Team:MIT/miRNA

From 2014.igem.org

(Difference between revisions)

Latest revision as of 03:50, 18 October 2014

Description
Outcome
Experiments

Low Sensor
High Sensor
L7ae
Single-Input
Multi-Input

Parts

miRNA DETECTOR MODULE

SUBGROUP MEMBERS: Gary Burnett, Jing Wei "Raymond" Liu, Raashed Raziuddin, Jiaqi Xie

Attributions: Jing Wei "Raymond" Liu (Description), Gary Burnett (Experiments), Kathryn Brink (Animations)

sensing Alzheimer's through multi-input miRNA-based logic

Description

miRNAs (microRNAs) are short, noncoding strands of RNA that facilitate gene silencing - a single miRNA degrades an mRNA through a process involving complementary base-pairing between the miRNA and part of the mRNA sequence. A cell’s miRNA profile comprises the relative levels of all the miRNAs produced by that cell. Because miRNAs play a key role in regulating gene expression, it ought to be expected that a liver cell’s miRNA profile would differ significantly from that of a neuron. But more surprisingly, miRNA profiles can discriminate between identical cells in different conditions.

Neurons afflicted with Alzheimer’s disease display an miRNA profile significantly different from that of healthy neurons (A blood based 12-miRNA signature of Alzheimer disease patients, Leidinger et al, 2013). The miRNA subgroup aimed to use this difference as an approach to detecting Alzheimer’s disease. Our goal was to build a set of genetic sensors to specifically detect the miRNA profile of a neuron with Alzheimer’s and initiate a specific biological response upon doing so.

Our strategy took its inspiration from a similar detection circuit demonstrated to respond to cancer onset (Multi-input RNAi-based logic circuit for identification of specific cancer cells, Xie et al, 2011) Through existing research, we identified six miRNAs that are critically up- or down-regulated in Alzheimer’s neurons. Using the inverting logic inherent to miRNAs, we designed detection circuits to release a response factor upon sensing either heightened or lowered levels of their target miRNA, and customized each circuit to use one of the six miRNAs as its input. Using the principles of combinational logic, we can integrate the inputs from all six of our miRNA sensors, and actuate our response only when all six miRNAs meet their critical threshold concentrations. This ensures excellent specificity for our circuit.

return to top

Outcome

The miRNA detection team built individual sensing constructs for each miRNA. We determined input-output relations for our sensors using flow cytometry and found that our sensors respond to miRNA levels by modulating the production of a fluorescent reporter, exactly as we had predicted.

Future work on our sensors will focus largely on implementation concerns - tuning as well as integration. Although we have shown that our sensors respond on a digital level, this does not accurately model the dynamic chemical conditions of the intracellular environment. We would thus like to refine our sensor control. In the ideal case, a small shift in a critical range of miRNA concentration will result in a large output signal, so that the treatment response is both specific and substantial.

We only tested binary combinatorial inputs for our sensors (one high and one low, or two of each). The ultimate goal is to use all six sensors in tandem with one another. When we use more sensors, we achieve greater precision, but as a tradeoff we gain more variables that require keeping track. There is also the complication that the various miRNAs are not biologically present at the same concentrations, meaning that each of our sensors must be individually tuned for optimal response to its own miRNA. Because all six of our sensors actuate the same response, we must also ensure that one sensor does not become overstimulated, activating our treatment even in the absence of input from the other sensors. These are all issues that can only be answered through extensive iterative testing.

The miRNA sensing team has established a conceptual grounding for a detection mechanism that responds to cellular conditions in the fashion of a true biological system. It is worthwhile to note that our strategy is not Alzheimer’s-specific, and can be implemented with any disease with a characteristic miRNA profile. This can be a novel approach for diseases with poorly understood etiologies, such as Parkinson’s (MicroRNA profiling of Parkinson's disease brains identifies early downregulation of miR-34b/c which modulate mitochondrial function, Minones-Moyano, 2011)

return to top

Experiments

return to top

Low Sensor Construction

By cloning an miRNA target site 3’ to a gene coding a reporter protein, we can easily create a sensor that produces reporter protein only when miRNA levels are low enough to permit translation. In our experiments, we used a fluorescent reporter as a placeholder for rtTA, which would activate our treatment circuit.

return to top

High Sensor Construction

Because miRNAs naturally silence genes, for our high sensor design we cloned miRNA target sites to a repressor protein that would block transcription of response protein at the low sensor. We chose to use the L7ae/K-turn to eliminate the possibility of crosstalk with other cellular activities.

return to top

Repression of L7ae

Before coming to any conclusions about the success of our constructs, we needed to make sure that the L7ae/k-turn system worked correctly. To do this we expressed k-turn:eGFP with and without the presence of constitutive L7ae. We used eBFP as our normalizing transfection marker.

L7ae Repression of 2x-Kturn-GFP. In the absence of L7ae, eBFP2 and GFP fluorescence show a positive relationship, as expected when co-expressing two constitutive fluorophores. However, upon the addition of L7ae into the system, GFP production is almost completely silenced. This indicates that our L7ae / 2x-Kturn system is viable to implement in our high sensors.

return to top

Single-Input miRNA Sensor Experiments

We tested the sensitivity of our sensor constructs individually for each of the six miRNA that are upregulated or downregulated in Alzheimer's neurons. Our experiments were conducted by transfecting HEK293 cells with our sensor constructs. Since there were no cell lines in existence that could naturally reproduce the exact miRNA expression profile of an Alzheimer's neuron, we needed to artifically alter the miRNA profile of an existing cell line. We discovered through research in literature that HEK293 cells do not endogenously express any of the miRNA's that we planned to sense for, thus they provided the perfect low miRNA environment. In order to create a high sensor environment in this cell line, we needed co-transfect siRNA along with our sensors.

