BU06:Executive Summary

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'''II. Project Specifics'''  
'''II. Project Specifics'''  
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The current project design is a simple one which will hopefully generate functional results and useful biobricks.  The design revolves around engineering competent E. Coli to express genes resulting in the production of light and luminescence.  The main task lies in the development of a biobrick containing the LuxCDABE operon from the Photorhabdus luminescens, and our team is convinced we have devised a solid plan to do so.
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(how the lux operon works?)
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A biobrick is a standardized plasmid containing an insert that codes for a protein function.  The insert is flanked by specific restriction enzyme sites EcoRI and XbaI on one end and SpeI and PstI on the other end.  The part can then be digested from the biobrick easily, connected to other parts and transformed into cells.  Another requirement of a biobrick is that the four restriction sites are not found anywhere within the part or else the insert will be digested into smaller pieces.
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The Lux operon the team will be inserting into a biobrick contains EcoRI digest sites on either end and an XbaI digest site in the middle.  XbaI digests a vector when the nucleotide sequence, TCTAGA occurs.  In order to alter the XbaI site, we plan to do a single point mutation to change a single base pair in the Lux operon sequence.  The most viable place to do so is in the middle of the digest site, where the codon CTA codes for the amino acid Leucine.  Other codons that code for the same protein Leucine include CTT and CTC, both of which occur at low frequency in Photorhabdus Luminescens, from which the operon originates, and in E. Coli K12, in which we want to insert the operon.  By performing this silent point mutation we hope to avoid any unnecessary and unforeseen damage to the gene coding region. 
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The EcoRI sites must also be removed from either end of the coding sequence, so that we can add the standard restriction enzyme sites.  EcoRI digests the plasmid when the sequence GAATTC occurs.  This DNA sequence can be removed by attaching primers to the end of the DNA sequence, halfway through the EcoRI sites and using Polymerase Chain Reaction to copy  only half of the site.  The sequence will no longer be recognized as an EcoRI site.  The operon can then be inserted into a standard biobrick construct, bracketing it with the appropriate restriction sites.

Revision as of 20:50, 20 June 2006


Proposal outline

  • Intro
    • Igem and synth. biology
    • previous successful projects and media reviews
    • who we are and what are our goals
    • prove igem concept
    • contribute novel parts to catalog (registry)
    • produce a working project
  • Project specifics
    • the plan: simple project, expected good results, extensions
    • technical: what it is: see Melissa's
    • results: modeling, characterizing, documenting in data sheet
  • materials/ lab req.
    • costs and time line
  • Fundraising cost, goals & sources
    • Goals and sources
  • timeline
    • lab training, lab planning - max people in shifts at lab -> lab teacher
    • schedule


Proposal Writing Teams: Please copy your material into the appropriate section below by Monday night June 19th, so we can all be ready for a group edit on Tuesday.


I. Intro

The International Genetically Engineered Machines competition (iGEM) is built around the central question of whether biological systems can be built from standard interchangeable parts and operated in living cells. iGEM was developed by Massachusetts Institute of Technology professors, primarily Tom Knight and Drew Endy, with their students, and is still hosted at MIT. Over the past three years of structured synthetic biology competitions, iGEM, has developed a "Registry" of hundreds of available and working parts, called "BioBricks". These parts are designed to be inserted into microorganisms to achieve human goals. The ultimate goal is to guide this area of molecular biology from a difficult and complicated series of individual experiments to a standardized engineering discipline, approachable to any engineer by using an online registry, similar to the McMaster-Carr catalog of electromechanical components.

In past years, teams have made such contributions as a bacterial "photographic film," a caffeine detector, and an inverter analogous to an electronic inverter. The competition has grown rapidly from five teams in the initial year, to 13 teams, to 40 international teams in this year's field of competitors. iGEM has been earning attention in the scientific and general press, as much for the success of its projects as for its unique pedagogical goals of bringing together undergraduates and graduates from widely divergent scientific and engineering backgrounds. Past coverage has included Nature, Science, and this year has been featured as the cover story of a recent issue of Scientific American.

BU's 2006 iGEM team is composed of a group of primarily undergraduate biomedical engineering students, reinforced with graduate students in a number of disciplines, including biology, electrical engineering and physics. Most have completed an introductory course in molecular biology and have some lab experience. Our Principal Investigator is Dr. Timothy Gardner, whose early work in the field of synthetic biology resulted in the development of the first biological toggle switch.

Our goals in participating in the competition are to help prove the basic iGEM principles by producing a functional biologically engineered system, contribute a novel bioluminescent part to the Registry, develop our molecular design skills, gain more experience in molecular biological laboratory techniques, and strengthen the synthetic biology community among schools and for the future growth of the industry. In addition, iGEM has been beneficial in providing thesis and research material for participants, and we hope to be able to take advantage of this to help guide our future academic careers.

