Team:NCTU Formosa/Test

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===MATLAB Introduction===
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===團隊交流===
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<p>MATLAB (matrix laboratory) is a numerical computing environment and fourth-generation programming language. It is developed by MathWorks, a company in United States. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, and Fortran. Although MATLAB is intended primarily for numerical computing, '''an optional toolbox''' uses the MuPAD symbolic engine, allowing access to symbolic computing capabilities. An additional package, Simulink, adds '''graphical multi-domain simulation''' and''' Model-Based Design''' for dynamic and embedded systems.</p>
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<div id="dialog" title="Basic dialog">
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<br>[[File:MO_fig.1.png|667px|center|Fig. Matlab]]
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<p>This is an animated dialog which is useful for displaying information. The dialog window can be moved, resized and closed with the 'x' icon.</p>
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</div>
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<div id="opener">Open Dialog</div>
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<div id="more1">111</div><div class="doo1">222</div>
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<div id="opener">Open Dialog</div>
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  {{:Team:NCTU Formosa/source/Test3}}
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<p>[[File:NCTU_Formosa_2014_HP_1.jpg|300px|thumb|right]]</p>
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{{:Team:NCTU Formosa/source/introo}}
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We invited Mingdao High school iGEM team to exchange ideas with us. We also held a pizza party to enhance more fun in this event.
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<div style="clear:both"></div>
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[[File:NCTU_Formosa_2014_HP_2.jpg|300px|thumb|right]]
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We asked Mingdao high school to give a brief introduction to their project－Odor Let It Die. It’s really an interesting and creative idea. Although they are just high school students, their English presenters clearly explained what problems they want to solve. In the discussion section, we gave them several feedback and suggestions to perfect their project.
 +
<div style="clear:both"></div>
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[[File:NCTU_Formosa_2014_HP_3.jpg|300px|thumb|right]]
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As for our presenting section, we successfully caught their eyes with our creative project－Operation Debug, which is to attract pests in the farm with PBAN.
 +
After our amazing presentation, we believed they not only learned more knowledge about synthetic biology but also impressed by the future development potential of this field.
 +
<div style="clear:both"></div>
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[[File:NCTU_Formosa_2014_HP_4.jpg|300px|thumb|right]]
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Because some high school students are pretty curious about our laboratory, so we guided them to pay a visit to lab at the end of this event. We introduce the equipment we usually use in the process of DNA synthesis.
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<div style="clear:both">
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====Video conferencing with Xiamen University ====
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===ANFIS Introduction===
 
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<p>Adaptive-Network-Based Fuzzy Inference System, in short ANFIS, is a power tool for constructing a set of fuzzy if-then rules to generate stipulated output and input pairs. Unlike system modeling using mathematical rules that lacks the ability to deal with ill-defined and uncertain system, '''ANFIS can transform human knowledge into rule base, and therefore, ANFIS can effectively tune membership functions, minimizing the output error.'''</p>
 
 +
<p></p>
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We had a video conferencing with the iGEM team of Xiamen University, China, in May. As both teams just started their own research projects at that time, the main topics of this video conferencing only consisted of a brief description or introduction of the protocols for each other’s project, how the research team was established and organized. According to this short conferencing, we knew the Xiamen team mainly consists of sophomores or juniors, whereas they were surprised to learn that almost 90% of our team members are freshmen.
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<p id="para1">Me too!</p>
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<p>And me!</p>
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===Single Unit===
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====Red Promoter====
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As shown in Figure 2,  the red promoter is consisted of P<sub>ompc</sub> and P<sub>lac</sub>. By multiplying the experimental data of P<sub>ompc</sub> + RBS + mGFP and P<sub>lac</sub> + RBS + mGFP, we would be able to build a model for the red promoter. This model, however, wouldn't be so accurate. To solve this problem, '''we used this model to train the actual experimental data of the red promoter by using ANFIS.''' Figure 2 is the result of such a training. We obtained '''a curve between our model and the actual experimental data.''' This curve is the representation of the new model that has been trained and supported by the actually experimental data of P<sub>red</sub>. This new model definitely contains a high degree of accuracy.
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[[File:NCTU_Pred-value.jpg|center|Figure 2. using ANFIS to modified the simulated data by experimental data to obtain a more accurate result.]]
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====Lux Promoter====
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===戶外考察===
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<p>We did the following modeling based on the data obtained from Imperial 2007 iGEM team.
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The data notes the strength of P<sub>lux</sub> under '''different concentrations of AHL''' and '''different time frames'''.</p>
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[[File:Plux_testbiobrick.jpg|400px|center|Figure 3. the biobrick to test expression of the lux promoter]]
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<p>
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Using ANFIS to train 76 sets of data and to test 20 sets of data, we ontained Figure 4. It shows that '''our training data exhibits a similar trend as the testing data''', even though '''the computer has no based knowledge of the trend'''. This simply means that our modeling has successfully simulated the actually data. </p>
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[[File:Nctu_Plux_train_wikifig.jpg|745px|center|Figure 4. The training and testing data using ANFIS system]]
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Figure 5 is the resultant graph from input 1 (time) and input 2 (AHL concentration). According to this graph, we can observe the output (fluorescence) has two peaks about AHL concentration(at concentration of 4 nM and 40 nM).
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That means '''we could achieve our regulation goal with little AHL.''' Also, pleas note that there is more output as time passes.
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[[file:Nctu_Plux_ahl_time_wikifig.jpg|500px|center|Figure 5. Input 1 is time (min), input 2 is AHL concentration, and output is fluorescence.]]
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====37 °C RBS====
 
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<p>We used Figure 6 biobrick to model our 37<sup>o</sup>C RBS's function at different
 
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temperatures.</p>
 
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[[File:Nctu_37rbs_biobricktest.jpg|400px|center|Figure 6. The biobrick used to test the temperature-regulated RBS function ]]
 
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<p>
 
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First, we did a experiment that test the fluroscence at different temperature and different time.
 
