IGEM:VGEM/2007/Projects

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==Projects==
==Projects==
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We have decided to focus on two of the following projects for the remainder of the summer, Bactierla Melanogenesis and Butanol Biosynthesis.
+
The following projects represent a small fraction of the plethora of project ideas that we brainstormed during the spring semester and early summer.  Many of our initial project ideas were either too expensive or depended on knowledge that does not exist yet.  Therefore, only a small percentage of these were deemed plausible near the beginning of the summer, but most eventually met similar roadblocks.  We will present our work on '''Harvesting Biomass and Light to Power Butanol Biosynthesis''' at the iGEM Jamboree in November. It is our wish that the 2008 VGEM Team will investigate the remaining designed projects in more detail.
 +
 
 +
----
 +
===Butanol Biosynthesis===
 +
----
 +
Coming up with alternative fuels is a real-world problem.  We're interested in using cheap, renewable feedstock to power efficient biofuel production.  More to come!
 +
====References====
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17372221&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host] by DeLong ''et al''
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17277079&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Light-powering E. coli with proteorhodopsin]
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16008504&ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumNew  Insights into metabolic properties of marine bacteria encoding proteorhodopsins]
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16707677&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum  Complete cellulase system in the marine bacterium ''Saccharophagus degradans'' strain 2-40T] by Weiner ''et al''
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16014479&ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Saccharophagus degradans, a versatile marine degrader of complex polysaccharides]
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17311090&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Plant Carbohydrate Scavenging through TonB-Dependent Receptors: A Feature Shared by Phytopathogenic and Aquatic Bacteria]
 +
*[http://aem.asm.org/cgi/content/abstract/68/1/53 Improvement of Cellulolytic Properties of Clostridium cellulolyticum by Metabolic Engineering]
 +
*[http://www3.interscience.wiley.com/cgi-bin/abstract/109792702/ABSTRACT?CRETRY=1&SRETRY=0 Butanol fermentation research: upstream and downstream manipulations]
 +
*[http://www3.interscience.wiley.com/cgi-bin/abstract/114109891/ABSTRACT Butanol production from agricultural residues: Impact of degradation products on ''Clostridium beijerinckii'' growth and butanol fermentation]
 +
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4NK4739-1&_user=709071&_coverDate=06%2F30%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=cd81c68d18f23cafdc69fa0d8a90c1b6 Bioproduction of butanol from biomass: from genes to bioreactors]
 +
*[http://aem.asm.org/cgi/content/full/73/9/3061?view=long&pmid=17337545 Dynamics of Genomic-Library Enrichment and Identification of Solvent Tolerance Genes for Clostridium acetobutylicum]
 +
*[http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bp050360w Butanol Production from Corn Fiber Xylan Using ''Clostridium acetobutylicum'']
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16685494&ordinalpos=10&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Bacterial acetone and butanol production by industrial fermentation in the Soviet Union: use of hydrolyzed agricultural waste for biorefinery]
 +
*[http://aem.asm.org/cgi/content/abstract/45/3/966 Butanol Production by a Butanol-Tolerant Strain of ''Clostridium acetobutylicum'' in Extruded Corn Broth]
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17289987&ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Challenges in engineering microbes for biofuel production] by Stephanopoulos
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16270654&ordinalpos=9&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Metabolic engineering] by Stephanopoulos
 +
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16041571&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus Global physiological understanding and metabolic engineering of microorganisms based on omics studies] by Park ''et al''
 +
<br />
----
----
===Bacterial Melanogenesis===
===Bacterial Melanogenesis===
----
----
-
 