We are convinced that our team has a plan designed for success. As a first-year team, we aspire to establish ourselves at the annual iGEM "Jamboree" as a major contender in the competition, and begin a tradition of Boston University iGEM excellence. The Jamboree is the primary opportunity for teams to present and promote their projects with documentation, results, and characterization of the biological systems they have built. We believe our participation will reflect well on ourselves and enhance BU's image as a front-runner in undergraduate synthetic biology. The support, academic, technical and financial, of the BU community will be a major component of our success.


II. Project Specifics

The current project design is a simple one which will hopefully generate functional results and useful biobricks.  The design revolves around engineering competent E. Coli to express genes resulting in the production of light and luminescence. The main task lies in the development of a biobrick containing the LuxCDABE operon from the Photorhabdus luminescens, and our team is convinced we have devised a solid plan to do so.

(how the lux operon works?)

A biobrick is a standardized plasmid containing an insert that codes for a protein function. The insert is flanked by specific restriction enzyme sites EcoRI and XbaI on one end and SpeI and PstI on the other end. The part can then be digested from the biobrick easily, connected to other parts and transformed into cells. Another requirement of a biobrick is that the four restriction sites are not found anywhere within the part or else the insert will be digested into smaller pieces.

The Lux operon the team will be inserting into a biobrick contains EcoRI digest sites on either end and an XbaI digest site in the middle. XbaI digests a vector when the nucleotide sequence, TCTAGA occurs. In order to alter the XbaI site, we plan to do a single point mutation to change a single base pair in the Lux operon sequence. The most viable place to do so is in the middle of the digest site, where the codon CTA codes for the amino acid Leucine. Other codons that code for the same protein Leucine include CTT and CTC, both of which occur at low frequency in Photorhabdus Luminescens, from which the operon originates, and in E. Coli K12, in which we want to insert the operon. By performing this silent point mutation we hope to avoid any unnecessary and unforeseen damage to the gene coding region.

The EcoRI sites must also be removed from either end of the coding sequence, so that we can add the standard restriction enzyme sites. EcoRI digests the plasmid when the sequence GAATTC occurs. This DNA sequence can be removed by attaching primers to the end of the DNA sequence, halfway through the EcoRI sites and using Polymerase Chain Reaction to copy only half of the site. The sequence will no longer be recognized as an EcoRI site. The operon can then be inserted into a standard biobrick construct, bracketing it with the appropriate restriction sites.


III. Materials/Lab Requirements


IV. Fundraising Costs, Goals & Sources

The BU iGEM team has ambitious fundraising goals but is confident we will attain our goals with our thorough fundraising plan. We have obtained starting funds that ensure our research will not be held back while we raise all the funds needed to complete the entire project.

The BU iGEM team has begun the process of applying for student organization status from the Student Activities Office which will provide a yearly stable structure for the group as well as yearly funds to ensure that the group always has base funds from which to operate. The group will be notified of acceptance and funds in early October.

The team is pursuing educational grants from several companies interested in funding innovative and collaborative projects such as iGEM. We are approaching two types of companies: those companies who work directly in synthetic biology and are committed to advancing this particular field and larger local companies in the area interested in funding innovative projects as part of their larger educational and community grants.

The team is looking into the feasibility of selling tee-shirts to team members, parents, students, and faculty to raise funds. These would also serve the dual purpose of providing and impressive presence at the November Jamboree.

The iGEM team is also hopeful that administrators, professors, and labs in the Engineering Department at Boston University will provide funds to the team in recognition of the great publicity that our successful participation in this competition will bring to the BU Engineering Department and for the opportunity this program brings to the students in our department. iGEM provides beneficial hands-on research experience to undergraduates in preparation for their Senior Project and also exposes students to one of the most cutting-edge fields in BioMedical Engineering. It is also a enlightening interdisciplinary project that bring together students from all specializations in Engineering.


V. Timeline



PUNCHY!

  • SB is a new field - Why is it interesting, no, essential!?
    • Standardization of genetic engineering to enable innovation
    • Improves collaboration, rate of innovation,
    • 'programmable' cells
    • when we do genetic engineering it should be like building a bridge--we can show that what we build will work; it's not a wild-ass guess whether or not it will work
    • specialization -- let people focus on their chosen area of expertise with the assumption that all the other levels of abstraction will just work
    • iGEM is about undergrads

Motivation factors for BU professors:

  • put boston university undergraduates at the center of an infrastructure of a 'revolutionary' (sorry) new field
  • opportunity to build a year-on-year franchise (a resource for getting kids molecular biology experience -- keep in mind there's not that many _mol bio_ labs in the dept)
  • let our undergrads socialize scientifically outside the university
  • complement/enhance senior project (one of our key differentiators--sorry to lapse into admin-speak)
  • bringing an engineering sensibility to biology is a huge deal for a biomedical engineering department centrally located in a city with a huge biomedical industrial complex
  • Jay Keasling/Amyris greatly reduced the cose of producing artemesin for huge # of people in need -- as the good Dr. Endy says we should make this routine so that it doesn't require $20m of Bill Gates' money and 100 (?) man-years of effort.
  • quantitative quantitative quantitative (BU BME professors' three favorite words)
  • growth in # of teams (5, one of which was BU) -> 12 -> 43 -> at least seven hundred next year
  • obvious opportunity for press coverage
  • biofactories
  • we have people doing tissue engineering; wouldn't they like to have predictable cells?
  • the Biological Century


