CRISPR Project Lab

CRISPRing lepidopterans to study wings

Schedule (F19)

Weekly Schedule

11/21 – WEEK 14 – Discussion

Before lab,

  • Update your lab notebook for Week 13 by midnight 11/15.
  • Complete the brief prelab on Canvas by TUESDAY midnight (prelab will open on Sunday evening).
  • Draft your discussion section: upload to Canvas and bring a print copy to lab for peer review.

In lab,

11/14 – WEEK 13 – Interpreting Results 

Before lab,

  • Update your lab notebook for Week 12 by midnight 11/8.
  • Complete the prelab on Canvas by TUESDAY midnight.
  • Create your figures, figure captions, and written results section based on your statistical analysis. Due on Canvas Assignments at start of lab.
  • Bring a print copy of your assignment to lab.
  • Bring your computer to lab.

In lab,

  • Interpreting your results.
  • Team video on a surprise topic!

After lab,

  • Complete the prelab on Canvas by TUESDAY midnight.
  • Write your Discussion section. Due on Canvas Assignments at start of lab.
  • Bring your computer to lab.

11/7 – WEEK 12 – qPCR analysis

Before lab,

  • BRING COMPUTERS TO LAB!

In lab,

  • qPCR analysis
    • F19 Sample IDs by group
    • Omit the following samples from your data before you analyze:
      • Plate B IAPV TC (in well F10)
      • Any row with a Cq value of 0
      • Any colony with an HE value of 0.
      • Instead of delta-delta Ct, consider comparing delta CtE values and their fold change
      • SEM = stdev.s / (sqrt(N-1))
    • 12 qPCR analysis how-to
  • Workshop: Making figures

After lab,

  • Update lab notebook by Friday
  • More TBD…

10/31 – WEEK 11 – Data Analysis (meet in Library 2130)

Before lab,

  • Complete the PreLab due Wednesday by midnight
  • BRING COMPUTERS TO LAB!

In lab, MEET IN LIBRARY ROOM 2130,

  • Classify each colony by an urbanization metric

After lab,

  • Update lab notebook by Friday
  • No PreLab this week. Good luck on the lecture exam.

10/18 – WEEK 10 – qPCR

Before lab,

In lab,

  • qPCR overview with Q&A
  • qPCR protocol instructions & SYBR green information
    • Discuss experimental design for our samples
    • We’ll run all of your Fall 2019 samples and water using primers: beta-actin (positive control), DWV, SBV, IAPV, Defensin-1, Abaecin
    • Set up qPCR reactions
    • Load into assigned wells on 96 well plate
  • Journal Club

10/9 – WEEK 9 – Data Assembly

Before lab,

  • Update lab notebook by Friday midnight (see “After Lab” from Week 8 for details).
  • Complete the PreLab due Wednesday by midnight
  • Writing Assignment – Introduction 2

In lab,

  • Repeat sizing for another gel to proofread. Data proofreading (for presence/absence of appropriate bands.
  • Workshop on figures & data presentation

After lab,

  • Update lab notebook by Friday
  • Complete the PreLab due Wednesday by midnight

10/11 – WEEK 8 – Gels

Before lab,

  • Update lab notebook from Week 7 Friday by midnight.
  • Complete the PreLab due Wednesday by midnight (this will focus on urbanization metric)
  • Writing Assignment – Introduction

In lab,

  • Electrophorese PCR samples in 2% agarose gel at 100 V for 45-60 minutes. Make a comprehensive gel map.
    • Ladder = GeneRuler 100 bp DNA ladder
  • Complete a gel video while you are loading your gel. Video Instructions: Training video (less than 60 seconds) to communicate to someone new to bench work how to load and run and gel with DNA, without making rookie errors.
  • Peer review introductions.
  • Results: View and size the bands, if any, on your gel and record the results in your notebook.
  • Data assembly
  • Midsemester Course/TA Evaluation

Data and info

  • Gel results – Section A:

  • Gel Results – Section B:

  • Abaecin expected PCR product size:

  • Defensin1 expected PCR product size:

After lab,

  • Update your lab notebook by Friday midnight, being sure to include gel running conditions, comparison of DWV with previous results, gel map and image, what the gel shows in words (results), a link to the full class results, and any issues.
  • Complete the PreLab due Wednesday by midnight
  • Revise your introduction with peer feedback and discussion with TAs and instructors during drop in hours or by appointment. Submit before lab your Writing Assignment – Introduction 2

10/3 – WEEK 7 – PCR with several loci

Before lab,

  • Peer-review the assigned methods.
  • Update your lab notebook.
    • that you have had an Intro to R Studio and what you can do with this information.
    • Relevant initial results for our project
    • An update on your current thinking about urbanization metrics for your paper
    • Any questions you would like to raise about the project (and please bring those to us in drop in hours or during lab)
  • Complete the PreLab due Wednesday by midnight.
  • Writing Assignment – Methods 2, a revision of your methodology. Upload to Canvas/Assignments before lab next week.

In lab,

26 – WEEK 6 – Intro to R Studio (meet in Library 2130)

Before lab

  • Update your lab notebook. Refer to gel images and details under WEEK 5 and PCR bead info under WEEK 4. Notebook this week should include:
    • how to load a gel, gel percentage (2%) and buffer information (TAE)
    • what samples you electrophoresed (sample ID, locus amplified)
    • an image of the gel with your samples and with the negative controls, indicating what is in each relevant well
    • a text explanation of your gel results and how they match the expectations
    • an interpretation of those results. For example, if you see a band at 149 bp for rps18, what does that mean for your study?
    • any other relevant details
    • your pipettor video
  • Reading: Burdine and McCluney 2019 (pdf on Canvas)
  • Complete the PreLab due Wednesday by midnight
  • Writing Assignment – Methods. Upload to Canvas/Assignments before lab next week.

