Template:Team:Vanderbilt/CSS

From 2014.igem.org

(Difference between revisions)
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</style>
</style>
 +
<script>
 +
/**
 +
* Created by Anna Hwang on 1/15/2015.
 +
*/
 +
 +
var leftPageBuilder = document.getElementById("left_page");
 +
var rightPageBuilder = document.getElementById("right_page");
 +
 +
function SubPageBuilderFactory() {
 +
    this.makeBuilder = function(pageNum) {
 +
        switch(pageNum) {
 +
            case 3:
 +
                return new ProjectSubPageBuilder();
 +
            case 4:
 +
                return new PartsSubPageBuilder();
 +
            case 5:
 +
                return new NotebookSubPageBuilder();
 +
            case 7:
 +
                return new AttributionsSubPageBuilder();
 +
            default:
 +
                return new SubPageBuilder();
 +
        }
 +
    };
 +
}
 +
 +
/**@class SubPageBuilder
 +
* @description Creates the correct SubPage based on the SubPageNum input and the pageNum passed to it upon
 +
* construction **/
 +
function SubPageBuilder() {
 +
    var maxSubPage = 1;
 +
 +
    this.getMaxSubPage = function() {
 +
        document.getElementById("igem_header").innerHTML = "for some reason here";
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        return maxSubPage;
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    };
 +
 +
    this.createSubPage = function (subPageNum) {};
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    this.addMultLI = function(ul, arr) {
 +
        for(var i = 0; i < arr.length; i++) {
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            var tmp = document.createElement("LI");
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            tmp.appendChild(document.createTextNode(arr[i]));
 +
            ul.appendChild(tmp);
 +
        }
 +
    };
 +
 +
    this.insertTextRow = function(table, names){
 +
        var row = table.insertRow();
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        row.style.textAlign="center";
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        for (var i = 0; i < names.length; i++) {
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            var str = row.insertCell(i);
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                str.innerHTML = names[i];
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        }
 +
    };
 +
 +
    this.createRowFromArray = function(table, elements) {
 +
        var row = table.insertRow();
 +
        row.style.textAlign="center";
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        for (var i = 0; i < elements.length; i++) {
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            var str = row.insertCell(i);
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            str.appendChild(elements[i]);
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        }
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    };
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 +
    this.createPhoto = function(src, alt, w, h, para) {
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        var img = document.createElement("img");
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        img.src = src;
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        img.alt = alt;
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        img.width = w;
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        img.height = h;
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        img.style.margin = "0px";
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 +
        var photo = document.createElement("div");
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        photo.style.backgroundColor = "floralwhite";
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        photo.style.position = "relative";
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        photo.style.display = "inline-block";
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        photo.style.width = img.width + "px";
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        photo.style.height = (img.height + 70) + "px";
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        photo.style.padding = "0.5em";
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        photo.style.margin = "1%";
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        photo.style.boxShadow = "0 0 3px rgba(0,0,0,0.3)";
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 +
        var text = document.createElement("p");
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        text.appendChild(document.createTextNode(para));
 +
        text.style.height = "65px";
 +
        text.style.textAlign = "right";
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        text.style.overflow = "auto";
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        text.style.fontStyle = "italic";
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        text.style.margin = "2px";
 +
 +
        photo.appendChild(img);
 +
        photo.appendChild(text);
 +
        return photo;
 +
    };
 +
 +
    this.createP = function(str){
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        document.getElementById("igem_header").innerHTML = "reached createP";
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        var p = document.createElement("p");
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        p.appendChild(document.createTextNode(str));
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        return p;
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    };
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 +
    this.createPlainIMG = function(src, alt, w, h){
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        var img = document.createElement("img");
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        img.src = src;
 +
        img.alt =  alt;
 +
        img.width = w;
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        img.height = h;
 +
        return img;
 +
    };
 +
 +
    this.createIMG = function(src, alt, w, h, f){
 +
        var img = document.createElement("img");
 +
        img.src = src;
 +
        img.alt =  alt;
 +
        img.width = w;
 +
        img.height = h;
 +
        img.className = "var_page_img";
 +
        img.style.float = f;
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        img.style.marginLeft = "1%";
 +
        img.style.marginRight = "1%";
 +
 +
        return img;
 +
    };
 +
}
 +
 +
function ProjectSubPageBuilder() {
 +
    var subPage = new SubPageBuilder();
 +
    subPage.maxSubPage = 5;
 +
 +
    document.getElementById("igem_header").innerHTML = "subPage.prototype = SbPageBuilder? : " + (Object.getPrototypeOf(subPage) == SubPageBuilder).toString();
 +
 +
    subPage.getMaxSubPage = function() {
 +
        return subPage.maxSubPage;
 +
    };
 +
 +
    subPage.createSubPage = function (subPageNum) {
 +
        switch(subPageNum){
 +
            case 1:
 +
                subPage.createIntroLeft();
 +
                subPage.createIntroRight();
 +
                break;
 +
            case 2:
 +
                subPage.createDesignLeft();
 +
                subPage.createDesignRight();
 +
                break;
 +
            case 3:
 +
                subPage.createMethodsLeft();
 +
                subPage.createMethodsRight();
 +
                break;
 +
            case 4:
 +
                subPage.createResultsDirectionsLeft();
 +
                subPage.createResultsDirectionsRight();
 +
                break;
 +
            case 5:
 +
                subPage.createCollaborationsLeft();
 +
                subPage.createCollaborationsRight();
 +
                break;
 +
        }
 +
    };
 +
 +
    subPage.createIntroLeft = function() {
 +
        var head = document.createElement("header");
 +
        head.appendChild(document.createTextNode("Introduction"));
 +
 +
        var text = "The production of plant essential oils and their derivatives represents an over 9 billion dollar " +
 +
            "industry when considering just their applications in the food and fragrance industries 1. A staggering 23 " +
 +
            "million kilograms of citrus oil alone are produced worldwide each year. Up until only a couple decades ago, " +
 +
            "the production of these essential oils was done exclusively by chemical extraction from plant material. " +
 +
            "However, the sudden emergence of synthetic biology a versatile and efficient tool has the potential to " +
 +
            "transform this immense industry, the products of which nearly everyone will come in contact with on a daily " +
 +
            "basis. ";
 +
 +
        var p1 = subPage.createP(text);
 +
        document.getElementById("igem_header").innerHTML = "reached intro left 2";
 +
 +
        var plant = subPage.createIMG("VU_greenhouse_plants.JPG", "VU greenhouse plants", 300, 300, "right");
 +
 +
        text = "By harnessing existing biosynthetic pathways and introducing enzymes taken from plants into more " +
 +
        "malleable model systems, it will be possible to significantly improve on current methods of the active " +
 +
        "components of essential oils, most notably the terpenoids. While most plants express terpenes in the range of " +
 +
        "parts per million and thus require very large scale operations to be commercially viable, early forays into the " +
 +
        "biological production of terpenes have proven that it is possible to improve yields 100-fold 2. We selected a " +
 +
        "total of nine different terpenes to produce (see table), each of which has practical applications which make " +
 +
        "them prime candidates for alternate means of production. The first aspect of our project involves using the " +
 +
        "great potential of synthetic biology to design a commercially-viable strategy for the production of any class " +
 +
        "of terpenoid. ";
 +
        var p2 = subPage.createP(text);
 +
 +
        text = "Just as important to the economic benefit of this approach is its environment benefit. With chemical " +
 +
        "terpene extraction being such a relatively inefficient process, it is necessary to process large amounts of " +
 +
        "plant material to get a substantive yield. This may not pose as significant of an issue for citrus growers, but" +
 +
        " many of the most prized compounds are taken from the rarest species of plant. The continuation of the status quo " +
 +
        "in terms of terpene extraction is not an environmentally sustainable solution. In our selection of terpenes, we " +
 +
        "placed a large emphasis on choosing compounds from some of the most rare species possible. ";
 +
        var p3 = subPage.createP(text);
 +
 +
        text = "The best example of this idea behind our project can be seen in the gene for santalene synthase. The only " +
 +
        "species know to have genes to produce this terpene are found in remote regions of India and Australia, and one " +
 +
        "of them is listed as a vulnerable species by the IUCN. The trees can live for hundreds of years, but are the " +
 +
        "target of widespread over-exploitation, to the point that, for example, the Indian government has banned the " +
 +
        "export of sandalwood. Synthetic biology can produce the exact same active ingredients of sandalwood oil in a " +
 +
        "way that is both more economically and environmentally sound. ";
 +
        var p4 = subPage.createP(text);
 +
 +
        text = "In order for our idea to truly be applicable to exotic and endangered species of plant, we had to take an " +
 +
        "approach that was quite different from the one most iGEM teams have historically taken. What we were looking for " +
 +
        "was a quick, inexpensive method of cloning genes that was also compatible with species that have not had their " +
 +
        "entire genomes sequenced. Often, iGEM teams resort to synthesizing their genes through third parties. However, " +
 +
        "this can be fairly costly especially given the moderately large size of many of these synthase genes, may take " +
 +
        "several weeks or even a month to finish synthesizing, and cannot be done unless the gene's sequence is known in " +
 +
        "its entirety. By going back to basics and taking raw plants as our source material, we were able to avoid these " +
 +
        "issues and demonstrated how our approach was a practically viable one.";
 +
        var p5 = subPage.createP(text);
 +
 +
        leftPageBuilder.appendChild(head);
 +
        leftPageBuilder.appendChild(p1);
 +
        leftPageBuilder.appendChild(plant);
 +
        leftPageBuilder.appendChild(p2);
 +
        leftPageBuilder.appendChild(p3);
 +
        leftPageBuilder.appendChild(p4);
 +
        leftPageBuilder.appendChild(p5);
 +
    };
 +
 +
    subPage.createIntroRight = function() {
 +
        var table = document.createElement("table");
 +
        table.style.margin = "auto";
 +
        var row = table.insertRow();
 +
 +
        var cell = row.insertCell(0);
 +
        cell.appendChild(subPage.createPhoto("VU_Cadenine.png", "Cadenine", 150, 150, "Cadenine"));
 +
        cell = row.insertCell(1);
 +
        cell.appendChild(subPage.createPhoto("VU_Carene.png", "Caderene", 150, 150, "Caderene"));
 +
        cell = row.insertCell(2);
 +
        cell.appendChild(subPage.createPhoto("VU_Humelene.png", "Humelene", 150, 150, "Humelene"));
 +
 +
        row = table.insertRow();
 +
        cell = row.insertCell(0);
 +
        cell.appendChild(subPage.createPhoto("VU_Myrcene.png", "Myrcene", 150, 150, "Myrcene"));
 +
        cell = row.insertCell(1);
 +
        cell.appendChild(subPage.createPhoto("VU_R_linalool.png", "R Linalool", 150, 150, "R Linalool"));
 +
        cell = row.insertCell(2);
 +
        cell.appendChild(subPage.createPhoto("VU_S_linalool.png", "S Linalool", 150, 150, "S Linalool"));
 +
 +
        row = table.insertRow();
 +
        cell = row.insertCell(0);
 +
        cell.appendChild(subPage.createPhoto("VU_Sabinene.png", "Sabinene", 150, 150, "Sabinene"));
 +
        cell = row.insertCell(1);
 +
        cell.appendChild(subPage.createPhoto("VU_Santalene.png", "Santalene", 150, 150, "Santalene"));
 +
        cell = row.insertCell(2);
 +
        cell.appendChild(subPage.createPhoto("VU_Zingiberene.png", "Zingiberene", 150, 150, "Zingiberene"));
 +
 +
        rightPageBuilder.appendChild(table);
 +
    };
 +
 +
    subPage.createDesignLeft = function() {
 +
        var head = document.createElement("header");
 +
        head.appendChild(document.createTextNode("Design"));
 +
 +
        var text = "Terpene biosynthesis in plants is part of larger pathways that metabolize isoprenoid intermediates. " +
 +
            "Genes encoding for enzymes known as synthases catalyze the terminal step in these pathways, from a precursor " +
 +
            "(commonly farnesyl pyrophosphate (FPP) or garnyl pyrophosphate (GPP)) to the final terpene product. As it " +
 +
            "happens, two well established and genetically manipulable model organisms- the bacterium Escherichia coli " +
 +
            "and baker's yeast Saccharomyces cerevisiae- produce moderate amounts of GPP and FPP as part of their " +
 +
            "endogenous non-mevalonate pathway (MEP) and mevalonate pathway (MEV) respectively3. All that is required " +
 +
            "for either of these organisms to begin producing terepenes is to introduce that single synthase gene. ";
 +
        var p1 = subPage.createP(text);
 +
 +
        text = "Yeast initially was our main target for a few advantages it appeared to have as a production platform. " +
 +
        "First, the MEV pathway is found in all eukaryotes including plants and fungi, so better yield were expected by " +
 +
        "choosing it over the MEP pathway in prokaryotes4. Second, it would be possible to physically integrate our gene" +
 +
        " into one of the yeast's chromosomes by using homologous recombination. An inducible promoter could be included" +
 +
        " to further increase production. Third, as a diploid the yeast could be made homozygous for the terpene gene. We" +
 +
        " soon found out that no exiting vector had all of the features we would want. Therefore, we designed our own new" +
 +
        " plasmid vector, pVU140006, that contained a number of important features and advances over previous plasmids for" +
 +
        " this purpose. See our parts page for more information on what special features we included and their relevance " +
 +
        "to the project";
 +
        var p2 = subPage.createP(text);
 +
 +
        leftPageBuilder.appendChild(head);
 +
        leftPageBuilder.appendChild(p1);
 +
        leftPageBuilder.appendChild(p2);
 +
    };
 +
 +
    subPage.createDesignRight = function() {
 +
        var img = subPage.createPhoto(
 +
            "Terpenoid_biosynthesis_pathway.png","Terpenoid Biosysnthesis Pathway", 700, 967,
 +
            "Terpenoid Biosysnthesis Pathway");
 +
        img.style.margin = "auto";
 +
        img.style.marginBottom = "1em";
 +
        rightPageBuilder.appendChild(img);
 +
    };
 +
 +
    subPage.createMethodsLeft = function() {
 +
        var head = document.createElement("header");
 +
        head.appendChild(document.createTextNode("Methods"));
 +
 +
        var text = "Our project had several co-dependent sub-project that were all worked on in parallel. These can " +
 +
            "roughly be divided into two categories: the first involving work on our synthase genes and the second" +
 +
