Team:OUC-China/Parts

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<h1>Summary</h1>
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<p>parts submitted : 33 Composite expression modules<br/>
 +
                        10 Generator<br/>
 +
                        4 Regulatory promoters<br/>
 +
                        1 Ribosome Binding Sites<br/>
 +
                        10 Coding proteins<br/>
 +
                        10 RNA </p>           
 +
<p>Total: <strong>68 Parts</strong></p>
 +
 +
<p>All 68 parts have been submitted to the registry and can be found <a
 +
href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2012&group=OUC-China">here</a>.</p>
-
An important aspect of the iGEM competition is the use and creation of standard  biological parts. Each team will make new parts during iGEM and will place them in the [http://partsregistry.org Registry of Standard Biological Parts]. The iGEM software provides an easy way to present the parts your team has created . The "groupparts" tag will generate a table with all of the parts that your team adds to your team sandbox.  Note that if you want to document a part you need to document it on the [http://partsregistry.org Registry], not on your team wiki.
+
<br/>
 +
<h1>Data for favorite parts</h1>
-
Remember that the goal of proper part documentation is to describe and define a part such that it can be used without a need to refer to the primary literature. The next iGEM team should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for  users who wish to know more.
+
<p><strong>Gvp cluster(<a href="http://partsregistry.org/Part:BBa_K737010">BBa_K737010</a>)</strong> is a 1 kbp part  
 +
contains 2 open reading frames coding for gas vesicle genes (gvpA gvpC-20) from Bacillus Planktothrix rubescens strain BC-
-
<groupparts>iGEM012 OUC-China</groupparts>
+
Pla 9402. Promotion of the sequence results in expression of gas vesicles, organelles made entirely out of protein. These
 +
 
 +
organelles contain gas and therefore provide bouyancy to the cell. This slows the rate of settling of the cells in
 +
 
 +
different water layer from Lake Zurich by gas vesicles, see Walsby 2002.</p>
 +
 +
<p><span>the expression situation of the Gas vesicle gene cluster in Escherichia coli JM109, from the picture, we can see
 +
 
 +
obviously gas vesicle due to the expression of bacteria produce clear separation phenomenon. The picture on the right of
 +
 
 +
the experimental group were liquid surface layer and intermediate layer of fluid sampling results, we can see that the
 +
 
 +
fluid layer surface bacteria volume density is obviously higher than that of the middle layer of fluid.</span></p>
 +
 
 +
 
 +
 +
<p><span>The picture shows the gas vesicle in the cells after expressed in the overall trend. We in the cultivation of the
 +
 
 +
cells into logarithmic phase after transferring them to test tube, quiet place and culture 36 hours after using Trace
 +
 
 +
stratified take liquid apparatus at the same time to each liquid layer for sampling. Then each layer of fluid samples of
 +
 
 +
blood count the number of cells with statistics. Results show that gas vesicle due to the existence of the cell
 +
 
 +
concentration in the test tube surface layer of fluid, and control group due to the action of gravity that most cells
 +
 
 +
sedimentation in the test tube bottom.</span></p>
 +
 +
<p><span>Graph of OD measurements at 600nm of both experience group and control group. From the experimental results can be
 +
 
 +
seen in the liquid surface .There cell number have significant abrupt transformation.</span></p>
 +
<p>Constitutive GVPA Generator (BBa_K737006) It contains a constitutive promoter, GvpA protein , GFP protein and a
 +
 
 +
terminator.This part can be used as a control of (J23106+P0412+R0011+B0034+GVPA+E0840). It can express GvpA protein and GFP
 +
 
 +
constantly. When it transformed with  (J23106+P0440+R0040+B0034+GVPC+E0840), the bacteria may can float with GFP!</p>
 +
 
 +
<p><strong>YtfJ_Comparator</strong>( <a href="http://partsregistry.org/Part:BBa_K737045">BBa_K737045</a>)  The leading
 +
 
 +
sequence involved in the YtfJ transcript which can act as the target of the sRNA, spot42. It enables strong competition
 +
 
 +
with the galk::GFP to interact with spot42 which shows great potential for constructing sRNA-mediated circuit.</p>
 +
<p>This device mean to test feasibility of N/P comparator,replacing Nitrate,Phosphate inputs by IPTG,aTc。Small RNA Spot42
 +
 
 +
controls the GFP mRNA translation by blocking the RBS in galK.The galK and E0040 is fused together using ClaI site to avoid
 +
 
 +
stop condon in standard scar.J23106 is a moderate promotor,and galK’s RBS is a moderate one.</p>
 +
 +
 
 +
<p>Spot42 sRNA is under control of aTc inducible device,the buffer RNA YtfJ is under control of IPTG inducible device.</p>
 +
 +
 
 +
 
 +
 
 +
<p><strong>Constitutive GVPC Generator</strong></p>(<a href="">BBa_K737007</a>)It contains a constitutive promoter, GvpC
 +
 
