PS
605-72259
Spring
2005
1-6-05 Version
2 credit hours, Tuesday-Thursday, 8:35-9:25 am
Instructors:
Neal Stewart
Matt Halfhill
Chhandak Basu
Mentewab Ayalew
Irina Teplova
This class is intended to be journal club where active class participation is the mechanism to explore the field of Plant Genomics. Each student will have the opportunity to lead the exploration of specific topics, and will present a combination of three lectures and/or journal club discussions on the assigned topics.
Grading
Each student will be graded based on this ratio: 60% lectures and journal clubs led/ 35% participation/ 5% Microarray analysis assignment. The lectures and journal clubs will each count for 20% of the student’s final grade, and will be assessed by five criteria (4 points for each): 1. Overall quality of presentation, 2. Scientific Accuracy, 3. Clarity, 4. Preparation, and 5. Evoking discussion. Participation will be assessed by active discussion during each class period. The Microarray analysis assignment will be given in week 2, and will be due on March 31.
92%-100%: A
90%-91%: A-
88%-89%: B+
82%-87%: B
80%-81%: B-
78%-79%: C+
72%-87%: C
70%-71%: C-
Honor statement
All images and figures used in presentations must be properly referenced.
UT Official Honor Statement: Students shall not plagiarize. Plagiarism is using the intellectual property or product of someone else without giving proper credit. The undocumented use of someone else's words or ideas in any medium of communication (unless such information is recognized as common knowledge) is a serious offense, subject to disciplinary action that may include failure in a course and/or dismissal from the University.
Class schedule and topics
In case of class cancellation
because of weather, etc., the class will be emailed to notify of
cancellation. Therefore the schedule
is subject to revision—generally responsibilities will be moved to the
following class meeting. So, if a student is scheduled to present a journal
club on Thursday, when it happens to snow, then it is understood that if class
is cancelled on Thursday that we’ll have that journal club the following
Tuesday.
Jan 13 Introduction of class and review of syllabus
Week 1
Jan 18 DNA
cloning using site-specific recombination
Lecture (Chhandak Basu)
Hartley, JL, Temple, GA, Brasch, MA (2000) DNA cloning using in vitro site-specific recombination. Genome Research 10:1788-1795.
Jan 20 DNA
cloning using site-specific recombination
Journal club (Irina Teplova)
doughnuts: Joshua
Curtis, MD, Grossniklaus, U (2003) A Gateway Cloning vector set for high-thoughput functional analysis of genes in planta. Plant Physiology 133:462-469.
Week 2
Jan 25 Microarray
analysis
Lecture: Reggie
Schena, M, Shalon, D, Davis, RW, Brown, PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.
Jan 27 Microarray analysis
journal club: Murali
doughnuts: Reggie
Lockhart, DJ et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology 14:1675-1680.
Week 3
Feb 1 Microarray analysis experimental design
Lecture: Alon
Alba, R et al. (2004) ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development. Plant Journal 39: 607-714.
Churchill, GA (2002) Fundamentals of experimental design for cDNA microarrays. Nature Genetics 32:490-495.
Feb 3 Microarray analysis experimental design
journal club: Oscar
doughnuts: Brian
Downie, A et al. (2004) Expression profiling of the response of Arabidopsis thaliana to methanol stimulation. Phytochemistry 65:2305-2316.
Week 4
Feb 8 Quantitative PCR
Lecture: Moon
Bustin, SA (2000) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. Journal of Molecular Endocrinology 25:169-193.
Feb 10 Quantitative PCR
Journal club: Joshua
doughnuts: Murali
Mentewab, A, Cardoza, V, Stewart, CN, Jr. (2005) Genomic analysis of the response of Arabidopsis thaliana to trinitrotoluene as revealed by cDNA microarrays. Plant Science, in press.
Week 5
Feb 15 Statistics
and microarray analysis
Lecture: Jason
Churchill, GA (2004) Using ANOVA to analyze microarray data. Biotechniques 37: 173-177.