            " involving the construction of a new, specially designed plasmid vector. We tried two different team " +
 +
            "structures over the year to see which would give the best results. For the Spring, we had the original " +
 +
            "idea of dividing members into independent groups, each working on a specific terpene. Each group was " +
 +
            "headed by a single group manager who would teach 4-5 new members the protocol that was to be preformed " +
 +
            "and then supervise that the work was carried out correctly. On occasion either the group managers or the" +
 +
            " organization president or wetware director would also given lessons to teach members about the techniques" +
 +
            " and theory involved at each step. All group managers were in turn trained by either the president " +
 +
            "or wetware director, both of whom had come with the experiment, acquired all the necessary primers and r" +
 +
            "eagents, wrote up the protocol, and had preformed it prior to any group-phase work for the purposes of t" +
 +
            "roubleshooting and predicting where issues may come up. The president or wetware director also helped the" +
 +
            " group manager in being present during all experiments for answering questions, preparing materials, and " +
 +
            "other forms of assistance.";
 +
        var p1 = subPage.createP(text);
 +
 +
        text = "Each group first planted seeds under the appropriate soil, humidity, and temperature conditions at the" +
 +
        " Vanderbilt Greenhouse. Once the majority of these grew into saplings with green leaves, Samples were flash froz" +
 +
        "en in liquid nitrogen in preparation for a genomic DNA extraction. After the extractions, nanodrop concentration" +
 +
        " readings and agarose gels confirmed the presence of high molecular weight genomic DNA. Groups then ran a PCR on" +
 +
        " their genomic DNA with primers specific to their synthase gene. More gels were run to check for PCR product. At" +
 +
        " this point, the semester was coming to an end, so groups were disbanded before most managed to isolate their sy" +
 +
        "nthase gene. Over the summer, the president and wetware director continued troubleshooting those genes which wer" +
 +
        "e not amplifying and eventually got each to the point where consistent PCR product bands were produced. ";
 +
        var p2 = subPage.createP(text);
 +
 +
        text = "Once we had clear banding patterns, it became clear that the number of introns in each of our genes (a " +
 +
        "variable which was unknown since most of the plants we worked with have not had their genomes sequenced) was too " +
 +
        "great for cloning and expression to be practical. Therefore, as soon as the fall semester began, we shifted strat" +
 +
        "egy to isolating RNA from our plants. This RNA could be converted to cDNA by reverse transcription, which would e" +
 +
        "liminate the issue with introns we were having. Several of our greenhouse plants were no longer available, so w" +
 +
        "e reduced the number of target terpenes we were focusing on. After extracting RNA and running an RT-PCR, severa" +
 +
        "l samples produced bands that corresponded roughly to where the synthase gene should be. These were gel extract" +
 +
        "ed. Because almost every synthase gene had restriction sites in them that prevented them from being RFC10 compa" +
 +
        "tible, we ligated the genes in pUC19 for site directed mutagenesis. After that, a second processing step would " +
 +
        "have been necessary to add the correct restriction sites to each gene to allow them to be integrated into pSB1C" +
 +
        "3 as a biobrick. In the interest of time, we synthesized a codon-optimized santalene synthase gene in order to " +
 +
        "skip these RFC10 processing steps, even though we had already successfully reverse transcribed cDNA of the san" +
 +
        "talene synthase gene. ";
 +
        var p3 = subPage.createP(text);
 +
 +
        text = "In the spring concurrent to work by the terpene groups, work began on plasmid construction. This was pre" +
 +
        "formed by the president, wetware director, and a handful of others rather than in group format. Each gene casset" +
 +
        "te for our final plasmid was first identified in an existing, readily available plasmid. All of these cassettes " +
 +
        "were extracted by PCR using those plasmids as templates. Overlap extension PCR was then done on the gel-purifie" +
 +
        "d product to add restriction sites and homology regions for the purposes of eventually combining all of the cas" +
 +
        "settes together into a single plasmid. By the end of the summer, only one final fragment remained to be inserte" +
 +
        "d to complete the intermediate plasmid pVU14004. Upon the successful creation of pVU14004, several restriction" +
 +
        " enzyme sites had to be removed by site directed mutagensis in order to make the plasmid RFC10 compatible. ";
 +
        var p4 = subPage.createP(text);
 +
 +
        leftPageBuilder.appendChild(head);
 +
        leftPageBuilder.appendChild(p1);
 +
        leftPageBuilder.appendChild(p2);
 +
        leftPageBuilder.appendChild(p3);
 +
        leftPageBuilder.appendChild(p4);
 +
    };
 +
 +
    subPage.createMethodsRight = function() {
 +
        var img1 = subPage.createPhoto("VU_experiment_1_diagram.png", "Experiment 1 Diagram",
 +
            421, 571, "Experiment 1 Diagram");
 +
        img1.style.margin = "auto";
 +
        img1.style.marginBottom = "1em";
 +
        var img2 = subPage.createPhoto("VU_experiment_2_diagram.png", "Experiment 2 Diagram",
 +
            484, 591, "Experiment 2 Diagram");
 +
        img2.style.margin = "auto";
 +
        img2.style.marginBottom = "1em";
 +
 +
        document.getElementById("right_page").appendChild(img1);
 +
        document.getElementById("right_page").appendChild(img2);
 +
    };
 +
 +
    subPage.createResultsDirectionsLeft = function() {
 +
        var head = document.createElement("header");
 +
        head.appendChild(document.createTextNode("Results and Directions"));
 +
 +
        var text = "Several factors contributed to the difficulty we experienced during the final phase of the project." +
 +
            " First, member engagement suffered a significant decline between the spring and fall semesters, to the point" +
 +
            " where only a small handful of people were left to preform all experiments. Second, the late realization tha" +
 +
            "t we had to change our cloning strategy to modified cDNA inserts effectively meant we had to start anew in l" +
 +
            "ate August despite having what was a good head start when we began in early March. Third, the RFC10 require" +
 +
            "ments added a substantial dimension of difficulty to the project since all of our starting material (both t" +
 +
            "he extracted gene cassettes for plasmid construction and the synthase genes) contained multiple sites that " +
 +
            "made them incompatible with the biobrick standard. Nevertheless, our team accomplished an enormous amount d" +
 +
            "uring our first year in competition. ";
 +
        var p1 = subPage.createP(text);
 +
 +
        text = "We successfully constructed pVU14004, which contains all of the cassettes needed to have all of function" +
 +
        "ality we had intended. However, this form of the plasmid has XbaI and EcoRI sites that make it incompatible with " +
 +
        "RFC10. These sites were successfully changed to missense mutations by site directed mutagenesis. The final step " +
 +
        "required to make pVU14006 is changing the multiple cloning site (MCS) to have the biobrick prefix and suffix. In" +
 +
        " its current form, the plasmid has a functional MCS but it does not yet have the specific order of EcoRI, XbaI," +
 +
        " SpeI, and PstI sites required by RFC10. ";
 +
        var p2 = subPage.createP(text);
 +
 +
        text = "For a listing of all the medal requirements we successfully fulfilled over the course of our project, " +
 +
        "please visit this page.";
 +
        var p3 = subPage.createP(text);
 +
 +
        document.getElementById("left_page").appendChild(head);
 +
        document.getElementById("left_page").appendChild(p1);
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        document.getElementById("left_page").appendChild(p2);
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        document.getElementById("left_page").appendChild(p3);
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 +
 +
    subPage.createResultsDirectionsRight = function() {
 +
        var table = document.createElement("table");
 +
        table.style.margin = "auto";
 +
 +
