Cell Physiology – Biology 456
Online Course Links at: http://faculty.fortlewis.edu/BYRD_S/
Instructor: Shere Byrd
Office: 790 Berndt, x7667
Email: byrd_s@fortlewis.edu
Office Hours: MWF 8:10-9:00, T 1:30-2:30, W 1:30-2:30, F 10:10-11; other times when my door is open
Posted on my website and on my office door. The easiest way to reach me is by email.
Course Description
This class will examine current topics in cell physiology. The course will examine these topics from the perspective
of current research in molecular biology, and pathologies that may be associated with dysfunction The text and
instructor will provide background information necessary for a more complete understanding of the topics
discussed.
Required Texts
1. Molecular Biology of the Cell, 4th ed. by Alberts et al., ISBN # 0-8153-3218-1. This comes with a CD “Cell Biology
Interactive” that has lots of cool animations related to topics covered in each chapter of the text – this is a great
study resource.
2. Dictionary of Cell and Molecular Biology. 3rd edition. JM Lackie and JAT Dow. Academic Press, San Diego,
CA., 1999.
3. Lab Manual (available at Basin Reproduction, 1437 E. 2nd Ave, 247-5212; call 24 hrs ahead so they have it
ready when you come to pick it up).
4. Packet of journal articles (also available at Basin Reproduction).
5. Powerpoint slides – will be posted on website
Grading
Lab Work (20% of final grade): Assignments may include pre-lab questions, lab reports, data analysis.
Questions on Papers (50% of final grade): variable points. We will read a set of primary journal articles and other
related materials about once every 10 days. Questions on these papers will be due on the day of class discussion
of the paper. You will receive a 0 if you are not in class to participate in the discussion, and are not ready
to turn in your answers to questions on the article at that time. You may drop the lowest grade for one of
these sets of questions.
Short Quizzes/Homework/In Class Activities (15% of final grade): variable points. Course participation will be
evaluated on days when paper discussions occur and when we solve problems in class. All students should be
ready and willing to contribute information regarding their understanding of the paper being discussed, including
material not necessarily found within the text of the paper (eg. more details regarding techniques used, results
presented, etc.).
Paper presentation (15% of final grade): 100 points. This will be a student-lead discussion of a paper you choose.
The paper will need to be approved by the instructor and be available to the rest of the class, one week prior to your
presentation. Your group (no more than 3 people) will make up a set of questions to be answered by the rest of the
class. These questions must also be approved by the instructor and be available to the class one week prior to
your presentation
Final grades will be based on a 90%-80%-70%-60%-50% scale, with no curving. 90%+ = A, etc.




