2012 Course Syllabus

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NOTE: Click on presentation titles to download the PowePoint or PDF file (when available).
Moore C.C. = CMORE Hale Moore Conference Center

Week 1: MICROBES AS DRIVERS OF BIOGEOCHEMICAL CYCLES

  • Visiting faculty: D. Bronk, S. Chisholm, P. Gasol, D. Repeta, A. White
  • Local Faculty: D. Böttjer, M. Church, D. Karl, M. Rappé, G. Steward

Saturday, May 26 thru Monday, May 28

Students arrive and check into Frear Hall at the University of Hawai‘i at Mānoa

UH Mānoa

Tuesday, May 29

Introduction / Orientation

C-MORE Hale

0830-0915

Matt Church: Welcome (5MB .ppt)

Moore C.C

0915-1045

Dave Karl: “Microbial Oceanography: Its Scope, Challenges and Opportunities” (42MB .pptx)

Moore C.C

 

 

Readings (PDFs):

 

1045-1100

Break

 

1100-1200

BioSafety (Steve Case)

Moore C.C.

1200-1300

Lunch (brown-bag)

MSB 307

1300-1415

Lab Safety (Hans Nielsen)

Moore C.C.

1415-1430

Break

 

1430-1630

Rad Safety (Irene Sakamoto)

Moore C.C.

1630-1800

Welcome Mixer

C-MORE Hale

Wednesday, May 30

Daily Theme: “Elemental Cycling in the Sea”

C-MORE Hale

0900-1015

Dan Repeta: “The ocean carbon cycle” (10MB .pptx)

Moore C.C

 

 

Readings (PDFs):

 

1015-1045

Break

 

1045-1200

Debbie Bronk: “Nitrogen cycling in the ocean” (6MB .ppt)

Moore C.C

 

 

Readings (PDFs):

 

1200-1400

Lunch (brown-bag)

MSB 307

1400-1515

Dave Karl: “Phosphorus in the Sea: New Views of an Old Cycle” (60MB .ppx)

Moore C.C

 

 

Readings (PDFs):

 

 

1515-1545

Break

 

1545-1700

Matt Church: “Cruise planning/information”

Moore C.C.

Thursday, May 31

Daily Theme: “Primary Production and Nutrient Cycling ”

C-MORE Hale

0900-1015

Angelicque White: “Remote sensing of primary productivity” (13MB. pptx)

Moore C.C

 

 

Readings (PDFs):

 

1015-1045

Break

 

1045-1200

Pep Gasol: “Bacterial production, growth efficiencies, leucine conversion factors and the energy limitation of oceanic bacteria” (10MB .pdf)

Moore C.C

 

 

Readings (PDFs):

 

1200-1400

Lunch (brown-bag)

MSB 307

1400-1515

Dan Repeta: “Substrate specificity in microbial carbon utilization” (112MB .ppt)

Moore C.C

 

 

Readings (PDFs):

 

1515-1545

Break

 

1545-1700

Debbie Bronk: “DON sources: methods and processes” (14MB .ppt)

Moore C.C

 

1800

Paradise Cove Luau (optional attendance)
Debbie Bronk is coordinating; please RSVP to Debbie if you plan to attend.

Paradise Cove

Friday, June 01

Daily Theme: “Detection of microbes and particles”

C-MORE Hale

0900-1015

Sallie Chisholm: “Phytoplankton Size and the multiple discoveries of Prochlorococcus (26MB .pdf)

Moore C.C

 

 

Readings (PDFs):

 

1015-1045

Break

 

1045-1200

Angelicque White: “Nitrogen fixation in the Gulf of California: A case study in the many ways we detect phytoplankton in the ocean” (16MB .pptx)

Moore C.C

 

 

Readings (PDFs):

 

1200-1400

Lunch (brown-bag)

MSB 307

1400-1515

Pep Gasol: “Flow cytometry to detect heterotrophs and their physiological status” (20MB .pdf)

Moore C.C

 

 

Readings (PDFs):

 

1515-1545

Break

 

1545-1630

Grieg Steward: “Introduction to molecular methods in microbial ecology”

Moore C.C

 

1630-1715

Matt Church: “Introduction to Station ALOHA”

Moore C.C.

