AVM BIOL368 Week 9: Difference between revisions
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*For rapid progressors we are looking at subject 3 and 10's first and last visits and for non-progressors we are looking at subject 12 and 13's first and last visits. These were chosen based on similar number of visits. | *For rapid progressors we are looking at subject 3 and 10's first and last visits and for non-progressors we are looking at subject 12 and 13's first and last visits. These were chosen based on similar number of visits. | ||
'''In-Class Structure Activity:''' | |||
*Convert a DNA sequence into an amino acid sequence using [http://web.expasy.org/translate/ ExPASY Translate tool]. | |||
**You will notice you are given multiple reading frame options. Since we are not given the complete open reading frame, the option to chose will be the reading frame that does not contain a stop codon. | |||
*Obtain the remaining sequences from the bedrock webpage. | |||
[[Image:Readingframeoptionsavmbiol368.png]] | |||
*Open [http://www.uniprot.org UniProt Knowledgebase (UniProt KB)] and search HIV-1 and gp120. | |||
**If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get? | |||
***You will get 563,418 results and 207,983 results respectively. | |||
**Use the entry with accession number "P04578" which corresponds to the reference entry for HIV gp120. | |||
***What types of information are provided about this protein in this database entry? | |||
****It is the env protein gp160 (gp41 and gp120 collectively) which binds to the CD4 receptor. All known information about this protein is available through this page. | |||
*Using [https://ppopen.informatik.tu-muenchen.de/ PredictProtein server] input an amino acid sequence from the Markham study. | |||
**This website gives a summary of the amino acid composition, predicted regions, etc. (Photo below). | |||
[[Image:AVMPredictprotienbiol368.png]] | |||
==Data and Files== | ==Data and Files== | ||
* [http://bioquest.org/bedrock/problem_spaces/hiv/ BEDROCK HIV Problem Space] | |||
** [http://bioquest.org/bedrock/problem_spaces/hiv/sequence_data.php Sequence Data] | |||
==Conclusion== | ==Conclusion== | ||
==Acknowledgments== | ==Acknowledgments== | ||
*Worked in collaboration with research partner [[User:Mia Huddleston| Mia Huddleston]] in class. | |||
**We agreed on our presentation topic for next week. | |||
*Template followed from week 9 assignment [http://openwetware.org/wiki/BIOL368/F16:Week_9 BIOL368/F16] | |||
*Help from our professor, [[User:Kam D. Dahlquist|Dr. Dahlquist]] in class. | |||
*Note: While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. | |||
[[User:Avery Vernon-Moore|Avery Vernon-Moore]] 19:45, 25 October 2016 (EDT) | |||
==References== | ==References== | ||
Line 27: | Line 48: | ||
#* [http://www.pnas.org/content/95/21/12568.long Publisher Full text] | #* [http://www.pnas.org/content/95/21/12568.long Publisher Full text] | ||
#*[http://www.pnas.org/content/95/21/12568.full.pdf+html PDF]. | #*[http://www.pnas.org/content/95/21/12568.full.pdf+html PDF]. | ||
#* [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=8099 Kwong et al. (1998) structure 1GC1] | |||
#*[http://www.uniprot.org UniProt Knowledgebase (UniProt KB)] | |||
#*[https://ppopen.informatik.tu-muenchen.de/ PredictProtein server] | |||
#*[http://web.expasy.org/translate/ ExPASY Translate tool] | |||
*{{Template: Avery_Vernon-Moore}} | |||
{{Template: Avery_Vernon-Moore}} |
Revision as of 16:55, 25 October 2016
Purpose
The purpose of this weeks lab is to define my HIV structure project and complete this in-class HIV structure activity.
Methods and Results
HIV Structure Project: What is your question?
- Does diversity and divergence increase within the amino acid sequences over time more within the rapid progressors compared to non-progressors?
Make a prediction about the answer to your question before you begin your analysis.
- Since divergence and diversity increases over time within the DNA sequences for all progressor types, and more so within the rapid progress ors, we would expect to see more diversity within the amino acid sequences over time within the rapid progressors.
Which subjects, visits, and clones will you use to answer your question?
- For rapid progressors we are looking at subject 3 and 10's first and last visits and for non-progressors we are looking at subject 12 and 13's first and last visits. These were chosen based on similar number of visits.
In-Class Structure Activity:
- Convert a DNA sequence into an amino acid sequence using ExPASY Translate tool.
- You will notice you are given multiple reading frame options. Since we are not given the complete open reading frame, the option to chose will be the reading frame that does not contain a stop codon.
- Obtain the remaining sequences from the bedrock webpage.
- Open UniProt Knowledgebase (UniProt KB) and search HIV-1 and gp120.
- If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
- You will get 563,418 results and 207,983 results respectively.
- Use the entry with accession number "P04578" which corresponds to the reference entry for HIV gp120.
- What types of information are provided about this protein in this database entry?
- It is the env protein gp160 (gp41 and gp120 collectively) which binds to the CD4 receptor. All known information about this protein is available through this page.
- What types of information are provided about this protein in this database entry?
- If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
- Using PredictProtein server input an amino acid sequence from the Markham study.
- This website gives a summary of the amino acid composition, predicted regions, etc. (Photo below).
Data and Files
Conclusion
Acknowledgments
- Worked in collaboration with research partner Mia Huddleston in class.
- We agreed on our presentation topic for next week.
- Template followed from week 9 assignment BIOL368/F16
- Help from our professor, Dr. Dahlquist in class.
- Note: While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Avery Vernon-Moore 19:45, 25 October 2016 (EDT)
References
- Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, 12568-12573. doi: 10.1073/pnas.95.21.12568
Weekly Assignments:
Assignment 1 Assignment 2 Assignment 3 Assignment 4 Assignment 5 Assignment 6 Assignment 7 Assignment 8 Assignment 9 Assignment 10 Assignment 11 Assignment 12 Assignment 14 Assignment 15
Individual Journals:
"Week 1: Create Wiki Page" Individual Journal 2 Individual Journal 3 Individual Journal 4 Individual Journal 5 Individual Journal 6 Individual Journal 7 Individual Journal 8 Individual Journal 9 Individual Journal 10 Individual Journal 11 Individual Journal 12 No Week 13 Assignment Individual Journal 14 Individual Journal 15
Class Journal 1 Class Journal 2 Class Journal 3 Class Journal 4 Class Journal 5 Class Journal 6 Class Journal 7 Class Journal 8 Class Journal 9 Class Journal 10 Class Journal 11 Class Journal 12 Class Journal 14 Class Journal 15