User talk:Nicole Anguiano

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Week 10 Feedback

  • Your annotated figure for the structure analysis redux looks really good!
  • For question 6, the TCA cycle genes will be induced if glucose is running out so that the cell can produce more ATP through aerobic respiration. Yeast do glycolysis/fermentation first until all the glucose runs out and only then do they switch over to aerobic respiration.
  • For question 7, all of the genes could be regulated by the same transcription factor. Eukaryotes do not use operons like prokaryotes.

Kam D. Dahlquist 13:48, 10 December 2014 (EST)

Microarray Data

  • Nicole, use the updated spreadsheet that I uploaded (it's got the same name as your Excel spreadsheet, so you should just be able to follow the link). I put the IDs in and deleted the control spots. The sheet I labeled "scaled_centering" is what you should use to go on to the next step in the analysis" Kam D. Dahlquist 20:04, 2 December 2014 (EST)

Week 8 Feedback

  • Thank you for submitting your assignment on time.
  • Your assignment was complete and thoroughly documented.

Kam D. Dahlquist 17:50, 22 October 2014 (EDT)

Week 7 Feedback

  • Thank you for submitting your assignment on time.
  • Your outline was complete and thorough.

Kam D. Dahlquist 17:49, 15 October 2014 (EDT)

Week 2 Feedback

  • Thank you for completing your assignment on time.
  • In the future, please combine your methods/results/answers to questions into one narrative.

Kam D. Dahlquist 19:23, 8 October 2014 (EDT)

Week 6 Feedback

  • Thank you for submitting your assignment on time.
  • You have answered all of the questions and documented your methods in your electronic notebook. In the future, make the methods/results/answers to questions one continuous narrative, instead of breaking it out into individual sections.
  • To clarify, the structure of the hOGG1 protein is actually a tertiary structure; it is a single polypeptide. It could be considered as being a quaternary structure because it is bound to DNA, but the protein structure itself is tertiary. The presence of absence of different domains does not determine the difference between a tertiary or quaternary structure. The number of polypeptide chains does.
  • This protein only has 3 domains. You might have been confused by the blue domain (see below).
  • To answer your questions from your shared journal reflection...
    • This exercise actually guided you through an attempt to understand protein function based on structure. You looked at the position of the oxidized base relative to the protein structure. It is often the arrangement of the molecule with respect to the binding partner that matters the most. As with many things, more experience at doing this helps.
    • Domains are a difficult concept to grasp because there is both a structural component to them and a functional component to them. In terms of structure, if you can cut the polypeptide backbone at just one or two spots and still get a fully folded section of the protein, then that section is a domain. This is often determined experimentally by cutting the polypeptide in vitro. When looking at the structure in Cn3D, you can ask do the different domains pass the "hula hoop" test. That is, can you pass a hula hoop around them and not touch another part (domain) of the protein. The purple and brown domains shown in Cn3D pass this test. The other is a functional definition in that the region of the protein has a single function. The blue domain doesn't pass the former test because the backbone would have to be cut in multiple places, but likely it passes the functional test. This can't be determined from the structure picture alone.

Kam D. Dahlquist 19:03, 8 October 2014 (EDT)

Week 5 Feedback

  • Thank you for completing your assignment on time.
  • It was helpful that you put the link to your presentation at the top of the page.
  • The documentation of your research project was very thorough. A couple of notes:
    • It would be better to give theta as a number instead of a fraction to facilitate comparisons.
    • As discussed in class, the way that you chose your clones was not truly "random".
  • In response to your shared journal reflection:
    • We were only looking at one narrow aspect of HIV infection, the genetic diversity and divergence of the gp120 V3 sequence. This is only one portion of one protein in the viral genome and we were only looking at sequence diversity and not relating it to function. In the next project, we will attempt to look at structure > function relationships. This also focuses on the virus itself. How the patient responds to the virus is also dependent on genetic and environmental factors of the patient.

Kam D. Dahlquist 17:45, 8 October 2014 (EDT)

Week 3 Feedback

  • Be sure to complete your assignments by the deadline.
  • Your assignment was complete, except for a few things for your outline. Be sure to explain all the figures and tables in your outline, even if you are not assigned to present them in class. Also, your outline was missing the comparison with other studies that Markham et al. (1998) talked about in their Discussion section.

Kam D. Dahlquist 17:08, 8 October 2014 (EDT)

Week 4 Feedback

  • I am giving feedback in reverse order from Week 4 to Week 2 because that will be most useful to you.
  • Thank you for submitting your Week 4 journal on time
  • You have performed a very thorough documentation of your work in your electronic lab notebook and have an excellent discussion of your results. A couple of minor points:
    • You can combine your methods/results/answers to questions into one narrative instead of separating it out by those sections. This will make things flow better and cut down on the redundancy of what you are saying in response to the questions.
    • You can make your images larger on the page. You are using the formatting that was used to create the "thumbnail" images on the User pages with the border and caption. In this case, larger images would be preferable to better see your results. You can leave out that code to see the image at its native size. If you still want to control the size of the image, there is wiki formatting you can look up that does so.
  • Looking forward to your research presentation next week.

Kam D. Dahlquist 18:27, 24 September 2014 (EDT)

Week 1 Redux

  • Thank you for completing all of the skills on the wiki checklist from Week 1 by this week's deadline.
  • Since your CMSI 499 is your research project, you don't need to list it separately under courses; it is already covered by your research section.

Kam D. Dahlquist 18:12, 10 September 2014 (EDT)

Week 1 Journal Feedback

  • I've finished reviewing your Week 1 assignment and have the following feedback for you. You will have the chance to earn back the points you missed on this assignment by fixing the items below by the Week 2 journal deadline of midnight on Wednesday, September 10.
  • Please be sure to submit all aspects of the assignment on time. Your e-mail to me, as well, as your personal interests/hobbies section of your user page were submitted late.
    • Each time you save a change on a wiki page, you should write something in the Summary field. You are doing it roughly half of the time, but the goal is to do it every time you save a change.
    • You did not technically make a link to a new wiki page, you just linked to existing pages within our wiki. This should be fulfilled by creating your Week 2 journal page.
    • Your external link to LMU should probably go to the LMU home page instead of MYLMU. People who click on that link will expect to go to a general info page, not to an intranet that they can't access.
    • You created a numbered list, but only on the Class Journal page. The assignment was to demonstrate a numbered list on your user page.
    • Make sure that you use multiple levels of headings, not just 2 equals signs, but 3 or more for subheadings.
    • Make sure that you "comment out" something on your user page. The only comments were the ones automatically placed there by OpenWetWare.
    • You need to upload an image file and display it on your page.
    • You need to upload another type of file and link to it on your page.
    • You can delete the automatic text from this talk page after you have read it. You can also delete the I'm a new member of OpenWetWare banner on your user page.
  • Please let me know if you need any assistance with making these changes. Kam D. Dahlquist 19:09, 3 September 2014 (EDT)
  • I've answered your question on my user talk page.