A
B	C
Low Sensor miR-144 in the presence and absence of siRNA-144 in HEK293 cells. Using red as our transfection marker and blue as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show repressed eBFP2 output. However the cytometry results in figure (A) shows that there is no difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment.

A
B	C
Low Sensor miR-181c in the presence and absence of siRNA-181c in HEK293 cells. Using red as our transfection marker and blue as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show repressed eBFP2 output. However the cytometry results in figure (A) shows that there is no difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment.

A
B	C
High Sensor miR-30d in the presence and absence of siRNA-30d in HEK293 cells. Using red as our transfection marker and green as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show an increase in GFP output. However the cytometry results in figure (A) shows that there is no difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment.

A
B	C
High Sensor miR-125b in the presence and absence of siRNA-125b in HEK293 cells. Using red as our transfection marker and green as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show an increase in GFP output. The cytometry results in figure (A) shows that there is difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment.

A
B	C
High Sensor miR-146a in the presence and absence of siRNA-146ain HEK293 cells. Using red as our transfection marker and green as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show an increase in GFP output. However the cytometry results in figure (A) shows that there is no difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment.

A
B	C
High Sensor let-7f in the presence and absence of siRNA-7f in HEK293 cells. Using red as our transfection marker and green as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show an increase in GFP output. The cytometry results in figure (A) shows that there is no difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment.

return to top

Multi-Input miRNA Sensor Experiments

Ideally, we would put all of our miRNA sensors together into one, large classifier circuit that is capable of testing all the miRNAs in the Alzheimer's profile at once. However, before we test 6 sensors in tandem, we decided to try some pairwise combinations of high and low sensors. This would give us important information that we could use to tune our system before making to jump to testing all of the sensors at once.

Two low sensors. We co-transfected the same low sensors from the previous Single Input miRNA Sensor Experiments using red as our transfection marker and blue as our output. Given the results of our previous experiments we hoped that the sensors, when exposed to the inhibiting siRNA, would show a more repressed eBFP2 output. However, the cytometry results in figure (A) show that there was still no difference between the 'on' and 'off' state.

Two high sensors.We co-transfected the same high sensors from the previous Single Input miRNA Sensor Experiments using red as our transfection marker and green as our output. Given the results of our previous experiments we hoped that the sensors, when exposed to the inhibiting siRNA, would show a similar amount of GFP output as before. However, the cytometry results in figure (B) show that there was still no difference between the 'on' and 'off' state.

C.1.

One low sensor and one high sensor. We co-transfected the same low and high sensors from the previous Single Input miRNA Sensor Experiments. In this figure we show red as our transfection marker and blue as the low sensor output. Given the results of our previous experiments we hypothesized that, when exposed to the inhibiting siRNA, the sensor output would show a similar amount of repressed eBFP2 output as before. The cytometry in figure (C.1.) confirm this by showing that there was still no difference between the 'on' and 'off' state.

C.2.

One low sensor and one high sensor. We co-transfected the same low and high sensors from the previous Single Input miRNA Sensor Experiments. In this figure we show red as our transfection marker and green as the high sensor output. Given the results of our previous experiments we hypothesized that, when exposed to the inhibiting siRNA, the sensor output would show a similar amount of GFP output as before. The cytometry in figure (C.2.) confirms this by showing that there was still no difference between the 'on' and 'off' state.

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Parts

full parts list available here
pENTR_hEF1a
MAV1212-RFP
pENTR_L7ae
MAV1212_hEF1a_L7ae
MAV1212_hEF1a_eBFP2
Low sensor: eBFP2_miR-144
Low sensor: eBFP2_miR-181c
High sensor: L7ae_miR-30d
High sensor: L7ae_miR-146a
High sensor: L7ae_miR-125b
High sensor: L7ae_miR-let-7f
Low sensor: eBFP2_miR-144_miR-181c

Retrieved from "http://2014.igem.org/Team:MIT/miRNA"

