Instructor: |
K. Jane Grande-Allen, Ph.D. ( grande@rice.edu ) 228 Keck Hall ext 3704 |
Meeting Time: |
101 Keck Hall - 10:00 - 10:50 am MWF |
Office Hours: |
12:00 - 1:00 pm Monday and Wednesday, and by appt. |
Course Material: The course pack is available from the Rice Bookstore. Additional handouts will be given out the class before they are needed. See the reading list at the end of the syllabus for the specific dates we will be covering the different components in the course pack.
Grading will be based on: |
Homework assignments (1 per unit) |
20% |
Group report |
25% |
4 quizzes (1 per unit) |
25% |
Midterm exam |
20% |
Participation in in-class discussions |
10% |
Final Course Grades (A, B, etc.) will be determined by the distribution of grades in the class, but you will not receive a letter grade lower than your average numerical grade (A=90, B=80, etc., Pass = 60 and above).
Discussion groups will be formed in the second class and you will have the same group partners all semester. Everyone in each discussion group:
- is expected to contribute equally to the discussion
- will rotate roles in recording discussion and reporting a summary to the class (roles will be observed and documented)
- is encouraged to study together for quizzes and the midterm exam
- will contribute to the group special topic report
Although discussion about homework is encouraged, turned in homework assignments are expected to represent individual work in accordance with the Rice Honor Code . Proper citations should be included for any and all work.
Expectations:
Of the Instructor
I am trying to teach you about important concepts in the field of Extracellular Matrix Biology and Mechanics. Although there will be some quantitative explanations of the topics and some demos, this is not a cookbook class. I will not be giving you all the information in class that you need to solve the homework problems. However, I will attempt to engage your attention and interest with information about current topics in the field and by using interactive teaching methods. I am here to learn as well.if I do not know the answer to your questions, I will try to find out and get back to you.
Of the Students
I expect you to take the initiative in understanding the material. If you do not understand something, discuss it with me, the TA, or your classmates, or venture to the library or online to seek more information. I expect you to take the concepts that you read about and that we discuss in class and apply these to the material in future lectures and in your own future.
New to cell biology? Refer to http://www.ncbi.nih.gov/entrez/query.fcgi?db=Books and search in the Molecular Biology of the Cell textbook, 3 rd edition. The other books, too, are a great resource.
Assignment Policy: ALL homework and project milestones are due in class by 10:00 a.m. on the date that they are due. If assignments totaling 10% or more of the final course grade are not turned in, the instructor retains the right to fail the student for the course. No late homework will be accepted without permission of the instructor before the homework is due. If an assignment is turned in late, the grade will be reduced 10% per day. If your assignment is late, you must write the number of days it is late on the first page (Honor Code). Illness and family emergencies will be dealt with on an individual basis.
All assignments (homework and group report milestones) should be neatly typed. Handdrawn figures and handwritten equations are acceptable but they need to be very easy to read. Using a computer to draw figures and type equations is encouraged. Neatness and correct grammar are important. Use a computer program (i.e., Excel, Matlab) to tabulate and plot data.
Attendance Policy: Students are required to attend all quizzes, exams and planned in-class discussion dates. The remaining lectures will have required attendance but given that class participation is 10% of your grade and that not all in-class discussions will be announced in advance, you are strongly encouraged to attend the lectures. Other classes and extracurricular activities are not valid excuses. Absences for job interviews and graduate/medical school interviews (documentation required) must be cleared in advance and any work must be made up.
A student choosing to miss one of these dates to attend another commitment must make up the quiz/exam at a time convenient to Dr. Grande-Allen. Missed in-class discussions (planned or unplanned) must be made up by meeting individually with Dr. Grande-Allen within 1 week of the missed class and having a 10-minute discussion about a slightly different but related topic of her choice.
If a convenient time cannot be established or the student chooses not to make up the quiz or discussion, the student will receive zero points for this particular quiz/discussion/exam in the final course grade. If you choose to miss a day, planning ahead will help. You can have another student turn in your homework for you.
Illness and family emergencies will be dealt with on an individual basis. Contact Dr. Grande-Allen immediately as soon as an emergency arises.
Disability accommodations: If you have a documented disability that will impact your work in this class, please contact me to discuss your needs. Additionally, you will need to register with the Disability Support Services Office in the Ley Student Center .
