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| Information pre-2010 can be found at [[SynBERC:SBWGLunchesArchive]]. | | Information pre-2010 can be found at [[SynBERC:SBWGLunchesArchive]]. |
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| ===Next meeting===
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| Spring 2009 Schedule
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| Invited Speaker
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| Date: May 13, 12-1pm, Star (Stata D463)
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| Speaker: Ty Thomson
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| We will have lunch with Ty Thomson (a SynBERC alum) who will describe a computational
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| system for modeling BioBrick parts.
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| Title: A framework for modeling BioBrick parts: Towards the predictable design of synthetic systems
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| The BioBricks framework was designed to facilitate the easy construction of a diverse array of
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| synthetic systems by optimizing the modularity and reusability of functional DNA parts. This is
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| made possible by a strong adherence to the principle of encapsulation in the design of the
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| individual BioBricks parts, wherein each component is meant to be functionally independent of the
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| system in which it is used. However, there is currently no standard in silico framework for
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| modeling systems composed of BioBrick parts that also offers this same level of functional
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| reusability. I will present a computational framework for modeling BioBrick parts that closely
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| mirrors the modularity of the parts themselves. This framework allows for the rapid computational
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| prototyping of synthetic systems, even by non-modelers, enabling researchers to design, explore,
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| test and optimize the behavior of synthetic systems prior to their actual construction in the
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| laboratory.
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| Ty Thomson sent the URL of the BioBrick framework info:
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| The URL is http://cellucidate.com/books/58389.
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|
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| SynBERC Student Exchange Talk
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| Date: May 1, 1-2 pm, 34-401 (Grier Room)
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| Speaker: Jonathan Goler
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| Abstract:
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| One of the necessary steps in the advancement of synthetic biology
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| is a method of producing sensors for myriad biological compounds. In-
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| Vitro selection (SELEX) of metabolites is a well-established method for
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| discovering RNA or DNA molecules that specifically bind an arbitrary
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| metabolite. We examines the dependence on Magnesium on a
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| selection for a biologically relevant molecule, para-Amino-Phenylalanine.
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| Since SELEX is typically carried out at 10 mM Mg2+, and cells typically
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| have approximately 1 mM Mg2+, we sought to know a) whether high-
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| affinity aptamers could be selected at such low, but biologically relevant
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| Magnesium levels; and b) whether structures derived from one magnesium
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| concentration are adaptable to different magnesium concentrations. Thus,
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| parallel selections were carried out at four magnesium concentrations(1,
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| 2.5, 5 and 10 mM). Each of the four selections succeeded in yielding pAF
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| binding RNA molecules, and reselection of isolates demonstrated that
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| molecules could be optimized for different magnesium concentrations, de-
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| pending on the requirements of the biological application.
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|
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| SynBERC Distinguished Lecture and Synthetic Biology Working Group Lunch Invited Speaker
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| Title: Acinetobacter baylyi ADP1 as a chassis for the directed evolution of genes and genomes
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| Date: April 22, 12-1pm, Kiva (Stata 449)
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| Speaker: Ichiro Matsumura
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| We will have lunch with Ichiro Matsumura as he speaks about a new model organism for synthetic
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| biology.
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| This talk will be webcast to the SynBERC research centers: Berkeley, Stanford, UCSF, and Harvard.
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| Abstract:
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| Synthetic biologists generally build upon the Escherichia coli chassis, which usually necessitates
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| a life of cloning. Acinetobacter baylyi sp. ADP1 offers two significant advantages over E. coli:
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| natural competence, and efficient homologous recombination. I will explain how these natural
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| advantages obviate cloning and streamline the directed evolution of genes and genomes. I will
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| also describe the engineering of a broad host range expression vector pBAV1K (Biobrick Accepting
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| Vector) that replicates and produces proteins in a wide variety of gram negative and gram positive
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| bacteria. These tools enable the facile laboratory evolution of genes and chromosomes, without
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| restriction digests or ligation reactions.
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| A video of the talk is available here: http://vimeo.com/4367036 (Thanks to Mac Cowell for filming
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| this.)
