Virginia United/2010/Readings/Responses/UVA/Assignment1

Assignment 1 Responses (Due Jan 25)
Example: Daniel R Tarjan 21:29, 24 January 2010 (EST)
 * Paper title
 * Response
 * Paper 2 title
 * Response

Building outside of the Box: iGEM and the Biobricks Foundation
Main points:


 * Creating an open sharing platform of DNA constructs
 * Building a Registry of biobrick parts
 * Developing tools to make engineering biological systems easier (BBF & iGEM)

IGEM:


 * Synthetic biology competition held at MIT
 * Teams identify a real world problem and prototype engineered genetic programs as possible solutions

Synthetic Biology:

1) Budget for de novo DNA synthesis -solution: share and reuse parts,Registry of parts 2) Challenges with gene synthesis -solution: optimize variable copy number vectors with enhanced transcriptional insulation 3) Too much time spent trying to understand how systems work -solution: abstraction hierarchy
 * Relies on the decoupling design
 * Uses abstraction to manage biological complexity
 * Limitations:

Registry of Parts:


 * Online catalog of parts
 * Purpose-streamline a process that can be used to make the integration of parts more reliable and efficient
 * iGEM competition fosters a quality control check by rewarding teams that contribute parts and improve technical standards

Biobrick Foundation:


 * Provide a legal framework for the collection of functional genetic elements encoding bio parts
 * RFC (request for comment)
 * Develop a contract between the inventor and user (determine terms of use,etc)
 * Reduce legal ambiguity around use and re-use of parts—BPA (Biobrick Public Agreement)

Five Hard Truths for Synthetic Biology
Challenges in the field:

1) Many of the parts are undefined -eliminate variations arising from experimental conditions and instruments by measuring promoter activity relative to a reference promoter (standard)

2) Circuitry is unpredictable -cells integrate genes in their genome unpredictably -requires trial and error process -computational modeling can be used for predictions -optimize the system with directed evolution: mutating DNA sequences, screening their performance, selecting the best candidates, repeat the process

3) Complexity is unwieldy -speed up biobrick assembly with assembler cells, selection cells, enzymes

4) Many parts are incompatible -genetic circuits can have unintended effects on host -solution: develop orthogonal systems that operate independently of the cell’s natural machinery

5) Variability crashes the system -i.e. growth conditions, noise, genetic mutations

Rohini Manaktala 23:59, 24 January 2010 (EST)

Building outside of the box: iGEM and the BioBricks Foundation
iGEM, inspired by other student-oriented engineering competition and a month-long course taught at MIT, grew rapidly since 2004. iGEM is now the largest synthetic biology event in the world. iGEM has been very successful for the past few years, and more and more students from high schools and universities are getting interested in synthetic biology. An engaging synthetic biology community forms as the competition goes along, and groups from different areas network and support each other. Yet, there are challenges and difficulties. First, there were some fund-raising issues for teams in different areas due to different cultural and economical backgrounds. Second, concerns about the whether undergraduate students could solve the puzzles within the biological systems still remain. Overall, the participation of iGEM is a well rewarding experience for students intertested in solving problems through the application of engineered biological systems.

Five Hard Truths for Synthetic Biology
1) Many of the parts are undefined
 * researchers find it unable to characterize all the parts within an engineered biological system
 * genes being introduced into the system work unpredictably in different configuration and conditions
 * most of the time, too complex to capture by standardized characterization

2) The circuitry is unpredictable
 * laborious process of trial and error
 * Reduce the guesswork by using computer modeling
 * directed evolution

3)The complexity is unwieldy
 * Solution:
 * Automated process to combine genetic parts, which might involve assembly using "robots"

4)Many parts are incompatible
 * Solutions:
 * orthogonal systems that operate independently
 * parallel systems which allow tweaking components without disrupting stability of the the biological system
 * physically isolate the synthetic network from the rest of the cell

