Course Schedule for BIOEN 304 (2008) - updated Sept. 08
This course is a mixture of basic physiology and engineering aspects related to physiology.
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Week
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Date
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Lecture
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304 Lab
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Book Chapters
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1
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Sept.24
Sept.26
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Transport – Diffusion, Membranes, Osmosis, Electropotentials, Nernst
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Expand 302 circuit to build
working photometer given few details about the LED, emission/detection
spectra
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Chap. 2,3,5
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2
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Sept. 29
Oct. 1
Oct. 3
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Kinetics
Capstone: N130 - mandatory
Capstone: N130 - mandatory
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Continue Week 1
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Handouts
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3
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Oct. 6
Oct. 8
Oct. 10
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Membrane Transport
Prof. Dan Ratner
Open, Closed Systems, Kinetics
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Data handling, acquisition, fitting, and Beer-Lambert law
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Chap. 4
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4
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Oct. 13
Oct. 15
Oct. 17
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Enzymes
Control of Pathways
Control of Pathways
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“Enzyme Kinetics” – by hand test of Trypsin/Chymotrysin
and whether there is moving data
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Handouts
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5
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Oct. 20
Oct. 22
Oct. 24
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Digestion, Food stuffs, vitamins
Physiology of Digestion
Physiology of Digestion
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Automation of Week 4 through digital interface.
True enzyme kinetics
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Chap 21
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6
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Oct. 27
Oct. 29
Oct. 31
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Metabolism – Energy
Organ systems in nutrition
Hormonal Control
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Examine two glucose assays,
Benedict’s and Glucose oxidase/peroxidase. Qualitative detection.
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Handouts
Chap 22
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7
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Nov. 3
Nov. 5
Nov. 7
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Integrated nutrition during
starvation and fed states
MidTerm Quiz
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No Lab this
week
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Chap 25,
Handouts
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8
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Nov. 10
Nov. 12
Nov. 14
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Hormonal Control Systems
Simulating Control Systems
Insulin Control System
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Two enzyme system, decoupling of signals. Direct
reference to previous 304 HW
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Chap 7,22
Handouts
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9
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Nov. 17
Nov. 19
Nov. 21
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Homeostasis
Special Dynamics
Kidney Function
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Simulation of blood or urine
samples. Instrumentation at the interface of biological samples. Satisfies
an ABET criterion K
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Handouts
Chap 19
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10
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Nov. 24
Nov. 26
Nov. 28
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Sensory Systems
Eye Function
Engineered Synthetic Retina
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Dissection and acquisition of pancreatic tissue sample
from dead rats
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Chap 10
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11
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Dec. 1
Dec. 2
Dec. 5
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Ear, structure and function
Pain, heat and other sensors
Artificial Neural Nets
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Analysis of tissue samples in terms of Trypsin and
Chymotrypsin
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Handouts and
Chap 10
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12
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Dec. 10
(830-1020)
GLD 322
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Final Exam in GLD 322
at 8.30 to 10.20
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No Lab this
week
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Grading will be based on Mastery-Based Grading which is based solely on a students' master of the material. In terms for breakdown, the final grade is based on the following partitioning:
Grades will be made available on the new Catalyst online grading system.
Textbook: Silverthorn, Human Physiology an Integrated Approach (3rd or 4th Edition or above)
In addition there is a very useful but optional pocket sized text book:
Color Atlas of Physiology (Thieme Flexibook) (Paperback)
Agamemnon Despopoulos and Stefan Silbernagl
Amazon Link
Class Meeting Times and Location:
M,W,F 9:30-10.20am in GLD (Gould) 322
Teaching Assistants:
Kassandra Thomson
Fan Lee
Familiarity with Matlab or some suitable programming language will be expected.
Class Project (graded as an assignment): Split into roughly 11 groups of 4 per team. Pick one of the following 6 papers and spend 10 mins discussing the paper in front of the class. Present next week on 17th and 19th of Nov (with spill over on to the 21st if necessary).
1. Calcium Control
Calcium Homeostasis and Parturient Hypocalcemia: An Integral Feedback Perspective
Review paper on Calcium Homeostasis
2. Chemotaxis Control
Control Analysis of Bacterial Chemotaxis Signaling
Tau-Mu Yi, Burton W. Andrews and Pablo A. Iglesias
Methods in Enzymology
Volume 422, 2007, Pages 123-140
Two-Component Signaling Systems, Part A
Health Series or Natural Sciences Stacks
3. Thyroid Control
AN IMPROVED MATHEMATICAL MODEL OF HUMAN THYROID HORMONE REGULATION
SARATCHANDRAN and CARSON and REEVE
Clinical Endocrinology
Volume 5 Issue 5, Pages 473 - 483
Health Science Library
4. Integral Rein Control in Insulin/Glucagon
Integral Rein Control in Physiology
Saunders P.T; Koeslag J.H; Wessels J.A2
Journal of Theoretical Biology, Volume 194, Number 2, September 1998, pp. 163-173(11), available online.
5. Integral Rein Control: Generalization
Integral Rein Control in Physiology II: a General Model
PETER T. SAUNDERS, JOHAN H. KOESLAG and JABUS A. WESSELSb
Journal of Theoretical Biology
Volume 206, Issue 2, 21 September 2000, Pages 211-220
Available online
Reading assignments for the last two weeks of term:
Chapter 10: Sections on Ear, Eye, Pain, Heat, Taste and Smell
Chapter 19: Kidney.
The remainder of term will be on these topics.
The Eye
The Ear
Other Senses and the Kidney
Two hour exam in room MEB 246
Wednesday, December 10, 2008,830-1020
Transport:
Diffusion, Fick's law, diffusion coefficients (units)
Stokes-Einstein Equation
Root mean square distance and time
Membrane bilipid layer
Diffusion through membranes
Transport by passive and facilitated diffusion, active transport
Channels (aquaporins etc)
Carriers - uniport, symport, antiport
Examples: Na/K ATPase etc.
Origin of resting potential
Nernst Equation
Osmosis - how to measure molecular weight using osmosis
Definitions for control coefficients, elasticities, and response coefficients.
Understanding the importance of the flux summation theorem.
State the connectivity theorems.
Understand the importance of the Response Coefficient relationship (R = C e).
Being able to derive a control equation when given summation and connectivity theorems.
Understanding the basic properties conferred by negative feedback.
Understanding why negative feedback can use useful in a physiological situation.
Difference between proportional and integral control
Digestion:
Challenges aced by digestion
Function of digestion
Basic Anatomy of digestive system
Anatomy of stomach and intestinal wall
Function of each part of the digestive system
Enzymes involved in digestion
Digestion of different food types
Hormonal control in the stomach and intestine
Difference in metabolism between different organs
Brain, Muscle, Adipose, Liver, RBC
Fasting and Starvation
Basic Circulatory System
Homeostasis
Different kinds of control strategies
Advantages and disadvantages of strategies
Insulin/Glucagon Control
Senses
Eye
Ear
Taste and Smell
Pain
TED Video on in silico biologically inspired sensors
Kidney
Anatomy
Basic Function
Basic Hormonal Control