Saturday, June 02
0830-1400

Symposium 1:

“Organic Matter Cycling in the Sea”

Moderated by Dave Karl
For more information, download the flyer PDF.

CMORE Hale Moore Conference Center

 

0830

Coffee

 

900-1000

Dan Repeta: “The composition of dissolved organic matter — how is it determined and what can it tell us?” (8MB .ppt)

 

1000-1100

Debbie Bronk: “DON bioavailability & approaches to study N uptake” (18MB .pptx)

 

1100-1130

Break

 

1130-1230

Angelicque White: “Dissolved organic phosphorus utilization” (25MB .pptx)

Readings (PDFs):

 

1230-1330

Pep Gasol: “Group-specific approach to describe the role of bacteria on organic matter cycling” (17 MB .pdf)

Readings (PDFs):

 

1330-1400

Wrap up discussion

 

1400-1600

Late lunch provided

 

Sunday, June 03

Hanauma Bay snorkeling with Ken

Free Day

[ Top of Page | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6a | Week 6b ]  [ Symposium 1 | Symposium 2 ]

Week 2: MICROBIAL OCEANOGRAPHY: GENOMES TO BIOMES

  • Visiting Faculty: E. Allen, S. Chisholm, E. DeLong, N. Krypides, J. Zehr
  • Local Faculty: D. Böttjer, M. Church, D. Karl, M. Rappé, G. Steward

Monday, June 04

Daily Theme: “Student Research Talks”

Moore C.C.

 

0900-1015

Student research talks

Moore C.C.

1015-1045

Break

 

1045-1200

Student research talks

Moore C.C.

1200-1330

Lunch (brown-bag)

MSB 307

1330-1500

Student research talks

Moore C.C.

1500-1530

Break

 

1530-1700

Cruise planning meeting

Moore C.C.

Tuesday, June 05

Daily Theme: “Introduction to marine microbial genomics

C-MORE Hale

0900-1015

Ed DeLong: “Introduction: Marine microbes and genomics” (40MB .ppt)

Moore C.C.

 

 

Readings (PDFs):

 

1015-1045

Break

 

1045-1200

Jon Zehr: “Ecology of marine N2 fixation: use of genes and genomics” (22MB .pptx)

Moore C.C.

 

1200-1330

Faculty brownbag lunch: Zehr & DeLong faculty introductory chat

MSB 307

1330-1500

Nikos Kyrpides: “Annotation of microbial genomes” (Part 1 9MB .pptx Part 2 4MB .pptx)

Moore C.C.

 

1500-1530

Break

 

1530-1700

Eric Allen: “Genome assembly: genomics & metagenomics” (19MB .pptx)

Moore C.C.

 

1800

Group Dinner (to be organized by students)

TBD

Wednesday, June 06

Daily Theme: “Comparative Genomics — Theory and applications

C-MORE Hale

0900-1015

Sallie Chisholm: “Genomics of the oceans most abundant phototroph and its phage partners” (29MB .pdf)

Moore C.C

 

 

Readings (PDFs):

 

1015-1045

Break

 

1045-1200

Jon Zehr: “Solving the mystery of an enigmatic N-fixing cyanobacterium” (29MB .pptx)

Moore C.C.

 

1200-1330

Faculty brownbag lunch: Kyrpides & Allen faculty introductory chat

MSB 307

1330-1700

Lectures & Computer Lab I: “Genomic and metagenomic web-based analytical tools”

Moore C.C.

1330–1500

Nikos Kyrpides: “Introduction to IMG and IMG/M ”
Lab: “Logging in and Surfing around IMG”
(Part 1 10MB .pptx;Part 2 6MB .pptx)

Moore C.C.

1530-1700

Eric Allen: “Introduction to CAMERA” (21MB .pptx)
Lab: “Logging in and Surfing around CAMERA”

Moore C.C.

Thursday, June 07

Daily Theme: “Metagenomics & metaranscriptomics

C-MORE Hale

0900-1015

Eric Allen: “Microbial metagenomics in extreme environments” (41MB .pptx)

Moore C.C.

 

1015-1030

Break

1030 -1200

Ed DeLong: “Marine microbial metatranscriptomics” (32MB .pptx)

Moore C.C

 

 

Readings (PDFs):

 

1200-1330

Lunch

MSB 307

1330-1700

Computer Lab II “Genomic and metagenomic analysis using IMG, IMG/M and CAMERA”
Nikos Kyrpides: “Annotating a new microbial genome using IMG”
Eric Allen: “Analyzing metagenomic datasets using CAMERA”

Moore C.C.

