2012 BME 3323L/5052L - Cellular Engineering Laboratory
(Finalized syllabus will be distributed on the first day of class)
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 3XXX 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
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The student will learn to identify, formulate and solve engineering problems

The student will learn about professional and ethical responsibility
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The student will learn to communicate effectively
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The student will learn about contemporary issues regarding the use of cells in BME research
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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
Office: J296, Biomedical Sciences Bldg
Phone: 273-8125
Email: bormerod@bme.ufl.edu
Website: http://stemcell.ufl.edu
Office Hours: Wednesdays 3:00-4:00pm.
Dr. Peter McFetridge
Office: J391, Biomedical Sciences Bldg
Phone: 273-9325
Email: pmcfetridge@bme.ufl.edu
Website:
Office Hours:
7.
Teaching Assistants:
Ms. Lan Hoang-Minh, M.E. and PhD Candidate
Phone: 273-8179
Email: hoang@ufl.edu
]
Office Hours: Wednesday 3-4 pm.
Ms. Cassandra Juran, PhD Student
Phone: 273-9518
Email: cassiejuf@gmail.com
Office Hours: Wednesday 3-4 pm.
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.
9.
Class/laboratory schedule
Class meets for: a) 1 - 50 min lecture per week (Mondays – Period 8; 2:50-3:50pm) b) 1 – cell feeding session per week (Mondays – Period 6 - arranged with TA) c) 1 – 180 min laboratory per week (Wednesdays – Periods 6-8; 12:50 to 3:50pm) d) 1 – 180 min laboratory (Fridays – Periods 6-8; 12:50 to 3:50pm)
10.
Meeting Location
Monday – HPNP G316

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 - 01/09/12
HPNP G319 - 50 Min
• Course overview/expectations
•
•
Introduction to Instructors/Teaching Assistants
Syllabus Overview
Laboratory 1 – Introduction to Cell Culture and the laboratory
Wednesday – 01/13/12
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
Laboratory 2 – Writing a Manuscript Style Research Report
Friday, January 13 th
, 2012
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 01/18/12 (bring 5 abstracts to class) .
Week 2
Lecture 2 - No class – Martin Luther King Day
Monday – 01/16/12
Room J280 BMSB (50 min)
Laboratory 3 – Working aseptically with cells
Wednesday – 01/18/12
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 – 01/20/12
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
Lecture 3- Introduction to Cell Culture, Thawing and Plating cells for an Experiment
Monday – 01/23/12
BMSB J280 (50 min)
Laboratory 5 – Ick, my cells look sick!
Wednesday – 01/25/12
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 – 01/27/12
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 – 01/30/12
BMSB J280 (50 min)
•
Feed Cells independently (at time specific by TA).
Laboratory 7 – Are my cells genetically stable?
Wednesday – 02/01/12
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 – 02/03/12
HHMI Laboratory (180 min)
Required Reading: Chapters 14 and 15
•
•
•
•
•
•
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
Hand in notebook page copy (0.5% of grade for module 1)
Week 5
Lecture 5 – Freezing cells, Record Keeping and GMP
Monday – 02/06/12
BMSB J280 (50 min)
•
Introduction to Cell Culture – Freezing Cells, Record keeping and GMP for clinical work
• Feed Cells Independently
Laboratory 9- Immunohistochemistry and evaluating your experiment effects
Wednesday – 02/08/12
HHMI Laboratory (180 min)
Required Reading: Freshney Chapter 19.
•
•
•
•
•
Discussion: Controls and effects
Introduction to data analysis
Experiment – Use antibodies to detect neurons and glia in your NPC cultures
Freeze Remaining Cells
Hand in notebook page copy (0.5% of grade for module 1)

