2010 Course Syllabus

UH Faculty: Matthew Church, David Karl, Michael Rappé, Grieg Steward, Debbie Millikan

Week 1: THE OCEAN AS A MICROBIAL HABITAT Visiting Faculty: Ken Denman, Mick Follows, Ken Johnson, Mary Jane Perry, Paul Falkowski
Monday 31 May Memorial Day	INTRODUCTION / ORIENTATION
0830-0915	Introductions	MSB 100
0900-1000	Paperwork — visa and tax forms	MSB 100
1000-1020	Break
1020-1130	Dave Karl: “Microbial Oceanography: Its scope, challenges, and opportunities” Readings (PDFs): Seascape Microbial Ecology: Habitat Structure, Biodeversity, and Ecosystem Function Microbial oceanography: paradigms, processes and promise A Sea of Change: Biogeochemical Variability in the North Pacific Subtropical Gyre Microbial oceanography in a sea of opportunity	MSB 100
1130-1300	Lunch	MSB Lanai
1300-1630	Student research talks (Part 1)	MSB 100
1630-	Informal Mixer	MSB Lanai
Tuesday 01 June	INTRODUCTION / ORIENTATION (continued)
0900-1045	Radiation Safety Training (Irene Sakimoto)	MSB 100
1045-1100	Break
1100-1130	Biosafety Training (Hubert Olipares)	MSB 100
1130-1300	Lunch (Campus Center Executive Dining Room) Self introductions: Karl, Steward
1300-1400	Laboratory Safety Training (Hans Nielsen)	MSB 100
1400-1500	Student research talks (Part 2)	MSB 100
1500-1700	Faculty research talks (Dave Karl, Grieg Steward, Matt Church, Mike Rappé, Debbie Millikan)	MSB 100
Wednesday 02 June	OCEAN BIOGEOCHEMICAL VARIABILITY
0830-0945	Ken Denman: “Observing ocean ecosystems: Needs, capabilities and gaps” Lecture (Powerpoint presentation saved as PDF): Observing Ocean Ecosystems: Needs, Capabilities, and the Future (12MB)	MSB 100
0945-1000	Break
1000-1115	Mick Follows: “Physical circulation of the ocean and nutrient supply” Reading (PDF): Physical Transport of Nutrients and the Maintenance of Biological Production (3.5MB)	MSB 100
1115-1300	Lunch (Campus Center Executive Dining Room) Self introductions: Denman, Follows
1300-1400	Paul Falkowski: “Coupled redox controls and nutrient cycling” Readings (PDFs): Redox control of N:P ratios in aquatic ecosystems The co-evolution of the nitrogen, carbon and oxygen cycles in the Proterozoic ocean	MSB 100
1400-1500	Mary Jane Perry : “Biological control of ocean nutrients” Readings (PDFs): The Marine Nitrogen Cycle: Overview and Challenges (2.9MB) The Oceanic Phosphorus Cycle Lecture (Powerpoint presentation): Biological control… (3MB; revised 06-14-10)	MSB 100
1520-1620	Ken Johnson: “Nutrient supply and metabolic balance in the oligotrophic ocean, Part I” Readings (PDFs): Vertical Nitrate Fluxes in the Oligotrophic Ocean Metabolic balance of the open sea Net production of oxygen in the subtropical ocean Eddy/Wind Interactions Stimulate Extraordinary Mid-Ocean Plankton Blooms Lecture (Powerpoint presentation): Nutrient supply and metabolic balance… Parts 1 and 2 (30MB)	MSB 100
1800-	Group Dinner	TBD
Thursday 03 June	PHYTOPLANKTON DYNAMICS IN THE OPEN SEA
0830-0945	Mary Jane Perry: “Detection of phytoplankton and their physiology from ships to satellites” Lecture (Powerpoint presentation): Detection of phytoplankton… Part 1 (13MB) Detection of phytoplankton… Part 2 (3MB; revised 06-14-10)	MSB 100
0945-1000	Break
1000-1115	Mick Follows: “Modeling marine microbes: Molecules to ecosystems” Readings (PDFs): Some Characteristics of Simple Types of Predation and Parasitism Population Growth in Micro-Organisms Limited by Food Supply A theoretical model for nutrient uptake in phytoplankton Lecture (PDF): Modeling molecules to ecosystems	MSB 100
