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Tentative Agouron Course Syllabus (edited 07/24/2006)

Theme Week 1: Visualizing microbes
Visiting faculty: Sieracki
Permanent faculty: Church/Karl/Steward
Overseeing Labs: Steward

Wednesday June 21, 2006 - Introductions

08:30-09:15 MSB 100 Introduction, outline of course syllabus (Church)
09:30-10:45 Lab safety Training (UH-EHSO)
10:45-12:00 Bio Safety Training (UH-EHSO)
12:00-13:00 Lunch
13:00-16:00 Rad safety training and course (UH-EHSO)
16:00-18:00 Dinner
18:00-19:30 MSB 100 Lecture: The emergence of microbial oceanography and the ocean as a habitat (Karl)

Thursday June 22, 2006 - Visualizing microbes

08:30-11:30 MSB 100 Lecture: Aquatic Cytometry: Visualizing and Mapping Microbes in the Ocean (Sieracki)/ Lecture: Virus aquaticus (Steward)
11:30-13:00 Lunch break
13:00-17:00 HIG 215
-Microscopes and stains for enumerating microplankton and viral abundances (Rappe, Steward)
17:00-18:30 Dinner
18:30-20:00 MSB 100 Colloquium: Should we study microbes at microbial scales, and if we should, how can we? (Sieracki)

Friday June 23, 2006 - Bacterial activity and elemental cycling

08:30-15:30 MSB 203/627/632
-Tutorial: Imaging microbes (Sieracki)
-Labs: flow cytometry and flow cam (Sieracki/Doggett)
11:00-13:00 Lunch
15:30-17:00 MSB 100 Lecture: Coupled C, N and P cycles (Karl)/ Discussion of microscopy lab results
17:00-19:00 Dinner
Evening off

Saturday June 24, 2006 - Student presentations

08:30-11:30 MSB 100 Student Presentations (6)
11:00-12:30 Lunch
12:30-14:30 MSB 100 Student presentation (6)

Sunday June 25, 2006 - Free day for activities around the island

Theme Week 2: Microbial Activity and Biomass
Visiting Faculty: Kirchman, Repeta, Williams
Permanent Faulty: Bidigare, Church, Johnson, Karl, Rappe, Steward
Overseeing Labs: Johnson

Monday June 26, 2006 - Historical developments and biomass

08:30-11:30 MSB 100 Lecture: (Williams): Geophysiology: from Pasteur and Hutton via Vernadsky, Redfield to Lovelock
1) Cybernetics, Homeostasis, Redfield and Nutrient Control in the Oceans
2) The Biosphere, Climate Stabilization, Lovelock and Daisyworld (Williams)
11:30-13:00 Lunch
13:00-17:00 MSB 203/POST 07:
-Microbial biomass by HPLC (Bidigare)
17:00-18:00 Break
18:00-19:30 MSB 100 Colloquium: Accuracy in Reporting and Citing Science (Williams)

Tuesday June 27, 2006 - The soil of the sea and organic matter production

08:30-11:30 MSB 100 Lecture: Dissolved Organic Matter- fuel for the microbial loop (Repeta)
Lecture: Lecture: Let's Build a Planktonic Food web from a set of Commandments from Physics and Thermodynamics – well and bit of Biology also (Williams)
11:30-12:30 Lunch/Break
1:00-16:00 MSB 100 Lecture: Light harvesting and oxygenic photosynthesis (Bidigare)/ Lecture: Respiration – the dark side of the moon (Williams)
16:00-18:00 Break/Dinner
18:00-19:30 MSB 100 Colloquium: The bomb, radiocarbon, and the
reactivity of dissolved organic matter (Repeta)