Friday, June 08

Daily Theme: “Metagenomics & metaranscriptomics (con’t)”

C-MORE Hale

0900-1200

Students working independently on genome/metagenome analyses

C-MORE Hale

1200-1400

Lunch

MSB 307

1400-1600

Regroup to discuss genome analyses

Moore C.C.

1600-1700

Matt Church: “Introduction to Station ALOHA” (15MB .pptx)

Moore C.C.

 

Saturday, June 09
0830-1400

Symposium 2:

“Marine bacteria and cyanobacteria — genotypes, phenotypes, and ecology”

Moderated by Grieg Steward
For more information, download the flyer PDF.

CMORE Hale Moore Conference Center

 

0830

Coffee

 

900-1000

Sallie Chisholm: “The power of Diversity: What Prochlorococcus can teach us about life” (49MB .pptx)

Readings (PDFs):

 

1000-1100

John Waterbury: “Ecology of marine cyanobacteria” (32MB .ppt)

 

1100-1130

Break

 

1130-1230

Eric Allen: “Marine microbial secondary lipids: from biomes to biotechnology” (9MB .pptx)

 

1230-1330

Ed DeLong: “Microbial community structure, function, and dynamics: An ‘omics’ perspective” (41MB .pptx)

 

1330-1400

Wrap up discussion

 

1400-1600

Late lunch reception

 

Sunday, June 10
0830-1500

 Loading Research Vessel Kilo Moana

Snug Harbor

[ Top of Page | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6a | Week 6b ]  [ Symposium 1 | Symposium 2 ]

Week 3 & 4: RESEARCH CRUISE IN THE SUBTROPICAL NORTH PACIFIC OCEAN

  • Faculty: K. Björkman, D. Böttjer, M. Church, M. Rappé, J. Waterbury

Monday, June 11 – Wednesday, June 20

RESEARCH CRUISE

R/V Kilo Moana

[ Top of Page | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6a | Week 6b ]  [ Symposium 1 | Symposium 2 ]

Week 4: LABORATORY AND GENOME ANALYSES

Wednesday, June 20

Return to Honolulu

R/V Kilo Moana

0800

Return to Snug Harbor, offload research vessel

Snug Harbor

1100-1200

Return to UH Mānoa campus; students check into Frear Hall

UH Mānoa

1400-1700

UH laboratory analyses

C-MORE Hale

Thursday, June 21
0900-1700

UH laboratory analyses

C-MORE Hale

Friday, June 22
0900-1700

UH laboratory analyses

C-MORE Hale

Saturday, June 23

Daily Theme: “UH faculty research talks”

C-MORE Hale

 

0900-1000

Daniela Böttjer: "Diazotroph activity and community structure at Station ALOHA under different CO2 conditions" (47MB .pptx)

Moore C.C.

1000-1100

Matt Church: “Dynamics of nitrogen cycling microorganisms in the open sea” (11MB .pptx)

Moore C.C.

1100-1130

Break

 

1130-1230

Dave Karl: “Elements of Microbial Oceanography” (32MB .pptx)

Moore C.C.

1200-1330

Lunch

Outside
C-MORE Hale

1330-1430

Karin Björkman: “Phosphorus in the Oligotrophic North Pacific Subtropical Gyre” (27MB .pptx)

Moore C.C.

1430-1530

Grieg Steward: “Viruses Rule the Sea” (10MB PDF)

Moore C.C.

1530-1600

Break

 

1600-1700

Mike Rappé: “The structure of bacterial communities in the NPSG” (45MB .pptx)

Moore C.C.

