Team:Lambert GA/Project

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Lambert iGEM Project
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       <h1>Our Project</h1>
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       <h2>Project Calendar:</h2>
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       <h1>Lambert iGEM Project</h1>
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       <h2>Biobricks:</h2>
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        Biobricks are defined as the “…standard for interchangeable parts, developed with a view to building biological systems in living cells” by the iGEM Parts website. Our contribution to CDA would be essential to biobrick because it will allow others to use the part in the future. The biobrick that is created will be mapped out and put into a database which is basically a free dictionary of biobricks. This compilation of biobricks allow others to use them in their experiments, expand on, or restructure. Without a database of biobricks, we would have a hard time expanding on our knowledge and would be continuously having to try to invent them for ourselves.
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       <h2>Jaemor Farms:</h2>
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    <h2>How we got our idea...</h2>
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        On November 25th, the Lambert iGEM team went to Jaemor Farms to interview the local farmers and producers of fresh fruits and vegetables. The main objective was to find out how spoiled produce really affected the agricultural industry, such as in amount of profit lost per year due to spoiled peaches. The team toured the farm, interviewed the farm’s owner, and had a great time eating fresh homemade desserts. We came back with some impressive statistics- in 2013, Jaemor Farms produced 700,350 pounds of peaches, 124,949 pounds of strawberries, 115,204 pounds of tomatoes, and 48,000 pounds of apples, among the over 300 different products produced. However, according to global stats, over 50% of fresh produce is lost to spoilage every year across the world. That translates to only half of all the peaches harvested that will make it to the grocery store. With this percentage in mind, the previous numbers cited now seem very small in retrospect. Hunger is a huge problem in less developed countries, and still plagues 1 out of every 6 person in the US. If the LHS iGEM team’s 2014 project is to succeed, it can potentially save world hunger in the long run by preventing food spoilage and increasing the “shelf-life” of fresh produce, which would then go to mean more food available for food aid or distribution to those that really need it.
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       <h2>Use of Cells for Chitin</h2>
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       <h2>What we did in the lab...</h2>
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        Chitin, which is mostly commonly found in the cell walls of fungi and the shells of crustaceans, is the second most abundant natural long-chain polymer. Due to the many industrial and medical applications of chitin’s deacetylated form, chitosan, the extraction of chitin from chemical and biological sources remains very important, especially to our experiment. Chitin and chitosan are mainly extracted through the demineralization, deproteinization, and other decomposition methods, of crustacean shells and fungi cell wall using acids and bases (mainly hydrochloric acid). The principal problem of this method is that dense acid concentrations cause hydrolysis (the cleavage of chemical bonds due the addition of water) of the polymer, which can potentially change the physical and chemical properties of the outcome, lowering the quality of the final product. This problem leads to more interest in more organic extractions through designer cells. Changing the plasmids of designer cells to express chitosan in the presence of chitin and chitin deacetylase allows for higher quality products, which allows more efficient applications and less acid-base dependency.
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      <h2>CDA Methodology and Results</h2>
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      <h3>pMAL Protein Expression Kit</h3>
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      <h3>Biobrick</h3>
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       <h2>How to get Chitosan Out of Cells</h2>
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       <h2>Assay Methodology and Results</h2>
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        Chitosan is a vital part of this project. Chitosan is produced from raw materials that naturally contain chitin. Chitosan’s biological sources are often crustacean shells, specifically shrimp shells, and its assay is greater than or equal to 75 percent (deacetylated). The manufacturing process of shrimp leaves behind a waste shell. This shell is then crushed to remove about 90 percent of the protein present. The crushed shells are washed with salt water and decalcified with a diluted form of hydrochloric acid. The shells are washed once again with recycled salt water and deproteinized with diluted sodium hydroxide. The treated shell produces chitin at this point. The chitin is put through deacetylation and treated with concentrated sodium hydroxide to produce chitosan.  
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       <h2> References</h2>
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      <p>Anitha, A., Sowmya, S., Kumar, P. T. S., Deepthi, S., Chennazhi, K. P., Ehrlich, H., . . . Jayakumar, R. Chitin and chitosan in selected biomedical applications. Progress in Polymer Science(0). doi: http://dx.doi.org/10.1016/j.progpolymsci.2014.02.008</p>
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      <p>Christodoulidou, A., Bouriotis, V., & Thireos, G. (1996). Two sporulation-specific chitin deacetylase-encoding genes are required for the ascospore wall rigidity of Saccharomyces cerevisiae. J Biol Chem, 271(49), 31420-31425.</p>
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      <p>Christodoulidou, A., Briza, P., Ellinger, A., & Bouriotis, V. (1999). Yeast ascospore wall assembly requires two chitin deacetylase isozymes. FEBS Lett, 460(2), 275-279. </p>
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      <p>Christodoulidou, A., Briza, P., Ellinger, A., & Bouriotis, V. (1999). Yeast ascospore wall assembly requires two chitin deacetylase isozymes. FEBS Lett, 460(2), 275-279. doi: http://dx.doi.org/10.1016/S0014-5793(99)01334-4</p>
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      <p>Jarmila, V., & Vavrikova, E. (2011). Chitosan derivatives with antimicrobial, antitumour and antioxidant activities--a review. Curr Pharm Des, 17(32), 3596-3607.</p>
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      <p>Liu, N., Chen, X.-G., Park, H.-J., Liu, C.-G., Liu, C.-S., Meng, X.-H., & Yu, L.-J. (2006). Effect of MW and concentration of chitosan on antibacterial activity of Escherichia coli. Carbohydrate Polymers, 64(1), 60-65. doi: http://dx.doi.org/10.1016/j.carbpol.2005.10.028</p>
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      <p>Martínez, J. P., Falomir, M. P., & Gozalbo, D. (2001). Chitin: A Structural Biopolysaccharide eLS: John Wiley & Sons, Ltd.</p>
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      <p>Martinou, A., Koutsioulis, D., & Bouriotis, V. (2003). Cloning and expression of a chitin deacetylase gene (CDA2) from Saccharomyces cerevisiae in Escherichia coli: Purification and characterization of the cobalt-dependent recombinant enzyme. Enzyme and Microbial Technology, 32(6), 757-763. doi: http://dx.doi.org/10.1016/S0141-0229(03)00048-6</p>
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      <p>Moussa, S. H., Tayel, A. A., & Al-Turki, A. I. (2013). Evaluation of fungal chitosan as a biocontrol and antibacterial agent using fluorescence-labeling. International Journal of Biological Macromolecules, 54(0), 204-208. doi:http://dx.doi.org/10.1016/j.ijbiomac.2012.12.029</p>
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      <p>Tsigos, I., Martinou, A., Kafetzopoulos, D., & Bouriotis, V. (2000). Chitin deacetylases: new, versatile tools in biotechnology. Trends in Biotechnology, 18(7), 305-312. doi: http://dx.doi.org/10.1016/S0167-7799(00)01462-1</p>
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      <p>Zakrzewska, A., Boorsma, A., Brul, S., Hellingwerf, K. J., & Klis, F. M. (2005). Transcriptional response of Saccharomyces cerevisiae to the plasma membrane-perturbing compound chitosan. Eukaryot Cell, 4(4), 703-715. doi: 10.1128/ec.4.4.703-715.2005</p>
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      <p>Zhang, H., Li, R., & Liu, W. (2011). Effects of Chitin and Its Derivative Chitosan on Postharvest Decay of Fruits: A Review. International Journal of Molecular Sciences, 12(2), 917-934.</p>
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      <p> (Anitha et al.; Christodoulidou, Bouriotis, & Thireos, 1996; A. Christodoulidou, P. Briza, A. Ellinger, & V. Bouriotis, 1999; Anna Christodoulidou, Peter Briza, Adi Ellinger, & Vassilis Bouriotis, 1999; Jarmila & Vavrikova, 2011; Liu et al., 2006; Martínez, Falomir, & Gozalbo, 2001; Martinou, Koutsioulis, & Bouriotis, 2003; Moussa, Tayel, & Al-Turki, 2013; Tsigos, Martinou, Kafetzopoulos, & Bouriotis, 2000; Zakrzewska, Boorsma, Brul, Hellingwerf, & Klis, 2005; Zhang, Li, & Liu, 2011)</p>
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    <p>Lõoke M, Kristjuhan K, Kristjuhan A. Extraction of genomic DNA from yeasts for PCR-based applications..  doi:10.2144/000113672. PubMed PMID: 21548894.</p>
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    <p>El Hadrami, A.; Adam, L.R.; El Hadrami, I.; Daayf, F. Chitosan in Plant Protection. Mar. Drugs 2010, 8, 968-987.</p>
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Latest revision as of 01:11, 21 June 2014

