20.109(F14):Module 2

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==Module 2==
==Module 2==
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'''Instructors:''' [[User:Shannon K. Alford |Shannon Hughes-Alford]], [[Natalie Kuldell]], [[User:AgiStachowiak| Agi Stachowiak]]<br>
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'''Instructors:''' [[User:Shannon K. Alford |Shannon Hughes]], [[Natalie Kuldell]], [[User:Noreen L. Lyell| Noreen Lyell]], [[User:AgiStachowiak| Agi Stachowiak]]<br>
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'''TA:''' [[User:Eric Ma|Eric Ma]]<br>
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'''TA:''' [[]]<br>
[[Image:Image M2 20.109(F10).jpg||thumb|left|300 px]] Getting systems that work right out of the box is something that we’ve come to expect from electrical and mechanical engineers. New car? Get some gas, turn the key and off you go! New digital camera? Charge the battery and then start taking pictures! Biological engineers—though notable in their achievements---have lagged behind in the design and construction of novel systems that work in reliable, scalable, intuitive ways. Biology simply does not always perform as intended. Moreover, tools for the design and testing stages of engineered living systems are not yet robust or standard. In this experimental module we’ll learn to design and tune a biological system—namely the bacterial photography system in which bacteria serve as pixels in a picture. The picture, though remarkable, is slow to develop, limited to two colors, and low in contrast. To improve the system, we’ll combine some powerful tools from biological science, namely genetics and evolution, with some of the fledgling tools in synthetic biology such as abstraction and standardization of biological parts, to improve and extend the performance of the bacterial photography system. In the process we may also learn something new about the natural systems upon which the engineered one is built.  
[[Image:Image M2 20.109(F10).jpg||thumb|left|300 px]] Getting systems that work right out of the box is something that we’ve come to expect from electrical and mechanical engineers. New car? Get some gas, turn the key and off you go! New digital camera? Charge the battery and then start taking pictures! Biological engineers—though notable in their achievements---have lagged behind in the design and construction of novel systems that work in reliable, scalable, intuitive ways. Biology simply does not always perform as intended. Moreover, tools for the design and testing stages of engineered living systems are not yet robust or standard. In this experimental module we’ll learn to design and tune a biological system—namely the bacterial photography system in which bacteria serve as pixels in a picture. The picture, though remarkable, is slow to develop, limited to two colors, and low in contrast. To improve the system, we’ll combine some powerful tools from biological science, namely genetics and evolution, with some of the fledgling tools in synthetic biology such as abstraction and standardization of biological parts, to improve and extend the performance of the bacterial photography system. In the process we may also learn something new about the natural systems upon which the engineered one is built.  
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==Assignments==
==Assignments==
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[[20.109(F12): Module 2 celebrations of learning| summary of Module 2 assignments]]<br>
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[[20.109(F14): Module 2 celebrations of learning| summary of Module 2 assignments]]<br>
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[[20.109(F12): Slides for Journal Club Presentation| Slides for Journal Club Presentation]]<br>
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[[20.109(F14): Slides for Journal Club Presentation| Slides for Journal Club Presentation]]<br>
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[[20.109(F12):Guidelines for oral presentations| Journal Club Presentation, M2D4 or M2D8]]<br>
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[[20.109(F14):Guidelines for oral presentations| Journal Club Presentation, M2D4 or M2D8]]<br>
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[[20.109(F12): Results and Discussion sections| System Engineering Results and Discussion]]<br>
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[[20.109(F14): Results and Discussion sections| System Engineering Results and Discussion]]<br>
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[[20.109(F12): System engineering research article| System Engineering Full Research Article]]<br>
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[[20.109(F14): System engineering research article| System Engineering Full Research Article]]<br>
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[[20.109(F12): System engineering research article| Guidelines for research article assignment]]<br>
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[[20.109(F14): System engineering research article| Guidelines for research article assignment]]<br>
==Useful sequence files==
==Useful sequence files==

Revision as of 06:52, 16 August 2014

20.109(F14): Laboratory Fundamentals of Biological Engineering

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Contents

Module 2

Instructors: Shannon Hughes, Natalie Kuldell, Noreen Lyell, Agi Stachowiak
TA: [[]]

Getting systems that work right out of the box is something that we’ve come to expect from electrical and mechanical engineers. New car? Get some gas, turn the key and off you go! New digital camera? Charge the battery and then start taking pictures! Biological engineers—though notable in their achievements---have lagged behind in the design and construction of novel systems that work in reliable, scalable, intuitive ways. Biology simply does not always perform as intended. Moreover, tools for the design and testing stages of engineered living systems are not yet robust or standard. In this experimental module we’ll learn to design and tune a biological system—namely the bacterial photography system in which bacteria serve as pixels in a picture. The picture, though remarkable, is slow to develop, limited to two colors, and low in contrast. To improve the system, we’ll combine some powerful tools from biological science, namely genetics and evolution, with some of the fledgling tools in synthetic biology such as abstraction and standardization of biological parts, to improve and extend the performance of the bacterial photography system. In the process we may also learn something new about the natural systems upon which the engineered one is built.


link to bacterial photography paper

Lablinks: day by day

Day 1: Testing an engineered biological system
Day 2: Measuring system performance
Day 3: Tools for system engineering
Day 4: Journal Club I
Day 5: Assessing re-tuned system
Day 6: Readout DNA
Day 7: Readout Protein
Day 8: Journal Club II

Assignments

summary of Module 2 assignments
Slides for Journal Club Presentation
Journal Club Presentation, M2D4 or M2D8
System Engineering Results and Discussion
System Engineering Full Research Article
Guidelines for research article assignment

Useful sequence files

pCph8
Cph8 ORF: sequence
Cph8 ORF: translated
KP mutant library
WT photography DNA, sequenced with NO496

Notes for Teaching Faculty

TA notes, mod 2
Personal tools