IGEM:PennState/2008: Difference between revisions

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<h2 style="color: #fff">Penn State's 2007 iGEM project: Diauxie Elimination</h2>
<h2 style="color: #fff">Penn State's 2007 iGEM project: Diauxie Elimination</h2>
<p style="color: #fff">Penn State won a Gold medal in the 2007 iGEM Jamboree!  We're proud of our work during the year and our registry submissions.</p>
<p style="color: #fff">Penn State won a Gold medal in the 2007 iGEM Jamboree!  We're proud of our work during the year and our registry submissions.</p>
<h3>Abstract:</h3>
<h3 style="color: #fff">Abstract:</h3>
<p style="color: #fff">Increasing energy demands have brought about the need for a renewable, efficient energy source.  Using microorganisms to convert biomass to fuel offers a promising alternative to traditional energy sources, but still faces developmental challenges. Microbes such as Escherichia coli have evolved to preferentially metabolize sugars in a process knows as diauxie.  Engineering bacteria to eliminate diauxie with the common lignocellulose sugar xylose would allow faster digestion of ordinary plant biomass while simultaneously reducing the costly sugar residues of wild type bacterial digests.  Such modified strains of E. coli need to reduce or eliminate glucose’s repression of catabolization proteins necessary to utilize the energy stored in xylose.  The effect of such augmentation would be readily assayed with fluorescent proteins placed downstream of xylose regulatory regions.</p>  
<p style="color: #fff">Increasing energy demands have brought about the need for a renewable, efficient energy source.  Using microorganisms to convert biomass to fuel offers a promising alternative to traditional energy sources, but still faces developmental challenges. Microbes such as Escherichia coli have evolved to preferentially metabolize sugars in a process knows as diauxie.  Engineering bacteria to eliminate diauxie with the common lignocellulose sugar xylose would allow faster digestion of ordinary plant biomass while simultaneously reducing the costly sugar residues of wild type bacterial digests.  Such modified strains of E. coli need to reduce or eliminate glucose’s repression of catabolization proteins necessary to utilize the energy stored in xylose.  The effect of such augmentation would be readily assayed with fluorescent proteins placed downstream of xylose regulatory regions.</p>  
<h2 style="color: #fff">Want to Join?</h2>
<p style="color: #fff">If you are interested in joining the team [[IGEM:PennState/Newmember|click here]].</p></font>
<p style="color: #fff">If you are interested in joining the team [[IGEM:PennState/Newmember|click here]].</p></font>


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<h2><font color="#FFFFFF">Fulltime Undergraduates</font></h2>
<h2><font color="#FFFFFF">Fulltime Undergraduates</font></h2>
*[[user:Nimrah Ahmed|<font color="#CCFFFF">Nimrah Ahmed</font>]]  
 
*[[user:yourusernamehere|<font color="#CCFFFF">Daniel Seong</font>]]
{|valign="top" style="background:none; border: 0; width: 500px; text-indent: 3em"
*[[user:Trevor Wiley|<font color="#CCFFFF">Trevor Wiley</font>]]  
|-
*[[user:GTobin|<font color="#CCFFFF">Garrett Tobin</font>]]
|class="teamm"| [[user:GTobin|<font color="#CCFFFF">Garrett Tobin</font>]]
*[[user:Shariful Alam|<font color="#CCFFFF">Shariful Alam</font>]]
|[[IGEM:PennState/Labbook/GarrettTobin08|<font color="#CCFFFF">Lab Notebook</font>]]
*[[user:yourusernamehere|<font color="#CCFFFF">Renae Patch</font>]]
|-
*[[user:samhita_banavar|<font color="#CCFFFF">Samhita Banavar</font>]]
|class="teamm"|[[user:Trevor Wiley|<font color="#CCFFFF">Trevor Wiley</font>]]
|[[IGEM:PennState/Labbook/Trevor Wiley|<font color="#CCFFFF">Lab Notebook</font>]]
|-
|class="teamm"|[[user:Nimrah Ahmed|<font color="#CCFFFF">Nimrah Ahmed</font>]]
|[[IGEM:PennState/Labbook/Nimrah Ahmed|<font color="#CCFFFF">Lab Notebook</font>]]
|-
|class="teamm"|[[user:yourusernamehere|<font color="#CCFFFF">Daniel Seong</font>]]
|[[IGEM:PennState/Labbook/yourname|<font color="#CCFFFF">Lab Notebook</font>]]
|-
|class="teamm"|[[user:Shariful Alam|<font color="#CCFFFF">Shariful Alam</font>]]
|[[IGEM:PennState/Labbook/Shariful Alam|<font color="#CCFFFF">Lab Notebook</font>]]  
|-
|class="teamm"|[[user:yourusernamehere|<font color="#CCFFFF">Berooke Alemayehu</font>]]
|[[IGEM:PennState/Labbook/yourname|<font color="#CCFFFF">Lab Notebook</font>]]
|}
 
