CHE.496/2009/Responses/a4

Engineering Principles

• Discussion leader: Maria

(Thaddeus)'s Response

• Idempotent Vector Design for Standard Assembly of Biobricks
  • Describes the usefulness and construction of Biobricks as well as the formatting of the Standard Assembly of Biobricks.
  • Consists of a double stranded DNA strand with four unique restriction sites flanking the gene of interest.
  • Each construct can be cut to either form a front or rear insert or vector.
  • After each round of cutting and inserting new inserts into the vector the construct will be identical to the construct before the new piece was inserted, allowing the process to be repeated in the exact same way.
  • Bases in between restriction sites were chosen carefully to prevent unwanted methylation and cutting of consruct.
  • Contain standard primers for the verification of sequence.
  • This article will be useful for the VGEM team because we will be using biobricks to create our machine and will be creating new biobricks as part of the project.

• Genetic parts to program bacteria
  • The article describes how cells can be programed by using simple devices that form circuits and complex behaviors when combined properly. It also describes the most successful parts.
  • Each circuit or device can only be used once in a biological machine because the biochemical reactions take place in the same space. This will require redundancy of parts to create complex machines.
  • Response of circuit is dependent on what state in the cell cycle the cell is. Devices must resist this dependence.
  • Sensors allow cells to gain information about the external environment.
  • Genetic circuits interpret and process the information from the sensors.
  • Actuators control cell behavior.
  • Debugging can be achieved either by replacing a non-compatible part of a protein with a known part or by applying selective pressure to a sensitive part of the machine under mutagenisis until a functioning machine evolves.
  • This article will be useful to the VGEM team because it breaks down the standard parts of a machine and identifies their function. We will be using these parts to construct our machine.

Thaddeus Webb 19:58, 18 February 2009 (EST)

Rohini's Response

Tom Knight’s article, “Idempotent Vector Design for Standard Assembly of Biobricks” discussed the method of standard vector assembly using the biobrick composition technique. Knight along with authors of various articles previously assigned for this class stress the necessity of having a standard set of reliable engineering mechanisms. By utilizing a standard and universal assembly technique, research in building biological systems from different genetic components can be greatly benefited. With the construction of standards, researchers can use previously manufactured components from other systems, outsource parts to various assemblies and be able to interchange parts between systems. Knight details the two step process of making a biobrick which is: a) prefixing a recipient with a donor component and b) post-fixing an insertion of a donor fragment into a recipient vector. The example used to illustrate this procedure is the transformation of the LacZα gene into a standard component that can be then used to test the effectiveness of the cloning technique. Knight also mentioned various challenges he faced dealing with his research. I did not realize that one has to be very selective in picking the restriction enzymes to cut the DNA sequence. The enzymes have to be able to withstand the environment of the experiment and other specificities. Overall, Knight’s research goal was to transform component parts during the assembly reaction while ensuring that distinct structural elements of the component remain unaltered. As a result, the component can be placed within a library of previously assembled components and made accessible for future complex assemblies.

I think researchers have found some interesting and revolutionary scientific applications that have the potential to advance the current treatments used within the field of medicine. I was amazed after reading about how scientists are working on discovering ways to create more operational commands in bacteria such as: synthesizing anti-malarial and cancer fighting drugs. They were able to begin working on their research only after realizing microorganisms can be programmed using synthetic constructs of DNA set with operational tasks. Voigt’s article, “Genetic Parts to Program Bacteria” discussed present challenges dealing with genetically engineering microorganisms. The two most prevalent problems are: cells can evolve and could potentially mutate and genetic parts interfere with one another within a system which means a genetic circuit can only be used once in design.

The information present in the two articles can be applied to the VGEM project. If we can work with standard components already available in the biobrick library then we can deal with fewer complexities.

Rohini Manaktala 8:10 p.m., 18 February 2009

Patrick's Response

• Idempotent Vector Design for Standard Assembly of Biobricks
• Genetic parts to program bacteria