Difference between revisions of "Team:USP UNIFESP-Brazil/Results"

 
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<h2> Description</h2>
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<h2> Results</h2>
 
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<p class="black">Spider silk is an amazing bionanomaterial due to its exceptional features. It exhibits high tensile strength, high fracture resistance, high elasticity and it has biocompatibility and low degradability.
 
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Some studies show silk can be compared to a synthetic polymer called Kevlar, that is made of aramid and is used to make body armor (Lewis). Silks are polymers composed of proteins. These proteins and their genes present specific repetitive sequences that are associated with silk properties, making it possible to handle it in order to obtain the most suitable material for each application. Moreover, some studies suggest that the terminal domains of silk proteins play important roles in the polymerization process. In this way, it can be possible to add N- and C- terminal domains in several interesting proteins or motifs and spun it with native proteins to obtain a customized silk.</p>
 
  
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                                <p class="black">The size of genes, their repetitive sequences and high content of Cytosine and Guanine establish a challenge to many expression systems. However Chlamydomonas reinhardtii has naturally high CG content on its genome and it could be able to deal with this problem, it can also perform post translational modifications and it can secrete complex proteins, easing the purification process. Furthermore, it exhibits low cost production, rapid growth, scalability and stable transgenic line generation, all desired characteristics to an expression system (Wijffels, Kruse, and Hellingwerf; Rosenberg et al.). It is important to highlight the low cost of microalgae cultivation, while production of antibodies in mammalian cells presents an average cost about US$150.00/per gram of raw materials and plants US$0.05/per gram (Dove), Maylfield has estimated that microalgae can reach US$ 0.002/liter (Rosenberg et al.; Mayfield, Franklin, and Lerner). Chlamydomonas reinhardtii also is Generally Recognized As Safe (GRAS), that is, it has low risk of being contaminated by virus, prions and bacterial endotoxins (Mayfield et al.). Easy purification and low risk of contamination are very significant issues when we are talking about making products to biomedical applications.</p>  
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<p class=black>Although we had to do a lot of unexpected troubleshooting, we managed to achieve some satisfying results at iGEM 2016! Check our list of main results here or go through our <a href=https://2016.igem.org/Team:USP_UNIFESP-Brazil/Notebook>Lab Notebook </a> for a REALLY complete view! </p>
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<p class=black>Doing iGEM in labs without an established molecular biology line was challenging, and although some features may seem small, they were surely fruits of hard work!</p>
  
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<img src="https://static.igem.org/mediawiki/2016/5/59/T--USP_UNIFESP-Brazil--cassetechlamydomonas.png" style="margin-bottom:20px; margin-top:0px; width=110%; align=center" />
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<h4 class= black><b>Positive results</b></h4>
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<p class="fig-label">Figure 1. Cassette construction to be inserted in C. renhardtii nuclear genome. Promoter hsp70A/rbcs2: fusion of the promoters hsp70A and rbcs2 (Eichler-Stahlberg et al.; Schroda, Blöcker, and Beck). Sh-Ble: resistance gene to Zeomycin. 2A: self-cleavage peptide from Foot and Mouth Disease Virus (FMDV) (Rasala et al.). SP: secretion signal peptide of the gene Ars1. GOI: gene of interest. His: histidine tag. RbcS2 3’ UTR: terminal sequence of the gene RbcS2 (Fuhrmann et al.). Introns were added as the figure shows (Eichler-Stahlberg et al.; Lumbreras et al.).</p>
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                                <p class="black">Our project was inspired by the UCLA’s projects presented at iGEM in 2014 and 2015 about synthetic silks. Like we said above, silks are very interesting material but one of the main problems is dealing with its high content of Cytosine and Guanine. Most of the expression systems are not able to deal with that, however we have known Chlamydomonas reinhardtii has naturally high CG content which makes it interesting as an expression chassis. One of UCLA’s projects was called Silk Functionalization: Developing the Next Generation of  Performance Fibers. The team has created a genetic construct using the Green Fluorescent Protein (GFP) inserted between N- and C- terminal domains of Bombyx mori’s silk to express proteins able to bind to native silk proteins. When this customized GFPs and native proteins were mixed and spun they were able to recognize each other by the terminal domains, making a fluorescent silk.</p>  
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<!--- <li class=black> We were able to purify a <i>Pfu</i>X7 polymerase and standardize a working PCR protocol </li> --->
  
