forming a loose chain between the two protein domains

load, loading — a load is a downstream element of a system or circuit (e.g. binding sites for a regulatory protein) that interacts with upstream elements and has an effect on the circuit function.

load driver — device used to engineer modularity in biological networks by mitigating retroactivity.

logic gate — an element implementing the notion of digital logic, e.g. an AND gate. The behavior of a logic gate can be expressed as a truth table.

Lux system, LuxI, LuxR — family of cell density-responsive transcriptional regulators that act as a quorum sensing system in bacteria.

M

machine — a set of parts that use energy to perform an action. A biological example is transcriptional machinery: a set of proteins that harness the energy of nucleotide triphosphate bonds to polymerize RNA transcripts.

marker — in the context of DNA assembly, a gene that enables the screening or selection of bacteria containing our desired marker. This could be a gene that is toxic to the cell (negative selection; e.g. ccdB), a gene that confers antibiotic resistance (positive selection; e.g. KanR), or a gene that turns the bacterial colonies some color (e.g. LacZ, or a fluorescent protein such as RFP)

mass-action kinetics — a method of modelling chemical reaction rates. In this kinetic scheme, the rate of a reaction is proportional to the product of the concentrations of reacting species.

master equation — a form of chemical kinetic equation that describes the time-evolution of all possible states of a chemical system. Master equations are commonly used in stochastic simulations in conjunction with the Gillespie algorithm simulations.

MoClo — modular cloning (MoClo). A hierarchical DNA assembly method built on Golden Gate technology. The use of a parts with standardized cloning sequences creates MoClo modularity. This modularity permits the automated construction of many MoClo constructs.

modularity — the engineering principle of interchangeable components. Modularity is an important aspect of design because it allows the reuse of (often-arduously-characterized) components. Some aspects of biology lend themselves well to modularity, e.g. 2A linker peptides and translational fusions.

module — a component that lends itself to be used in a modular manner.

modRNA — modified mRNA (modRNA). Synthetic, chemically-modified mRNA that can be transfected into cells to induce expression of a protein of interest. Chemical modifications at the 5' end allow the transcript to evade harmful immune responses and prevent it from being degraded thus allowing prolonged protein expression.

metabolator — a synthetic, oscillating circuit published by Fung et al. in 2005 that couples species oscillations to flux through a metabolic pathway. The use of acetyl-CoA as one of the oscillating (and actuating) species allows the sensing of glycolytic flux.

monomer — the basic unit of a polymer. A nucleotide is the monomer of a strand of DNA, which is a polymer of deoxyribonucleic acids

motif — a commonly-reproduced pattern that has a similiar function across multiple systems. Examples of regulatory network motifs are negative autoregulation and feed-forward loops. Nucleotide sequence motifs are commonly-found sequences of nucleotides that may serve as transcription factor binding sites. Amino acid sequence motifs may reproduce common protein structures such as alpha helices.

miRNA — a microRNA is a functional RNA that can inhibit the expression of a gene by either inhibiting translation through mostly unknown mechanisms or destabilizing the mRNA through the use of enzymes in the RNA interference, or RNAi pathway. Not all organisms have the RNAi pathway. Notable exclusions are all prokaryotes and baker's yeast, S. cerevisiae.

Michaelis-Menten kinetics — a chemical kinetic scheme for describing the rates of enzyme-catalyzed processes. Its simplest formulation considers three processes: the binding of substrate to enzyme, the unbinding of the substrate-enzyme complex, and the conversion of the enzyme-substrate complex to the product and the enzyme. Using mass-action kinetics and the assumption that enzyme concentrations are much smaller than substrate concentrations, we get an equation for the rate of product ($P$) production (initial velocity): $v = \frac{d[P]}{dt} = \frac{V_{max}[S]}{K_M+[S]}$ where $V_{max}$ is the maximal velocity (saturating substrate conditions) and $K_M$ is the Michaelis constant (the substrate concentration at half-maximal velocity). More complex Michaelis-Menten formulations must be used if the release of the product from the enzyme-product complex is slow, ordered-binding is required, or inhibitors are present.

mKate — A far-red fluorescent protein.

mRNA — messenger RNA is a functional RNA comprising codons to be translated by ribosomes to proteins. In eukaryotic systems, mRNA that has not been processed is referred to as precursor mRNA (pre-mRNA). This pre-mRNA is typically processed through the removal of exons, the addition of a poly(A) tail, and the addition of a 5' cap to create mature mRNA. Mature mRNA is what is translated by ribosomes.

multimer — a protein made up of multiple monomers. Notably, many transcription factor are active only in their multimeric form. Multimerization allows the emergence of cooperativity.

multiple cloning site, MCS — a designed stretch of DNA with recognition sites for many common restriction enzymes.

