Comparative Animal Physiology

Review the following:

• Laws of Thermodynamics
  • Diffusion
  • Osmosis
• Thermodynamics of chemical reactions
  • Endergonic Reactions vs. Exergonic Reactions
• Structure and function of biological membranes
  • Active transport
  • Intermediary metabolisms
    • Glycolysis
    • Krebs Cycle
    • Electron transport/oxidative phosphorylation

Review basic characteristics of the following animal groups (refer to Lab Schedule and links)

Phylogeny/Anatomy lab packet

Animal physiology lab exam preparatory PDF

Feb 24: Protists, Cnidaria, Rotifers (check-out videos on the web)

Mar 2: Platyhelminthes, Protostomes: Annelids, (Molluscs), Arthropods

Earthworm structures

Brain
Pharynx
Hearts (pseudohearts)
Dorsal aorta
Seminal vesicles
Crop
Gizzard
Ventral nerve cord
Ventral blood vessel
Clitellum

Grasshopper structures

Crop
Gastric caeca (caecum)
Eggs in ovary
Ventral nerve cord
Ovipositor

Mar 9: Deuterostomes: (Echinoderms), Chordata:

• Cat anatomy
  • Muscles

Mar 16: Cat anatomy: Viscera

Mar 23: Cat anatomy: Circulatory system

Mar 30: Cat anatomy: Brain + Review for lab practical exam

April 5: Lab practical exam

More cat anatomy websites: 

• Wiki
• Cascade

NIH Visible Human Project

Lab exam preparation

Note: You will NOT be tested on the histology of gut and gonads (Refer to this PDF)

Protozoa (Not a phylum)
Cnidaria
Platyhelminthes
Annelida
Mollusca
Arthropoda
Echinodermata
Chordata

Topics to be studied this term:

Homeostasis/allostasis
Feeding/digestion
Metabolism
Gas exchange/respiration
Circulation
Osmoregulation/excretion
Neurophysiology

How to succeed in this class

The work in this class will encourage you to think like a physiologist. What is the significance of homeostasis? How are structure and function related?  What are persuasive methods, experiments, and observations by which to study physiology? Take responsibility for your own learning. You will find the work much more rewarding if you come to class prepared, having read the assignment carefully so that you can participate in discussions. Be a considerate listener to contributions of others; attendance in class and lab is required. Be on time! If you must miss a class, it is your responsibility to get the assignment and come to the next class prepared. Please do not email me or leave phone messages for trivial matters (e.g. Is it ok for me to be late? Can you put the assignment in my box? Etc.)

Please check my office hours (posted outside my office, Dickinson 108) or make an appointment with me at the end of class. If you are having difficulty with the work, please come talk to me!

For those interested in medicine: Nothing in medicine makes sense except in the light of evolution

Checklist for essays

• The essays are typed
• The first page includes your name
• The entire document is double-spaced
• The questions are NOT rewritten as part of your response essays
• Each essay in response to each question is numbered
• There is a response to each question
• Each essay begins with a specific claim (E.g. The heart rate will increase...)
• Each claim is supported by a discussion of the specific underlying mechanism(s). (E.g. The permeability of the membrane to potassium will decrease and that will cause...)
• Every sentence has content and specificity. No extraneous sentences. The essays are concise. Only mechanisms relevant to the question are discussed
• Each essay is proofread with attention to the logic of your argument
• Each essay is proofread and checked for clarity, spelling, grammar, and punctuation. (No fragments)
• You use your own words in each essay
• If you submit more than one sheet, the sheets must be stapled together in the correct order
• The essay set is submitted on time

ASSIGNMENTS

Required Reading

1. Animal Physiology. Hill, Wyse, and Anderson. 2nd Edition (2008) or 3rd Edition (2012). Sinauer.
2. Photographic Atlas for the Zoology Laboratory. Van De Graaff & Crawley.
3. Additional papers to be assigned by professor          
4. Lab material from lab classes

Required work

• 1 paper response report (before midterm)
• 2-3 essay problem sets (typically 1 before midterm and 2 after midterm)
• 1 lab practical exam (before midterm)
• 1 physiology research poster (end of term)
• 1 physiology research presentation (end of term)

Late papers are not accepted. All assignments must be submitted in order to pass. Remarks that I write on your assignments are first and foremost, feedback, in order to encourage more sophisticated problem solving. If you do not understand my comments, please come see me. Class participation is required. Prepare for the lab before the lab. In order to succeed in the lab, you will need to attend to the work (whether the phylogeny and anatomy of the first part of term or the physiology experiments in the second part of term) beyond the set lab time of Wednesday morning.

How to read a paper

• Attend to abstract, figures, tables, and legends
• What is (are) the question(s)
• Read through once for overview
• Read again, and take notes
• Understand methods
• Interpret figures without looking at the narrative
• Do methods used permit the conclusions drawn?
• The thesis of this paper is...

