Team:Baltimore US/Notebook/ProjectIdeaNotes

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==Possible Projects==
====Project: DIY-Gem====
Creating the set of educational tools and learning resources to allow comprehension and accessibility to the core techniques associated with Synthetic Biology. We've discussed creating e.coli that can be added to the bb system that can actually produce the major enzymes used in these techniques so that beginner's can "grow their own", saving the $1 a ul that some of these can cost. We have the sequence for Pol1 (J)
for Taq Aquaticus, and can put it into e. coli, but it contains a Pst1 site dead in the center of it's sequence so we'd have to create a new sequence and test it's viability, prior to formatting it in the bb format. The Pfu polymerase from Pyroclase Fusarium is usually used with BB, as it has enhanced error protection mechanisms and can withstand higher temperature cycling. The patent on Pol1 has expired. Patents exist on Pst1, none on exist on EcoR1, Xbe and Spe, couldn't find patent or sequence information, need more research. Other implementation of the DIY-Bio structure involves the construction of inexpensive hardware that is utilized in the process of synthetic biology research, i.e. microgram scales, centrifuges, PCR thermocyclers, Gel Electrophoresis kits, Devices for volumetrics, histobots, DNA sequencers/synthesizers and enhanced microscopy equipment. Many of these hw pieces have already been hacked by various groups within the DIY-Bio communities, however our goal would be to create those pieces necessary for us to continue to experiment/collaborate past the end of the iGEM timeframe. <br>
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====Project: Children of Men====
Bio-remediation oriented project to sequester/breakdown excessive estrogen levels that are currently responsible for turning the bass populations in Maryland tributaries into intersex species. Apparently 100% of the Male Bass populations are currently intersex meaning that they are carrying eggs due to the high-levels of hormone disruptors such as Estrogen that are not being cleaned by Maryland's current water treatment facilities. Researchers at Washington State have posited using Ammonia based microbials in bio-reactor systems to help break down estrogen, and there are supposedly BB parts that can be used as Estrogen Receptors. Failure to act, could conceivably lead to a sterile future for mankind, aka "The Children of Men" scenario from the science fiction film of same name. <br>
Similar Bio-remediation scenarios were presented to deal with excess Nitrogen fixation, Pfisteria Sensors and petroleum digestion in response to the Gulf tragedy. <br>
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====Project: ANN====
Artificial neural networks offer powerful tools for pattern recognition, discriminant analysis and machine learning.  Originally developed as a model of human cognitive activity, artificial neural networks have been adopted by 
statistical modelers for their capacity to partition high-dimensional parameter spaces and "learn" to classify inputs through teaching and reinforcement.  The massively parallel nature of artificial neural networks have provided motivation to implement them in-vitro rather than in-silico.  Indeed, steps toward in vitro implementation have been taken by a number of previous iGEM teams.  We hope to improve upon these efforts.

In particular, we wish to provide tools for the construction of a multi-layer feed forward net with back-propagation of error.  Owing to the parallel nature of the net, implementation must consist of the development of a single computational unit along with the processes by which units can be rationally composed.  Such a project will require the completion of several subtasks.

The first item is the acceptance of input by the user.  We intend to employ cellular signaling mechanisms for communicating with the input layer.  Between network layers, we intend to employ the addressible conjugation method developed by Berkeley 2006.After input has been received by a node in a given layer of the net, it must be weighted, summed, and fed through a non-linear threshold function.  Weighting may be accompolished by molecular AND gates which limit the expression of the input protein to levels which may be governed by the concentrations of "weighting proteins" within the cell.  Summing and thresholding may then be naturally accomplished by cellular metabolism.  Output may be given to the user through the expression of fluorescent 
proteins.  Lastly, back-propagation of error may be accomplished by separate channels of addressing plasmids which up- or down-regulate rates of conjugation in the previous layer.

The above constitutes an ambitious program which may exceed the scope of the summer.  We wish to focus our efforts upon techniques for parallel, asynchronous addressible conjugation, especially so as to permit input from multiple nodes in the previous layer and allow computation of multiple input instances through a single generation of cells.
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