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<li class=black style="font-size:20px" >We were able to design and clone in pSB1C3 a protein domain part (<a href= http://parts.igem.org/Part:BBa_K2136002>BBa_K2136002</a>) and a working gene expression cassete for microalgae (<a href=http://parts.igem.org/Part:BBa_K2136010>BBa_K2136010</a>) ! </li>
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<li class=black>We could efficiently transform and characterize the expression of a codon optimized version of mCherry in Chlamydomonas reinhardtii by many methods, such as fluorescence spectrum, FPLC elution spectrum, DIY fluorescence and plate reading throughout cell growth! You can check this all in our <a href = https://2016.igem.org/Team:USP_UNIFESP-Brazil/Description>Description</a> and <a href = https://2016.igem.org/Team:USP_UNIFESP-Brazil/Proof>Proof of Concept</a> pages!
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                                <p class="black">From this idea we thought: “Silk is a very interesting material and could be expressed in Chlamydomonas reinhardtii, a model organism that has many advantages and that remains underexplored. What could be put in place of a GFP to express in microalgae? What biomolecule could take advantage of this amazing silk feature? It has to work while immobilized... Why not enzymes? There are many studies about enzymes immobilization, enzymes are very appropriate and useful in many applications around the world!”. But we knew it could not to be any enzyme linked to silk, we knew it need to address technical, social and economic issues. So we read that spider silk has been studied to many biomedical applications, like the treatment of burn victims. Then we studied about burns in order to find an interesting enzyme that could solve some problem and we learned that one of the most important problems affecting burn victims is sepsis. In this way, we sought for antimicrobial enzymes and we found the endolysins. Endolysins are very interesting enzymes because they are able to combat multiresistant bacterias and they are specific, avoiding problems like the antibiotic resistance.</p>  
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<li class=black> We could also multimerize our synthetic MaSp1 Type2 construct, 2-mer, at the DNA level, achieving constructs with 4-mer and 8-mer ! This multimerization was done twice trhough simple “cut-and-paste” reactions with restriction and ligation. You can read more about this at the <a href=https://2016.igem.org/Team:USP_UNIFESP-Brazil/Experiments> Experiments</a> page!</li>
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                                <p class="black">So we decided to make a project about spider silk production in microalgae, creating possibilities to future works with silk proteins from this amazing organism model, like the association between them and endolysins by UCLA’s approach in order to make an antimicrobial silk to be applied on burn victims to combat sepsis.</p>
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<h4 class=black ><b>Negative results</b></h4>
  
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<ul><li class=black> We tried to multimerize our synthetic  MaSp1 Type2 construct through USER fusion(Nour-Eldin, Fernando, and Halkier), but were not able to get proper clones with multimers, as expected in our <a href=https://2016.igem.org/Team:USP_UNIFESP-Brazil/Experiments> Experiments</a> page.  We had difficulties regarding the primers, having to wait until September before having proper ones available here, so we lacked the time for proper troubleshooting. However, we still believe it is a valid option for the assembly of multiple fragments (and we will continue to try it at our lab!). </li>
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<li class=black> We could not clone and detect the enzybiotics in a expression plasmid, although we tried it repeatedly, as can be seen in in our<a href=https://2016.igem.org/Team:USP_UNIFESP-Brazil/Notebook> Lab Notebook </a> . This could be due to some toxicity of the parts as well as high background/inefficiency of cells. A good method for screening enzybiotics that we did not have the time to try would be testing the <i>E. coli</i> lysate or the <i>C. reinhardtii</i> supernatant against <i>Staphylococcus aureus</i> cultures in 96 well plates. Efficient clones would increase cell lysis and decrease the OD600. </li>
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<h2>References</h2>
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<p class="black">Eichler-Stahlberg, Alke et al. “Strategies to Facilitate Transgene Expression in Chlamydomonas Reinhardtii.” Planta 229.4 (2009): 873–883. Print.</p>
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<p class="black">Fuhrmann, Markus et al. “A Synthetic Gene Coding for the Green Fluorescent Protein (GFP) Is a Versatile Reporter in Chlamydomonas Reinhardtii.” The Plant journal: for cell and molecular biology 19.3 (1999): 353–361. Print.</p>
 
  
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<p class="black">Lewis, Randolph V. “Spider Silk: Ancient Ideas for New Biomaterials.” Chemical reviews 106.9 (2006): 3762–3774. Print.</p>
 