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|
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|
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| Talk: Adp1: A model organism for Synthetic Biology/TBA
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| Date April 15, 12-1pm, Kiva
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| Speaker: Jason Kelly
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|
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|
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| Talk: Protein domain construction and its relationship to assembly standards
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| Date: March 18, 12-1pm, 34-401B
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| Speaker: The discussion will be led by Tom Knight
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| Protein coding regions containing multiple domains. We will discuss the construction of
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| multi-domain proteins and possible replacements for current assembly strategies to make these
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| easier to build. The BBF RFC's for much of this discussion are already online here in RFC 11,
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| 13, and 14:
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| http://openwetware.org/wiki/The_BioBricks_Foundation:RFC
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| A draft version of BBF RFC 15, which uses a new family of parts to add new capabilities to the
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| existing BioBrick standard is available here:
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| http://openwetware.org/wiki/The_BioBricks_Foundation:BBFRFC15
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|
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|
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| Talk: Registry Discussion
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| Date: February 4th and 11th, 12-1pm, Kiva (Stata 449)
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| Speakers: Reshma Shetty, Meagan Lizarazo, Barry Canton, and Randy Rettberg.
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| Abstract:
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| The Registry has been presented as a "catalog" of biological parts. It has also been referred to as
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| a collection of poor quality parts. For several months, Reshma and Barry have been converting the
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| Registry into a better catalog and have been curating the parts. They will present this work.
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| Spring is the time of the year when many changes are made to the Registry and the iGEM
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| infrastructure.
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| Randy will describe some of those changes and ask for comments.
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| Finally, we have described a hierarchy of Systems -> Devices -> Parts. The Registry has Parts
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| but does not deal explicitly with Devices. We will present some of our thoughts on how devices
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| should be represented.
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| The presentations will be limited to allow for lots of discussion and suggestions.
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|
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| Invited Speaker: Peter Carr from MIT Media Lab (with Farren Isaacs, Bram Sterling, Harris Wang,
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| George Church, and Joseph Jacobson)
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| Talk: Genome Engineering and the Construction of New Genetic Codes
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| Date: 2/18/09, 12-1pm, G449
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| Abstract: Our capacity to engineer genetic material is moving beyond the level of single genes to
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| the scale of genomes. Still, our ability to paint effectively on a canvas as large as a genome is
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| modest, dwarfed by our growing ability to synthesize DNA, which is in turn dwarfed by our ability
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| to sequence.
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| We present the rE. coli project, a collaborative effort to re-engineer the genetic code of E.
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| coli strain MG1655. The goal of this work is to remove all instances of one type of codon (the
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| amber stop codon, i.e. TAG) from the genome, replacing them with a synonymous codon (ochre, TAA).
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| On a practical level, this strain will provide a plug-and-play opportunity for those advancing
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| work on non-natural amino acid incorporation. It will also be the first step towards generating
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| an "orthogonal" genetic code, i.e. defining an organism which is unable to make use of exogenous
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| genetic material. Microorganisms engineered with orthogonal genetic codes would be unable to
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| utilize antibiotic resistance genes from their environment. In a more distant envisioning, crops
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| with such a feature would be unable to cross with wild strains.
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| We will discuss current progress and challenges in engineering at this scale. In particular for
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| genome-scale design projects, one must consider the two broad categories of failure modes: the
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| foreseeable and the unforeseen. Potentially complex interactions between components (some of
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| questionable or unknown function) virtually guarantee that not all concerns can be accounted for
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| at the outset of a project. Robust design modules coupled with flexible troubleshooting
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| hierarchies are required—we will give examples of these principles applied to the rE. coli work.
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|
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| Special section:
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| The SBWG is invited to watch: “Hypothetical Risks, The Cambridge City Council hearings on DNA
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| experimentation in Cambridge.” in room 26-152, on 3/3, from 11:30-1 pm. Thanks to Natalie
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| Kuldell for arranging this.