This project is an extension of work that was done at Biosource Genetics Corporation in 1990.  What we would like to do is program bacteria to produce melanin in response to a red light stimulus.  This inducible melanin production has various applications including making melanin for monitoring cellular processes.  In this way, melanin would serve as a biomarker or indicator similar to the GFP but would be easily visible to the naked eye.
This project is an extension of work that was done at Biosource Genetics Corporation in 1990.  What we would like to do is program bacteria to produce melanin in response to a red light stimulus.  This inducible melanin production has various applications including making melanin for monitoring cellular processes.  In this way, melanin would serve as a biomarker or indicator similar to the GFP but would be easily visible to the naked eye.
 +
 +
We have designed a light-inducible system in ''E. coli'' capable of manufacturing and secreting melanin.  This biological machine is built from two standard biological parts, a melanin generator and a red light-inducible plasmid.  This project has a very simple design: the melanin producing gene mel from Streptomyces is linked to the red-light inducer designed by UT Austin in the iGem 2006 competition.
 +
 +
''Motivation''
 +
<br />
 +
 +
According to the American Cancer Society, skin cancer is the most common form of all cancers.  It accounts for nearly half of all cancers in the United States.  Due to its natural defense mechanism, skin must first be exposed to UV radiation before melanogenesis begins.  Thus, we thought it would be convienient to be able to produce melanin in response to another harmless wavelength.  This technology may, in the future, lead to treatments for albinism and a safe alternative for cosmetic tanning.  Melanin may also be used as a natural indicator in the laboratory as well as an acoustic material.  According to a study by Kono, et. al., melanin is capable of absorbing ultrasound.
 +
 +
Additionally, we would like to be able to use the melanin secretion system as an indicator in our ethylene detection project.  Theoretically, more and more melanin would be secreted as various produce items become riper and produce more ethylene, causing the indicator to become darker on a gradient.
 +
 +
''Background''
 +
<br />
 +
 +
In humans, melanin is found in the skin, hair, iris, adrenal gland, inner ear, and various pigment-producing regions of the brain.
 +
 +
Melanin is the primary determinant of skin color.  The process of tanning originates in specialized cells called melanocytes.  When stimulated by ultraviolet radiation, these cells produce melanin, which then migrates to the neighboring keratinocytes.  The melanin accumulates above the receiving cells' nuclei in order to protect genetic material from from mutations caused by the sun's ionizing radiation. 
 +
 +
Though there are many types of melanin, they are all polymers which contain derivatives of the amino acid tyrosine.  Melanin is an aggregate of smaller component molecules; the various types of melanin have differing proportions and bonding patterns of the component molecules.  Three types of melanin found in humans include eumelanin, pheomelanin, and neuromelanin.  Eumelanin, which produces a brown-black color, is most common. 
====References====
====References====
Line 12: Line 53:
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=1367455 ''Melanin production in Escherichia coli from a cloned tyrosinase gene'' by Della-Cioppa G, Garger SJ, Sverlow GG, Turpen TH, Grill LK.]
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=1367455 ''Melanin production in Escherichia coli from a cloned tyrosinase gene'' by Della-Cioppa G, Garger SJ, Sverlow GG, Turpen TH, Grill LK.]
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16306980&ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum ''Synthetic biology: engineering Escherichia coli to see light'' by Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA.]
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16306980&ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum ''Synthetic biology: engineering Escherichia coli to see light'' by Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, Voigt CA.]
 +
*Wu, Corrina. Unraveling the Mystery of Melanin. Sept 18, 1999. Vol 156, No 12.
 +
*[http://www.mbceo.com/science/more_information.php?c=Melanin Information and Facts About Melanin]
 +
<br />
----
----
===Ethylene Biosensor===
===Ethylene Biosensor===
Line 51: Line 95:
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WBK-45R75CJ-28&_user=709071&_coverDate=05%2F15%2F1996&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=d973de9610ebed952565617b9dea7b44 Expression of biologically active isoforms of the tumor angiogenesis factor VEGF in ''Escherichia coli''] by Siemeister et al.
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WBK-45R75CJ-28&_user=709071&_coverDate=05%2F15%2F1996&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=d973de9610ebed952565617b9dea7b44 Expression of biologically active isoforms of the tumor angiogenesis factor VEGF in ''Escherichia coli''] by Siemeister et al.
----
----
-
 
-
===Butanol Biosynthesis===
 
-
----
 
-
Coming up with alternative fuels is a real-world problem.  We're interested in using cheap, renewable feedstock to power efficient biofuel production.  More to come!
 
