Zachary T. Goldstein Week 9

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Electronic Lab Notebook

Purpose

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.

Data and Files

Scientific Conclusion

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. The specific clones chosen are:


HIV Structure in-Class Activity

BIOL368/F16

All class assignments:


All individual assignments:


All shared journals:

User: Zachary T. Goldstein

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