Courses

I teach two courses during the Spring semester, an undergraduate genetics class (L311) and a section on plant development in our graduate course on development (L587).

Warning: This is not the offical web page for these courses! If you are enrolled in L311 or L587, you must use Oncourse for offical course information.

L311 Genetics

Instructor: Dr. Scott Michaels (Myers Hall 316A, 856-0302, michaels@indiana.edu, for email please include L311 on the subject line.)

Textbook: Genetics – From Genes to Genomes, 2nd edition by Lee Hartwell, et al. (McGraw-Hill, 2004) and Study Guide/Solutions Manual by Debra Nero. These can be purchased at the I.U. Bookstore.

Lee Hartwell and colleagues have written a superb genetics textbook, now in its 2nd edition. It is lively, current, weaves in the new and exciting frontier of genomics, and deals with important genetic issues that face society today. Note that short answers are provided for the odd-number problems at the back of the textbook. Longer answers are provided for all problems in the Solutions Manual.

Discussion Groups, times and locations: TBA.

Problem Sets and Discussion Groups: Each Friday of a non-exam week, problems covering the week's material will be assigned. This assignment will consist of problems from the textbook (for which some answers are given in the back of the book, and all answers are given in the Solutions Manual), and 3-5 "for credit" problems (for which answers are not provided). You should work through the problem sets, individually or with other members of the class, before your next Discussion Group session. In Discussion Group, students will meet to discuss concepts and solve problems. The "for credit" problems must be turned in by 5:00 pm the following Thursday – they can be given to your AI/UTI at the end of Discussion Group, or delivered to the L311 "drop box" outside the Molecular Biology Institute office, Myers Hall 150.

Working in small groups: The best way to learn the language and skills of genetics is to discuss and work through genetics problems with others. Furthermore, the very best way to learn a difficult concept is to teach it. I encourage all of you to form study groups and get together at least once a week, to work through or at least check over the problems in the problem sets. There is no penalty to any student for helping fellow students do well in this course.

Web Site: I use Oncourse to post lecture handouts, reading assignments, problems sets, keys to problem sets, exams, keys to exams, supplementary information, notes to the class, and other miscellaneous items. If you are not yet familiar with Oncourse, you can get information and help at that site at http://oncourse.iu.edu/. If you are familiar with Oncourse, you can use your username and password to access the BL BIOL L311 13290 GENETICS site. Documents will be under “Schedule”. Lecture handouts will be posted on Oncourse by 6pm the evening prior to the corresponding lecture.

Exams: There will be 4 exams. Three exams are scheduled during the semester. The 3 exams given during the semester will cover the material (in-class material, reading assignments, and problem sets) from the 3-4 weeks preceding the exam week. Part of the final exam will cover the material from the last 3 weeks of class and part will be comprehensive. The comprehensive component will be on using the genetic tools you learn throughout the semester. Each exam will be composed of problems similar to those given in class and found on the weekly assignments. Because the problems on the exam will be similar (but not identical) to the in-class and assigned problems, participating in class discussions and doing the assignments is the best way to study.

Everyone must take the final exam.It is your responsibility to check to make sure that you do not have a conflict in your final exam schedule. If you have a conflict (i.e., another exam scheduled at the same time, notify me immediately). Students who miss the final exam (for whatever reason) will receive a score on it of "0" and a final course grade calculated using that score. Any student with a justifiable absence should petition, as soon as possible, for a hearing with the Committee on Absence in the Dean of Students office. With the approval of that committee, the final grade may be converted to an "I" or calculated from the grades for the 3 mid-semester exams. If a mid-semester exam has also been missed, then the usual procedure is to complete another section of L311 within one year, according to the procedures of that section.

Exam Scores: Each mid-semester exam is worth 100 points, and the final is worth 120 points. In tallying your total course score, I will drop the lowest score among your 3 mid-semester exam scores. For this reason, there will be absolutely no make-up exams for any reason. If you miss a mid-semester exam (due to illness, a conflicting athletic event, a funeral, or any other unexpected circumstance), that exam score is the one that will be dropped. The final exam score cannot be dropped.

