Bio113 Lab Schedule - Dr. C. Fall 2013

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.

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

Bio 113 Lab Schedule - Dr. C. Fall 2014

List of Protocols Used in Bio113

Practice Calculations

Dr. Campbell's Bio113 Page