SynBERC:MIT: Difference between revisions

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  Talk: Engineering Zinc Finger Nucleases for Highly Efficient Genome Modification.
  Talk: Engineering Zinc Finger Nucleases for Highly Efficient Genome Modification.
   
   
  Zinc finger proteins and nucleases are a critical technology for synthetic biology since they can cut,   
  Zinc finger proteins and nucleases are a critical technology for synthetic biology since they can cut,   
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  Jocelyn Kaiser's Science Now article 'DNA "Scissors" Go Open Source' and Patrick Barry's ScienceNews
  Jocelyn Kaiser's Science Now article 'DNA "Scissors" Go Open Source' and Patrick Barry's ScienceNews
  article 'Choose Your Own Splicer'  
  article 'Choose Your Own Splicer'  


  Date: Wednesday, November 5, 2008
  Date: Wednesday, November 5, 2008

Revision as of 11:08, 3 November 2008

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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 Isadora Deese. 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 1pm. Usually in 32-D463

Next meeting

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.

Zinc finger proteins and nucleases are a critical technology for synthetic biology since they can cut,   
splice, or tweak genes.  We are pleased to invite Joung as a speaker as he has developed a new 
technique for engineering zinc-finger proteins where everything is transparent.  His technique has the 
potential to allow open source engineering of zinc finger proteins.  You may be pleased to know that
Dr. Joung makes many of his plasmids available through Addgene for distribution to  academic
researchers.  Dr. Joung's work has in a number of ways countered Sangamo BioSciences, the "Microsoft" 
of zinc finger proteins, which is currently planning to sell custom zinc finger nucleases through 
Sigma-Aldrich at a cost of $25,000 per set.  This description of Dr. Joung's work was adapted from
Jocelyn Kaiser's Science Now article 'DNA "Scissors" Go Open Source' and Patrick Barry's ScienceNews
article 'Choose Your Own Splicer' 

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: TBA

Date: Wednesday, December 3rd, 2008/TBA

Time: 1:00-2:00 pm

Location: TBA






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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