5)Variability crashes the system
 * Solutions:
 * Synchronize blinking by relying on cell-cell communication
 * Use more accurate DNA replication machine

Applications: bio-fuel production

Yong Y. Wu 16:28, 25 January 2010 (EST)

Building outside of the Box: iGEM and the Biobricks Foundation

 * This article, published in Nature last December, describes the goals and challenges faced by the two leading organizations in the new field of synthetic biology. The first, iGEM, is an international contest that, in spite of its highly competitive nature, is built on principles of collaboration and the sharing of “parts”.  In addition to encouraging the development of novel “parts” the competition differs from other traditional competitions in that it also desires to see the improvement and expansion of previous ones.  To accomplish this, awards besides the “grand prize” are available and in a variety of fields.  Any team can get a “gold metal”.  The second organization, the BioBricks Foundation, focuses less on the development of the parts themselves and instead on how the information and technology can be shared (BioBricks was established by many people from iGEM).  In this sense, they work to prepare the field for the future, particularly in the legal sector, as it continues to grow.  While iGEM and the BioBricks Foundation work on different aspects of synthetic biology, both are dedicated to fostering a community of sharing and collaboration, and both face the same problems in 1.)obtaining funding and 2.) developing standards in a field that until recently has been growing independently in different laboratories (and thus use different standards).
 * This article has given me further insight into the iGEM competition. I like that there are ways of rewarding teams for their research beyond the “grand prize”.  The opportunity to create new parts that may potentially be used by future teams (or even by researchers in the field itself) is really cool.  The work being done by BioBricks is equally exciting because it shows the enthusiasm of people in the field (all the seminars and conferences) and the anticipation that the field is going to continue to grow (demonstrated by the need for improvements to the legal system to accommodate collaboration).

Five Hard Truths for Synthetic Biology

 * The Five Hard Truths for Synthetic Biology focuses on the five major obstacles the field needs to overcome.  The first roadblock is that most of the parts are undefined.  While a Registry of Standard Biological parts has been created, and has 5,000 parts listed, many are of bad quality and will “fail” when used a second time.  The second obstacle to be overcome is the unpredictable nature of the circuitry in living organisms.  The resulting ‘trial and error” system of experimentation required is very time consuming.  The third problem, similar to the second, is that these circuits are incredibly complex.  Large scale projects require huge teams with considerably large funds, and are intimidating to initiate.  The fourth major problem is that many parts are incompatible; a circuit working in one cell can have drastically different results when moved to a new type of host. Finally, the natural differences in cells, their variability, pose problems in assessing and controlling the circuits and their products.  In spite of these five “hard truths” many researchers are still successfully expanding synthetic biology.  In fact, much of the progress has arisen to directly combat these issues.   For example, the registry of parts is now requiring the sequences of samples and documentation on their performances.  BIOFAB has just been launched to professionally characterize parts.  The unpredictability of circuits is being reduced by computer modeling and sometimes even directed evolution (based on screening and selecting processes).  The complexity of systems is being improved by the creation of entire systems that will reduce time (using assembler cells, selection cells, and phagemids).  To overcome the incompatibility of parts, protein synthesis pathways independent of those naturally occurring in cells are being developed.  They run entirely separate and are based on specific sequences that flag down their own set of ‘O-ribosomes’.  Even a physical separation of these systems using special new membrane bound compartments is in development. Finally, the variability of the cells can sometimes be considered an advantage because it allows cells to respond differently.  Even so, attempts are being made to improve the stability of DNA and its replication to overcome variability.
 * While this article focuses on the difficulties the field’s scientists are facing, I found it incredibly interesting for its descriptions of proposed solutions. A lot of research focuses on preparing the field for the future- on changes and improvements of pre-existing cellular mechanisms that will allow the standardization and use of parts to happen more easily.  I found the development of entire new O-mRNA and O ribosomes incredibly interesting because it’s a clever way of obtaining a desired product through the addition of a new network instead of the complete rewiring of the old one.

