Marine Functional Genomics & Biotechnology
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Transcript of Marine Functional Genomics & Biotechnology
Textbook
No textbook required. The key reference book is ‘Microbial Functional Genomics’. You don’t have to buy it. My copy will be available for you.
I will also provide your lecture note.
Literature references
1. One key reference paper will be provide for each topic. You should read it because some exam question will be from these papers!!!!
2. You are also encouraged to read original source articles. They will enhance your understanding of the material.
Grading
15% class participation30% midterm (March 1) and final exam (May 10)25% topic discuss and presentation (April 17, 24, & 26)
Instructors• Leading Instructor
Guangyi Wang, Associate Professor, Dept of Oceanography956-3744, [email protected]
• Visiting InstructorsGrieg Steward, Assistant Professor, Department of Oceanography956-6775, [email protected] Johnson, Assistant Professor, Department of Oceanography, 956-0844, [email protected] Presting, Assistant Professor, Department of Molecular Biosciences & Bioengineering, 956-8861, [email protected] Church, Assistant Researcher, Department of Oceanography, 956-8779, [email protected]
On-site Visit
• Visiting UH Biotechnology Facility (TBA).
1. To be familiar with diversity and cataloging of natural microbes.
2. To understand genomics view of microbes.
3. To learn general approaches to understand the function of microbes (cultured and uncultured) through genomics analysis.
4. To apply functional genomics approaches in marine science, drug discovery, bacterial pathogenesis, and environmental toxicology.
Course Objectives
5. To appreciate benefits of microbial functions to our society.
6. To develop skills to integrate microbial physiological and biochemical information into applied sciences.
7. To be prepared for professional career in environmental science and biotechnology.
Course Objectives (continued)
Course Organization
• Basic information for functional genomics• Functional genomics of marine microbes• High-throughput technology (DNA
microarray and proteomics• Applications of genomics in environment
sciences and biotechnology
Course Outline• Lecture 1-3: general introduction and basic molecular info for
microbial genomics and function• Lecture 4-6: microbial diversity and molecular phylogeny• Lecture 7-12: functional, comparative, and evolutionary
genomics• Lecture 13-16: Molecular and high-throughput technology for
functional genomics• Lecture 17-18: application of genomics approach in natural
habitats• Lecture 19-23: Application of genomics in marine microbial
ecology• Lecture 24-25: Application of genomics in pathology and
environmental biotechnology• Lecture 26-27: Application of genomics in antibiotic discovery
and environmental toxicology
Importance of Microbial FunctionAbundance and Biomass
a) Each of us contain 10 to 100 times (1014-15) more bacterial than own cells (1013).
(Whitman et al, 1998)
Photo courtesy of M. Church
b) 500 billion tons of carbon (half of the total carbon in the global biomass) and 90% of global nitrogen and phosphoreous).
Foundation of our biospheresPhototrophic microbes produce oxygen
Completion of biogeochemical cyclesWithout microbes, many geochemical cycles can not be completed in many natural habitats.
Physiological and biochemical versatility
The frontier of lifesurvive and even thrive under the most extreme environmental conditions.
Fundamental to the survival of most higher organisms (endosymbionts)
A huge biomedical and biotechnological potential (non-cultured prokaryotes)
Problems and ChallengesUnknown and uncultured majority
(Schleifer, 2004)
What to do?Reveal and organize uncultured microbes using
16S rRNA genes
localize them in natural habitats
Delong 2005)
Metagenomics approach
From Functional Genomics to Life
DNA RNA protein
Phenotype & function
ProteomicsDNA microarray
Potential ApplicationsDrug discovery
Time ofdevelopment
Body region, physiology, pharmacology, pathology
Environmental and biomedical sciences
Summary
• Importance of environmental microbes• Approaches.• Challenge and opportunity of functional
genomics in environmental science and biotechnology.
