20.109(F07):Module 1

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(New page: {{Template:20.109(F07)}} <div style="padding: 10px; width: 640px; border: 5px solid #666699;"> ==Module 1== '''Instructors:''' Drew Endy and Natalie Kuldell '''TA:''' In this...)
Current revision (06:14, 24 August 2007) (view source)
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==Module 1==
==Module 1==
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'''Instructors:''' [[Drew Endy]] and [[Natalie Kuldell]]
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'''Instructors:''' [[Drew Endy]], [[Natalie Kuldell]], and [[User:AgiStachowiak| Agi Stachowiak]]
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'''TA:'''
 
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In this experiment, we will consider the genome of a virus, namely the bacteriophage M13. M13 is a self-assembling nano-machine with a compact genome that has been optimized by evolution to commandeer its bacterial host. Approximately 1000 new viruses are generated from a single infection event.  Imagine harnessing this production. What could we build and what  natural processes could we better understand? One approach we’ll take is to modify the existing genome in a subtle but useful way, namely by adding a peptide-tag that can be presented on the bacteriophage coat. We’ll examine how this modification affects the coat protein’s expression and overall phage production. Another approach we’ll take is to start from scratch, undertaking a full throttle redesign of the bacteriophage genome. We’ll employ a commercial DNA synthesis company to compile the redesigned genomic program and then we’ll see if it encoded infective M13 and if the genome of the bacterial host affects bacteriophage production. Through these investigations we’ll ask: is nature’s M13 genome “perfect” or can we do better?   
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'''TA:''' [[Laure-Anne Ventouras]]
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In this experiment, we will consider the genome of a virus, namely the bacteriophage M13. M13 is a self-assembling nano-machine with a compact genome that has been optimized by evolution to commandeer its bacterial host. Approximately 1000 new viruses are generated from a single infection event.  Imagine harnessing this production. What could we build and what  natural processes could we better understand? One approach we’ll take is to modify the existing genome in a subtle but useful way, namely by adding a useful sequence-tag that modifies the bacteriophage coat. We’ll examine how this modification affects the coat protein’s expression and overall phage production. Another approach we’ll take is to start from scratch, undertaking a full throttle redesign of the bacteriophage genome. We’ll employ a commercial DNA synthesis company to compile the redesigned genomic program and then we’ll see if it encoded infective M13 and if the genome of the bacterial host affects bacteriophage production. Through these investigations we’ll ask: is nature’s M13 genome “perfect” or can we do better?   
[[Image:Macintosh HD-Users-nkuldell-Desktop-GnmEng coverart S07.jpg|thumb|500px|center|M13-coated coli from M. Russel<br> Map of M13 genome from M. Blaber]]
[[Image:Macintosh HD-Users-nkuldell-Desktop-GnmEng coverart S07.jpg|thumb|500px|center|M13-coated coli from M. Russel<br> Map of M13 genome from M. Blaber]]
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[[20.109(S07):Start-up genome engineering | Module 1 Day 1: Start-up genome engineering]]<br>
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[[20.109(F07):Start-up genome engineering | Module 1 Day 1: Start-up genome engineering]]<br>
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[[20.109(S07): Agarose gel electrophoresis| Module 1 Day 2: Agarose gel electrophoresis]]<br>
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[[20.109(F07): Agarose gel electrophoresis| Module 1 Day 2: Agarose gel electrophoresis]]<br>
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[[20.109(S07): DNA ligation and bacterial transformation| Module 1 Day 3: DNA ligation and bacterial transformation]]<br>
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[[20.109(F07): DNA ligation and bacterial transformation| Module 1 Day 3: DNA ligation and bacterial transformation]]<br>
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[[20.109(S07): Examine candidate clones| Module 1 Day 4: Examine candidate clones]]<br>
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[[20.109(F07): Examine candidate clones| Module 1 Day 4: Examine candidate clones]]<br>
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[[20.109(S07): Western analysis| Module 1 Day 5: Western analysis]]<br>
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[[20.109(F07): M13.1 | Module 1 Day 5: M13.1]]<br>
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[[20.109(S07): Probe western| Module 1 Day 6: Probe western]]<br>
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[[20.109(F07): Western analysis| Module 1 Day 6: Western analysis]]<br>
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direct link to [[20.109%28S07%29:_Genome_engineering_essay]]<br>
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[[20.109(F07): Probe western| Module 1 Day 7: Probe western]]<br>
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direct link to [[20.109:Module 1:RefactorM13| M13 refactoring workpage]]<br>
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[[20.109(F07): Module 1 oral presentations| Module 1 Day 8: Oral Presentations]]<br>
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direct link to [http://parts.mit.edu/r/parts/partsdb/part_info.cgi?part_name=BBa_M1307| hard info for BBa_M1307]
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direct link to the requirements for the genome engineering [[20.109(F07):_Genome_engineering_assessment| portfolio]]<br>
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direct link to [[20.109(F07):Module 1:RefactorM13 | working page]] for M13 refactoring
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[[20.109(S07): TA's notes for module 1| TA notes, mod 1]]
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[[20.109(F07): TA's notes for module 1| TA notes, mod 1]]

Current revision

20.109(F07): Laboratory Fundamentals of Biological Engineering

Home        People        Schedule Fall 2007        Assignments        Lab Basics        OWW Basics       
Genome Engineering        Expression Engineering        Biomaterials Engineering              

Module 1

Instructors: Drew Endy, Natalie Kuldell, and Agi Stachowiak


TA: Laure-Anne Ventouras

In this experiment, we will consider the genome of a virus, namely the bacteriophage M13. M13 is a self-assembling nano-machine with a compact genome that has been optimized by evolution to commandeer its bacterial host. Approximately 1000 new viruses are generated from a single infection event. Imagine harnessing this production. What could we build and what natural processes could we better understand? One approach we’ll take is to modify the existing genome in a subtle but useful way, namely by adding a useful sequence-tag that modifies the bacteriophage coat. We’ll examine how this modification affects the coat protein’s expression and overall phage production. Another approach we’ll take is to start from scratch, undertaking a full throttle redesign of the bacteriophage genome. We’ll employ a commercial DNA synthesis company to compile the redesigned genomic program and then we’ll see if it encoded infective M13 and if the genome of the bacterial host affects bacteriophage production. Through these investigations we’ll ask: is nature’s M13 genome “perfect” or can we do better?

M13-coated coli from M. Russel Map of M13 genome from M. Blaber
M13-coated coli from M. Russel
Map of M13 genome from M. Blaber

Module 1 Day 1: Start-up genome engineering
Module 1 Day 2: Agarose gel electrophoresis
Module 1 Day 3: DNA ligation and bacterial transformation
Module 1 Day 4: Examine candidate clones
Module 1 Day 5: M13.1
Module 1 Day 6: Western analysis
Module 1 Day 7: Probe western
Module 1 Day 8: Oral Presentations
direct link to the requirements for the genome engineering portfolio
direct link to working page for M13 refactoring

TA notes, mod 1
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