N

NAND gate — a negated AND gate: outputs false if all inputs are true and true otherwise.

negative autoregulation — a common regulatory network motif where the result of a process represses itself. An example would a repressor that represses its own transcription. Negative autorgulation can be harnessed to achieve faster convergence to steady state without the energetic waste of increased degradation. It can also increase the stability of a species concentrations or induce oscillations depending on parameters.

network — a group of two or more interacting sub-units. Each sub-unit is called a node and the interactions between nodes are termed edges. In synthetic biology, networks can be used to describe many different systems. Protein-protein interaction networks have proteins as nodes and the edges between them can be binding interactions. Microbiome studies may describe microbial species as nodes and define the edges as influences on growth rate.

node — the smallest sub-unit of a particular network

noise — irregular fluctuations that accompany a signal. Noise is an important consideration of biological system design because all interactions must be accomplished through chemical reactions. Chemical events produce noise due to their dicrete and stochastic nature. Digital devices are desireable because they have the ability to prevent the propagation of noise through a system.

NOR gate — a negated OR gate: outputs true if no input is present and false otherwise.

NOT gate; inverted buffer — a negated buffer gate. Outputs TRUE if the input is FALSE and outputs FALSE if the input is TRUE.

nuclease — an enzyme that creates a cut in the DNA (or RNA in some cases) backbone. Some nucleases are sequence specific, others are not. Some depend on the methylation state or other modifications of the substrate DNA.

nucleoside — a glycosylamine that is can be thought of as a nucleotide without any phosphate groups. This term is commonly seen in the form of deoxynucleoside triphosphates (dNTPs), a necessary reagent for PCR reactions.

nucleotide — the monomeric unit of DNA and RNA. A nucleotide comprises: a nitrogenous base, a five-carbon sugar (ribose or deoxyribose), and at least one phosphate group.

nucleus — a membrane-bound compartment found in most eukaryotic cells. It typically contains most of the cell's genetic information and entrance and exit of large molecules to and from the nucleus is mediated my nuclear pore complexes in the nuclear membrane.

nullcline — the set of system states that result in no change of a single state. The intersections of all nullclines are system equilibria. In the case of a two-species chemical kinetic model, there will be two nullclines and each will be a curve in a two-dimensional plane. While all nullcline intersections are equilibria, these are not guaranteed to be stable equilibria.

O

ODE — see ordinary differential equation

OFP — Output fluorescent protein. A fluorescent reporter for a circuit's output.

oligo, oligomer, oligonucleotide — short polymers of nucleotides usually less than 200 nucleotides in length. They are typically chemically synthesized and have many uses in biotechnology. DNA oligos can be used as primers for PCR, targets in DNA microarrays, and as probes for Southern blots.

oncolytic — cancer-killing, used in the context of viruses that have the ability to specifically infect and kill cancerous cells.

one-pot reaction — a reaction occurring in a single test tube vs. having multi-step reactions that need to be combined appropriately. Preferred, as it reduces the manual work, material losses etc. compared to multi-pot reactions.

operator — the sequence of DNA to which a transcription factor binds. Operators sequences can be varied to alter the binding affinity of their respective transcription factor.

operon — is a functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter.

OR gate — a digital logic element that produces a high output (1, true) if and only if any of the inputs (typically there are two) are high; otherwise, a low output (0, false) is produced.

ordinary differential equation — (ODEs) are differential equations that are a function of one independent variable and its derivatives. In the scope of this course, ODEs will most commonly be used to represent the time-evolution of chemical systems.

origin of replication, origin, ori — the location in a genome (or within a replicating plasmid) at which DNA replication is initiated. Genes near origins of replication will typically have higher copy numbers on average.

orthogonality — an engineering principle in which components of a system are able to interact independently of each other. An example of an orthogonal set of repressors would be a set of proteins where each protein binds its own operator sequence, but does not bind to the operator sequence of any of the other repressors. Such a set of orthogonal repressors was published by the Voigt Lab in 2014.

oscillator — a biomolecular system characterized by the periodic rise and fall of chemical species. Canonical synthetic biology include the metabolator and the repressilator.

overhang — a short stretch of single-stranded DNA that "hangs off" a region of double-stranded DNA. Two overhangs are compatible if they can anneal to form a double-stranded DNA with no gaps (there can be nicks in the backbone but no missing basepairs)

