Bee Project F15

Schedule and Due dates

(This schedule will likely change as the project develops. The most current version will always be at this link: bio2355.biosci.gatech.edu/bee-project-f15-schedule/)

Genetics Lab Notebook Guidelines and Rubric (on the last page!)
Genetics Lab Report Guidelines and Rubric (on the last page!)

8/20 – WEEK 1 (meet in CULC 481)

Before lab reading: BeeBasicsBook before lab (read pages 1-12, 30, 31)

In lab,

Basic bee biology & tour the bees
Explore hive status history at bees.gatech.edu
How to read a scientific paper
In-lab Reading: 1 Mattila & Seeley 2007 ScienceAfter lab,
Find a paper on honey bee genetics that might inform an question that we can test in lab, read the paper and write a 3 sentence synopsis. Bring a copy of the paper and your synopsis to class. If you’d like to vet your paper choice with an instructor, send us an email or drop by office hours. Search tips include:
- Use keywords in Web of Science like Apis mellifera, genetics, subfields of genetics, genetics assays or techniques, interested aspects of bee biology
- do a cited reference search on authors doing bee work, such as the Mittila and Seeley paper, to see what other work has come from that research group.

8/27 – WEEK 2 (meet in CE 123)

Before Lab,

Print your found paper on honey bee genetics
Print a 3 sentence synopsis.
Watch this video on micropipetting (this is a library resource, so you’ll need to be on campus and/or logged into a campus account) and complete the pre-lab on t2.
Review the hive status information on bees.gatech.edu.
Prepare any honey bee questions for Dr. Leavey.
Come dressed for wet lab: lab coat, long pants, close-toed shoes.

In lab,

Lab Safety (Alison Onstine)
Project brainstorming and drafting some ideas
Bee Consult (Dr. Jennifer Leavey)
Pipettor introduction and activity

After lab,

Read ___________.
Complete the pre-lab by Wednesday 11:55 pm.

9/3 – WEEK 3 (Meet in CE 123)

Before lab,

Read 2 Seeley & Tarpy 2007 queen promiscuity lowers disease
Prepare a carefully-worded proposed research question, including as much detail as possible
Complete the pre-lab by Wednesday 11:55 pm
Please bring your laptop to lab if convenient.

In lab,

Finalize research question
Lab notebook set-up
Protocol assessment and pilot DNA-Isolation-Protocol-Chelex
Gel Electrophoresis of DNA isolation samples and controls

After lab,

Create first lab notebook entry on DNA isolation pilot and research question.
Gel photos from DNA isolations: Gel file names indicate which lab section HP1 or HP2 and which Gel are depicted. Gels are oriented with wells at the top, the opposite orientation from how we loaded them in lab. If you have questions about which samples are yours, or how to read the gel, ask a TA!

9/10 – WEEK 4 (Meet in CE 123)

Before lab,

Writing Assignment: Use the protocol for DNA Isolation from last week to craft a Gel Electrophoresis Protocol. Due on t2/Assignments/Week 4 and paper at the start of lab.

In lab,

After lab,

No pre-lab for next week. Good luck on the lecture exam!

9/17 – WEEK 5

Before lab,

Read Solignac et al 2003 500 msats
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)
Writing Assignment: Bring a print-out of your revised or original Gel Electrophoresis protocol from last week.

In lab,

PCR pilot to test 7 loci on several of our bee DNA isolations.
05 2355 F15 Microsatellite primers

After lab,

Pre-lab on t2
Writing Assignment: Write a methods-plus portion of your project report. (see below)

9/24 – WEEK 6

Before lab,

Pre-lab on t2
Writing Assignment: Write a methods-plus portion of your project report.
- Model your writing to the style from the methods section of Delaney et al 2011 or another paper that you deem to include sufficient detail to replicate the experiment.
- Use complete sentences (not numbered protocol steps) for the methods we’ve done to date, and use bullet points to list the parts that we haven’t done yet.
- Before your methods, write a 1 sentence statement of the overall objective or purpose of the project
- Underneath your methods, list questions that you have about current and upcoming protocols, analysis, etc.