Megan E. Barron 21:34, 25 January 2010 (EST)

Five Hard Truths for Synthetic Biology
Many Parts are Undefined
 * Many parts have not been efficiently characterized, and this leads to variations in measurements
 * The registry of standard Biological Parts has requested documentation of part performance to improve quality
 * Methods for limiting variation in part performance has been proposed by BIOFAB (comparing promoter to a reference).

The Circuitry is Unpredictable


 * Parts may not function as expected. Tedious trial and error methods are often employed to perfect part function
 * Computational models can help to reduce time and optimize part efficiency without trial and error procedures.
 * Directed evolution may also be used to refine imperfect part designs by mutating DNA sequences and analyzing performance.

The Complexity is Unwieldy


 * Larger circuits can be constructed more quickly and efficiently by using artificially designed bacteria to "cut and stitch" DNA parts.

Many Parts are Incompatible


 * Parts remain unpredictable which may include incompatibility with natural biological systems
 * Orthogonal systems have been developed to act individually, thus lowering chances of variations in cell activity
 * Isolation of the synthetic network has also been proposed.

Variability Crashes the System


 * Circuits must be able to withstand "fluctuations" in the molecular activities of cells
 * Fluctuations may be due to varying amounts of protein production units amongst cells
 * Cell to Cell communication can be used to initiate synchronized blinking.
 * Changing genome sites so that they are less prone to mutations is another proposed solution

Building outside of the Box: iGEM and the Biobricks Foundation
Synthetic Biology


 * Synthetic biology combines the works to combine engineering with biological systems
 * In order for this process to work effectively, communities must collaborate
 * IGEM and Biobricks are two community based efforts to expand the field of biological engineering

Genesis of IGEM

of biological engineering
 * Competition first started in MIT in which teams from across the world produce innovative mechanisms

A Competition Matures


 * Over a 100 universities from 26 countries participate in the competition
 * The Registry of Standard Biological Parts became a resource for providing DNA encoding parts to participants
 * Teams are rewarded for "contributing and documenting" biological parts compatible with approved standards

IGEM Community


 * Participants have formed a community in which they engage in sharing parts and proposing solutions to problems
 * IGEM is focused more on education

BioBricks Foundation


 * Not for profit organization founded by IGEM people
 * Provide a legal framework for open collection of genetic elements
 * Technical standards for parts are also provided
 * Has run several workshops on technical standards
 * Actively involved in the community and has diversified the field of synthetic biology


 * Arjun Athreya 22:54, 25 January 2010 (EST):

Building outside of the Box: iGEM and the Biobricks Foundation

 * The iGEM competition and the Biobricks Registry of parts are providing a framework to develop opensource synthetic biology tools and platforms.
 * The most of the parts in the Registry are added by iGEM teams. This presents a problem because they do not have the time or sometimes skill to properly verify and characterize most of the parts that are submitted.  The iGEM experience acts as a filter for poorly functioning parts in that teams that have a poor experience with a part will pass their experience forward to the benefit of other teams.
 * Rewards within the competition reward those who advance the field and the registry significantly.
 * The competition aspect of the iGEM experience adds to the quality of work yet can be costly on a human and financial level.
 * The biobricks foundation seeks to streamline synthetic biology by providing a framework for using biological tools without invoking costly patents.
 * Request for Comments will provide an important set of standards to govern the registry.
 * The iGEM competition and the biobricks foundation are attempting to provide and organizational framework for the field of synthetic biology to grow within.

Five Hard Truths for Synthetic Biology

 * Biological engineering is difficult because the basic units have not been characterized.
 * The biological parts are unpredictable and combining them can have unintended consequences. In other words, biology is complicated.
 * There are many parts and many chassis. Some parts do not work with certain chassis or with each other becuase of crosstalk within a system.
 * Engineering is based on standardization and repeatability whereas life is based on variance and noise.


 * User:Thaddeus Webb 22:54, 25 January 2010 (EST):