Difference between revisions of "20.109(S11):Module 2"

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==Module 2==
 
==Module 2==
 
   
 
   
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'''Instructors:''' [http://web.mit.edu/be/people/weiss.htm Ron Weiss] and [[User:AgiStachowiak| Agi Stachowiak]]
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'''Instructors:''' [http://web.mit.edu/be/people/weiss.htm Ron Weiss] and [http://openwetware.org/wiki/User:AgiStachowiak | Agi Stachowiak]
  
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'''TA:''' [[User:Adrian_Randall| Adrian Randall]]
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'''TA:''' [http://openwetware.org/wiki/User:Adrian_Randall | Adrian Randall]
  
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As engineers, we would like to make useful objects that behave in a predictable fashion. As biological engineers, we face unique challenges in implementing our ideas: the biological machines we create may evolve, their components may not always play nicely together, and slight variations in the environment might substantially affect their function. In this module, we will work on understanding and improving an edge detection system effected by bacteria. By way of diffusible signals and photosensitivity, a single (i.e., genetically identical) cell population is able to copy the outline of an image placed above it. However, the system can be finicky, with low contrast, poor resolution, and little margin for variability in preparation. Using a more easily manipulatable system (not based on light) as a tool, we will attempt to improve system robustness and transfer our knowledge to improve the light-based system.  
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As engineers, we would like to make useful objects that behave in a predictable fashion. As biological engineers, we face unique challenges in implementing our ideas: the biological machines we create may evolve, their components may not always play nicely together, and slight variations in the environment might substantially affect their function. In this module, we will work on understanding and improving an edge detection system effected by bacteria. By way of diffusible signals and photosensitivity, a single (i.e., genetically identical) cell population is able to copy the outline of an image placed above it. However, the system can be finicky, with low contrast, poor resolution, and little margin for variability in preparation. Using a more easily manipulatable system (not based on light) as a tool, we will attempt to improve system robustness and consider how to transfer our knowledge to improve the original edge detector.  
  
 
[[Image:S11-M2_frontpage-pic.JPG|thumb|center|300px|'''Edge detection image''' A Petri dish with bacteria expressing the edge detection system is shown. The original system displays poor contrast.]]
 
[[Image:S11-M2_frontpage-pic.JPG|thumb|center|300px|'''Edge detection image''' A Petri dish with bacteria expressing the edge detection system is shown. The original system displays poor contrast.]]
  
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We thank 20.109 instructor [[Natalie Kuldell]] for helpful discussions during early module development, as well as for her prior work in developing a [http://openwetware.org/wiki/20.109(F10):Module_2 related module]. We also thank Lisa Foo, '12, for her contributions to pilot experiments, particularly in obtaining the light:''lacZ'' transfer function.
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We thank 20.109 instructor [http://openwetware.org/wiki/Natalie_Kuldell ] for helpful discussions during early module development, as well as for her prior work in developing a [http://openwetware.org/wiki/20.109(F10):Module_2 related module]. We also thank Lisa Foo, '12, for her contributions to pilot experiments, particularly in obtaining the light:''lacZ'' transfer function.
  
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[[20.109(S11):Explore model system (Day1)| Module 2 Day 1: Explore model system]]<br>
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[http://openwetware.org/wiki/20.109(S11):Explore_model_system_(Day1) | Module 2 Day 1: Explore model system]<br>
 
[[20.109(S11):Complete DNA design (Day2)| Module 2 Day 2: Complete DNA design]]<br>
 
[[20.109(S11):Complete DNA design (Day2)| Module 2 Day 2: Complete DNA design]]<br>
 
[[20.109(S11):Prepare DNA for cloning (Day3)| Module 2 Day 3: Prepare DNA for cloning]]<br>
 
[[20.109(S11):Prepare DNA for cloning (Day3)| Module 2 Day 3: Prepare DNA for cloning]]<br>
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Note: spring break week occurs between day 4 and day 5 of lab.
 
Note: spring break week occurs between day 4 and day 5 of lab.
  
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[[20.109(S11):Prepare candidate clones in model cell strain (Day5)| Module 2 Day 5: Prepare candidate clones in model cell strain]]<br>
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[http://openwetware.org/wiki/20.109(S11):Prepare_candidate_clones_in_model_cell_strain_(Day5) | Module 2 Day 5: Prepare candidate clones in model cell strain]<br>
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[[20.109(S11):Evaluate DNA and choose clone (Day6)| Module 2 Day 6: Evaluate DNA and choose clone]]<br>
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[http://openwetware.org/wiki/20.109(S11):Evaluate_DNA_and_choose_clone_(Day6) | Module 2 Day 6: Evaluate DNA and choose clone]<br>
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[[20.109(S11):Assay modified model system (Day7)| Module 2 Day 7: Assay modified model system]]<br>
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[http://openwetware.org/wiki/20.109(S11):Assay_modified_model_system_(Day7) | Module 2 Day 7: Assay modified model system]<br>
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[[20.109(S11):Wrap-up analysis and modelingb (Day8)| Module 2 Day 8: Wrap-up analysis and modeling]]<br>
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[http://openwetware.org/wiki/20.109(S11):Wrap-up_analysis_and_modelingb_(Day8) | Module 2 Day 8: Wrap-up analysis and modeling]<br>
  
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[[20.109(S11): System engineering report | System engineering research article]]<br>
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[http://openwetware.org/wiki/20.109(S11):_System_engineering_report  | System engineering research article]<br>
  
 
[[20.109(S11): TA notes for module 2| TA notes, mod 2]]
 
[[20.109(S11): TA notes for module 2| TA notes, mod 2]]

Revision as of 02:01, 8 March 2011


20.109(S11): Laboratory Fundamentals of Biological Engineering

20.109(S11) frontpg.JPG

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Module 2

Instructors: Ron Weiss and | Agi Stachowiak

TA: | Adrian Randall

As engineers, we would like to make useful objects that behave in a predictable fashion. As biological engineers, we face unique challenges in implementing our ideas: the biological machines we create may evolve, their components may not always play nicely together, and slight variations in the environment might substantially affect their function. In this module, we will work on understanding and improving an edge detection system effected by bacteria. By way of diffusible signals and photosensitivity, a single (i.e., genetically identical) cell population is able to copy the outline of an image placed above it. However, the system can be finicky, with low contrast, poor resolution, and little margin for variability in preparation. Using a more easily manipulatable system (not based on light) as a tool, we will attempt to improve system robustness and consider how to transfer our knowledge to improve the original edge detector.

Edge detection image A Petri dish with bacteria expressing the edge detection system is shown. The original system displays poor contrast.

We thank 20.109 instructor [1] for helpful discussions during early module development, as well as for her prior work in developing a related module. We also thank Lisa Foo, '12, for her contributions to pilot experiments, particularly in obtaining the light:lacZ transfer function.

| Module 2 Day 1: Explore model system
Module 2 Day 2: Complete DNA design
Module 2 Day 3: Prepare DNA for cloning
Module 2 Day 4: Ligate DNA and transform bacteria

Note: spring break week occurs between day 4 and day 5 of lab.

| Module 2 Day 5: Prepare candidate clones in model cell strain
| Module 2 Day 6: Evaluate DNA and choose clone
| Module 2 Day 7: Assay modified model system
| Module 2 Day 8: Wrap-up analysis and modeling

| System engineering research article

TA notes, mod 2
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