1120-1300	Lunch (Campus Center Executive Dining Room) Self introductions: Johnson, Perry
1300-1400	Ken Johnson: “Nutrient supply and metabolic balance in the oligotrophic ocean, Part II”	MSB 100
1400-1500	Ken Denman: “Responses of marine ecosystems to a changing climate: physical oceanographic and biogeochemical linkages” Lecture (Powerpoint presentation saved as PDF): Responses of Marine Ecosystems to a Changing Climate (6.5MB)	MSB 100
1500-1700	Cruise planning discussion	MSB 315
Friday 04 June	MICROBIAL OCEANOGRAPHY: PROJECTIONS, DYNAMICS, AND THE HUMAN DIMENSION
0830-1030	Mick Follows: “Ocean Data View Tutorial ”	MSB 315
1030-1045	Break
1045-1145	Peter Mouginis-Mark: “The Hawai‘ Space Flight Program”	MSB 100
1200-1330	Lunch (Campus Center Executive Dining Room) Self introductions
1400-1500	Ken Johnson: “Iron: the other limiting nutrient” Readings (PDFs): Glacial-Interglacial CO2 change: The Iron Hypothesis Mesoscale Iron Enrichment Experiments 1993\962005: Synthesis and Future Directions Lecture (Powerpoint presentation, parts 1 and 2): Iron: the other limiting nutrient (19MB)	MSB 100
1500-1600	Mary Jane Perry: “How might projected changes to the ocean influence plankton biology?” Lecture (Powerpoint presentation): Climate change… Part 1 (7.7MB; revised 06-14-10)	MSB 100
1600-1700	Ken Denman: “A planetary status update and lessons from the IPCC report”	MSB 100
Saturday 05 June	Symposium 1: “Observations and Predictions in a Changing Ocean” Moderated by Dave Karl
0830-1700	Speakers: Ken Johnson, Monterey Bay Aquarium Research Institute How do we observe biogeochemical cycles at the global scale in a changing world? (Reading: Observing Biogeochemical Cycles at Global Scales with Profiling Floats and Gliders) (View embedded video of his presentation) Jon Zehr, University of California at Santa Cruz Detecting global change: temporal and spatial dynamics of N cycling microbes (View embedded video of his presentation; includes Dave Karl’s opening comments) Mick Follows, Massachusetts Institute of Technology Modeling marine microbes: past, present, and prospects (View embedded video of his presentation; download the presentation PDF) Mary Jane Perry, University of Maine, Darling Marine Center Ocean carbon credits — is it possible to document biological carbon removal? Ken Denman, University of Victoria Ocean acidification, marine ecosystems, and geoengineering our climate (View embedded video of his presentation Coffee service begins at 8:30 am; presentations begin at 8:45 am. Lunch will be provided. Please RSVP to Sharon Sakamoto by Wednesday, June 02. Lunch will be provided; reception to follow at the East-West Center Download the advertisement flyer PDF.	UH William Richardson School of Law, Classrm 2
Sunday 06 June	Free Day for students to explore O‘ahu
[ Top of Page ] Week 2: THE MICROBIAL OCEAN VIEWED THROUGH THE LENS OF GENES & GENOMES Visiting Faculty: Edward DeLong, Jonathan Zehr, Nikos Kyrpides, Roman Stocker, Ger van den Engh, Carlos Pedros-Alio, Farooq Azam
Monday 07 June	INTRODUCTION TO MARINE MICROBIAL GENOMICS AND METAGENOMICS