We need one million dollars!

awesome proposal team!!! i posted the outline and additional points we came up with on the proposal meeting. when you write up the executive summary don't be intimidated to be as creative as possible. there is no true or false in this write up. more over feel comfortable to post/save your summaries on this page (with your name at the bottom so we will have a common place to go over them together in the meeting, cut and paste the appropriate parts and have a place to observe eachother work and comment outside of our get togethers. When we will meet on friday we will collect the ideas we like from every summary and put it all together into an awesome summary. (Nadav 06/13/06)

  • proposal
    • convincing that we are scientific/professional
    • more specifics of plan
    • success stories
    • actual literature
    • road map
    • celebrity backers
    • list of tools and materials
    • how much money we need
  • Brochure
    • what is synthetic biology
    • how does igem relate
    • potential excitement success
    • what we are doing?
  • why?
    • reasons to help- prestige and senior project
    • opportunities for undergraduates
  • how
    • road map
    • list of needs
    • tools, materials, practical ways to help

We are a group of Undergraduate students from BU who participated in a molecular biology course during the Spring 2006 semester. Our professor, Timothy Gardner, and Professor Drew Endy (MIT) introduced us to the world of synthetic biology. Synthetic Biology is a new field of research that integrates science and engineering in order design biological systems that carry out specific functions, such as programming bacteria to work as a biological toggle switch. Fascinated by the opportunities given by this novel we field of research we decided to participate in the iGEM 2006 competition. Because of the complexity involved in designing and building biological systems we decided to attempt to implement three ideas, each more complicated than the previous one. Moreover, the more complicated ideas are built off of the simpler ideas


Synthetic Biology is the new field of biological engineering aimed at innovating and enhancing all bioengineering by introducing standardizations of methods and results. This effort to create modular designs in biology ultimately lends to greater efficiency and speed at which research and engineering may be conducted. In specifying biological parts, engineers may be able to more accurately predict the outcomes of a design, as well as using and contributing to all other work in Synthetic Biology. The fundamentals of this field are grounded in the collaborative interaction between engineers and researchers. This is materialized in the annual iGEM competition at MIT. The Boston University iGEM 2006 team aims to contribute to this promising field by offering designs consisting of previously confirmed genetic parts as well as newly created parts.


The BU iGEM team, a group of undergraduate researchers from Boston University, are very excited by the opportunities presented by the third annual International Genetically Engineered Machines Competition (iGEM). iGEM is an international competition between Universities, in which groups of undergraduates from different schools work to create an innovative and useful biological system. The standardization of these bio-systems as parts, formally called biobricks, is at the forefront of synthetic biology. Biological engineers use these biobricks to develop new biological systems more efficiently. The possibilities are endless. The BU team hopes that through their work in iGEM, they can help in the effort to reduce the cost and increase the accessibility of synthetic biology technologies. As a starting point, the team has designed a bio-system that will produce light under specific conditions. The design requires the creation of a new biobrick for light emission, which is then combined with a light detection biobrick created and added to the registry of parts for iGEM 2005. In order to complete our design we will require financial backing. Thank you for your time and consideration.


the 21st century introduces synthetic biology! igem - international genetichaly engineered machine competition is an anual cosmopolitan competition participated by schools from all around the world that is designed to promote the novel and rapidaly expanding field of thynthetic biology with the goals of standarizing it and promoting free information sharing. the competition is going to be held for the fourth time in november in an event called "The Jamboree" that is held at MIT. we are a group of students from boston University who decided to form agroup and participate in the competition backed by our world known faculty and professors, Jim Collins and Timothy Gardner we came up with exciting and novel ideas we would like to develop for the competition starting with a biological night light, biological chemical detector and light excited bacteria. developments from previous igem competitions include biological photophilm and biological counter. all of our ideas are based on the chemotaxis protein and luxR operon and require the help of synthetic biology companies to synthesis the sequences needed. in order to develop our ideas we need funding of $10,000 in order to buy the raw materials and essential lab equipment in return to the funding we offer publication and fame for the companies who are willing to support us, more over a spectacular insight to the world of synthetic biology as a whole and igem as the core of it.

Nadav (06/15/06)

proposal outline

  • Intro
    • Igem and synth. biology

-previous successful projects and media reviews

    • who we are and what are our goals

-prove igem concept -contribute novel parts to catalog (registry) - produce a working project

  • Project specifics
    • the plan: simple project, expected good results, extensions
    • technical: what it is: see Melissa's
    • results: modeling, characterizing, documenting in data sheet
  • materials/ lab req.
    • costs and time line
  • Fundraising cost, goals & sources
    • Goals and sources
  • timeline
    • lab training, lab planning - max people in shifts at lab -> lab teacher
    • schedule
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