<h2><font color="#FFFFFF">High School Student</font></h2>
{|valign="top" style="background:none; border: 0; width: 500px; text-indent: 3em"
|class="teamm"| [[user:samhita_banavar|<font color="#CCFFFF">Samhita Banavar</font>]]
|[[IGEM:PennState/Labbook/GarrettTobin08|<font color="#CCFFFF">Lab Notebook</font>]]
|}


<h2><font color="#FFFFFF">Affiliated Undergraduates</font></h2>
<h2><font color="#FFFFFF">Affiliated Undergraduates</font></h2>


*[[IGEM:PennState/2007/user:GKho|<font color="#CCFFFF">George Khoury</font>]]
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|[[IGEM:PennState/2007/user:GKho|<font color="#CCFFFF">George Khoury</font>]] ||
|-
|class="teamm"|[[user:Galen Lynch|<font color="#CCFFFF">Galen Lynch</font>]]
|[[IGEM:PennState/Labbook/yourname|<font color="#CCFFFF">Lab Notebook</font>]]
|}


<h2><font color="#FFFFFF">Graduate Students</font></h2>
<h2><font color="#FFFFFF">Advisory Assistance</font></h2>


*[[IGEM:PennState/2006/user:Megan_Marshall|<font color="#CCFFFF">Megan Marshall</font>]]
*[[IGEM:PennState/2006/user:Megan_Marshall|<font color="#CCFFFF">Megan Marshall</font>]]
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<h2><font color="#FFFFFF">Lab Notebooks</font></h2>
*[[IGEM:PennState/Labbook/CommonBook|<font color="#CCFFFF">General Lab Notebook</font>]]
*[[IGEM:PennState/Labbook/Nimrah Ahmed|<font color="#CCFFFF">Nimrah Ahmed</font>]]
*[[IGEM:PennState/Labbook/yourname|<font color="#CCFFFF">Daniel Seong</font>]]
*[[IGEM:PennState/Labbook/Trevor Wiley|<font color="#CCFFFF">Trevor Wiley</font>]]
*[[IGEM:PennState/Labbook/Shariful Alam|<font color="#CCFFFF">Shariful Alam</font>]]
*[[IGEM:PennState/Labbook/yourname|<font color="#CCFFFF">Galen Lynch</font>]]
*[[IGEM:PennState/Labbook/GarrettTobin08|<font color="#CCFFFF">Garrett Tobin</font>]]
*[[IGEM:PennState/Labbook/yourname|<font color="#CCFFFF">Renae Patch</font>]]
*[[IGEM:PennState/Labbook/SamhitaBanavar|<font color="#CCFFFF">Samhita Banavar</font>]]


<h2><font color="#FFFFFF">Fun Stuff</font></h2>
<h2><font color="#FFFFFF">Fun Stuff</font></h2>
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<font color="#646B86" size="6"><html><blink>></blink></html>Project</font>
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<html><font face="Tahoma" color="#FFFFFF" size="6"><blink>></blink>Project</font>
</html>
*[http://2008.igem.org/Team:PennState <font color="#CCFFFF">2008 Penn State iGEM Project Site</font>]
*[http://2008.igem.org/Team:PennState/Notebook <font color="#CCFFFF">2008 Lab Notebook</font>]