P

pathway — a series of interactions among molecules in a cell that result in a certain product or change in the cell. An example is a metabolic pathway where a linked-set of chemical reactions, catalyzed by enzymes, result in a product or set of products.

part — a part is a process in the context of design. Not to be confused with a physical part, which is likely to be involved with many processes that make design and abstraction difficult. Parts can be hierarchical. The inputs to parts are state variables and the outputs are rates of change of those state variables due to the process at hand. Example: the process of converting some particular substrate to a product is a part and can be composed of smaller parts, say the binding of the substrate to the enzyme doing the conversion, the actual conversion, the release of the product from the enzyme.

partial differential equations — (PDEs) are functions that contain multivariable functions and their derivatives. A common application of PDEs to biological systems is in the modeling of molecular diffusion.

PCR, polymerase chain reaction — a thermocycled reaction involving repeated rounds of primer annealing, primer extension and dsDNA denaturing to amplify and/or modify DNA sequences. Read more about it in the biology section of PS0.

perturbation, perturb — a deviation from the normal state of a system due to an outside influence. From an engineering perspective, we want to design systems that are robust to perturbations. That is: they are able to adjust their functions to still achieve their purpose. A method commonly used to make a system robust to perturbations is negative auto-regulation.

PEST tag — C-terminal tag that can be added to proteins to increase their endogenous degradation rate. Termed "PEST" because the peptide is rich in proline (P), glutamate (E), serine (S), and threonine (T).

phase plane — the trajectory of a system plotted in a two-dimensional state space. This graphical method is useful in the stability analysis of two-state systems. In a phase plane, the x and y axes represent a range of values for each of system's states. The vector field overlaid on the state space represents the derivative of the states with respect to time. For example: take a system with two states: (\x\) and $y$ which are on the x and y axes, respectively. Each vector in the vector field is $< \frac{dx}{dt}, \frac{dy}{dt} >$ for the values of $x$ and $y$ at that point. The stability of an equilibrium point can be determined by the shape of its surrounding vector field. If the surrounding vectors converge on the point, it is a stable equilibrium. If they diverge from the point, the equilibrium is unstable and any perturbations from that point would cause the system to fall away from the equilibrium.

phenotype — the set of observable characteristics of an organism resultant of the interactions between an organism's environment and its genotype.

physical part — in biology, a piece of DNA that might be involved in any number of processes. Example: ribosome binding site. In electrical engineering, some electrical component, e.g. a transistor

plasmid — a relatively small circular piece of DNA, usually on the order of tens of kilobases or less. Typical features of a plasmid include the origin of replication, a multiple cloning site and a marker, such as an antibiotic resistance gene.

plate reader — a device for measuring the absorbance, luminescence, or fluorescence of bulk cell culture, e.g. suspended bacteria. The name comes from reading the values of these properties in standard multi-well plate format, e.g. 96-well plates, where each well contains a sample.

polymerase — an enzyme that catalyzes polymerization from monomers.

positive autoregulation — a regulatory motif where a gene product activates its own production. This motif can exhibit bistability if a gene's basal production rate is below its switching threshold. Compared to negative autoregulation, a system exhibiting positive autoregulation will take longer to converge to a given steady state.

primer — a short, single-stranded DNA used in DNA replication. A primer binds a region of single-stranded DNA to form a primer-template complex which allows DNA polymerase to synthesize the complementary strand (primer extension). Since most DNA polymerases are only able to catalyze the addition of a nucleotide to the 3' end of a DNA strand, primers are necessary for elongation. Primers are a necessary reagent for PCR.

processive, processitivity — an enzyme is processive if it acts on a polymeric substrate and catalyzes a reaction on several of the monomeric subunits after binding the polymer. For example, DNA polymerase is a processive enzyme, as it binds the primer-template complex and then proceeds to create a new strand of DNA by moving along the template. Higher processivity means that the enzyme stays and acts on the polymer for longer (e.g. a DNA polymerase can process thousands of nucleotides after a single binding event). Other processive enzymes include some exonucleases (keep on chewing up the DNA, base by base) and helicases (unwind double-stranded DNA).

prokaryote, prokaryotic — an organism without a nucleus, e.g. bacteria.

promoter — a region of DNA that drives the expression of a gene following it on a piece of DNA. Most promoters are directional, meaning they drive the expression of a gene only on one side (3') of it. Some promoters are bidirectionally and will drive the expression on both the 5' and 3' side of it.

propagation, propagate — in terms of plasmids, propagation is the ability of a plasmid to be replicated by its host organism. A properly-propagating plasmid will have an origin of replication that is able to recruit the DNA replication machinery of the organism. A plasmid that does not propagate will ultimately be diluted out of a replicating cell line due to cellular divisions.

protease — an enzyme that catalyzes the cleavage of peptide bonds; proteases chew up proteins

protein — a polymer of amino acids that typically fold into a particular shape (though proteins with less-defined shapes exist). Some proteins are multimeric, meaning they are a complex of many copies of the same amino acid sequences. Many proteins are enzymes, allowing them to catalyze specific reactions. Proteins are created in the process of translation using information encoded in codons in a messenger RNA.

