Welcome to 20.109 Laboratory Fundamentals of Biological Engineering

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Welcome to 20.109 Laboratory Fundamentals of
Biological Engineering
Orientation Lecture Spring 2008
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Introducing 20.109

• Why youre here
• course mission
• the art of investigation
• What youll do
• three experimental modules
• assessments/communication
• course logistics

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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

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20.109 Laboratory Fundamentals of Biological
Engineering
Course Mission

• To prepare students to be the future of
  Biological Engineering

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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?
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Engineering Principles Modern Biology
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How Doctors() People Think
even engineers!
() J. Groopman
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Puzzles hindsight bias
Why is it better to have round manhole covers
than square ones?
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?
(cf. invention of PCR)
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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?
Most popular answer 31 remainder 12!
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Framing effect
Politics tax cuts vs. tax relief vs. tax
responsibility
Science policy GM foods or nanotechnology benefi
ts frame vs. risks frame
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How Engineers Succeed
Bias leads investigations astray
How do we fight bias?
Your data should be true even if your story is
wrong. Darcy Kelley, Columbia (The
Canon, N. Angier)
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20.109 Laboratory Fundamentals of Biological
Engineering
Course Mission

• To prepare students to be the future of
  Biological Engineering

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DNA Engineering (B. Engelward)
Module 1
Protein Engineering (A. Jasanoff)
Module 2
Biomaterials Engineering (A. Stachowiak)
Module 3
openwetware.org/wiki/20.109(S08)
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DNA Engineering EGFP recombination
web.mit.edu/engelward-lab/animations/DSBR.html
Recombocell image from Dominika Wiktor, Engelward
lab.

• LabAnalytical Skills
• DNA manipulation
• PCR, recombination, gels
• Cell culture
• bacterial ( DNA)
• mammalian ( protein)
• Flow cytometry
• statistical analysis
• Discuss primary research article

• 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

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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

• LabAnalytical Skills
• Assess protein features
• DNA mutagenesis and sequencing
• Characterize protein
• identity, amount, fluorescence
• More error analysis
• low vs. high-throughput
• MATLAB modeling

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Biomaterials Engineering Cartilage gel

• LabAnalytical Skills
• 3D cell culture
• Fluorescence microscopy
• Measure message
• isolate RNA
• RT-PCR
• Measure one protein (from mixture)
• ELISA

• Experimental Goals
• Design Culture conditions
• Study how cell environment
• affects viability and morphology.
• Measure collagen contents for
• chondrocytes cultured differently.

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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
Neal Lerner Atissa Banuazizi
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After 20.109, you should be able to

• Implement laboratory protocols
• Design novel experiments with

• appropriate controls
• 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

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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