Week 3
This journal entry is due on Thursday, September 19, at 12:01am Pacific time.
Contents
Overview
The purpose of this assignment is:
- To acquaint you with four major biological databases and the information that is typically documented, gathered, or collected regarding a gene.
- To relate a paper and pencil gene model to actual gene sequences and tools used to manipulate them on the web.
- To give you additional practice time with editing the wiki and managing files.
Individual Journal Assignment
- Store this journal entry as "gene name Week 3" (i.e., this is the text to place between the square brackets when you link to this page). Each partner will contribute to one journal page for this week.
- Create the following set of links. (HINT: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.) Each partner would invoke their template on the shared page.
- Link to your journal entry from your user page.
- Link back from your journal entry to your user page.
- Link to this assignment from your journal entry.
- Don't forget to add the "Journal Entry" category to the end of your wiki page.
Homework Partners
You are expected to work with your homework partner, in order to complete the assignment. For this week, you and your partner will work together on one wiki page. Homework partners for this week are: You must give the details of the interaction with your partner in the Acknowledgments section of your journal assignment. Homework partners for this week are:
- Christina and Naomi : RAD53 / YPL153C
- DeLisa and Joey: CMR2 / YOR093C
- Emma and Michael ASP1 / YDR321W
- Ivy and Aby: HSF1/YGL073W
- Kaitlyn and Iliana ILT1/YDR090C
- Marcus and David: CDC28/YBR160W
- Mihir and Jonar: FAS2 / YPL231W
Paper and Pencil Assignment
You will turn in individually the completed paper and pencil assignment that was handed out in class on Thursday, 9/12/19. The paper copy is due at the beginning of class on Thursday, 9/19/19.
“My Favorite Gene”
With your homework partner, you will create a wiki page (one page shared by both partners) that displays the relevant information for a “favorite gene.” (OK, so maybe you don’t really have a favorite gene—but it makes for a fun assignment title)
For this exercise (and the rest of the semester), we will focus on budding yeast (a.k.a. Baker's yeast, Brewer's yeast, Saccharomyces cerevisiae) as a model organism. A model organism is used for research because it has some property that makes it easy to study the phenomenon of interest. Budding yeast is a simple, single-celled eukaryote that shares fundamental properties with human cells, yet is much easier to study. A lot of foundational work in understanding cancer, for example, was performed in yeast.
For the Week 3 exercise, you will select your favorite yeast gene to highlight.
- To choose your gene, visit the Saccharomyces Genome Database (SGD), a model organism database that aims to be a one-stop shop for yeast data.
- You can search for a gene or protein in the search field or browse the resources at the site through the various tabs. If you do not already have a gene in mind that you want to find, the curators at SGD maintain a blog to highlight interesting research. Browse through the Research Spotlights or Yeast and Human Disease categories for inspiration.
- You may not use the same gene as another group. Gene choices are first-come, first-served. To claim your gene, edit this page, listing the gene you have chosen next to the names of you and your homework partners.
- Once you have identified your gene, you will look it up in four different databases and create a summary of what you have learned about your gene on you and our partner's wiki page. The four databases are:
- SGD itself
- NCBI Gene Database
- Ensembl
- UniProt
- The summary should be one paragraph about the function of your gene based on what you have read in each of the four databases. This is one paragraph that synthesizes information, not one paragraph per database.
- Provide the following additional information about your gene on your wiki page:
- What is the standard name, systematic name, and name description for your gene (from SGD)?
- What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
- Provide hyperlinks to the specific pages for your gene in each of the above databases.
- What is the DNA sequence of your gene?
- What is the protein sequence corresponding to your gene?
- Go to the ExPASy tool and translate the DNA sequence of your gene. Which reading frame encodes the protein sequence? Take a screenshot of your results, display it on your wiki page, and state which frame it is.
- What is the function of your gene?
- What was different about the information provided about your gene in each of the parent databases?
- Were there differences in content, the information or data itself?
- Were there differences in presentation of the information?
- Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
- Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
- Please make the image something scientific (not like the random images seen on the SGD blog posts).
- If a 3D structure of the protein your gene encodes is available, you can choose to embed a rotating image of the structure on your page using the FirstGlance in Jmol software. This is optional, a different static image would be OK, too.
- Include Acknowledgments and References sections on your wiki page. Both partners should sign the Academic Honesty statement with their wiki signatures.
- You need to cite the specific database page from which you derived your information for each of the questions.
- When answering the free-form questions, be sure to paraphrase.
- Store your journal entry in the shared Class Journal Week 3 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
- Link to your journal entry from your user page.
- Link back from the journal entry to your user page.
- NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.
- Sign your portion of the journal with the standard wiki signature shortcut (
~~~~). - Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).
Read & Reflect
- Ford, Paul. “What is Code?” Business Week, June 11, 2015. This is a long article—but quite worthwhile. If you can read it in one sitting, go right ahead; we will focus on specific parts at various points in the semester.
This week focuses on the first two sections of this article: “The Man in the Taupe Blazer” and “Let’s Begin.”
- Pull out a quote from the first two sections of “What is Code?” that you find particularly interesting. Explain why this quote is particularly resonant for you.
- What is something from the first two sections that you need further explanation of or that you want to know more about?
- Also, out of the four databases you accessed for this assignment (SGD itself, NCBI Gene Database, Ensembl, UniProt), which did you like the best, and why? Which did you like the least, and why? (Refer back to the question about differences in content or presentation that you noted on your gene's wiki page.)