Q

qPCR — quantitative PCR. A method of determining amount of a DNA sequence of interest that is present in a sample. By monitoring the amplification of a strand of DNA during PCR, the original quantity can be extrapolated. qPCR can be used to monitor gene expression by reverse transcribing mRNA into cDNA and then quantifying the cDNA through qPCR.

quorum sensing — the ability of an organism to detect population density. The canonical quorum sensing system is the AHL-Lux system first described in Aliivibrio fischeri (formerly classified as Vibrio fischeri). Quorum sensing systems have been co-opted by synthetic biologists to engineer cell-to-cell communication systems.

R

rate constant — in a mass-action kinetics model, the proportionality constant (typically denoted by $k$) between the rate of a chemical reaction and the product of its constituent chemical species' concentrations. Different reaction orders will have different rate constant units. A first-order reaction will have units of $[s^{-1}]$, whereas a second-order reaction will have units of $[M^{-1}s^{-1}]$, where $M$ can be any concentration units, but is typically molarity.

rate of change — how much a dependent variable changes for a given change in an independent variable. Graphically, it is the slope of a line where the independent variable is on the x-axis and the dependent variable is on the y. The rate of change at any point can be determined by taking the first derivative of a function with respect to the independent variable.

RBP, RNA-binding protein — a protein that binds to an RNA sequence as its substrate. Naturally, these proteins serve a variety of roles in post-transcriptional regulation. Recently, bacteriophage coat proteins such as PP7 and MS2 have been used to target RNA sequences that have had RBP binding sites integrated into them. Fusion of these RBPs to fluorescent proteins allows the real-time monitoring of mRNA transcription.

RBS, ribosome binding site — a sequence upstream of the start codon that recruits ribsomes and allows translation. RBSs are well-defined in prokaryotic systems and are also known as Shine-Dalgarno sequences. Recruitment of ribosomes in eukaryotic systems is more complex and less-understood. RBS "strength" is a large factor in protein production rate and is determined by local RNA secondary and tertiary structure. RBS calculators allow the control of relative translation rates across different RBSs.

recognition site, recognition sequence — the specific sequence recognized by a DNA-binding protein. Most commonly referred to when discussing the cut sites for restriction enzymes.

recombinase, recombination — the insertion or deletion of DNA sequence from a strand mediated by recombinases. Cre recombinase -- from a bacteriophage -- is a commonly-used recombinase that effects site-specific recombination between two Lox sites. Recombination is the basis of Gateway cloning technology.

regulatory element — any element that regulates gene expression. Examples of cis-acting regulatory elements are operators, promotors, and leader peptides. Trans-acting regulatory elements are diffusible molecules such as transcription factors or trans-acting RNA in a toehold switch system.

response — how a system reacts to an input. Much information about a system's internal workings can be gleaned from observing its response to different types of input.

replication — the process of producing two identical copies of DNA from a single double helix. DNA replication begins at specific sequences termed origins of replication and requires polymerases, dNTPs, and other factors.

replicon — a DNA or RNA molecule that replicates from a single origin of replication. Most prokaryotic chromosomes are a single replicon, while eukaryotic chromosomes typically have multiple replicons. "Replicon" is sometimes used to describe self-amplifying RNAs (RepRNA), which have the ability to replicate themselves within a transfected cell to provide continuous protein production.

reporter — in the context of gene expression, a reporter allows the easy determination of transcription from a given promoter. Good reporters have an obvious phenotype, such as the blue phenotype for LacZ in the presence of X-gal, or the fluorescence of a fluorescent protein. Quantification of protein production from a promoter as a function of reporter fluorescence is also possible.

repressilator — one of the earliest oscillating synthetic circuits published by Elowitz and Leibler in 2000. It accomplishes oscillations through the use of a three-repressor ring oscillator circuit topology. The circuit was able to oscillate, but had issues with robustness.

repressor, repression — the suppression of gene expression from a promoter by a protein. Important repressors in synthetic biology are TetR, LacI, and cI (lambda repressor). Some repressors are inducible.

restriction, restriction enzyme — enzymes that cut DNA in a site-specific manner. Typically, each restriction enzyme has a certain restriction site that it recognizes. Standard restriction enzymes that cut within their recognition site are the basis of traditional cloning methods. Type IIS restriction enzymes, such BsaI, cut at a location outside of their recognition site and enable DNA assembly without the producing scar regions. Type IIS restriction enzymes are the basis of Golden Gate cloning methods.

retroactivity — when the input/output behavior of an upstream model is affected by presence of downstream module(s). Retroactive effects can be reduced through the use of load driver circuits.