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|
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| Invited Speaker: Nils Gilman from Monitor 360
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| Date: 12-1pm, Grier Room (34-401), 3/4
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| Talk: Computer Hacking: What can Garage Biotechnology Learn?
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| Abstract: The subject will be the diversity of computer hacking scenes today, how they got that
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| way, and what this may tell us about the possible futures of biohacking. The DIYbio community
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| is also invited.
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|
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| Summer/Fall 2008 Schedule: including the Synthetic Biology Lecture Series @ the Synthetic Biology Working Group Lunch
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|
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| *Invited Speakers: Mikhail Shapiro (MIT, Biological Engineering) and Vivek Murthy, MD, MBA (Harvard Medical School/Brigham and Women's Hospital)
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|
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| Talk: Epernicus founders reveal a new social networking site for scientists
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|
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| Abstract: *Epernicus** is a networking platform for scientists that was created by
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| researchers at MIT and Harvard. It helps scientists search efficiently for
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| specific expertise and people in their real world scientific networks.
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| Epernicus also makes it easy for researchers to learn about their colleagues
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| and to stay connected with fellow scientists in their current and past labs,
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| departments, and institution.
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|
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| Date: Wednesday, July 9th, 2008
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|
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| Time: 1:00-2:00 pm
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|
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| Location: 68-181
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|
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| *Invited Speaker: Andres Leschziner, Ph.D. (Harvard University, Molecular and Cellular Biology)
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|
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| Talk: Looking at chromatin remodeling using Three-Dimensional Electron Microscopy
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|
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| Abstract: Three-Dimensional Electron Microscopy (3D EM) has emerged as a
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| powerful technique for structural characterization. Near-atomic resolution
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| structures of macromolecular assemblies imaged as "single particles" (i.e.
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| in the absence of a crystalline array) are now being obtained. Arguably one
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| of 3D EM's most exciting prospects is its potential ability to visualize, at
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| high resolution and under physiological conditions, the conformational
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| flexibility central to the function of many macromolecules. I will discuss
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| the technique and some of the challenges we face to make this prospect a
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| reality and will illustrate this using examples from our work on the
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| ATP-dependent chromatin remodeling complex RSC.
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|
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| Date: Wednesday, July 23, 2008
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|
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| Time: 1:00-2:00 pm
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|
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| Location: 68-121
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|
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| *Invited Speaker: J. Keith Joung, M.D., Ph.D. (Harvard Medical School, Pathology; Massachusetts General Hospital, Center for Cancer Research)
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|
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| Talk: Engineering Zinc Finger Nucleases for Highly Efficient Genome Modification.
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|
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| Abstract: Zinc finger nucleases are a critical technology for synthetic biology since they can cut,
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| splice, or tweak genes with high efficiency in a variety of cell types including Drosophila, C.
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| elegans, plants, and humans. A bottleneck in the application of ZFN technology has been the generation
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| of highly specific engineered zinc-finger arrays. Dr. Joung's lab has recently described OPEN
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| (Oligomerized Pool ENgineering), a rapid, publicly available strategy for constructing multifinger
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| arrays, which is more effective than the previously published modular assembly method. Using OPEN, Dr.
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| Joung and colleagues have constructed 37 highly active ZFN pairs which induced targeted alterations
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| with high efficiencies (1%-50%) at 11 different target sites located within three endogenous human
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| genes (VEGF-A, HoxB13, and CFTR), an endogenous plant gene (tobacco SuRA), and a chromosomally
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| integrated EGFP reporter gene. OPEN provides an "open-source" method for rapidly engineering highly
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| active zinc-finger arrays, thereby enabling broader practice, development, and application of ZFN
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| technology for biological research and gene therapy.
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|
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| Date: Wednesday, November 5, 2008
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|
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| Time: 12:00-1:00 pm
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|
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| Location: Kiva Seminar Room 32-G449, Stata Center
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|
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| *Invited Speaker: Edward Boyden, Ph.D.
