Bhamilton18 Week 4

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Electronic Notebook for Week 4

Content Portion

To begin this assignment I utilized Dr. Dionisio's starter zip file. The file came with a template of a chrome html page as well as an image. While creating our, Katie Wright and my's, website I used the html page as a template to start my own coding/editing, but deleted image that was linked to the URL.

To begin, Katie and I began researching "our favorite gene" the ASP1 gene located on the SGD website, https://www.yeastgenome.org/locus/S000002729#reference

  • This website along with NCBI Gene Database, Ensembl, and UniProt, were used to complete this assignment.*

Looking at each individual website we found the "content" needs.I.e. the standard name, systematic name, and name description for your gene, gene ID (found on all 4 websites*), DNA sequence*, protein sequence*, function*, and located differences between each site. We found the following:

  • Standard name: ASP1
  • Systematic name: YDR321W
  • Name description for your gene: "This Gene codes for L-asparaginase, which depletes levels of L-asparagine by hydrolyzing L-ASP into aspartic acid and ammonia. This molecule can be used to treat acute lymphoblastic leukemia. It also has low glutaminase activity and dependence." (This portion was paraphrased by Katie Wright based on the SGD Overview Page)
  • Gene ID: S000002729 (for SGD and Ensembl), P38986 (for UniProt) and 85192 (for NCBI)
  • DNA sequence:

ATGAAAAGCGATTCAGTTGAAATCACTACCATCTGCCCAGATGTTGAAAATTCTCAGTTT
GTTGTGCAAAGCAACTGTCCAGAGACTATTCCAGAGATTCTAAAGTCTCAAAATGCCGCT
GTGAATGGCAGCGGCATCGCTTGCCAACAACGTAGCTTACCAAGAATCAAAATCTTGGGT
ACCGGTGGTACTATTGCATCGAAAGCTATAGACTCCTCTCAAACTGCCGGCTATCATGTT
GACCTGACCATCCAAGATCTATTGGATGCCATTCCAGATATATCCAAGGTCTGTGACATT
GAATATGAGCAACTATGCAACGTGGATTCTAAAGACATAAACGAGGATATTCTTTATAAA
ATTTATAAGGGCGTCTCAGAATCGTTGCAGGCTTTTGACGGTATAGTTATTACCCATGGG
ACTGATACGCTATCTGAAACTGCATTCTTTATTGAAAGTACTATTGATGCTGGCGACGTT
CCTATTGTTTTTGTTGGTTCGATGCGTCCTTCAACCAGCGTTTCTGCTGATGGCCCTATG
AACCTTTACCAAGCAATTTGCATTGCTTCAAATCCAAAATCTAGAGGAAGAGGTGTTCTT
GTTTCCTTGAATGACCAAATTTCCTCTGGTTACTACATTACTAAGACGAATGCAAATAGT
TTGGATTCTTTTAATGTTAGACAAGGCTATTTAGGAAATTTTGTCAACAATGAAATTCAC
TACTATTATCCTCCTGTGAAACCGCAAGGTTGCCACAAATTCAAACTGAGAGTGGACGGT
AAGCATTTTAAATTACCAGAGGTTTGCATTTTATATGCTCACCAAGCCTTTCCGCCAGCT
ATAGTCAACTTAGTGGCAGATAAGTATGATGGTATTGTTCTTGCTACCATGGGTGCTGGT
TCATTGCCGGAGGAGGTCAATGAAACCTGCATGAAATTGAGTTTGCCGATCGTATATTCC
AAGAGATCGATGGATGGTATGGTGCCTATTGCCAACGTACCAAAGAAAGGTTCAAAGGAG
GATAATCTCATCGCATCTGGTTATCTAAGCCCTGAAAAGAGCAGAATCTTGTTACAATTA
TGTTTGGCAGGTAACTACACGTTGGAAGAAATTAAACATGTTTTCACTGGCGTCTATGGT
GGGTGA

  • Protein sequence:

MKSDSVEITTICPDVENSQFVVQSNCPETIPEILKSQNAAVNGS
GIACQQRSLPRIKILGTGGTIASKAIDSSQTAGYHVDLTIQDLLD
AIPDISKVCDIEYEQLCNVDSKDINEDILYKIYKGVSESLQAFDG
IVITHGTDTLSETAFFIESTIDAGDVPIVFVGSMRPSTSVSADGP
MNLYQAICIASNPKSRGRGVLVSLNDQISSGYYITKTNANSLDSF
NVRQGYLGNFVNNEIHYYYPPVKPQGCHKFKLRVDGKHFKLPEVC
ILYAHQAFPPAIVNLVADKYDGIVLATMGAGSLPEEVNETCMKLS
LPIVYSKRSMDGMVPIANVPKKGSKEDNLIASGYLSPEKSRILLQ
LCLAGNYTLEEIKHVFTGVYGG

  • Function: ASP1 codes for L-ASPase, an enzyme that depletes levels of asparagine in the blood when expressed in humans. (Also paraphased/explained to me by Katie Wright)

Coding Portion

Once the content was found, we began editing/coding our html page. First we utilized the Bootstrap website to find out a basis for formatting, image uploading and unique personal touches to the site. Unique touches such as color changes, the initial title of the page with the faded text, and the table section after the first question.

