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  test and optimize the behavior of synthetic systems prior to their actual construction in the   
  test and optimize the behavior of synthetic systems prior to their actual construction in the   
  laboratory.  
  laboratory.  
Ty Thomson sent the URL of the BioBrick framework info:
The URL is http://cellucidate.com/books/58389.


  SynBERC Student Exchange Talk
  SynBERC Student Exchange Talk

Revision as of 08:27, 20 May 2009

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SynBERC Research @ MIT

Short summaries of MIT SynBERC research projects.

Lab Video Tours

MIT lab video tours

Synthetic Biology Working Group lunches

Overview

Synthetic Biology Working Group lunches are an opportunity for anyone in the Boston-area who is interested in synthetic biology to get together and discuss current issues and topics in the field. Each lunch discussion is led by someone (selected at the end of lunch the previous week) and focuses on a particular topic. The style of the lunch is really meant to be a discussion rather than a presentation. Therefore, discussion leaders frequently give a chalk talk or only have a handful of slides to help structure discussion.

  • New Program for Summer/Fall 2008: Within the context of the standard lunches we will invite a group of selected speakers to provide 30 minute talks/30 minute discussions, on areas of emerging or historical importance for Synthetic Biology as part of our Synthetic Biology Lecture Series. To nominate a speaker for an invited talk, email Julie Norville (norville.at.obvious.edu.)

Announcements regarding Synthetic Biology Working Group lunches are sent to synthbio AT mit. To join the mailing list, go here or contact Julie Norville. All are welcome to attend.

If you've previously led a discussion at SBWG lunch, please consider posting your slides or notes at the appropriate link below.

The spring schedule will likely be Wed at noon. Usually in 32-D463

Next meeting

Spring 2009 Schedule 

Invited Speaker
Date: May 13, 12-1pm, Star (Stata D463) 
Speaker: Ty Thomson
We will have lunch with Ty Thomson (a SynBERC alum) who will describe a computational 
system for modeling BioBrick parts.
Title: A framework for modeling BioBrick parts: Towards the predictable design of synthetic systems
The BioBricks framework was designed to facilitate the easy construction of a diverse array of 
synthetic systems by optimizing the modularity and reusability of functional DNA parts.  This is 
made possible by a strong adherence to the principle of encapsulation in the design of the 
individual BioBricks parts, wherein each component is meant to be functionally independent of the 
system in which it is used.  However, there is currently no standard in silico framework for 
modeling systems composed of BioBrick parts that also offers this same level of functional 
reusability.  I will present a computational framework for modeling BioBrick parts that closely 
mirrors the modularity of the parts themselves.  This framework allows for the rapid computational 
prototyping of synthetic systems, even by non-modelers, enabling researchers to design, explore, 
test and optimize the behavior of synthetic systems prior to their actual construction in the  
laboratory. 
Ty Thomson sent the URL of the BioBrick framework info: 
The URL is http://cellucidate.com/books/58389. 

SynBERC Student Exchange Talk
Date: May 1, 1-2 pm, 34-401 (Grier Room)
Speaker: Jonathan Goler
Abstract: 
One of the necessary steps in the advancement of synthetic biology 
is a method of producing sensors for myriad biological compounds. In- 
Vitro selection (SELEX) of metabolites is a well-established method for 
discovering RNA or DNA molecules that specifically bind an arbitrary 
metabolite. We examines the dependence on Magnesium on a 
selection for a biologically relevant molecule, para-Amino-Phenylalanine. 
Since SELEX is typically carried out at 10 mM Mg2+, and cells typically 
have approximately 1 mM Mg2+, we sought to know a) whether high- 
affinity aptamers could be selected at such low, but biologically relevant 
Magnesium levels; and b) whether structures derived from one magnesium 
concentration are adaptable to different magnesium concentrations. Thus, 
parallel selections were carried out at four magnesium concentrations(1, 
2.5, 5 and 10 mM). Each of the four selections succeeded in yielding pAF 
binding RNA molecules, and reselection of isolates demonstrated that 
molecules could be optimized for different magnesium concentrations, de- 
pending on the requirements of the biological application. 