  
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<p class="black">Lumbreras, Victoria et al. “Efficient Foreign Gene Expression in Chlamydomonas Reinhardtii Mediated by an Endogenous Intron.” The Plant journal: for cell and molecular biology 14.4 (1998): 441–447. Print.</p>
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<h4 class=black><b> References: </b></h4>
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<p class=black>Nour-Eldin, Hussam H., Geu-Flores Fernando, and Barbara A. Halkier. “USER Cloning and USER Fusion: The Ideal Cloning Techniques for Small and Big Laboratories.” Methods in Molecular Biology. N.p., 2010. 185–200. Print.<p>
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<p class="black">Mayfield, S. P., S. E. Franklin, and R. A. Lerner. “Expression and Assembly of a Fully Active Antibody in Algae.” Proceedings of the National Academy of Sciences 100.2 (2003): 438–442. Print.</p>
 
  
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<p class="black">Mayfield, Stephen P. et al. “Chlamydomonas Reinhardtii Chloroplasts as Protein Factories.” Current opinion in biotechnology 18.2 (2007): 126–133. Print.</p>
 
  
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<p class="black">Rasala, Beth A. et al. “Robust Expression and Secretion of Xylanase1 in Chlamydomonas Reinhardtii by Fusion to a Selection Gene and Processing with the FMDV 2A Peptide.” PloS one 7.8 (2012): e43349. Print.</p>
 
  
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<p class="black">Rosenberg, Julian N. et al. “A Green Light for Engineered Algae: Redirecting Metabolism to Fuel a Biotechnology Revolution.” Current opinion in biotechnology 19.5 (2008): 430–436. Print.</p>
 
  
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<p class="black">Schroda, M., D. Blöcker, and C. F. Beck. “The HSP70A Promoter as a Tool for the Improved Expression of Transgenes in Chlamydomonas.” The Plant journal: for cell and molecular biology 21.2 (2000): 121–131. Print.</p>
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<p class="black">Wijffels, René H., Olaf Kruse, and Klaas J. Hellingwerf. “Potential of Industrial Biotechnology with Cyanobacteria and Eukaryotic Microalgae.” Current opinion in biotechnology 24.3 (2013): 405–413. Print.</p>
 
  
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Latest revision as of 08:56, 19 October 2016

AlgAranha Team USP_UNIFESP-Brazil

iGEM 2016

Results

Although we had to do a lot of unexpected troubleshooting, we managed to achieve some satisfying results at iGEM 2016! Check our list of main results here or go through our Lab Notebook for a REALLY complete view!

Doing iGEM in labs without an established molecular biology line was challenging, and although some features may seem small, they were surely fruits of hard work!

Positive results

  • We were able to design and clone in pSB1C3 a protein domain part (BBa_K2136002) and a working gene expression cassete for microalgae (BBa_K2136010) !
  • We could efficiently transform and characterize the expression of a codon optimized version of mCherry in Chlamydomonas reinhardtii by many methods, such as fluorescence spectrum, FPLC elution spectrum, DIY fluorescence and plate reading throughout cell growth! You can check this all in our Description and Proof of Concept pages!
  • We could also multimerize our synthetic MaSp1 Type2 construct, 2-mer, at the DNA level, achieving constructs with 4-mer and 8-mer ! This multimerization was done twice trhough simple “cut-and-paste” reactions with restriction and ligation. You can read more about this at the Experiments page!

Negative results

  • We tried to multimerize our synthetic MaSp1 Type2 construct through USER fusion(Nour-Eldin, Fernando, and Halkier), but were not able to get proper clones with multimers, as expected in our Experiments page. We had difficulties regarding the primers, having to wait until September before having proper ones available here, so we lacked the time for proper troubleshooting. However, we still believe it is a valid option for the assembly of multiple fragments (and we will continue to try it at our lab!).
  • We could not clone and detect the enzybiotics in a expression plasmid, although we tried it repeatedly, as can be seen in in our Lab Notebook . This could be due to some toxicity of the parts as well as high background/inefficiency of cells. A good method for screening enzybiotics that we did not have the time to try would be testing the E. coli lysate or the C. reinhardtii supernatant against Staphylococcus aureus cultures in 96 well plates. Efficient clones would increase cell lysis and decrease the OD600.

References:

Nour-Eldin, Hussam H., Geu-Flores Fernando, and Barbara A. Halkier. “USER Cloning and USER Fusion: The Ideal Cloning Techniques for Small and Big Laboratories.” Methods in Molecular Biology. N.p., 2010. 185–200. Print.