Difference between revisions of "Cfrench:CaseStudy1"

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* [http://ieeexplore.ieee.org/xpl/topAccessedArticles.jsp?punumber=4290605 Our paper in IET synthetic biology]
* [http://ieeexplore.ieee.org/xpl/topAccessedArticles.jsp?punumber=4290605 Our paper in IET synthetic biology]
* [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFX-4XC50FY-2H&_user=809099&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000043939&_version=1&_urlVersion=0&_userid=809099&md5=7f39f7bb7fc23b44f71bf166f7afe545 Our article in Desalination]
* [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFX-4XC50FY-2H&_user=809099&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000043939&_version=1&_urlVersion=0&_userid=809099&md5=7f39f7bb7fc23b44f71bf166f7afe545 Our article in Desalination]
* [http://wwwa.vito.be/english/environment/environmentaltech2d.htm VITO's BioMet biosensors]
===The iGEM project arsenic sensor===
===The iGEM project arsenic sensor===

Revision as of 04:58, 28 October 2009

Synthetic Biology Case Study 1: Development of an arsenic biosensor


Each module is composed of two parts. The first part consists of several lectures. The second part consists of a two-hour exemplar case study presented by one or more of the teachers or Institute members, demonstrating a successful scientific research achievement, such as a publication. The exemplar case study should cover an introduction to the problem, types of existing data, need for collaboration with researchers from a different scientific discipline, how the problem was tackled, and remaining open questions. The exemplar case study will provide students with ideas for their own case studies.

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.

Arsenic is also significantly toxic to people. One particularly unfortunate example is the case of groundwater in Bangladesh and West Bengal. During the 1970s, this region was plagued by waterborne diseases such as cholera, due to contaminated surface water. To solve this problem, NGOs drilled many tube wells to supply clean groundwater for drinking, washing and cooking. Unfortunately, 15-20 years later, many cases of skin cancer and other symptoms of chronic arsenic poisoning (arsenicosis) began to appear, and only then was it discovered that the wells had been drilled through arsenic-contaminated sediments. This was a great surprise, especially to the British Geological Survey (BGS), which had done the surveys for the project, as arsenic was not normally associated with such sediments. This has led to reexamination of other groundwaters, and the discovery that such contamination is actually quite widespread. The current WHO recommended limit for arsenic in drinking water is 10 ppb, though many regions are still operating to an older standard of 50 ppb.

This led to demand for a cheap, rapid and simple field test that could be used to measure arsenic levels in groundwater. This can be used to test wells on a regular basis (as the arsenic level within a well can change over time) and also to monitor the performance of filters which have been installed to remove arsenic, so as to know when the filter medium needs to be replaced. The standard test for this purpose is the Gutzeit test, which reduces arsenate/arsenite to volatile (and toxic) arsine gas (AsH3), which reacts with mercuric bromide (mercury is also a toxic heavy metal) to produce a coloured spot. There are a number of obvious issues with this test, not the least of which is that it is barely sensitive enough, giving a significant percentage of false negative results at 50 ppb arsenic. Also, interpretation of the coloured spot is rather subjective. Improved designs are available, such as the 'Arsenator', which address some of these issues, but it is clear that there is room for an improved test.

The iGEM project arsenic sensor

Further characterization and optimization

Alternative: an endospore-based biosensor

Alternative 2: an autochromogenic system producing lycopene

Requirements for the non-biological components

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