Dahlquist:SURP 2019 Schedule

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Week 1

Week 2

Alice

  • Alice updated protocol with links to archived files on GitHub.
  • TO DO (Alice): Organize the main stem results for each strain so that the same profile is all down one column, add it to the summary PowerPoint.
  • TO DO (Alice): For profiles that are the same across strains, she will determine whether the Gene Ontology terms are the same or different for the profile. She can use Microsoft Excel to do this based on a protocol on this page. Searches for a tool that can compare two GO term lists turned up the following:

Alyssa & Susanne

  • Alyssa created protocol page for Preparing Cheek Cell Lysate based on the BIOL 478 Lab 5 prep list and protocol.
  • Alyssa and Susanne prepared 24 tubes of 0.9% saline.
  • They prepped cheek cell lysate from 5 individuals, three of whom were the same from the Spring BIOL 478 class. These were performed as repeats so that we could verify that we got the same results as before.
  • They performed the PCR reaction on those samples + lysate from the three matching individuals from BIOL 478, ran the gel, and purified the PCR products according to this protocol.
  • The three control PCR products were sent to be sequenced.

Week 3

Alyssa & Susanne

Completed

  • Set up search alerts for PubMed for several variations on key terms
  • Analyze sequencing results: Susanne updated her notebook and uploaded edited text files to Box. Blast2Seq to reference sequence on the protocol page.
  • Set up cited reference alerts for key articles through Web of Science.
  • RFLP analysis complete for the PCR samples prepped during Week 3.
  • TOPO cloning of 448 bp fragment TT sample, CC sample.
    • Prepare LB liquid media and plates for cloning (6/4/19).
    • Perform control PCR from TOPO kit (6/5/19).
    • Perform TOPO cloning reaction on vector-only control, vector+control insert, TT sample, CC sample (6/5/19).
    • Transform with the above + pUC19 control plasmid + negative control (water) (6/5/19).
    • Pick transformants: streak on fresh plate (6/6/19).

Week 4

Alice

  • Began modeling experiments
    • Variable inclusion of strain data for db5
      • Made a list of experiments in Excel to keep track.
      1. wt-only
      2. wt + each strain individually
      3. wt + 2 strains
      4. wt + 3 strains
      5. wt + 4 of the five deletion strains (in other words, leaving one deletion strain out)

Alyssa & Susanne

TO DO

  • Computer work:
    • Scan through the Web of Science results for the Tishkoff paper; alternately do a cited reference search on the Lewinsky et al. (2005) paper.
    • Look at dbSNP to make a list of SNPs in the region, then search for their related papers in PubMed.
    • Start to flag papers in bibliography as "Key papers" that we want to read in more depth. One needs to be selected for journal club given in week 5 of SURP.
    • Need to mark FaqI restriction sites on reference sequence on protocol page.
  • Lab work:
  • PCR (gel), and restriction digests (gel) to confirm cloning.
  • Sequence clones, need 15 to 20 μL of purified plasmid and PCR DNA at concentrations between 50-100 ng/μL for Laragen

Completed

Alyssa & Susanne

  • Inoculate O/N cultures (Sunday 6/9/19).
  • Mini-preps (gel), 6/10/19


Week 5

Alice

TO DO

Alyssa & Susanne

TO DO

Journal Clubs

Week 2 (May 28, 2019)

Week 3 (June 3, 2019)

Week 4 (June 10, 2019)

Week 5 (June 17, 2019)

Week 6 (June 24, 2019)

  • Research presentations

SURP Workshops

  • Thursday, May 30, 12:00-1:00, UH 3999 (McIntosh Center): Making Research Relevant Across Cultures (Alyssa, Susanne, Dr. D)
  • Wednesday, June 5, 11:30-12:30, WHH 118 (Library): Are You LinkedIn, or Left Out? (Alyssa, Susanne)
  • Thursday, June 20, 12:00-1:30, WHH 117 (Library): Abstract Writing Workshop (Susanne)
  • Wednesday, June 26, 12:00-1:00, WHH 117 (Libary): I am Good at Stuff: Crafting an Effective Resume (Alyssa)