Sunday, June 24

Free Day for students to explore O‘ahu

Free Day

[ Top of Page | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6a | Week 6b ]  [ Symposium 1 | Symposium 2 ]

Week 5: LABORATORY AND GENOME ANALYSES

Monday, June 25
0900-1700

UH laboratory analyses

C-MORE Hale

Tuesday, June 26
0900-1700

UH laboratory analyses

C-MORE Hale

Wednesday, June 27
0900-1700

UH laboratory analyses

C-MORE Hale

Thursday, June 28
0900-1700

UH laboratory analyses

C-MORE Hale

Friday, June 29
0900-1700

Shark’s Cove snorkeling with Ken

Free Day

Saturday, June 30
0900-1700

UH laboratory analyses

C-MORE Hale

[ Top of Page | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6a | Week 6b ]  [ Symposium 1 | Symposium 2 ]

Week 6 (part 1): MICROBIAL OCEANOGRAPHY IN THE 21ST CENTURY

  • Visiting Faculty: S. Chisholm, M. Follows, K. Johnson, O. Schofield
  • Local Faculty: D. Böttjer, M. Church, D. Karl, M. Rappé, G. Steward

Sunday, July 01

Daily Theme: “Ocean biogeochemistry: from observations to models”

C-MORE Hale

0900-1015

Mick Follows: “Physical circulation of the ocean and nutrient supply to the euphotic zone” (173MB .pptx)

Moore C.C.

 

1015-1030

Break

 

1030-1200

Oscar Schofield: “Emerging assets and capabilities for observing ocean dynamics” (150MB PDF)

Moore C.C.

 

1200-1330

Lunch (brown-bag)

MSB 307

1330-1445

Ken Johnson: “Observing microbial processes at the global scale” (29MB .pptx)

Moore C.C

 

 

Readings (PDFs):

 

1500-1530

Break

 

1445-1700

Mick Follows: Hands on Ocean Data View tutorial
Students and Faculty: Synthesis of cruise data

Moore C.C.

Monday, July 02

Daily Theme: “Oceanography: Predictions, projections, and the human dimension

C-MORE Hale

0900-1015

Sallie Chisholm: “From Synthetic Biology to Geoengineering: Where is the biosphere headed?” (19MB .pptx)

Moore C.C

 

 

Readings (PDFs):

 

1015-1030

Break

 

1030-1200

Ken Johnson: “Iron: the other limiting nutrient” (24MB .pptx)

Moore C.C

 

 

Readings (PDFs):

Moore C.C.

1200-1330

Lunch (brown bag)

MSB 307

1330-1445

Mick Follows: “Models of ocean biogeochemistry and ecology: Do we have predictive capability?” (155MB .pptx)

Moore C.C.

 

1445-1500

Break

 

1500-1615

Oscar Schofield: “Hot days in polar seas and trended changes in the melting polar seas” (300MB PDF)

Moore C.C.

 

1615-1730

Students and Faculty: Synthesis of cruise data

Moore C.C.

Tuesday, July 03

Daily Theme: “Detecting plankton biomass, physiology, and metabolism

C-MORE Hale

0900-1015

Ken Johnson: “Observing ocean metabolism from profiling floats” (11MB .pptx)

Moore C.C.

 

 

Readings (PDFs):

 

1015-1030

Break

 

1030-1200

Oscar Schofield: “Techniques for measuring plankton biomass and physiology” (27MB .pptx)

Moore C.C.

 

1200-1330

Lunch (brown bag)

MSB 307

1330-1445

Mick Follows: “Models of microbial physiology: A potted history”

Moore C.C.

 

1445-1700

Mick Follows: Hands-on microbial modeling tutorial: "Resource competition and the paradox of the plankton”

Moore C.C.

1700

BBQ at Kaimana Beach

Kaimana Beach

Wednesday, July 04
Independence Day

Free Day to explore O‘ahu

Free Day

[ Top of Page | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6a | Week 6b ]  [ Symposium 1 | Symposium 2 ]

Week 6 (con’t): SYNTHESIS AND INTEGRATION

Thursday, July 05
0900-1700

Synthesis of cruise/genome data, preparing final presentations

C-MORE Hale

Friday, July 06

Symposium and End of Course

C-MORE Hale

1000-1200

Student Research Symposium (52MB .pptx)
Summer course farewell video (154MB .wmv opens in a new window)

Moore C.C.

 

1200-1330

Lunch

 

1330-1430

Course evaluations

Moore C.C.

1730-2000

Farewell Gala – End of course

Waikiki Aquarium

Saturday, July 07

Free day to explore O‘ahu

Free Day

Sunday, July 08

Students check out of Frear Hall

UH Mānoa

[ Top of Page | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6a | Week 6b ]  [ Symposium 1 | Symposium 2 ]