Difference between revisions of "Help:Glossary"

Revision as of 18:53, 7 June 2017

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

0-9 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

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.

0-9

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 Help: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

T

Tag

Small functional sequences of amino acids.

Transfer function

The ratio of output and input in a system.

U

V

W

X

Y

Z