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-<li><a href="#top">Top</a></li>
 <li><a href="#description">Description</a></li>
 <li><a href="#outcome">Outcome</a></li>
 <li><a href="#experiments">Experiments</a></li>
-<li><a href="#parts">Parts</a></li>
+<ul>
+<li><a href="#1">Low Sensor </a></li>
+<li><a href="#2">High Sensor </a></li>
+<li><a href="#3">L7ae </a></li>
+<li><a href="#4">Single-Input </a></li>
+<li><a href="#5">Multi-Input </a></li>
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-<h1>miRNA Detector Module <a name="top" /></h1><br />
-<div style="float:left;clear:none"><img src="https://static.igem.org/mediawiki/2014/a/a7/MIT_protein_receptor.jpg"></div>
+<h3 align= "center" style="font-size:42px; color:teal">miRNA DETECTOR MODULE <a name="top" ></a></h3>
-<div align="center">
+<center>
+<p style="font-size:12px" align=center><i><b>SUBGROUP MEMBERS: Gary Burnett, Jing Wei "Raymond" Liu, Raashed Raziuddin, Jiaqi Xie </b></i></p>
+<p style="font-size:12px" align=center><i>Attributions: Jing Wei "Raymond" Liu (Description), Gary Burnett (Experiments), Kathryn Brink (Animations)</i></p>
+<font size=4>sensing Alzheimer's through multi-input miRNA-based logic</font><br /><br />
+</center>
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-		<option value="https://static.igem.org/mediawiki/2014/9/96/MIT_flip_book_placeholder.jpg">Overview</option>
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+		<option value="https://static.igem.org/mediawiki/2014/f/f3/MIT_mirna_high_sensor2.png">2</option>
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+		<option value="https://static.igem.org/mediawiki/2014/6/61/MIT_mirna_low_sensor2.png">5</option>
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+by <a href="http://javascriptsource.com">The JavaScript Source</a></font> -->
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+<h2>Description</h2><a name="description"></a>
+miRNAs (microRNAs) are short, noncoding strands of RNA that facilitate gene silencing - a single miRNA degrades an mRNA through a process involving complementary base-pairing between the miRNA and part of the mRNA sequence. A cell’s miRNA profile comprises the relative levels of all the miRNAs produced by that cell. Because miRNAs play a key role in regulating gene expression, it ought to be expected that a liver cell’s miRNA profile would differ significantly from that of a neuron. But more surprisingly, miRNA profiles can discriminate between identical cells in different conditions.</br>
+</br>
+Neurons afflicted with Alzheimer’s disease display an miRNA profile significantly different from that of healthy neurons (A blood based 12-miRNA signature of Alzheimer disease patients, Leidinger et al, 2013). The miRNA subgroup aimed to use this difference as an approach to detecting Alzheimer’s disease. Our goal was to build a set of genetic sensors to specifically detect the miRNA profile of a neuron with Alzheimer’s and initiate a specific biological response upon doing so.</br>
+</br>
+Our strategy took its inspiration from a similar detection circuit demonstrated to respond to cancer onset (Multi-input RNAi-based logic circuit for identification of specific cancer cells, Xie et al, 2011) Through existing research, we identified six miRNAs that are critically up- or down-regulated in Alzheimer’s neurons. Using the inverting logic inherent to miRNAs, we designed detection circuits to release a response factor upon sensing either heightened or lowered levels of their target miRNA, and customized each circuit to use one of the six miRNAs as its input. Using the principles of combinational logic, we can integrate the inputs from all six of our miRNA sensors, and actuate our response only when all six miRNAs meet their critical threshold concentrations. This ensures excellent specificity for our circuit.</br> <br><a href="#top">return to top</a>
+<h2>Outcome</h2><a name="outcome" ></a>
-<p><center>
+The miRNA detection team built individual sensing constructs for each miRNA. We determined input-output relations for our sensors using flow cytometry and found that our sensors respond to miRNA levels by modulating the production of a fluorescent reporter, exactly as we had predicted. </br>
+</br>
+Future work on our sensors will focus largely on implementation concerns - tuning as well as integration. Although we have shown that our sensors respond on a digital level, this does not accurately model the dynamic chemical conditions of the intracellular environment. We would thus like to refine our sensor control. In the ideal case, a small shift in a critical range of miRNA concentration will result in a large output signal, so that the treatment response is both specific and substantial. </br>
+</br>
+We only tested binary combinatorial inputs for our sensors (one high and one low, or two of each). The ultimate goal is to use all six sensors in tandem with one another. When we use more sensors, we achieve greater precision, but as a tradeoff we gain more variables that require keeping track. There is also the complication that the various miRNAs are not biologically present at the same concentrations, meaning that each of our sensors must be individually tuned for optimal response to its own miRNA. Because all six of our sensors actuate the same response, we must also ensure that one sensor does not become overstimulated, activating our treatment even in the absence of input from the other sensors. These are all issues that can only be answered through extensive iterative testing. </br>
