CRISPR Project Lab

CRISPRing lepidopterans to study wings

Bee Project F16

Due Dates

  • Final lab Notebook – Nov 22nd by 11:59 pm
  • Final Lab Report –Nov 22nd by 11:59 pm (email in advance to petition for extension)
  • Group Poster – Dec 1st by end of lab

Guidelines and Rubrics

Weekly Schedule

12/6 – WEEK 16 – BEE PARTY

  • Please stop by the Bee Party on Tuesday 12/6 from 11 am – 1 pm in CULC 205Q to see the amalgam poster, have some bee-shaped festive snacks, and maybe win a door prize! (This is just for fun, not required for the course.)

12/1 – WEEK 15 – Group Posters (Meet in CULC 481)

Before lab,

  • Prelab on t2 due Wed by midnight
  • Bring your laptop, lab report, your data files, and any references you found compelling to explain our research.

In lab,

After lab,

  • Please complete CIOS and the t2 project evaluation

11/24 – WEEK 14 – Happy Thanksgiving!

No class meeting

11/17 – WEEK 13 – Results & Discussion Working Session

Before lab,

  • 11/17: Results & Figures/Tables & Discussion draft: Peer Review (due in lab next week and on t2). The more you can put onto paper, the more helpful the feedback will be. Instructors are available by appointment to discuss. Our expectation is that you use a minimum of one rigorous statistical approach on the full dataset. You learned three examples today, and there are other options if you have more stats background. Beyond that, you are welcome to present data, ideas, and analyses when possible on subsets of the data or other questions.

In lab,

  • Thank you cards with a report by virus and hive for each beekeeper.
    • Everyone signs every card
    • Reports divided up among teams. Make a group template for report format.
  • Instructor overview of what should be in the results/discussion.
  • Peer Review Results, Figures/Tables, Discussion
  • Working session on your analysis and writing. Ask for peer or instructor guidance.
  • REMINDER: Error bars should be standard error of the mean:
    • SEM = (Standard Deviation) / √(N – 1)
    • In excel, the formula is = (STDEV(range))/(SQRT((range)-1)))

After lab,

  • Tuesday 11/22: Upcoming: PROJECT LAB REPORT DUE 11/22 BY MIDNIGHT to t2, to get this out of the way before the holiday. If you have a compelling need for an extension, you may pitch your request ahead of time to Dr. Spencer by email to have a 7-day extension.
  • Tuesday 11/22: Upcoming: LAB NOTEBOOK DUE 11/22 BY MIDNIGHT (extended by 1 day). Our expectation was that you worked on this each week, so no extensions on this deadline. Please start revising now if you have entries that need attention! Please go back and make any updates to previous entries. Your entire notebook will be graded as a single document after the due date.
  • No lab next week. Happy Thanksgiving!

11/10 – Week 12 – Data Analysis

Before lab,

  • Complete the pre-lab.
  • Incorporate results from colonies 11, 16:
    • Labeling error: Two samples are labeled 1105ACE. Because both have the same result (no bands). One of these samples is 1101ACE.

virus-samples-from-colonies-11-16

In lab

After lab,

  • Please read through these and mark your calendars to reflect the revised due dates:
  • 11/11: Update lab notebook by midnight tomorrow. This is the last real update you’ll do on your lab notebook, as next week will be a writing and synthesizing workshop. Your entry should include what statistical approaches you’ll do, and how to do them, including what lines of code, links to data files, etc. You are not constrained to use R, but I wanted to expose you to this very useful and flexible programming language. Here’s a compelling blog post on why R is a valuable data science tool:
    https://www.r-bloggers.com/why-you-should-learn-r-first-for-data-science/
  • 11/11: Upload Data file to t2/Assignments by midnight tomorrow. This is the excel file you’ve created that contains colony, urbanization metric, and virus numbers, etc. We don’t need your work, your figures, etc, just the data you plan to use for your various analyses.
  • 11/17: Results & Figures/Tables & Discussion draft: Peer Review (due in lab next week and on t2). The more you can put onto paper, the more helpful the feedback will be. Instructors are available by appointment to discuss. Our expectation is that you use a minimum of one rigorous statistical approach on the full dataset. You learned three examples today, and there are other options if you have more stats background. Beyond that, you are welcome to present data, ideas, and analyses when possible on subsets of the data or other questions.
  • Tuesday 11/22: Upcoming: PROJECT LAB REPORT DUE 11/22 BY MIDNIGHT to t2, to get this out of the way before the holiday. If you have a compelling need for an extension, you may pitch your request ahead of time to Dr. Spencer by email to have a 7-day extension.
  • Tuesday 11/22: Upcoming: LAB NOTEBOOK DUE 11/22 BY MIDNIGHT (extended by 1 day). Our expectation was that you worked on this each week, so no extensions on this deadline. Please start revising now if you have entries that need attention! Please go back and make any updates to previous entries. Your entire notebook will be graded as a single document after the due date.

