Course Materials

Lecture	Day	Date	Lecture Topic	Online Handouts/Readings
1.	Th	Aug. 28	Course overview, requirements, class photos, Introduction to plant biology	Outline Howell Ch.1 pp. 9-20 Required reading:   Taiz & Zeiger   Chapter 1, p 1-10 (overview/review); p. 17-22; 29-30 Howell  Ch. 1 p. 9-20 on differences between plant and animal development
2.	Tu	Sep. 2	Introduction to plant biology and development	Outline Required reading: Taiz & Zeiger, Chapter 1, pp 1-10; p. 17-22; 29-30; Taiz & Zeiger Ch. 15, pp. 349-357; 363-365 on Plant Cell walls.
3.	Th.	Sep. 4	Plant life cycle and reproduction	Outline Moore et al., Ch 10, 2nd Edition pp. 211-215 Chrispeels & Sadava pp. 214- 217 on seeds Required reading: Howell Chapter 1, pp. 9-20 on differences between plant and animal development and model plant systems*; Moore et al., Ch 10, 2nd Edition pp. 211-215*; Chrispeels & Sadava pp. 214- 217* on seeds. *PDF available on class website.  Both text books are on reserve in Biology Library.
4.	Tu.	Sep. 9	Plant Development I: embryogenesis and meristems	Outline Required reading: Chrispeels & Sadava pp. 214- 217 (link to PDF above) Taiz and Zeiger 4th Ed. Ch. 16 pp. 377-384; 398-400
5.	Th	Sep. 11	Shoot Development and Clonal Analysis	Outline Problem Set 1 Required readinFg: Taiz and Zeiger Ch. 16 4th ed. pp. 398-402 on SAM development; focus on mutants discussed in class. Supplemental reading: Bowman and Eshed review
6.	Tu	Sep. 16	CLONAL ANALYSIS II, Root Development & Transition to Flowering	Outline Required reading: Jegla and Sussex, 1989.  Dev. Biol. 131:215-225, Taiz and Zeiger 4th Ed. Ch. 16 pp. 402-405; 409 (on roots); Ch.4. pp 56-58 on roots; Ch. 25 pp. 635-637; 641-643 (flowering).
7.	Th	Sep. 18	Plant tissue culture & Molecular biology review	Outline Mol Bio review sheet Tissue Culture protocol Problem Set 2 Study Guide Lectures 1-8 Problem Set 1 Key Required reading: Taiz and Zeiger 4th Ed. Ch. 19 pp. 467-471, 488 (on auxin). Ch. 21 pp 543-546, 552 (bottom)- 554; 556-558 (on cytokinin). Supplementary reading: Glick and Pasternak Chapters on Molecular Biology Chapter 3 Chapter 4
8.	Tu	Sep. 23	Agrobacterium-mediated DNA transfer into plants: genetic engineering in nature	Outline Problem Set 2 Key Key for 2007 Midterm Required reading:Taiz & Zeiger Ch. 21 pp 548-549, 556-557 (on reserve) Glick and Pasternak Ch. 17 pp 513-520 Brock “Microbiology” pp 683-685 (on reserve) Supplementary reading: Lecroix 2006 and Tzfira & Citovsky 2002
	Th	Sep. 25	Mid-term exam #1 (covering lectures 1-8)	Exam 1 Key
9.	Tu	Sep. 30	Plant Transformation I: Agrobacterium tumefaciens-based:	Outline Required reading: Horsch et al, 1985 Science Glick and Pasternak Ch. 17 pp 517-523; 529-532 (PDF posted with lecture of 9/23) Supplemental reading: On in planta transformation by A. Bent, 2000
10.	Th	Oct. 2	Plant Transformation II: Physical transformation, plastid transformation	Outline Problem Set 3 Required reading: Glick and Pasternak Ch. 17 pp 520-523; 529-532* on physical TF (PDF posted previously) . Bock and Khan, 2004. Trends Biotech 22: 311-318 Supplemental reading: R. Bock 2007 Curr. Opin. Biotech 18:100-106
11.	Tu	Oct. 7	Cloning tissue-specific genes and promoters: T-DNA tagging, promoter trapping, etc.	Outline Required reading: Farrar et al, 2003. Plant J. 33:61-73. Glick and Pasternak Ch. 4 pp. 64-73; 75-80 (PDF posted with lecture of 9/18) Supplementary Reading: Springer Review on Gene Traps: Plant Cell. 2000 Watson “Recombinant DNA” : pp. 87-92 on cloning genes; pp. 94-100 on PCR (text on reserve in library)
