Help:Glossary

A compedium and index of terms found in the Registry and synthetic biology indexed alphabetically

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This glossary is always under construction! You can contribute by adding entries or simply linking them to relevant information. If you write a more comprehensive article, please add a short description on this page in addition to the link.

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3OC6HSL: A small signalling molecule of the acyl-homoserine lactone family.

A

Abstraction Hierarchy: A hierarchy in which individuals work independently at each level.
acyl-homoserine lactones (acyl-HSLs): Small signalling molecules

B

BioBrick Component: A portion of a Biobrick device that is available as a BioBrick product. A protein coding region is a BioBrick device if it is available as a BioBrick product and documented in the BioBrick Data Book.
BioBrick Device: A BioBrick system consisting of one or more BioBrick components that together instantiate a full logical or functional process. Normally, this consists of input protein coding regions that code for the input proteins and a BioBrick computational body that processes the input proteins and generates TIPS at the output sites.

C

canonical model: a simplified model that adequately represents the components and interactions under study (the actual system may or may not be structured like the canonical model).
cell-to-cell signalling: communication between an individual cell and its neighbors in culture or on a plate.
chassis: the cell that contains and supports a synthetic biology system
composable: capable of combining to make a larger whole. In the context of BioBricks, the assembly of two BioBricks creates a new, single BioBrick that can, in turn, be used in downstream assemblies.

D

E

F

G

Generator: A part which produces proteins in reponse to some stimuli.

H

I

Inverter: Receives the concentration of repressor A and, via gene expression, outputs the concentration of repressor B.

J

K

L

LVA Tag: A tag for degradation.
Lux: An operon for self-regulation production of luminescent proteins.

M

[http: //openwetware.org/wiki/Miniprep/Kit-free_high-throughput_protocol Miniprep]; A process for isolating small amounts of plasmid DNA from bacteria by lysing the cells and precipitating chromosomal DNA and other cell structures.

N

O

Output High (O_H): This is an output characteristic from a transfer function (see "output curve" entry below)
Output Curve: The current formula idealizing the output curve for <math>(a*c)/(1 + ((i/b)^n)</math>

P

PlateMate Plus: A robot utilized by iGEM to produce large numbers of identical 384-well distribution plates.
PoPS: Polymerase Per Second: A measure of number of times that an RNA Polymerase passes out of the regulatory region and into the protein coding region of a BioBrick.
Protein Coding Region: A section of DNA that can cause the generation of a specific protein. In BioBricks, this includes the BioBrick prefix and suffix, the Ribosome Binding Site (RBS), the codons for the protein's amino acids, and the stop codon.
Protein Generator: A part which is able to produce proteins in response to some stimuli.

Q

Quad Part Inverter (QPI): QPI refers to a Quad-Part Inverter, that is, a PoPS-based inverter composed of four sub-parts: a ribosome binding site, a coding region for a repressor protein (ie. cI lambda), a Help:Terminators, and the promoter (ie. pLamdba) which is regulated by the coded repressor protein

R

Regulatory Region: The canonical model of a BioBrick component asserts that proteins generated as a result of other logical or cellular processes (see Protein Coding Region) as well as other active molecules interact with the computational body of a BioBrick component to produce the output signal. The genetic code of the computational body is represented by a Regulatory Region of DNA.
Reporter: A gene that helps visualize or quantify the output of a device or part.
Restriction enzymes: An enzyme that recognizes a particular sequence of bases in DNA, and then cuts the DNA's backbones at that point.
Ribosome Binding Site

S

Small Molecule Sensors: A small molecule sensor can trigger gene expression when a small molecule becomes present in a cell's environment. Generally, each sensor is specific only to one or a range of small molecules. These sensors are generally surface proteins that can bind to a small molecule ligand. Upon binding, the surfact protein changes conformation, causing one or more intra-cell signals to induce gene expression. A common method of creating a small molecule sensor is to find (discover or literature research) a cellular pathway that is induced by a certain molecule. The surface protein(s) and intial promotors of the mechanism can be isolated from the wild type cellular pathway and made into a BioBrick part. The isolated surface protein + promotor can be put upstream of a new expression gene and inserted into a cell.

Signalling Molecules: A molecules involved in (generally) intercellular signalling methods

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Contents

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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