Difference between revisions of "Categories"

Latest revision as of 16:22, 30 May 2013

We have redesigned the Registry for the iGEM 2013 season. Part of the redesign includes the catalog system. You can also look through the old catalog pages if you couldn't find what you're looking for.

Basic Parts

The main four elements of a transcriptional unit are: promoter - RBS - protein coding region - terminator. Here we present each category and sub category.

Icon	List
		Promoters (?): A promoter is a DNA sequence that tends to recruit transcriptional machinery and lead to transcription of the downstream DNA sequence.
		Ribosome Binding Sites (?): A ribosome binding site (RBS) is an RNA sequence found in mRNA to which ribosomes can bind and initiate translation.
		Protein coding sequences (?): Protein coding sequences encode the amino acid sequence of a particular protein. Note that some protein coding sequences only encode a protein domain or half a protein. Others encode a full-length protein from start codon to stop codon. Coding sequences for gene expression reporters such as LacZ and GFP are also included here.
			Protein domains (?): Protein domains are portions of proteins cloned in frame with other proteins domains to make up a protein coding sequence. Some protein domains might change the protein's location, alter its degradation rate, target the protein for cleavage, or enable it to be readily purified.
		[[1]]	Protein generators (?): There are three major types of Protein Generators. Those devices composed of a promoter, an RBS, a protein coding region and a terminator. The second group don't have a promoter, allowing you to select your own. The final group is composed of a single piece of DNA, not of basic parts.
		[[2]]	Reporters (?): Reporters are an output that allow you to monitor the function of genetic circuit. They can be fluorescent proteins, colored chromoproteins or pH generator parts.
		[[3]]	Inverters (?): Intervers take an input and produce the opposite output. An inverter will take a high input and produce a low output and vice versa. Inverters are considered the basic building block of all digital circuits, making them of particular interest to synthetic biologists.
		[[4]]	Receivers and senders (?): Cell-cell signalling devices allow communication between an individual cell and its neighbors in culture or on a plate. This capability allows synchronized behavior across a cell population or the communication of information between cells hosting different systems. A cell can send a signal and it can receive an averaged signal from all its neighbors carrying the same signalling device.
		[[5]]	Measurement devices (?): These systems allow measurement of the relative strength of some types of basic parts. Usually promoters, ribosome binding sites and terminators are good candidates for measurement when it is not being repressed. They all require external validation of the operating conditions such as plasmid copy number and cell metabolism.
		Terminators (?): A terminator is an RNA sequence that usually occurs at the end of a gene or operon mRNA and causes transcription to stop.

Icon	List
		Awards (?): Award winning parts from previous iGEM competition can be found in these pages.
		Plasmid backbones (?): A plasmid is a circular, double-stranded DNA molecules typically containing a few thousand base pairs that replicate within the cell independently of the chromosomal DNA. A plasmid backbone is defined as the plasmid sequence beginning with the BioBrick suffix, including the replication origin and antibiotic resistance marker, and ending with the BioBrick prefix.
Chassis
		Escherichia coli chassis (?): Most parts in the Registry operate in E. coli.
		Bacillus subtilis chassis (?): Bacillus subtilis is a model gram-positive bacterium.
		Cell-free chassis (?): In vitro transcription/translation systems can be useful for some synthetic biological systems.
		Escherichia coli (?): Most parts in the Registry function in E. coli.
		Yeast (?): Yeast are simple eukaryotes.
		Bacteriophage T7 (?): Bacteriophage T7 is an obligate lytic phage of E. coli.
		Bacillus subtilis (?): Bacillus subtilis is a model gram-positive bacterium.
		MammoBlocks (?): MammoBlocks are a new category of BioBrick introduced by the MIT iGEM team in 2010 and continued in 2011. There are now dozens of MammoBlocks suitable for rapid expression in mammalian cells.
		Mesoplasma florum (?): Mesoplasma florum is a particularly simple model organism.
		Magnetotaxis (?): magnetotactic strain AMB-1 with BioBrick-compatible toolkit enables development of synthetic biology into magnetotaxis and beyond.
Collections and Kits
Functions
		Biosafety: Parts and devices improving biological containment.
		Biosynthesis: Parts involved in the production or degradation of chemicals and metabolites are listed here.
		Cell-cell signaling and quorum sensing: Parts involved in intercellular signaling and quorum sensing between bacteria.
		Cell death: Parts involved in killing cells.
		Coliroid: Parts involved in taking a bacterial photograph.
		Conjugation: Parts involved in DNA conjugation between bacteria.
		Motility and chemotaxis: Parts involved in motility or chemotaxis of cells.
		Odor production and sensing: Parts the produce or sense odorants.
		DNA recombination: Parts involved in DNA recombination.
		Viral vectors: Parts involved in the production and modification of Viral vectors.
test	[Most Documented]	Most Documented (?): The most highly documented parts on the Registry can be found in this list.
test	[Most Used]	Most Used (?): The most highly used parts on the Registry can be found in this list.
		iGEM 2012 | iGEM 2011 | iGEM 2010 | iGEM 2009 | iGEM 2008 | iGEM 2007 | iGEM 2006 | iGEM 2005 | Labs | Courses
		Translational units (?): Translational units are composed of a ribosome binding site and a protein coding sequence. They begin at the site of translational initiation, the RBS, and end at the site of translational termination, the stop codon.

Other types of parts

Catalog	List
		DNA (?): DNA parts provide functionality to the DNA itself. DNA parts include cloning sites, scars, primer binding sites, spacers, recombination sites, conjugative tranfer elements, transposons, origami, and aptamers.
		Plasmids (?): A plasmid is a circular, double-stranded DNA molecules typically containing a few thousand base pairs that replicate within the cell independently of the chromosomal DNA. If you're looking for a plasmid or vector to propagate or assemble plasmid backbones, please see the set of plasmid backbones. There are a few parts in the Registry that are only available as circular plasmids, not as parts in a plasmid backbone, you can find them here. Note that these plasmids largely do not conform to the BioBrick standard.
		Primers (?): A primer is a short single-stranded DNA sequences used as a starting point for PCR amplification or sequencing. Although primers are not actually available via the Registry distribution, we include commonly used primer sequences here.
		Genome Integration (?): The miniTn7 BioBrick tool kit is a set of fully BioBrick-compatible vectors based on Tn7 transposon for the integration of parts into microbial genomes.