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Day 2 - Chemistry Session: Protein Biosynthesis: Encoding Unnatural Amino Acids and Evolving in Cells - Lei Wang

"Proteins are involved in virtually every life process." 20 amino acids are encoded by 61 of the 64 codons. To generate interesting protein properties, there are two avenues: to increase the building blocks (i.e. genetically encode unnatural amino acids), and 2. to permute and recombine the existing AAs ...

DNA Synthesis Panel

J. D. Kittle - Coda genomics CODA (Computationally Optimized DNA Assembly), also incorporates its patented Translation Engineering TM into the design of the gene. John Danner - Codon Devices Mission: to eliminate construction as a barrier to synthetic biology (Drew's point #4). Key enabling technologies: CAD design environment -> multiplexed oligo synthesis & purification ...

"On a system for engineering genetic machines" - Drew Endy

This is Drew's Synthetic Biology Central Dogma: Recombinant DNA PCR Sequencing Synthesis Standardization Abstraction We've got the first three. Four is coming, and that means we need to talk about five and six. When synthesis becomes trivial, the barriers to innovation will be largely informational, dependant on our ability as a community to organize and ...

"Engineering nucleic acid-based molecular sensors for probing and programming cellular systems" - Christina Smolke

If we are interested in programming cellular behavior, then we need to be concerned with the network of biomolecules that interact to cause certain behaviors. DNA -> pre-mRNA->mRNA -> [export] -> [translation complex] -> proteins all fall under the auspices of "biomolecules." "We tend to think of the molecules we ...

"Cell-free gene expression in synthetic vesicles" - Vincent Noireaux

To build a cell you could start from the top down and reduce it's genome to the minimum size: ~400 genes. Or you could take a bottom-up approach and attempt to build a cell molecule-by-molecule with the "molecules of life." The idea is to develop an artificial cell as a programmable ...

"A novel genome vector for giant DNA assembly" - Mitsuhiro Itaya

Megacloning. The purpose of Itaya's work was push DNA cloning to the limit by cloning the entire 3.2 Mb genome of Synechocystis into B. subtilis. The work took several years, and is summarized at the Proceedings of the National Academy of Sciences, which also published this paper.

"Engineering artificial cytoskeletons" - Dyche Mullins

"The fundamental problem of cellular medicine: More is different" Consider a chemotactic cell. The cell's motility is derived from a motile actin network - constant polymerization and protrusion and debranching and depolymerization. Not enough is known about the "strokes" of the motility engine - that is to say, how ...

"DNA Origami" - Paul Rothemund

Richard Feynman once challenged the world to produce print the information in the encyclopedia britannica in a space no larger than that of a head of a pin. Science has since developed techniques that could potentially be used to accomplish this goal, but may be "impractical" for a variety ...

"Biologically inspired nanofabrication" - Dan Morse

Consider the silica structures that comprise the shells of diatoms. The precision of nanoscale architectual control of the silica shell fabrication process exceeds human technology. The fabrication process is very mild, by human standards: low temperatures, high yields, etc. The scale of production is enourmous - "gigatons!" Much ...

"Magnetite biominerlization in bacteria" - Arash Komeili

Thus begins the MATERIALS SESSION and ends the ENERGY SESSION. Magnetotactic bacteria have organelles called magnetosomes with which they can orient in (geo)magnetic fields. They prefer oxic-anoxic interfaces in their environment. By orienting against the geomagnetic field, they can control for lateral motion and search simply in a vertical ...

October 17th 2008
Tags: food No Comments

Cuchi Cuchi 1

Thai cocktail It's like an effervescent thai foot massage... For your tongue. It even taste a little gingery, but it lacks Ginger. A syrupy lime kick transitions into basilness, somehow ending with licorice. Yum! Caip They say it's been made impure with all the extra ingredients.. But it's like ...
August 1st 2008
Tags: Uncategorized No Comments

Eastern Standard Cocktails

Notes from my exploration of eastern standard's cocktail menu: Old Cuban: reminds me of a mojito + champagne - it's very tasty. Periodista: "rum for the intrepid reporter" - a little more than simply a mojito in a cocktail glass (with delicious ice crystals), the periodista is a citrusy drink with a ...
July 14th 2008
Tags: diybio No Comments

DIYbio 3 - Gel Electrophoresis

Thanks to everyone for a great meeting: Michael, Jason, Sophia, Benny, Topher, Ricardo, Alex, Alec, nublabs, and everyone else. Overview: DIYbio 2 & 3 were focused on gel electrophoresis - we started by researching all the amateur gel protocols we could find online (notably the MacGuyver Project and the MAKE protocol, ...
July 9th 2008
Tags: code No Comments

RubyU class 1 setup notes

My notes for getting all the prerequisites for Matt Knox's 1st RubyU class (hosted by Sermo) set up on my MacBook Pro (10.5).  Also see the friendfeed RubyU room. == getting prereqs installed == ruby > anvil:rubyclass macowell$ ruby -verison > ruby 1.8.6 (2008-03-03 patchlevel 114) [i686-darwin9.2.2] gems See http://www.rubygems.org/read/chapter/1 > anvil:rubyclass macowell$ gem environment > - ...
June 11th 2008
Tags: conference, diybio No Comments

DIYbio in 5 minutes - O’Reilly Ignite Boston 3

DIYbio in 5 minutes - O'Reilly ignite Boston from mac cowell on Vimeo. Here is an overview of DIYbio in 5 minutes - recorded at O'Reilly's Ignite Boston 2008.

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