Spring 2013 Syllabus - Biomedical Engineering - University of Florida

2013 BME 3323L - Cellular Engineering Laboratory
Section 01E0
1. Catalog Description
(3 credit hours)
The Cellular Engineering Laboratory will teach students the fundamentals of cell culture for
use in Biomedical Engineering applications employed in academic and industrial settings.
Students will acquire skills in cell culture, experiment design, quantitative analyses, notebook
keeping, report writing and oral presentation in a team setting. Students will be exposed to
the concepts of oversight (obtaining IACUC and IRB approval) and good manufacturing
practice as prerequisites for generating clinical grade technologies using animal and human
cells.
2. Pre-requisites and Co-requisites
Pre-requisites:
BSC 2010, CHM 2046
Co-requisites:
BCH 4024
PCB 3717 Cell & Systems Physiology
3. Course Objectives
1) To introduce the student to the concept of cell culture as a BME research tool.
2) To introduce the student to the concept of growing healthy cells in an in vitro
environment, that is critical to conducting successful in vitro research.
3) To give student hands-on experience growing cells in an in vitro environment.
4) To introduce the student to the concept of designing an experiment and executing,
analyzing and summarizing data derived from an experiment.
5) To give students hands on experience deriving answers to questions asked by biomedical
engineers using in vitro techniques.
4. Contribution of course to meeting the professional component
Students will learn to design and conduct experiments, as well as to analyze and interpret
data.
The student will learn to function in teams to work on multidisciplinary problems
The student will learn to identify, formulate and solve engineering problems
The student will learn about professional and ethical responsibility
The student will learn to communicate effectively
The student will learn about contemporary issues regarding the use of cells in BME
research
The student will learn to use the techniques, skills and modern engineering tools
necessary for engineering practice
5. Relationship of course to program outcomes

6. Instructors:
Dr. Brandi K. Ormerod (Module 1)
Office: J296, Biomedical Sciences Bldg
Phone: 273-8125
Email: bormerod@bme.ufl.edu
Website: http://stemcell.ufl.edu
Office Hours: Mondays 4:00-5:00pm.
Dr. Peter McFetridge (Module 2)
Office: J391, Biomedical Sciences Bldg
Phone: 273-9325
Email: pmcfetridge@bme.ufl.edu
Website:
Office Hours: TBA
7. Teaching Assistants:
Mr. Vikram Munikoti (Module 1)
Phone: 273-8179
Email: vmunikoti@ufl.edu
Office Hours: Thursday 2-3 pm.
TBA (Module 2)
8. Meeting Times
Course meets thrice per week
One 50 minute lecture period Mondays
One 3hr lab period on Wednesdays
One 3hr lab period on Fridays
**students will be expected to feed cells independently on Mondays at a time pre-arranged
by the teaching assistant for Module 1.
Don’t be late – you will lose part of your participation grade!
9. Class/laboratory schedule
Class meets for:
a) 1 - 50 min lecture per week (Mondays – Period 8; 3:00-3:50pm)
b) 1 – cell feeding session per week (Mondays – Period 6 - arranged with TA)
c) 1 – 180 min laboratory per week (Wednesdays – Periods 8-10; 3:00-6:00pm)
d) 1 – 180 min laboratory (Fridays – Periods 8-10; 3:00-6:00pm)
10. Meeting Location
Monday – BLK (Black Hall) Rm 415.
Monday Cell Feedings, Wednesday and Friday – HHMI Lab located in the Lobby of the
Biomedical Sciences Building.

11. Material and Supply Fees – TBA
12. Textbooks and Software Required
1) Culture of Animal Cells
R. Ian Freshney
2005, 5 th Edition
ISBN 0471453293
2) Laboratory Manual for Cellular Engineering
Brandi K. Ormerod and Lan Hoang-Minh
2009, 1 st Edition
Instructor prepared and distributed
3) Publication Manual of the American Psychological Association, 6 th Edition
American Psychological Association
ISBN 978-1-4338-0561-5
Other Requirements:
Standard laboratory notebook with carbon copy pages and lined paper
3 Ring Binder to Compile Protocols and Handouts
Hair ties (elastic bands) to tie back long hair
Safety Glasses
Closed toe shoes
13. Recommended Reading
1) Culture of Cells for Tissue Engineering
G. Vunjak-Novakovic and R. Ian Freshney
2006, Volume 7 of Culture of Specialized Cells
ISBN-13 978-0-471-62935-1
ISBN-10 0-471-62935-9