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|
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| Talk: Tools for Synthetic Neuroscience and Neurotechnology
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|
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| Abstract: Our brains and nervous systems mediate everything we perceive, feel, decide, and do--and
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| act as our ultimate interface to the world. An outstanding challenge for humanity is to understand
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| these neuromedia interfaces at a level of abstraction that enables us to engineer their
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| functions--repairing pathology, augmenting cognition, and revealing insights into the human
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| condition. The Synthetic Neurobiology group invents and applies tools to analyze and engineer brain
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| circuits in both humans and model systems. Our current neuroengineering focus is on devising
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| technologies for controlling the processing within specific neural circuit targets in the brain.
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| Many of these tools involve "optogenetic" components that sensitize neurons to being controlled
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| with light. We hope that this synthetic neurobiology approach to the brain will help us better
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| understand--and engineer improvements upon--the nature of human existence.
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|
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| Date: Wednesday, December 3rd, 2008
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|
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| Time: 1:00-2:00 pm
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|
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| Location: Kiva Seminar Room 32-G449, Stata Center
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|
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|
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| -------------------
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|
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|
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|
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|
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|
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|
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|
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|
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| Notes from prior Spring 2008 schedule:
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|
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| *[[SynBERC:MIT/Calendar/2008-4-2]]: 69th of restarted MIT SBWG lunch
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| **Wednesday 4/2 (1:00-2:00p EST), 32-D463, MIT
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|
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| *3/26 - cancel, spring break?
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| *4/2 - Jake Beal, follow up on spatial computing
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| *4/9 - held for SynBERC seminar with Dan Gibson
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| *4/16 - Justin Buck
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| *4/23 - open
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| *4/30 - open
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|
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| *Barry on Registry of Standard Biological Models
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|
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| ===Previous meetings===
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| {{hide|1=
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| *[[SynBERC:MIT/Calendar/2008-6-18]]: ??th of restarted MIT SBWG lunch
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| **Wednesday 6/18 (2:00-2:00p EST), 32-D463, MIT
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| *[[SynBERC:MIT/Calendar/2008-3-26]]: 69th of restarted MIT SBWG lunch
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| **Wednesday 3/26 (4:00-5:00p EST), 32-D463, MIT
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| *[[SynBERC:MIT/Calendar/2008-3-19]]: 68th of restarted MIT SBWG lunch
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| **Wednesday 3/19 (12:00-1:00p EST), 32-D463, MIT
| |
| *[[SynBERC:MIT/Calendar/2008-3-12]]: 67th of restarted MIT SBWG lunch
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| **Wednesday 3/12 (1:00-2:00p EST), 32-D463, MIT
| |
| *[[SynBERC:MIT/Calendar/2008-2-27]]: 66th of restarted MIT SBWG lunch
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| **Wednesday 2/27 (1:00-2:00p EST), 32-D463, MIT
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| *[[SynBERC:MIT/Calendar/2008-2-20]]: 65th of restarted MIT SBWG lunch