RFP — Red fluorescent protein.

ribosome — a protein-RNA complex that is responsible for translating mRNAs into polypeptides.

riboswitch — a cis-acting regulatory element found in mRNA transcripts. Riboswitches form structures whose conformations are affected by small molecules. These conformational changes have the ability to turn expression of a transcript "ON" or "OFF". This switching is accomplished through a variety of mechanisms.

ribozyme — an RNA molecule that is capable of catalyzing chemical reactions. Many ribozymes of interest (hammerhead and hairpin) catalyze RNA cleavage and ligation reactions in cis.

ring oscillator — an electrical engineering term used to describe a device with an odd number of NOT gates linked together. This accomplishes oscillation due to delayed feedback and ultimate inversion of signal (from an odd number of NOT gates) A biological implementation of a ring oscillator is the repressilator.

RNA — ribonucleic acid; polymeric molecules made up of nucleotide monomers. Have many biological functions from information carrying (mRNA) to catalytic activity (ribozymes).

RNAi, RNA interference — a biological process by which double-stranded RNA (dsRNA) inhibits the expression of genes complementary to its sequence. RNAi is thought to have evolved for defense against viruses (some of which have dsRNA genomes) and it has been shown to have an important role during development. This system can also exploited to induce artificial gene knockdown through the introduction of synthetic dsRNAs or vectors that express siRNAs. While most eukaryotes have RNAi machinery, S. cerevisiae notably lacks it. Prokaryotes also do not possess RNAi machinery.

RNAP — RNA polymerase; the protein complex that transcribes RNA from DNA. In prokaryotes RNAP, promoter specificity is determined by the presence of a sigma factor and the complex usually binds to the -35 and -10 elements (35bp and 10bp upstream of the start codon) of genes. Occlusion of these sites through transcription factor binding is a common mechanism of genetic repression. In eukaryotes, mRNA transcription is carried out by RNA polymerase II, but other RNAP types are responsible for the production of transfer RNAs, ribosomal RNAs, and some regulatory RNAs.

RNA-seq — RNA sequencing. A method of obtaining a snapshot of genetic transcripts present in an organism. mRNAs can be isolated from a cell by their poly(A) tail and then reverse transcribed into cDNA. Next-generation sequencing methods can then be used to sequence this cDNA, which allows the reconstruction of the cell's transcriptome.

robustness — a description of a system's ability to maintain desired functionality despite faults and perturbations. In the context of synthetic biology, a genetic circuit would be considered robust if it could maintain functionality after accruing mutations and also in different cellular states (e.g. both exponential growth and stationary phase).

rtTA — The reversed tetracycline trans-activator is analogous to tTA, except that the function of Dox is reversed. Dox stabilizes the DNA binding domain, facilitating promoter binding and activation of gene expression of promoters with tetracycline responsive elements (TREs). Referred to as the Dox-on system.

S

S. cerevisiae, Sachharomyces cerevisiae — a single-celled species of yeast which is commonly used in syntetic biology. Notably this eukaryotic organism does not have RNAi machinery.

scaffold — a structure on which elements can be brought together to be close in space. For example, the enzymes involved in the same pathway can be brought together in proximity on an RNA scaffold by fusing the enzymes with RNA-binding proteins and thus increase the efficiency of the pathway, as substrates do not need to diffuse far to reach the next enzyme in the pathway.

scalability — the ability to add more components to a system.

scar sequence — an unavoidable sequence arising from technicalities of a DNA assembly process. For example, Gateway assembly leaves a scar after the recombination occurs.

screening — a method to obtain a set of organisms (e.g. a bacterial colony) with a particular genotype or phenotype by considering many members of a large pool of variants. Each member is assessed for its suitability, causing more work than selection, where the undesired members are eliminated.

selection — a method to obtain a set of organisms (e.g. a bacterial colony) with a particular genotype or phenotype by selectively removing undesired organisms from a large pool of variants. Selection can be positive (organisms with a trait survive to the next round) or negative (organisms that do not have a trait survive to the next round). This approach can be less work than screening, as only "interesting" organisms have to be analyzed, rather than all organisms.