<h2>In The News</h2>
<h2>In The News</h2>


*[[IGEM:PennState/Publications/Synthetic Sports: A Bacterial Relay Race|<font color="#000000">Synthetic Sports: A Bacterial Relay Race</font>]]
*[[IGEM:PennState/Publications/Synthetic Sports: A Bacterial Relay Race|<font color="#000000">Synthetic Sports: A Bacterial Relay Race</font>]]
*[[IGEM:PennState/Publications/Posters|<font color="#000000">PSU iGEM Posters</font>]]
*[[IGEM:PennState/Publications/Posters <font color="#000">PSU iGEM Posters</font>]]
*[https://www.engr.psu.edu/NewsEvents/EPS/v22n2_2006spring/igem.htm<font color="#000000">Ready. Set. Grow!?</font>]
*[https://www.engr.psu.edu/NewsEvents/EPS/v22n2_2006spring/igem.htm<font color="#000">Ready. Set. Grow!?</font>]
*[http://www.ainewsletter.com/newsletters/aix_0512.htm#biobricks_conjugate <font color="#000000">AI Newsletter</font>]
*[http://www.ainewsletter.com/newsletters/aix_0512.htm#biobricks_conjugate <font color="#000">AI Newsletter</font>]
*[http://publications.nigms.nih.gov/findings/mar07/findings_mar07.pdf <font color="#000000">Government Report</font>]
*[http://publications.nigms.nih.gov/findings/mar07/findings_mar07.pdf <font color="#000">Government Report</font>]
*[http://www.mrsec.psu.edu/highlights/publications/publications2006.pdf <font color="#000000">MRSEC Publications</font>]
*[http://www.mrsec.psu.edu/highlights/publications/publications2006.pdf <font color="#000">MRSEC Publications</font>]


<h2>Tasks</h2>
<h2>Tasks</h2>
*[[IGEM:PennState/News/WebsiteTasks|<font color="#000">Website Tasks</font>]]
*[[IGEM:PennState/2007/News/MeetingNotes|<font color="#000">Group Meeting Minutes</font>]]


*[[IGEM:PennState/News/WebsiteTasks|<font color="#000000">Website Tasks</font>]]
<h2>Team Utilities</h2>
*[[IGEM:PennState/2007/News/MeetingNotes|<font color="#000000">Group Meeting Minutes</font>]]
*[http://tools.neb.com/NEBcutter2/index.php <font color="#000">NEB Cutter</font>]
*[http://www.neb.com/nebecomm/DoubleDigestCalculator.asp <font color="#000">Double Digest Finder</font>]
*[http://tanager.biotec.psu.edu/|<font color="#000">Oligo orders</font>]
*[http://www.geneart.com/|<font color="#000">Plasmid Orders (Geneart)</font>]
*[http://partsregistry.org/Help:BioBrick_Prefix_and_Suffix|<font color="#000">BioBrick Prefix & Suffix</font>]
*[http://www.sciencegateway.org/tools/bacteria.htm <font color="#000">OD Calculator</font>]