0900-1015	Ed DeLong : “Marine microbes and genomics” Readings (PDFs): The Uncultured Microbial Majority Genomic perspectives in microbial oceanography Molecular diversity and ecology of microbial plankton The microbial ocean from genomes to biomes Resourceful heterotrophs make the most of light in the coastal ocean Additional readings (PDFs): CAMERA: A Community Resource for Metagenomics (5MB) The metagenomics RAST server — a public resource for the automatic phylogenetic and functional analysis of metagenomes MEGAN analysis of metagenomic data	MSB 100
1015-1045	Break
1045-1200	Jon Zehr : “Functional genomics and transcriptomics of the marine nitrogen cycle”	MSB 100
1200-1330	Faculty brownbag lunch (Campus Center Room 220) Self introductions: DeLong, Zehr
1330-1500	Mike Rappé: “Pelagibacter — the most abundant heterotroph in the oceans” Readings (PDFs): SAR11 marine bacteria require exogenous reduced sulphur for growth Genome Streamlining in a Cosmopolitan Oceanic Bacterium The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity Lecture (PDF): Pelagibacter — the most abundant heterotroph… (10.8MB)	MSB 100
1500-1530	Break
1530-1700	Ed DeLong: “Marine microbial metagenomics”	MSB 100
1800-	Group Dinner	TBD
Tuesday 08 June	GENOME ASSEMBLY AND ANALYSES — APPLICATIONS AND THEORY
0900-1015	Nikos Kyrpides: “Annotation of microbial genomes ” Readings (PDF): The integrated microbial genomes system: an expanding comparative analysis resource Lectures (PowerPoint): Microbial Genome Annotation (6.5MB) DOE JGI Production Genomics Facility	MSB 100
1015-1045	Break
1045-1200	Jon Zehr: “New players in the N cycle revealed by population metagenomics”	MSB 100
1200-1330	Faculty brownbag lunch (Campus Center Room 220) Self introductions: Kyrpides, Rappé
1330-1700	Lecture & Computer Lab I — Genomic and metagenomic analytical tools DeLong: “Genomic and metagenomic tools on the web” (PDF of presentation, 8.8MB) Kyrpides: “Introduction to IMG and IMG/M” Lab: Logging in and Surfing around IMG	MSB 315
Wednesday 09 June
0900-1015	Mike Rappé: “Genomic perspectives on ubiquitous, newly cultivated marine planktonic bacteria” Lecture (PDF): “High throughput” cultivation and strain HIMB100 (34.7MB)	MSB 100
1015-1045	Break
1030-1200	Ed DeLong: “Marine metatranscriptomics” Lecture (PDF): Marine metatranscriptomics (17.8MB)	MSB 100
1200-1330	Lunch (Campus Center Room 220) Self introductions
1330-1700	Lecture & Computer Lab II — Genomic and metagenomic analysis using IMG and IMG/M Kyrpides: “The future of genomics” Lab: Annotating a newly sequenced microbial genome using IMG The Integrated Microbial Genome (IMG) systems (15.5MB Powerpoint)	MSB 315
Thursday 10 June	THE OCEAN AT THE CELLULAR SCALE
0830-0945	Roman Stocker: “Life at low Reynolds numbers” Lecture (PDF): Intro notes and “Life at low Peclet and Reynolds numbers”	MSB 100
0945-1000	Break
1000-1115	Ger van den Engh: “Principles and practices in flow cytometry (Part 1)”	MSB 100
1115-1300	Lunch (Campus Center Room 220) Self introductions: Stocker, van den Engh
1300-1700	Lab (Kyrpides): “Annotating a newly sequenced microbial genome using IMG”	MSB 315
1800-	Group Dinner	TBD
Friday 11 June
0830-1015	Lab (Kyrpides): “Annotating a newly sequenced microbial genome using IMG”	MSB 315
1015-1030	Break
1030-1145	Lab (Kyrpides): “Annotating a newly sequenced microbial genome using IMG”	MSB 315
1200-1330	Lunch (MSB Lanai)
1330-1445	Roman Stocker: “Chemotaxis and microbial movement in the sea” Lecture (PDF): Motility and chemotaxis, in general and in the Ocean (3.4MB)	MSB 100
1445-1600	Ger van den Engh: “Principles and practices in flow cytometry (Part 2)”	MSB 100