During lab,

Gel images from last week: 5PCRpilotgels or 05PCRpilotgels
DNA purification using an Ethanol Precipitation protocol. Resuspend DNA in 30 ul purified sterile water.
Repeat pilot PCR.
- Section HP1 repeated with original primer set: Am553, Am010, Am052, Am061. Gel images under Week 7.
- Section HP2 changed to a new primer set: AM043, Am059, and Am125. Gel images under Week 7.

After lab,

Update lab notebook.
Complete pre-lab.

10/1 – WEEK 7

Before lab,

Download 06 PCR pilot 2 gels and complete pre-lab on t2.

In lab,

Assess the data so far, make a plan for today’s bench work, act on your plan.
Calculate length of the PCR products for the loci that amplified.
- 07 Calculate Size of DNA Fragments (file contains semi-log paper)
Overview of how to create an outline for your introduction
Literature searching for strong papers to help you write your introduction (need 3 minimum, and you might need/want more. Note that Matilla and Seeley 2007 had 11 in their 2 paragraph introduction!)

After lab,

No pre-lab for next week. Good luck on the lecture exam!
If you WANT to revise your methods, please bring hard copy/upload revised version to t2 by the beginning of lab next week. We’ll take the average of the two grades, so no need to do this if you are happy with your work and your grade.
Please update your lab notebooks, and include all information you determined about and collected on your samples this week.
Look over the results of your PCR, if any, using the gels below:

10/8 – WEEK 8

Before lab,

No pre-lab. Good luck on the lecture exam!

In lab,

Review the gels below from a test PCR that Dr. Spencer ran. The lane key is below the gels.

DNA samples 17, 59, and 61 were purified isolates. All others were chelex DNA isolates. 3-01 and 3-02 are positive controls from DNA isolated by the F14 class.

HP1 decided to run a test PCR with various bees and loci. Each student tested 4 bees (2 from each hive) against 1 one locus, and each locus was tested by 4 different students.

In HP2, each student ran PCR with four bees. We will not run gels on all the samples but will provide you the opportunity to run your negative controls in lab next week to confirm that your PCR tubes are contaminant free.

After lab,

Writing Assignment due next week (in lab and on t2): “Full Sentence Outline” of your Introduction and Literature Cited for the bee genotyping project:
- include at least 3 primary literature references (in-text citations and full list in literature cited)
- outline the scientific ideas that will help your reader understand your hypothesis or research question.
- use the lab report guidelines and rubric to guide your content and organization.
- Introduction Full Sentence Outline Instructions
No pre-lab for next week. Happy Fall Break!

10/15 – WEEK 9

Before lab,

No Pre-lab this week. Happy Fall Break!
Upload your writing assignment and print TWO copies to bring to lab.

In lab,

HP1: Paternity Analysis PCR. Hand in your PCR
HP2: Run gels from last week’s PCR. Planning for the Virus Detection Project
Reverse Transcriptase PCR blog entry

After lab,

Please update your lab notebooks within 24 hours of lab.

10/22 – WEEK 10 – Genotype analysis in CE 206 Computer Lab

Before lab,

In lab,

Meet in the computer lab, login to the PC platform on the lab computer and open PeakScanner. Download the F15.zip folder from t2 resources
- HANDOUT: 10 Scoring Genotypes HANDOUT
Score the genotypes for all bees at loci Am098 and Am125 into the google spreadsheet for your lab section.

After lab,

Please update your lab notebooks within 24 hours of lab.
Writing Assignment: Introduction
- As you write, please modify your hypothesis to reflect existing evidence rather than expecting results from the virus detection assay that we will pilot later in the semster. Examples of existing evidence include hive status information at bees.gatech.edu, hive founder information from our conversation with Dr. Leavey, or published information in the scientific literature.

10/29 – WEEK 11– Genotype analysis in CE 206 Computer Lab

Before lab,

Complete your Writing Assignment: Introduction and upload to t2. Bring two hard copies to class: one to submit and one for peer-review.
- As you write, please modify your hypothesis to reflect existing evidence rather than expecting results from the virus detection assay that we will pilot later in the semster. Examples of existing evidence include hive status information at bees.gatech.edu, hive founder information from our conversation with Dr. Leavey, or published information in the scientific literature.

