A compedium and index of terms found in the Registry and synthetic biology indexed alphabetically
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.
- Abstraction Hierarchy
- A hierarchy in which individuals work independently at each level.
- acyl-homoserine lactones (acyl-HSLs)
- Small signalling molecules
- 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.
- 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.
- the cell that contains and supports a synthetic biology system
- 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.
- A part which produces proteins in reponse to some stimuli.
- Receives the concentration of repressor A and, via gene expression, outputs the concentration of repressor B.
- LVA Tag
- A tag for degradation.
- An operon for self-regulation production of luminescent proteins.
- A process for isolating small amounts of plasmid DNA from bacteria by lysing the cells and precipitating chromosomal DNA and other cell structures.
- 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>
- PlateMate Plus
- A robot utilized by iGEM to produce large numbers of identical 384-well distribution plates.
- 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.
- 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
- 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.
- 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
- 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
- Small functional sequences of amino acids.
- Transfer function
- The ratio of output and input in a system.