Bio113 Lab Schedule - Dr. C. Fall 2012

Your two oral presentations should 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 two 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.

Date	Topics			Lab Manual Word Files
August 30	Introduction Learning Objectives		1) Brainstorm how to learn in lab 2) Safety Issues 3) How to Use a "Pipetman" 4) Synthetic Biology Introduction (PDF version) 5) Touch of Greatness	Lab Manual Week #1 Practice Calculations
			Information	Learning Objectives for Information
September 6	Information Learning Objectives		Before Lab... 1) Answer 4 Questions 2 ) Create a Registry account (top right link, apply for account) 3) Take online skills Quiz #1 During Lab... 4) Review of Synthetic Biology 5) Basics of cloning DNA parts 6) Registry of Parts 7) Registry of Functional Promoters 8) Use PubMed to find regulatable bacterial promoter 9) CATME first week	Lab Manual Week #2 Skills Quiz #1
September 13	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 20	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 J100091 During Lab... 4) use the Loligator to get oligos ready for ligation 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 27	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) spot cells from each strain for next week (on LB + amp plates) 5) quantify Synergy data (use Excel) 6) update data in Registry and enter data into RFP database 7) outline method to genotype each person for TAS2R38 8) one volunteer/group for next Wednesday 4 pm 9) CATME peer review	Lab Manual Week #5
October 4	Information Learning Objectives		Before Lab... 1) 4 pm day before lab, start colony PCR (new primers) 2) Answer 4 Questions During Lab... 3) isolate genomic DNA from hair 4) eletrophores colony PCR products on gel with MW marker 5) set up PCR for TAS2R38 alleles 6) Update RFP database for your promoter 7) Take skills quiz #2 8) CATME peer review	Lab Manual Week #6 Skills Quiz #2
October 11	Information Learning Objectives		Before Lab... 1) Answer 4 Questions During Lab... 2) prepare DNA for sequencing 3) use ApE to analyze sample DNA sequences 4) prepare for oral and written presentations 5) CATME peer review	Lab Manual Week #7
October 18	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 DNA sequence 6) predict PTC taste then determine taste status 7) prepare for oral reports 8) CATME peer reivew	Lab Manual Week #8
			Evolution	Learning Objectives for Evolution
October 25	Oral Report on Synthetic Biology Information Learning Objectives	Evolution Learning Objectives	Before Lab... 1) print 3 iBOP cards, bring to lab 2) Read evolution story 3) Practice oral presentations 4) Answer 4 Questions During Lab... 5) Oral reports on promoter study 6) CATME peer reivew 7) Take promoter post-survey (EC) 8) Design MIC experiment and perform experiment	Lab Manual Week #9
Nov 1	Written Report on Synthetic Biology Information Learning Objectives	Evolution Learning Objectives	Before Lab... 1) Read about Goldilocks evolution 2) Answer 4 Questions During Lab... 3) submit written reports on promoter study 4) CATME peer reivew 5) Design and perform first directed evolution experiment 6) Walk and collect plant material for toxicity comparisons 7) Extract compounds and let dry 8) Skills Quiz #3	Lab Manual Week #10 Skills Quiz #3
November 8		Evolution Learning Objectives	Before Lab... 1) How do cells resist your antibiotic? 2) Antibotic resistance worst case is here... 2) Answer 4 Questions During Lab... 3) Start brine shrimp toxicity test 4) analyze directed evolution data 5) conduct next directed evolution experiment 6) CATME peer reivew	Lab Manual Week #11
November 15		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) statistical analysis of toxicity data 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 reivew	Lab Manual Week #12
November 22			Thanksgiving Break	Week #13
November 29		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 reivew 6) analyze directed evolution data 7) prepare for final oral presentation	Lab Manual Week #14
December 6		Oral Report on Antibiotic Resistance Evolution Learning Objectives	Before Lab... 1) print iBOP and bring to lab 2) Answer 4 Questions During Lab... 3) Oral presentation on evolution of antibiotic resistance 4) CATME peer reivew 5) Skills Quiz #4 6) Fellowships for you 7) course evaluations	week #15 lab manual Skills Quiz #4

Bio 113 Lab Schedule - Dr. C. Fall 2012

List of Protocols Used in Bio113

Practice Calculations

Dr. Campbell's Bio113 Page