-
====References====
 
-
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17372221&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host] by DeLong ''et al''
 
-
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17277079&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Light-powering E. coli with proteorhodopsin]
 
-
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16008504&ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSumNew  Insights into metabolic properties of marine bacteria encoding proteorhodopsins]
 
-
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16707677&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum  Complete cellulase system in the marine bacterium ''Saccharophagus degradans'' strain 2-40T] by Weiner ''et al''
 
-
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16014479&ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Saccharophagus degradans, a versatile marine degrader of complex polysaccharides]
 
-
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17311090&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Plant Carbohydrate Scavenging through TonB-Dependent Receptors: A Feature Shared by Phytopathogenic and Aquatic Bacteria]
 
-
*[http://aem.asm.org/cgi/content/abstract/68/1/53 Improvement of Cellulolytic Properties of Clostridium cellulolyticum by Metabolic Engineering]
 
-
*[http://www3.interscience.wiley.com/cgi-bin/abstract/109792702/ABSTRACT?CRETRY=1&SRETRY=0 Butanol fermentation research: upstream and downstream manipulations]
 
-
*[http://www3.interscience.wiley.com/cgi-bin/abstract/114109891/ABSTRACT Butanol production from agricultural residues: Impact of degradation products on ''Clostridium beijerinckii'' growth and butanol fermentation]
 
-
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4NK4739-1&_user=709071&_coverDate=06%2F30%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=cd81c68d18f23cafdc69fa0d8a90c1b6 Bioproduction of butanol from biomass: from genes to bioreactors]
 
-
*[http://aem.asm.org/cgi/content/full/73/9/3061?view=long&pmid=17337545 Dynamics of Genomic-Library Enrichment and Identification of Solvent Tolerance Genes for Clostridium acetobutylicum]
 
-
*[http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bp050360w Butanol Production from Corn Fiber Xylan Using ''Clostridium acetobutylicum'']
 
-
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16685494&ordinalpos=10&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Bacterial acetone and butanol production by industrial fermentation in the Soviet Union: use of hydrolyzed agricultural waste for biorefinery]
 
-
*[http://aem.asm.org/cgi/content/abstract/45/3/966 Butanol Production by a Butanol-Tolerant Strain of ''Clostridium acetobutylicum'' in Extruded Corn Broth]
 
-
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17289987&ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Challenges in engineering microbes for biofuel production] by Stephanopoulos
 
-
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16270654&ordinalpos=9&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Metabolic engineering] by Stephanopoulos
 
-
*[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16041571&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus Global physiological understanding and metabolic engineering of microorganisms based on omics studies] by Park ''et al''
 

Current revision

Contents

Projects

The following projects represent a small fraction of the plethora of project ideas that we brainstormed during the spring semester and early summer. Many of our initial project ideas were either too expensive or depended on knowledge that does not exist yet. Therefore, only a small percentage of these were deemed plausible near the beginning of the summer, but most eventually met similar roadblocks. We will present our work on Harvesting Biomass and Light to Power Butanol Biosynthesis at the iGEM Jamboree in November. It is our wish that the 2008 VGEM Team will investigate the remaining designed projects in more detail.


Butanol Biosynthesis


Coming up with alternative fuels is a real-world problem. We're interested in using cheap, renewable feedstock to power efficient biofuel production. More to come!

References



Bacterial Melanogenesis


This project is an extension of work that was done at Biosource Genetics Corporation in 1990. What we would like to do is program bacteria to produce melanin in response to a red light stimulus. This inducible melanin production has various applications including making melanin for monitoring cellular processes. In this way, melanin would serve as a biomarker or indicator similar to the GFP but would be easily visible to the naked eye.

We have designed a light-inducible system in E. coli capable of manufacturing and secreting melanin. This biological machine is built from two standard biological parts, a melanin generator and a red light-inducible plasmid. This project has a very simple design: the melanin producing gene mel from Streptomyces is linked to the red-light inducer designed by UT Austin in the iGem 2006 competition.