        var cTitles = ["Terpene",
 +
            "Plant Genomic DNA Extraction Success",
 +
            "PCR-isolation of Synthase Gene",
 +
            "Plant RNA Extraction success",
 +
            "Synthase Gene Reverse-Transcription success",
 +
            "Terpene Production in E.coli/yeast success"];
 +
 +
        subPage.insertTextRow(table, cTitles);
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 +
            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(redX, "red x", 32, 32, "red x"),
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            subPage.createPlainIMG(redX, "red x", 32, 32, "red x")];
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(redX, "red x", 32, 32, "red x")];
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(redX, "red x", 32, 32, "red x")];
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            subPage.createPlainIMG(redX, "red x", 32, 32, "red x"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(redX, "red x", 32, 32, "red x")];
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(greenCheck, "green check", 32, 32, "green check"),
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            subPage.createPlainIMG(redX, "red x", 32, 32, "red x"),
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            subPage.createPlainIMG(redX, "red x", 32, 32, "red x")];
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        subPage.createRowFromArray(table, row1);
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        subPage.createRowFromArray(table, row2);
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        subPage.createRowFromArray(table, row3);
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        subPage.createRowFromArray(table, row4);
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        subPage.createRowFromArray(table, row5);
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        subPage.createRowFromArray(table, row6);
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        subPage.createRowFromArray(table, row7);
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        subPage.createRowFromArray(table, row8);
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        subPage.createRowFromArray(table, row9);
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 +
 +
    subPage.createCollaborationsLeft = function() {
 +
        var head = document.createElement("header");
 +
        head.appendChild(document.createTextNode("Results and Directions"));
 +
 +
        var text = "In addition to our own wetware project, our team led fruitful collaborations with a total of three" +
 +
            " other iGEM teams. First, we played a major role in assisting Vanderbilt's microfluidic division with the b" +
 +
            "iological aspect of their project. We prepared the biobrick parts they tested in their microfluidic device" +
 +
            ", including transforming the E. coli they used to study their quorum-sensing fluorescent oscillator circui" +
 +
            "t. Second, we provided feedback to Vanderbilt's software division about their own project involving a prog" +
 +
            "ram to aid in the manipulation of genetic sequences. We used the program as if it were for a real project " +
 +
            "and gave them suggestions on how to make their program easier to use and more useful to biologists. ";
 +
        var p1 = subPage.createP(text);
 +
 +
        var building = subPage.createPhoto("Ravenwood_high_school.jpg", "Ravenwood High School", 250, 250, "Ravenwood High School");
 +
        building.style.float = "left";
 +
        building.style.margin = "1%";
 +
 +
        text = "Last but not least, we provided significant assistance and guidance to the Ravenwood Raptors high schoo" +
 +
        "l iGEM team. In a series of conversations with Dr. Amanda Benson, we planned a smaller scale version of our ow" +
 +
        "n project that involved only a single terpene synthase gene. After visiting the high school and presenting our" +
 +
        " idea, the students voted to choose it for their project. We also provided the primers and sage genomic DNA te" +
 +
        "mplate they used in their experiments. ";
 +
        var p2 = subPage.createP(text);
 +
 +
        leftPageBuilder.appendChild(head);
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        leftPageBuilder.appendChild(p1);
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        leftPageBuilder.appendChild(building);
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        leftPageBuilder.appendChild(p2);
 +
    };
 +
 +
    subPage.createCollaborationsRight = function() {
 +
        var header = document.createElement("header");
 +
        header.appendChild(document.createTextNode("References"));
 +
 +
        var text1 = "1. USDA Industrial Uses Reports. Essential Oils Widely Used in Flavors and Fragrances. September 1995.";
 +
        var text2 =
 +
            "2. Ajikumar PK, Tyo K, Carlsen S, Mucha O, Phon TH, Stephanopoulos G. Terpenoids: opportunities for biosynth" +
 +
            "esis of natural product drugs using engineered microorganisms. Mol Pharm. 2008;5(2):167-90.";
 +
        var text3 =
 +
            "3. Dudareva N, Klempien A, Muhlemann JK, Kaplan I. Biosynthesis, function and metabolic engineering of plant " +
 +
            "volatile organic compounds. New Phytol. 2013;198(1):16-32.";
 +
        var text4 =
 +
            "4.Martin VJ, Pitera DJ, Withers ST, Newman JD, Keasling JD. Engineering a mevalonate pathway in Escherichia " +
 +
            "coli for production of terpenoids. Nat Biotechnol. 2003;21(7):796-802.";
 +
 +
        var p1 = subPage.createP(text1);
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        var p2 = subPage.createP(text2);
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        var p3 = subPage.createP(text3);
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        var p4 = subPage.createP(text4);
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 +
        p1.style.fontStyle = "italic";
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        p2.style.fontStyle = "italic";
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        p3.style.fontStyle = "italic";
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        p4.style.fontStyle = "italic";
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 +
        rightPageBuilder.appendChild(header);
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        rightPageBuilder.appendChild(p1);
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        rightPageBuilder.appendChild(p2);
 +
        rightPageBuilder.appendChild(p3);
 +
        rightPageBuilder.appendChild(p4);
 +
    };
 +
 +
    return subPage;
 +
}
 +
 +
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("VU_San_psb_confirmation.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("VU_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);
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        var img3 = subPage.createPhoto("Sabinene_synthesis_pathway.gif",
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            "Sabinene Synthesis Pathway",
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            "Sabinene Synthesis Pathway");
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        rightPageBuilder.appendChild(img3);
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function NotebookSubPageBuilder() {
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    var subPage = new SubPageBuilder();
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    subPage.maxSubPage = 3;
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    subPage.getMaxSubPage = function() {
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        return subPage.maxSubPage;
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    };
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    subPage.createSubPage = function(subPageNum) {
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        document.getElementById("igem_header").innerHTML = "reachd createSubPage (notebook)";
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                subPage.createSpring2014Left();
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                subPage.createSummer2014Left();
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                subPage.createSummer2014Right();
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                subPage.createFall2014Left();
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                subPage.createFall2014Right();
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                break;
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        document.getElementById("igem_header").innerHTML = "reachd createsummer2014left";