RESEARCH PROJECT

RESEARCH PROPOSAL:

Submit your research proposal in outline form

1. What is your research question?
2. Description of methods including: What you will measure?
3. How will you analyze your data? (You might want to draw a graph of what the data might look like; the point is to think about your axes, independent and dependent variables)
4. Cite 2 references from the primary literature in this format:

Ballenge, E, B. and S.K. Sessions. 2009. Explanation for missing limbs in deformed amphibians. J. Exp. Biol. 312B: 12-25.

Sessions, S. K., R. A. Franssen, and V. L. Horner. 1999. Morphological clues from multilegged frogs: are retinoids to blame? Science 284: 800-802

Ideas for physiology research project

Dependent variables that can be measured in the lab

Instructions for poster

RESEARCH ANIMALS (Not an exhaustive list)

EVOLUTION OF ANIMAL DIVERSITY

UC Berkeley website about evolution
Animal Tree of Life (2013)
Regulating evolution. Carroll et al 2008.
The origins of form. Carroll 2005.
How limbs develop
Homologs, orthologs, paralogs
Chipman (2010) Parallel evolution of segmentation

Particularly important to orient you to questions in lab:

Doolittle (2000) Uprooting the tree of life
Davis and Patel (1999) The origin and evolution of segmentation
Mindell and Meyer (2001) Homology evolving
Balavoine (2003)  Evolution of coelom/segmentation in bilateralia
Aortic arches

HOMEOSTASIS

Too Much of a Good Thing: Dilemma in Our DNA (2015)
Schmidt-Nielsen (1994) How are control systems controlled Part 1; Part 2

2nd edition text Ch. 1
     Pg. 391-404; 380-383
3rd edition text Ch. 1
     Pg. 419-430; 407-409

Portner et al (2010) Fish thermal biology and global climate change   
Englert (2003) Sussing out stress
Fuller et al (2010) Physiological mechanism in coping with climate change
Mykles et al (2010) Homeostasis of insects and crustaceans-neuropeptides
Romero et al (2009) The reactive scope model — A new model integrating homeostasis, allostasis, and stress

FEEDING/DIGESTION

2nd edition text
   Ch. 5; Nutrient homeostasis: Pg. 409-411
3rd edition text
   Ch. 6; Nutrient homeostasis: Pg. 436-439

Secor & Diamond (1998) A vertebrate model of extreme physiological regulation
Moog (1981) The lining of the small intestine
Insulin resistance
Karasov & Diamond (1988) Interplay between physiology and ecology in digestion
Secor (2008) Digestive physiology of the Burmese python: broad regulation of integrated performance
Marino (2011) Central insulin and leptin-mediated autonomic control of glucose homeostasis
Murphy & Bloom (2006) Gut hormones and the regulation of energy homeostasis
Grenham et al (2011) Brain–gut–microbe communication in health and disease

METABOLISM

2nd edition text - Ch. 7; Ch. 6
    Aerobic and anaerobic metabolism. Ch. 7
    Body mass and metabolic rate. Pg. 154-163
3rd edition text - Ch. 8; Ch. 7
    Aerobic and anaerobic metabolism. Ch. 8
    Body mass and metabolic rate. Pg. 173-180

Exercise and the brain
Kelly (2012) Irisin, Light my fire
Nadel (1985) Physiological adaptations to aerobic training
Taigen & Beuchat (1984) Anaerobic threshold of anuran amphibians
Burgomaster (2006) Effect of short-term sprint interval training on human skeletal muscle carbohydrate metabolism during exercise and time-trial performance
Greer et al (2000) Comparison of caffeine and theophylline ingestion: exercise metabolism and endurance
Mayberg et al (2002) Neuroanatomy of placebo effect (glucose metabolism in the brain)
Smil (2000) Laying down the law
Roberts et al (2010) A New Model for the Body Size–Metabolism Relationship
Noakes (2012) Fatigue is a brain-derived emotion that regulates the exercise behavior to ensure the protection of whole body homeostasis
Westerblad (2002) Muscle Fatigue: Lactic Acid or Inorganic Phosphate the Major Cause?
Pontzer  et al (2012) Hunter-gatherer energetics and human obesity
     New York Times synopsis of above paper
Links to George A. Brooks' papers:
    Active muscle and whole body lactate kinetics after endurance training in men
    Effects of exercise intensity and training on lipid metabolism in young women

GAS EXCHANGE/RESPIRATION

    2nd edition text - Ch. 22 (Mechanics of breathing); Ch. 23 (Transport of O2 and CO2, especially Pg. 587-594 and 606-607)
    3rd edition text - Ch. 23 (Mechanics of breathing); Ch. 24 (Transport of O2 and CO2, especially Pg. 623-631 and 642-643)