sensing — the process of detecting levels of inputs from the outside or within a cell.

sensitivity — how well a method can pick up true positives; calculated by dividing the number of true positives by the number of true positives added to the number of false negatives. Also see specificity

sequencing — the process of determining the nucleic acid sequence of a piece of DNA or of a whole organism

shRNA — short hairpin RNA, a synthetic mimic of miRNA. A single molecule of RNA folds into a stem structure with a hairpin on one end to give rise to an shRNA.

sigmoid, sigmoidal, sigmoidicity — a sigmoidal function (sigmoid) has a stretched-out S shape. There are many sigmoidal functions, for example the logistic function ($f(x) = \frac{1}{1 + e^{-x}}$) but also the generalized Hill function $f(x) = \frac{x^n}{x^n + K^n}$ relevant to many biological processes.

signal — a function conveying information. A signal can take and be encoded in many forms, e.g. the voltage of a wire or the concentration of a chemical species. Systems can act on signals to modify them or to produce new signals.

signal-flow graph — a way of depicting information (signal) flow in systems. A directed graph is created where nodes are the system (state) variables and directed connections between the nodes indicate functional connections and can be annotated with e.g. mathematical functions explaining the relationships.

siRNA — an artificial double-stranded RNA that mimics miRNA. Sometimes chemically modified to increase the potency of the siRNA.

specificity — how well a method can distinguish between true positives and false positives; also called the true negative rate and calculated by dividing the number of true negatives by the number of true negatives added to the number of false positives. Often at odds with sensitivity (increasing specificity typically decreases sensitivity; this can be observed with a receiver operating characteristic curve, which plots 1 minus specificity against sensitivity).

state variable — a variable dedicated to describing a state of a system, e.g. the concentration of a species, the volume of a cell or any other measurable quantity

stateful — having a state, having memory. For example, a toggle switch is stateful since it has two states. Combinational logic circuits are not stateful, they do not have any memory of previous inputs or states.

stability analysis — a mathematical technique for determining at which conditions systems are stable.

steady state — a state of the system which does not evolve over time, given that there are no perturbations. Steady states can be stable or unstable, indicating their response to small perturbations (stable means the system returns to the steady state and unstable means it does not)

stochastic — random, non-deterministic. A stochastic model enables modeling of discrete systems containing a small number of species, where deterministic, continuous models may give inappropriate predictions. Stochastic simulations enable predicting properties other than the mean, bulk behaviour of a system. Stochastic simulations can show unexpected properties of systems which deterministic-continuous models might not.

strain — a particular variant of a bacterium, virus, or plant. For example, the E. coli strain BL21(DE3) has a particular genotype setting it apart from other strains and making it useful for some applications and not others.

strand of DNA, RNA — a single molecule of DNA or RNA. Such a strand has directionality, typically depicted as going from 5' (the end of the strand with the phosphate group) to 3' (the end of the strand with the -OH group).

switch — a device which has state, e.g. on/off, like a lightbulb; also see toggle.

system — a collection of devices and other components operating together to carry out some set of functions.

T

tag, tagging — a tag enables an experimenter to follow or extract a particular molecule, molecular species or even whole cells. Certain tags, e.g. the His-tag enable experimenters to enrich for species containing the tag using columns (a nickel column for the His-tag). Fluorescent tags enable measurement with devices like plate readers or flow cytometers.

TALE, TALER, TALEN — Transcription activator-like effectors (TALEs) are DNA binding proteins that have a "code" relating just two specific amino acids in their DNA-binding regions to a nucleotide in the DNA that is recognized. This "code" has been used by researchers to create a variety of TALE proteins that bind specific DNA operator sites. TALE operator sites can be placed near transcriptional start sites to block RNA polymerase binding and thus repress gene expression. TALEs used for this purpose are called TALE repressors, or TALERs. TALEs can also be modified to have nuclease activity, and cut DNA at specific locations in the genome. These are refered to TALE nucleases, or TALENs.

terminator, termination — the process of termination is the stopping of transcription. This occurs due to particular sequences, terminator sequences, within the DNA. Some terminators cause termination by causing the RNA to fold in structures that cause the RNA polymerase to release it. Others recruit proteins which pull the freshly synthesized (nascent) RNA out of the RNA polymerase or cause the release by other mechanisms.

TetO — Operator sequence for TetR protein binding.