Saturday 12 June	Symposium 2: “The cellular sea” Moderated by Grieg Steward (View embedded video of his opening remarks)
0830-0845	Coffee	UH William Richardson School of Law, Classrm 2
0845-0900	Introductory comments by moderator
0900-1000	Roman Stocker, Massachusetts Institute of Technology Cells and gradients in the sea (View embedded video of his presentation)
1000-1030	Break
1030-1130	Ger van den Engh, BD Biosciences A new flow cytometric method for resolving phytoplankton populations (View embedded video of his presentation)
1130-1300	LUNCH (provided for all on site)
1300-1400	Michael Sieracki, Bigelow Laboratory for Ocean Sciences Interrogating microbes, one cell at a time: Who are you and what are you doing? (View embedded video of his presentation)
1400-1500	Carles Pedrós-Alió, Institut de Ciéncies del Mar The genomes of marine flavobacteria: a manual to survive in the surface of the ocean (View embedded video of his presentation)
1500-1520	Short break
1520-1620	Farooq Azam, Scripps Institution of Oceanography Ocean biogeochemistry: one drop at a time
1620-1645	General discussion as time permits
1650-1900	Symposium Mixer / Reception (in the Edwin S.N. Wong Hospitality Suite in the Stan Sherriff Center, a short walk from the symposium site)
	Please RSVP to Sharon Sakamoto by Wednesday, June 09. Download the advertisement flyer PDF.
Sunday 13 June	Free Day for students to explore O‘ahu
0845-1400	Kayaking around windward O‘ahu (Ken Doggett)
[ Top of Page ] Week 3: FOUNDATIONS OF MICROBIAL OCEANOGRAPHY Visiting Faculty: Susana Agusti, Farooq Azam, Carlos Duarte, Carlos Pedros-Alio, Michael Sieracki
Monday 14 June	THE NEW GENERATION OF MICROBIAL OCEANOGRAPHY
0830-0945	Farooq Azam: “Observing ocean microbes and biogeochemistry at the microscale”	MSB 100
0945-1000	Break
1000-1115	Carlos Pedrós-Alió: “Marine Microbial Diversity: Dipping into the Rare Biosphere”	MSB 100
1115-1315	Lunch (Campus Center Executive Dining Room) Self introductions: Azam, Sieracki
1315-1430	Michael Sieracki: “Changes in observing technologies provide insight into new and old microbial processes”	MSB 100
1500-1800	Cruise planning meeting	MSB 315
Tuesday 15 June	THE MICROBIAL LOOP: CONCEPTS, PATTERNS, AND PROCESSES
0830-0945	Farooq Azam: “The microbial loop: Then and Now”	MSB 100
0945-1000	Break
1000-1115	Susana Agusti: “Mortality and cell death in the sea”	MSB 100
1115-1315	Lunch (Campus Center Executive Dining Room) Self introductions: Pedros-Alio, Agusti
1315-1430	Carlos Duarte: “Heterotrophic Activity in the Sea Revisited” Reading (PDF): How to write consistently boring scientific literature New! Lecture (PDF): Heterotrophic activity… (15.6MB)	MSB 100
1430-1545	Carlos Pedrós-Alió: “The scientific presentation as theater”	MSB 100
1600-1800	Cruise planning meeting	MSB 315
1800-	Group Dinner	TBD
Wednesday 16 June	MICROBIAL OCEANOGRAPHY OF THE EUPHOTIC ZONE
0830-0945	Carlos Duarte: “Ecology and microbial oceanography of the top meter of the sea” New! Lecture (PDF): Too close, yet so far: Exploring Microbial Ecology in the Top Meter of the Ocean (9MB)	MSB 100
0945-1000	Break
1000-1115	Michael Sieracki: “Novel phototrophs of the sea”	MSB 100
1115-1315	Lunch (Campus Center Executive Dining Room) Self introductions: Duarte
1315-1430	Carlos Pedrós-Alió: “A bestiary for the XXI century”	MSB 100