+</br>
+The miRNA sensing team has established a conceptual grounding for a detection mechanism that responds to cellular conditions in the fashion of a true biological system. It is worthwhile to note that our strategy is not Alzheimer’s-specific, and can be implemented with any disease with a characteristic miRNA profile. This can be a novel approach for diseases with poorly understood etiologies, such as Parkinson’s (MicroRNA profiling of Parkinson's disease brains identifies early downregulation of miR-34b/c which modulate mitochondrial function, Minones-Moyano, 2011) </br><br><a href="#top">return to top</a>
+<h2>Experiments</h2><a name="experiments" ></a>
+<img src="https://static.igem.org/mediawiki/2014/1/17/MIT_results.jpg"><br>
-<font face="arial, helvetica" size"-2">Free JavaScripts provided<br>
+<br><a href="#top">return to top</a>
+<a name="1"></a><h3>Low Sensor Construction</h3>
-by <a href="http://javascriptsource.com">The JavaScript Source</a></font>
+By cloning an miRNA target site 3’ to a gene coding a reporter protein, we can easily create a sensor that produces reporter protein only when miRNA levels are low enough to permit translation. In our experiments, we used a fluorescent reporter as a placeholder for rtTA, which would activate our treatment circuit.</br>
-</center><p>
+<table align=center><tr><td align=center>
-<a name="description"></a>
+<a href="https://static.igem.org/mediawiki/2014/d/d7/MIT_low_sensor_schematic.png"> <img src="https://static.igem.org/mediawiki/2014/d/d7/MIT_low_sensor_schematic.png" width=50% align=center> </a></br>
-<h2>Outcome</h2><a name="outcome" ></a>
+</td></tr></table>
+<br><a href="#top">return to top</a>
+<a name="2"></a><h3>High Sensor Construction</h3>
+Because miRNAs naturally silence genes, for our high sensor design we cloned miRNA target sites to a repressor protein that would block transcription of response protein at the low sensor. We chose to use the L7ae/K-turn to eliminate the possibility of crosstalk with other cellular activities. </br>
-Vivamus maximus lectus diam, quis luctus tortor blandit sed. Pellentesque ullamcorper urna ut elit gravida, eget pretium orci maximus. Nam dignissim diam tristique placerat aliquet. Nullam nulla nulla, porttitor nec lorem quis, scelerisque rutrum odio. Suspendisse potenti. Vestibulum vel metus metus. Nam eu tempus mauris. Sed et mattis ex. Curabitur eu purus fringilla mi molestie fermentum sit amet non arcu. Aliquam erat volutpat.<br />
+<table align=center><tr><td align=center>
+<a href="https://static.igem.org/mediawiki/2014/e/ec/MIT_high_sensor_schematic.png"> <img src="https://static.igem.org/mediawiki/2014/e/ec/MIT_high_sensor_schematic.png" width=50% align=center></a> </br>
+</td></tr></table>
+<br><a href="#top">return to top</a>
+<a name="3"></a><h3>Repression of L7ae</h3>
-Duis egestas lorem elit, eu suscipit lacus lacinia eget. Vivamus ultrices aliquet justo a consequat. Sed turpis quam, posuere ut interdum sed, rutrum a turpis. Nam malesuada eu dui at ultrices. Etiam mollis bibendum erat sit amet ultrices. Proin id tellus tellus. Fusce ultricies aliquam consequat.<br />
+Before coming to any conclusions about the success of our constructs, we needed to make sure that the L7ae/k-turn system worked correctly. To do this we expressed k-turn:eGFP with and without the presence of constitutive L7ae. We used eBFP as our normalizing transfection marker. </br><br>
-Duis vel massa ac justo tempus eleifend. Vestibulum pulvinar eu orci at consequat. Quisque ultrices mi vel porta finibus. Nunc luctus porttitor felis id blandit. Integer id enim et orci dapibus finibus et in mauris. Donec tortor dolor, viverra vitae mi ac, mattis gravida nisi. Suspendisse potenti. Quisque ac metus in tortor tincidunt laoreet. Nullam fermentum porta porta. Praesent pharetra sem non purus mollis pulvinar. Donec posuere orci id orci elementum, vel eleifend lorem vehicula. In pharetra mauris risus, vel iaculis eros gravida sit amet. Donec eu cursus quam. Morbi nisi odio, ullamcorper at dolor et, facilisis feugiat diam. Sed et ante luctus, condimentum nunc nec, ullamcorper enim. Nunc faucibus massa tincidunt ipsum varius egestas.<br />
+<table align="center" width=75%><tr>
+<tr><td align=center>
+<a href="https://static.igem.org/mediawiki/2014/3/34/MIT_L7ae_Repression_of_KxKturnGFP.png"> <img src="https://static.igem.org/mediawiki/2014/3/34/MIT_L7ae_Repression_of_KxKturnGFP.png" width=100% align=center> </a></br>
+</td></tr>
+<tr><td><p><b>L7ae Repression of 2x-Kturn-GFP. </b>In the absence of L7ae, eBFP2 and GFP fluorescence show a positive relationship, as expected when co-expressing two constitutive fluorophores. However, upon the addition of L7ae into the system, GFP production is almost completely silenced. This indicates that our L7ae / 2x-Kturn system is viable to implement in our high sensors. </p></td></tr>
+</table>