Problem Set Scores: Each problem set is worth 6 points. The highest 9 scores from the 10 problem sets will be counted.

Exam Regrades: If you want your exam to be regraded you must return it to your AI or UTI within one week of the date the exams are returned. You must also attach a sheet that 1) states your reason(s) for requesting a regrade, and 2) contains the following statement in your own handwriting “This exam has not been altered in any way since it has been returned to me”, and 3) it must be signed by you.

Academic misconduct (Cheating): DON’T DO IT! The University's policies on academic misconduct are described in the Schedule of Classes. Incidents must be reported to the Dean of Students.

Maximum points are:

Highest 2 scores among 3 mid-semester exams 200 points

Final exam 120 points

Problem sets (highest 9 scores among 10 problem sets) 54 points

Total 374 points

Final grades: Final grades will be assigned based on the following scale:

A: 90 - 100%

Bs: 80 - 89.9%

Cs: 70 - 79.9%

Ds: 60 - 69.9%

Fs: <59.9%

Plus and minus grades will also be given.

Question and answer sessions: In addition to in-class review sessions, I will hold question and answer sessions from 7:00 to 8:30 pm the evening before each mid-semester exam.

Withdrawal: You may drop this course up until the automatic withdrawal deadline. After that, an Incomplete will be granted only if you are passing the course and have a medical excuse; a note from a health professional will be required.

Class Cancellation Policy: Class will be cancelled if IU is closed. If for any reason I need to cancel a class, I will send our L311 AI or a Biology Department faculty member to announce the cancellation.

Course Syllabus:

L587 Developmental Biology
Plant Development

Class Format:

The course will consist of three components: presentation of background information (by instructor), careful and critical reading of one or two key papers (by you) for each class meeting, and discussion of the assigned readings and other recent papers. Background information for most topics will be presented during one class period, and discussion of the relevant reading assignment will occur during the next class period. Although this breaks up the topics a bit, the background often helps to make the reading assignment easier to understand.

Web Site: I will use Oncourse to post lecture notes and PDF files for required readings. If you are not yet familiar with Oncourse, you can get information and help at that site at http://oncourse.iu.edu/. If you are familiar with Oncourse, you can use your username and password to access the BL BIOL L587 1391 DEVELOPMENTAL BIOLOGY site. Documents will be under “Schedule”. Lecture handouts will be posted on Oncourse by 6pm the evening prior to the corresponding lecture.

Grading:

Class participation/paper presentation: The course is intended to be a discussion of the relevant topics. For this to happen, students must actively participate in discussion of the material under consideration. Therefore, we will keep track of the level of participation and will factor this in when assigning grades. Obviously, to participate you must be in class. Attendance will be monitored. Each of you will lead the discussion of two of the reading assignments. You will have approximately 30 minutes at the beginning of the class period in which to cover the reading assignment for that day. You should provide a brief introduction to the paper that puts it into the appropriate historical context, if necessary. You should then lead us through a discussion of the key experiments. In doing so, you should keep the following points in mind: 1. What question was the experiment designed to test? 2. How did the authors go about testing it? 3. What results did they obtain? 4. How did they interpret them? and 5. Do you agree with their interpretation? Finally you should provide a brief discussion of the key conclusions from the paper(s). Keep in mind that 30 minutes is generally not enough time to cover an entire paper (and certainly not 2). Therefore you will need to identify and focus your attention on the key experiments. Presentations that run significantly beyond the 30 minutes allotted will be marked down.

Schedule of topics:

Manipulation of plant development- Genetically modified organisms (GMOs)

Introduction to plant development and self-incompatibility

The shoot apical meristem

Plant hormones-Cytokinins

Plant hormones-Gibberellins

Plant hormones-Auxin

Plant hormones-Ethylene

Plant hormones- Abscisic Acid

Nodulation

Plasmodesmata

Red light responses

Blue light responses

Regulation of flowering by photoperiod

Regulation of flowering by cold

The ABCs of floral development

Schedule of topics:

Introduction to plant development and self-incompatibility

Assigned paper:

Takayama, S., et al., Direct ligand-receptor complex interaction controls Brassica self-incompatibility. Nature, 2001. 413(6855): p. 534-8.