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| **Wednesday 2/20 (1:00-2:00p EST), 32-D463, MIT
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| *[[SynBERC:MIT/Calendar/2008-2-14]]: 64th of restarted MIT SBWG lunch
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| **Thursday 2/14 (1:00-2:00p EST), 68-180, MIT
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| *[[SynBERC:MIT/Calendar/2008-2-6]]: 63th of restarted MIT SBWG lunch
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| **Wednesday 2/6 (3:00-4:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
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| *[[SynBERC:MIT/Calendar/2008-1-23]]: 62th of restarted MIT SBWG lunch
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| **Wednesday 1/23 (1:00-2:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-1-16]]: 61th of restarted MIT SBWG lunch
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| **Wednesday 1/16 (1:00-2:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-1-9]]: 60th of restarted MIT SBWG lunch
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| **Wednesday 1/9 (11:00a-12:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
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| *[[SynBERC:MIT/Calendar/2007-12-19]]: 59th of restarted MIT SBWG lunch
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| **Wednesday 12/19 (11:00a-12:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-12-12]]: 58th of restarted MIT SBWG lunch
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| **Wednesday 12/12 (11:00a-12:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
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| *[[SynBERC:MIT/Calendar/2007-12-5]]: 57th of restarted MIT SBWG lunch
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| **Wednesday 11/28 (11:00a-12:00p EST), 68-181, MIT
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| *[[SynBERC:MIT/Calendar/2007-11-28]]: 56th of restarted MIT SBWG lunch
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| **Wednesday 11/28 (11:00a-12:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-11-14]]: 55th of restarted MIT SBWG lunch
| |
| **Wednesday 11/14 (11:00a-12:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-11-7]]: 54th of restarted MIT SBWG lunch
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| **Wednesday 11/7 (11:00a-12:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-10-31]]: 53th of restarted MIT SBWG lunch
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| **Wednesday 10/31 (11:00a-12:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-10-24]]: 52th of restarted MIT SBWG lunch
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| **Wednesday 10/24 (11:00a-12:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-10-17]]: 51th of restarted MIT SBWG lunch
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| **Wednesday 10/17 (11:00a-12:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-10-10]]: 50th of restarted MIT SBWG lunch
| |
| **Wednesday 10/10 (11:00-12:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-10-3]]: 49th of restarted MIT SBWG lunch
| |
| **Wednesday 10/3 (11:00-12:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-9-26]]: 48th of restarted MIT SBWG lunch
| |
| **Wednesday 9/26 (12:00-1:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-9-19]]: 47th of restarted MIT SBWG lunch
| |
| **Wednesday 9/19 (12:00-1:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-9-12]]: 46th of restarted MIT SBWG lunch
| |
| **Wednesday 9/12 (12:00-1:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-9-5]]: 45th of restarted MIT SBWG lunch
| |
| **Wednesday 9/5 (12:00-1:00p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-8-29]]: 44th of restarted MIT SBWG lunch
| |
| **Wednesday 8/29 (12:30-1:30p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-8-22]]: 43th of restarted MIT SBWG lunch
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| **Wednesday 8/22 (12:30-1:30p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-8-15]]: 42th of restarted MIT SBWG lunch
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| **Wednesday 8/15 (12:30-1:30p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-8-8]]: 41th of restarted MIT SBWG lunch
| |
| **Wednesday 8/8 (12:30-1:30p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
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| **'''Contains notes and references for the BioBricks parts wanted list'''
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| *[[SynBERC:MIT/Calendar/2007-8-1]]: 40th of restarted MIT SBWG lunch
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| **Wednesday 8/1 (12:30-1:30p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-7-25]]: 39th of restarted MIT SBWG lunch
| |
| **Wednesday 7/25 (12:30-1:30p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
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| **'''Contains notes and references from the BioBricks tutorial'''
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| *[[SynBERC:MIT/Calendar/2007-7-18]]: 38th of restarted MIT SBWG lunch
| |
| **Wednesday 7/18 (12:30-1:30p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-7-11]]: 37th of restarted MIT SBWG lunch