-In tincidunt ante sed erat mollis sagittis a pulvinar sem. Quisque ac scelerisque ex. Vestibulum in turpis vel quam malesuada hendrerit. Suspendisse finibus sem tortor, vel convallis velit vehicula at. Duis tincidunt aliquet quam eget malesuada. Nulla vitae euismod erat. Sed ullamcorper molestie augue cursus suscipit. Vestibulum varius mollis purus, vitae posuere nisi egestas nec. Cras placerat molestie velit, tristique elementum erat. Duis non sagittis mi. Nunc tempus consectetur vestibulum. Nulla facilisi. Vivamus imperdiet semper suscipit. Duis a leo quis mauris facilisis ornare id nec erat. Proin vitae metus hendrerit, gravida risus non, finibus velit. Maecenas consequat nisi quis nisi mollis, sed porta nisl tempor.<br />
+<br><a href="#top">return to top</a>
+<a name="4"></a><h3>Single-Input miRNA Sensor Experiments</h3>
-Ut molestie viverra nulla tincidunt egestas. Ut in lacinia nulla. Duis aliquet, est ut tempor interdum, libero lorem maximus dolor, vitae pulvinar purus nunc ut est. Sed at risus consequat, commodo purus sed, pellentesque turpis. Sed fringilla lorem felis, id tincidunt nunc porta vitae. Aliquam laoreet magna at magna vestibulum, fermentum tempor lacus aliquet. Sed diam nisi, sollicitudin in rhoncus vel, interdum molestie orci. Proin sit amet erat sem. Donec at lacinia felis, non aliquam nisl. Curabitur risus mauris, viverra a scelerisque id, vulputate nec magna. <br />
+We tested the sensitivity of our sensor constructs individually for each of the six miRNA that are upregulated or downregulated in Alzheimer's neurons. Our experiments were conducted by transfecting HEK293 cells with our sensor constructs. Since there were no cell lines in existence that could naturally reproduce the exact miRNA expression profile of an Alzheimer's neuron, we needed to artifically alter the miRNA profile of an existing cell line. We discovered through research in literature that HEK293 cells do not endogenously express any of the miRNA's that we planned to sense for, thus they provided the perfect low miRNA environment. In order to create a high sensor environment in this cell line, we needed co-transfect siRNA along with our sensors.
-<h2>Experiments</h2><a name="experiments" ></a>
-<img src="https://static.igem.org/mediawiki/2014/1/17/MIT_results.jpg"><br>
-Suspendisse luctus lobortis feugiat. Aenean vel velit rhoncus, molestie tellus non, egestas nulla. Interdum et malesuada fames ac ante ipsum primis in faucibus. Nam eleifend tortor eget tincidunt semper. Suspendisse porttitor mollis ullamcorper. Maecenas commodo ante nec diam rhoncus tristique. Ut varius leo a libero cursus posuere. Duis consectetur metus tincidunt mauris dictum venenatis. Maecenas sit amet urna elementum, tristique justo sed, eleifend ex. Fusce nec volutpat ligula, id venenatis ligula. Fusce in hendrerit tellus. Nam eu rutrum orci. Morbi ac augue vitae sapien varius posuere. Suspendisse sit amet odio est. Pellentesque rutrum, purus a faucibus dictum, magna libero iaculis odio, in dapibus nisl lacus sed tellus. Integer faucibus risus dolor, in blandit est interdum ut.
+<table align="center" width=75%>
-Quisque volutpat gravida bibendum. Nullam fringilla magna nisl. Phasellus pulvinar lacus velit, ac bibendum est vehicula vitae. Duis porta nec nisi in molestie. Phasellus id sem fermentum turpis finibus condimentum. Etiam semper semper ligula, in ornare odio congue et. Proin accumsan est sed vulputate blandit.
+<tr><td colspan=2 align=center><p align=left><b>A</b></p>
+<a href="https://static.igem.org/mediawiki/2014/a/a3/HEK293_Single_Input_Sensor_miR-144.png"> <img src="https://static.igem.org/mediawiki/2014/a/a3/HEK293_Single_Input_Sensor_miR-144.png" align=center width=100%> </a></br>
+</td></tr>
-Morbi aliquet lacus eros, condimentum vulputate lectus blandit vel. Morbi ac nibh a elit placerat convallis. Curabitur finibus nibh at diam aliquet, vel consequat turpis ullamcorper. Proin suscipit malesuada quam. In hac habitasse platea dictumst. Morbi posuere hendrerit ipsum, nec porta nisl sollicitudin vitae. In justo urna, hendrerit quis quam in, tempus ultricies velit. Fusce hendrerit, diam nec sodales dignissim, tortor nulla cursus massa, sed pharetra lacus magna at sapien. Praesent euismod sodales felis ut efficitur. Praesent lacinia, felis non efficitur condimentum, arcu dui mollis orci, non placerat libero ipsum eu leo. Ut cursus imperdiet nisi at aliquam. Sed leo tortor, blandit sed mattis sit amet, semper a erat. Donec consectetur velit id arcu viverra, a faucibus neque efficitur. Vestibulum ullamcorper elit arcu, id elementum nisi dignissim in. Etiam gravida nibh at neque elementum, id semper nisi pharetra. Integer quis ante non elit porta efficitur.
+<tr><td><p align=left><b>B</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/7/7d/144_no_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/7/7d/144_no_sirna.png"  align=right width=100%> </a></br>
+</td>
-Vestibulum viverra et orci volutpat ornare. Sed tincidunt in nisi ut consectetur. Nullam lacinia sed nisl vel vestibulum. Duis non dui id odio tincidunt laoreet. Suspendisse potenti. Mauris ut ligula nunc. Suspendisse tristique, metus id pharetra placerat, tellus ante convallis ligula, eu placerat dui orci quis purus.
+<td><p align=left><b>C</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/6/6d/144_yes_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/6/6d/144_yes_sirna.png"  align=left width=100%> </a></br>