14. Course Outline
Module 1 – Working with Cultured Cells
Week 1
Lecture 1 ‐ Introduction to the Cell Engineering Laboratory Course
Monday - 01/07/13 (50 Min)
Introduction and what’s expected
• Course overview/expectations
• Introduction to Instructors/Teaching Assistants
• Syllabus Overview
Laboratory 1 – Writing a Manuscript Style Research Report
Wednesday – 01/09/13
HHMI Lab – 180 min
Required Reading: Look through the APA publication Manual and Read Freshney Chapters 2, 7 and 16.
Learn how to write a research report
Practicum: Learn how to cite, reference and do database searches with Amy Buhler from the
Marsten Engineering Library
Assignment: Gather 5 abstracts that describe how culture conditions (cell density,
adherence, free floating, retinoic acid, fetal bovine serum, etc) influence neural
progenitor/stem cell differentiation – due Wed 01/16/13 (bring 5 abstracts to class).
Laboratory 2 – Introduction to Cell Culture and the laboratory
Friday – 01/11/13
HHMI Lab – 180 min
Required Reading: Freshney, Chapter 1
Discussion: Learn about Animal and Human Cell Culture in Academia and Industry
Discussion: Lab and Cell Safety, IACUC and IRB (regulating animal and human cells)
Discussion: Keeping a good lab notebook
Meet your labmates – teamwork for the term!
Practicum: Take a Laboratory Tour
Week 2
Lecture 2‐ Introduction to Cell Culture, Thawing and Plating cells for an Experiment
Monday – 01/14/13
Laboratory 3 – Working aseptically with cells
Wednesday – 01/16/13
HHMI Laboratory (180 min)
Required Reading: Freshney Chapters 3-6.
• Discussion: Design your adult NPC experiment (using info from publications and discussions)
• Turn in 5 Abstracts about NPCs for up to 2% of your grade
• Introduction: Learn Aseptic Technique for Keeping your Cell Cultures Clean

• Practicum - Using Equipment in the Laboratory – Pipetting and Centrifuging 101
• Hand in notebook page copy (0.5% of grade for module 1)
Laboratory 4 – Thawing and Plating Cells
Friday – 01/18/13
HHMI Laboratory (180 min)
Required Reading: Freshney Chapters 7-10 and 19.
• Discussion: Finalize your NPC experiment hypothesis/research design
• Introduction: Learn how to thaw, plate and count cells (choices, choices, choices)
• Video: Thawing cells
• Practicum – Thawing, counting and plating neural progenitor cells
• Practicum – Use the hemocytometer to quantify live/dead neural progenitor cells
• Hand in notebook page copy (0.5% of grade for module 1)
Week 3
No Lecture – Martin Luther King Day
Monday – 01/21/13 Lecture (50 min)
Laboratory 5 – Ick, my cells look sick!
Wednesday – 01/23/13
HHMI Laboratory (180 min)
Required reading Freshney Chapters 12 and 18
• Practicum: Feed and check your NPCs
• Discussion: Factors that affect the happiness of your cells including infections
• Introduction to bacterial, yeast, and mold infections.
• Practicum: Contamination Exercise
• Hand in notebook page copy (0.5% of grade for module 1)
Laboratory 6 – Passage your Cells
Friday – 01/25/13
HHMI Laboratory (180 min)
Required reading Freshney Chapters 12, 18 and 26
Discussion: Cell Passaging
Discussion: Expanding cells for an experiment - How many flasks or chambers???
Practicum: Passage your NPCs
Hand in notebook page copy (0.5% of grade for module 1)
Week 4
Lecture 4‐ Reagents and Quality Control
Monday – 01/28/13 Lecture (50 min)
• Feed Cells independently (at time specific by TA).