Wednesday June 28, 2006 - Linking Function and activity

08:30-11:30 BEACH Lab-Snug Harbor
-Tutorial: Measuring PP (Johnson)
-Lab: 14C primary production/FRRf
11:30-13:00 Lunch
13:00-16:00 BEACH Lab-Snug Harbor
-Lab Tutorial: Bacterial production (Steward)
-Lab: 3H-TdR/Leu incorporation rates
16:00-18:00 Break/dinner
18:00-19:30 MSB 315 Cruise planning discussion (everyone)

Thursday June 29, 2006 - Production and Respiration

08:30-11:30 MSB 100 Lectures: 1. Biomass production by heterotrophic bacteria in the oceans
2. Linking structure and function of marine heterotrophic prokaryotes (Kirchman)
11:30-13:00 Lunch/Break
13:00-16:00 MSB 203: Precruise meeting with OTG-ship support
Discussion of previous lab results
16:00-18:00 Dinner (UH)
18:00-19:30 MSB 100 Colloquium: Abundance and activity of photoheterotrophic microbes in the oceans (Kirchman)

Friday June 30, 2006 - Food Webs and Nutrients

08:30-11:30 MSB 100 The Ocean Carbon Budget: Can we Make Sense from Nonsense (Williams)
11:30-13:00 Lunch break
13:00-16:00 MSB 203
-Lab tutorial: Measuring nutrients in the sea (Bjorkman/Mahaffey)
-HIG 215: SRP/DOP concentrations in SW (Bjorkman/Mahaffey)
16:00-19:00 break/dinner

Saturday July 1, 2006

East-West Center
Symposia 1: Controls and structure of the microbial loop
Speakers: Williams/Repeta/Steward/Kirchman
Provocateur: Church

15:00-18:00 Mixer/reception

Sunday July 2, 2006

08:30-11:30 HIG 215: Organize for cruise/staging materials
11:30-13:00 Lunch
17:00-18:30 Dinner

WEEK 3: Cruise planning/Cruising

Monday July 3, 2006

08:30-11:30 Load vessel for cruise
11:30-14:00 Lunch break Snug harbor
14:00-16:00 Continue loading vessel
16:00-18:00 Dinner (UH)

Tuesday July 4, 2006 - OFF FOR HOLIDAY

Wednesday July 5, 2006

08:00 Check out of campus housing and onto KM
10:00 Depart on KM

July 5-July 10, 2006 - AT SEA Church, Rappe, Williams

Monday July 10, 2006

08:00-12:00 Arrive Snug Harbor, offload vessel
Lunch on vessel
13:00 Check back into campus housing
15:00-16:30 POST 126 Lecture: (P. Hacker)

Theme Week 4 topic: Emerging Technologies
Visiting Faculty: Cullen, DeLong, Zehr, Williams
Permanent Faculty: Bidigare, Church, Johnson, Karl, Rappe
Overseeing Labs: Rappe

Tuesday July 11, 2006 - Cell signatures and molecular detection of activity

08:30-11:30 POST 126: Lecture: Activities of microorganisms: from theoretical considerations to applications in detecting organism function (Zehr)
11:30-14:00 Break/lunch
14:00-16:00 HIG 215: Lab tutorial: Identification of marine microbes (Rappe)
Nucleic acid extraction and PCR (Rappe)
17:00-18:00 Dinner/break
18:00-19:30 MSB 100: Colloquium: Tools for measuring in situ microbial activity - biomarkers, FISH and isotope analyses (DeLong)

Wednesday July 12, 2006 - Diversity

08:30-11:30 POST 126 Lecture: Behavior, physiology and the niche of marine phytoplankton (Cullen)/ Lecture: Genomic and metabolic diversity of marine Bacteria and Archaea (DeLong)
11:30-13:00 Lunch break
13:00-16:00 HIG 215: Lab Tutorial: Pitfalls and promises of techniques to screen microbes (Rappe)
Lab: Fingerprinting communities-TRFLP/cloning (Rappe)
16:00-18:00 Dinner break
18:00-19:30 MSB 315 Begin planning 2nd cruise