+</td>
+</tr>
-Aliquam accumsan massa vitae ex iaculis, quis cursus arcu blandit. Sed mauris libero, pharetra sed nulla et, rhoncus euismod risus. Duis ullamcorper ut elit molestie consectetur. Nunc at sapien id lacus semper eleifend. Duis in fermentum odio. Suspendisse venenatis venenatis molestie. Fusce iaculis ante a aliquam bibendum. Duis erat quam, viverra id urna nec, malesuada vulputate augue. Duis vel aliquam lorem, a porta massa. Interdum et malesuada fames ac ante ipsum primis in faucibus. Ut ipsum dui, iaculis id vehicula non, dictum nec ipsum. Cras sit amet erat eleifend, euismod nibh ut, viverra dolor. Duis vehicula semper quam ut laoreet. Vivamus tempor felis sed mi blandit lacinia.
+<tr><td colspan=2>
-<h2>Parts</h2><a name="parts" ></a>
+<p><b>Low Sensor miR-144 in the presence and absence of siRNA-144 in HEK293 cells.</b> Using <b>red</b> as our transfection marker and <b>blue</b> as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show repressed eBFP2 output. However the cytometry results in figure (A) shows that there is no difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment.</p>
+</td></tr>
+</table>
-Suspendisse ornare turpis vitae quam ultrices, in interdum nunc fringilla. Donec volutpat leo justo, in vestibulum quam dictum vel. Fusce cursus elit non lacus rutrum porttitor. In enim odio, tincidunt ut facilisis ac, convallis non nisl. Nunc semper lorem nulla, et imperdiet mi faucibus ut. Mauris fermentum, ex in faucibus accumsan, lectus augue ornare tortor, id mattis massa felis et felis. Sed imperdiet dictum nibh at pellentesque. Donec et tincidunt orci, sit amet lobortis enim. Pellentesque facilisis semper eleifend. Cras varius ut nisl vel aliquet. Fusce mattis mollis ligula. Morbi elementum ac tortor at auctor. In scelerisque, mauris ac condimentum tristique, tortor sem porta dui, aliquet aliquam erat magna eget tortor.
+<table align="center" width=75%>
-Vestibulum non nibh mauris. Pellentesque nibh eros, semper eu erat ac, ornare lobortis orci. Etiam eget ultrices elit, nec faucibus erat. Suspendisse potenti. Fusce enim libero, luctus id condimentum eget, venenatis vitae augue. Aenean pellentesque tempor lectus, et ultricies augue varius sit amet. Sed imperdiet congue diam, quis fringilla magna porttitor at. Mauris pellentesque tincidunt nisi a lobortis. Sed eget fringilla dui, ut ultrices enim. Maecenas pulvinar dictum tristique. Suspendisse sodales condimentum egestas. Integer at felis nulla. Curabitur dignissim interdum justo non varius.
+<tr><td colspan=2 align=center><p align=left><b>A</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/0/07/MIT_HEK293_Single_Input_Sensor_miR-181c.png"> <img src="https://static.igem.org/mediawiki/2014/0/07/MIT_HEK293_Single_Input_Sensor_miR-181c.png" width=100% align=center> </a></br>
+</td></tr>
-Fusce finibus lacus at tincidunt tempor. Pellentesque ullamcorper dictum blandit. Integer in porttitor nunc. Aliquam sodales ac velit id egestas. Phasellus mauris mauris, consectetur eget est sit amet, mollis rutrum eros. Etiam in risus id tellus dapibus lobortis posuere vitae risus. Sed vel justo sem. Proin eu tellus finibus, egestas nisl sed, aliquam tellus. Proin pretium lorem ultrices tincidunt gravida. Sed dolor urna, semper in fringilla a, rutrum sed quam. Sed pretium sapien enim, at dictum sapien dapibus a. Aenean a imperdiet turpis, eu lobortis eros. Praesent convallis, leo vitae consectetur vehicula, arcu odio tincidunt sem, eget venenatis mi purus vitae erat.
+<tr>
+<td align=center><p align=left><b>B</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/0/08/181c_no_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/0/08/181c_no_sirna.png" width=100% align=right> </a></br>
+</td>
-Praesent non urna commodo, imperdiet ex quis, luctus diam. Pellentesque semper quam vel felis commodo semper. Sed vel elit sed urna tempus mollis vel vitae metus. Vivamus id tellus ligula. Duis eget auctor diam. Maecenas et libero at leo sodales congue. Pellentesque at dui quis arcu hendrerit dignissim vel quis dui. Curabitur finibus, ante vel tristique volutpat, lacus arcu varius purus, ut eleifend diam nunc sed est. Phasellus sed fringilla justo.
+<td align = center><p align=left><b>C</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/5/5a/181c_yes_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/5/5a/181c_yes_sirna.png" width=100% align=left> </a></br>
+</td>
+</tr>
-Etiam venenatis rutrum lorem, dignissim dignissim odio egestas in. Duis tempor ultricies porttitor. In vitae hendrerit est. Sed id dolor nec ante maximus vestibulum nec vel velit. Curabitur pellentesque varius dui sed sagittis. Praesent vitae enim id arcu dictum imperdiet in a libero. Morbi sit amet risus quis lectus vestibulum hendrerit. Etiam non consectetur justo, quis tincidunt ex. Nam varius arcu at quam blandit elementum. Nam sit amet odio a ante tristique molestie nec a turpis. Phasellus mi lorem, venenatis feugiat dignissim quis, gravida vitae nibh. Aliquam sodales ex enim, fringilla finibus ipsum tincidunt in. Donec felis tortor, auctor sit amet luctus non, mattis vitae dui.
+<tr><td colspan=2 width=75%>
