Team:Vanderbilt/PartsSubPageBuilder

From 2014.igem.org

(Difference between revisions)
(Created page with " function PartsSubPageBuilder() { var subPage = new SubPageBuilder(); subPage.maxSubPage = 3; subPage.getMaxSubPage = function() { return subPage.maxSubPage;...")
 
Line 1: Line 1:
-
 
function PartsSubPageBuilder() {
function PartsSubPageBuilder() {
     var subPage = new SubPageBuilder();
     var subPage = new SubPageBuilder();
Line 79: Line 78:
     subPage.createBBa_K1322231Right = function() {
     subPage.createBBa_K1322231Right = function() {
-
         var img1 = subPage.createPhoto("VU_Santalene_biosynthesis_path.gif",
+
         var img1 = subPage.createPhoto("http://parts.igem.org/wiki/images/f/f4/VU_Santalene_biosynthesis_path.gif",
             "Santalene Biosynthesis Path",
             "Santalene Biosynthesis Path",
             450, 122.25,
             450, 122.25,
Line 86: Line 85:
         img1.style.marginBottom = "1em";
         img1.style.marginBottom = "1em";
-
         var img2 = subPage.createPhoto("VU_San_psb_confirmation.jpg",
+
         var img2 = subPage.createPhoto("http://parts.igem.org/wiki/images/6/62/Vanderbilt_San_psb.jpg",
             "San PSB Confirmation",
             "San PSB Confirmation",
             500, 290,
             500, 290,
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     subPage.createpVU14006Right = function() {
     subPage.createpVU14006Right = function() {
-
         var img3 = subPage.createPhoto("VU_pVU14006.jpg",
+
         var img3 = subPage.createPhoto("http://parts.igem.org/wiki/images/1/13/Vanderbilt_pVU14006.jpg",
             "pVU14006",
             "pVU14006",
             698, 448,
             698, 448,
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     subPage.createBBa_K1322001SabineneSynthaseRight = function() {
     subPage.createBBa_K1322001SabineneSynthaseRight = function() {
-
         var img3 = subPage.createPhoto("Sabinene_synthesis_pathway.gif",
+
         var img3 = subPage.createPhoto("http://parts.igem.org/wiki/images/9/9c/Sabinene_synthesis_pathway.gif",
             "Sabinene Synthesis Pathway",
             "Sabinene Synthesis Pathway",
             597, 192,
             597, 192,