<h2>Protocols</h2>
<h2>Protocols</h2>
*[[IGEM:PennState/2006/Growthmedia|<font color="#000000">Growth Media</font>]]
*[[IGEM:PennState/2006/Growthmedia|<font color="#000">Growth Media</font>]]
*[[IGEM:PennState/2006/Cloning|<font color="#000000">Cloning</font>]]  
*[[IGEM:PennState/2006/Cloning|<font color="#000">Cloning</font>]]   
**[[IGEM:PennState/2006/PreparingChemicallyCompetentCells|<font color="#000000">Preparing chemically competent cells</font>]]
**[[IGEM:PennState/2006/GrowingParts|<font color="#000">Growing Parts (Innoculation)</font>]]  
**[[IGEM:PennState/2006/GrowingParts|<font color="#000000">Growing Parts</font>]]  
**[[IGEM:PennState/2006/PreparingChemicallyCompetentCells|<font color="#000">Preparing chemically competent cells</font>]]
**[[IGEM:PennState/2007/Dnaprep|<font color="#000000">Telt Method DNA Prep</font>]]  
**[[IGEM:PennState/2008/PreparingElectrocompetentCells|<font color="#000">Preparing Electrocompetent cells</font>]]
**[[IGEM:PennState/2006/Restriction|<font color="#000000">Restriction</font>]]  
**[[IGEM:PennState/2007/Dnaprep|<font color="#000">Telt Method DNA Prep</font>]]  
**[[IGEM:PennState/2006/Ligation|<font color="#000000">Ligation</font>]]  
**[[IGEM:PennState/2006/Restriction|<font color="#000">Restriction</font>]]  
**[[IGEM:PennState/2006/Transformation|<font color="#000000">Transformation</font>]]
**[[IGEM:PennState/2006/Ligation|<font color="#000">Ligation</font>]]  
*[[IGEM:PennState/2006/Lambda Techniques|<font color="#000000">Lambda Techniques</font>]]
**[[IGEM:PennState/2006/Transformation|<font color="#000">Transformation</font>]]
*[[IGEM:PennState/2006/dnagels|<font color="#000000">Agarose Gel</font>]]
*[[IGEM:PennState/2006/dnagels|<font color="#000">Agarose Gel</font>]]
**[[IGEM:PennState/2006/sybrgreen|<font color="#000000">Working with Sybr Green I</font>]]
**[[IGEM:PennState/2008/TAEBuffer|<font color="#000">TAE Buffer</font>]]
*[http://openwetware.org/wiki/Silver:_PCR <font color="#000000">PCR</font>]
**[[IGEM:PennState/2006/sybrgreen|<font color="#000">Working with Sybr Green I</font>]]
**[[IGEM:PennState/2007/FreezeandSqueeze|<font color="#000000">PCR Purification Freeze and Squeeze</font>]]
*[http://openwetware.org/wiki/Silver:_PCR <font color="#000">PCR</font>]
*[[IGEM:PennState/2006/Plate-Reading|<font color="#000000">Plate-reading</font>]]
**[[IGEM:PennState/2007/FreezeandSqueeze|<font color="#000">PCR Purification Freeze and Squeeze</font>]]
*[[IGEM:PennState/2006/StrainConstruction|<font color="#000000">Strain Construction</font>]]   
*[[IGEM:PennState/2006/Plate-Reading|<font color="#000">Plate-reading</font>]]
*[[IGEM:PennState/2006/Eikenplates|<font color="#000000">Eiken Agar Plates</font>]]
*[[IGEM:PennState/2006/StrainConstruction|<font color="#000">Strain Construction</font>]]   
*[[IGEM:PennState/2006/PSUinventory|<font color="#000000">Inventory</font>]]
*[[IGEM:PennState/2006/Eikenplates|<font color="#000">Eiken Agar Plates</font>]]
*[[IGEM:PennState/2006/PSUinventory|<font color="#000">Inventory</font>]]


<h2>Progress</h2>
<h2>Progress</h2>
*[[IGEM:PennState/2007/Progress_Project_Development|<font color="#000000">Project Development Overview</font>]]
*[[IGEM:PennState/2007/Progress_Project_Development|<font color="#000">Project Development Overview</font>]]
*[[IGEM:PennState/2007/Progress_Cloning|<font color="#000000">Cloning</font>]]
*[[IGEM:PennState/2007/Progress_Cloning|<font color="#000">Cloning</font>]]
*[[IGEM:PennState/2007/Progress_Registry Parts|<font color="#000000">Submitted Registry Parts</font>]]
*[[IGEM:PennState/2007/Progress_Registry Parts|<font color="#000">Submitted Registry Parts</font>]]
*[[IGEM:PennState/2007/Microcentrifuge_tube_lists|<font color="#000000">Microcentrifuge Tube Lists</font>]]
*[[IGEM:PennState/2007/Microcentrifuge_tube_lists|<font color="#000">Microcentrifuge Tube Lists</font>]]
*[[IGEM:PennState/2006/Progress_motility|<font color="#000000">Motility results</font>]]
*[[IGEM:PennState/2006/Progress_motility|<font color="#000">Motility results</font>]]
*[[IGEM:PennState/2007/Storage|<font color="#000000">Glycerol Stock Inventory</font>]]
*[[IGEM:PennState/2007/Storage|<font color="#000">Glycerol Stock Inventory</font>]]