| |
| **Wednesday 7/11 (12:30-1:30p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-6-20]]: 36th of restarted MIT SBWG lunch
| |
| **Wednesday 6/20 (12:30-1:30p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-6-13]]: 35th of restarted MIT SBWG lunch
| |
| **Wednesday 6/13 (12:30-1:30p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-6-6]]: 34th of restarted MIT SBWG lunch
| |
| **Wednesday 6/6 (12:30-1:30p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-5-30]]: 33th of restarted MIT SBWG lunch
| |
| **Wednesday 5/30 (12:30-1:30p EST), 68-181, MIT
| |
| *[[SynBERC:MIT/Calendar/2007-5-22]]: 32th of restarted MIT SBWG lunch
| |
| **Tuesday 5/22 (12-1p EST), 56-614, MIT
| |
| *[[SynBERC:MIT/Calendar/2007-5-15]]: 31th of restarted MIT SBWG lunch
| |
| **Tuesday 5/15 (12-1p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-5-8]]: 30th of restarted MIT SBWG lunch
| |
| **Tuesday 5/8 (12-1p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4D/D463.gif D463], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-5-1]]: 29th of restarted MIT SBWG lunch
| |
| **Tuesday 5/1 (12-1p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:Seminar series/Remy Chait]]: 28th of restarted MIT SBWG lunch
| |
| **Tuesday 4/24 (12-1p EST), [http://whereis.mit.edu/map-jpg?mapterms=68&mapsearch=go 68]-181, MIT
| |
| *[[SynBERC:MIT/Calendar/2007-4-17]]: 27th of restarted MIT SBWG lunch
| |
| **Tuesday 4/17 (12-1p EST), Meet at [http://maps.google.com/maps?f=q&hl=en&q=320+Charles+St,+Cambridge,+Massachusetts+02141&sll=37.0625,-95.677068&sspn=38.638819,64.335938&layer=&ie=UTF8&z=16&ll=42.368532,-71.0865&spn=0.008815,0.015707&om=1&iwloc=addr 320 Charles St Cambridge, MA 02141] at 12pm
| |
| *[[SynBERC:MIT/Calendar/2007-4-10]]: 26th of restarted MIT SBWG lunch
| |
| **Tuesday 4/10 (12-1p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-4-3]]: 25th of restarted MIT SBWG lunch
| |
| **Tuesday 4/3 (12-1p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-3-28]]: 24th of restarted MIT SBWG lunch
| |
| **Wednesday 3/28 (12-1p EST), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-3-20]]: 23th of restarted MIT SBWG lunch
| |
| **Tuesday 3/20 (12-1p), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-3-13]]: 22th of restarted MIT SBWG lunch
| |
| **Tuesday 3/13 (12-1p), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-3-6]]: 21th of restarted MIT SBWG lunch
| |
| **Tuesday 3/6 (12-1p), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-2-27]]: 20th of restarted MIT SBWG lunch
| |
| **Tuesday 2/27 (12-1p), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-2-13]]: 19th of restarted MIT SBWG lunch
| |
| **Tuesday 2/13 (12-1p), 68-181, MIT
| |
| *[[SynBERC:MIT/Calendar/2007-2-6]]: 18th of restarted MIT SBWG lunch
| |
| **Tuesday 2/6 (12-1p), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-1-31]]: 17th of restarted MIT SBWG lunch
| |
| **Wednesday 1/31 (1-2p), [http://whereis.mit.edu/map-jpg?mapterms=32&mapsearch=go 32]-[http://www.csail.mit.edu/resources/maps/4G/G449.gif G449], MIT
| |
| *[[SynBERC:MIT/Calendar/2007-1-24]]: 16th of restarted MIT SBWG lunch
| |
| **Wednesday 1/24 (1-2p), 56-614, MIT
| |
| *[[SynBERC:MIT/Calendar/2007-1-17]]: 15th of restarted MIT SBWG lunch
| |
| **Wednesday 1/17 (1-2p), 56-614, MIT
| |
| *[[SynBERC:MIT/Calendar/2007-1-10]]: 14th of restarted MIT SBWG lunch
| |
| **Wednesday 1/10 (1-2p), 32-G449, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-12-20]]: 13th of restarted MIT SBWG lunch
| |
| **Wednesday 12/20 (1-2p), 68-180, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-12-13]]: 12th of restarted MIT SBWG lunch
| |
| **Wednesday 12/13 (1-2p), 68-180, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-12-6]]: 11th of restarted MIT SBWG lunch
| |
| **Wednesday 12/06 (1-2p), 68-180, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-11-29]]: 10th of restarted MIT SBWG lunch
| |
| **Wednesday 11/29 (1-2p), 68-180, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-11-15]]: 9th of restarted MIT SBWG lunch
| |
| **Wednesday 11/15 (1-2p), 68-180, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-11-08]]: 8th of restarted MIT SBWG lunch
| |
| **Wednesday 11/08 (1-2p), 68-180, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-11-01]]: 7th of restarted MIT SBWG lunch
| |
| **Wednesday 11/01 (1-2p), 32-G449, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-10-25]]: 6th of restarted MIT SBWG lunch
| |
| **Wednesday 10/25 (1-2p), 32-G449, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-10-18]]: 5th of restarted MIT SBWG lunch
| |
| **Wednesday 10/18 (1-2p), 68-180, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-10-11]]: 4th of restarted MIT SBWG lunch
| |
| **Wednesday 10/11 (1-2p), 32-G449 (Kiva conference room), MIT
| |
| *[[SynBERC:MIT/Calendar/2006-10-4]]: 3rd of restarted MIT SBWG lunch
| |
| **Wednesday 10/4 (1-2p), 68-180, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-9-27]]: 2nd of restarted MIT SBWG lunch
| |
| **Wednesday 9/27 (1-2p), 32-D463, MIT
| |
| *[[SynBERC:MIT/Calendar/2006-9-20]]: 1st of restarted MIT SBWG lunch
| |
| **Wednesday 9/20 (1-2p), 32-G449
| |
| **Please feel free to add yourself to the agenda.
