User talk:Chloe Jones

Week 7 Feedback

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

— Kam D. Dahlquist 17:48, 15 October 2014 (EDT)

Week 2 Feedback

• Thank you for submitting your assignment on time.
• Don't forget to add your template to your individual journal page so that all of the links requested in the assignment are present.
• 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 19:26, 8 October 2014 (EDT)

Week 6 Feedback

• Thank you for submitting your assignment on time.
• You completed all of the questions and documented your methods completely in your electronic lab 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.
• I think you have some confusion as to exactly what is being oxidized. It is the G base in the DNA that is being oxidized, not the amino acids in the protein. The job of the DNA glycosylase enzyme is to remove the damaged DNA base from the DNA strand. Oxidation is anyreaction in which electrons are lost, so in general, amino acids and proteins can both be oxidized. In practice, certain atoms in certain bases or amino acids have a higher propensity to being oxidized than others, hence the evolution of an enzyme that is specific for removing oxidized guanosine.
• Also, what exactly do you want to know about the roles of atoms in proteins?

— Kam D. Dahlquist 18:42, 8 October 2014 (EDT)

Week 5 Feedback

• Be sure to submit your journal assignment on time.
• Your research project was complete, but you could have included some more details regarding your methods in your electronic notebook.
• The overall organization of your wiki page is a little confusing with tables and text and figures interspersed. It would be easier to read if it was in a more linear order and some of the figures were larger.
• In answer to your shared journal reflection...
  • I agree with you that if we could somehow follow the evolution of individual clones of the HIV virus, we would learn some valuable information. However, doing that is technically impossible. The way the study was done, blood samples of the patients were taken at 6 month intervals and the sequences of the virus found in the blood were analyzed. There is no way to track how one particular sequence mutated into a different one unless we were able to tag it somehow and put it back into the patient. Some sequences that were there at one visit might also completely disappear due to the immune system of the patient and others would evolve and take their place. Unfortunately, there is just no way for us to know what is happening to individual viruses within the patient. Let me know if this now makes sense.

— Kam D. Dahlquist 18:04, 8 October 2014 (EDT)

Week 3 Feedback

• Thank you for completing your assignment on time.
• All of the content of your bibliography, vocabulary terms, and outline was complete except that you did not include the comparison with other studies that Markham et al. (1998) talked about in their Discussion section.

— Kam D. Dahlquist 17:10, 8 October 2014 (EDT)

Week 4 Feedback

• I am giving feedback in reverse order from Week 4 to Week 2 because this feedback will be most relevant to you now.
• Thank you for submitting your work on time.
• Don't forget to add your template to each of your individual journal pages. Because you omitted the template, you are missing the link to your user page and assignment page from your individual journal page and the category.
• Overall, you need to provide more detail in your electronic notebook. Be careful to state exactly what you did following the protocol and to record all the relevant information. The following were missing or needed to be clarified in your notebook:
  • Activity 1/Part 2: did you download 4-6 sequences into Word and confirm that they were in FASTA format?
  • Activity 1/Part 3: you did not show the practice tree you generated for this section or discuss how you relate the specific topology of the tree you created to the differences in sequences.
  • Activity 2/Part 1:
    • Please list the subjects and clones you chose for this part of the exercise. I found it in your concluding paragraph, but it should be listed here as well.
    • Please answer whether the clones from each subject clustered together.
    • Your discussion of whether some subject's clones showed more diversity than others is found in your concluding paragraph, but should also be answered here.
    • Briefly discuss your tree and the evolutionary relationships.
  • Activity 2/Part 2:
    • Please show all of the alignments you generated for this section of the activity. There should be an alignment for each subject individually and one for each pair of subjects compared.
    • There is an error in the way you calculated the min and max differences. Those numbers should be between 1 and 285, because they are the minimum and maximum number of nucleotide differences between clones. If the percent difference was 0.1, then you should multiply 0.1 X 285, which would be 28.5, then round to the nearest integer, which would be 28. It seems you multiplied by much larger numbers.
  • One other note. When reporting numbers < 0, please use leading zeros. For example, say 0.1 instead of just .1.
• I think I understand your research question, but I just want to clarify what you mean by subjects 1 and 2 overlapping on the phylogenetic tree.

— Kam D. Dahlquist 17:47, 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 18:15, 24 September 2014 (EDT)

• I forgot to add that I discussed your question with you and it has been clarified for me. I look forward to your presentation next week!

