Bio 113 Lab Schedule - Dr. C. Fall 2014

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

Print, read and sign the safety form.

Learning Objectives for Lab Course

List of Protocols Used in Bio113

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

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 28

Introduction

Learning Objectives

 

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
optional... Touch of Greatness

Lab Manual Week #1

Practice Calculations

     
Information
Learning Objectives
for Information
September 4

Information

Learning Objectives

 

Before Lab...
1) Answer 4 Questions

2 ) Create a Registry account (top right link, apply for account)

3) Radio show about Synthetic Biology
(7 minutes)

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

Lab Manual Week #2

September 11

Information

Learning Objectives

 

Before Lab...
1) Answer 4 Questions
2) What is golden gate assembly (GGA)?
Detailed Method and Summary of Lab

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 Wednesday 4 pm

7) CATME peer review

Lab Manual Week #3
September 18

Information

Learning Objectives

 

Before Lab...
1) 4 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) transform E. coli cells (+ control plasmid J04450)
7) design promoter experiment (with controls)
8) one volunteer/group for next Wednesday 4 pm
9) CATME peer review

Lab Manual Week #4
September 25

Information

Learning Objectives

 

Before Lab...
1) 4 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
October 2

Information

Learning Objectives

 

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 9

Information

Learning Objectives

 

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 16

Information

Learning Objectives

Evolution

Learning Objectives

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 23

Oral Report on Synthetic Biology

Information

Learning Objectives

Evolution

Learning Objectives

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 30

Written Report on Synthetic Biology

Information

Learning Objectives

Evolution

Learning Objectives

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 6  

Evolution

Learning Objectives

Before Lab...
1) How do cells resist your antibiotic?
2) Antibotic 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 13  

Evolution

Learning Objectives

Before Lab...
1) Look up TAS2R38 gene
2) View TAS2R38 genome browser
3) Wikigenes TAS2R38
4) What is MRSA?
5) Answer 4 Questions

During Lab...
6) Discuss toxicity data
7)Fisher Exact test
8) prepare graphics for written taste/toxicity report
9) analyze directed evolution data
10) conduct experiments to determine if your bacteria are resistant to the antibiotic
11) CATME peer review

Lab Manual Week #12

November 20  

Written Report on Tasting

Evolution

Learning Objectives

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 27    

Thanksgiving Break

Week #14

December 4  

Oral Report on Antibiotic Resistance

Evolution

Learning Objectives

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


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