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        var header = document.createElement("header");
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        header.appendChild(document.createTextNode("Spring 2014"));
 +
 +
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        var p_m31 = subPage.createP("March 31st");
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        var p_a25 = subPage.createP("April 25th");
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        var p_a29 = subPage.createP("April 29th");
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        var m30 = document.createElement("ul");
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        var m31 = document.createElement("ul");
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        var a1 = document.createElement("ul");
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        var a2 = document.createElement("ul");
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        var a3 = document.createElement("ul");
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        var a4 = document.createElement("ul");
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        var a5 = document.createElement("ul");
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        var a7 = document.createElement("ul");
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        var a24 = document.createElement("ul");
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        var a25 = document.createElement("ul");
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        var a27 = document.createElement("ul");
 +
        var a29 = document.createElement("ul");
 +
 +
        var text = [["Extracted genomic DNA from 100 mg of Arabidopsis thaliana leaves using a Viogene DNA extraction kit. Samples were " +
 +
        "labeled ZIN for zingiberene."],
 +
            ["Two samples were prepared and nanodropped. The concentration of the first w" +
 +
            "as 2.6 ng/ul, and the second was 3.5 ng/ul of DNA, indicating a minimal yield of DNA."]];
 +
        subPage.addMultLI(m27, text);
 +
 +
        text = [["Extracted genomic DNA from 100 mg of Picea abies needles using the same extr" +
 +
        "action kit and protocol. Samples were labeled CAR for carene."],
 +
            ["Two samples were prepared and nanodropped. The concentration of the first w" +
 +
            "as 2.6 ng/ul, and the second was 3.5 ng/ul of DNA, indicating a minimal yield of DNA."]];
 +
        subPage.addMultLI(m30, text);
 +
 +
        text = [["Ran a 0.6 % argarose gel on the DNA extracted from ZIN and CAR, as well as the column flow-throu" +
 +
        "gh from the kit."],
 +
            ["ZIN1, ZIN2, CAR1, and CAR2 all show a faint but distinct DNA band above the highest rung on the DNA l" +
 +
            "adder (>10kb), showing the presence of DNA. No bands were seen on the kit flow-through. Indicates successful g" +
 +
            "enomic extraction."],
 +
            ["Preformed a second genomic extraction on Picea abies to improve yield. Nanodrop shows CAR3 to be " +
 +
            "at 6.2 ng/ul and CAR4 to be 11.5 ng/ul."],
 +
            ["Extracted genomic DNA from Gossypium hirsutum. Samples nanodroppped: CAD1 1.8 ng/ul and CAD2 7.8 ng/ul."]];
 +
        subPage.addMultLI(m31, text);
 +
 +
        text = [["Ran a gel on CAR3, CAR4, CAD1, and CAD2. Brighter genomic DNA bands were seen on the cadinene camples" +
 +
        " than before, but cadinene samples showed significant smearing near the top of the gel."]];
 +
        subPage.addMultLI(a1, text);
 +
 +
        text = [["Extracted genomic DNA from Salvia officinalis . Samples nanodropped: SAB1 7.5 ng/ul, and SAB 11.4 ng/ul."],
 +
            ["Extracted genomic DNA from Mentha citrata . Samples nanodropped: LNR1 3.4 ng/ul, LNR2 6.2 ng/ul, LNR3 7.3 ng/ul"],
 +
            ["E. coli containing p404GALS and pDZ207 from Addgene were grown on LB plates with ampicilin. These were min" +
 +
            "iprepped using a Viogen kit. Samples nanodropped: p404GALS (A) 130.2 ng/ul, p404GALS (B) 112.3 ng/ul, pDZ2" +
 +
            "07 (A) 145.3 ng/ul, pDZ207 (B) 84.1 ng/ul."]];
 +
        subPage.addMultLI(a2, text);
 +
 +
        text = [["Extracted genomic DNA again from Arabidopsis thaliana . Sample nanodropped: LNS1 53.4 ng/ul, LNS2 585.2 ng/ul"],
 +
            ["Ran gel on LNR1, LNR2, LNR3, LNS1, LNS2, SAB1, and SAB2. All show high weight DNA bands, with Linalool (S) sampl" +
 +
            "es having the brightest."]];
 +
        subPage.addMultLI(a3, text);
 +
 +
        text = [["Extracted genomic DNA from Zingiber zermbet . Sample nanodropped: HUM1 31.9 ng/ul and HUM2 18.6 ng/ul"],
 +
            ["Extracted genomic DNA from Ocimum basilicum . Sample nanodropped: GER1 2.3 ng/ul"]];
 +
        subPage.addMultLI(a4, text);
 +
 +
        text = [["Extracted genomic DNA from Santalum album seeds since the sapling was still not fully grown. Sample nan" +
 +
        "odropped: SAN1 53.8 ng/ul and SAN2 28.4 ng/ul"]];
 +
        subPage.addMultLI(a5, text);
 +
 +
        text = [["Extracted genomic DNA from Perilla frutescens . Sample nanodropped: MYR1 632.8 ng/ul and MYR2 958.6 ng/ul"],
 +
            ["Extracted genomic DNA from Perilla frutescens . Sample nanodropped: MYR1 632.8 ng/ul and MYR2 958.6 ng/ul"]];
 +
        subPage.addMultLI(a7, text);
 +
 +
        text = [["Preformed PCR using zingiberene synthase primers on LNS2 genomic DNA and using linalool (S) synthase p" +
 +
        "rimers on the sample template."],
 +
            ["Ran gel on PCR product. Resulted in no visible bands formed."]];
 +
        subPage.addMultLI(a24, text);
 +
 +
        text = [["Took 1.8 ul of HUM1 genomic DNA and preformed a PCR with humelene synthase primers."],
 +
            ["Ran gel on PCR product. Resulted in three total bands, one faint around 1.2 kb, and two bands very close " +
 +
            "in size just under 3.0 kb."],
 +
            ["Both ~3 kb bands were gel extracted, combining across all four lanes. Samples nanodropped: HUM-top 8.5 ng/u" +
 +
            "l, HUM-bottom 10.6 ng/ul."]];
 +
        subPage.addMultLI(a25, text);
 +
 +
        text = [["Preformed PCR using linalool (R) synthase primers on LNR3 genomic DNA."],
 +
            ["Ran gel on PCR product. Resulted in no visible bands formed."]];
 +
        subPage.addMultLI(a27, text);
 +
 +
        text = [["Preformed PCR using myrcene synthase primers on MYR2 genomic DNA."],
 +
            ["Ran gel on PCR product. Smeared bands on gel but no distinct bands."],
 +
            ["Preformed overlap-extension PCR on the gel extracted humelene samples (both HUM-top and HUM-bottom) to add " +
 +
            "epitope tag sequence."],
 +
            ["Ran gel on OE-PCR product. Only extremely faint bands were visible."]];
 +
        subPage.addMultLI(a29, text);
 +
 +
        leftPageBuilder.appendChild(header);
 +
 +
        leftPageBuilder.appendChild(p_m27);
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        leftPageBuilder.appendChild(m27);
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        leftPageBuilder.appendChild(p_m30);
 +
        leftPageBuilder.appendChild(m30);
 +
 +
        leftPageBuilder.appendChild(p_m31);
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        leftPageBuilder.appendChild(m31);
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        leftPageBuilder.appendChild(p_a1);
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        leftPageBuilder.appendChild(a1);
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 +
        leftPageBuilder.appendChild(p_a2);
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        leftPageBuilder.appendChild(a2);
 +
 +
        leftPageBuilder.appendChild(p_a3);
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        leftPageBuilder.appendChild(a3);
 +
 +
        leftPageBuilder.appendChild(p_a4);
 +
        leftPageBuilder.appendChild(a4);
 +
 +
        leftPageBuilder.appendChild(p_a5);
 +
        leftPageBuilder.appendChild(a5);
 +
 +
        leftPageBuilder.appendChild(p_a7);
 +
        leftPageBuilder.appendChild(a7);
 +
 +
        leftPageBuilder.appendChild(p_a24);
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        leftPageBuilder.appendChild(a24);
 +
 +
        leftPageBuilder.appendChild(p_a25);
 +
        leftPageBuilder.appendChild(a25);
 +
 +
        leftPageBuilder.appendChild(p_a27);
 +
        leftPageBuilder.appendChild(a27);
 +
 +
        leftPageBuilder.appendChild(p_a29);
 +
        leftPageBuilder.appendChild(a29);
 +
    };
 +
 +
    subPage.createSpring2014Right = function() {
 +
        var img1 = subPage.createPhoto("VU_Genomic_DNA_bands_check_LNS.JPG", "Genomic DNA bonds check", 395.2, 516.8,
 +
        "An example of a gel showing high molecular weight (>10 kb) bands corresponding to successfully " +
 +
        "extracted plant genomic DNA (in this case, samples LNS1 and LNS2 from Arabidopsis DNA");
 +
 +
        var img2 = subPage.createPhoto("VU_humelene_genomic_dna_pcr.JPG", "Humelene Genomic DNA PCR", 374, 348.5,
 +
            "PCR products resulting from primers targeted to hmelene synthase using Zingiber genomic" +
 +
            "DNA as a template. The sixth ladder band down corresponds to 3000 bp.");
 +
 +
        var img3 = subPage.createPhoto("VU_labeled_PCON_Gel.JPG", "Labeled PCON Gel", 374, 348.5,
 +
            "Labeled PCON Gel");
 +
 +
        rightPageBuilder.appendChild(img1);
 +
        rightPageBuilder.appendChild(img2);
 +
        rightPageBuilder.appendChild(img3);
 +
    };
 +
 +
    subPage.createSummer2014Left = function() {
 +
        var header = document.createElement("header");
 +
        header.appendChild(document.createTextNode("Summer 2014"));
 +
 +
        var p_may = subPage.createP("May");
 +
        var p_june = subPage.createP("June");
 +
        var p_july = subPage.createP("July");
 +
 +
        var may = document.createElement("ul");
 +
        var june = document.createElement("ul");
 +
        var july = document.createElement("ul");
 +
 +
        var text = [["Continued troubleshooting PCR reaction conditions for all of the terpenes that failed " +
 +
                    "to amplify. Tried adjusting template concentration, adding DMSO, changing thermocycler program, hot " +
 +
                    "start PCR, new polymerase and dNTPs."],
 +
                    ["Re-did genomic extractions for those that produced less than 50 ng/ul of genomic DNA. " +
 +
                    "Used this new template in further PCRs."],
 +
                    ["Extracted the Gal10 gene from our template plasmid and a kanomycin resistance gene borde" +
 +
                    "red by LoxP sites."]];
 +
        subPage.addMultLI(may, text);
 +
 +
        text = [["All of the gene cassettes for plasmid construction that were successfully extracted so far" +
 +
        " were ligated together and inserted into the MCS of pUC19. This formed our first intermediate plasmid."]];
 +
        subPage.addMultLI(june, text);
 +
 +
        text = [["Finally reached the point that all terpene genes were consistently amplifying with the " +
 +
        "synthase gene primers. The genomic DNA sample for sabinene was completely used before this point, " +
 +
        "although all other of the 8 terpenes showed clear bands.."]];
 +
        subPage.addMultLI(july, text);
 +
 +
        leftPageBuilder.appendChild(header);
 +
        leftPageBuilder.appendChild(p_may);
 +
        leftPageBuilder.appendChild(may);
 +
        leftPageBuilder.appendChild(p_june);
 +
        leftPageBuilder.appendChild(june);
 +
        leftPageBuilder.appendChild(p_july);
 +
        leftPageBuilder.appendChild(july);
 +
    };
 +
 +
    subPage.createSummer2014Right = function() {
 +
        var img = subPage.createPhoto("VU_genomic_DNA_PCR.jpg",
 +
            "The results of the genomic DNA PCR on all of the plant species.",
 +
            554, 735,
 +
            "The results of the genomic DNA PCR indicated each gene had a large fraction of introns. " +
 +
            "None of the genes had a distinct band at exactly the right weight corresponding with what " +
 +
            "the intron-less cDNA size would be.");
 +
        rightPageBuilder.appendChild(img);
 +
    };
 +
 +
    subPage.createFall2014Left = function() {
 +
        document.getElementById("igem_header").innerHTML = "reachd createsummer2014left";
 +
        var header = document.createElement("header");
 +
        header.appendChild(document.createTextNode("Spring 2014"));
 +
 +
        var p_aug = subPage.createP("August");
 +
        var p_sept = subPage.createP("September");
 +
        var p_s17 = subPage.createP("September 17th");
 +
        var p_s18 = subPage.createP("September 18th");
 +
        var p_s19 = subPage.createP("September 19th");
 +
        var p_s20 = subPage.createP("September 20th");
 +
        var p_s26 = subPage.createP("September 26th");
 +
 +
        var p_o5 = subPage.createP("October 5th");
 +
        var p_o7 = subPage.createP("October 7th");
 +
        var p_o9 = subPage.createP("October 9th");
 +
        var p_o10 = subPage.createP("October 10th");
 +
        var p_o11 = subPage.createP("October 11th");
 +
        var p_o12 = subPage.createP("October 12th");
 +
        var p_o13 = subPage.createP("October 13th");
 +
        var p_o14 = subPage.createP("October 14th");
 +
        var p_o15 = subPage.createP("October 15th");
 +
        var p_o16 = subPage.createP("October 16th");
 +
 +
        var aug = document.createElement("ul");
 +
        var sept = document.createElement("ul");
 +
        var s17 = document.createElement("ul");
 +
        var s18 = document.createElement("ul");
 +
        var s19 = document.createElement("ul");
 +
        var s20 = document.createElement("ul");
 +
        var s26 = document.createElement("ul");
 +
 +
        var o5 = document.createElement("ul");
 +
        var o7 = document.createElement("ul");
 +
        var o9 = document.createElement("ul");
 +
        var o10 = document.createElement("ul");
 +
        var o11 = document.createElement("ul");
 +
        var o12 = document.createElement("ul");
 +
        var o13 = document.createElement("ul");
 +
        var o14 = document.createElement("ul");
 +
        var o15 = document.createElement("ul");
 +
        var o16 = document.createElement("ul");
 +
 +
        var text = [["Moved the lab into its new space before the start of the semester."],
 +
            ["Created the plasmid intermediate pVU1400A, which is missing only a single insert to become pVU14004."]];
 +
        subPage.addMultLI(p_aug, text);
 +
 +
        text = [["Ran RNA extraction on all the plants that were still available. This excluded Myrcene and " +
 +
        "Linalool (R) since both Perilla frutescens and Mentha aquatica had withered over the summered."],
 +
            ["Repeated RNA extractions on those which showed appreciable concentration on the nanodrop. Event" +
 +
            "ually all 7 remanining terpenes had plant RNA in appreciable quantities (most between 20-50 " +
 +
            "ng/ul, with a few less than 10 and a few more than 100 ng/ul)."]];
 +
        subPage.addMultLI(p_sept, text);
 +
 +
        text = [["Digested plasmid intermediate grown in demethylated bacteria with ClaI. Ligated final " +
 +
            "insert into vector. No transfomants grow after 24 hours."],
 +
            ["Diagnostic digest shows the ClaI enzyme is cutting properly. pUC19 positive control for transforma" +
 +
            "tions show that the competent cells are working."]];
 +
        subPage.addMultLI(p_s17, text);
 +
 +
        text = [["Ran reverse transcription PCR on extracted RNA to isolate synthase cDNA. Humelene and sabinene " +
 +
        "show clear positive results, santalene shows amplification at smaller region, and cadinene shows no" +
 +
        " cDNA bands."]];
 +
        subPage.addMultLI(p_s18, text);
 +
 +
        text = [["Made liquid cultures of K546546 in preparation for mutagenesis. Also made glycerol stock to store at -80."],
 +
            ["Diagnostic digest of ligation of pVU1400A intermediate and the final insert needed to make " +
 +
            "finished plasmid. Gel clearly shows bands in exactly the correct positions for each of three " +
 +
            "comparison conditions, proving that the creation of pVU14004 was finally successful.."]];
 +
        subPage.addMultLI(p_s19, text);
 +
 +
        text = [["Miniprep of K546546 liquid cultures (1 ml ). First culture tube concentration of 85.7 ng/ul " +
 +
                "DNA, second 105.1 ng/ul."],
 +
                ["RNA extracted arabadopsis and Picea abies to improve yield and quality. Carene still failed to " +
 +
                "get an RNA concentration greater than 10 ng/ul, while Arabidopsis produced 107 ng/ul with a go" +
 +
                "od A260/A280 ratio."],
 +
                ["Miniprep of K546546 liquid cultures (1 ml ). First culture tube concentration of 85.7 ng/ul " +
 +
                "DNA, second 105.1 ng/ul"]];
 +
        subPage.addMultLI(p_s20, text);
 +
 +
        text = [["RT-PCR done on humelene, linalool (S), sabinene, and zingiberene. Sabinene produces clear " +
 +
        "bands, while zingiberene shows one faint band at roughly the correct size. Positive controls are also " +
 +
        "run to confirm that the reverse transcription step is not the cause of any failures to amplify."]];
 +
        subPage.addMultLI(p_s26, text);
 +
 +
        text = [["RT-PCR done on humelene, sabinene, and santalene. Sabinene again produces clear bands,and " +
 +
        "santalene does as well although much fainter. Both bands were gel extracted to yield a small " +
