20.109:Module 4

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==Module 4==
==Module 4==
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'''Instructors:''' Angela Belcher and [[Natalie Kuldell]]
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'''Instructors:''' [[Angela Belcher]] and [[Natalie Kuldell]]
'''TA:''' [[Chandni Valiathan]]
'''TA:''' [[Chandni Valiathan]]
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In this experimental module we will study an unusual protein, one that allows yeast to bind a metal, gold. Over the next few weeks we will purify yeast based on this binding property, and then we’ll vary some experimental condition to improve the yeast/gold interaction. Using your optimized conditions, we will screen a library of yeast to isolate a new gold-binding strain. The DNA encoding the new gold-binding protein will be sequenced and, with any luck, we’ll elucidate some amino acid requirements for the yeast/metal interaction.
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“Invention” is a wonderful word, derived from words meaning, “scheme” and “a finding out.” Inventors draw on materials provided by the natural world, refining and combining them in insightful ways, to make something useful. In this experimental module we will invent materials by manipulating biological systems, namely the bacteriophage M13 and its bacterial host.  In one experiment,  we will revisit the host/phage interface and try to build a simpler one, infecting a strain bearing a minimal bacterial genome using a refactored phage genome. In a second experiment, we  will use a very slightly modified phage, presenting four additional glutamic acids on the major coat protein p8, to build a nanowire that we’ll visualize on the transmission electron microscope. In a final experiment we will let the phage themselves do the building, watching them self-assemble on a polymer-surface, visualizing their structures with an atomic force microscope. Drawing on a rich stockroom of biological elements and a good but incomplete understanding of their behavior, we’ll hope to invent some novel and useful materials.
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[[Image:Macintosh HD-Users-nkuldell-Desktop-yeastbuddingandbound.png|center|400px|'''S. cerevisiae shown budding (top) and bound to CdS (bottom)''']]
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[[Image:Macintosh HD-Users-nkuldell-Desktop-Mod4 coverartS07.png|thumb|400px|center| TEM of M13E4 after CoCl2/NaBH4 treatment, image by Natalie Kuldell, Anthony Garratt-Reed and KiTae Nam]]
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[[20.109(S07):Bio-material engineering/Screening library | Module 4 Day 1: Screening library]]<br>
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[[20.109(S07): Bio-material engineering/Optimizing panning | Module 4 Day 2: Optimizing panning]]<br>
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[[20.109(S07): Growth of phage materials| Module 4 Day 1: growth of phage materials]] <br>
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[[20.109(S07): Bio-material engineering/Rescreening gold binders | Module 4 Day 3: Rescreening gold binders]]<br>
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[[20.109(S07): Testing redesigned genomes| Module 4 Day 2: testing redesigned genomes]]<br>
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[[20.109(S07): Bio-material engineering/PCR of gold binding candidates | Module 4 Day 4: PCR of gold binding candidates]]<br>
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[[20.109(S07): Building phage nanowires| Module 4 Day 3: building phage nanowires]]<br>
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[[20.109 (S07): Research proposal, module 4| Module 4 Day 5: Student presentations]]<br>
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[[20.109 (S07): Transmission electron microscopy| Module 4 Day 4: Transmission Electron Microscopy (TEM)]] <br>
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[[20.109(S07): Bio-material engineering/Sequence analysis | Module 4 Day 6: Sequence analysis]]<br>
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[[20.109 (S07): Atomic force microscopy| Module 4 Day 5: Atomic Force Microscopy (AFM)]]<br>
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[[20.109(S07): Biomaterial engineering, TA notes| TA notes Module 4]]
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[[20.109(S07):Student presentations, module 4| Module 4 Day 6: student presentations]]<br>
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[[20.109(S07): TA's notes for module 4| TA notes, mod 4]]
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Current revision

20.109: Laboratory Fundamentals of Biological Engineering

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Genome Engineering        Biophysical Signal Measurement        Expression Engineering        Biomaterial Engineering       

Module 4

Instructors: Angela Belcher and Natalie Kuldell

TA: Chandni Valiathan

In this experimental module we will study an unusual protein, one that allows yeast to bind a metal, gold. Over the next few weeks we will purify yeast based on this binding property, and then we’ll vary some experimental condition to improve the yeast/gold interaction. Using your optimized conditions, we will screen a library of yeast to isolate a new gold-binding strain. The DNA encoding the new gold-binding protein will be sequenced and, with any luck, we’ll elucidate some amino acid requirements for the yeast/metal interaction.

S. cerevisiae shown budding (top) and bound to CdS (bottom)


Module 4 Day 1: Screening library
Module 4 Day 2: Optimizing panning
Module 4 Day 3: Rescreening gold binders
Module 4 Day 4: PCR of gold binding candidates
Module 4 Day 5: Student presentations
Module 4 Day 6: Sequence analysis

TA notes Module 4
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