Latest revision as of 22:41, 25 January 2015

function PartsSubPageBuilder() {

   var subPage = new SubPageBuilder();
   subPage.maxSubPage = 3;
   subPage.getMaxSubPage = function() {
       return subPage.maxSubPage;
   };
   subPage.createSubPage = function(subPageNum) {
       switch(subPageNum){
           case 1:
               subPage.createBBa_K1322231Left();
               subPage.createBBa_K1322231Right();
               break;
           case 2:
               subPage.createpVU14006Left();
               subPage.createpVU14006Right();
               break;
           case 3:
               subPage.createBBa_K1322001SabineneSynthaseLeft();
               subPage.createBBa_K1322001SabineneSynthaseRight();
               break;
       }
   };
   subPage.createBBa_K1322231Left = function() {
       var header = document.createElement("header");
       header.appendChild(document.createTextNode("BBa_K1322231: Optimized Santalene Synthase"));
       var text1 =
           "BBa_K1322231 is a codon-optimized biobrick part encoding the gene for alpha-santalene synthase (E" +
           "C 4.2.3.82). The enzyme catalyze the conversion of the common isoprenoid intermediate farnesyl pyrophospha" +
           "te (FPP) into the sesquiterpene (+)-alpha-santelene in a single step. Traces of (-)-beta-santalene and ber" +
           "gamontene have previously been shown to be produced by this enzyme as well. ";
       var text2 =
           "The gene, derived from a relative of the exotic sandalwood tree, has been demonstrated to produce function" +
           "al terpene product in both yeast (Scalcinati et al 2012) and E. coli (data pending). This is possible due to" +
           " several endogenous pathways that produce FPP as an intermediate, including the MEV and MEP pathways.";
       var text3 =
           "In addition to being a prized fragrance, with what is often described as a warm, sweet woody scent, the " +
           "sandalwood oil has been investigated for a number of other practical applications, including as a chemopr" +
           "otective against carcinogenesis (Banaerjee, Ecavade, and Rao 1993) and inhibitors of viral reproduction " +
           "(Koch et al 2008). ";
       var text4 =
           "Our biobrick has additional functionality added to it beyond just the coding sequence for santalene synth" +
           "ase. Immediately before the start codon is a yeast consensus sequence to permit efficient translation of " +
           "the gene transcript in S. cerevisiae. Toward the end of the sequence there is also a sequence added inside" +
           " the reading frame that encodes for a strep tag. The strep tag is a small, eight amino acid epitope tag th" +
           "at is translated onto the C terminus of the recombinant polypeptide. Its small size ensures that it will " +
           "not likely interfere with protein function, yet in most situations it is still prominent enough that the " +
           "common molecule streptavidin (in the form of Strep-tactin) can recognize and bind to it. Because anti-str" +
           "eptavidin antibodies are widely available, this opens the way for a range of possibilities, including sim" +
           "ple confirmation assays of synthase expression by western blotting and quick purification of the synthase" +
           " enzyme. ";
       var text5 =
           "We confirmed our part succesfully ligated into pSB1C3 by a diagnostic digest of miniprepped plasmid. While " +
           "none of the samples had the santalene insert cleanly cut out, two observations were made which confirmed th" +
           "at in the fourth miniprepped sample, santalene had been successfully integrated. First, the size of the uncu" +
           "t fourth plasmid is equal to pSB1C3 plus the santalene synthase gene. Second, it was later noticed that the" +
           " plasmids were grown in a non-demethylated strain of E. coli. This would explain why no inserts were cut ou" +
           "t, since one enzyme used, ApaI, was dam methylation sensitive. This would also explain why the digested prod" +
           "uct is consistently larger than the undigested, since the linearized DNA should be above the uncut supercoil" +
           "ed form (Tirabassi 2014).";
       var p1 = subPage.createP(text1);
       var p2 = subPage.createP(text2);
       var p3 = subPage.createP(text3);
       var p4 = subPage.createP(text4);
       var p5 = subPage.createP(text5);
       leftPageBuilder.appendChild(header);
       leftPageBuilder.appendChild(p1);
       leftPageBuilder.appendChild(p2);
       leftPageBuilder.appendChild(p3);
       leftPageBuilder.appendChild(p4);
       leftPageBuilder.appendChild(p5);
   };
   subPage.createBBa_K1322231Right = function() {
       var img1 = subPage.createPhoto("VU_Santalene_biosynthesis_path.gif",
           "Santalene Biosynthesis Path",
           450, 122.25,
           "Santalene Biosynthesis Path");
       img1.style.margin = "auto";
       img1.style.marginBottom = "1em";
       var img2 = subPage.createPhoto("Vanderbilt_San_psb.jpg",
           "San PSB Confirmation",
           500, 290,
           "San PSB Confirmation");
       img2.style.margin = "auto";
       img2.style.marginBottom = "1em";
       rightPageBuilder.appendChild(img1);
       rightPageBuilder.appendChild(img2);
   };
   subPage.createpVU14006Left = function() {
       var header = document.createElement("header");
