- Open Ocean:
  - Case study 1: Effects of ocean acidification on marine animal in times of ocean warming. Guest speaker: Dr. Shallin Busch, NWFSC-NOAA

  - Case study 2: Harmful algal blooms and red tide problems: impact of domoic acid on the US west Coast. Sources: Local newspapers and other news media, scientific papers, NOAA outreach education website
    - News media (These are some examples. There should be more recent news by the time this class is taught:
      - Seattle Times: “Toxic algae bloom might be largest ever” (published on June 15, 2015)
http://www.seattletimes.com/seattle-news/health/toxic-algae-bloom-might-be-largest-ever/
      - Seattle Times: “Toxic algae grows even worse; crab-fishing closure double in size” (published on August 5, 2015)
http://www.seattletimes.com/seattle-news/toxic-algae-blooming-in-warm-water-from-california-to-alaska/
      - King 5: “Toxic algae threatens shellfish future” (published on July 17, 2015)
http://www.king5.com/story/tech/science/environment/2015/07/17/toxic-algae-domoic-acid-research-marine-mammals-shellfish/30327447/
      - USA Today: “What you need to know about toxic algae blooms” (published on August 7, 2015)
http://www.usatoday.com/story/news/nation-now/2015/08/07/algae-blooms-economy-west-coast-toxic-bloom/31222581/
      - Santa Cruz Sentinel News: “Domoic acid: behind health warnings, a marine mystery” (published on May 2, 2014)
http://www.santacruzsentinel.com/general-news/20140502/domoic-acid-behind-health-warnings-a-marine-mystery
      - Inquisitr: “‘The blob’, domoic acid: extremely poisonous toxic bloom poses serious threat to west” (published June 23, 2015)
http://www.inquisitr.com/2192946/the-blob-domoic-acid-extremely-poisonous-toxic-bloom-poses-serious-threat-to-west-coast/
      - King 5: “Massive algae bloom causing seizures in sea lions” (published June 17, 2015)
http://www.king5.com/story/tech/science/environment/2015/06/16/noaa-toxic-algae-bloom-domoic-acid-sea-lion/28841659/

    - Papers:
      - Harmful algal blooms on the U.S. west coast, by Vera trainer et al.
(Pdf available online)
      - Domoic acid production near California coastal upwelling zones, June 1998
http://onlinelibrary.wiley.com/doi/10.4319/lo.2000.45.8.1818/pdf
      - Harmful algal blooms and red tide problems on the U.S. west coast
http://onlinelibrary.wiley.com/doi/10.4319/lo.1997.42.5_part_2.1076/pdf
      - Effects of marine toxins on the reproduction and early stages of development of aquatic organisms
http://www.ncbi.nlm.nih.gov/pubmed/20161971

    - NOAA Outreach:
      - http://www.nwfsc.noaa.gov/hab/habs_toxins/marine_biotoxins/da/
      - http://www.nwfsc.noaa.gov/news/features/west_coast_algal_bloom/index.cfm
      - http://montereybay.noaa.gov/new/2015/hab.html

- Estuaries:
  - Case study 1: Homing in Pacific salmon: physiological mechanisms and ecological basis. Guest speaker: Dr. Andy Dittman, NWFSC-NOAA

  - Case study 2: Hypoxia in two extremes: under the ice and on coral reefs. Sources: Book Chapters (Books: Fish life in special environments, Ed. Sebert, Onyango and Kapoor; and Extremophile fishes, Ed. Riesch, Tobler and Plath)

  - Extremophile fishes, Ch 2 (Low-oxygen life styles), pp 9-35.
    - Hypoxic habitats
    - Divergent selective environments

  - Fish life in special environments, Ch 7, pp 169-193.
    - The crucian carp-a master of hypoxic survival
      - Respiratory adaptations
      - The anoxic brain
      - Circulatory adaptations
    - Hypoxia in coral reef teleosts
      - Coral gobies: the most extreme coral dwellers
      - Cardinal fishes: mouthbrooding vs. hypoxic survival


- Polar and tropical aquatic environments:
  - Case study 1: In the dark: a review of ecosystem processes during the Artic polar night. Sources: Review paper 
http://www.sciencedirect.com/science/article/pii/S0079661115001858

  - Case study 2: Adaptations to living at sub-zero; Hemoglobinless icefish and mitochondrial function in the cold. Sources: Book chapters (Books: Fish life in special environments, Ed. Sebert, Onyango and Kapoor)
    - Fish life in special environments, Ch 5 and 6, pp 131-169
      - Antifreeze proteins
      - Cardiovascular system
      - Respiratory and other adaptations
      - Mitochondrial function
        - Does mitochondrial abundance and oxidative capacity indicate compensation for cold temperature?
      - Evolutionary adaptation to the cold: Changes in lipid composition

- Deep Ocean:
  - Case study 1: Hydrothermal vents, functional adaptations and host-microbial symbiotic relationship. Sources: Review paper, and chapter from book (Book: Marine Biology, an ecological approach, Ed. Nybakken and Bertness)
    - Papers: 
      - Ecology of deep-sea hydrothermal vent communities: a review
http://onlinelibrary.wiley.com/doi/10.1029/93RG01280/abstract
      - Microbiology of deep-sea hydrothermal vents
(Pdf provided)
  
  - Case study 2a: Pressure and life: Biological strategies. 
(PDF provided)

  - Case study 2b: Sampling at the dee sea. Source: Chapter from book (Book: Marine Biology, an ecological approach, Ed. Nybakken and Bertness), and NOAA outreach education website/Okeanos Explorer: Exploring deep waters off Hawaii: Mission plan.
    - Marine Biology, an ecological approach, Ch 4, pp 144-195
      - Sampling the Deep Sea
    - Okeanos Explorer: Exploring deep waters off Hawaii: Mission plan
http://oceanexplorer.noaa.gov/okeanos/explorations/ex1504/background/plan/welcome.html
    - Can't Bring Deep-sea Samples Up? Send a Lab Down
http://www.whoi.edu/oceanus/feature/cant-bring-deep-sea-samples-up-send-a-lab-down