Biology 423L Syllabus 2014 Laboratory Experiments in Genetics

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1 Biol 423L Laboratories in Genetics 1 Biology 423L Syllabus 2014 Laboratory Experiments in Genetics Lecture: Monday at 12:00 noon in Wilson Hall 128 Laboratories: Section 001: Tuesday at 2:00 p.m. in Wilson room 242 Section 002: Wednesday at 2:00 p.m. in Wilson room 242 Course materials available on Sakai Text book: Genetic Analysis by Sanders and Bowman. I strongly recommend buying the text but one copy will be at the reserve circulation desk in the undergraduate library available for two hours at a time. There is no course pack. All lab protocols, reading lists and most reading materials will be available on Sakai. A new version of the protocol will be available one week before each lab. Print out the protocol, read it carefully and bring it to class. Instructor: Sarah Grant sgrant@ .unc.edu Telephone: Office hours: by appointment ( me if you want to set up a meeting). Friday afternoons are optimal. TA: Duncan Mcpherson damcpher@ .unc.edu Office hours: TBA Holcomb davidholcomb@unc.edu Office hours: TBA Reports: Due in laboratory period 2 weeks after exercise finished. Penalty for handing in late: 50% off if handed in by 5:00 Wednesday for Section 001 and Thursday for section 002. Otherwise your report will not be graded and your grade will be recorded as 0 points. Exceptions can be made in unusual circumstances by arrangement ( to TA or instructor, preferably before due date) Reports will be handed back one week after being turned in. Lab reports will make up 50% of the final grade. They will be graded out of 25 points: 5 for participation, 5 for abstract and introduction, 10 for methods and results and 5 for discussion. See Course Information on web site for instructions on how to prepare lab reports. Regrade requests: Lab reports: Submit graded pdf with grader s comments to Dr. Grant. Explain your complaint in writing. You can submit the

2 Biol 423L Laboratories in Genetics 2 complaint by with the graded PDF attached. I reserve the right to regrade the entire paper, not just evaluate your complaint. Midterms: Submit your correction in writing to Dr Grant s mailbox with the exam. I reserve the right to regrade the entire test, Dr. Grant to make sure she looks in her mailbox for your request. If the problem is incorrect addition of marks, discuss that directly with Dr. Grant (after class is fine). Exams etc: Homework quizzes and in-class quizzes: 5% of final grade. 2 midterms for 10% of final grade each. Final exam: 25% of final grade Lab reports for a total of 50% of the grade. Syllabus Date Topic August 19/20 First meeting: Plant fast plant seeds for two experiments August 25 First Lecture: Mendelian Genetics Readings for class: Sanders and Bowman: Read Chapter 2 for a review of the principles relevant to this week s lab. Focus on dihybrid cross: section 2.2 and 2.3 pp and Chi-square test: section 2.5 pp Review epistasis: Section 4.4 pp FAST PLANTS: Williams et al. (1986) Vol. 232 pp PDF available on web site; You can find more information at the home page for Wisconsin Fast Plants, Aug 26/27. Mendelian Genetics: fast plants and corn kernel color TA: Duncan Report on Mendelian Genetics due Sept. 9/10. Sept 1 Labor Day no lecture Sept 2/3. A. Complementation of alleles B. Mating for transposon mutagenesis. TA: Duncan and David You will need to come back on day 2 and 3 after the lab to finish the experiments. Readings: Yeast complementation: Sanders and Bowman Chapter 3, pp (figure 3.15). Section 4.4 pp , Section 5.18 p See Sakai Resources site for the following PDFs from A Classroom Guide to Yeast Experiments: Genetics of Baker s Yeast.

3 Biol 423L Laboratories in Genetics 3 Baker s Yeast and its Life Cycle A Closer Look at Adenine-requiring Mutants in Yeast- Conjugation in bacteria: review Bacterial conjugation: Sanders and Bowman Section 6.1 pp Transposons and transposon mutagenesis: Sanders and Bowman Section 13.5 pp and p Optional reading available as Pdfs on Sakai site Resources: Suicide plasmid: Herrero et al J. Bacteriology 172: Mini Tn 5 transposon: De Lorenzo et al J. Bacteriology 172: Erin Garcia research: Anderson et al 2012 Plos Genetics e doi: /journal.pgen Report on yeast complementation due Sept. 16/17. Report on transposon mutagenesis due Oct. 14/15. Sept. 8 Mutagenesis of yeast and Selection of transposon mutations Readings: Review of mutation: Sanders and Bowman section pp Mutation screen Section 16.1 pp Transposon tagging: p.550. Gene replacement: Section 17.1 pp , Figure 17.12, and Genetic Analysis box See Sakai Resources site for the following PDFs from A Classroom Guide to Yeast Experiments: The Response of Yeast to Radiation A Closer Look at Biological Consequences of UV exposure A Closer Look at Repair of DNA Sept. 9/10 Mutations in yeast and Transposon mutagenesis in Burholderia TA: Duncan You will need to come back every day this week to finish the experiments. Times will be worked out with the TA during the lab class. Report on Yeast mutations due Sept. 23/24. Report on Mendelian Genetics due this week. Sept. 15 Selection of insertion mutants Meet in lab classroom Select candidate mutant bacteria in the lab class and prep cultures for DNA purification this week. Sept. 16/17 DNA purification see week 2 for the protocol. Readings: review of DNA structure and replication: Sanders and Bowman Section pp Qiagen DNA purification kit protocol- available on Sakai Report on Transposon mutation work due Oct.14/15.

