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Intro:
http://herocoli.com/
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DateWeekClassInstructorsExperimental HWHardwareWetwareVideos?
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Module 1SYN BIO BOOT CAMP
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September 131George Church, Megan Palmer, David KongBuild hardwarepower supply, transilluminator (blue LED), pcr, electroporation, centrifuge...MAKE INTEGRATED THING
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September 202Bio DesignGeorge ChurchPCR from a colony / electrophersis (part preparation)
1. cutting genes from a plasmid, run out on a gel and see sizes
-cutting a gene, put it into another plasmid, see some fluorescence? Rolling circle amplification?		thermocycler / heating block, gel electrophoresis, transilluminator; spectrophotometer: measure DNA concentrationStarting plasmid (with indigo?), restriction enzymes, Carolina stain? gel extraction kit?
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September 273Next generation Synthesis Joseph JacobsonDNA assembly (indigo? blue of blue collar or GFP to BFP/CFP) - 0. primer design 1. PCR from input plasmid to generate gblock 2. modified golden gate to build larger constructthermocycler, gel electrophoresis, transilluminator, electroporation, centrifugeOligos, polymerase, restriction enzymes...BUY DNA CENTRALLY AND DISTRIBUTE OLIGOScomprehensive library of 5mers that you ligated...
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October 44Bio Production Patrick Boyle(indigo /lycopene?) Assays from ginkgo? Measure growth curve for E. Coli; put two genes together and co-express? Build a simple reporter, like a licopene production, look at a simple geneelectroporation, spectrophotometer, turbidity meter? (plating?) Amino? SynbiotaSucrose gel extraction protocol (nature methods) Bellot et al.
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October 115Biomolecule Sensors Vatsan Raman(indigo /lycopene?)

What is the sensor output measurement? color independent sensor...color too specialized. Connect with colormetric or fluorescence? Vatsan sends Manu a sample or a fold scope. Design, MUST BUILD. Sensors as a circuit entity or as a way to turn something on or off...have 3 cell types mixed together, pull out the winner? Sensor as a control device? Split GFP as a potential sensor? They make one protein and in a time dependent way turn one or other off...sensors are control elements...add one more plasmid that expresses the sensor to the existing two....growth curves for sensor calibration?		Fold Scope to image bio sensor??? Do long exposure with mobile?Zack sun Synvitro Bio
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October 186Synthetic Minimal CellsKate AdamalaGlucose sensors from paper-based IVT

Make in cell-free something toxic in cells (e.g., could only be made in an artificial cell)

Double-emulsion microfluidic systems

Make you own cell-free extract? put it on paper and share...mail IVT to each other and compare. Send it by regular mail. Worked in exterme enviroments, it worked everywhere!!!		Microfluidics intro here (3DP, laser cut), MAKE IVT WITH PAPER CENTRIFUGE, centrifuge and liquid nitrogen!!! dry ice ethanol bath for dry ice bathJim Collins / freeze-dried IVT? Zika sensor? Buy from MicroArray? 9 uL IVT, 3 uL plasmid. IVT will survive for a few days in fridge. Last time sent 75 uL per site, good for 100 uL of reaction mix...Kate, can she make it in her lab?*make bio summit logo with paper?
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October 257Gut Microbiome David KongGut on a Chip...conjugation experiment? A sender-receiver experiment (one population that has retrons, but when you mix they all fluoresce?)
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Module 2BIO FABRICATION AND IMAGING
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November 183D Bio Printing Fio OmenettoSilk printing, Embed silk in gel? Do coatings / gratings?Danny will teach us to build bio printers?
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November 89Synthetic Development Bio Nina TandonMake a mouse heart, image silk, mouse heart?Build low-cost fluorescence scope? centrifuge, shaker...
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November 1510Imaging 1: Principles of FISSEQ + Expansion MicroscopyEvan Daugharty and Boyden LabBe really tough about asking does it work every day? How robust is it? Build a washing device on day 1...Image microtubulesPrinciples of FISSEQ + Expansion Microscopy; Paper microscope / LEDFei Chen
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November 22BREAK (Thanksgiving)-
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November 2911Imaging 2: DNA PaintWilliam Shih / Peng Yin and Boyden Lab?Image what you bio printing using expansion microscopy...DNA Paint -> short oligos, bind transiently, depending on binding events get flashing with TIRF. Peng has DIY TIRF? $10k. Expansion microscopy + DNA Paint. Expansion microscopy with foldscope?continuous washing system? peristaltic pump?4 day protocol, Faster with existing immunohistochemistry samples
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Module 3DARWIN FOR 2 WEEKS
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December 612Gene DrivesKevin EsveltWhite / Red colonies, easy to distinguish. Do one cross. Measure how close to 100% it is. Concepts of escape, reversal. Can get most concepts. RESPONSIBLE SCIENCE.Electroporator, transilluminator
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December 1313Genome Engineering John Glass, George ChurchLambda Red? CRISPR experiment? Retron (RNA-based) | traffic light reporter with yeast? prokaryote / eukaryote option? DO MAGE. Do electroporation, possible chemically competent cells, ELECTROPORATION. A sensor strain that Vatsan has engineered. Select with GFP and screen with the color. Grow up the colony it's colored.Electroporator...centrifuge...Lambda Red in bacteria? CRISPR in yeast(what's the point of genome engineering in bacteria?) John and george talk about therapeutic uses?
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EEnd module 3
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January 201814Final presentations
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*Thomas / JOGL?crispr based modification of something in yeast post conjugation in e. coli
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pre-crispr life, what would we have done.
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