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Dr. Chung-Jui
Tsai
Professor
Office: FRES
164
Email: chtsai@mtu.edu; Phone: 487-2914
FW5085, Fall 2007
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Syllabus Expectations &
Assignments
Lecture Slides
1. Introduction to Biotechnology and Functional
Genomics handouts
[Reading]
Relative
Differences: The Myth of 1%. Science 316: 1836 (2007).
[HW1] Omics
(due 9/12/07)
2. Recombinant DNA Technology handouts
[News] Medical News Today 9/7/07: Human source of
stem cells identified with potential to repair muscle (Danielle)
[Animation] Sanger Sequencing and Cycle
Sequencing,
3. Gene Discovery handouts
[Reading] Suppression subtractive hybridization. PNAS 93: 6025-6030
(1996).
[Reading] A decade of differential display. BioTechniques
33: 338-346 (2005).
[HW2] Degenerate primers (due 9/21/07) GenBank ClustalW OligoAnalyzer
4. Expressed Sequence Tags handouts
[Reading]
A hitchhiker’s guide to expressed sequence tag (EST)
analysis. Briefs in Bioinformatics 8: 6-21 (2006).
[News] Scientific American 9/17/07: Synthetic
genes give cells something to remember (Mike)
[HW3] EST
assembly (due 9/28/07) CAP3
5. New Sequencing Technologies handouts
[Reading]
The race for the $1000 genome. Science 311: 1544-1546
(2006).
[Animation] 454 Sequencing (Genome Sequencer
FLX, Roche)
[Animation] Solexa
Sequencing (Illumina)
6. Microarray handouts
[Reading] ESTs, cDNA
microarrays, and gene expression profiling. Plant Journal 39: 697-714
(2004).
[Reading]
Microarrays go mainstream. Nature Methods 1: 263 - 270
(2004).
[News] Science Daily 9/21/07: Mechanism for the
in vivo transport of siRNA (Kate)
7.
Microarray Data Analysis handouts
[HW4] Microarray Data Analysis (due 10/10/07) dataset1 dataset2 Cluster & TreeView
Manual
8.
DNA Markers and Genome Sequencing handouts
[News] Science News 9/29/07: Unexpected Archive:
Mammoth hair yields ancient DNA (Lindsey)
9.
Association Genetics handouts
[Reading]
Linkage disequilibrium: Ancient history drives the new genetics. Human Heredity
59: 118-124 (2005).
10.
Plant Tissue Culture handouts
[News] NobelPrize.org 10/8/07: The Nobel Prize in
Physiology/Medicine 2007 (gene targeting in mice) (Eric W)
11.
Agrobacterium-mediated Transformation and T-DNA Transfer Mechanism handouts
[Reading] The
transfer of DNA from Agrobacterium tumefaciens into plants: A feast of
fundamental insights. Plant Journal 23: 11-28 (2000)
[Reading] Transformation of
plant science in our time – the contribution of Jozef
S. Schell (1935-2003). Plant Physiology 132: 1119-1121 (2003)
12.
Direct Transformation and In-Planta Transformation handouts
[Reading]
T-strand integration in maize protoplasts after codelivery of a T-DNA substrate and virulence genes.
PNAS 94: 11726-730 (1997)
[Reading]
Arabidopsis in planta transformation. Uses,
mechanisms, and prospects for transformation of other species. Plant Physiol 124: 1540-1547 (2000)
[News]
MSNBC 10/15/07: Plant gene modified to fight pollution (Tara )
13. Regulation of Gene
Expression handouts
[Reading]
AGRIS and AtRegNet. A
platform to link cis-regulatory elements and
transcription factors into regulatory networks. Plant Physiol
140: 818-829 (2006)
14. Antisense Technology
handouts
15.
Post-transcriptional Gene Silencing and RNAi handouts
[Reading]
RNA interference. Nature 418: 244-251 (2002)
[Reading]
Plant Pathology and RNAi: A brief history. Annual Review of Phytopathology
43: 191-204 (2005)
[Animation] Nature Reviews RNAi animation by
Arkitek Studios.
16.
Micro RNAs and Small RNAs handouts
[Reading]
Elucidation of the small RNA component of the transcriptome.
Science 309: 1567-1569 (2005)
[Reading]
MicroRNA gets down to business. Nature Biotechnology
25: 631-638 (2007)
[News] ScienceDaily
10/12/07: Genome update defines landscape of breast and colon cancers (Eric M)
17.
Forward and Reverse Genetics handouts
[News] ChronicleOnline
10/22/07: Cornell researchers identify natural herbicide that controls weeds
around some common lawn grasses (John)
18.
Proteomics handouts
[News] Science News 11/10/07: Smarty Gene:
Breast-fed kids show DNA-aided IQ boost (Mark)
[Reading] Functional genomics studied by
proteomics. BioAssays 26: 901-915 (2004)
19.
Metabolomics handouts
[Reading]
Towards the plant metabolome and beyond. Nature
Reviews Molecular Cell Biology 8: 167-174 (2007)
20.
Ecological Genomics handouts
[Reading]
Evolutionary and ecological functional genomics.
Nature Reviews Genetics 4: 649-655 (2003)
[Reading]
Functional genomics and ecology, a tale of two scales.
New Phytologist 176: 735-739 (2007)
21. Genetically Modified
Organisms handouts
22. Systems Biology
(Guest Lecture by Dr. Harding) handouts
[News] BCC Press Office 12/5/07: The Richard Dimbleby Lecture 2007: Dr. J. Craig Venter – A
DNA-Driven World
Dec 14 @ 9 am:
Term paper presentations by Kate, Danielle, Tara, Mike, Eric W
·
Michael
Brodeur-Campbell (Chemical Engineering): Genetic engineering
of microorganisms for next-generation biofuels production.
·
Danielle
Dusold (Biology): Bioremediation
of polycyclic aromatic hydrocarbons by Pseudomonads:
Methods for determining of the mode of assimilation and implications in biotechnology.
·
Kate
Tay (Biology): Transcription
factors involved in Arabidopsis thaliana root hair development.
·
Tara
Waybrant (Biology): A brief review
of evolutionary genomics.
·
Eric
Winder (Biology): Creation of novel protein-based nanosensor device components for detection of biological
and environmental toxins.
Dec 17 @ 9 am:
Term paper presentations by Lindsey, John, Mark, Eric M
·
Mark
Griep (ME-EM): Advanced DNA detection
utilizing carbon nanotube-based technology.
·
Eric
Minner (Biomedical Engineering): Changes in gene expression after spinal cord injuries.
· John Saida
Shaik (FRES): Genetic
engineering of plastids for vaccines and therapeutic protein production.
·
Lindsey
Tuominen (FRES): Recent biotechnological
advances in the production of Taxol® (Paclitaxel).