4 Biol 423L Laboratories in Genetics 4 Report on Yeast alleles due this week. Sept. 22 Transformation, restriction digestion and cloning. Readings: Sanders and Bowman: PCR Section 7.5 pp , p. 540 Natural Bacterial transformation Section 6.4 pp Recombinant DNA technology: Section pp Gene libraries: Section 16.4 and 16.5 pp Sept. 23/24 Transformation of Burkholderia, restriction digestion and cloning In E. coli. and Duncan You will need to come back on day 2 and 3 to complete the experiments. Report on E. coli transformation and restriction digestion due Oct. 7/8 (short report) Report on Yeast mutations due this week. Sept. 29 Midterm Readings for lab: Drosophila life cycle: Sanders and Bowman page 678 figure 20.4 (a) Sex-linked inheritance: Sanders and Bowman section 3.3 and 3.4 pp (mostly for interest) Three point cross: Sanders and Bowman Chapter 5: pp Focus on sections 5.2, 5.3 and 5.5. Mapping in Humans: Sanders and Bowman Section 5.5 pp Positional cloning of Huntington syndrome gene Section 16.1 pp Sept. 30/Oct1 Drosophila three point cross Oct. 1/2, Oct 15/16. Oct. 29/30. Finish transposon mutagenesis up to Selection of mutants. Report on Transposon mutation work due Oct. 14/15. Report on Drosophila 3 point cross due Nov. 11/12. Oct. 6 C. elegans as a Model System and Epigenetics Readings for class: Sanders and Bowman Section 15.3 pp and Section 17.3 pp Required Reading: Tabara et al., 1999 Cell 99: , describe how this paper identifies genes required for the gene silencing mechanism as part of your report..oct. 7/8 C. elegans Genetics and RNAi Help from Megan Brady mmbrady@ .unc.edu You will need to come back on each day after the lab to continue experiments. Times for all returns will be organized by the TA during the lab period.

5 Biol 423L Laboratories in Genetics 5 Report on C. elegans Genetics and RNAi due Oct. 21/22. Report on cloning lab due this week. Oct. 13 Finish C. elegans lab. Meet in lab room (Wilson 242) open lab room at 11 and allow students to come late leaving room open until 1. Oct. 14/15. Drosophila three-point cross 2: test cross and sex-linkage. Fall break: Thurs Oct. 16 and Friday Oct. 17 Report due Nov. 11/12. Report on Transposon mutagenesis due this week. Oct. 20 Mapping, Forensics (DNA sequence analysis, PCR, dispersal of man, trees of relationship). Readings: PCR: Sanders and Bowman pp , 256 VNTR Fig and Animation Chapter 7 slide show #120. Gel electrophoresis: pp , polymorphisms pp Micro and Tiling arrays pp Oct 21/22 Forensics For discussion in class: Foster et al 1998 Nature 396: Underhill et al Ann. Hum. Genet. 65: Optional Reading: Nakamura et al., NAR 16:9364. Forensics report due Oct. 28/29 (short report) Report on C. elegans and epigenetics due this week. Oct. 27 Midterm 2 Oct 28/29 Drosophila 3 pt cross scoring test cross progeny. Report on Drosophila 3 pt cross due Nov. 11/12. Report on C. elegans and epigenetics due in lab this week. Nov. 3 DNA Analysis and Mapping in Humans Readings: Mapping in Humans: Sanders and Bowman Section 5.5 pp Positional cloning of Huntington syndrome gene Section 16.1 pp

6 Biol 423L Laboratories in Genetics 6 Nov. 4/5 DNA analysis. Analysis of DNA of transposon insertions Readings: Sanders and Bowman: DNA sequencing: pp Animation in slide show Ch. 7 #127 and pp Annotation pp Report due at end of lab period. Forensics report due this week. Nov. 10 Mapping in a model organism Readings for class: Physical Mapping of genes: Sanders and Bowman Section 16.1 pp Lukowitz et al., 2000 Plant Physiol. 123: Nov. 11/12 TA: Duncan Mapping in Arabidopsis Report on Mapping in Arabidopsis due Nov. 25/26 Report on 3 point cross due this week. Nov. 17 QTL and GWAS mapping Reading: Sanders and Bowman: Ch. 21 pp , 732 Nov.18/19. QTL mapping in mouse. Report on mapping in mouse due Dec 2/3. Report on DNA sequence analysis due this week. Nov. 24. QTL lab results. Map based cloning of the gene for Cystic Fibrosis Readings for class: Pearson 2009 Nature 460; No lab this week due to Thanksgiving Holiday Dec. 1 Association mapping for human diseases. Guest lecturer Dr. Karen Mohlke Reading: Sanders and Bowman pp GWAS papers, Dec 2/3 GWAS exercise Report due at end of lab period Dec noon-3 pm Final Exam 128 Wilson Hall