marine functional genomics & biotechnology · course outline • lecture 1-3: general...

Marine Functional Genomics & Biotechnology

Guangyi Wang, Ph.D.guangyi@hawaii.edu

Spring, 2007

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, guangyi@hawaii.edu

• Visiting InstructorsGrieg Steward, Assistant Professor, Department of Oceanography956-6775, grieg@hawaii.eduZackary Johnson, Assistant Professor, Department of Oceanography, 956-0844, zij@hawaii.eduGernot Presting, Assistant Professor, Department of Molecular Biosciences & Bioengineering, 956-8861, gernot@hawaii.eduMatthew Church, Assistant Researcher, Department of Oceanography, 956-8779, mjchurch@hawaii.edu

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.