1445-1600	Carlos Duarte: “Microbial Oceanography as a Business” — open discussion to follow lecture New! Lecture (PDF): Microbial Oceanography as a Business (14MB)	MSB 100
Thursday 17 June	Cruise Preparations
0830	Students depart dorms to UH Marine Center, Snug Harbor (1 Sand Island Access Road)
0900	Arrive R/V Kilo Moana to load research vessel	Snug Harbor
1500	Students take cabs back to UH
Friday 18 June
0900-1015	Grieg Steward: Viral ecology in the marine environment
1015-1030	Break
1030-1145	Matt Church: Ecosystem variability in the Subtropical North Pacific Ocean
1200-1300	Lunch
1300-1400	Debbie Millikan: “Marine Symbioses” (revised 06-16-10)
Saturday 19 June	Free Day to explore O‘ahu
Sunday 20 June	RESEARCH CRUISE Download the research plan (Word .doc). Readings (PDFs) The transient oasis: Nutrient-phytoplankton dynamics and particle export in Hawaiian lee cyclones Physical and bio-optical observations of oceanic cyclones west of the island of Hawai‘i (3.8MB) Diatoms in the desert: Plankton community response to a mesoscale eddy in the subtropical North Pacific Influence of a cyclonic eddy on microheterotroph biomass and carbon export in the lee of Hawaii Mesoscale Eddies Drive Increased Silica Export in the Subtropical Pacific Ocean	Kilo Moana
0645	Students take cabs to UH Marine Center at Snug Harbor (revised 06-14-10)
0700	Arrive R/V Kilo Moana for 0800 departure (revised 06-14-10)	Snug Harbor
[ Top of Page ] Week 4: AT SEA / RETURN TO HONOLULU / LAB ANALYSIS
Monday 21 June – Friday 25 June	RESEARCH CRUISE	Kilo Moana
Saturday 26 June	Return to Honolulu
0900	Return to Snug Harbor aboard R/V Kilo Moana	Snug Harbor
1300	Students check into Frear Hall	Frear Hall
Sunday 27 June	UH laboratory analyses
[ Top of Page ] Week 5: LAB ANALYSIS / STUDENT PRESENTATIONS / TO BOSTON
Monday 28 June
0900-1700	UH laboratory analyses	MSB
Tuesday 29 June
0900-1700	UH laboratory analyses	MSB
Wednesday 30 June
0900-1700	UH laboratory analyses	MSB 315
Thursday 01 July
0900-1700	Data analyses and preparation for student presentations	MSB 315
Friday 02 July	Student Presentations
0900-1300	Preparation for student presentations	MSB 315
1300-1500	Student research presentations	MSB 100
1600	Mixer/reception	TBA
Saturday 03 July	Depart for Boston
1200	Students check out of Frear Hall	Frear Hall
1530	Depart for airport	HNL
1800	Depart for Honolulu for Boston, MA, to attend Gordon Research Conference (GRC)	BOS
Sunday 04 July Independence Day	Boston / Gordon Reseach Conference
1200	Arrive Boston	BOS
1400	Shuttle to GRC from Embassy Suites, Boston, MA	Boston
1800	Dinner, evening presentations GRC, Tilton, NH	Tilton, NH
[ Top of Page ] Week 6: GORDON RESEARCH CONFERENCE
Monday 05 July – Friday 09 July	Students attend Gordon Research Conference	Tilton, NH
Friday 09 July	Depart
0730	Breakfast GRC	Tildon, NH
0900	Depart Tilton, NH for Boston, MA	Tilton, NH
1200	Arrive Logan Airport, depart Boston and return home	BOS
[ Top of Page ] Jump to: [ Week 1 \| Week 2 \| Week 3 \| Week 4 \| Week 5 \| Week 6 ] [ Symposium 1 \| Symposium 2 ]

2010 Course Syllabus

Week 1: THE OCEAN AS A MICROBIAL HABITAT

Symposium 1: “Observations and Predictions in a Changing Ocean”

Week 2: THE MICROBIAL OCEAN VIEWED THROUGH THE LENS OF GENES & GENOMES

Symposium 2: “The cellular sea”

Week 3: FOUNDATIONS OF MICROBIAL OCEANOGRAPHY

Week 4: AT SEA / RETURN TO HONOLULU / LAB ANALYSIS

Week 5: LAB ANALYSIS / STUDENT PRESENTATIONS / TO BOSTON

Week 6: GORDON RESEARCH CONFERENCE