| |
| *[[SynBERC:MIT/Calendar/2006-8-30]]: Kickoff Meeting @ MIT
| |
| **Wednesday 8/30 (4-5p), 68-574 or immediately local surrogate
| |
| }}
| |
|
| |
| ==Proposed topics==
| |
| Past and present research topics for synthetic biology working group lunches. Please add to the list.
| |
|
| |
| #Electronics device families (introduction by TK) - [[SynBERC:MIT/Calendar/2006-9-27]]
| |
| #Abstraction hierarchies
| |
| ##Parts -> Devices -> Systems
| |
| ##Biological layer model (AC)
| |
| #'''DEVICES''': Composability? Device family specification? Interfaces within families? Interfaces across families? Eventually parts datasheet? Eventually standards?
| |
| ##Transcriptional device families (RS and CAF) - [[SynBERC:MIT/Calendar/2006-10-4]], [[SynBERC:MIT/Calendar/2006-10-11]]
| |
| ##Post-translational device families (SS) - [[SynBERC:MIT/Calendar/2007-2-13]]
| |
| ##Biosynthetic device families (KJP lab) - [[SynBERC:MIT/Calendar/2006-10-18]], [[SynBERC:MIT/Calendar/2006-10-25]]
| |
| ##Ribozyme device families (AC) - [[SynBERC:MIT/Calendar/2007-1-10]], [[SynBERC:MIT/Calendar/2007-1-17]] and [[SynBERC:MIT/Calendar/2007-1-24]] and [[SynBERC:MIT/Calendar/2007-3-28]]
| |
| ##Translation device families?
| |
| #'''PARTS''': [[SynBERC:MIT/Calendar/2007-2-6]]
| |
| ##Terminators
| |
| ##Coding regions
| |
| ##RBSs
| |
| ##Promoters
| |
| ##Composability and characterization - [[SynBERC:MIT/Calendar/2006-11-01]]
| |
| #'''CHASSIS''': Why do we want different kinds? What kinds? What are the simplest systems that work?
| |
| ##Minimal chassis
| |
| ##Mesoplasma florum - [[SynBERC:MIT/Calendar/2006-12-13]]
| |
| ##E. coli standard strain and rE. coli - [[SynBERC:MIT/Calendar/2006-12-6]]
| |
| ##Yeast
| |
| ##Power supply - [[SynBERC:MIT/Calendar/2006-11-15]]
| |
| ##Vectors - [[SynBERC:MIT/Calendar/2007-1-31]]
| |
| #Synthesis technologies
| |
| ##What is state of the art?
| |
| ##What are the good ideas?
| |
| ##How do we get more investment?
| |
| ##Can the fabs constrain what people synthesize?
| |
| #What does the CAD tool look like? - [[SynBERC:MIT/Calendar/2007-7-18]], [[SynBERC:MIT/Calendar/2007-8-1]]
| |
| #Human practice
| |
| #Differentiation and cell to cell communication. Development. Programmed pattern formation. (Arthur Lander, Radhika)
| |
| #[[Synthetic Biology:BioBricks/Standardization|Standards]] (also see talk page)
| |
| #Load issues
| |
| #*What demands on the chassis are of most concern to us? Replication, transcription, [[Endy:Translation demand|translation]], Enzyme activity?