Storey, JD, Tibshirani, R (2003) Statistical significance for genomewide studies. Proceedings of the National Academy of Science 100:9440-9445.
Feb 17 Statistics and microarray analysis
Journal club: Kellie
doughnuts: Alon
Reymond, PR, et al. (2004) A conserved transcript pattern in response to a specialist and generalist herbivore. Plant Cell 16:3132-3147.
Week 6
Feb 22 RNAi
Lecture: Murali
Waterhouse, PM, Helliwell, CA (2003) Exploring plant genomes by RNA-induced gene silencing. Nature Reviews Genetics 4:29-38.
Feb 24 RNAi
Journal club: Moon
doughnuts: Kellie
Ogita, S, Uefuji, H, Morimoto, M, Sano, H (2004) Application of RNAi to confirm theobromine as the major intermediate for caffeine biosythesis in coffee plants with potential for construction of decaffeinated varieties. Plant Molecular Biology 54:931-941.
Week 7
Mar 1 RNAi
Journal Club: Byung-guk
Guo, HS, Fei, JF, Chua, NH (2003) A chemical-regulated inducible RNAi system in plants. Plant Journal 24:383-392.
Mar 3 RNAi
Journal club: Reggie
doughnuts: Moon
Mathieu, O, Bender, J (2004) RNA-directed DNA methylation. Journal of Cell Science 117:4881-4888.
Week 8
Mar 8 RNAi
Journal club: Alon
Isaacs, FJ, et al. (2004) Engineered riboregulators enable post-transcriptional control of gene expression.
Mar 10 RNAi
Journal club: Kellie
doughnuts: Oscar
Roth, BM, Pruss, GJ, Vance, VB (2004) Plant viral suppressors of RNA silencing. Virus Research 102:97-108.
Week 9
Mar 15 Regulation
of eukaryotic gene expression
Lecture: Oscar
Zhang, JZ (2003) Overexpression analysis of plant transcription factors. Current Opinion in Plant Biology 6:430-440.
Mar 17 Regulation of eukaryotic gene expression
Journal club: Ryan
doughnuts: Byung-guk
Yen, L, et al. (2004) Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 431:471-476.
Spring Break
Mar 22 No Class (Spring Break)
Mar 24 No Class (Spring Break)
Week 10
Mar 29 Regulation of eukaryotic gene expression
Journal club: Byung-guk
Harbison, CT, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431:99-104.
Mar 31 Regulation of eukaryotic gene expression
Journal club: Brian
doughnuts: Jason
Hashimoto, S, et al. (2004) 5’-end SAGE for the analysis of transcriptional start sites. Nature Biotechnology 9:1146-1149.
Microarray analysis assignment due
Week 11 Open week for review of previous topics
Apr 5 Discussion of Microarray analysis assignment
Apr 7
Week 12
Apr 12 Proteomics
Lecture: Brian
de Hoog, CL, Mann, M (2004) Proteomics. Annual Review of Genomics and Human Genetics 5:267-293.
Apr 14 Proteomics: 2D gels
Journal club: Ryan
doughnuts: Ment
Righetti, PG, et al. (2004) Critical survey of quantitative proteomics in two dimensional electrophoresis approaches. Journal of Chromatography 1051:3-17.
Week 13
Apr 19 Proteomics: Mass spectrometry
Journal club: Joshua
Newton, RP, Brenton, AG, Smith, CJ, Dudley, E (2004) Plant proteome analysis by mass spectrometry: principles, problems, pitfalls and recent developments. Phytochemistry 65:1449-1485.
Apr 21 Proteomics: Bioinformatic approaches
Journal club: Jason
doughnuts: Chhandak
Blueggel, M, Chamrad, D, Meyer, HE (2004) Bioinformatics in proteomics. Current Pharmaceutical Biotechnology 5:79- . TENATIVE
Last Week
Apr 26 Guest Lecture (Last Day of Class)