12.	Th	Oct. 9	cDNA synthesis, engineering recombinant genes	Outline Required reading: Farrar et al, 2003. Plant J. 33:61-73. (PDF posted with 10/7 lecture) Glick and Pasternak Ch. 4 pp. 75-80 on cDNA synthesis (PDF with previous lectures). Supplementary Reading: Springer Review on Gene Traps: Plant Cell. 2000 ( PDF posted with 10/7 lecture) Topping et al on promoter trapping. Plant J. 1994 Watson “Recombinant DNA” : pp.; pp. 85-87 on cDNA pp. 94-100 on PCR (text on reserve in library)
13.	Tu	Oct. 14	Methods for monitoring transgene expression	Outline Problem Set 3 Key Required reading; Glick & Pasternak Ch. 18 pp. 538- 547 on engineering insect resistance Supplementary Reading: Chrispeels et al, Ch. 16 on Pest Control; especially pp. 433-439; Watson Recombinant DNA on DNA & RNA blots p. 127-130; Lodish et al. Molec. Cell Biology (pp. 92-97 in 3rd Edition). On PAGE and Westerns Glick and Pasternak, Ch. 9 pp.228-230 on ELISA Glick and Pasternak Ch. 15, pp. 456-470 on Bt-toxin;
14.	Th	Oct. 16	Protein engineering at the codon level: engineering insect resistance using Bt toxin	Outline Problem Set 4 Required reading Vaughn et al 2005, Crop Sci 45: 931-938 High et al 2004 Trends Plant Sci. G+P: Ch. 18 pp. 538- 547 on engineering insect resistance (posted 10/14) Losey et al: 1999. Nature 399:214 Hodgson, 1999.Nature Biotech 17:627. Supplementary Reading: Chrispeels et al, Ch. 16 on Pest Control; especially pp. 433-439 (posted 10/14) Schuler et al, 1998 on insect resistant transgenic plants Glick & Pasternak Ch. 8, pp. 456-470 on Bt-toxin; Glick & Pasternak Ch. 8 pp 191-198- Site-directed mutagenesis Watson Recomb. DNA pp. 131-132 & Fig. 6-3 on site-directed mutagenesis. Research article by Perlak et al, 1991 Kota et al, 1999 PNAS- engineering BT expression in plastids Are Bt crops safe? Mendelsohn et al, 2003 Pimentel and Raven, 2000
15.	Tu	Oct. 21	Developmental engineering I: flower color, sense suppression, & RNAi	Outline Study Guide Lectures 9-16 Required reading: Losey et al: 1999. Nature 399:214 (PDF posted 10/16) Hodgson, 1999. Nature Biotech 17:627 (PDF posted 10/16) Glick and Pasternak Ch. 18 pp. 566-569 on manipulating anthocyanin levels. Taiz & Zeiger pp. 326-328 Supplementary Reading: Are Bt crops safe? Mendelsohn et al, 2003; (PDF posted 10/16) Pimentel and Raven, 2000; (PDF posted 10/16) Napoli et al, Plant Cell 1990 Watson et al, Ch. 9. Review on RNAi by Waterhouse et al, 2001
16.	Th	Oct. 23	Developmental engineering II: male sterility	Outline Problem Set 4 Key Problem Set 5 Problem Set 5 Key Required reading: Mariani et al. 1990. Nature 347:737 on engineering male sterility Chrispeels Ch. 9 pp 224- 227 Chrispeels Ch. 14 pp. 368-371 4. Supplementary Reading: Mariani et al. 1992. Nature 357:384-387.(PDF from last year) Review by C. Chase, 2005 on Genetically engineered cms
	Tu	Oct. 28	Mid-term exam #2 (covering lectures 9-16)	2007 Exam 2 Key 2008 Exam 2 Key
17.	Th	Oct. 30	Developmental engineering III: Ripening	Outline Student presentation info Suggested topics Required reading: Oeller et al. 1991. Science. 254:437-439 Glick and Pasternak, Ch 18: pp. pp. 564-566 Taiz and Zeiger Chapter 22 on Ethylene, pp. 572-577; 581-584 Supplementary Reading: Hamilton et al, 1990. Nature 346:284 Klee et al. 1991
18.	Tu	Nov. 4	Biochemical engineering I: Amino acid metabolism, herbicide action and resistance	Outline Required reading: Glick and Pasternak Ch. 18. pp 554-556 Chrispeels & Sadava Ch. 17. Focus on pp. 454-470 on weeds, herbicides & herbicide resistance Supplementary Reading: Cheung et al, 1988. PNAS 85: 391-395 on engineering resistance to atrazine. Shah et al, 1986. Science 233: 478 on engineering resistance to glyphosate Castle et al, 2004. Science 304:1151 on detoxifcation of glyhposate.