All assignments must be typewritten, with computer-generated tables and graphs imported appropriately
into the text. Web resources are a fine starting point, but should not replace peer-reviewed, library
resources.
Homework (questions on papers assigned) and labs must be turned in on time for full credit. There will be
5% loss in possible points per day late. No late assignment will be accepted after the instructor has graded
and turned that assignment back.
As with any course, plagiarism of any written or other assignment will result in a failing (F) grade.
Students with disabilities have equal access and equal opportunity in this course. If you require reasonable
accommodations to fully participate in course activities or meet course requirements, you must register
with Disability Services, 280 Noble Hall, 247-7459. If you qualify for services, bring your letter of
accommodation to me as soon as possible.
Syllabus
This is a tentative syllabus. Please come to class for the most up-to-date information. Adjustments may be made at
any time during the trimester.
Date
TOPICS
M 1.08.07
Overview of cell physiology and course format
W 1.10
How do cells metabolize fuels; enzymes; free energy
F 1.12.
Equilibrium constants; activated carrier molecules
Readings for Week 1
MBC – Chapter 1, Chapter 14
Packet 1 - paper 1 (Fisler and Warden)
Lab Manual – Exercise 1
ASSIGNMENT
PKt 1 papers/questions
Lab hmwk problems
M 1.15
Energy generation in mitochondria vs. chloroplasts
W 1.17
Electron transport; redox potentials
F 1.19
Pathologies associated with altered metabolism
Readings for Week 2
MBC – Chapter 14 (continued)
Packet 1 – paper 2 (Tajima et al.)
Lab Manual – Exercise 1 (continued)
M 1.22
Paper discussion
W 1.24
How do cells develop into specific cell types/tissues?
F 1.26
Basic mammalian differentiation (embryology)
Readings for Week 3
MBC – Chapter 21 (pp 1157-1170; 1223-1242)
Packet 2 – paper s 1 & 2 (Lanza & Rosenthal; Cohen & Leor)
Lab Manual – Exercise 2
Questions on pkt 1 due
Pkt 2papers/questions
M 1.29
Control of stem cell fates
W 1.31
Treatment technologies utilizing stem cells
F 2.2
Public issues related to stem cell use
Readings for Week 4
MBC – Chapter 22 (pp 1259-1267; 1283-1296; 1308-1311)
Packet 2 – paper 3 (Xiaohua et al.)
Lab Manual – Exercise
M 2.5
Paper discussion
W 2.7
How do cells move/move things?
F 2.9
Actin filaments in the cytoskeleton; assembly
Readings for Week 5
MBC – Chaper 16
Packet 3 – paper 1 (Van Noorden et al.)
Lab Manual - Exercise
M 2.12
Traditional and non-traditional myosins
W 2.14
Cell/organelle movement
F 2.16
Extracellular matrix and cell movement
Readings for Week 6
MCB – Chapter 19 (pp 1080-1118); Chapter 23 (pp 1313-1326)
Packet 3 – paper 2 (Wong and Gumbiner)
Lab Manual – Exercise
Questions on pkt 2 due
Pkt 3 papers/questions
Group1 paper/questions due
M 2.19
Issues related to movement – metastasis
W 2.21
Paper discussion
F 2.23
Membrane channels, transport, membrane potential
Readings for Week 7
MBC – Chapter 11 (pp 615-647; 654-666)
Packet 3 – paper 2 (Wong and Bumbiner); Paper selected by group 1
Lab Manual – Exercise
M 2.26
Transporter families
W 2.28
Multi-drug resistance in disease
F 3.2
Group 1 paper presentation
Readings for Week 8
MBC – Chapter 11 (continued)
Paper selected by group 1
Lab Manual - Exercise
SPRING BREAK
Questions on pkt 3 due
Q on Group 1 paper due
March 3-11
M 3.12
Membrane potential, Nernst equation, patch clamping
W 3.14
Learning and membrane potential
F 3.16
Impairment of learning by stress
Group 2 paper/questions due
Readings for Week 9
MBC - Chapter 11 (continued)
Paper selected by group 2; paper on maternal stress and learning (Gi et al.)
Lab Manual – Exercise
M 3.19
Cell and organism ageing
W 3.21
Apoptosis – mechanisms and control
F 3.23
Group 2 paper presentation
Readings for Week 10
MBC – Chapter 17 (pp. 1010-1025;
Paper on Telomers and aging (Homayoun et al.)
Lab Manual – Exercise
M 3.26
The immune system; cell types
W 3.28
Cellular immunity
F 3.30
Antibody mediated immunity
Readings for Week 11
MBC – Chapter 24
Paper selected by group 3
Lab Manual – Exercise
Q on Group 2 paper due
Group 3 paper/questions due
M 4.2
MHC proteins; grafts; autoimmune problems
W 4.4
Immune system therapeutics
F 4.6
Viruses, pathogens, and parasites
Readings for Week 12
MBC – Chapter 24 (continued); Chapter 25
Paper selected by group 3
Lab Manual - Exercise
M 4.9
Group 3 paper presentation
W 4.11
Mechanism of pathogen invasion
F 4.13
How to fight an invader?
Readings for Week 13
MBC – Chapter 25 (continued)
Paper selected by group 4 (if needed)
Lab Manual - Exercise
Q on Group 3 paper due
Paper and Q from group 4 (if needed)
M 4.18
Developing therapies for worldwide protection
W 4.20
Public policy for global health; US Disease protection strategies
F 4.22
Group 4 paper presentation (if necessary)
Q on Group 4 paper due
Readings for Week 14
Chapter 6, Epilogue, The changing face of public health and future global prophylaxis. From: Betrayal of Trust: the
collapse of global public health.. Laurie Garrett, 2000, Hyperion Press, New York, NY
See Syllabus for dates of paper discussions/questions due
Read the papers in the order presented.
Questions on specific papers in each packet can be found on the course website:
http://faculty.fortlewis.edu/byrd_s
Packet #1
Fisler JS, and Warden CH. Uncoupling proteins, dietary fat, and the metabolic syndrome. Nutrition & Metabolism
Sept., 2006, 3:38
Tajima D, Masaki T, Hidaka S, Kakuma T, Sakata T, Yoshimatsu H. Acute central infusion of leptin modulates fatty
acid mobilization by affecting lipolysis and mRNA expression for uncoupling proteins. Exp Biol Med (Maywood).
2005 Mar; 230(3):200-6.
Packet #2
Lanza, R. and N. Rosenthal. The Stem Cell Challenge. Scientific American., June 2004, pp 92-99.
Cohen, S., and J Leor. Rebuilding broken hearts. Scientific American, 102(19), 2000, pp. 45-51
Xiaohua X, Zenglu X, Yuanyuan X, Guanghui C. Selective Down-Regulation of Extracellular Matrix Gene
Expression by Bone Marrow Derived Stem Cell Transplantation Into Infarcted Myocardium. Circ J 2005; 69: 1275–
1283
Packet #3
Van Noorden, CJF, Meade-Tollin LC, Bosman, FT. Metastasis. American Scientist, 86:2, 1998, 130
Wong AST, Gumbiner, BM. Adension-independent mechanism for suppression of tumor cell invasion by Ecadherin. J. Cell Biol 161(6), 2003, 1191-1203.
Additional papers
Gi Hoon Son,Dongho Geum, Sooyoung Chung, Eun Joo Kim, Ji-Hoon Jo, Chang-Mee Kim, Kun Ho Lee, Hyun
Kim, Sukwoo Choi, Hyun Taek Kim, Chang-Joong Lee, and Kyungjin Kim. Maternal Stress Produces Learning
Deficits Associated with Impairment of NMDA Receptor-Mediated Synaptic Plasticity
The Journal of Neuroscience, March 22, 2006, 26(12):3309-3318
Homayoun Vaziri, Franpois Schachter, Irene Uchida, Lan Weit Xiaoming Zhu, Rita Effros,
Daniel Cohen, and Calvin B. Harley. Loss of Telomeric DNA during Aging of Normal and Trisomy
21 Human Lymphocytes. Am. J. Hum. Genet. 52:661-667, 1993
Garrett, Laurie. Chapter 6, Epilogue, The changing face of public health and future global prophylaxis. From:
Betrayal of Trust: the collapse of global public health. 2000, Hyperion Press, New York, NY
Lab Schedule
Due to the nature of some of the experiments we will be undertaking, you may need to come in to lab outside of
regular lab hours to either prepare for the experiment, or make examinations for your results.
Please bring a calculator and a lab notebook to every lab. All labs meet in 3020 Berndt.
Date
Lab Project
January 8
No Lab
January 15
Project 1 – Isolation of pyruvate kinase activity in mouse liver; Quantification of liver protein
(differential centrifugation; protein standard curve)
January 22
Assessment of protein kinase activity; PAGE electrophoresis and transfer to nitrocellulose
(PAGE and protein transfer)
January 29
Western blotting for pyruvate kinase; plating CHO cells for culture/immunohistochemistry
(enzyme linked spectrophotometry; cell culture techniques)
February 5
Staining and immunohistochemistry for actin filaments, mitochondria, and nuclei
(cell fixation, staining, fluorescence microscopy)
February 12
Fluorescence microscopy and cell photography (guest supervisor)
February 19
Calcium signaling in CHO cells in response to hormonal stimulation
(effects of carbachol and atropine; quantification of fluorescence intensity)
February 26
Flex lab
SPRING BREAK
March 12
Isolation and quantification of total RNA from Xenopus oocytes
March 19
RT-PCR for phospholipase-C from Xenopus RNA
March 26
Quantification of RT-PCR products by agarose gel electrophoresis
April 2
Cell signaling by the MAPK pathway in stimulated Xenopus oocytes
April 9
Analysis of phosphorylationof MAPK target proteins by ELISA
Supplies needed:
January 15:
 3 live mice (for livers)
January 22:



