CHE.496/2008/Responses/a4

Responses Page:

Genetic Programming

• Patrick Gildea Response

• • • File:JA response4 1.27.08.doc

• • • • Patrick Gildea 16:28, 27 January 2008 (CST):

• • Idempotent Vector Design for Standard Assembly of Biobricks
    • The purpose of this article was to make a case for the standardization of assembly techniques for biobricks to ensue that structural elements of the biobricks remain the same as all the biobricks transform into the module as a whole. In addition, the article goes through the standard sequence they chose as a basis for biobrick components - on the upstream end by EcoRI and XbaI restriction sites, and on the downstream end by SpeI and PstI restriction sites. For a module to be inserted into an assembly vector – specific restriction enzymes are used to cut the DNA (in the regulatory sequence) and insert the biobrick components at the restriction sites that have been cut. In order for this technique to be useful, the assembly vector cannot contain any other sites that the restriction enzymes could cut into. I am not 100% sure, but the restriction enzyme discussed in the article is applicable to a broad spectrum of organisms that can be used to insert biobrick modules. This is important because as a standard, this technique has to apply to many different types of assembly vectors. This article is relevant for the 2008 project because we need to understand how to fit in our biobrick module into the assembly vector without changing the structure or function of our biobrick components. For example, accidental creations of ATG start codons that could potentially start mutations, as well as other scenarios. Furthermore, this area of standardization needs to be explored – the article mentions different assembly vectors that add different functionalities to the assembly process (such as the NOMAD system). Research into different assembly vectors and investigations into what functionalities, benefits/disadvantages could provide a better basis of standardization.

• • Genetic parts to program bacteria
    • The purpose of this article is to discuss how biobricks are being used to program organisms via cell-based sensors and circuits. In other words, frameworks for synthetic biology (akin to VLSI for electronics in the 1980’s) are being developed in order to design biological systems with process and data abstraction in mind. A list of genetic parts and their description is given, which is very valuable for looking at parts that program bacteria (Table 1). The common types of tools are discussed: sensors and how they work with different types of inputs (i.e. u.v. light, cytoplasmic regulatory proteins); circuits such as switches, inverters, logic gates, etc. The descriptions and their use of different tools used to govern the behavior of a bacterial organism is the most valuable part of the paper because it gives us all a run-through on the different tools that can be used and ideas for more complex systems can arise from thinking about the different ways these tools can be used in different combinations. These concepts of the tools can be applied toward design ideas of programming bacteria for a specific purpose. In other words, we can use the knowledge in this paper as a source of general knowledge to be applied to whatever project design we come up with. Another part of the paper that is especially beneficial is the debugging and tuning of complex systems with different techniques described. For the project in 2008, we may have to use one of these techniques depending on what we design. Knowing what tools to apply to a problem is half the solution of solving a problem.

• Patrick Gildea 16:08, 27 January 2008 (CST):

• Kevin Hershey Response
  • Idempotent Vector Design for Standard Assembly of Biobricks
    • This articles primary purpose is to illustrate the design components of the biobricks. It begins by discussing the aspect of standardization using the analogy of a screw, where standardizing the thread of a screw helped the industry tremendously. The article then gets to the meat of the topic, discussing the design of biobricks. The most important design is the location of the restriction enzymes. The standard format is as follows: Eco RI, Xba 1, insert, Spe 1, Pst 1. This allows users to 'plug and play' devices into the biobrick as long as they keep the sequences standard. The advantage to this format is that if an insert is added to an existing biobrick, it cannot be broken again. In other words, if the Eco RI and Xba 1 are chosen to be ligated, the sequence is lost, and the biobrick does not have a risk of being fragmented after it has been constructed.
  • Genetic parts to program bacteria
    • In this article, Christopher Voigt discusses the engineering currently being done in synthetic biology. That is to say, some examples of how synthetic biology is currently being used and created. His figure showing the different switches and sensors is very useful, especially as a precursor to using the Standardized Registry of Biological Parts. Voigt then goes into detail of different two component systems, sensors and inputs, genetic circuits, and actuators. Voigt then goes into detail on debugging and tuning. The main point from this article is the ability of synthetic biologists to build complex systems from their standardized parts.
• User:KPHershey 12:01, 27 January 2008 (EST)