 +
        "(<10 ng/ul) amount of DNA."],
 +
        ["Extracted DNA was ligated into pUC19 and transformed into E. coli."]];
 +
        subPage.addMultLI(p_o5, text);
 +
 +
        text = [["Site direction mutagenesis kit and specially designed primers were used to mutagenize K546546 " +
 +
        "at its BglI site, sabinene cDNA at its XbaI and EcoRI sites, and pVU14004 at its EcoRI and XbaI sites."],
 +
            ["Mutagenesis product was transformed into E. coli."]];
 +
        subPage.addMultLI(p_o7, text);
 +
 +
        text = [["Minipreps were done on 5 ml liquid cultures of mutagenized pVU14004, sabinene, and K546546. " +
 +
        "Four liquid cultures were made for each, and both sabinene and pVU14004 were done in duplicate."],
 +
            ["Diagnostic digests were done on miniprepped plasmid to check if the restriction sites were " +
 +
            "mutagenized. pVU14004 appeared to have lost its XbaI site but not its EcoRI site, sabinene shows " +
 +
            "a size that suggests it failed to ligate as an insert into pUC19, and K546 shows only a single " +
 +
            "band at around its starting weight."]];
 +
        subPage.addMultLI(p_o9, text);
 +
 +
        text = [["All 8 minipreps of sabinene ligated into pUC19 were digested with SpeI and ApaI to check for " +
 +
        "the synthase insert. Only one, Sab B2, shows a second band at the right size."]];
 +
        subPage.addMultLI(p_o10, text);
 +
 +
        text = [["Santalene synthase was ligated into pVU14004 and pSB1C3. E. coli was transformed and incubated."],
 +
            ["The sites that failed to show mutagenesis were mutagenized again using and transformed into E. " +
 +
            "coli. K546546 had its AgeI site mutagenized."]];
 +
        subPage.addMultLI(p_o11, text);
 +
 +
        text = [["All liquid cultures were miniprepped, producing 8 samples of pVU14004 with confirmed XbaI " +
 +
        "mutagenesis, 4 pVU14004 with no sites confirmed, 4 sabinene, and 6 samples produced from santalene in " +
 +
        "pVU14004. None of the plates with santalene in pSB1C3 produced colonies."],
 +
            ["Diagnostic digests were run on all miniprepped plasmid (K546- AgeI, BglI, SphI. Sabinene- EcoRI, " +
 +
            "BamH1. Santalene in pVU- ApaI, XbaI. pVU- EcoRI, XbaI, BamHI, KpnI). Santalene appeared not to have " +
 +
            "ligated into pVU14004. Sabinene did not have its EcoRI site removed by mutagenesis. K546546 had at least" +
 +
            " one cut, but the second sample may have had one site mutagenized."],
 +
            ["Santalene was re-ligated into pSB1C3 and transformed."]];
 +
        subPage.addMultLI(p_o12, text);
 +
 +
        text = [["Santalene in pSB1C3 was miniprepped to good yield. Each of 4 replicates was digested with " +
 +
        "SpeI and ApaI to test for ligation. The ApaI enzyme appears not have cut, but the fourth sample showed an " +
 +
        "uncut plasmid size which corresponded to that of pSB1C with santalene successfully inserted."]];
 +
        subPage.addMultLI(p_o13, text);
 +
 +
        text = [["Ligated santalene synthase again into pVU14004 and transformed into E. coli."]];
 +
        subPage.addMultLI(p_o14, text);
 +
 +
        text = [["One colony grew and was put in liquid culture."],
 +
            ["Culture miniprepped and digested. Again no gene insertion was detectable."]];
 +
        subPage.addMultLI(p_o15, text);
 +
 +
        text = [["Transformed pVU14004 into a dam- strain of E. coli to address the methylation sensitivity of ApaI."],
 +
            ["Finished planning and acquiring materials for GC-MS confirmation of terpene presence."]];
 +
        subPage.addMultLI(p_o16, text);
 +
 +
        leftPageBuilder.appendChild(header);
 +
 +
        leftPageBuilder.appendChild(p_aug);
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        leftPageBuilder.appendChild(aug);
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        leftPageBuilder.appendChild(p_sept);
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        leftPageBuilder.appendChild(sept);
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        leftPageBuilder.appendChild(p_s17);
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        leftPageBuilder.appendChild(s17);
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 +
        leftPageBuilder.appendChild(p_s18);
 +
        leftPageBuilder.appendChild(s18);
 +
 +
        leftPageBuilder.appendChild(p_s19);
 +
        leftPageBuilder.appendChild(s19);
 +
 +
        leftPageBuilder.appendChild(p_s20);
 +
        leftPageBuilder.appendChild(s20);
 +
 +
        leftPageBuilder.appendChild(p_s26);
 +
        leftPageBuilder.appendChild(s26);
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        leftPageBuilder.appendChild(p_o5);
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        leftPageBuilder.appendChild(o5);
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 +
        leftPageBuilder.appendChild(p_o7);
 +
        leftPageBuilder.appendChild(o7);
 +
 +
        leftPageBuilder.appendChild(p_o9);
 +
        leftPageBuilder.appendChild(o9);
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 +
        leftPageBuilder.appendChild(p_o10);
 +
        leftPageBuilder.appendChild(o10);
 +
 +
        leftPageBuilder.appendChild(p_o11);
 +
        leftPageBuilder.appendChild(o11);
 +
 +
        leftPageBuilder.appendChild(p_o12);
 +
        leftPageBuilder.appendChild(o12);
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 +
        leftPageBuilder.appendChild(p_o13);
 +
        leftPageBuilder.appendChild(o13);
 +
 +
        leftPageBuilder.appendChild(p_o14);
 +
        leftPageBuilder.appendChild(o14);
 +
 +
        leftPageBuilder.appendChild(p_o15);
 +
        leftPageBuilder.appendChild(o15);
 +
 +
        leftPageBuilder.appendChild(p_o16);
 +
        leftPageBuilder.appendChild(o16);
 +
    };
 +
 +
    subPage.createFall2014Right = function() {
 +
        var img1 = subPage.createPhoto("VU_First_RT_PCR_results_cad_hum_sab_san.JPG",
 +
            "Results of a reverse transcription PCR, showing the cDNA amplified from plant RNA template.",
 +
            346, 417,
 +
        "Results of a reverse transcription PCR, showing the cDNA amplified from plant RNA template.");
 +
 +
        var img2 = subPage.createPhoto("VU_Diagnostic_Digest_10-9.JPG",
 +
            "Diagnostic digest produces bands of exactly the correct size (from left to right, 2700, 2700," +
 +
            "and 950, 2700, and 1700, confirming that pVU14004 was successfully constructed.",
 +
            303, 314,
 +
            "Diagnostic digest produces bands of exactly the correct size (from left to right, 2700, 2700," +
 +
            "and 950, 2700, and 1700, confirming that pVU14004 was successfully constructed.");
 +
 +
        var img3 = subPage.createPhoto("VU_PVU14004_Conf_9_19.jpg",
 +
            "10-9 Diagnostic digest",
 +
            340, 286.375,
 +
            "10-9 Diagnostic digest");
 +
 +
        var img4 = subPage.createPhoto("VU_10-11_diagnostic_digest.JPG",
 +
            "10-11 Diagnostic digest",
 +
            331.5, 381.8,
 +
            "10-11 Diagnostic digest");
 +
 +
        rightPageBuilder.appendChild(img1);
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        rightPageBuilder.appendChild(img2);
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        rightPageBuilder.appendChild(img3);
 +
        rightPageBuilder.appendChild(img4);
 +
    };
 +
 +
    return subPage;
 +
}
 +
 +
function AttributionsSubPageBuilder() {
 +
    var subPage = new SubPageBuilder();
 +
    subPage.maxSubPage = 2;
 +
 +
    subPage.getMaxSubPage = function() {
 +
        return subPage.maxSubPage;
 +
    };
 +
 +
    subPage.createSubPage = function(subPageNum) {
 +
        switch(subPageNum){
 +
            case 1:
 +
                document.getElementById("igem_header").innerHTML = "case 1 of attributions";
 +
                subPage.createIntro();
 +
                subPage.createProfFacul();
 +
                break;
 +
            case 2:
 +
                subPage.createStaffRes();
 +
                subPage.createSponsors();
 +
                break;
 +
        }
 +
    };
 +
 +
    subPage.createIntro = function() {
 +
        document.getElementById("igem_header").innerHTML = "beginning of createIntro";
 +
        var header = document.createElement("header");
 +
        header.appendChild(document.createTextNode("Our Attributions"));
 +
        document.getElementById("igem_header").innerHTML = "1 of createIntro";
 +
 +
        var text = "While Vanderbilt University's iGEM team is driven by its undergraduates, our work is indebted to " +
 +
            "the generosity of our mentors and gracious sponsors. Vanderbilt iGEM prides itself in being a team run by un" +
