CHE.496/2009/Responses/a8

Biological Machines

• Discussion leader: Rohini

Rohini's Response

Designing Biological Systems

• Main Point- review progress made in the field of synthetic biology
• Synthetic biology- seeks to modify or mimic biological systems by using natural cellular components as well as generate unnatural chemical systems
• Overall, the construction of systems is the product of iterative cycles of computer modeling, biological assembly and testing

The four developments that synthetic biologists have to wait for before engineering whole organisms are:

• inexpensive DNA synthesis, rapid and inexpensive DNA sequencing, collection of components that are well-characterized, adoption of engineering approaches

• Role mathematical modeling plays in designing gene circuits:

Ex.- repressilator, use of a quantitative model of the system was important in determining the parameters in which the system is oscillatory

• Two ways of achieving bistability in a network: creating a positive feedback loop and creating mutual repression

• Synthetic switches in both pro/eukaryotes can be mediated via RNA devices (engineered riboregulators)
• By introducing specific mutations in portions of the RNA sequences, the switching behavior of the system can be altered
• Certain evolutionary precursors gave rise to diverse types of organisms because they had design features that were easier for evolution to work

• Challenge in engineering bacteria- the cell wall makes it impossible for cells to communicate by cell contact

• Example of a synthetic circuit that has implemented artificial cell-cell interaction:

Pulse generator- the receiver cell responds to the signal sent by the sender cell with a pulse of GFP. The system demonstrated that receiver cells respond to a varying response to sender cells based on the rate of increase of inducer concentration and their distance from the sender cell

• Example of engineered signaling pathway in a system:

-Reprogramming of an allosteric protein signaling switch in yeast

• Metabolic engineering-integrating new pathway into a cell to synthesize a key metabolite.
• Example: synthesis of artemisinin, component in antimalarial drug

• Two strategies for studying the simplest organism:

1) Top-down approach: organisms are simplified further through the removal of nonessential genetic elements 2) Bottom-up approach: synthesis of artificial cells is attempted, component by component

• Problems with using PCR to synthesize DNA:

-too laborious, high rate of errors and repair is done by site-directed mutagenesis -“copy, cut and paste” manner using polymerases, restriction endonucleases and ligases

• Currently used technique for synthesizing DNA:

-coupling of large scale oligo synthesis on microfluidic microarrays with mismatch error correction and a single step polymerase assembly to the build the gene

• Proposed engineering approaches to make work within the field of synthetic biology easier:

-use of well-characterized parts, standardization, abstraction

Biology by design: reduction and synthesis of cellular components and behavior

• The article discusses two types of work that goes on within the field of synthetic biology. It mentions that the field encompasses the design and construction of new biological parts, devices and systems. But, it also discusses the re-design of existing, natural biological systems for useful purposes such as the development of therapeutics, renewable energies.

• The biggest challenge that scientists face in creating simple biological systems is predicting the system behavior

• Steps for engineering gene circuits:

-Determine the design goal, pick suitable host organisms, identify necessary parts, model, explore circuit dynamics, implement/test/debug

• Florescent protein helps in monitoring synthetic circuits by monitoring in vivo protein levels

• Microfluidics-manipulating small amounts of fluids using microsized channels help in the integration of complex chemical or biological procedures into a single process that is faster

• Reverse sorting:cells scanned at a high flow rate until a fluorescent cell is detected and then flow is stopped and reversed allowing the cell to be measured and diverted into a collection tube. The purpose is to isolate rare cells or to make multiple measurements of the cell.

Rohini Manaktala 16:30, 11 March 2009 (EST)