Further reading:

1. Nasrallah, J.B., Recognition and rejection of self in plant reproduction. Science, 2002. 296(5566): p. 305-8.
2. Chookajorn, T., et al., INAUGURAL ARTICLE: Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand. Proc Natl Acad Sci U S A, 2004. 101(4): p. 911-7.
3. Vanoosthuyse, V., et al., Interaction of calmodulin, a sorting nexin and kinase-associated protein phosphatase with the Brassica oleracea S locus receptor kinase. Plant Physiol, 2003. 133(2): p. 919-29.

The shoot apical meristem

Assigned paper:

Reddy, G.V. and E.M. Meyerowitz, Stem-cell homeostasis and growth dynamics can be uncoupled in the Arabidopsis shoot apex. Science, 2005. 310(5748): p. 663-7.

Further reading:

1. Baurle, I. and T. Laux, Apical meristems: the plant's fountain of youth. Bioessays, 2003. 25(10): p. 961-70.
2. Gallois, J.L., et al., Combined SHOOT MERISTEMLESS and WUSCHEL trigger ectopic organogenesis in Arabidopsis. Development, 2002. 129(13): p. 3207-17.
3. Rojo, E., et al., CLV3 is localized to the extracellular space, where it activates the Arabidopsis CLAVATA stem cell signaling pathway. Plant Cell, 2002. 14(5): p. 969-77.

Plant hormones-Cytokinin

Assigned paper:

Inoue, T., et al., Identification of CRE1 as a cytokinin receptor from Arabidopsis. Nature, 2001. 409(6823): p. 1060-3.

Further reading:

1. Hutchison, C.E. and J.J. Kieber, Cytokinin signaling in Arabidopsis. Plant Cell, 2002. 14 Suppl: p. S47-59.
2. Werner, T., et al., Cytokinin-deficient transgenic Arabidopsis plants show multiple developmental alterations indicating opposite functions of cytokinins in the regulation of shoot and root meristem activity. Plant Cell, 2003. 15(11): p. 2532-50.
3. Sun, J., et al., The Arabidopsis AtIPT8/PGA22 gene encodes an isopentenyl transferase that is involved in de novo cytokinin biosynthesis. Plant Physiol, 2003. 131(1): p. 167-76.
4. Kakimoto, T., CKI1, a histidine kinase homolog implicated in cytokinin signal transduction. Science, 1996. 274(5289): p. 982-5.

Plant hormones-Gibberellins

Assigned paper:

1. Ueguchi-Tanaka, M., M. Ashikari, M. Nakajima, H. Itoh, E. Katoh, M. Kobayashi, T.Y. Chow, Y.I. Hsing, H. Kitano, I. Yamaguchi, and M. Matsuoka, GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin. Nature, 2005. 437(7059): p. 693-8.

Further reading:

1. Ogawa, M., et al., Gibberellin biosynthesis and response during Arabidopsis seed germination. Plant Cell, 2003. 15(7): p. 1591-604.
2. McGinnis, K.M., et al., The Arabidopsis SLEEPY1 gene encodes a putative F-box subunit of an SCF E3 ubiquitin ligase. Plant Cell, 2003. 15(5): p. 1120-30.
3. Singh, D.P., A.M. Jermakow, and S.M. Swain, Gibberellins are required for seed development and pollen tube growth in Arabidopsis. Plant Cell, 2002. 14(12): p. 3133-47.
4. Sun, T., Gibberellin signal transduction. Curr Opin Plant Biol, 2000. 3(5): p. 374-80.

Plant hormones-Auxin

Assigned paper:

Dharmasiri, N., S. Dharmasiri, and M. Estelle, The F-box protein TIR1 is an auxin receptor. Nature, 2005. 435(7041): p. 441-5.

