Cfrench:CaseStudy1

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===Statement of Philosophy===
===Statement of Philosophy===
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My original training was in BioProcess Engineering. Much of the material focused on designing processes around the activities of living things, such as microorganisms. The biological activities of the microorganisms formed an integral part of the process, but basically we just had to accept the characteristics of the organisms available (barring minor modifications possible through mutation-selection programs, etc.), so the non-biological parts of the process had to be designed around the characteristics of the organisms. Synthetic biology changes all that. Now we can (aspire to) design the characteristics of the organism, the biological component of the process, just as we can design the non-biological parts.
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My original training was in BioProcess Engineering. Much of the material focused on designing processes around the activities of living things, such as microorganisms. The biological activities of the microorganisms formed an integral part of the process, but basically we just had to accept the characteristics of the organisms available (barring minor modifications possible through mutation-selection programs, etc.), so the non-biological parts of the process had to be designed around the characteristics of the organisms. Synthetic biology changes all that. Now we can (aspire to) design the characteristics of the organism, the biological component of the process, just as we can design the non-biological parts. The microorganism becomes just another part of the system, its design to be optimized just like the design of all the other parts. In this case study, we will consider an example of the development of a system, involving design and optimization of both the biological and non-biological components.
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===Starting Points===
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Arsenic (As, z=33) is a metalloid element related to phosphorus (group 15, p3 in the outer electron shell). Like phosphorus, it forms oxyanions, mainly arsenate (+5 oxidation state; AsO4, 3-) and arsenite (+3 oxidation state, AsO3, 3-). Arsenic is quite toxic, due to its ability to interfere with phosphate-dependent processes. Bacteria are often exposed to arsenate and arsenite in the environment, and most bacteria seem to possess a conserved mechanism for dealing with it, consisting of an arsenic detoxification operon. In the simplest case this consists of three genes: ''arsC'', encoding arsenate reductase, which reduces arsenate to arsenite; ''arsB'', encoding an arsenite efflux pump; and ''arsR'', encoding a repressor which binds to the promoter of the operon, releasing only when it binds arsenate or arsenite.
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[[French_Lab|Back to main page]]
[[French_Lab|Back to main page]]

Revision as of 10:41, 22 October 2009

Synthetic Biology Case Study 1: Development of an arsenic biosensor

Statement of Philosophy

My original training was in BioProcess Engineering. Much of the material focused on designing processes around the activities of living things, such as microorganisms. The biological activities of the microorganisms formed an integral part of the process, but basically we just had to accept the characteristics of the organisms available (barring minor modifications possible through mutation-selection programs, etc.), so the non-biological parts of the process had to be designed around the characteristics of the organisms. Synthetic biology changes all that. Now we can (aspire to) design the characteristics of the organism, the biological component of the process, just as we can design the non-biological parts. The microorganism becomes just another part of the system, its design to be optimized just like the design of all the other parts. In this case study, we will consider an example of the development of a system, involving design and optimization of both the biological and non-biological components.

Starting Points

Arsenic (As, z=33) is a metalloid element related to phosphorus (group 15, p3 in the outer electron shell). Like phosphorus, it forms oxyanions, mainly arsenate (+5 oxidation state; AsO4, 3-) and arsenite (+3 oxidation state, AsO3, 3-). Arsenic is quite toxic, due to its ability to interfere with phosphate-dependent processes. Bacteria are often exposed to arsenate and arsenite in the environment, and most bacteria seem to possess a conserved mechanism for dealing with it, consisting of an arsenic detoxification operon. In the simplest case this consists of three genes: arsC, encoding arsenate reductase, which reduces arsenate to arsenite; arsB, encoding an arsenite efflux pump; and arsR, encoding a repressor which binds to the promoter of the operon, releasing only when it binds arsenate or arsenite.



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