Laboratory 7 – Are my cells genetically stable?
Wednesday – 01/30/13
HHMI Laboratory (180min)
Required Reading: Chapter 17
• Feed your cells
• Introduction to genetic stability, passaging, and dissociation methods.
• Practicum - Karyotype cells – please be diploid!!!
• Assignment: Turn in your notebook page (0.5% of your Module 1 grade).
Laboratory 8 – Analyzing phenotypes
Friday – 02/01/13
HHMI Laboratory (180 min)
• Discussion: How do I collect data? Multiple ways to count cell phenotypes…
Introduction to immunohistochemistry, microscopy and FACS.
Experiment – Passage and count cells (remaining plate not in your experiment).
Fix cells in plate 1 and store in TBS for immunohistochemistry
Fix cells in plate 2 and store in TBS for flow cytometry
Assignment: Turn in your notebook page (0.5% of your Module 1 grade).
Week 5
Lecture 5 – Freezing cells, Record Keeping and GMP
Monday – 02/04/13 – Lecture (50 min)
• Introduction to Cell Culture – Freezing Cells, Record keeping and GMP for clinical work
• Feed Cells Independently
Laboratory 9 ‐
Wednesday – 02/06/13 - Laboratory (3hr)
• Fix Cells
• Experiment preparation – design, plate preparation, calculations, media prep, etc
Hand in notebook page copy (0.5% of grade for module 1)
Laboratory 10 –
Friday – 02/08/13 - Laboratory (2h)
• Plate cells for experiment
• Freeze Cells
• Hand in notebook page copy (0.5% of grade for module 1)
• Hand in methods section of report for feedback
Week 6
Lecture 6 – Quantitation and Data Analysis – Morphological Analyses
Monday – 02/11/13 - Lecture (50 min)
Laboratory 11 – Microscopy Analysis
Wednesday – 02/13/13 - Laboratory (180 min)
Antibody Staining

• Fix cells for Immunohistochemistry
• Immunohistochemistry
• Hand in notebook page copy (0.5% of grade for module 1)
Laboratory 12‐ FAC Analysis
Friday – 02/15/13 - Laboratory (180 min)
Analysis of Antibody Staining
• Continue counting cells using microscopy
• Hand in notebook page copy (0.5% of grade for module 1)
Week 7
Lecture 7 – Quantitation and Data Analysis – Molecular Analyses
Monday – 02/18/13 - Lecture (50 min)
Laboratory 13‐ Work on Paper Write Up
Wednesday – 02/20/13
HHMI Laboratory (180 min)
• Discussion: Data Interpretation.
• Practicum: write and questions about data analysis, IEEE format, content, etc.
Laboratory 14‐ Work on Paper Write Up
Friday – 02/22/13
HHMI Laboratory (180 min)
• Discussion: Questions regarding style and content of paper sections.
• Practicum: Write and questions about data analysis, IEEE format, content, etc.
Week 8
Lecture 8 ‐ Review
Monday – 02/25/13 - Lecture (50 min)
• Review (Weeks 1-7)
• Report due before class
• Fill out teacher evaluation (0.5% of grade)
Laboratory 15 – Exam #1
Wednesday – 02/27/13 - Laboratory (180 min)
• All material learned in weeks 1-7 (lecture, textbook and laboratory) will be tested
Laboratory 16 – no class
Friday – 02/29/13 – Laboratory (180 min)

15. Module 2: Course Outline (Tentative)
Module 2 /1– Hydrogels as scaffolds for engineering 3D tissues
Week 9
No classes – Spring Break
Week 10 (Group A), Week 13 (Group B)
Monday – 03/11/13 - Lecture (50 min) –
Experimental overview (two sections – ‘Hydrogels’ and ‘ex vivo derived tissue implants’)
Introduction to Instructors/Teaching Assistants
Overview/expectations
Lab books, write-ups continued
Wednesday – 03/13/13 - Laboratory (3h)
Introduction to Hydrogels (Alginate) and mechanics
o Session 1: Prepare hydrogels (different %weight protein), and cell cultures, seed
cells to begin 3 week culture period. Multiple samples set for continued analysis
over 3 week period.
o Session 2: Prepare hydrogels, biomechanical analysis
Friday – 03/15/13 - Laboratory (3h)
Swap sections from Wednesday
o Session 2: Prepare hydrogels (different %weight protein), and cell cultures, seed
cells to begin 3 week culture period. Multiple samples set for continued analysis
over 3 week period.
o Session 1: Prepare hydrogels, biomechanical analysis – compressive stress strain
analysis
Research Assignment – search for publications that describe 2D vs. 3D culture conditions
and discuss pros and cons of each approach – due date TBA
Week 11 (Group A), Week 14 (Group B)
Monday – 03/18/13 - Lecture (50 min) –
Experimental overview (two sections – ‘Hydrogels’ and ‘ex vivo derived tissue implants’)
Feeding cells
Wednesday – 03/20/13 - Laboratory (3h)
Continued analysis of engineered construct T0+ 1 week
o Session 1: Alamar Blue assay to assess approximate cell density and metabolysm