Motivation

According to the American Cancer Society, skin cancer is the most common form of all cancers. It accounts for nearly half of all cancers in the United States. Due to its natural defense mechanism, skin must first be exposed to UV radiation before melanogenesis begins. Thus, we thought it would be convienient to be able to produce melanin in response to another harmless wavelength. This technology may, in the future, lead to treatments for albinism and a safe alternative for cosmetic tanning. Melanin may also be used as a natural indicator in the laboratory as well as an acoustic material. According to a study by Kono, et. al., melanin is capable of absorbing ultrasound.

Additionally, we would like to be able to use the melanin secretion system as an indicator in our ethylene detection project. Theoretically, more and more melanin would be secreted as various produce items become riper and produce more ethylene, causing the indicator to become darker on a gradient.

Background

In humans, melanin is found in the skin, hair, iris, adrenal gland, inner ear, and various pigment-producing regions of the brain.

Melanin is the primary determinant of skin color. The process of tanning originates in specialized cells called melanocytes. When stimulated by ultraviolet radiation, these cells produce melanin, which then migrates to the neighboring keratinocytes. The melanin accumulates above the receiving cells' nuclei in order to protect genetic material from from mutations caused by the sun's ionizing radiation.

Though there are many types of melanin, they are all polymers which contain derivatives of the amino acid tyrosine. Melanin is an aggregate of smaller component molecules; the various types of melanin have differing proportions and bonding patterns of the component molecules. Three types of melanin found in humans include eumelanin, pheomelanin, and neuromelanin. Eumelanin, which produces a brown-black color, is most common.

References



Ethylene Biosensor

NOTE: This project has been put on the back burner.


During one of our brainstorming sessions we were discussing possible biosensors and came up with a fairly practical project idea: an ethylene biosensor. Why sense ethylene? Mature fruit produce and release ethylene as they ripen. Measuring the concentration of gaseous ethylene on or near the surface of the ripening fruit would allow for the indirect measurement of its degree of ripeness.

References


Synthetic Biological Clock

NOTE: This project has been put on the back burner.


The synthetic biological clock was one of our earliest project ideas and involves the coupling of Elowitz and Leibler's repressilator system to some actuator such as fluorescence or aroma generation. We would like to link MIT's 2006 iGEM project to the repressilator and create an aroma therapy clock in addition to linking green, yellow and red fluorescent proteins to the repressilator to make a molecular traffic light. Future applications of controlled synthetic oscillatory systems include internal, autonomous drug delivery technology.

References


Cellular Photosignalling

NOTE: This project has been put on the back burner.


This system incorporates the idea of the repressilator on a larger scale, using three distinct cell types that are chemically isolated from each other (i.e., not sharing medium) and are each equipped with genes that enable bioluminescence and photosensing. Cell type 1 is bioluminescent at a particular wavelength (e.g., blue). Cell type 2 produces yellow bioluminescence unless it perceives blue light. Cell type 3 produces bioluminescence at yet another wavelength (e.g., green) unless it senses yellow light. Green light represses cell type 1 blue bioluminescence. Thus, engineered cell-cell communication with light is possible, creating a "wireless" repressilator system.

References


Directed Angiogenesis

NOTE: This project has been put on the back burner.


Angiogenesis is crucial in many biological and disease processes. Usually stufied in the context of uncontrolled tumor growth, it is also a necessary element of wound healing and tissue engineering. A major problem with the application of engineered tissues is a lack of perfusion of the essential nutrients to keep the tissue alive, healthy, and properly integrated with the surrounding natural tissue. We would like to develop a natural phototaxis system in engineered bacteria which can be exploited to induce angiogenesis at targeted areas within the body. These living machines are programmed so that once they have arrived, they produce and secrete their payload (e.g., VEGF) and can be compared to "cellular dumptrucks".

References

Expression of biologically active isoforms of the tumor angiogenesis factor VEGF in Escherichia coli by Siemeister et al.


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