Phosphoenol pyruvate ,Monopotassium Salt,Sigma Prod. No. P-7127 100 mg $54.50
*
*
Fructose 1,6-Diphosphate, Sodium Salt, Sigma Prod. No. F-4757 $30.70
Pyruvate kinase , Sigma P1506-1KU $27
*
January 29:
 Goat Pyruvate kinase antibody
AbD Serotec #7894-9988
$141.00
http://www.biocompare.com/matrixsc/3194/2/6/2042/Pyruvate+Kinase.html

Secondary antibody anti-goat AP conjugate

CHO cells with M1 receptor


Ham’s F12 medium with G418*
Fetal bovine serum*
Feb 5






ATCC CRL-1984
Paraformaldehyde Sigma P6148-500g
Phalloidin
Cytoskeleton, Inc. (Cytoskeleton.com) PHDR1
MitoTracker
Invitrogen M7514
Cover slips
Slides
Antifade kit (Invitrogen P7481)
Feb 19
 Fluo-4 AM (Invitrogen F 14210)
 Pleuronic
(Sigma P 1300-500G)
 Carbachol
 atropine
March 12
 gravid Xenopus (Xenopus express LB OP XL FM) two @$25 each
http://www.xenopus.com/products.htm#lb
 Absolutely RNA miniprep kit
(Stratagene 400800)
 One-Step RTPCR (Invitrogen 10928-042)
 RNAsin
(Promega N2511)
 Progesterone (Sigma P3972-5g)
 Metformin (Sigma D150959-5g)
 Insulin (Sigma I 5500-50mg)
 Inhibitor cocktail (Sigma P-2714) 2@34.30
 Deoxycholate (Sigma 238392-25g)
 Sodium orthovanadate (Sigma S6508-10g)
$330
*
$25.40
$93.00*
$178*
$166
$162*
$59*
$50
$210
$438
$93*
$27
$56.90
$42.00
68.60*
25.50*
22.30
March 19
 ERK1/2 Elisa Kit (Biosource International KHO 0091)
$525
http://www.biosource.com/content/catalogContent/detail2.asp?partnum=KHO0091&product=ERK1%2F2+%5Bp
TpY185%2F187%5D