Zachary T. Goldstein Week 9: Difference between revisions

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#***First visit clones: 6,1,2
#***First visit clones: 6,1,2
#***Last visit clones: 4,9,13
#***Last visit clones: 4,9,13
=HIV Structure in-Class Activity=




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=References=
=References=
 
*[[BIOL368/F16:Week 9]]
 
*[https://www.ncbi.nlm.nih.gov/orffinder/ NCBI Open Reading Frame Finder]
*[http://web.expasy.org/translate/ ExPASY Translate tool]
*[http://www.uniprot.org UniProt Knowledgebase (UniProt KB)]
*[https://ppopen.informatik.tu-muenchen.de/ PredictProtein server]




Revision as of 15:04, 27 October 2016

Electronic Lab Notebook

Purpose

  • The purpose of this assignment was to explore programs and databases that give information on proteins, analyze gene regions, and study the relationship between structure and function of amino acids so that we can design our structure HIV-1 project question and hypothesis. Additionally we identified which subjects and clones we want to use in our study.

Methods and Results

  • Each translation gives 6 reading frames: +1,+2,+3,-1,-2,-3.
  • A complete open reading frame includes a start codon which is a multiple of 3 away from a stop codon...this is not possible given sequences because we only have a segment of the protein.
  • We do not want a stop codon in our sequences, out of the 6 frames given, you decide which one the true reading frame is based on whether there is a stop codon. No stop codon means it is the true frame.
  • 1/6 frames should not have a stop codon in it, it may include a Methionine, but the Methionine is not necessarily the start codon.
  1. How do you know which of the six frames is the correct reading frame (without looking up the answer)?
    • The reading frame that does not include a stop codon because we are analyzing a middle segment, in this case it is Frame 1.
  2. If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
    • 206,000 results
  3. What types of information are provided about this protein in this database entry via "P04578" search?
    • This database reveals information about the proteins functions, where it is located, where certain information are published, links to enzyme and pathway related databases, protein family related databases, names/alternative names/gene names, organisms in which it can be found, sub-cellular location, interactions with other molecules, structure, and much more.
  4. Paste one of the amino acid sequences from Markham et al. (1998) into the input field and submit. Explore the types of information provided. How does this information relate to what is stored in the UniProt database?
    • It is a lot less comprehensive but more visually pleasing. It gives different types of information such as an interactive figure that you can zoom in on, sequence length, number of alligned proteins, and a figure denoting amino acid composition. There are links within the program that take you to the UniProt database for further information.

Data and Files

GO BACK AND GET SCREEN SHOTS

Scientific Conclusion

  • In this lab software was used to analyze proteins and amino acid structure in preparation for studying how structure relates to function. The main conclusion of our assignment was that we decided what our question and hypothesis will be for our HIV-1 structure project. We concluded that, because a lower dS/dN ratio indicates a higher nonsynonymus mutation rate (given that nonsynonmous mutations change structure more than synonymous mutations), subjects from the Markham study who had ratios of 0 would demonstrate high variation in amino acid structure, and consequently function. We concluded that we would also included sequences from subjects demonstrating the highest ratio values to accentuate the difference in data during analysis and the tree formation.

HIV Structure Research Project

  1. What is your question?
    • Will subjects demonstrating a low dS/dN ratio value show high variation and dissimilar relationships between each other when examining their respective amino acid sequences and will subjects demonstrating high dS/dN ratio values show low variation and closer relationships when examining their amino acid sequences both individually and comparatively.
  2. What is your prediction before performing analysis?
    • If we extract and compare subjects from the Markham paper who exhibited very high and very low non-synonymous mutation rates and compare the amino acid sequences from their last visits, we will find high variation between them both structurally and functionally because the subjects with lower ratios will have experienced more mutations which caused changes in their amino acid sequencing.
  3. Which subjects, visits, and clones will you use to answer your question?
    • Subjects were selected with the same criteria from week 6 presentation Media:HIV1Presentaionzachandshivum.pdf due to selection for "extreme" dS/dN values. Eight subjects were chosen, the four exhibiting the highest dS/dN ratios and the four exhibiting the lowest dS/dN ratios. Due to inconsistencies in subject's visits, we decided to use three clones from the subjects' first (of which everyone's is the same) visit and last (of which some subjects were different) visit. For example, Subject 2's last visit was after 4 years, but subjects 4's last visit was only after 1.5 years. Random selection was used to determine which 3 clone sequences were compared within each visit. The specific clones chosen are:
      • Subject 2
        • First visit clones: 1,6,4
        • Last visit clones: 8,6,1
      • Subject 4
        • First visit clones: 1,2,3
        • Last visit clones: 8,10,7
      • Subject 5
        • First visit clones: 2,5,1
        • Last visit clones: 3,4,5
      • Subject 7
        • First visit clones: 7,9,3
        • Last visit clones: 7,4,5
      • Subject 9
        • First visit clones: 4,2,5
        • Last visit clones: 1,4,7
      • Subject 11
        • First visit clones: 7,5,4
        • Last visit clones: 7,6,3
      • Subject 13
        • First visit clones: 2,1,3
        • Last visit clones: 2,5,6
      • Subject 14
        • First visit clones: 6,1,2
        • Last visit clones: 4,9,13


Acknowledgements

  • I received help on this assignment and collaborated on our HIV structure project question, hypothesis, and subject selection with User: Jordan T. Detamore
  • While I received help on this assignment everything was completed by me and was not copied from anybody else

Zachary T. Goldstein 19:54, 25 October 2016 (EDT)Zachary T. Goldstein

References



BIOL368/F16

All class assignments:


All individual assignments:


All shared journals:

User: Zachary T. Goldstein

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