In lab,

Peer-review of introduction
Compare data from two lab groups, discuss common patterns and decisions on calling alleles for each locus.
Learn how to determine maternal and paternal genotypes

After lab,

Continue to work with the dataset to create your final version of binned alleles per bee, maternal and paternal genotypes, and a minimum and maximum predicted number of fathers per hive. You may collaborate with peers to generate your final table of genotypic values, which should be an appendix your Full Lab Report, due on 12/3 at the end of your lab period.
If you have access to a PC or the PC platform on your Mac, you can download PeakScanner yourself from:
https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600583&tab=Overview

11/5 – WEEK 12 – Genotype analysis in Computer Lab

Before lab,

Read Sguazza et al 2013 detection of bee viruses by multiplex pcr
Complete pre-lab on RT-PCR

In lab,

Score genotypes for loci Am052 and Am059, confirming that the ABI well ID is correct for your PCR tube in this document: 2355 F15 ABI well IDs, apis microsatellites
Clean up the data.
Create a dataset of alleles within each locus and bin them in the class google doc spreadsheet.
Determine the maternal genotypes for each locus.
- How many alleles should each worker inherit from the queen?
- How many alleles does the queen have?
- List the queen’s at each locus alleles
Assign paternity by colony
- sort by colony
- identify queen’s genotype for each locus. Identify problems and recheck.
- remove rows with data for only one locus unless unique (none are unique)
- subtract off Mom’s alleles to create Dad’s genotype for each row.
How many dad’s do the data predict?
How might allelic diversity affect parentage assignment?
What are the types of scientific uncertainty in your data (scoring uncertainty, bee samples size per colony, number of loci, etc)?

After lab,

Update your lab notebook
Optional: Revise your Introduction by Sunday midnight and resubmit (please add “RESUBMIT” to the end of your filename).
To consider:

11/12 – WEEK 13 – RNA Isolation and cDNA synthesis in CE 123 wet lab

Before lab,

No pre-lab this week. Good luck on the lecture exam!

In lab,

RNA isolation (read pages 2-7 of the protocol: RNA isolation – GeneJet RNA Purification Kit)
Single strand cDNA synthesis
13 – RNA Isolation and cDNA synthesis PROTOCOL

After lab,

Update your lab notebook

11/19 – WEEK 14 –Virus detection PCR in CE 123 Wet Lab, then finalize CULC01 & CULC10 parentage analysis in CE 206

Before lab,

Pre-lab on t2

In lab,

PCR of virus cDNA using primers from Sguazza et al 2013 simultaneous detection of bee visurs by multiplex pcr Table 1 (note, we will not screen for acute bee paralysis virus (ABPV))
Positive controls are drawn from Scharlaken et al 2008 control genes
Protocol for PCR: 14 – PCR to detect viruses
TAs will run gels on Friday and post results here.
Gels 1-4 (across then down)
Gels 5,6
Gels 7-11(across then down)
Notes: Tubes 12 and 13 may have been switched on gel 2. Map of gel lane contents on last page of this protocol file: 14 – PCR to detect viruses

After lab,

Update your lab notebook.
If you’d like for 15% of your course grade to be weighted toward an additional assignment of a grant proposal on surveying the GT Honey Bee Project hives for the presence of bee viruses, then consult the rubric below and create a full draft proposal. The final proposal will be due the Tuesday of exams week, but we encourage you to present a draft before Thanksgiving for comment and feedback.
- 2355 Mini-Grant RUBRIC

11/26 – THANKSGIVING HOLIDAY – No class meeting

12/03 – WEEK 15 – Paper Due – No class meeting

Due: Final Paper due at 6 pm on t2 and as a paper copy. Paper copies should be delivered to CULC 474 by 6 pm. Genetics Lab Report Guidelines and Rubric (on the last page!)
Dr. Spencer is available in CULC 474 for drop in office hours during lab time from 12:05 to 5:55 pm.
Genetics Lab Notebook Guidelines and Rubric (on the last page!) – Due Friday 6 pm

12/08 – EXAMS WEEK – OPTIONAL: Mini-Grant Proposal due Tuesday by midnight on t2

OPTIONAL 15% of course grade for Mini-Grant on Virus screening project.
RUBRIC: 2355 Mini-Grant RUBRIC
Students may opt not to complete this mini-grant. In that case, course grade will consist of remaining assessments proportional to their weights are listed in the syllabus.
Bee Poster F15 – Virus Detection