In lab, MEET IN LIBRARY ROOM 2130

  • Intro to R Studio with Mr. Jay Forrest
  • Discussion of urbanization metrics relevant to bee ecology of virus spread
  • Workshop: Introduction
  • Peer-review of methods on Canvas

9/19 – WEEK 5 – Gel electrophoresis

Before lab

  • Complete the Prelab in Canvas by midnight Wednesday.
  • Writing Assignment – Half Abstract: Draft the first half of your abstract, following the ideas in the Workshopping the Abstract handout (Writing the Abstract #1-3) and the Lab Report Rubric. Submit to Canvas/Assignments before class on Thursday 9/19.
  • Reading (timing optional): Tesovnik et al 2017

In lab,

  • Pipettor video
  • Gel loading practice
  • Load & run gel of PCR products for ~1 hour at 100 V
  • Workshopping the Methods.
  • Image your gel and analyze the outcomes. The loci are DWV (Sguazza et al 2013) and rps18 (Scharlaken et al 2008, expected size 149 bp).

After lab,

  • Update lab notebook by Friday; include your pipettor video
  • Reading: Burdine and McCluney 2019 (see Canvas)
  • Complete the PreLab due Wednesday by midnight
  • Writing Assignment – Methods

9/12 – WEEK 4 – PCR

Before lab

  • Watch the DNALC animation on PCR, and read the Polymerase Chain Reaction handout. You may also view this video on PCR (this is proprietary library resource, so you’ll need to log in to the library or view from a campus computer) to gain a more nuanced understanding of PCR.
  • Download from Canvas Sguazza et al 2013 . Bring a print or e-copy of the paper to class. If you have 10 minutes before lab, please look at Table 1, section 2.4, and section 3.2.
  • No PreLab this week. Good luck on the lecture exam.

In lab,

  • Review importance of labeling for every sample and every tube
  • PCR of bee cDNA (protocol) using PCR beads (bead information)
  • Journal Club: Reading in lab and discussion of Sguazza et al 2013
  • Experimental Design discussion and Workshopping the Abstract
  • Conducting a literature search

After lab,

  • Complete the Prelab in Canvas by midnight Wednesday.
  • Writing Assignment – Half Abstract: Draft the first half of your abstract, following the ideas in the Workshopping the Abstract handout (Writing the Abstract #1-3). Submit to Canvas/Assignments before class on Thursday 9/19.

9/5 – WEEK 3 – RNA to cDNA 

Before lab,

  • Update lab notebook by Friday, including a revision of your hypothesis using feedback from lab, using the Genetics Lab Notebook Rubric.
  • Because we are diving right in to some involved benchwork next week, we have modified your preparation for lab. Instead of reading the Sguazza et al 2013 (save that for later), please read this Reading on RNA isolation and Reverse Transcription and the Protocol for RNA isolation & cDNA synthesis to isolate RNA and synthesize cDNA. We will save the pipettor video for a later date as well.
  • Consider, are there bee genes or viral genes with known primers that you’d like to explore?
  • After working through the previous items, complete PreLab on Canvas, due Wednesday before midnight.
  • Before lab, work through the Protocol – RNA isolation & cDNA synthesis to decide what to save and what to discard at each step.

In lab,

After lab,

  • Refer to the lab notebook guidelines and rubric, then update your lab notebook by Friday midnight.
  • No reading or Prelab for next week.

8/29 – WEEK 2 – Lab Safety & Pipettors / Dilutions / Solutions

Before lab,

  • Download and read Youngsteadt et al 2015 using the basics provided in “How to read a scientific paper.” Bring a copy of the paper and your reading notes to class next time to help facilitate discussion.
  • Complete the Prelab on Canvas/Quizzes by Wednesday midnight.
  • Come dressed for wet lab: lab coat, long pants, close-toed shoes.

In lab,

  • Lab safety, Safety quiz and paperwork
  • Workshop: pipettors/dilutions/solutions
  • Create your lab notebook
  • Journal club: Discussion of Youngsteadt et al 2015
  • Project planning

 After lab,

  • Before Friday midnight, update your lab notebook with relevant lab safety notes, pipettor/dilutions/solutions notes, and project background/introduction information in your own words. From fresh, draft and craft a possible research question in your own words. This research question may be similar to one of those presented in class or very different.
  • Read Squazza et al 2013 (download here or from Canvas module “Week 2”)
  • Complete your Pre-lab Week 3 by Wednesday midnight. (Opens on Monday.)

8/22 – WEEK 1 – Urban Honeybee Genetics

Before lab

  • Please read: BeeBasicsBook before lab (read pages 1-12, 30, 31)

In lab,

  • We’ll solicit student learning goals for the course, learn basic bee biology & tour the beehives on campus.
  • We’ll meet our off-campus collaborators virtually and learn what types of hive samples they can donate to our research project.
  • After we review the syllabus and the plan for the semester, we’ll consider How to read a scientific paper for practice in advance of your reading assignment for next week.

After lab,

  • Download and read Youngsteadt et al 2015 using the basics provided in “How to read a scientific paper.” Bring a copy of the paper and your reading notes to class next time to help facilitate discussion.
  • Complete the Prelab on Canvas/Quizzes by Wednesday midnight.