BIOE464
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Integration Courses
BIOE321 - Cellular Engineering
BIOE425 - Pharmaceutical Engineering
BIOE464 - Extracellular Matrix
BIOE592 - Sensory Neuroengineering

 

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BIOE464 - Extracellular Matrix

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

 

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