SynBERC Distinguished Lecture and Synthetic Biology Working Group Lunch Invited Speaker
Title: Acinetobacter baylyi ADP1 as a chassis for the directed evolution of genes and genomes
Date: April 22, 12-1pm, Kiva (Stata 449) 
Speaker: Ichiro Matsumura 
We will have lunch with Ichiro Matsumura as he speaks about a new model organism for synthetic
biology.
This talk will be webcast to the SynBERC research centers: Berkeley, Stanford, UCSF, and Harvard.
Abstract: 
Synthetic biologists generally build upon the Escherichia coli chassis, which usually necessitates
a life of cloning. Acinetobacter baylyi sp. ADP1 offers two significant advantages over E. coli:
natural competence, and efficient homologous recombination. I will explain how these natural 
advantages obviate cloning and streamline the directed evolution of genes and genomes.  I will 
also describe the engineering of a broad host range expression vector pBAV1K (Biobrick Accepting 
Vector) that replicates and produces proteins in a wide variety of gram negative and gram positive 
bacteria.  These tools enable the facile laboratory evolution of genes and chromosomes, without  
restriction digests or ligation reactions.
A video of the talk is available here: http://vimeo.com/4367036 (Thanks to Mac Cowell for filming  
this.)



Talk: Adp1: A model organism for Synthetic Biology/TBA
Date April 15, 12-1pm, Kiva
Speaker: Jason Kelly 


Talk: Protein domain construction and its relationship to assembly standards
Date: March 18, 12-1pm, 34-401B
Speaker: The discussion will be led by Tom Knight
Protein coding regions containing multiple domains.  We will discuss the construction of 
multi-domain  proteins and possible replacements for current assembly strategies to make these
easier to build.  The BBF RFC's for much of this discussion are already online here  in RFC 11,
13, and 14:
http://openwetware.org/wiki/The_BioBricks_Foundation:RFC 
A draft version of BBF RFC 15, which uses a new family of parts to add new capabilities to the  
existing BioBrick standard is available here:
http://openwetware.org/wiki/The_BioBricks_Foundation:BBFRFC15



Talk: Registry Discussion
Date: February 4th and 11th, 12-1pm, Kiva (Stata 449)
Speakers: Reshma Shetty, Meagan Lizarazo, Barry Canton, and Randy Rettberg.
Abstract:
The Registry has been presented as a "catalog" of biological parts. It has also been referred to as 
a collection of poor quality parts. For several months, Reshma and Barry have been converting the 
Registry into a better catalog and have been curating the parts. They will present this work.
Spring is the time of the year when many changes are made to the Registry and the iGEM 
infrastructure.
Randy will describe some of those changes and ask for comments.
Finally, we have described a hierarchy of Systems -> Devices -> Parts.  The Registry has Parts
but does not deal explicitly with Devices. We will present some of our thoughts on how devices 
should be represented.
The presentations will be limited to allow for lots of discussion and suggestions.

Invited Speaker: Peter Carr from MIT Media Lab (with Farren Isaacs, Bram Sterling, Harris Wang, 
George Church, and Joseph Jacobson)
Talk: Genome Engineering and the Construction of New Genetic Codes
Date:  2/18/09, 12-1pm, G449
Abstract: Our capacity to engineer genetic material is moving beyond the level of single genes to
the scale of genomes. Still, our ability to paint effectively on a canvas as large as a genome is
modest, dwarfed by our growing ability to synthesize DNA, which is in turn dwarfed by our ability 
to sequence.
We present the rE. coli project, a collaborative effort to re-engineer the genetic code of E.
coli strain MG1655. The goal of this work is to remove all instances of one type of codon (the 
amber stop codon, i.e. TAG) from the genome, replacing them with a synonymous codon (ochre, TAA). 
On a practical level, this strain will provide a plug-and-play opportunity for those advancing 
work on non-natural amino acid incorporation. It will also be the first step towards generating 
an "orthogonal" genetic code, i.e. defining an organism which is unable to make use of exogenous 
genetic material. Microorganisms engineered with orthogonal genetic codes would be unable to 
utilize antibiotic resistance genes from their environment. In a more distant envisioning, crops 
with such a feature would be unable to cross with wild strains.
We will discuss current progress and challenges in engineering at this scale. In particular for 
genome-scale design projects, one must consider the two broad categories of failure modes: the  
foreseeable and the unforeseen. Potentially complex interactions between components (some of  
questionable or unknown function) virtually guarantee that not all concerns can be accounted for 
at the outset of a project. Robust design modules coupled with flexible troubleshooting 
hierarchies are required—we will give examples of these principles applied to the rE. coli work.

Special section: 
The SBWG is invited to watch: “Hypothetical Risks, The Cambridge City Council hearings on DNA 
experimentation in Cambridge.” in room 26-152, on 3/3, from 11:30-1 pm.  Thanks to Natalie 
Kuldell for arranging this.

Invited Speaker: Nils Gilman from Monitor 360
Date: 12-1pm, Grier Room (34-401), 3/4
Talk: Computer Hacking: What can Garage Biotechnology Learn?  
Abstract: The subject will be the diversity of computer hacking scenes today, how they got that 
way, and what this may tell us about the possible futures of biohacking.  The DIYbio community 
is also invited.

