Bio 113 Lab Schedule - Dr. C. Fall 2016

Lab meets Thursday, either at 8:15 am or 1:40 pm in Watson 147.

Read the safety form. Hard copies for signing will provided for you in lab.

Learning Objectives for Lab Course

List of Protocols Used in Bio113

We will use CATME to facilitate fair assessment of lab group projects.

lab schedule

Your two oral presentations will be divided into four sections: Introduction; Materials and Methods; Results; Discussion. Each person will present one section and change sections for the second presentation. The oral presentations must be pledged to indicate that each person made substantial contributions. You will not know which section you are presenting until 1 hour before lab, therefore you should learn all 4 parts.

For your last written lab reports, each person must write his or her own (including figure legends), though you may confer about the content. The figures may be shared resources since they were produced as a team. Put your name as the first author and your labmates names as coauthors.

Grading will be based on these grading rubrics.

Date
Topics
Lab Manual
Word Files
August 25

Introduction

 

1) Safety Issues
2) Submit info to CATME for Team maker
3) How to Use a "Pipetman"
4) Synthetic Biology Introduction (PDF version)
5) TOSLS survey

Lab Manual Week #1

Practice Calculations

     
Information
Learning Objectives
for Information
September 1

Information & Cells

 

Before Lab...
1) Answer 4 Questions

2 ) Create a Registry account (top right "login", apply for new account)

3) Radio show about Synthetic Biology
(7 minutes)

During Lab...
4) Basics of cloning DNA parts
5)
Registry of Parts
6) Use PubMed to find regulatable bacterial promoter
7) CATME first week

Lab Manual Week #2

September 8

Information & Cells

 

Before Lab...
1) Answer 4 Questions
2) What is golden gate assembly (GGA)?
Overview and Detailed explainations

During Lab...
3) Find regulatable promoter DNA sequence
4) generate oligos from GGA Oligator
5) name sequences and send for synthesis
6) one volunteer/group for next Wed. 4:30 pm

7) CATME peer review

Lab Manual Week #3
September 15

Information & Cells

 

Before Lab...
1) 4:30 pm day before lab, boil oligos (one per group)
2) Answer 4 Questions
3) View the receiving plasmid
J119137

During Lab...
4) get oligos ready for ligation (calculations last week)
5) do GGA ligation for oligos
6) do paper GGA activity
7) transform E. coli (+ control plasmid J04450)
8) design promoter experiment (with controls)
9
) one volunteer/group for next Wed. 4:30 pm
10) CATME peer review

Lab Manual Week #4
September 22

Information & Cells

 

Before Lab...
1) 4:30 pm day before lab, start cells growing (+/- treatment).
2) Answer 4 Questions

During Lab...
3) test cells in Synergy machine
4) quantify Synergy data (use Excel)
5) update data in Registry
6) outline method to genotype each person for TAS2R38
7) CATME peer review

Lab Manual Week #5
September 29

Information

 

Before Lab...
1) Answer 4 Questions

During Lab...
2) isolate genomic DNA from hair
3) set up PCR (v2) for TAS2R38 alleles (see lab manual)
4) Finalize your Registry exprience for your promoter

5) CATME peer review

Lab Manual Week #6

October 6

Information & Cells

 

Before Lab...
1) Answer 4 Questions

During Lab...
2) prepare DNA for sequencing
3) separate PCR products on gel with MW marker
4) use ApE to analyze sample DNA sequences
5) calculate the molecular weight of your PCR product
6) prepare for oral and written presentations

7) CATME peer review

Lab Manual Week #7
October 13

Information & Cells

Evolution & Cells

Before Lab...
1) Skim the JAMA paper
2) Watch 6 minute video
3) Answer 4 Questions

During Lab...
4) Test E. coli and B. subtilis for antibiotic sensitivity
5) Analyze your personal DNA sequence
6) predict PTC taste then determine taste status

7) prepare for oral reports
8) CATME peer review

Lab Manual Week #8
     
Evolution
Learning Objectives for Evolution
October 20

Information & Cells

Oral Report Grading Rubric

Evolution & Cells

Before Lab...
1) read iBOP cards (I'll print copies)

2) Read evolution story
3) Practice oral presentations
4) Answer 4 Questions

During Lab...
5) Oral reports on promoter study
6) CATME peer review
7) Design and perform first directed evolution experiment

Lab Manual Week #9
October 27

Information & Cells

Written Report Grading Rubric

Evolution & Cells

 

Before Lab...
1) Read about Goldilocks evolution
2) Answer 4 Questions
3) Bring plant material for toxicity testing

During Lab...
4) submit written reports on promoter study
5) CATME peer review
6) analyze directed evolution data
7) conduct second directed evolution experiment
8) Bring plant material for toxicity comparisons
9) Extract compounds and let dry

Lab Manual Week #10

November 3
 

Evolution & Cells

Before Lab...
1) How do cells resist your antibiotic?
2) Antibiotic resistance worst case is here...

3) Answer 4 Questions

During Lab...
4) Start brine shrimp toxicity test
5) analyze directed evolution data
6) conduct next directed evolution experiment
7) CATME peer review

Lab Manual Week #11
November 10  

Evolution & Cells

Before Lab...
1) View TAS2R38 gene
2) View TAS2R38 genome browser
3)
View Wikigenes TAS2R38
4) What is MRSA?
5) Answer 4 Questions
6) Lab manual is long this week. Read about Chi square statistics before coming to lab.

During Lab...
7) Discuss toxicity data
8) Chi square test using R
9) prepare graph for written taste/toxicity report
10) analyze directed evolution data
11) conduct experiments to determine if your bacteria are resistant to the antibiotic
12) CATME peer review

Lab Manual Week #12

November 17
 

Evolution & Cells

Written Report Grading Rubric

Before Lab...
1) Read CDC recommendations
2) Read about good microbes
3) Answer 4 Questions

During Lab...
4) submit written reports on taste/toxicity
5) CATME peer review
6) analyze directed evolution data

7) prepare for final oral presentation

Lab Manual Week #13
November 24    

Thanksgiving Break

Week #14

December 1
 

Evolution & Cells

Oral Report Grasding Rubric

Before Lab...
1) prepare oral presentation

During Lab...
2) Oral presentation on evolution of antibiotic resistance
3) CATME peer review
4) Fellowships for you
5) course evaluations

week #15 lab manual


Practice Calculations

Dr. Campbell's Bio113 Page


Copyright 2016 Department of Biology, Davidson College, Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu