Team:UC Davis/Potentiostat Design

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   <h2>Software</h2>
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    <li><img src="https://static.igem.org/mediawiki/2014/1/13/UCDavis_Full_Potentiostat.png"/></li>
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    <li><img src="https://static.igem.org/mediawiki/2014/5/53/UCDavis_Cheapstat.png" height="400px"/></li>
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    <li><img src="https://static.igem.org/mediawiki/2014/5/5d/UCDavis_CircuitAbstract.png"/><div style="position:absolute"><h2>Circuit Abstract</h2></div></li>
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    <li><img src="https://static.igem.org/mediawiki/2014/0/09/UCDavis_TeensyPinout.png"/></li>
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A potentiostat is an instrument capable of maintaining a voltage bias between electrodes. The bias encourages diffusion but more importantly the transfer of electrons which are recorded, and ultimately related to the species present in solution. When faced with the decision to buy or build our potentiostat, we found that the available solutions did not fit our needs. We decided to create our own. We developed an abstract and found a microcontroller with a 16-bit ADC (13 bit ENOB). We then designed, modeled, built and tested our potentiostat under a range of conditions. We went on to create a catalog of prototypes. The final product is the OliView potentiostat: <b>The first arduino-compatible potentiostat to incorporate a 16-bit ADC.</b>
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<img src="https://static.igem.org/mediawiki/2014/1/13/UCDavis_Full_Potentiostat.png" height="250px" style="float:left;margin-right:20px;" />Our biosensor required a potentiostat. A potentiostat is an instrument capable of maintaining a voltage bias between electrodes. <br><br>The bias encourages diffusion but more importantly the transfer of electrons which are recorded, and ultimately related to the species present in solution. We were faced with the decision to buy or build. <br><br>Unfortunately, publication quality potentiostats can range in the tens of thousands of dollars. We needed a cheaper solution if we wanted our device to be consumer friendly. We researched the literature for potentiostat circuits, and were presented with the CheapStat.
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<h3 style="color:#212f20;margin-bottom: 0;">Inspiration and Iteration</h3>
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<img src="http://web.chem.ucsb.edu/~kwp/cheapstat/cheaplayout.png" height="250px"/><img src="https://static.igem.org/mediawiki/2014/0/03/CheapStatActual.png" height="250px"/>
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The CheapStat is a budget friendly device developed at UC Santa Barbara several years ago. We aspired to build this circuit and modify the software for our purposes, however, the microcontroller on the CheapStat was controlled predominantly in machine level code. The learning curve seemed unreasonable considering our deadline, so we had to find another solution.<br><br>We were forced to build our own. With a clean slate, we wanted to create a device that would fulfill our needs, but also be welcomed by the iGEM community. We aimed to match the performance of the CheapStat, but also improve in three ways: increase the effective range of the instrument, decrease the cost of the circuit, and convert to an arduino-friendly microcontroller. In this capacity, we have succeeded.<br><br> We modeled our circuit after the CheapStat, eventually including more than 30 components. We went on to create five iterative prototypes. The schematic and board files for the various prototypes are all available <a href="https://2014.igem.org/Team:UC_Davis/Potentiostat_Design_Software">here</a>. <br><br>
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<b>To read more about the OliView hardware, click <a href="https://2014.igem.org/Team:UC_Davis/Potentiostat_Design_Inspiration_Iteration" class="brightlink">here</a>.</b>
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<img src="http://web.chem.ucsb.edu/~kwp/cheapstat/cheaplayout.png" height="250px" style="float:right;margin-left:20px;" />The CheapStat is a budget friendly device developed at UC Santa Barbara several years ago. We aspired to build this circuit and modify the software for our purposes, however, the microcontroller on the cheapStat was controlled predominantly in machine level code. The learning curve seemed unreasonable considering our deadline, so we had to find another path.<br><br>We were ultimately forced to build our own. With a clean slate, we wanted to create a device that would fulfill our needs, but also be welcomed by the iGEM community. We aimed to match the performance of the cheapStat, but also improve in three ways: increase the effective range of the instrument, decrease the cost of the circuit, and convert to an arduino-friendly microcontroller. <br><br> We modeled our circuit after the cheapStat, eventually including more than 30 components. We went on to create five iterative prototypes. The schematic and board files are all available <a href="https://2014.igem.org/Team:UC_Davis/Potentiostat_Design_Software">here</a>. To read more about our inspiration and circuit design, click <a href="https://2014.igem.org/Team:UC_Davis/Potentiostat_Design_Inspiration_Iteration">here</a>.  
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Flowchart!!! Kunkel!!! DNA!!!<br><br>
 
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Once we had identified the aldehyde dehydrogenases we wanted to screen for specificities, we needed order DNA so we could express the enzymes and assay them in the lab. For enzymes identified in the literature, sequences were pulled from UniProt Knowledge Base. We ordered DNA from Life Technologies, cloned the genes into the pET29b-(+) plasmid vector using the Gibson assembly method, and transformed the assembled plasmids into BLR strain E. coli for expression.  For our engineered mutants, Kunkel mutagenesis was used to introduce desired mutations into the plasmid DNA. Expressed aldehyde dehydrogenase enzymes were purified using affinity chromatography.<br><br>
 
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Click on “Build” to learn more about how we turned DNA sequences into enzymes
 
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<img src="https://static.igem.org/mediawiki/2014/d/d2/OliViewScreenShot.png" height="250px" style="float:left;margin-right:20px;margin-bottom:20px;" />The OliView software was written in C++ within the Qt Creator IDE. The backend of the software includes the GNU-licensed library QCustomPlot for graphing, and the open-source biquad library by Nigel Redmon, for digital signal processing. These elements have been incorporated with more than 1,200 lines of UC Davis code to create a feature-rich environment for controlling the OliView potentiostat. Our progress was updated through the UCDiGEM <a href="http://github.com/UCDiGEM/OliView" class="brightlink">OliView Github</a> . We included features for statistical analysis as well a .CSV exporting feature<br><br>
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The downloads section includes all the files necessary to build and run the OliView system. Schematic and board files for the OliView potentiostat are provided in Eagle V6.6 format. CAM processing files have been optimized for production by <a href="http://www.seeedstudio.com">Seeed Studios, Inc</a>.
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<b>To read more about the OliView software, click <a href="https://2014.igem.org/Team:UC_Davis/Potentiostat_Design_Software" class="brightlink">here</a>.</b>
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PLATE READER!!! CURVES!!!<br><br>
 
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To determine the specificity profiles of our aldehyde dehydrogenases, we needed to develop a simple, high-throughput assay which we could ultimately use to determine the aldehyde composition of a sample of olive oil. We developed a simple spectrophotometric plate assay which measures the concentration of NADH in a solution. Using this assay, we screened all 26 aldehyde dehydrogenases against 16 aldehyde substrates and identified four enzymes with unique specificities. We created full Michaelis-Menten curves and calculated the kinetic constants for the four enyzmes we identified on all sixteen aldehyde substrates. We also developed a protocol for extracting aldehydes from olive oil which could be used with our plate assay. <br><br>
 
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Latest revision as of 22:13, 9 December 2014

UC Davis iGEM 2014

Hardware

Hardware

Software

Software

Build Your Own

Build Your Own
> <

  • Circuit Abstract



A potentiostat is an instrument capable of maintaining a voltage bias between electrodes. The bias encourages diffusion but more importantly the transfer of electrons which are recorded, and ultimately related to the species present in solution. When faced with the decision to buy or build our potentiostat, we found that the available solutions did not fit our needs. We decided to create our own. We developed an abstract and found a microcontroller with a 16-bit ADC (13 bit ENOB). We then designed, modeled, built and tested our potentiostat under a range of conditions. We went on to create a catalog of prototypes. The final product is the OliView potentiostat: The first arduino-compatible potentiostat to incorporate a 16-bit ADC.

Hardware

The CheapStat is a budget friendly device developed at UC Santa Barbara several years ago. We aspired to build this circuit and modify the software for our purposes, however, the microcontroller on the CheapStat was controlled predominantly in machine level code. The learning curve seemed unreasonable considering our deadline, so we had to find another solution.

We were forced to build our own. With a clean slate, we wanted to create a device that would fulfill our needs, but also be welcomed by the iGEM community. We aimed to match the performance of the CheapStat, but also improve in three ways: increase the effective range of the instrument, decrease the cost of the circuit, and convert to an arduino-friendly microcontroller. In this capacity, we have succeeded.

We modeled our circuit after the CheapStat, eventually including more than 30 components. We went on to create five iterative prototypes. The schematic and board files for the various prototypes are all available here.

To read more about the OliView hardware, click here.

Software

The OliView software was written in C++ within the Qt Creator IDE. The backend of the software includes the GNU-licensed library QCustomPlot for graphing, and the open-source biquad library by Nigel Redmon, for digital signal processing. These elements have been incorporated with more than 1,200 lines of UC Davis code to create a feature-rich environment for controlling the OliView potentiostat. Our progress was updated through the UCDiGEM OliView Github . We included features for statistical analysis as well a .CSV exporting feature

The downloads section includes all the files necessary to build and run the OliView system. Schematic and board files for the OliView potentiostat are provided in Eagle V6.6 format. CAM processing files have been optimized for production by Seeed Studios, Inc.

To read more about the OliView software, click here.

Thanks

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