+<p><b>Low Sensor miR-181c in the presence and absence of siRNA-181c in HEK293 cells.</b> Using <b>red</b> as our transfection marker and <b>blue</b> as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show repressed eBFP2 output. However the cytometry results in figure (A) shows that there is no difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment.</p>
+</td></tr>
+</table>
+<table align="center" width=75%>
+<tr><td colspan=2 align=center><p align=left><b>A</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/2/28/MIT_HEK293_Single_Input_Sensor_miR-30d.png"> <img src="https://static.igem.org/mediawiki/2014/2/28/MIT_HEK293_Single_Input_Sensor_miR-30d.png" width=100% align=center> </a></br>
+</td></tr>
+<tr>
+<td align=center><p align=left><b>B</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/d/d2/30d_no_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/d/d2/30d_no_sirna.png" width=100% align=right> </a></br>
+</td>
+<td align = center><p align=left><b>C</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/9/9d/30d_yes_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/9/9d/30d_yes_sirna.png" width=100% align=left> </a></br>
+</td>
+</tr>
+<tr><td colspan=2 width=75%>
+<p><b>High Sensor miR-30d in the presence and absence of siRNA-30d in HEK293 cells.</b> Using <b>red</b> as our transfection marker and <b>green</b> as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show an increase in GFP output. However the cytometry results in figure (A) shows that there is no difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment.</p>
+</td></tr>
+</table>
+<table align="center" width=75%>
+<tr><td colspan=2 align=center><p align=left><b>A</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/9/90/MIT_HEK293_Single_Input_Sensor_miR-125b.png"> <img src="https://static.igem.org/mediawiki/2014/9/90/MIT_HEK293_Single_Input_Sensor_miR-125b.png" width=100% align=center> </a></br>
+</td></tr>
+<tr>
+<td align=center><p align=left><b>B</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/8/8b/125b_no_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/8/8b/125b_no_sirna.png" width=100% align=right> </a></br>
+</td>
+<td align = center><p align=left><b>C</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/4/45/125b_yes_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/4/45/125b_yes_sirna.png" width=100% align=left> </a></br>
+</td>
+</tr>
+<tr><td colspan=2 width=75%>
+<p><b>High Sensor miR-125b in the presence and absence of siRNA-125b in HEK293 cells.</b> Using <b>red</b> as our transfection marker and <b>green</b> as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show an increase in GFP output. The cytometry results in figure (A) shows that there is difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment. </p>
+</td></tr>
+</table>
+<table align="center" width=75%>
+<tr><td colspan=2 align=center><p align=left><b>A</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/3/34/HEK293_Single_Input_Sensor_miR-146a.png"> <img src="https://static.igem.org/mediawiki/2014/3/34/HEK293_Single_Input_Sensor_miR-146a.png" width=100% align=center> </a></br>
+</td></tr>
+<tr>
+<td align=center><p align=left><b>B</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/7/74/146a_no_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/7/74/146a_no_sirna.png" width=100% align=right> </a></br>
+</td>
+<td align = center><p align=left><b>C</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/b/b7/146a_yes_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/b/b7/146a_yes_sirna.png" width=100% align=left> </a></br>
+</td>
+</tr>
+<tr><td colspan=2 width=75%>
+<p><b>High Sensor miR-146a in the presence and absence of siRNA-146ain HEK293 cells.</b> Using <b>red</b> as our transfection marker and <b>green</b> as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show an increase in GFP output. However the cytometry results in figure (A) shows that there is no difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment.</p>
+</td></tr>
+</table>
+<table align="center" width=75%>
+<tr><td colspan=2 align=center><p align=left><b>A</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/e/e9/MIT_HEK293_Single_Input_Sensor_let7f.png"> <img src="https://static.igem.org/mediawiki/2014/e/e9/MIT_HEK293_Single_Input_Sensor_let7f.png" width=100% align=center> </a></br>
+</td></tr>
+<tr>
+<td align=center><p align=left><b>B</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/4/40/7f_no_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/4/40/7f_no_sirna.png" width=100% align=right> </a></br>
+</td>
+<td align = center><p align=left><b>C</b></p><br>
+<a href="https://static.igem.org/mediawiki/2014/9/9e/7f_yes_sirna.png"> <img src="https://static.igem.org/mediawiki/2014/9/9e/7f_yes_sirna.png" width=100% align=left> </a></br>
+</td>
+</tr>
+<tr><td colspan=2 width=75%>
+<p><b>High Sensor let-7f in the presence and absence of siRNA-7f in HEK293 cells.</b> Using <b>red</b> as our transfection marker and <b>green</b> as our output, we expected that the sensor, when exposed to the inhibiting siRNA, would show an increase in GFP output. The cytometry results in figure (A) shows that there is no difference between the 'on' and 'off' state. This conclusion is reinforced by the microscopy in (B) and (C). On the left the sensor is in a low miRNA environment, and on the right the sensor is in a high miRNA environment.</p>
+</td></tr>
+</table>
+<br><a href="#top">return to top</a>