 +
protein , GFP protein and a terminator.This part can be used as a control of (J23106+P0440+R0040+B0034+GVPC+E0840). It can
 +
 
 +
express GvpC protein and GFP constantly. When it transformed with  (J23106+P0412+R0011+B0034+GVPA+E0840), the bacteria may
 +
 
 +
can float with GFP!</p>
 +
<p>Here is the result of SDS-polyacrylamide gel electrophoresis. We can see GFP and GvpC protein directly. Lane 4 is top10
 +
 
 +
control group, lane 3 is constitutive GvpA and GFP generator, lane 5 is constitutive GvpC and GFP generator. The upper
 +
 
 +
white boxes are in the position about 26KD are GFP protein (25.8KD). The lower white box in the position of about 20KD is
 +
 
 +
GvpC-20 (20KD). Because the MW(molecular weight) of GvpA protein is too small, it’s very difficult to see it on the SDS-
 +
 
 +
polyacrylamide gel. But the expression of GFP suggests it may be expressed.
 +
Some papers say that GvpA is difficult to see is that GvpA is too hydrophobic to run out of sample hole.</p>
 +
 +
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Revision as of 14:50, 25 September 2012

Summary

parts submitted : 33 Composite expression modules
10 Generator
4 Regulatory promoters
1 Ribosome Binding Sites
10 Coding proteins
10 RNA

Total: 68 Parts

All 68 parts have been submitted to the registry and can be found here.


Data for favorite parts

Gvp cluster(BBa_K737010) is a 1 kbp part contains 2 open reading frames coding for gas vesicle genes (gvpA gvpC-20) from Bacillus Planktothrix rubescens strain BC- Pla 9402. Promotion of the sequence results in expression of gas vesicles, organelles made entirely out of protein. These organelles contain gas and therefore provide bouyancy to the cell. This slows the rate of settling of the cells in different water layer from Lake Zurich by gas vesicles, see Walsby 2002.

the expression situation of the Gas vesicle gene cluster in Escherichia coli JM109, from the picture, we can see obviously gas vesicle due to the expression of bacteria produce clear separation phenomenon. The picture on the right of the experimental group were liquid surface layer and intermediate layer of fluid sampling results, we can see that the fluid layer surface bacteria volume density is obviously higher than that of the middle layer of fluid.

The picture shows the gas vesicle in the cells after expressed in the overall trend. We in the cultivation of the cells into logarithmic phase after transferring them to test tube, quiet place and culture 36 hours after using Trace stratified take liquid apparatus at the same time to each liquid layer for sampling. Then each layer of fluid samples of blood count the number of cells with statistics. Results show that gas vesicle due to the existence of the cell concentration in the test tube surface layer of fluid, and control group due to the action of gravity that most cells sedimentation in the test tube bottom.

Graph of OD measurements at 600nm of both experience group and control group. From the experimental results can be seen in the liquid surface .There cell number have significant abrupt transformation.

Constitutive GVPA Generator (BBa_K737006) It contains a constitutive promoter, GvpA protein , GFP protein and a terminator.This part can be used as a control of (J23106+P0412+R0011+B0034+GVPA+E0840). It can express GvpA protein and GFP constantly. When it transformed with (J23106+P0440+R0040+B0034+GVPC+E0840), the bacteria may can float with GFP!

YtfJ_Comparator( BBa_K737045) The leading sequence involved in the YtfJ transcript which can act as the target of the sRNA, spot42. It enables strong competition with the galk::GFP to interact with spot42 which shows great potential for constructing sRNA-mediated circuit.

This device mean to test feasibility of N/P comparator,replacing Nitrate,Phosphate inputs by IPTG,aTc。Small RNA Spot42 controls the GFP mRNA translation by blocking the RBS in galK.The galK and E0040 is fused together using ClaI site to avoid stop condon in standard scar.J23106 is a moderate promotor,and galK’s RBS is a moderate one.

Spot42 sRNA is under control of aTc inducible device,the buffer RNA YtfJ is under control of IPTG inducible device.

Constitutive GVPC Generator

(BBa_K737007)It contains a constitutive promoter, GvpC protein , GFP protein and a terminator.This part can be used as a control of (J23106+P0440+R0040+B0034+GVPC+E0840). It can express GvpC protein and GFP constantly. When it transformed with (J23106+P0412+R0011+B0034+GVPA+E0840), the bacteria may can float with GFP!

Here is the result of SDS-polyacrylamide gel electrophoresis. We can see GFP and GvpC protein directly. Lane 4 is top10 control group, lane 3 is constitutive GvpA and GFP generator, lane 5 is constitutive GvpC and GFP generator. The upper white boxes are in the position about 26KD are GFP protein (25.8KD). The lower white box in the position of about 20KD is GvpC-20 (20KD). Because the MW(molecular weight) of GvpA protein is too small, it’s very difficult to see it on the SDS- polyacrylamide gel. But the expression of GFP suggests it may be expressed. Some papers say that GvpA is difficult to see is that GvpA is too hydrophobic to run out of sample hole.

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