       header.appendChild(document.createTextNode("pVU14006"));
       var text1 = "As a shuttle vector, pVU14006 is capable of expression both in E. coli and S. cerevisiae. It has r" +
           "esistance markers to both ampicillin and kanomycin, making selection convenient in both bacteria and yeas" +
           "t. For cloning in bacteria, it has a prokaryotic origin of replication taken out of pUC19. Two regions of" +
           " base pair homology with the S. cerevisiae genome allow it to efficiently integrate into the yeast genome" +
           ". Genomic integration has a number of advantages, including the potential for increased product yield. Th" +
           "ere is a multiple cloning site with a range of different restriction enzymes to make the plasmid compatib" +
           "le with almost all of the most commonly used restriction enzymes, including those used in RFC10 compatibl" +
           "e biobricks.";
       var text2 = "A Gal1 inducible promoter is upstream of where the protein coding gene would be inserted. This prom" +
           "oter is strongly repressed by glucose and further allows the protein coding gene to be transcriptionally up-" +
           "regulated upon the addition of galactose. Changing which of these two carbohydrates are present in the growt" +
           "h media therefore gives an enormous degree of control over the level of gene expression. Finally, a CYC1 te" +
           "rminator is present to ensure proper termination of transcription.";
       var p1 = subPage.createP(text1);
       var p2 = subPage.createP(text2);
       leftPageBuilder.appendChild(header);
       leftPageBuilder.appendChild(p1);
       leftPageBuilder.appendChild(p2);
   };
   subPage.createpVU14006Right = function() {
       var img3 = subPage.createPhoto("Vanderbilt_pVU14006.jpg",
           "pVU14006",
           698, 448,
           "pVU14006");
       img3.style.margin = "auto";
       img3.style.marginBottom = "1em";
       rightPageBuilder.appendChild(img3);
   };
   subPage.createBBa_K1322001SabineneSynthaseLeft = function() {
       var header1 = document.createElement("header");
       header1.appendChild(document.createTextNode("BBa_K1322001- All-RFC Compatible Fluorescent Oscillator"));
       var header2 = document.createElement("header");
       header2.appendChild(document.createTextNode("Sabinene Synthase"));
       var rheader = document.createElement("header");
       rheader.appendChild(document.createTextNode("References"));
       rheader.style.fontSize = "1em";
       var text1 = "As part of our collaboration with Vanderbilt Microfluidics, we were working with the existing bio" +
           "brick K546546, which encodes a self-regulating fluorescent oscillating system. We wanted to make this par" +
           "t compatible with all major RFC standards, and did so by using our site-directed mutagenesis kit with spe" +
           "cially designed primers. The sequence changes were designed so that the part should function equally well" +
           " as it did before. For a gel showing confirmation, please see our lab notebook under October 11th.";
       var text2 = "Although it is not yet RFC10 compatible and thus will not appear in the registry until later, we h" +
           "ave successfully extracted the gene for sabinene synthase out of raw plant RNA. Following successful mutag" +
           "enesis, we plan to add the biobrick prefix and suffixes so that this part can be made available at the reg" +
           "istry for other iGEM teams to use.";
       var ref1 = "Scalcinati et al.: Combined metabolic engineering of precursor and co-factor supply to increa" +
           "se α-santalene production by Saccharomyces cerevisiae. Microbial Cell Factories 2012 11:117";
       var ref2 = "Banerjee, Ecavade and Rao: Modulatory influence of sandalwood oil on mouse hepatic glutathione S-tr" +
           "ansferase activity and acid soluble sulphydryl level. Cancer Letters, 68 (1993) 105 - 109 Koch et al: Inhi" +
           "bitory effect of essential oils against herpes simplex virus type 2. Phytomedicine 2008;15(1-2):71-8. ";
       var ref3 = "Rebecca Tirabassi, How to identify supercoils, nicks and circles in plasmid preps. Bitesizebio. Oc" +
           "tober 8, 2014.";
       var p1 = subPage.createP(text1);
       var p2 = subPage.createP(text2);
       var p_ref1 = subPage.createP(ref1);
       var p_ref2 = subPage.createP(ref2);
       var p_ref3 = subPage.createP(ref3);
       p_ref1.style.fontStyle = "italic";
       p_ref2.style.fontStyle = "italic";
       p_ref3.style.fontStyle = "italic";
       p_ref1.style.fontSize = "0.75em";
       p_ref2.style.fontSize = "0.75em";
       p_ref3.style.fontSize = "0.75em";
       leftPageBuilder.appendChild(header1);
       leftPageBuilder.appendChild(p1);
       leftPageBuilder.appendChild(header2);
       leftPageBuilder.appendChild(p2);
       leftPageBuilder.appendChild(rheader);
       leftPageBuilder.appendChild(p_ref1);
       leftPageBuilder.appendChild(p_ref2);
       leftPageBuilder.appendChild(p_ref3);
   };
   subPage.createBBa_K1322001SabineneSynthaseRight = function() {
       var img3 = subPage.createPhoto("Sabinene_synthesis_pathway.gif",
           "Sabinene Synthesis Pathway",
           597, 192,
           "Sabinene Synthesis Pathway");
       img3.style.margin = "auto";
       img3.style.marginBottom = "1em";
       rightPageBuilder.appendChild(img3);
   };
   return subPage;

}