+<a name="5"></a><h3>Multi-Input miRNA Sensor Experiments</h3>
+Ideally, we would put all of our miRNA sensors together into one, large classifier circuit that is capable of testing all the miRNAs in the Alzheimer's profile at once. However, before we test 6 sensors in tandem, we decided to try some pairwise combinations of high and low sensors. This would give us important information that we could use to tune our system before making to jump to testing all of the sensors at once.</br>
+<table align="center" width=75%>
+<tr><td align=center><p align=left><b>A</b></p>
+<a href="https://static.igem.org/mediawiki/2014/4/4e/MIT_HEK293_Multi_Input_Sensor_miR-144_miR-181c.png"> <img src="https://static.igem.org/mediawiki/2014/4/4e/MIT_HEK293_Multi_Input_Sensor_miR-144_miR-181c.png" width=100% align=center> </a></br>
+</td></tr>
+<tr><td>
+<p><b>Two low sensors. </b> We co-transfected the same low sensors from the previous Single Input miRNA Sensor Experiments using <b>red</b> as our transfection marker and <b>blue</b> as our output. Given the results of our previous experiments we hoped that the sensors, when exposed to the inhibiting siRNA, would show a more repressed eBFP2 output. However, the cytometry results in figure (A) show that there was still no difference between the 'on' and 'off' state.</p>
+</td></tr>
+</table><br>
+<table align="center" width=75%>
+<tr><td align=center><p align=left><b>B</b></p>
+<a href="https://static.igem.org/mediawiki/2014/a/a2/MIT_HEK293_Multi_Input_Sensor_miR-125b_miR-30d.png"> <img src="https://static.igem.org/mediawiki/2014/a/a2/MIT_HEK293_Multi_Input_Sensor_miR-125b_miR-30d.png" width=100% align=center> </a></br>
+</td></tr>
+<tr><td>
+<p><b>Two high sensors.</b>We co-transfected the same high sensors from the previous Single Input miRNA Sensor Experiments using <b>red</b> as our transfection marker and <b>green</b> as our output. Given the results of our previous experiments we hoped that the sensors, when exposed to the inhibiting siRNA, would show a similar amount of GFP output as before. However, the cytometry results in figure (B) show that there was still no difference between the 'on' and 'off' state.</p>
+</td></tr>
+</table><br>
+<table align="center" width=75%>
+<tr><td align=center><p align=left><b>C.1.</b></p>
+<a href="https://static.igem.org/mediawiki/2014/f/fa/MIT_HEK293_Multi_Input_Sensor_miR-144_miR-30d_%28Green%29.png"> <img src="https://static.igem.org/mediawiki/2014/f/fa/MIT_HEK293_Multi_Input_Sensor_miR-144_miR-30d_%28Green%29.png" width=100% align=center> </a></br>
+</td></tr>
+<tr><td>
+<p><b>One low sensor and one high sensor.</b> We co-transfected the same low and high sensors from the previous Single Input miRNA Sensor Experiments. In this figure we show <b>red</b> as our transfection marker and <b>blue</b> as the low sensor output. Given the results of our previous experiments we hypothesized that, when exposed to the inhibiting siRNA, the sensor output would show a similar amount of repressed eBFP2 output as before. The cytometry in figure (C.1.) confirm this by showing that there was still no difference between the 'on' and 'off' state.</p>
+</td></tr>
+<tr><td align=center><p align=left><b>C.2.</b></p>
+<a href="https://static.igem.org/mediawiki/2014/a/a9/MIT2014_HEK293_Multi_Input_Sensor_miR-144_miR-30d_%28Blue%29.png"> <img src="https://static.igem.org/mediawiki/2014/a/a9/MIT2014_HEK293_Multi_Input_Sensor_miR-144_miR-30d_%28Blue%29.png" width=100% align=center> </a></br>
+</td></tr>
+<tr><td>
+<p><b>One low sensor and one high sensor. </b> We co-transfected the same low and high sensors from the previous Single Input miRNA Sensor Experiments. In this figure we show <b>red</b> as our transfection marker and <b>green</b> as the high sensor output. Given the results of our previous experiments we hypothesized that, when exposed to the inhibiting siRNA, the sensor output would show a similar amount of GFP output as before. The cytometry in figure (C.2.) confirms this by showing that there was still no difference between the 'on' and 'off' state.</p>
+</td></tr>
+</table>
+</table><br><a href="#top">return to top</a>
+<h2>Parts</h2><a name="parts" ></a>
+<a href="https://2014.igem.org/Team:MIT/Parts">full parts list available here</a><br>
+<a href="http://parts.igem.org/Part:BBa_K1391016">pENTR_hEF1a</a><br />
+<a href="http://parts.igem.org/Part:BBa_K1391017">MAV1212-RFP</a><br />
+<a href="http://parts.igem.org/Part:BBa_K1391018">pENTR_L7ae</a><br />
+<a href="http://parts.igem.org/Part:BBa_K1391019">MAV1212_hEF1a_L7ae</a><br />
+<a href="http://parts.igem.org/Part:BBa_K1391020">MAV1212_hEF1a_eBFP2</a><br />
+<a href="http://parts.igem.org/Part:BBa_K1391021">Low sensor: eBFP2_miR-144</a><br />
+<a href="http://parts.igem.org/Part:BBa_K1391022">Low sensor: eBFP2_miR-181c</a><br />
+<a href="http://parts.igem.org/Part:BBa_K1391023">High sensor: L7ae_miR-30d</a><br />
+<a href="http://parts.igem.org/Part:BBa_K1391024">High sensor: L7ae_miR-146a</a><br />
+<a href="http://parts.igem.org/Part:BBa_K1391025">High sensor: L7ae_miR-125b</a><br />
+<a href="http://parts.igem.org/Part:BBa_K1391026">High sensor: L7ae_miR-let-7f</a><br />
+<a href="http://parts.igem.org/Part:BBa_K1391027">Low sensor: eBFP2_miR-144_miR-181c</a><br />
 </td>
 </tr></table>