Summer/Fall 2008 Schedule: including the Synthetic Biology Lecture Series @ the Synthetic Biology Working Group Lunch

  • Invited Speakers: Mikhail Shapiro (MIT, Biological Engineering) and Vivek Murthy, MD, MBA (Harvard Medical School/Brigham and Women's Hospital)
Talk: Epernicus founders reveal a new social networking site for scientists

Abstract: *Epernicus** is a networking platform for scientists that was created by
researchers at MIT and Harvard.  It helps scientists search efficiently for
specific expertise and people in their real world scientific networks.
Epernicus also makes it easy for researchers to learn about their colleagues 
and to stay connected with fellow scientists in their current and past labs,
departments, and institution.

Date: Wednesday, July 9th, 2008

Time: 1:00-2:00 pm

Location: 68-181
  • Invited Speaker: Andres Leschziner, Ph.D. (Harvard University, Molecular and Cellular Biology)
Talk: Looking at chromatin remodeling using Three-Dimensional Electron Microscopy

Abstract: Three-Dimensional Electron Microscopy (3D EM) has emerged as a 
powerful technique for structural characterization. Near-atomic resolution 
structures of macromolecular assemblies imaged as "single particles" (i.e. 
in the absence of a crystalline array) are now being obtained. Arguably one 
of 3D EM's most exciting prospects is its potential ability to visualize, at 
high resolution and under physiological conditions, the conformational 
flexibility central to the function of many macromolecules. I will discuss 
the technique and some of the challenges we face to make this prospect a 
reality and will illustrate this using examples from our work on the 
ATP-dependent chromatin remodeling complex RSC.

Date: Wednesday, July 23, 2008

Time: 1:00-2:00 pm

Location:  68-121
  • Invited Speaker: J. Keith Joung, M.D., Ph.D. (Harvard Medical School, Pathology; Massachusetts General Hospital, Center for Cancer Research)
Talk: Engineering Zinc Finger Nucleases for Highly Efficient Genome Modification.

Abstract: Zinc finger nucleases are a critical technology for synthetic biology since they can cut, 
splice, or tweak genes with high efficiency in a variety of cell types including Drosophila, C. 
elegans, plants, and humans. A bottleneck in the application of ZFN technology has been the generation 
of highly specific engineered zinc-finger arrays. Dr. Joung's lab has recently described OPEN 
(Oligomerized Pool ENgineering), a rapid, publicly available strategy for constructing multifinger 
arrays, which is more effective than the previously published modular assembly method. Using OPEN, Dr. 
Joung and colleagues have constructed 37 highly active ZFN pairs which induced targeted alterations 
with high efficiencies (1%-50%) at 11 different target sites located within three endogenous human 
genes (VEGF-A, HoxB13, and CFTR), an endogenous plant gene (tobacco SuRA), and a chromosomally 
integrated EGFP reporter gene. OPEN provides an "open-source" method for rapidly engineering highly 
active zinc-finger arrays, thereby enabling broader practice, development, and application of ZFN 
technology for biological research and gene therapy.

Date: Wednesday, November 5, 2008

Time: 12:00-1:00 pm

Location:  Kiva Seminar Room 32-G449, Stata Center
  • Invited Speaker: Edward Boyden, Ph.D.
Talk: Tools for Synthetic Neuroscience and Neurotechnology 

Abstract: Our brains and nervous systems mediate everything we perceive, feel, decide, and do--and 
act as our ultimate interface to the world. An outstanding challenge for humanity is to understand 
these neuromedia interfaces at a level of abstraction that enables us to engineer their 
functions--repairing pathology, augmenting cognition, and revealing insights into the human 
condition. The Synthetic Neurobiology group invents and applies tools to analyze and engineer brain  
circuits in both humans and model systems. Our current neuroengineering focus is on devising 
technologies for controlling the processing within specific neural circuit targets in the brain. 
Many of these tools involve "optogenetic" components that sensitize neurons to being controlled 
with light. We hope that this synthetic neurobiology approach to the brain will help us better 
understand--and engineer improvements upon--the nature of human existence. 

Date: Wednesday, December 3rd, 2008

Time: 1:00-2:00 pm

Location: Kiva Seminar Room 32-G449, Stata Center






Notes from prior Spring 2008 schedule:

  • 3/26 - cancel, spring break?
  • 4/2 - Jake Beal, follow up on spatial computing
  • 4/9 - held for SynBERC seminar with Dan Gibson
  • 4/16 - Justin Buck
  • 4/23 - open
  • 4/30 - open
  • Barry on Registry of Standard Biological Models

Previous meetings

 

Proposed topics

Past and present research topics for synthetic biology working group lunches. Please add to the list.