Thursday July 13, 2006 - Scaling and informatics

08:30-11:30 POST 126 Lecture: Technologies to sample pelagic ecosystems on scales that matter (Cullen) / Lecture: (Bidigare-Eddies talk)
11:00-13:00 Lunch break
13:00-16:00 MSB 314 Lab Tutorial: Databases and web resources to analyze and compare genomic sequences (DeLong)
16:00-18:00 Dinner break
18:00-19:30 MSB 100 Colloquium: Spatial and temporal distributions of functional groups in the nitrogen cycle (Zehr)

Friday July 14, 2006

08:30-11:30 MSB 315 organize for cruise
11:30-13:00 Lunch break
18:00 MSB 100 Colloquium: Science, Society and Ocean Fertilization for Carbon Credits (Cullen)

Saturday July 15, 2006

Symposium 2: Have advances in gene technology aided microbial ecology?
08:30 East-West Center
Speakers: DeLong/Zehr/Cullen/Johnson
Provocateur: Karl

-Environmental genomics - from genotype, to phenotype, to community dynamics (DeLong)
-Big things come in small packages (and how molecular techniques have started to unwrap those packages)-(Johnson)
-Molecular ecology of marine N2-fixing microorganisms: from genes to function (Zehr)

15:00-18:00 Mixer/reception

Sunday July 16, 2006

08:00 Check out of UH housing
10:00 Load vessel
12:00- Depart Snug Harbor on KM

WEEK 5: Cruising again

July 16-21, 2006 - AT SEA - Church, Bidigare, Rappe, Letelier, Johnson

Friday July 21, 2006

08:00-12:00 Offload KM (lunch on board vessel)
13:00 Check into UH housing
Rest of day off to unpack and begin processing samples

Theme Week 6 Topic: Modeling and synthesis
Visiting faculty: Doney, Duarte
Permanent Faculty: Bidigare, Church, Johnson, Karl, Rappe

Saturday July 22, 2006 - Sensing microbes from space

08:30-11:30 MSB 100 Lecture: (Letelier)/ Lecture: Bio-optics photosynthesis models (Bidigare)
11:30-13:00 lunch break
13:00-15:00 Colloquium: Doney

Sunday July 23, 2006 - Analyzing complex systems

08:30-11:30 MSB 100 Lecture: Comparative analyses of marine microbial systems: searching for pattern (Duarte)/Lecture: Physical forcing and plankton variability (Bidigare)
11:30-13:00 lunch break
13:00-16:00 Laboratory work on samples from cruises

Monday July 24, 2006 - Experiments and observations

08:30-11:30 MSB 114 Lecture: Experimental approaches in marine microbial ecology: micro-, meso- and macrocosm experiments (Duarte)/Lectures: Prochlorococcus as a model marine microbe (Johnson)
11:30-13:00 lunch break
13:00-16:00 Laboratory work on samples from cruises
18:00-19:30 MSB 114 Colloquium: Deconstructing the Carbon Budget of the Ocean: Paradigms and Aesthetics at Play (Duarte)

Tuesday July 25, 2006 - Laboratory work on samples

08:30-16:00 Laboratory work on samples from cruises
18:30-19:30 MSB 114 Initial student data presentations from cruise

Wednesday July 26, 2006 - Modeling fluxes and inventories

08:30-11:30 MSB 114 Lecture: (Doney)/Colloquium: The role of publication in the scientific process (Duarte)
11:30-13:00 lunch break
13:00-16:00 Students assemble lab group presentations

Thursday July 27, 2006 - Communicating your data

13:00-16:00 MSB 114 Student’s lab group symposia

17:30-21:00 Waikiki Aquarium: Farewell mixer

Friday July 28, 2006 - Looking ahead

08:30-11:30 MSB 114 Lecture: Challenges and opportunities in microbial oceanography: A future prospectus (Karl)

Saturday July 29, 2006 - Free Day

Sunday July 30, 2006 - Check out of UH campus housing