2014 Course Syllabus

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Week 1: The Ocean as a Habitat

  • Faculty: Phil Boyd, Curtis Deutsch, Alyson Santoro, John Cullen, Dan Repeta
  • All Lectures in the Moore Conference Center, Daniel K. Inouye C-MORE Hale.

Tuesday, May 27

Welcome and laboratory safety training

0830–0915

Welcome

0915–1030

Lecture: An Introduction to Microbial Oceanography (Karl)

Readings (PDFs):

1030–1045

Coffee break

1045–1145

Lab safety (Hans Nielsen)

1145–1315

Lunch

1315–1415

Biosafety (Steve Case)

1415–1430

Break

1430–1630

Radiation safety (Irene Sakimoto)

1630–

Welcome Mixer

Wednesday, May 28

Processes and patterns in microbial carbon and nutrient cycles

0900–1015

Lecture: The marine carbon cycle: pools, inventories, fluxes (Repeta)

Readings (PDFs):

1015-1045

Coffee break

1045–1200

Lecture: Processes controlling carbon and nutrient distributions and cycling (Deutsch)

1215-1330

Lunchtime introductions (Campus Center, 203E)

1330–1445

Lecture: The Microbial Marine Nitrogen Cycle (Santoro)

Readings (PDFs):

1500–1530

Break

1530–1645

Lecture: The ocean P cycle (Karl)

Readings (PDFs):

1645–1845

Student Research Talks

Thursday, May 29

Plankton productivity and organic matter production

0830–0945

Lecture: Light, nutrients, and primary productivity PDF (Cullen)

Readings (PDFs):

0945–1015

Coffee break

1015–1130

Lecture: Plankton community structure and the biological pump (Boyd)

Readings (PDFs):

1130–1300

Lunchtime introductions (Campus Center, 203E)

1315–1430

Lecture: Plankton growth, stoichiometry and nutrients (Deutsch)

1430–1500

Break

1500–1730

Student Research Talks

Additional Lecture

Lecture: Microbial processes in the mesopelagic (Santoro)

Readings (PDFs):

1730–2000

Pavel Medal in Microbial Oceanography Reception

Friday, May 30

Plankton ecology and biogeochemistry

0900–1015

Lecture: Measures and models of ocean productivity PDF (Cullen)

1015–1045

Coffee break

1045–1200

Lecture: The HNLC condition and iron biogeochemistry (Boyd)

Readings (PDFs):

1215–1330

Lunchtime introductions (Campus Center, 203E)

1345–1500

Lecture: Promises and pitfalls of ocean biogeochemical models (Deutsch)

1530–1645

Lecture: Dissolved organic matter: distributions and composition (Repeta)

Readings (PDFs):

1700–1830

Introduction to Station ALOHA (Church)

Saturday, May 31

Plankton ecology and biogeochemistry

0900–1015

Lecture: Behavior, physiologies, and niches of marine plankton PDF (Cullen)

Readings (PDFs):

1015–1045

Break

1045–1200

Lecture: Plankton biogeochemistry in a future ocean (Boyd)

Readings (PDFs):

1200–1330

Lunch (provided)

1330–1445

Lecture: Ecology and physiology of planktonic archaea (Santoro)

Readings (PDFs):

1445–1500

Break

1500–1615

Lecture: Organic matter reactivity and microbial substrate utilization (Repeta)

Readings (PDFs):

1630–1800

Reception

Sunday, June 01

 Free day to snorkel and explore with Ken

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Week 2: Microbial oceanography through the lens of genomics

  • Faculty: Ginger Armbrust, Penny Chisholm (virtually), Ed DeLong, Craig Nelson, Carlos Pedros-Alio, Grieg Steward, John Eppley, Thomas Bibby
  • All Lectures in the Moore Conference Center, C-MORE Hale

Monday, June 02

0900–1015

Lecture: Cellular life and function (Growth, reproduction, introduction to DNA, RNA, transcription, translation, and regulation) (Steward)

1015–1045

Coffee break

1045–1130

Lecture: Microbial phylogeny and genomics 101 (DeLong)

Readings (PDFs):

1200–1330

Lunchtime introductions

1345–1500

Lecture: Introduction to eukaryotic marine phytoplankton (Armburst)

1500–1515

Break

1515–1630

Lecture: Culture-independent approaches to studying microorganisms; plate count anomaly, 16S rRNA genes, PCR, cloning, FISH (Nelson)

1630–1730

Cruise planning meeting

Tuesday, June 03

Microbial ecology and diversity

0900–1015

Lecture: Introduction to major marine bacterial lineages (Pedrós-Alió)

1015–1045

Coffee Break

1045–1200

Lecture: Microbial phylogeny and genomics 101 (DeLong)

Readings (PDFs):

1200–1400

Lunchtime introductions

1400–1515

Lecture: Modern rRNA tag surveys and statistical analyses (Nelson)