19.	Th	Nov. 6	Biochemical engineering II: Carbon fixation, carbon source allocation, & manipulation of carbon storage in plants	Outline Required reading: Moore et al, Chapter 7 on Photosynthesis, focus on pp. 143-154. Nawrath et al 1994.. Proc. Natl. Acad. Sci. 91: 12760-12764 Scheller & Conrad, 2005. Curr. Op. Plant. Biol. 8:188-196. Focus on section on PHA. Supplementary Reading: Chrispeels and Sadava Ch 10, pp. 243- 251; Taiz and Zeiger, Ch, 7, 8, 10, focus on: pp. 132-137; 139-143; 156-165; 221-230. Gross & Kalra, 2002. Science 297:803-807 (PDF from last year) van Beilen & Poirier, 2008. Plant J. 54: 684 on Biomass for biofuels & biopolymers (new PDFattached)
20.	Tu	Nov. 11	Biofuels and the role of plant biotechnology	Outline Problem Set 6 Required reading: Durrett, et al. Plant triacylglycerols as feedstocks for the production of biofuels. The Plant Journal (2008) 54, 593–607.
21.	Th	Nov. 13	Manipulating carbon storage in plants: Biodegradable plastics & oils	Outline Required reading: Nawrath et al. 1994. Proc. Natl. Acad. Sci. 91: 12760-12764; (posted 11/6) Scheller & Conrad, 2005. Curr. Op. Plant. Biol. 8:188-196. Focus on section on PHA. (posted 11/6) Taiz&Zeiger, Ch. 11 pp. 278-283; Chrispeels and Sadava Ch. 19 pp. 510-516. Supplementary Reading: Gross & Kalra, 2002. Science 297:803-807; (posted 11/6) van Beilen & Poirier, 2008. Plant J. 54: 684 on Biomass for biofuels & biopolymers.(posted 11/6) Dyer et al, 2008 Plant J. High-Value oils from plants
22.	Tu	Nov. 18	Modification of Plant oils & Introduction to plant-pathogen interactions	Outline Required reading: Taiz&Zeiger, Ch. 11 pp. 278-283 on lipid metabolism; #Chrispeels and Sadava Ch. 19 pp. 510-516 on plant oils (PDF posted with previous lecture) Taiz and Zeiger: pp. pp. 315-318; 338-342; p. 412 on HR Supplementary Reading: Dyer et al, 2008. High-value oils from plants, The Plant J. 54:640; (PDF posted with previous lecture) Voelker et al. 1992. Science 257:72 Glick and Plasternak Chapter 18: pp. 547-554 and 556-560. Crispeels and Sadava Chapter 15 especially pages 404-411 Pages 390-399 and 400-413
23.	Th	Nov. 20	Engineering resistance to pathogens	Outline Problem set 7 Required reading: Huang et al, 2006. Proc. Nat. Acad. Sci. 103:14302 Taiz and Zeiger: pp. pp. 315-318; 338-342; p. 412 on HR #Crispeels and Sadava Chapter 15 especially pages 404-413 (PDF posted with previous lecture) Supplementary Reading: Glick and Pasternak Chapter 18: pp. 547 - 554; 556-560. (PDF posted with previous lecture)
24.	Tu	Nov. 25	Student Presentations Asona Lui C. Lai & M. Strother E. Hanly & Cicy Li	Outline Outline Outline Study Guide for Final
	Th	Nov. 27	Thanksgiving break
25	Tu	Dec. 2	Student Presentations Cara Clure & Kenneth Smith Peter Jin & Varun Sundarum Helene Burks	Outline Outline Outline Problem Set 6 Key Problem Set 7 Key Problem Set 8 Key
26.	Th	Dec. 4	Student Presentations Christine Ding & Inez Oh Jon Wignes & Aaron Schneider	Outline Outline Study Guide for student presentations
	W	Dec. 17	FINAL EXAM: 6 - 8 pm (Exam Group XX)	2007 Final 2007 Final Key 2008 Final Key

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