Our Project

Project Calendar:

How we got our idea...

What we did in the lab...

CDA Methodology and Results

pMAL Protein Expression Kit

Biobrick

Assay Methodology and Results

References

Anitha, A., Sowmya, S., Kumar, P. T. S., Deepthi, S., Chennazhi, K. P., Ehrlich, H., . . . Jayakumar, R. Chitin and chitosan in selected biomedical applications. Progress in Polymer Science(0). doi: http://dx.doi.org/10.1016/j.progpolymsci.2014.02.008

Christodoulidou, A., Bouriotis, V., & Thireos, G. (1996). Two sporulation-specific chitin deacetylase-encoding genes are required for the ascospore wall rigidity of Saccharomyces cerevisiae. J Biol Chem, 271(49), 31420-31425.

Christodoulidou, A., Briza, P., Ellinger, A., & Bouriotis, V. (1999). Yeast ascospore wall assembly requires two chitin deacetylase isozymes. FEBS Lett, 460(2), 275-279.

Christodoulidou, A., Briza, P., Ellinger, A., & Bouriotis, V. (1999). Yeast ascospore wall assembly requires two chitin deacetylase isozymes. FEBS Lett, 460(2), 275-279. doi: http://dx.doi.org/10.1016/S0014-5793(99)01334-4

Jarmila, V., & Vavrikova, E. (2011). Chitosan derivatives with antimicrobial, antitumour and antioxidant activities--a review. Curr Pharm Des, 17(32), 3596-3607.

Liu, N., Chen, X.-G., Park, H.-J., Liu, C.-G., Liu, C.-S., Meng, X.-H., & Yu, L.-J. (2006). Effect of MW and concentration of chitosan on antibacterial activity of Escherichia coli. Carbohydrate Polymers, 64(1), 60-65. doi: http://dx.doi.org/10.1016/j.carbpol.2005.10.028

Martínez, J. P., Falomir, M. P., & Gozalbo, D. (2001). Chitin: A Structural Biopolysaccharide eLS: John Wiley & Sons, Ltd.

Martinou, A., Koutsioulis, D., & Bouriotis, V. (2003). Cloning and expression of a chitin deacetylase gene (CDA2) from Saccharomyces cerevisiae in Escherichia coli: Purification and characterization of the cobalt-dependent recombinant enzyme. Enzyme and Microbial Technology, 32(6), 757-763. doi: http://dx.doi.org/10.1016/S0141-0229(03)00048-6

Moussa, S. H., Tayel, A. A., & Al-Turki, A. I. (2013). Evaluation of fungal chitosan as a biocontrol and antibacterial agent using fluorescence-labeling. International Journal of Biological Macromolecules, 54(0), 204-208. doi:http://dx.doi.org/10.1016/j.ijbiomac.2012.12.029

Tsigos, I., Martinou, A., Kafetzopoulos, D., & Bouriotis, V. (2000). Chitin deacetylases: new, versatile tools in biotechnology. Trends in Biotechnology, 18(7), 305-312. doi: http://dx.doi.org/10.1016/S0167-7799(00)01462-1

Zakrzewska, A., Boorsma, A., Brul, S., Hellingwerf, K. J., & Klis, F. M. (2005). Transcriptional response of Saccharomyces cerevisiae to the plasma membrane-perturbing compound chitosan. Eukaryot Cell, 4(4), 703-715. doi: 10.1128/ec.4.4.703-715.2005

Zhang, H., Li, R., & Liu, W. (2011). Effects of Chitin and Its Derivative Chitosan on Postharvest Decay of Fruits: A Review. International Journal of Molecular Sciences, 12(2), 917-934.

(Anitha et al.; Christodoulidou, Bouriotis, & Thireos, 1996; A. Christodoulidou, P. Briza, A. Ellinger, & V. Bouriotis, 1999; Anna Christodoulidou, Peter Briza, Adi Ellinger, & Vassilis Bouriotis, 1999; Jarmila & Vavrikova, 2011; Liu et al., 2006; Martínez, Falomir, & Gozalbo, 2001; Martinou, Koutsioulis, & Bouriotis, 2003; Moussa, Tayel, & Al-Turki, 2013; Tsigos, Martinou, Kafetzopoulos, & Bouriotis, 2000; Zakrzewska, Boorsma, Brul, Hellingwerf, & Klis, 2005; Zhang, Li, & Liu, 2011)

Lõoke M, Kristjuhan K, Kristjuhan A. Extraction of genomic DNA from yeasts for PCR-based applications.. doi:10.2144/000113672. PubMed PMID: 21548894.

El Hadrami, A.; Adam, L.R.; El Hadrami, I.; Daayf, F. Chitosan in Plant Protection. Mar. Drugs 2010, 8, 968-987.

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