11/3 – Week 11 – Data Assembly

Before lab,

  • Complete the pre-lab.

In lab,

  • Return Intros and give some general comments
  • Data Assembly Workshop:
  1. On your teams, discuss options for Urban/Rural categorization for each hive (15 minutes)
  2. Assemble data in class gsheet, initial, and proofread. Once finalized, no more editing, only downloading for your own use.
  3. Brainstorming session: How would you graphically present data points? Should we average or pool the 5 different samples from each colony?
  4. Brainstorming session: What statistical approach or test would you use for each of the graphical presentations ideas.

After lab, please update lab notebook by Friday midnight:

  • Align your urban/rural classification of each hive site with the class data, and upload an excel file or gsheet link containing your working dataset.
  • Record your intended graphical presentation (sketch or description) and the statistical comparison you propose to use. If you don’t have a name for the statistical text, then provide a specific description or a sketch figure of what you want to compare.
  • What’s due: Figures and Tables in draft form in lab next week and uploaded to t2.

10/27 – WEEK 10 – Gels and data pooling

Before lab,

  • Writing Assignment: Revise your Introduction by next lab. Upload to t2 as well as bringing a print copy to class. This version will be graded.
  • Our hive locations file is linked in your email. Please do not share the details of these hive locations with anyone outside our class. Lab Notebooks incorporating this link should have visibility set to private. We’ll need an Urban/Rural definition by Week 11 to complete our data analysis, so plan to work on this for next week.
  • Complete the Prelab on t2: Before lab on Thursday, please complete the t2/Prelab called TA & Lab Assessment. This assessment is anonymous so that you can give us an honest assessment without penalty. Please remember that constructive feedback that incorporates why is so much more useful to us than words like “good” and “bad.” If 90% of the class completes the TA & Lab Assessment, then we’ll give everyone five bonus Pre-lab points to top up missed or skipped prelab questions. We still have two prelabs coming up later this semester.

In lab,

  • For each sample, combine your five loci into 2 wells, carefully recording what is in each well. Keep the negative control in its own well. Electrophorese your PCR products on a 2.0% agarose gel at 100 V for 45-60 minutes, or until good size separation for PCR products ranging from 150–775 bp. Record the gel number and gel lanes that contain your samples. Visualize using UV, calculate band sizes using the gel doc software, print your gel (invert the image—bands dark, gel background light) for your lab notebook and lab report, and record your results.
  • Add your sample results for presence/absence of each RNA virus to the class dataset gsheet shared by t2 email.
  • Urban/Rural workshop – while your gels are running.
  • Gel results (lab section A):

group-a group-b group-c group-d group-e group-f group-g group-h group-j group-k

  • Gel results for lab section B:

group-l group-m group-n group-p group-q group-s group-t group-w group-x group-z

  • Colonies 11, 16:

virus-samples-from-colonies-11-16

After lab,

  • Update your lab notebook and add your data to the class gsheet (we’ll do the gsheet data pooling in lab next week).
  • We’ll need an Urban/Rural definition by Week 11 to complete our data analysis, so plan to work on this for next week.
  • Complete the Prelab on t2/PreLabs.

10/20 – WEEK 9 – PCR on cDNA 

Before lab,

  • Writing Assignment: Write your Introduction and upload to t2 as well as bringing a print copy to class for peer review.

In lab,

  • PCR on all five cDNA samples with five RNA virus loci
  • Peer review of Introduction

After lab,

  • Update your lab notebook
  • Writing Assignment: Revise your Introduction by next lab. Upload to t2 as well as bringing a print copy to class. This version will be graded.
  • Complete the TA evaluation on t2/PreLabs.

10/13 – WEEK 8 – RNA isolation/cDNA synthesis

Before lab,

  • No pre-lab

In lab,

After lab,

  • Update your lab notebook
  • Writing Assignment: Write your Introduction and upload to t2 as well as bringing a print copy to class for peer review.

10/6 – WEEK 7 – Gel Electrophoresis on PCR pilot

Before lab,

  • Writing Assignment: Write your METHODS section for our experiment. Use the rubric at the end of the Genetics Lab Report Guidelines. Upload to t2 and bring a print copy to lab.
  • Complete the Prelab on t2.