<h2>Background</h2>
<h2>Background</h2>
*[[IGEM:PennState/history|<font color="#000000">History of Penn State iGEM</font>]]
*[[IGEM:PennState/history|<font color="#000">History of Penn State iGEM</font>]]
*[[iGEM:PennState/2006 | <font color="#000">Penn State iGEM 2006 on OpenWetWare</font>]]
*[http://parts.mit.edu/wiki/index.php/Penn_State_2005 Penn State <font color="#000"> iGEM 2005</font>]
*[http://parts.mit.edu/wiki/index.php/Penn_State_University_2006 <font color="#000">Penn State iGEM 2006</font>]


<h2>Links</h2>
<h2>Links</h2>
*[http://parts.mit.edu/registry Parts registry]
*[http://parts.mit.edu/registry <font color="#000">Parts registry</font>]
*[http://parts.mit.edu/igem iGEM wiki]
*[http://parts.mit.edu/igem iGEM <font color="#000">wiki</font>]
*[[iGEM:PennState/2006|Penn State iGEM 2006 on OpenWetWare]]
*[http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=10119&window=7964&begin=10568 | <font color="#000">Lambda Phage Genome</font>]
*[http://parts.mit.edu/wiki/index.php/Penn_State_2005 Penn State iGEM 2005]
*[http://mycoplasmas.vm.iastate.edu/lab_site/methods/DNA/precip.html <font color="#000"> Ethanol Precipitation</font>]
*[http://parts.mit.edu/wiki/index.php/Penn_State_University_2006 Penn State iGEM 2006]
*[http://tanager.biotec.psu.edu/ Oligo orders]
*[http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=10119&window=7964&begin=10568 Lambda Phage Genome]
*[http://mycoplasmas.vm.iastate.edu/lab_site/methods/DNA/precip.html Ethanol Precipitation]
*[http://0-www.ncbi.nlm.nih.gov.ilsprod.lib.neu.edu/blast/bl2seq/wblast2.cgi]
*[http://0-www.ncbi.nlm.nih.gov.ilsprod.lib.neu.edu/blast/bl2seq/wblast2.cgi]
*[http://www.sciencegateway.org/tools/bacteria.htm OD Calculator]
 
 
 
 
 
 
 
 
 
 
 
 
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Latest revision as of 19:53, 14 July 2008

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What iGEM is All About

The International Genetically Engineered Machines (iGEM) Competition is an annual undergraduate research competition hosted by MIT. The project aim is to develop Synthetic Biology through the creation of an open registry of parts, or biobricks. Each part in the registry is an analyzed strain of DNA with several specific restriction sites at each end of the fragment. These strains can be anything from promoters to genes, allowing easy assembly and reassembly of these parts into genetic circuits. The [2007 Jamboree] consisted of 54 teams from 19 countries who presented their findings.

Penn State's 2007 iGEM project: Diauxie Elimination

Penn State won a Gold medal in the 2007 iGEM Jamboree! We're proud of our work during the year and our registry submissions.

Abstract:

Increasing energy demands have brought about the need for a renewable, efficient energy source. Using microorganisms to convert biomass to fuel offers a promising alternative to traditional energy sources, but still faces developmental challenges. Microbes such as Escherichia coli have evolved to preferentially metabolize sugars in a process knows as diauxie. Engineering bacteria to eliminate diauxie with the common lignocellulose sugar xylose would allow faster digestion of ordinary plant biomass while simultaneously reducing the costly sugar residues of wild type bacterial digests. Such modified strains of E. coli need to reduce or eliminate glucose’s repression of catabolization proteins necessary to utilize the energy stored in xylose. The effect of such augmentation would be readily assayed with fluorescent proteins placed downstream of xylose regulatory regions.

Want to Join?

If you are interested in joining the team click here.




<html><blink>></blink></html>People

Fulltime Undergraduates

Garrett Tobin Lab Notebook
Trevor Wiley Lab Notebook
Nimrah Ahmed Lab Notebook
Daniel Seong Lab Notebook
Shariful Alam Lab Notebook
Berooke Alemayehu Lab Notebook

High School Student

Samhita Banavar Lab Notebook

Affiliated Undergraduates

George Khoury
Galen Lynch Lab Notebook

Advisory Assistance

Faculty


Fun Stuff


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<html><font face="Tahoma" color="#FFFFFF" size="6"><blink>></blink>Project</font> </html>

In The News

Tasks


Team Utilities

Protocols

Progress

Background

Links







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