Further reading:

1. Kepinski, S. and O. Leyser, Plant development: an axis of auxin. Nature, 2003. 426(6963): p. 132-5.
2. Fu, X. and N.P. Harberd, Auxin promotes Arabidopsis root growth by modulating gibberellin response. Nature, 2003. 421(6924): p. 740-3.
3. Benkova, E., et al., Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell, 2003. 115(5): p. 591-602.

Plant hormones-Ethylene

Assigned paper:

Potuschak, T., et al., EIN3-dependent regulation of plant ethylene hormone signaling by two arabidopsis F box proteins: EBF1 and EBF2. Cell, 2003. 115(6): p. 679-89.

Further reading:

1. Guo, H. and J.R. Ecker, The ethylene signaling pathway: new insights. Curr Opin Plant Biol, 2004. 7(1): p. 40-9.
2. Lanahan, M.B., et al., The never ripe mutation blocks ethylene perception in tomato. Plant Cell, 1994. 6(4): p. 521-30.
3. Hall, A.E. and A.B. Bleecker, Analysis of combinatorial loss-of-function mutants in the Arabidopsis ethylene receptors reveals that the ers1 etr1 double mutant has severe developmental defects that are EIN2 dependent. Plant Cell, 2003. 15(9): p. 2032-41.

Plant hormones- Abscisic Acid

Assigned paper:

1. Razem, F.A., A. El-Kereamy, S.R. Abrams, and R.D. Hill, The RNA-binding protein FCA is an abscisic acid receptor. Nature, 2006. 439(7074): p. 290-4.

Further reading:

1. Finkelstein, R.R., S.S. Gampala, and C.D. Rock, Abscisic acid signaling in seeds and seedlings. Plant Cell, 2002. 14 Suppl: p. S15-45.
2. White, C.N., et al., Gibberellins and seed development in maize. I. Evidence that gibberellin/abscisic acid balance governs germination versus maturation pathways. Plant Physiol, 2000. 122(4): p. 1081-8.
3. Suzuki, M., et al., Viviparous1 alters global gene expression patterns through regulation of abscisic acid signaling. Plant Physiol, 2003. 132(3): p. 1664-77.
4. McCarty, D.R., et al., Molecular Analysis of viviparous-1: An Abscisic Acid-Insensitive Mutant of Maize. Plant Cell, 1989. 1(5): p. 523-532.

Nodulation

Assigned paper:

Krusell, L., et al., Shoot control of root development and nodulation is mediated by a receptor-like kinase. Nature, 2002. 420(6914): p. 422-6.

Further reading:

1. Cullimore, J.V., R. Ranjeva, and J.J. Bono, Perception of lipo-chitooligosaccharidic Nod factors in legumes. Trends Plant Sci, 2001. 6(1): p. 24-30.
2. Ehrhardt, D.W., R. Wais, and S.R. Long, Calcium spiking in plant root hairs responding to Rhizobium nodulation signals. Cell, 1996. 85(5): p. 673-81.
3. Shaw, S.L. and S.R. Long, Nod factor elicits two separable calcium responses in Medicago truncatula root hair cells. Plant Physiol, 2003. 131(3): p. 976-84.

Plasmodesmata

Assigned paper:

Kim, I., et al., Cell-to-cell movement of GFP during embryogenesis and early seedling development in Arabidopsis. Proc Natl Acad Sci U S A, 2005. 102(6): p. 2227-31.

Further reading:

1. Heinlein, M., Plasmodesmata: dynamic regulation and role in macromolecular cell-to-cell signaling. Curr Opin Plant Biol, 2002. 5(6): p. 543-52.
2. Escobar, N.M., et al., High-throughput viral expression of cDNA-green fluorescent protein fusions reveals novel subcellular addresses and identifies unique proteins that interact with plasmodesmata. Plant Cell, 2003. 15(7): p. 1507-23.
3. Kim, J.Y., Z. Yuan, and D. Jackson, Developmental regulation and significance of KNOX protein trafficking in Arabidopsis. Development, 2003. 130(18): p. 4351-62.