Animation of oxygen transport in the blood
Climate Change Affects Marine Fishes Through the Oxygen Limitation of Thermal Tolerance (2007)
Tracheal respiration in insects (2003)
    Watch movie
Good short discussion of insect tracheal system
Parke (2006) Breath-holding and its breakpoint
Farmer (2010) Unidirectional airflow in the lungs of alligators
Farmer (2012) The Pulmonary Anatomy of Alligator mississippiensis and its Similarity to the Avian Respiratory System
Schmidt-Nielsen (1971) How birds breathe (link to cool video)
Bartecchi et. al (1995) The global tobacco epidemic
Warkentin (2002) Oxygen availability and hatching plasticity in frogs
Gans et. al (1969)  Bullfrog ventilation: How does the frog breathe
Gorr et al (2010) Hypoxia tolerance
Burggren & Bemis (1992) Metabolism and Ram Gill Ventilation in Juvenile Paddlefish, Polyodon spathula (Chondrostei: Polyodontidae)
Harris & Milsom (1994) The ventilatory response to hypercapnia in hibernating golden-mantled ground squirrels, Spermophilus lateralis
Orgeig (2007) The anatomy, physics, and physiology of gas exchange surfaces: is there a universal function for pulmonary surfactant in animal respiratory structures?
Evans (2010) A brief history of the study of fish osmoregulation: the central role of the Mt. Desert Island Biological Laboratory

CIRCULATION

    2nd edition text - Ch. 24 (Really good chapter)
         Pg. 622-626 Mammal & bird hearts and circulation
         Pg. 627-629 Fish heart
         Pg. 631-634 Amphibian and reptile hearts
         Pg. 612-618 Mammalian heart physiology
    3rd edition text - Ch. 25 (Still really good chapter)
         Pg. 658-662 Mammal & bird hearts and circulation
         Pg. 664-666 Fish heart
         Pg. 668-670 Amphibian and reptile hearts
         Pg. 648-652 Mammalian heart physiology

Mammalian heart function animation
Riquelme et al (2011) Fatty Acids Identified in the Burmese Python Promote Beneficial Cardiac Growth (Note relationship to python digestion articles)
Johansen (1968) Aneurysms
Schmidt-Nielsen (1981) Countercurrent systems in animals
Cantin (1986) The heart as endocrine gland
Robinson (1986) The heart as suction pump
Moon et al (1995) The physiology of decompression illness
Hicks (1994) Adrenergic and cholinergic regulation of intracardiac shunting
Overgaard et al (2002) Cardiac shunting
Brainerd (1997) Efficient fish not faint-hearted
Burrgren (2000) Vertebrate hearts
Cardiac shunting in reptiles (Review)

OSMOREGULATION/EXCRETION

    2nd edition text - Ch. 28
    3rd edition text - Ch. 29

Animation of function of loop of henle (University of Colorado)
Evans (2010) A brief history of the study of fish osmoregulation: the central role of the Mt. Desert Island Biological Laboratory
Berridge (1970) A structural analysis of intestinal absorption
Schmidt-Nielsen (1963) Amoeba proteus: studying the contractile vacuole by micropuncture
Schmidt-Nielsen (1995) The renal concentrating mechanism in insects and mammals: a new hypothesis involving hydrostatic pressure
Ortiz et al (1998) Osmoregulation in wild and captive West Indian manatees
Mylkes et al (2010) Insects, crustaceans and neuropeptides
Charmantier et al (1998) Ontogeny of osmoregulation
Pruitt et al (2006) Effect of peristaltic contraction of renal pelvic wall on solute concentration
      Video of contractions of pelvic wall
Schmidt-Nielsen (2011) On the function of the mammalian renal papilla and the peristalsis of the surrounding pelvis
    "We are left without a full explanation of the concentrating mechanism of the mammalian renal papilla." Bodil Schmidt-Nielsen (2011)
Pinter (2009) Effect of peristaltic contractions of the renal pelvic wall on solute concentrations of the renal inner medulla in the hamster

NEUROPHYSIOLOGY

2nd edition text - Ch. 11, 12
     Pg. 277-285 Resting potential; Passive membrane properties
     Pg. 285-296 Ionic basis of AP (Voltage clamp, Patch clamp)
     Pg. 297-301 Propagation of AP
     Pg. 303-321 Synaptic function
3rd edition text - Ch. 12, 13
     Pg. 301-309 Resting potential; Passive membrane properties
     Pg. 309-320 Ionic basis of AP (Voltage clamp, Patch clamp)
     Pg. 320-324 Propagation of AP
     Pg. 327-344 Synaptic function

Class comportment and common decency

It is important for all of us to come together as a group interested in discussing problems in animal physiology. Each of us is a part of this group, and as such, our behavior is not just about each of us as individuals, but also about being members of a group.

Be respectful and attentive. Do not arrive late, as it is disrespectful and disruptive. Do not leave the room during class, as it is disrespectful and disruptive. Plan your time. Use the bathroom before class. Bring water, tissues, lozenges, etc. with you. Do not engage in any activity that you would avoid at a job interview (E.g. Do not pick your nose or skin, do not slouch, play with your hair, chew on your nails, etc.) Turn off your cell phone before coming to class. Do not surf the web or check your email during class.

Class attendance is required. Plan your work. All assignments must be submitted on time in order to pass this class. Frequently I write assignments on the board or project them in class so be prepared to write them down. If you must miss a class, it is your responsibility to get the assignment and find out from another student about missed work. If you plan to miss class before or after Long Weekend or Thanksgiving, either change your plans or do not take this class. If you plan to miss the last class, either change your plan, or do not take this class. An absence is an absence with no distinction between excused and not.

The work is the thing.