User talk:Isabel Gonzaga

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Week 10 Feedback

  • Question 3: Actually X and Y are pretty similar. Your correlation coefficient is not 1, but 0.72 is actually pretty high for this type of data. The curves for these two genes definitely have the same shape and are induced/repressed at the same time points as each other.
  • Question 7: Eukaryotes do not use operons. They would regulated genes using the same transcription factor, but they would not need to be arranged in the same location on the chromosome.

Kam D. Dahlquist 13:55, 10 December 2014 (EST)

Sample Data Relationship

I think there is a typo in your paper for the legend for figure 1. Probably that data is all from strain 1254 and not H37Rv. I found the following samples in the sdrf.txt file:

Mtb 1254 40 min. 0.05 mM DETA/NO (7 replicates)
GSM886377
GSM886364
GSM886347
GSM886327
GSM886320
GSM886295
GSM886253
Mtb 1254 control vs. 2h hypoxia (3 replicates)
GSM886373
GSM886232
GSM886273
Mtb 1254 day 0 vs. low oxygen day 4 (6 replicates)
GSM886355
GSM886348
GSM886339
GSM886294
GSM886264
GSM886248

Kam D. Dahlquist 19:59, 18 November 2014 (EST)

Week 8 Feedback

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

Kam D. Dahlquist 17:51, 22 October 2014 (EDT)

Week 7 Feedback

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

Kam D. Dahlquist 17:50, 15 October 2014 (EDT)

Week 2 Feedback

  • Thank you for submitting your assignment on time.
  • You could have provided some more specific details about the methods you used. In the future, combine the methods, results, and answers to questions into one combined narrative.

Kam D. Dahlquist 19:25, 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.
  • 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.
  • 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.
    • 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 18:54, 8 October 2014 (EDT)


Week 5 Feedback

  • Thank you for submitting your assignment on time.
  • The documentation of your research is very thorough.
  • A couple of notes regarding your wiki formatting:
    • It is customary to use 2 equals signs for the largest headings on your page since the page title itself uses 1 equal sign.
    • Please format your figures so that they are larger on the page. It is difficult to read the smaller figures.
  • In response to your shared journal reflection...
    • I'm not sure what you mean when you say that you are not certain about the functioning of the gene; do you mean gp120? Hopefully next week's journal club article will shed some light on that. The theta statistic is attempting to give one number to sum up the average genetic distance between a group of clones. The minimum and maximum values give an idea of the range of genetic diversity between clones, but theta tries to sum it up in one number. Theta can then be compared more easily to other theta values than trying to compare the min/max values because those could be outliers in the sample. Let me know if you have further questions.

Kam D. Dahlquist 17:54, 8 October 2014 (EDT)

Week 3 Feedback

  • Thank you for completing your assignment on time. Your bibliography, vocabulary list, and outline were all complete and accurate.

Kam D. Dahlquist 17:12, 8 October 2014 (EDT)

Week 4 Feedback

  • I am giving feedback in reverse order from Week 4 to Week 2 because that will be more useful to you right now.
  • Thank you for submitting your work on time.
  • Here is feedback on the electronic notebook pahow rt of the assignment regarding the Exploring HIV Evolution activity:
    • Do not separate your methods and results section; they should be integrated into one narrative that describes what you did, how you did it and the result of what you did.
    • You have started a good practice of providing hyperlinks to the resources you used. You could improve this by being more specific. For example, instead of just linking to GenBank, you could link to the individual record you looked at.
    • Activity 1/Part 2: you said that you downloaded 5 records into word, but which ones did you choose? did you confirm that they were in FASTA format?
    • Activity 1/Part 3: you did not show the tree or talk about how you relate the topology of the tree to differences in sequences.
    • Activity 2/Part 1: complete.
    • Activity 2/Part 2:
      • You did not show the trees for the individual subjects or the pairwise comparisons.
    • Concluding paragraph: complete.
    • Research question: complete--I look forward to seeing your results!

Kam D. Dahlquist 18:08, 24 September 2014 (EDT)

  • One more comment for next week, make sure to include some screenshots of the multiple sequence alignments and distance matrices, not just the trees.

Kam D. Dahlquist 18:14, 24 September 2014 (EDT)

Week 1 Redux

  • Thank you for making the changes listed below by this week's journal deadline. Here are some additional observations:
    • It looks like you will need to take extra biology classes next semester to graduate!
    • Make sure that you utilize the headings feature of the wiki. Make subheadings by using 3, 4, or 5 equals signs for your headers. This will be useful for your journal club outline on the Week 3 Assignment.
    • It looks like you put in all the links to the assignments, individual journal pages, and shared journal pages on your User page. You should move these over to your template.

Kam D. Dahlquist 18:23, 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.
    • I would like you to list all upper division courses in biology, chemistry, math, and computer science you have taken, not just the ones from the current semester.
    • Each time you save a change on a wiki page, you should write something in the Summary field. You are doing it roughly 2/3 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.
    • Make sure you know the difference of how to link to a page within the OpenWetWare wiki versus linking to a page external to the wiki. Also, make sure that you know how to format the labels on the links. Please fix the formatting of your links.
    • Please make a link to an external web site.
    • 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.
    • Make sure that you label your links correctly. The link you labled as "Isabel Gonzaga Week 1" actually goes to the Class Journal Week 1 page. Please change the label on this.
    • 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 18:57, 3 September 2014 (EDT)
  • I've answered your question on my user talk page.
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