TetR — DNA binding protein commonly used for regulation of TRE promoters. Binds TetO operator sequence in the DNA.

thermocycler — a machine that can rapidly change temperatures in a programmable fashion, e.g. in loops (cycles of steps). Used for running reactions like PCR.

thermostable — resistant to high temperature. A thermostable enzyme is still active at elevated temperatures (e.g. near boiling) and have been found in organisms that live in extreme environments, e.g. deep sea thermal vents.

timescale separation — a method for simplifying time-dependent systems. It is often the case that a system has processes which have timescales (how long it takes for the system to reach equilibrium) differing by one or more orders of magnitude. For example, the timescale of transcription factors binding to DNA is short, as the binding equilibrium is reached within milliseconds or less. However, the process of producing a mature protein can take minutes or more. Hence, when analyzing a system where both processes occur, the binding can be considered to be at equilibrium when discussing how the protein dynamics look like.

timing diagram — a diagram showing how a system behaves and evolves over time. For digital systems, a timing diagram shows the state of the system (and possibly signals within the system) at each tick of a clock. Often a timing diagram is depicted as a table, where each row shows a signal and each column shows an instance of time. The value in the table is the value of the particular signal at the particular time. Another way to depict the timing diagram is to draw a value trace over time for each signal and stack them such that time flows left to right.

tissue — an organized collection of similar cells. Multiple tissues make up organs.

toggle, toggle switch — a system which can switch between multiple states and stay in the target state even if the input is removed. For example, a light switch is a toggle, as the light remains on after the toggle (switch) is set to the correct state even if the input stimulus (the finger that flicks the switch) is no longer present.

topology — in the context of regulatory networks, the topology refers to the way the nodes (e.g. genes) are connected (which kinds of arrows go from which nodes to which nodes). An abstract gene-regulatory network has some topology that could be implemented by many ways by choosing the suitable components for each node.

toxin — a substance (small molecule, peptide, protein) that kills cells or even whole organisms. Toxin-antitoxin pairs can be useful in biotechnology where the presence of the antitoxin confers resistance to the toxin, enabling selection. Producing a toxin as the output of a circuit can be used in medical applications, e.g. to kill cancerous cells or infectious bacteria.

trans-activation domain, TAD — A domain of a transcription factor that interacts with the transcriptional machinery, cofactors, and/or chromatin modifying machinery (eukaryotes only) in order to facilitate formation of the transcriptional initiation complex (TIC).

transcript, transcription — transcription is the process of creating an RNA transcript based on information in DNA. A promoter drives transcriptino and decides when and how much transcript is made.

transcription factor, TF — A protein that binds operator sequences in the promoter or enhancer regions distal from the promoter. Activates or represses transcription depending on the presence of a trans-activation or trans-repression domain, respectively. Also can contain a signal-sensing domain, which allows for external regulation of DNA-binding or cellular localization, eg by small molecules or hormones.

transcriptional fusion — a mechanism for generating several transcripts from the same input. For example, using the same promoter for different genes causes all of the genes to be transcribed if the appropriate input is present. Several transcripts can sometimes also be produced if processing of a single transcript creates several, e.g. if there is a self-cleaving RNA element in the transcript. These transcripts are produced in equal amounts, but can contain different information.

transfection — the process of introducing new genetic material into cells, mostly used when talking about mammalian cells (similar to transformation in bacteria).

transformation — the process of introducing new genetic material into cells, mostly used when talking about bacterial cells (similar to transfection in mammalian cells). Transformation can be performed by electrical and/or chemical means, e.g. by electroporation.

transient — temporary. A transient signal is much shorter than a proper signal, but can potentially be confused with one. In complicated systems, transient signals can sometimes arise during input transitions, causing the output to temporarily be incorrect. These must be taken into consideration and e.g. filtered out.

transistor — a device that amplifies or switches signals.

transition region — a region in the input range of a transfer function where the output changes from one state (e.g. "low") to another (e.g. "high"). It is often desirable that the transition region is small.

translation — the process of creating a peptide (sequence of amino acids, e.g. a protein or enzyme) based on the sequence of an mRNA. The ribosome is the key enzyme in this process, which also requires tRNAs charged with amino acids.

translational fusion — a protein fusion where the two proteins are translated together. The coding sequences of translationally fused proteins are on the same mRNA and form a single polypeptide chain when translated

TRE, pTRE— Tetracycline-responsive element. A promoter that contains operator sequences (TetO) for a TetR protein to bind. The TRE promoter contains multiple TetO sites and a minimal CMV core promoter.

tRNA — transfer RNA. These special RNAs have a particular structure and many chemical modifications. They are charged with amino acids; the charged tRNAs are then used in protein synthesis. The tRNA has a three nucleotide anticodon loop, which complements a three nucleotide codon on an mRNA in the ribosome, enabling the ribosome to create a new peptide based on the sequence of an mRNA.

