Download Course Mission

Welcome to 20.109
Laboratory Fundamentals of
Biological Engineering
Orientation Lecture
Spring 2008
Introducing 20.109
• Why you’re here
– course mission
– the art of investigation
• What you’ll do
– three experimental modules
– assessments/communication
– course logistics
20.109 Laboratory Fundamentals
of Biological Engineering
Course Mission
 To prepare students to be the
future of Biological Engineering
 To teach cutting edge research skill and
technology through authentic investigation
 To inspire rigorous data analysis and
its thoughtful communication
20.109 Laboratory Fundamentals
of Biological Engineering
Course Mission
 To prepare students to be the
future of Biological Engineering
20.109 Laboratory Fundamentals
of Biological Engineering
Course Mission
 To prepare students to be the
future of Biological Engineering
We inform, you create!
Your goals and interests?
Engineering Principles + Modern Biology
Make stuff!
Measure
Model
Manipulate
pdb.org
How Doctors(*) People Think
…even engineers!
Scientists are like detectives
Bias leads investigations astray
Hindsight bias
Attribution error
Framing effect
(*)
J. Groopman
Puzzles: hindsight bias
Why is it better to have round manhole covers
than square ones?
Round covers cannot be dropped down the
manhole, no matter how you turn them.
A woman had two sons who were born on the
same hour of the same day of the same year.
But they were not twins. How could this be so?
They were triplets!
(cf. invention of PCR)
Rote learning: attribution error
Your school district must drive 1128 kids to
school each day, and 36 kids can fit on a
bus. How many buses do you need?
31
36
1128
108
48
Most popular answer: 31 remainder 12!
Framing effect
Politics: “tax cuts” vs. “tax relief” vs. “tax responsibility”
Science: what carries and controls genetic information?
(The Canon, N. Angier; Images all from public domain)
2
4
1
3
Science policy: GM foods or nanotechnology
benefits frame vs. risks frame
?5?
How Engineers Succeed
Bias leads investigations astray
How do we fight bias?
Appropriate controls
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Reluctant interpretation
Community vigilance
“Your data should be true even if your story is wrong.”
~ Darcy Kelley, Columbia
(The Canon, N. Angier)
20.109 Laboratory Fundamentals
of Biological Engineering
Course Mission
 To prepare students to be the
future of Biological Engineering
 To teach cutting edge research skill and
technology through authentic investigation
 To inspire rigorous data analysis and
its thoughtful communication
Module 1
Module 2
Module 3
DNA Engineering (B. Engelward)
Protein Engineering (A. Jasanoff)
Biomaterials Engineering (A. Stachowiak)
openwetware.org/wiki/20.109(S08)
DNA Engineering: EGFP recombination
web.mit.edu/engelward-lab/animations/DSBR.html
Recombocell image from Dominika Wiktor, Engelward lab.
Experimental Goals
Design: PCR primers
 Truncate EGFP gene (5’)
 Make and test 5 plasmid
 Transfect mouse cells with
EGFPs (full and )
 Test for spontaneous DNA
recombination by fluorescence
Lab+Analytical Skills
 DNA manipulation:
PCR, recombination, gels
 Cell culture
bacterial ( DNA)
mammalian ( protein)
 Flow cytometry
statistical analysis
 Discuss primary research article
Protein Engineering: Calcium sensor redesign
Experimental Goals
Design: protein modification
 Mutagenize wild-type plasmid
 Express and purify protein in a
bacterial host
 Assess effect of mutation on
protein production and behaviour
Lab+Analytical Skills
 Assess protein features
 DNA mutagenesis and sequencing
 Characterize protein
identity, amount, fluorescence
 More error analysis
low vs. high-throughput
MATLAB modeling
Biomaterials Engineering: Cartilage gel
Experimental Goals
Design: Culture conditions
 Study how cell environment
affects viability and morphology.
 Measure collagen contents for
chondrocytes cultured differently.
Lab+Analytical Skills
 3D cell culture
 Fluorescence microscopy
 Measure message
isolate RNA
RT-PCR
 Measure one protein (from mixture)
ELISA
Communication and Grading
Major Assessments
50% Written Work
Module 1 - lab report
Module 2 - portfolio
Module 3 - essay
30% Oral Presentations
Module 2 - journal article
Module 3 - research proposal
Day-to-day Assessments
10% Homework Assignments
5% In-lab Daily Quizzes
5% Lab Notebooks
Neal Lerner
Atissa Banuazizi
After 20.109, you should be able to…
• Implement laboratory protocols
• Design novel experiments with
appropriate controls
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• Organize a lab notebook
• Interpret qualitative data
• Analyze quantitative data
• Recognize utility of models
• Examine the scientific literature
• Communicate to various audiences, in various styles
• Present salient points of your own and others’ ideas
Course Logistics
Lecture
Tuesdays and Thursdays 11-12, 13-3101
Lab
Tuesdays and Thursdays 1-5, 13-3095
Wednesdays and Fridays 1-5, 13-3095
There are no “make-up” labs
You will perform experiments in pairs.
Collaboration with integrity is encouraged: assignments
can be worked on together but must be submitted individually.
Work must be turn in on time:
lab notebooks - end of lab
assignments - beginning of lab or lecture