1515–1545

Break

1545–1700

Lab Practical: Computer analyses of rRNA tag sequences (Nelson)

Wednesday, June 04

Genomics and meta-omics

0900–1015

Lecture: Prochlorococcus: The Power of Diversity I (Chisholm)

1015–1045

Coffee Break

1030–1200

Lecture: Eukaryotic phytoplankton ecology (Armburst)

1200–1400

Lunchtime introduction

1400–1515

Lecture: Marine planktonic virus ecology (Steward)

1515–1530

Break

1530–1700

Lecture: The scientific presentation as theater (Pedros-Alio)

Reading (PDF): How to Give a Killer Presentation Lessons from TED by Chris Anderson

1800–

Group Dinner

Thursday, June 05

Comparative Genomics

0900–1015

Lecture: Prochlorococcus: The Power of Diversity II ( (Chisholm)

1015–1045

Coffee Break

1045–1200

Lecture: Genomics of marine Flavobacteria (Pedrós-Alió)

Reading (PDF): Beatriz Fernandez-Gomez et al. 2013. Ecology of marine Bacteroidetes: a comparative genomics approach. The ISME Journal 7, 10261037

1200–1400

Lunchtime introductions — Bibby (Campus Center, 203E)

1400–1530

Lecture: Genomic insights into diatom ecology & physiology (Armbrust)

1530–1545

Break

1545–1700

Lab: Photophysiology & molecular biology of marine cyanobacteria (Bibby)

Friday, June 06

 

0900–1015

Lecture: Integrating Ďomics, biogeochemistry and ecology (DeLong)

Readings (PDFs):

1015–1045

Coffee Break

1045–1200

Lecture: Statistical analyses in microbial ecology (Nelson)

1200–1330

Lunchtime introductions

1400–1515

Computer Lab: Microbial metagenomic analysis tools — lab practical (DeLong/Eppley)

1530–1545

Break

1530–1700

Computer Lab: Microbial metagenomic analysis tools - lab practical (DeLong/Eppley)

Saturday, June 07

Free Day to Explore O‘ahu

Sunday, June 08

Load R/V Kilo Moana for research cruise
Note: Closed-toed shoes required; also make sure to bring sunscreen and a hat

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Weeks 3 and 4: Research Cruise

  • Possible Faculty/staff: Church, Steward, Doggett, Clemente, Björkman, Searson

Monday, June 09

Depart Snug Harbor aboard R/V Kilo Moana

Monday, June 16

Return to Snug Harbor, offload ship and check into dorms
Begin laboratory analyses afternoon of June 16

Tuesday, June 17

 

0800–1130

Biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)

1130–1330

Lunchtime introductions (TBD)

1330–1730

Biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)

Wednesday, June 18

 

0800–1130

Biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)

1130–1330

Lunchtime introductions (TBD)

1330–1730

Biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)

Thursday, June 19

 

0800–1130

Students complete biogeochemical laboratory analyses (LLN, LLP, PSi, PPO4, LLSi, PC/PN, flow cyto)

1130–1330

Lunchtime introductions (TBD)

1330–1730

Students begin molecular laboratory analyses (sequencing tutorial)

Friday, June 20

 

0800–1130

Molecular laboratory analyses (Amplicon sequencing)

0130–1330

Lunchtime introductions (Campus Center, TBD)

1330–1730

Molecular laboratory analyses (Amplicon sequencing)

Saturday, June 21

 

0800–1130

Molecular laboratory analyses (Metagenomics)

1130–1330

Lunchtime introductions (Campus Center, TBD)

1330–1730

Molecular laboratory analyses (Metagenomics)

Sunday, June 22

Free Day to Explore O‘ahu

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Week 5: Laboratory Analyses and Synthesis

Monday, June 23

 

0800–1130

Molecular laboratory analyses (Metagenomics)

1130–1330

Lunchtime introductions (Campus Center, TBD)

1330–1730

Molecular laboratory analyses (Metagenomics)

Tuesday, June 24

 

0800–1130

Molecular laboratory analyses (Metagenomics)

1130–1330

Lunchtime introductions (Campus Center, TBD)

1330–1730

Molecular laboratory analyses (Metagenomics)

Wednesday, June 25

 

0900–1015

Student break out groups working on data analyses

1015–1030

Break

1030–1200

Student break out groups working on data analyses

1200–1400

Lunchtime introductions (Campus Center, TBD)

1400–1700

Student break out groups working on data analyses

Thursday, June 26

 

0900–1015

Students working on presentations

1015–1030

Break

1030–1200

Students working on presentations

1200–1400

Lunchtime introductions (Campus Center, TBD)

1400–1700

Students working on presentations

Friday, June 27

 

0900–1030

Student Final Presentation

1030–1100

Break

1100–1200

Student evaluations

1200–1400

Lunchtime introductions (Campus Center, TBD)

1400–1700

Student evaluations, lab check out

1800–2100

Farewell Gala at Willows Restaurant

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