— Kam D. Dahlquist 18:28, 24 September 2014 (EDT)

Week 1 Redux

• Thank you for making the requested changes by this week's deadline. Here are some further comments:
  • You should be in the habit that each time you save a change on a wiki page, you should write something in the Summary field that is just above the row of buttons. This should be a short description of the changes you made. These show up when you view the list of changes on the History tab. You're doing it roughly half or less the time now and you should aim for every time you save a change.
  • You have made a list of links to the Assignment and Class Journal pages on your User page. You should move this over to your template instead. Also, don't forget to add the [[Category:BIOL368/F14]] to your template so that it appears on your user page and all of your journal pages.
  • Make sure that when you are linking to a page within our wiki, you use the within-wiki formatting, like [[BIOL368/F14]] instead of the format for linking to an external site, like [http://www.openwetware.org/wiki/BIOL368/F14]. Right now the links on your template should be like the former, but are formatted like the latter.
  • Be sure you know how to make sub-headings by using the equal signs. This will be useful when making your outline for the Week 3 Assignment.
  • Are you sure that the file you uploaded is a .pdf format? It's opening as if it is actually a .png image.

— Kam D. Dahlquist 18:42, 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 your assignment on time. Your e-mail to me and the question you posted on my talk page came after the deadline.
• In terms of the content of your user page:
  • I suggest that you put your on campus box address instead of your actual home address, to protect your privacy.
  • 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.
• It seems that you are a still a little unsure of how to do some of the wiki skills. Specifically:
  • Each time you save a change on a wiki page, you should write something in the Summary field that is just above the row of buttons. This should be a short description of the changes you made. These show up when you view the list of changes on the History tab.
  • You did create a link to a page within our wiki called Chloe Jones, however, don't confuse this with your actual user page which is User:Chloe Jones. You should remove the former link from your 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 go to the People page and link your name there to your user page.
  • 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.
  • Be sure to add the BIOL368/F14 category to your template so that it appears on your User page and other pages.
  • 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.
• I think that you should still consider yourself a biologist. Don't sell yourself short. Even though you may not have as much experience and knowledge as someone who has a Ph.D. and multiple years of experience, as a senior biology major, you still have much more knowledge and experience than the average person on the street!
• Please let me know if you need any assistance with making these changes. — Kam D. Dahlquist 18:42, 3 September 2014 (EDT)
• I've answered your question on my user talk page.

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Hello, Chloe Jones! This is a welcome message from OpenWetWare. By the way, we've announced you on the home page! You can leave messages to any OWW member by editing their User_talk pages like this one. And don't forget to personalize your User Page so that we can get to know you better! We've included some tips below to get you started.

Basic Wiki Instructions

• Don't be afraid to edit! As with all pages on the wiki, all versions are saved so its easy to undo. If you have any questions feel free to send us an email.

1. Start off by clicking the 'edit' button to the right of this section, or at the top of the page.
2. Now you should see the text of this section as text within an editor box. There are several buttons in the editor box, but don't worry about those for now. Just type something in the box, scroll down to the bottom, and hit the 'Preview' button.
3. You should see the web-page and text box views, but now with your edits! Don't forget to save your changes by clicking 'Save Page'!
4. Editing pages is as easy as that. There are of course many ways to format your text. The easiest way to learn is to find an OWW page with the formatting you like, click on the edit button again, and see for yourself how it was created in the text box. Here's an extensive list of formating examples. Or look at this OpenWetWare introductory tutorial.
5. When you are done, remove these instructions by clicking the edit button for this section again, erase everything you see in the text box and click 'Save Page'. (And remember you can always retrieve these by clicking on the 'history' tab at the top of this page.)

Note that these instructions apply to any page on OWW. Feel free to contribute to OWW by editing pages to add content, update them, or even correct mistakes. OWW relies on an active community to manage our growing resource of open access information, and we need your help!

Personal/Lab Info

We have gone ahead and filled in some information you provided us in your membership application on your User Page. Please take a moment to embellish this and tell the community a little more about you. Put links to your lab pages, your projects and your interests. If you run out of ideas, take a look at some of the other User pages. For example, check out User:Julius_B._Lucks, User:Jason_R._Kelly and User:Reshma_P._Shetty.

You'll also notice that we have put an 'image' placeholder at the top of your User Page. We encourage you to upload an image of yourself to give OWW a more personal feel. To upload an image, click on the Upload file link on the left-hand side (toolbar). Choose a file from your computer, and remember the file name. After you have uploaded the image, you should see it loaded on its own page. Go back to your User Page, click on edit, and replace 'OWWEmblem.png' with the name of your file that you have uploaded in the second line of this page.