Laboratory 10 – Analyzing proportions of neurons and glia with FACs
Friday – 02/10/12
•
•
•
HHMI Laboratory (180 min)
•
•
Discussion: Analyzing cell phenotypes with Flow Cytometry
Video on Flow Cytometry: http://probes.invitrogen.com/resources/education/tutorials/4Intro_Flow/player.ht
ml
Practicum: Analyze your cells with your TA using Flow Cytometry
Hand in notebook page copy (0.5% of grade for module 1)
Hand in methods section of report for feedback and 2% of grade
Week 6
Lecture 6 – Quantitation and Data Analysis – Morphological Analyses
Monday – 02/13/12
BMSB J280 (50 min)
Laboratory 11 – Analyzing proportions of neurons and glia with microscopy
Wednesday – 02/15/12
•
•
HHMI Laboratory (180 min)
•
•
Discussion: Analyzing cell phenotypes using microscopy
Presentation on how to use the EVOs systems: http://www.authorstream.com/Presentation/Obama-55030-evos-customer-training-t-
Entertainment-ppt-powerpoint/
Practicum: Count Cells
Hand in notebook page copy (0.5% of grade for module 1)
Laboratory 12- Using and reporting statistics
Friday – 02/17/12
HHMI Laboratory (180 min)
•
•
•
Discussion: T-tests, ANOVAs, correlations, dependent and independent variables
Bring your data to class so that we can run statistical tests.
Hand in notebook page copy (0.5% of grade for module 1)
Week 7
Lecture 7 – Quantitation and Data Analysis – Molecular Analyses
Monday – 02/20/12 - Lecture (50 min)
• Hand in Preliminary results section (2% of grade).
Laboratory 13- Work on Paper Write Up
Wednesday – 02/22/12
HHMI Laboratory (180 min)

Laboratory 14- Work on Paper Write Up
Friday – 02/24/12
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
• Discussion: Data Interpretation.
• Practicum: write and questions about data analysis, IEEE format, content, etc.
Lecture 8 - Review
•
•
Monday – 02/27/12 - Lecture (50 min)
•
Review (Weeks 1-7)
Report due before class
Fill out teacher evaluation (2% of grade)
Laboratory 15 – Exam #1
Wednesday – 02/29/12
HHMI Laboratory (180 min)
•
All material learned in weeks 1-7 (lecture, textbook and laboratory) will be tested
Laboratory 16 – no class
Friday – 03/02/11 – Laboratory (180 min)

15.
Module 2: Course Outline
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 – 03/12/12 - 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 – 03/14/12 - 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 – 03/16/12 - 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 – 03/19/12 - Lecture (50 min) –

Experimental overview (two sections – ‘Hydrogels’ and ‘ ex vivo derived tissue implants’)

Feeding cells
Wednesday – 03/21/12 - 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 – 03/23/12 - 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 – 03/26/12 - Lecture (50 min) -

Experimental overview (two sections – ‘Hydrogels’ and ‘ ex vivo derived tissue implants’)

Results – what are they going to mean.
Wednesday – 03/28/12 - 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 – 03/30/12 - 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 – 04/02/12 - Lecture (50 min) -
Wednesday – 04/04/12 - Laboratory (3h)
Friday – 04/06/12 - Laboratory (3h)
Week 15
Monday – 04/09/12 - Lecture (50 min) -
Wednesday – 04/11/12 - Laboratory (3h)
Friday – 04/13/12 - Laboratory (3h)
Week 16
Monday – 04/16/12 - Lecture (50 min) -
Wednesday – 04/18/12 - Laboratory (3h)
Friday – 04/20/12 - Laboratory (3h)

Report #2 Due
Week 16
Monday – 04/23/12 - Lecture (50 min)

Review – weeks 9-14
Wednesday – 04/25/12 - 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
Report Methods
Report Results
Full Report
Exam
2%
2%
2%
15%
20%
Lab Note Book Pages 10%
50%
Module 2
Report
Exam#2
15%
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 reminder 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
Counseling.
- SHCC mental Health, Student Health Care Center, 392-1171, Personal and
Counseling.
Career
- 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.