| |
| #**Are we regularly placing high demands on the chassis with our existing systems?
| |
| #*What chassis responses to an applied demand are of relevance? Growth rate, protein synthesis capacity?
| |
| #**Can we specify a threshold demand level above which the chassis response is so severe as to render the our engineered systems inoperable?
| |
| #Selection against our systems [[SynBERC:MIT/Calendar/2006-12-20]]
| |
| ##e.g. IS elements are showing up in our devices!
| |
| #Statistics of codon pairs (UC Irvine folks)
| |
| #iGEM 2010 - [[SynBERC:MIT/Calendar/2006-11-08]]
| |
| #Registry 2.0 - [[SynBERC:MIT/Calendar/2007-6-20]]
| |
| #Publishing (with CS on Oct 20) - held separately
| |
| #Controlled transcriptional termination as an implementation for logic - Chris Anderson
| |
| #Designing enzymatic reactions by splitting catalytic activity and substrate specificity potentially by scaffolds - John Dueber? ask Adam Arkin for someone to talk about this
| |
| #What is the obvious list of things to do?
| |
| ##Parts characterization
| |
| ##How do we get basic tasks done?
| |
| #Experience with different parts: RBSs, promoters, terminators - Jen? Chris Anderson? Curt and Hal Alper
| |
| #Web of registries - Randy
| |
| #Repetitive sequences and potential for recombination - ask Graham Walker, someone in Philadelphia
| |
| #Registry of models - Barry and Vincent
| |
| #Bacterial counter and how you implement it - Tom or Gerry - [[SynBERC:MIT/Calendar/2007-5-30]]
| |
| #How do I get a computer inside my cell? - Tom
| |
| #Human practices - Michael Rossi
| |
| #Writing DNA - Maia, Farren?, Church lab, Adam Arkin, Sasha and polony sequencing - [[SynBERC:MIT/Calendar/2007-4-3]]
| |
| #Noncoding RNAs - Ron Breaker
| |
| #Materials - Angie Belcher, Julie Norville - [[SynBERC:MIT/Calendar/2007-5-8]]
| |
| #Education in SB - Natalie and Scot and Austin and Michael and Shawn? - [[SynBERC:MIT/Calendar/2007-3-20]], [[SynBERC:MIT/Calendar/2007-5-22]]
| |
| ##Curriculum
| |
| ##Workshop implementation
| |
| ##Materials
| |
| ##Bootcamp
| |
| #Security - are we ok with the current investments in biotechnology? - Drew, Gautam? Phil Sharp and Gerry Fink and Jonathan King and Noam Chomsky and Ed Hammond - [[SynBERC:MIT/Calendar/2007-6-6]], [[SynBERC:MIT/Calendar/2007-6-13]]
| |
| #*Must act in the absence of perfect knowledge
| |
| #Impact of big pharma and big ag and big energy on our field
| |
| #Inteins and Fran Perler from NEB - [[SynBERC:MIT/Calendar/2007-4-10]]
| |
| #Brian Baynes and Codon Devices - future of DNA synthesis technology
| |
| #Ownership, sharing and innovation - [[SynBERC:MIT/Calendar/2007-5-1]], [[SynBERC:MIT/Calendar/2007-9-26]]
| |
| ##IP around DNA fabrication technology (synthesis and automated assembly)
| |
| ##How do we incent contributions? i.e. documentation of parts in the Registry
| |
| ##Historical examples around IP
| |
| ##SynBERC OSI model
| |
| ##BBF work
| |
| #Bioenergy - [[SynBERC:MIT/Calendar/2007-5-15]]
| |
| #Please add your topic to the list.
| |
|
| |
| ==Room locations for Spring==
| |
| Usually 32-D463 except for the following dates
| |
|
| |
| *May 7 - 68-180
| |
| *May 28 - no room booked
| |