truth table — a tool for summarizing the behavior of a digital logic device or circuit. Each digital input has a column, followed by columns for each output. All combinations of input values (each can be 0 or 1) are enumerated in the table and the corresponding output values are listed. By convention, the rows are ordered such that the binary numbers formed by the input assignments are increasing, e.g. with two inputs the combinations would go as 00, 01, 10, 11.

tTA — The tetracycline trans-activator is a fusion of a tetracycline-destabilizing DNA binding domain and the VP16 trans-activation domain. Thus, in the presence of Dox (an analog of tetracycline) tTA can no longer bind to its target promoter - this system is referred to as Dox-off because in the absence of Dox, it activates gene expression at target promoters with tetracycline-responsive elements (TREs).

tunability — a property of components and systems, referring to the ability to tweak aspects of their performance, e.g. the strength of a promoter.

Type IIs restriction enzyme — these restriction enzymes cleave double-stranded DNA in a location that is outside the recognition sequence of the enzyme. They are particularly useful for DNA assembly, as they enable creating arbitrary overhang sequences. Commonly used Type IIs enzymes include BsaI and BbsI, which are both used in Golden Gate / MoClo assembly.

U

UAS, pUAS — Upstream activation sequence, a specific sequence of DNA recognized by Gal4. The UAS promoter contains multiple UAS sites and a minimal CMV core promoter.

ultrasensitivity — ultrasensitive responses have a small transition region between the low and high states of a transfer function. A digital step-function is ideally ultrasensitive, as the transition region is minimal. Ultrasensitive responses can arise from cooperativity in the binding interactions that implement the transfer function; higher cooperativity increases the sensitivity as only a small change is necessary to push the system from one state to another when close to the transition region.

unstable steady state — a steady state for which any perturbation causes the system to leave that state and not return (e.g. it goes to a different steady state, one that is stable).

upstream — a region of DNA is upstream of a sequence if it is on the 5' side of the sequence of interest, it is always relative to some reference, e.g. the promoter is upstream of the coding strand of a gene.

UTR — untranslated region. Sequences in the 5' and 3' ends of an mRNA that are transcribed, but not translated. UTRs often harbor regulatory elements, for example protein binding sites (including the ribosome binding site), miRNA binding sites, secondary structures (e.g. riboswitches).

V

variance — a statistical measure describing the spread of a random variable around its mean. A tight distribution has small variance and thus most of the values are close to the mean. The variance is related to the standard deviation by $Var(X) = \sigma^2$. Mathematically, $Var(X) = E[(X - E[X])^2]$; the variance is the expectation of the square of the difference of the random variable from its mean. The variance can also be calculated by taking the difference of the expectation of the square of the variable and the expectation of the variable, squared: $Var(X) = E[X^2] - (E[X])^2$.

vector — an ordered set of values, for example coordinates in a space ($x, y, z$, which is often also taken as an "arrow" from the origin to this point, i.e. as having direction) or concentrations of chemical species $[A], [B], [C]$.

vesicle — vesicles are lipid bilayer structures that contain liquid and materials of interest. DNA, RNA and proteins can all be delivered to cultured cells using vesicles created in a mixture of the desired payload. As the vesicles form, they encapsulate the nucleic acids and proteins in the mixture. The vesicles can merge with the cell outer layer or be endocytosed, both leading to the delivery of the payload (though through different biological mechanisms). Reagents are commercially available for this purpose, optimized for different payload types, amounts, and sizes.

VP16 — Herpes simplex virus (HSV) viral protein 16 (VP16) trans-activation domain (TAD). Stongly activates gene expression in eukaryotic cells when fused to a DNA binding protein, commonly Gal4.

W

Watson strand — the sense strand (complementary to the Crick strand). This strand matches the mRNA sequence after T-s are replaced with U-s).

X

X-gal — a colorless galactose derivative. When cleaved by β-galactosidase (encoded by the LacZ gene), gives rise to two products: galactose and an indole. The indole spontaneously forms a dimer, which has a blue color. This allows to test for the presence of β-galactosidase activity (and by extension the activity or presence of the LacZ gene).

XNOR — negated exclusive OR function. True only if both inputs are false or both inputs are true, false otherwise. For more inputs, true only if an even number of inputs (including 0, no inputs) are true and false otherwise.

XOR — exclusive OR function. True only if one input is true, but not both and false otherwise. For more inputs, true only if an odd number of inputs are true and false otherwise.