  • Color changes code: 
<div class="p-3 mb-2 bg-info text-white">Content Questions</div>
-The div creates the border/color for the text box on the website. The "Content Questions represents the given title of whatever you want the title to be, as seen in blue on our website.
  • Initial Title with Faded Text:
<h1>ASP-1<small class="text-muted">The Gene of the Decade</small></h1>
-The h1 represents the header and the "text-muted" represents the faded part of the text, as seen at the top of our website.
  • Table Section (Two Types):
<dl class="row"><dt class="col-sm-3">Standard Name:</dt>
  <dd class="col-sm-7">ASP1</dd>
</dl>
-The dl represents the creation of the table, and the dt represents the columns created. The col-sm-7 or 3 are where the text will be placed on the page, i.e. how far apart they are and what portion of the page with be covered. 
 <table class="table table-striped table-inverse">
            <thead>
              <tr>
                <th>Website Title</th>
                <th>Presentation Differences</th>
                <th>Content Differences</th>
              </tr>
            </thead>
            <tbody>
              <tr>
                <th scope="row">SGD</th>
                <td>Easiest to find answers for and well-labeled when searching information. Multiple tabs for further knowledge and explaination of the gene.</td>
                <td>Most thorough in content compared to the other four sites. Did not contain the protein sequence, but did have the DNA sequence.</td>
              </tr>
            </table>
-The table class gives the table a look of dark grays alternating in brighter and darker gray for a "striped" look. The thead represents the start/top line of the table, while tr starts the next row. The th code represents the header to each column and can be increased or decreased with an addition th tag. The th scope begins the row and a label for it, and td represents the preceding column items.

After Inserting the content in Unstyled lists under each question, I began adding stylistic changes.

  • Unstyled lists:
<ul class="list-unstyled">
  <ul>
    <li></li>
  </ul>
</ul>
-The ul class tag makes a unstyled lists which begins without a bullet point and then once an additional ul and li are added a bullet point appears. The second ul represents a "tab" of sorts and the li represents the beginning of a list.

Then for inserting hyperlinks I followed Dr. Dionisio's template and did the following code: 

 <a href=". . .">Description</a>
-The a href creates a hyper reference to a given URL. The "Description" section is what will be underlined and "clickable."

When choosing a photo for our page we looked for uncopyrighted images on the ASP1 gene. We wanted to focus on a microscope shot to give an idea of the genes shape and size.

  • To insert the photo, we once again used Dr. Dionisio's template as well as the Bootstrap Tutorial in order to center the photo.Here is the code:
 <div class="text-center">
      <img src="Saccharomyces_cerevisiae_SEM(640px).jpg" class="rounded" alt="Screenshot of ASP1 Gene">
      <figcaption class="figure-caption"> Image of Saccharomyces cerevisiae generated by a scanning electron microscope.</figcaption>
 </div>
-The img src represents the desired image to be added to the page. The class gives a look to the image, i.e. rounded edges. And the alt represents a description of the image. The figcaption is a caption that is added underneath the image on the page.

* See Reference/Acknowledgments Section for citations

Current Zip File for "Our Favorite Gene" Website

  1. Katie and Blair's Zip File

Acknowledgments

  1. I utilized the Bootstrap Tutorial Page for formatting help, table formation, image upload and unique style elements (i.e colors).
  2. I worked with my homework partner Katie Wright to collaborate on homework questions as well as the cs file uploads. We met in person going over our website look and content to post.
  3. Used Dr. Dionisio's starter zip file as a template for our website.
  4. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

References

  1. ASP1 asparaginase ASP1 [Saccharomyces cerevisiae S288C] - Gene - NCBI. (2017, September 14). Retrieved September 25, 2017, from https://www.ncbi.nlm.nih.gov/gene/851920
  2. ASP1 [Saccharomyces cerevisiae] - Protein - NCBI. Retrieved September 25, 2017, from https://www.ncbi.nlm.nih.gov/protein/KZV12561.1?report=fasta
  3. ASP1. Retrieved September 25, 2017, from https://www.yeastgenome.org/locus/S000002729#reference
  4. Das Murtey, M., & Ramasamy, P. (2016, October 14). [SEM Image of Brewer's Yeast]. Retrieved September 25, 2017, from https://upload.wikimedia.org/wikipedia/commons/thumb/9/95/Saccharomyces_cerevisiae_SEM.jpg/640px-Saccharomyces_cerevisiae_SEM.jpg
  5. LMU BioDB 2017. (2017). Week 4. Retrieved September 21, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_4
  6. Gene: ASP1. (2017, August 9). Retrieved September 25, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core%3Bg
  7. L-asparaginase 1. (2017, July 05). Retrieved September 25, 2017, from http://www.uniprot.org/uniprot/P38986
  8. Starr, B. (2017, March 2). Feed a Cold, Starve a Cancer? Retrieved September 25, 2017, from https://www.yeastgenome.org/blog/feed-a-cold-starve-a-cancer


Category Links
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