In lab,

After lab,

  • Update your lab notebook with your gel results, being careful to identify which lane your group’s results are in. Hover over the gels to find yours, right click to download the file for your use. If your positive control lane has not PCR product, check in with Dr. Spencer before lab to discuss what may have gone awry in your RNA isolation protocol. 2% agarose run at 100V with LO DNA Marker (Bionexus)

2355a-group-a-and-b-10-6-2016 2355b-group-z-and-m-10-6-2016 2355b-group-t-and-w-10-6-2016 2355b-group-s-and-p-10-6-2016 2355b-group-n-and-x-10-6-2016 2355b-group-l-and-q-10-6-2016 2355a-group-j-and-k-10-6-2015 2355a-group-g-and-h-10-6-2015 2355a-group-f-and-e-10-6-2015 2355a-group-c-and-d-10-6-2015

  • No writing assignment or prelab. Good luck on the lecture exam!

9/29 – WEEK 6 – PCR on cDNA pilot

Before lab,

  • Writing Assignment: Write your methods section for our experiment, including Week 5 and upcoming Week 6 steps. Use the rubric at the end of the Genetics Lab Report Guidelines. Upload to t2 and bring a print copy to class.

In lab,

After lab,

  • Update your lab notebook

9/22 – WEEK 5 – RNA isolation/cDNA synthesis pilot

Before lab,

  • Watch the video on PCR (this is proprietary library resource, so you’ll need to log in to the library or view from a campus computer)
  • Complete the Pre-lab on t2

In lab,

After lab,

  • Update your lab notebook
  • Writing Assignment (see week 6)

9/15 – WEEK 4 – PCR pilot gels, Protocols

Before lab,

  • Writing Assignment
  • No Pre-lab

During lab,

  • Gel loading practice and run gel of PCR products
    • Load 10-15 ul of sample mixed with 2-5 ul loading dye
    • Load 10 ul of LO DNA Marker (Bionexus)
    • Electrophoresis in 2% agarose in 1X TAE for up to 60 min
    • Positive Controls reactions (using PCR beads)

03-gel-of-positive-controls-2016-09-09-18-12-55

04-student-trial-pcr-gel-section-a-2016-09-15

  • Hypothesis Score Card
  • How to create a protocol
    • Examine the PCR protocol. What are the key elements? How could you make it better?
    • Draft a protocol for riding a bike, etc.
    • Examine the RNA Purification Kit instructions

After lab,

  • Update lab notebook by Friday to include the results of your PCR, gel electrophoresis protocol, revised experimental hypothesis
  • Watch the video on PCR (this is proprietary library resource, so you’ll need to log in to the library or view from a campus computer)
  • Complete the Pre-lab on t2

9/9 – WEEK 3 – PCR Pilot

Before lab

  • Download and read Sguazza et al 2013 detection of bee viruses by multiplex pcr using the basics provided in “dissecting a scientific paper.” Bring a copy of the paper and your reading notes to class next time to help facilitate discussion. Focus particularly on the methodology in this paper.

In lab,

  • PCR pilot of human DNA using two human genes

95 for 3 min
34 cycles of : 95 for 30s, 60 for 60s, 72 for 60s
72 for 10 minutes

After lab,

  • Writing Assignment: State our research question and create a detailed hypothesis in your own words. List three background pieces of evidence that you’ll need to support your hypothesis; one of these should include an idea and citation for how to define urban v. rural. The remainder of ideas do not need to be supported with citations at this point.

9/2 – WEEK 2 – Project Planning (meet in CE 123)

Before lab

  • Download and read Youngsteadt et al 2015 using the basics provided in “dissecting a scientific paper.” Bring a copy of the paper and your reading notes to class next time to help facilitate discussion. 
  • Create your lab notebook and title it: F16A or B – Last, First Name – Project Name. For now you can leave the project name undecided, and update that once we’ve settled on a research question (due by Friday 8/26).

In lab,

After lab,

  • For your notebook entry, repeat this exercise on your own. Your final question may be very similar to one of those presented in class or very different. Regardless, it should be your original work in your own words. (We will pull viable options from these and put them forward for finalization next week.)
  • Reading for next week: Sguazza et al 2013 detection of bee viruses by multiplex pcr

8/25 – WEEK 1 – Bee Overview (meet in CULC 481)

Before lab

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

In lab,

  • What do you want to learn in this course
  • Basic bee biology & tour the bees
  • Syllabus overview and plan for the semester
  • Dissecting a scientific paper
  • In-lab Reading: Youngsteadt et al 2015 abstract

After lab,

  • Download and read Youngsteadt et al 2015 using the basics provided in “dissecting a scientific paper.” Bring a copy of the paper and your reading notes to class next time to help facilitate discussion. 
  • Create your lab notebook and title it: F16A or B – Last, First Name – Project Name. For now you can leave the project name undecided, and update that once we’ve settled on a research question.