Red light responses

Assigned paper:

Matsushita, T., N. Mochizuki, and A. Nagatani, Dimers of the N-terminal domain of phytochrome B are functional in the nucleus. Nature, 2003. 424(6948): p. 571-4.

Further reading:

1. Seo, H.S., et al., LAF1 ubiquitination by COP1 controls photomorphogenesis and is stimulated by SPA1. Nature, 2003. 424(6943): p. 995-9.
2. Klin, K.A. and G.C. Whitelam, Light signals, phytochromes and cross-talk with other environmental cues. J Exp Bot, 2004. 55(395): p. 271-6.
3. Kaczorowski, K.A. and P.H. Quail, Arabidopsis PSEUDO-RESPONSE REGULATOR7 is a signaling intermediate in phytochrome-regulated seedling deetiolation and phasing of the circadian clock. Plant Cell, 2003. 15(11): p. 2654-65.
4. Kircher, S., et al., Nucleocytoplasmic partitioning of the plant photoreceptors phytochrome A, B, C, D, and E is regulated differentially by light and exhibits a diurnal rhythm. Plant Cell, 2002. 14(7): p. 1541-55.

Blue light responses

Assigned paper:

Kagawa, T., et al., Arabidopsis NPL1: a phototropin homolog controlling the chloroplast high-light avoidance response. Science, 2001. 291(5511): p. 2138-41.

Further reading:

1. Cashmore, A.R., Cryptochromes: enabling plants and animals to determine circadian time. Cell, 2003. 114(5): p. 537-43.
2. Somers, D.E., et al., ZEITLUPE encodes a novel clock-associated PAS protein from Arabidopsis. Cell, 2000. 101(3): p. 319-29.
3. Yang, H.Q., et al., The C termini of Arabidopsis cryptochromes mediate a constitutive light response. Cell, 2000. 103(5): p. 815-27.

Regulation of flowering by photoperiod

Assigned paper:

Valverde, F., et al., Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science, 2004. 303(5660): p. 1003-6.

Further reading:

1. Suarez-Lopez, P., et al., CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature, 2001. 410(6832): p. 1116-20.
2. Simpson, G.G. and C. Dean, Arabidopsis, the Rosetta stone of flowering time? Science, 2002. 296(5566): p. 285-9.
3. Izawa, T., et al., Phytochrome mediates the external light signal to repress FT orthologs in photoperiodic flowering of rice. Genes Dev, 2002. 16(15): p. 2006-20.
4. Kobayashi, Y., et al., A pair of related genes with antagonistic roles in mediating flowering signals. Science, 1999. 286(5446): p. 1960-2.

Regulation of flowering by cold

Assigned papers:

Sung, S. and R.M. Amasino, Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature, 2004. 427(6970): p. 159-64.

Further reading:

1. Bastow, R., et al., Vernalization requires epigenetic silencing of FLC by histone methylation. Nature, 2004. 427(6970): p. 164-7.
2. He, Y., S.D. Michaels, and R.M. Amasino, Regulation of flowering time by histone acetylation in Arabidopsis. Science, 2003. 302(5651): p. 1751-4.
3. Sung, S. and R.M. Amasino, Vernalization and epigenetics: how plants remember winter. Curr Opin Plant Biol, 2004. 7(1): p. 4-10.
4. Michaels, S.D. and R.M. Amasino, FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell, 1999. 11(5): p. 949-56.

The ABCs of floral development

Assigned paper:

Lenhard, M., et al., Termination of stem cell maintenance in Arabidopsis floral meristems by interactions between WUSCHEL and AGAMOUS. Cell, 2001. 105(6): p. 805-14.

Further reading:

1. Lohmann, J.U. and D. Weigel, Building beauty: the genetic control of floral patterning. Dev Cell, 2002. 2(2): p. 135-42.
2. Pelaz, S., et al., B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature, 2000. 405(6783): p. 200-3.
3. Lohmann, J.U., et al., A molecular link between stem cell regulation and floral patterning in Arabidopsis. Cell, 2001. 105(6): p. 793-803.