"

From 2012.igem.org

Revision as of 14:24, 26 September 2012 (view source) Jjkoehorst (Talk | contribs) (→Faulty parts) ← Older edit		Revision as of 14:25, 26 September 2012 (view source) Jjkoehorst (Talk | contribs) (→Faulty parts) Newer edit →
Line 83:		Line 83:
	[[File:biobrick_availability.PNG|300px|left|thumb|''Table 1'']]		[[File:biobrick_availability.PNG|300px|left|thumb|''Table 1'']]
	[[File:Biobrick_sequencing2.PNG|300px|left|thumb|''Table 2'']]		[[File:Biobrick_sequencing2.PNG|300px|left|thumb|''Table 2'']]
-	[[File:Biobrick_status.PNG|300px|left|thumb|''Table 3'']]	+	[[File:Biobrick_status.PNG|295px|left|thumb|''Table 3'']]
	<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/>		<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/>

---

Revision as of 14:25, 26 September 2012

Contents 1 Parts 2 Parts we made 3 Parts we used 4 Parts we ordered 4.1 Parts we standardized 4.2 Faulty parts

Parts

In the Open Access scientific community that iGEM is, the Registry of Standard Parts plays a crucial role. As teams construct new parts and devices, they make them available to anyone who might want to use, add or improve them. However, the current registry is not only hard to navigate (see The Constructor), it also turns out to contain non-functioning and even non-existent parts. To work towards a better Open Source future, we think it is of great importance that apart from quantity, the quality of the registry should improve as well. It is up to all users to make this happen. We tried to contribute to the quality of the registry not only by sending in our bricks (which were all sequenced), but also by validating other bricks and improving some[1, 2].

Parts we made

<groupparts>iGEM012 Wageningen_UR</groupparts>

Parts we used

For our project, we used few bricks from the 2012 Spring Distribution Kit. A list is included below.

Part	Name	Description
BBa_B0015	Terminator	double terminator (B0010-B0012)
BBa_I13522	pTet GFP	Untagged GFP behind a constitutive promoter.
BBa_J04450	RFP Coding Device	RFP Coding Device (iptg + Cap induced, pSB1C3 backbone)
BBa_J04500	IPTG inducable promotor with RBS	R0010.B0034
BBa_K197038	BBb - BseRI/AcuI entry vector	This part is and entry vector in BBb Format. It is flanked by BamHI, BseRI, BglII, and AcuI sites and is used in the 2AB Layered Assembly scheme developed at UC Berkeley.

Parts we ordered

For our project, we ordered few bricks from the iGEM Registry. A list is included below.

Part	Name	Description
BBa_K197021	EILD	One peptide of a heterodimeric leucine zipper that dimerizes with KILR.
BBa_K197022	KILR	A heterodimeric peptide that dimerizes to EILD. This can be used for adhering two cells together to evolve new two cell chemistry and functions.
BBa_J3901	PrFe-mRFP1	This device coupled the promoters PI and PII of rus operon from Acidithiobacillus ferrooxidans with a monomeric red fluorescent protein (BBa_E1010) used as a signal, showing specific sensorbility response to iron ions presence.
BBa_I765010	Iron promoter -EYFP reporter	Iron promoter expresion is reported by the trascription of EYFP reporter.

Parts we standardized

Two of these parts (BBa_K197021 and BBa_K197022) were in a non-standard backbone and format. For both parts, we tried to brick them by adding standard pre- and suffixes and inserting them in the pSB1C3 standard backbone. Unfortunately, this only worked for one of the parts. We uploaded the standardized version of BBa_K197022 on the registry as BBa_K883600.

Faulty parts

Even though the Registry constitutes the main repository for the iGEM competition, it contains a large number of parts that have a questionable status. Only 20% of all biobricks have been validated (Table 3). This relates to 4.083 validated parts in a registry of 19.976. A mere 5% of all biobricks have been sequenced and only 35% of all biobricks are available. Therefore, users of biobricks have the responsibility to sequence used constructs and assess their validity, which they can describe in the experience tab of the registry page. Such initiatives improve the quality of the Registry and benefits all users.

The other two parts we ordered from the registry were parts BBa_J3901 and BBa_I765010. After repeated growth experiments, these parts didn’t seem to function the way they are supposed to and we decided to sequence them. Although the results confirmed our suspicions, we were still quite shocked to see them: Both parts completely lacked a promotor that was supposed to be in there (and which was the main reason we ordered it). We documented our findings on the experience page of both parts [1, 2] of course, but we hope that our findings are not representative for the registry as a whole.