Latest revision as of 20:06, 28 October 2008

MSUSB iGEM 08

Team

Project

Papers and Notebook

Overall project

Project Details

In Depth Description of our Project

We began work in May obtaining cDNA samples of Phanerochaete Chrysosporium. We initially worked with the Mississippi State University Forest Products Lab, but we could never get any PCR results. We contacted the University of Wisconsin Forest Products Lab (Jill Gaskell) and obtained samples of cDNA from PC (BKM strain and RP strain). We got no results from this either. At this point, we consulted Jill and she advised that we make our primers more specific for the noncoding regions of the gene. This worked and we obtained our gene (LipA).

The Experiments

We were able to obtain a purified Lignin Peroxidase from PC by doing sequential PCRs of the non coding region and then the coding region. There was difficulty in cloning the gene into the plasmids we used, pGEM and pPIC6alpha. However, once we were able to clone the gene into pGEM, it was easily cloned into pPIC6alpha as well. However, this work required the whole summer and we had to work around classes. We have been able to BioBrick our part and get it into Pichia for testing. At this point we are in the middle of testing the gene and the enzyme activity.

Results

We have isolated a Lignin Peroxidase gene from Phanerochaete Chrysosporium. The gene is highly analogous to many other Lignin Peroxidase genes, especially Lignin Peroxidase A. It was sequenced and uploaded to GenBank for comparisons and showed an extremely high degree of homology with other Lignin Peroxidases. The gene has been put into standard BioBrick format, but it has not been characterized due to time constraints. This, as well as development of a functional system will be part of our future work.

Our Part

We made a coding part for Lignin Peroxidase. It is currently in testing and will hopefully be done by the Jamboree. This part can be used for a biomass degradation system. There has also been talk that this type of enzyme has promise in breaking down synthetic polymers like plastics. This would be incredibly cool and we think people should try and tackle this problem.

@@ Line 17: / Line 17: @@
 <!--End Tabs-->
+[[Image:MStateblob.JPG|200 px|right]]
-[[Image:Plants2plants.JPG|center]]
+= '''Overall project''' =
-{|align="justify"
-|You can write a background of your team here.  Give us a background of your team, the members, etc.  Or tell us more about something of your choosing.
-|
-|-
-|
-'''Lignin is a ubiquitous, extremely complex biopolymer found in plant cells.  It is the most recalcitrant part of the cell wall, and only a few organisms possess the machinery necessary for its degradation.  As a result, a huge proportion of the earth's biomass resources are trapped in a highly degradation resistant lignin matrix.  To make these resources viable for energy and chemical needs, lignin must be broken down to separate the chemical components of biomass.'''
-|-
-|
-'''Mississippi State seeks to benefit the uses of non-food material biomass as a source of energy. Though ethanol and other biofuels offer an alternative to fossil fuels, their extraction from food crops is unrealistic and puts enormous economic strain on both food products and the further development of natural fuels. Biomass waste contains a huge amount of unused cellulose and hemicellulose, the raw materials for biofuel production. In addition, Lignin has been shown to be a source of biogasoline, which conforms better than any current biofuel to the existing energy infrastructure. As a result, this project will develop a better method for natural degradation of biomass to reduce the costs and complications involved with current methods.'''
-|[[Image:Bandit2.JPG|right|250 px]]
-|-
-|
-'''We seek to isolate a single gene from the Lignin Peroxidase gene family.  This gene will be sequenced, tested, characterized, and submitted to the registry in BioBrick format.  Our project is vital to developing a biological process for degrading biomass.  Lignin Peroxidase initiates this process, so we see fit that this technology must be the first developed.  We want to make our resources a reality, and this project is the first step.'''
-|-
-|
-|align="center"|[[Team:Mississippi_State | Team Example 2]]
-|}
-[[Image:Learnmore.JPG|250 px|Team:Mississippi State/Project]][[Image:Seewhatwedid.JPG|250 px|Team:Mississippi State/Notebook]][[Image:Meetourteam.JPG|250 px|Team:Mississippi State/Team]]
-<!--- The Mission, Experiments --->
-{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
-!align="center"|[[Team:Mississippi_State|Home]]
-!align="center"|[[Team:Mississippi_State/Team|The Team]]
-!align="center"|[[Team:Mississippi_State/Project|The Project]]
-!align="center"|[[Team:Mississippi_State/Parts|Parts Submitted to the Registry]]
-!align="center"|[[Team:Mississippi_State/Modeling|Modeling]]
-!align="center"|[[Team:Mississippi_State/Notebook|Notebook]]
-|}
-(''Or you can choose different headings.  But you must have a team page, a project page, and a notebook page.'')
-== '''Overall project''' ==
-*[[Team:Mississippi_State/So Far|So Far]]
-*[[Team:Mississippi_State/What We've Done And Why|What We've Done And Why]]
-*[https://2008.igem.org/Judging Requirements]
-*[http://dspace.mit.edu/bitstream/1721.1/21168/1/biobricks.pdf BioBrick Design]
-*[http://mit.edu/endy/www/scraps/comic/AiSB.vol1.pdf An Intro to SynBio]
-Your abstract
 == Project Details==
+*[[Team:Mississippi State/project description|In Depth Description of our Project]]
+We began work in May obtaining cDNA samples of Phanerochaete Chrysosporium.  We initially worked with the Mississippi State University Forest Products Lab, but we could never get any PCR results.  We contacted the University of Wisconsin Forest Products Lab (Jill Gaskell) and obtained samples of cDNA from PC (BKM strain and RP strain).  We got no results from this either.  At this point, we consulted Jill and she advised that we make our primers more specific for the noncoding regions of the gene.  This worked and we obtained our gene (LipA).
+=== The Experiments ===
+We were able to obtain a purified Lignin Peroxidase from PC by doing sequential PCRs of the non coding region and then the coding region.  There was difficulty in cloning the gene into the plasmids we used, pGEM and pPIC6alpha.  However, once we were able to clone the gene into pGEM, it was easily cloned into pPIC6alpha as well.  However, this work required the whole summer and we had to work around classes.  We have been able to BioBrick our part and get it into Pichia for testing.  At this point we are in the middle of testing the gene and the enzyme activity.
-=== Part 2 ===
+[[Image:CalebBioBricks.JPG|400 px]][[Image:SamBioBricks.JPG|400 px]]
+== Results ==
+We have isolated a Lignin Peroxidase gene from Phanerochaete Chrysosporium.  The gene is highly analogous to many other Lignin Peroxidase genes, especially Lignin Peroxidase A.  It was sequenced and uploaded to GenBank for comparisons and showed an extremely high degree of homology with other Lignin Peroxidases.  The gene has been put into standard BioBrick format, but it has not been characterized due to time constraints.  This, as well as development of a functional system will be part of our future work.
-=== The Experiments ===
+='''Our Part'''=
+We made a coding part for Lignin Peroxidase.  It is currently in testing and will hopefully be done by the Jamboree.  This part can be used for a biomass degradation system.  There has also been talk that this type of enzyme has promise in breaking down synthetic polymers like plastics.  This would be incredibly cool and we think people should try and tackle this problem.
-=== Part 3 ===
-== Results ==

Team:Mississippi State/Project

From 2008.igem.org