 +
            "dergraduates, for undergraduates. All project design and data analysis, lab work and experimentation, fundr" +
 +
            "aising and outreach, and all the other work done by the team was all preformed by undergraduate student vo" +
 +
            "lunteers. However outside companies, faculty and staff, institutions, and individuals all have made contri" +
 +
            "butions that have been essential in our team's growth and success. We would like to take the time to speci" +
 +
            "ally thank each one of them.";
 +
 +
        document.getElementById("igem_header").innerHTML = "2 of createIntro";
 +
        var p = subPage.createP(text);
 +
        document.getElementById("igem_header").innerHTML = "middle of createIntro";
 +
 +
        leftPageBuilder.appendChild(header);
 +
        leftPageBuilder.appendChild(p);
 +
        document.getElementById("igem_header").innerHTML = "end of createIntro";
 +
    };
 +
 +
    subPage.createProfFacul = function() {
 +
        var header = document.createElement("header");
 +
        header.appendChild(document.createTextNode("Professors and Faculty"));
 +
        var img1 = subPage.createPhoto("VU_Chrissy_marasco.JPG",
 +
            "Chrissy Marasco",
 +
            300, 300,
 +
            "Dr. Chrissy Marasco for her role as the team's principle faculty adviser, with " +
 +
            "contributions to both the administrative and scientific work of our team");
 +
 +
        var img2 = subPage.createPhoto("VU_Kevin_seale.jpg",
 +
            "Kevin Seale",
 +
            300, 300,
 +
            "Kevin Seale for his role as our team's administrative adviser, providing lab " +
 +
            "space and equipment, and offering assistance through the SyBBURE program");
 +
 +
        var img3 = subPage.createPhoto("VU_Kathy_friedman.jpg",
 +
            "Kathy Friedman",
 +
            300, 300,
 +
            "Kathy Friedman for her role as our team's scientific adviser, offering technical" +
 +
            " assistance during project planing and troubleshooting");
 +
 +
        var img4 = subPage.createPhoto("VU_Ian_macara.jpg",
 +
            "Ian Macara",
 +
            300, 300,
 +
            "Ian Macara for providing our team with lab space, materials, and equipment for the fall semester and beyond");
 +
 +
        var img5 = subPage.createPhoto("VU_Mark_woelfle.jpg",
 +
            "Mark Woelfle",
 +
            300, 300,
 +
            "Mark Woelfle for providing our team with lab space and equipment for the spring semester");
 +
 +
        var img6 = subPage.createPhoto("VU_Amanda_benson.jpg",
 +
            "Amanda Benson",
 +
            300, 300,
 +
            "Amanda Benson for her technical support and guiding collaboration with Ravenwood High School's iGEM team");
 +
 +
        rightPageBuilder.appendChild(header);
 +
        rightPageBuilder.appendChild(img1);
 +
        rightPageBuilder.appendChild(img2);
 +
        rightPageBuilder.appendChild(img3);
 +
        rightPageBuilder.appendChild(img4);
 +
        rightPageBuilder.appendChild(img5);
 +
        rightPageBuilder.appendChild(img6);
 +
    };
 +
 +
    subPage.createStaffRes = function() {
 +
        var header = document.createElement("header");
 +
        header.appendChild(document.createTextNode("Staff and Resources"));
 +
        var img1 = subPage.createPhoto("VU_Greenhouse_ertelt.jpg",
 +
            "Vanderbilt Greenhouse and Jonathan Ertelt",
 +
            300, 300,
 +
            "VU Greenhouse and Jonathan Ertelt for assistance growing and maintaining our various plants");
 +
 +
        var img2 = subPage.createPhoto("VU_mass_spec.jpg",
 +
            "Mass Spec at Vanderbilt Mass Spectrometry Core",
 +
            300, 300,
 +
            "Vanderbilt Mass Spectrometry Core for agreeing to analyze our samples for terpenoid content and " +
 +
            "discussing ways to extract terpene for analysis");
 +
 +
        var text = "Dr. Steven Baskauf for general assistance in running our lab.";
 +
        var p1 = subPage.createP(text);
 +
 +
        text = "Charles Sissom and Sara Samoray for protocol advice, equipment t" +
 +
        "raining, and assistance in running our lab.";
 +
        var p2 = subPage.createP(text);
 +
 +
        text = "Anthony Tharp for access to common equipment resources.";
 +
        var p3 = subPage.createP(text);
 +
 +
        text = "Vanderbilt Environmental Health and Safety for training in pro" +
 +
        "per lab practice and safe waste disposal.";
 +
        var p4 = subPage.createP(text);
 +
 +
        text = "University of Massachusetts Medical Center, especially Dr. Aviva Joseph, for tec" +
 +
        "hnical advice related to our genetic constructs.";
 +
        var p5 = subPage.createP(text);
 +
 +
        document.getElementById("left_page").appendChild(header);
 +
        document.getElementById("left_page").appendChild(img1);
 +
        document.getElementById("left_page").appendChild(img2);
 +
        document.getElementById("left_page").appendChild(p1);
 +
        document.getElementById("left_page").appendChild(p2);
 +
        document.getElementById("left_page").appendChild(p3);
 +
        document.getElementById("left_page").appendChild(p4);
 +
        document.getElementById("left_page").appendChild(p5);
 +
    };
 +
 +
    subPage.createSponsors = function() {
 +
        var header = document.createElement("header");
 +
        header.appendChild(document.createTextNode("Sponsors"));
 +
 +
        var img1 = [subPage.createPlainIMG("VU_SyBBURE.png", "SyBBURE", 300, 146),
 +
                    subPage.createPlainIMG("VU_VIIBRE.png", "VIIBRE", 300, 69)];
 +
        var img2 = [subPage.createPlainIMG("VU_Biomatters.png", "Biomatters", 300, 101),
 +
                    subPage.createPlainIMG("VU_School_of_Engineering.jpg", "Vanderbilt School of Engineering", 300, 51)];
 +
 +
        var table = document.createElement("table");
 +
        table.style.width = "80%";
 +
        table.style.margin = "auto";
 +
 +
        subPage.createRowFromArray(table, img1);
 +
        subPage.createRowFromArray(table, img2);
 +
 +
        document.getElementById("right_page").appendChild(header);
 +
        document.getElementById("right_page").appendChild(table);
 +
    };
 +
 +
    return subPage;
 +
}
 +
 +
/**
 +
* Created by Anna Hwang on 1/15/2015.
 +
*/
 +
 +
var leftPage = document.getElementById("left_page");
 +
var rightPage = document.getElementById("right_page");
 +
 +
var leftButton = document.getElementById("left_button");
 +
var rightButton = document.getElementById("right_button");
 +
 +
var factory = new SubPageBuilderFactory();
 +
 +
/**@class Page
 +
* @description A class in charge of creating, updating, and destroying pages between page turns.
 +
* @param pageNum: the page number of the page (e.g. Home = 1, Team = 2, ...)
 +
* **/
 +
function Page(pageNum) {
 +
 +
    document.getElementById("igem_header").innerHTML = "reached Page constr: 1";
 +
    var subPageNum = 1;
 +
    var builder = factory.makeBuilder(pageNum);
 +
    var maxSubPage = builder.getMaxSubPage();
 +
 +
    this.destroyPage = function() {
 +
        while(leftPage.hasChildNodes()) {
 +
            leftPage.removeChild(leftPage.childNodes[0]);
 +
        }
 +
        while(rightPage.hasChildNodes()) {
 +
            rightPage.removeChild(rightPage.childNodes[0]);
 +
        }
 +
    };
 +
 +
 +
    this.turnPage = function(dir) {
 +
        subPageNum += dir;
 +
        this.destroyPage();
 +
        builder.createSubPage(subPageNum);
 +
    };
 +
 +
 +
    this.getSubPageNum = function () {
 +
        return subPageNum;
 +
    };
 +
 +
    this.getMaxSubPage = function() {
 +
        return maxSubPage;
 +
    };
 +
}
 +
 +
 +
var thisPage = new Page(thisPageNum);
 +
thisPage.turnPage(0);
 +
 +
/**@description These functions cause the Buttons on the page to change the SubPage when clicked.**/
 +
leftButton.onclick=function(){
 +
    thisPage.turnPage(-1);
 +
    updateButtons(thisPage.getSubPageNum());
 +
};
 +
 +
rightButton.onclick=function(){
 +
    thisPage.turnPage(1);
 +
    updateButtons(thisPage.getSubPageNum());
 +
};
 +
 +
function updateButtons(subPageNum) {
 +
    document.getElementById("igem_header").innerHTML = "reached updateButtons";
 +
    if(subPageNum == 1) {
 +
        leftButton.style.visibility = "hidden";
 +
        rightButton.style.visibility = "visible";
 +
    }
 +
    else if(subPageNum == thisPage.getMaxSubPage()) {
 +
        leftButton.style.visibility = "visible";
 +
        rightButton.style.visibility = "hidden";
 +
    }
 +
    else {
 +
        leftButton.style.visibility = "visible";
 +
        rightButton.style.visibility = "visible";
 +
    }
 +
}
 +
 +
</script>
</html>
</html>

Revision as of 07:22, 25 January 2015

Retrieved from "http://2014.igem.org/Template:Team:Vanderbilt/CSS"