SynBERC:SBWGLunchesArchive

This page contains archived information about old SBWG lunches (pre-Fall 2010).

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 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'''

Each date is 12-1 pm

Stata (Bld. 32) Rm: G449 June 10- Discussion led by Kevin Solomon

Stata(Bld. 32) Rm: D463 June 24- Invited Lecture by Magdelena Bezanilla

The ease of molecular genetic manipulation in the plant model, Physcomitrella patens Magdalena Bezanilla, Assistant Professor of Biology, University of Massachusetts Amherst Follow link to see video: http://blip.tv/file/2285207/ Our lab studies the molecular control of polarized growth in plant cells. We are using the facile reverse genetics afforded by the moss Physcomitrella patens to establish a molecular pathway controlling polarized growth in plants. Physcomitrella is amenable to gene replacement by homologous recombination, RNA interference, rapid regeneration of whole plants from single cells, and has the potential for high-throughput studies. We have recently used RNAi to simultaneously silence nine genes within the actin-binding formin family and have demonstrated that plant class II formins are essential for polarized growth, while class I formins appear to be involved in cell division. We have used homologous recombination to tag the endogenous locus of one of the class II formin genes and determine its subcellular localization. Using in vitro assays, we demonstrated that class I and class II formins have strikingly different properties with respect to actin elongation. In combination with in vivo rescue experiments, we demonstrated that rapid actin elongation is necessary for polarized growth. This study exemplifies how Physcomitrella patens represents an exciting plant model, highly amenable to molecular genetic manipulation. This organism may be of interest as a potential model organism for DIYbiology.

Stata (Bld. 32) Rm: G449 July 8 Discussion with MIT iGEM Team

Stata (Bld. 32) Rm: D463 July 22

Stata (Bld. 32) Rm: D463 August 5 Paul Steiner Gene synthesis is one of the major bottlenecks faced by synthetic biologists. A number of companies will happily synthesize genes for a fee, but such service is opaque and introduces total dependence on an external organization. The alternative, doing syntheses oneself, is often time-consuming and error-prone. I believe this is due to the lack of a robust software tools.

I'll present an algorithm that quickly finds an optimal set of oligos for PCR-based synthesis of a given DNA sequence. An optimal set is defined as one that contains no potentially mispriming oligos and has maximally uniform overlap melting temperature. This algorithm places no restrictions on oligo length or overlap size -- both can vary within the set. I've implemented a tool using this algorithm in Common Lisp.

When trying to synthesize a coding region, the protein sequence encoded by a DNA sequence is often the only concern. From the perspective of oligo design, this means there are many sequences to choose from. I'll show how my algorithm could theoretically be extended and used with existing codon optimization problems to simultaneously optimize codons and design oligos for synthesis.

Stata (Bld. 32) RmL D463 August 19 Synthetic Biology Teaching Materials

To comment on the food, email Maria dot Konizeski at sebastians dot com (if food doesn't arrive call 617-758-0112 and reference SBWG lunch and the room number)