  1. Electronics device families (introduction by TK) - SynBERC:MIT/Calendar/2006-9-27
  2. Abstraction hierarchies
    1. Parts -> Devices -> Systems
    2. Biological layer model (AC)
  3. DEVICES: Composability? Device family specification? Interfaces within families? Interfaces across families? Eventually parts datasheet? Eventually standards?
    1. Transcriptional device families (RS and CAF) - SynBERC:MIT/Calendar/2006-10-4, SynBERC:MIT/Calendar/2006-10-11
    2. Post-translational device families (SS) - SynBERC:MIT/Calendar/2007-2-13
    3. Biosynthetic device families (KJP lab) - SynBERC:MIT/Calendar/2006-10-18, SynBERC:MIT/Calendar/2006-10-25
    4. 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
    5. Translation device families?
  4. PARTS: SynBERC:MIT/Calendar/2007-2-6
    1. Terminators
    2. Coding regions
    3. RBSs
    4. Promoters
    5. Composability and characterization - SynBERC:MIT/Calendar/2006-11-01
  5. CHASSIS: Why do we want different kinds? What kinds? What are the simplest systems that work?
    1. Minimal chassis
    2. Mesoplasma florum - SynBERC:MIT/Calendar/2006-12-13
    3. E. coli standard strain and rE. coli - SynBERC:MIT/Calendar/2006-12-6
    4. Yeast
    5. Power supply - SynBERC:MIT/Calendar/2006-11-15
    6. Vectors - SynBERC:MIT/Calendar/2007-1-31
  6. Synthesis technologies
    1. What is state of the art?
    2. What are the good ideas?
    3. How do we get more investment?
    4. Can the fabs constrain what people synthesize?
  7. What does the CAD tool look like? - SynBERC:MIT/Calendar/2007-7-18, SynBERC:MIT/Calendar/2007-8-1
  8. Human practice
  9. Differentiation and cell to cell communication. Development. Programmed pattern formation. (Arthur Lander, Radhika)
  10. Standards (also see talk page)
  11. Load issues
    • What demands on the chassis are of most concern to us? Replication, transcription, 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?
  12. Selection against our systems SynBERC:MIT/Calendar/2006-12-20
    1. e.g. IS elements are showing up in our devices!
  13. Statistics of codon pairs (UC Irvine folks)
  14. iGEM 2010 - SynBERC:MIT/Calendar/2006-11-08
  15. Registry 2.0 - SynBERC:MIT/Calendar/2007-6-20
  16. Publishing (with CS on Oct 20) - held separately
  17. Controlled transcriptional termination as an implementation for logic - Chris Anderson
  18. Designing enzymatic reactions by splitting catalytic activity and substrate specificity potentially by scaffolds - John Dueber? ask Adam Arkin for someone to talk about this
  19. What is the obvious list of things to do?
    1. Parts characterization
    2. How do we get basic tasks done?
  20. Experience with different parts: RBSs, promoters, terminators - Jen? Chris Anderson? Curt and Hal Alper
  21. Web of registries - Randy
  22. Repetitive sequences and potential for recombination - ask Graham Walker, someone in Philadelphia
  23. Registry of models - Barry and Vincent
  24. Bacterial counter and how you implement it - Tom or Gerry - SynBERC:MIT/Calendar/2007-5-30
  25. How do I get a computer inside my cell? - Tom
  26. Human practices - Michael Rossi
  27. Writing DNA - Maia, Farren?, Church lab, Adam Arkin, Sasha and polony sequencing - SynBERC:MIT/Calendar/2007-4-3
  28. Noncoding RNAs - Ron Breaker
  29. Materials - Angie Belcher, Julie Norville - SynBERC:MIT/Calendar/2007-5-8
  30. Education in SB - Natalie and Scot and Austin and Michael and Shawn? - SynBERC:MIT/Calendar/2007-3-20, SynBERC:MIT/Calendar/2007-5-22
    1. Curriculum
    2. Workshop implementation
    3. Materials
    4. Bootcamp
  31. 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
  32. Impact of big pharma and big ag and big energy on our field
  33. Inteins and Fran Perler from NEB - SynBERC:MIT/Calendar/2007-4-10
  34. Brian Baynes and Codon Devices - future of DNA synthesis technology
  35. Ownership, sharing and innovation - SynBERC:MIT/Calendar/2007-5-1, SynBERC:MIT/Calendar/2007-9-26
    1. IP around DNA fabrication technology (synthesis and automated assembly)
    2. How do we incent contributions? i.e. documentation of parts in the Registry
    3. Historical examples around IP
    4. SynBERC OSI model
    5. BBF work
  36. Bioenergy - SynBERC:MIT/Calendar/2007-5-15
  37. 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
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