o Session 2: Biomechanical analysis of constructs (as previous week – compressive
stress - strain analysis)
Friday – 03/22/13 - Laboratory (3h)
Swap sections from Wednesday
o Session 2: Alamar Blue assay to assess approximate cell density and metabolysm
o Session 1: Biomechanical analysis of constructs (as previous week – compressive
stress - strain analysis)
Week 12 (Group A), Week 15 (Group B)
Monday – 03/25/13 - Lecture (50 min) -
Experimental overview (two sections – ‘Hydrogels’ and ‘ex vivo derived tissue implants’)
Results – what are they going to mean.
Wednesday – 03/27/13 - Laboratory (3h)
Continued analysis of engineered construct T0+ 2 weeks
o Session 1: Cell counts/Alamar Blue assays
o Session 2: Biomechanical analysis of constructs (as previous week – compressive
stress - strain analysis)
Friday – 03/29/13 - Laboratory (3h)
Continued analysis of engineered construct T0+ 2 week
o Session 1: Cell counts/Alamar Blue assays
o Session 2: Biomechanical analysis of constructs (as previous week – compressive
stress - strain analysis)
Module 2/2
Week 13 (Group A), Week 16 (Group B)
Ex vivo derived scaffolds for engineering cardiovascular implants
Monday – 04/01/13 - Lecture (50 min) -
Wednesday – 04/03/13 - Laboratory (3h)
Friday – 04/05/13 - Laboratory (3h)
Week 14
Monday – 04/08/13 - Lecture (50 min) -
Wednesday – 04/10/13 - Laboratory (3h)
Friday – 04/12/13 - Laboratory (3h)

Week 15
Monday – 04/15/13 - Lecture (50 min) -
Wednesday – 04/17/13 - Laboratory (3h)
Friday – 04/19/13 - Laboratory (3h)
Report #2 Due
Week 16
Monday – 04/22/13 - Lecture (50 min)
Review – weeks 9-14
Wednesday – 04/24/13 - Laboratory (3h)
Exam# 2 - weeks 9-14
16. Attendance and Expectations
Class participation is required and part of the final grade Grading – methods of evaluation
(e.g., Lab notebook pages, Reports, Exams)
17. Grading
Module 1
Report Intro 2%
Report Methods 2%
Report Results 2%
Full Report 15%
Exam 20%
Lab Note Book Pages 10%
50%
Module 2
Report 15%
Exam#2 25%
Lab Note Book Pages 10%
50%
18. Grading Scale
A A- B+ B B- C+ C C- D+ D D- E
> 90 87-89 84-86 80-83 77-79 74-76 70-73 67-69 64-66 60-63 57-59 < 56
19. Make-up Exam Policy
Midterm and Final Exam can be made up in extreme circumstances if a Doctor’s note is
presented or death certificate (regarding someone in the immediate family) is presented
before the start of the exam.
20. Honesty Policy
All students admitted to the University of Florida have signed a statement of academic
honesty committing themselves to be honest in all academic work and understanding that
failure to comply with this commitment will result in disciplinary action. This statement is a

eminder to uphold your obligation as a UF student and to be honest in all work submitted
and exams taken in this course and all others.
21. Accommodation for Students with Disabilities
Students Requesting classroom accommodation must first register with the Dean of Students
Office. That office will provide the student with documentation that he/she must provide to
the course instructor when requesting accommodation.
22. UF Counseling Services
Resources are available on-campus for students having personal problems or lacking clear
career and academic goals. The resources include:
- University Counseling Center, 301 Peabody Hall, 392-1575, Personal and Career
Counseling.
- SHCC mental Health, Student Health Care Center, 392-1171, Personal and
Counseling.
- Center for Sexual Assault/Abuse Recovery and Education (CARE), Student Health
Care Center, 392-1161, sexual assault counseling.
- Career Resource Center, Reitz Union, 392-1601, career development assistance and
counseling.
23. Software Use
All faculty, staff and student of the University are required and expected to obey the laws and
legal agreements governing software use. Failure to do so can lead to monetary damages
and/or criminal penalties for the individual violator. Because such violations are also against
University policies and rules, disciplinary action will be taken as appropriate. We, the
members of the University of Florida community, pledge to uphold ourselves and our peers
to the highest standards of honesty and integrity.