Lecture Schedule (subject to change)
Date |
Lecture # |
Topic |
Assignment and Events |
Part 1: Cell Biology Basis for Matrix Mechanics |
1/12/2004 |
1 |
Course Overview, Cell structure and organization |
|
1/14/2004 |
2 |
Cell phenotypes, Cellular responses to stresses |
Assign groups |
1/16/2004 |
3 |
Cell Signaling and Communications |
Homework 1 assigned |
1/19/2004 |
|
MLK Jr. Holiday - no class |
|
1/21/2004 |
4 |
Cell Binding/Adhesions, Integrins |
|
1/23/2004 |
5 |
Go over homework, planned in-class discussion
Handouts about group reports |
Vishal will lead class Homework 1 DUE |
1/26/2004 |
6 |
Receptor-Ligand Binding Models |
|
1/28/2004 |
7 |
Quiz and Receptor-Ligand Binding Models continued |
|
1/30/2004 |
8 |
Mechanical Properties of Cells |
Groups turn in report title |
2/2/2004 |
9 |
Mechanical Properties of Cells continued |
|
Part 2: Extracellular Matrix Constituents and Analysis |
2/4/2004 |
10 |
Collagen Structure and Mechanics |
|
2/6/2004 |
11 |
Collagen continued |
|
2/9/2004 |
12 |
Elastin Structure and Mechanics |
|
2/11/2004 |
13 |
Proteoglycans/GAGs Structure and Mechanics |
Homework 2 assigned |
2/13/2004 |
14 |
Class cancelled for HSEMB |
Preliminary report bibliography due |
2/16/2004 |
15 |
Proteoglycans and GAGs continued |
|
2/18/2004 |
16 |
Go over homework assignment
Quiz and planned in-class discussion |
Homework 2 DUE |
2/20/2004 |
17 |
Glycoproteins Structure and Mechanics
(Basement Membranes) |
|
2/23/2004 |
18 |
Biology/Biochemistry Techniques and Demos |
|
2/25/2004 |
19 |
Biology/Biochemistry Techniques and Demos continued; Discussion; Review for midterm |
Preliminary report outline due |
2/27/2004 |
20 |
Midterm |
|
3/1/2004 |
|
Spring Break - no class |
|
3/3/2004 |
|
Spring Break - no class |
|
3/5/2004 |
|
Spring Break - no class |
|
Part 3: The Roles of Matrix in Tissues and Organs |
3/8/2004 |
21 |
Tissue Organization, Tissue Types, Cell lineages |
|
3/10/2004 |
22 |
Tissue Organization continued |
|
3/12/2004 |
23 |
Tissue Origins, Cells, Functions, Connective Tissues |
|
3/15/2004 |
24 |
Definition and Organization of Organs |
Homework 3 assigned |
3/17/2004 |
25 |
Organs continued + preliminary group presentations |
5 minute presentations
Homework 3 assigned |
3/19/2004 |
26 |
Experimental Techniques for tissue mechanics |
|
3/22/2004 |
27 |
Experimental Techniques continued
Schedule HW3 recitation with Vishal |
Homework 3 DUE |
3/24/2004 |
28 |
Quiz and planned in-class discussion |
Homework 3 DUE |
Part 4: Matrix Production, Turnover, and Degradation |
3/26/2004 |
29 |
Cellular Production of Matrix |
Vishal will teach class |
3/29/2004 |
30 |
Cellular Production of Matrix |
|
3/31/2004 |
31 |
Matrix-Matrix Interactions |
Homework 4 assigned |
4/2/2004 |
32 |
Matrix and Tissue Turnover Rates (Half-Lifes) |
Detailed outline due |
4/5/2004 |
33 |
Tissue Degradation |
|
4/7/2004 |
34 |
Quiz and planned in-class discussion
Go over homework assignment |
Homework 4 DUE |
4/9/2004 |
35 |
Tissue Degradation |
Homework 4 DUE |
4/12/2004 |
36 |
Michaelis-Mentin Models of enzyme-substrate kinetics |
|
4/14/2004 |
37 |
Quiz and Michaelis-Mentin Models continued |
|
4/16/2004 |
38 |
Tissue remodeling: variations, impact on mechanics |
Final Group reports DUE |
4/19/2004 |
39 |
Tissue Aging |
|
4/21/2004 |
40 |
Group report presentations (2) |
|
4/23/2004 |
41 |
Group report presentations (1)
>Fill out course evaluation forms |
|
Finals wk |
|
Last group report presentations (2) |
|
Readings Schedule (subject to change)
Students are expected to have READ the appropriate material for that day.
Date |
|
1/12/2004 |
Introduction to Cells (Chapter 1) in Essential Cell Biology |
1/14/2004 |
Banes chapter in Functional Tissue Engineering, and Chiquet paper regulation of ECM synthesis by mechanical stress |
1/16/2004 |
Cell Communications (Chapter 16) in Essential Cell Biology |
1/21/2004 |
Chapter 19 from Molecular Biology of the Cell, 4th Edition |
1/30/2004 |
Cytoskeleton chapter (Ch 17) of Essential Cell Biology |
2/2/2004 |
Handouts |
2/4/2004 |
Ottani articles and bone article |
2/6/2004 |
Collagen sections from Guidebook |
2/9/2004 |
chapter in ECM Assembly and Structure, also DeBelle article |
2/11/2004 |
Chapters in ECM Assembly and Structure AND Guidebook |
2/13/2004 |
Fibronectin chapter in ECM Assembly and Structure, Quondomatteo article about basement membranes |
2/16/2004 |
Handouts |
2/20/2004 |
Handouts |
3/8/2004 |
Chapter 22 from Molecular Biology of the Cell, 4th Edition |
3/12/2004 |
Tissues Chapter from Biomaterials |
3/15/2004 |
Handouts |
3/19/2004 |
Chapters 1-2 from Biomechanics: Mechanical Properties of Living Tissues |
3/26/2004 |
Handouts |
3/31/2004 |
Handouts |
4/2/2004 |
Handouts |
4/5/2004 |
MMP article by Stamenkovic (J Pathology 2003) |
4/7/2004 |
Handouts |
4/9/2004 |
Section on ECM-degrading enzymes from Guidebook |
4/12/2004 |
Section C - Enzymes in Biochemistry Instant Notes |
4/16/2004 |
Chapters 1-3 from Basic Pathology Textbook, 7th edition |
4/19/2004 |
article by Robert and Labat-Robert, Biogerontology, 2000, chapter by Sames in PG book, aging chapter in Elastin book |