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
 * 3) Parts -> Devices -> Systems
 * 4) Biological layer model (AC)
 * 5) DEVICES: Composability? Device family specification? Interfaces within families? Interfaces across families?  Eventually parts datasheet?  Eventually standards?
 * 6) Transcriptional device families (RS and CAF) - SynBERC:MIT/Calendar/2006-10-4, SynBERC:MIT/Calendar/2006-10-11
 * 7) Post-translational device families (SS) - SynBERC:MIT/Calendar/2007-2-13
 * 8) Biosynthetic device families (KJP lab) - SynBERC:MIT/Calendar/2006-10-18, SynBERC:MIT/Calendar/2006-10-25
 * 9) 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
 * 10) Translation device families?
 * 11) PARTS: SynBERC:MIT/Calendar/2007-2-6
 * 12) Terminators
 * 13) Coding regions
 * 14) RBSs
 * 15) Promoters
 * 16) Composability and characterization - SynBERC:MIT/Calendar/2006-11-01
 * 17) CHASSIS: Why do we want different kinds? What kinds?  What are the simplest systems that work?
 * 18) Minimal chassis
 * 19) Mesoplasma florum - SynBERC:MIT/Calendar/2006-12-13
 * 20) E. coli standard strain and rE. coli - SynBERC:MIT/Calendar/2006-12-6
 * 21) Yeast
 * 22) Power supply - SynBERC:MIT/Calendar/2006-11-15
 * 23) Vectors - SynBERC:MIT/Calendar/2007-1-31
 * 24) Synthesis technologies
 * 25) What is state of the art?
 * 26) What are the good ideas?
 * 27) How do we get more investment?
 * 28) Can the fabs constrain what people synthesize?
 * 29) What does the CAD tool look like? - SynBERC:MIT/Calendar/2007-7-18, SynBERC:MIT/Calendar/2007-8-1
 * 30) Human practice
 * 31) Differentiation and cell to cell communication. Development.  Programmed pattern formation.  (Arthur Lander, Radhika)
 * 32) Standards (also see talk page)
 * 33) Load issues
 * 34) *What demands on the chassis are of most concern to us? Replication, transcription, translation, Enzyme activity?
 * 35) **Are we regularly placing high demands on the chassis with our existing systems?
 * 36) *What chassis responses to an applied demand are of relevance? Growth rate, protein synthesis capacity?
 * 37) **Can we specify a threshold demand level above which the chassis response is so severe as to render the our engineered systems inoperable?
 * 38) Selection against our systems SynBERC:MIT/Calendar/2006-12-20
 * 39) e.g. IS elements are showing up in our devices!
 * 40) Statistics of codon pairs (UC Irvine folks)
 * 41) iGEM 2010 - SynBERC:MIT/Calendar/2006-11-08
 * 42) Registry 2.0 - SynBERC:MIT/Calendar/2007-6-20
 * 43) Publishing (with CS on Oct 20) - held separately
 * 44) Controlled transcriptional termination as an implementation for logic - Chris Anderson
 * 45) Designing enzymatic reactions by splitting catalytic activity and substrate specificity potentially by scaffolds - John Dueber? ask Adam Arkin for someone to talk about this
 * 46) What is the obvious list of things to do?
 * 47) Parts characterization
 * 48) How do we get basic tasks done?
 * 49) Experience with different parts: RBSs, promoters, terminators - Jen? Chris Anderson? Curt and Hal Alper
 * 50) Web of registries - Randy
 * 51) Repetitive sequences and potential for recombination - ask Graham Walker, someone in Philadelphia
 * 52) Registry of models - Barry and Vincent
 * 53) Bacterial counter and how you implement it - Tom or Gerry - SynBERC:MIT/Calendar/2007-5-30
 * 54) How do I get a computer inside my cell? - Tom
 * 55) Human practices - Michael Rossi
 * 56) Writing DNA - Maia, Farren?, Church lab, Adam Arkin, Sasha and polony sequencing - SynBERC:MIT/Calendar/2007-4-3
 * 57) Noncoding RNAs - Ron Breaker
 * 58) Materials - Angie Belcher, Julie Norville - SynBERC:MIT/Calendar/2007-5-8
 * 59) Education in SB - Natalie and Scot and Austin and Michael and Shawn? - SynBERC:MIT/Calendar/2007-3-20, SynBERC:MIT/Calendar/2007-5-22
 * 60) Curriculum
 * 61) Workshop implementation
 * 62) Materials
 * 63) Bootcamp
 * 64) 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
 * 65) *Must act in the absence of perfect knowledge
 * 66) Impact of big pharma and big ag and big energy on our field
 * 67) Inteins and Fran Perler from NEB - SynBERC:MIT/Calendar/2007-4-10
 * 68) Brian Baynes and Codon Devices - future of DNA synthesis technology
 * 69) Ownership, sharing and innovation - SynBERC:MIT/Calendar/2007-5-1, SynBERC:MIT/Calendar/2007-9-26
 * 70) IP around DNA fabrication technology (synthesis and automated assembly)
 * 71) How do we incent contributions? i.e. documentation of parts in the Registry
 * 72) Historical examples around IP
 * 73) SynBERC OSI model
 * 74) BBF work
 * 75) Bioenergy - SynBERC:MIT/Calendar/2007-5-15
 * 76) Please add your topic to the list.

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

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

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

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Notes from prior Spring 2008 schedule:


 * SynBERC:MIT/Calendar/2008-4-2: 69th of restarted MIT SBWG lunch
 * Wednesday 4/2 (1:00-2:00p EST), 32-D463, MIT


 * 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