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Choosing 100 sets of data to do machine learning, then we tested 20 sets of data. '''As Figure 7 shown, the curve can classify 4 groups fit in 27<sup>o</sup>C,32<sup>o</sup>C,37<sup>o</sup>C and 42<sup>o</sup>C.'''
 
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</p>
 
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[[File:Nctu_37_random_test.jpg|745px|center|Figure 7.The figure shows 100 training data composed by 4 different temperture (blue dot), and simulated result (red star).]]
 
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<p>To test the accuracy of our model, we randomly chose 20 pairs of data which is not include in our training data to do the independent test, and the test result is shown in Figure 8. The blue dot in the figure represents the real experimental data that we randomly choose from our whole dataset, and the red star represents simulated result of our model. '''It is obviously showed that our model can accurately predict the biobrick function in any condition by using ANFIS.'''</p>
 
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[[File:37rbs_test.png|745px|center|Figure 8. The blue dots represents the real experimental data. The red star represents simulated result of our model.]]
 
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[[File:37rbs_model.jpg|center|500px|Figure 9. Input 1= Time (hr), Input 2= Temperature (degree Celsius), Output = Normalized expression (AU).]]
 
 +
====Dinning Together in Feng Wu====
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<p>From Figure 9, the maximum output is obtained at 37 <sup>o</sup>C. Under the same time frame, the output (the normalized expression of the reporter gene) is maximized at 37 <sup>o</sup>C while minimized at 25 <sup>o</sup>C. There is a dramatic decrease in the output below 30 <sup>o</sup>C and the outputs around 37<sup>o</sup>C are much higher. '''This modeling demonstrates that using 37 <sup>o</sup>C RBS is a plausible approach for achieving gene expression through temperature.''' </p>
+
'''Experience Sharing of Capturing Bloodsucking Flies in the farm：'''<br>
 +
　Dr. Tzeng told us the livestock farmers used to borrow the Insect light trap from them to capture the Bloodsucking Flies. To our surprise, he said the light trap can capture thousands of insects at just one night. Aditionally, they also had some cooperation program with livestock farmers. At that time, they used many different interesting approaches, like colors & light to test the behavior of Bloodsucking Flies. This experience sharing made us learn some basic methods of testing insects’ behavior.
 +
<p></p>
 +
'''The Art of Insect Rearing for Them：'''<br>
 +
　Dr. Tzeng told us insect rearing is not only a branch of knowledge, but a kind of art. For example, when malaria was a pandemic disease all over the world, some related research had difficulty in obvious progression, because Anopheles gambiae had not been reared successfully at that time. However, since a researcher from United Kingdom had success in rearing Anopheles gambiae in lab, the malaria disease had been completely researched, and the health life of human had been improved. This concept raised a great inspiration for how to do the research of our project.
 +
<p></p>
 +
'''Suggestion of Our Harmful Insects--Bactrocera dorsalis：'''<br>
 +
　Dr. Tzeng told us the bactrocera dorsalis is a serious problem for Taiwanese agriculture, which causes 17 billions dollors of loss every year. Our government had used many methods ( like：air drop many non-fertility bactrocera dorsalis to the farm ), trying to solve this problem, but finally failed. Dr. Tzeng suggested Bactrocera dorsalis as the target harmful insect of our project to solve the main problem of Taiwanese agricultural insects damage.
 +
<p></p>
 +
'''Discussion about Ecological Equilibrium Problem of Our Project：'''<br>
 +
　As for the ecological equilibrium problem of our project, Dr. Tzeng thought foundamentally we human farm in the area, having caused harm to nature. If you persist in the ecological equilibrium problem, then you have to ask yourself why you do farming and cause harm to the environment？Dr. Tzeng gave us a special view point, highlighting in the beginning, we human who do farming to survive have caused harm to the environment, so we shouldn’t inspect the ecological equilibrium problem of capturing insects.
 +
<p></p>
 +
'''Experience Sharing of Dengue Fever Prevention and Control：'''<br>
 +
　Dr. Tzeng shared the interesting experience of his presentation about Dengue Fever Prevention and Control at many town offices and also introduced there are two kinds of dengue fever vector mosquito, one is Aedes albopictus outdoors and the other is aedes aegypti indoors. We not only learned simple knowledge of dengue fever but also realized the feeling of helping people with professional knowledge.
-
======Reference======
+
 
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<div class="rev">
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====Visitation of their Department Building====
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<ol start="1">
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<li>iGEM 2007 Imperial  https://2007.igem.org/Imperial</li>
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<div class=BOX>　　　　　　　　
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</ol>
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<table border=0 width=90%>
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<td align=center>[[File:NCTU_Formosa_2014_HP_5.jpg|300px|thumb|center]]</td>
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<td align=center>[[File:NCTU_Formosa_2014_HP_6.jpg|300px|thumb|center]]</td>
 +
</table>
</div>
</div>
 +
'''Explanation of the Real Function of Mosquito PBAN：'''<br>
 +
　In fact, the mosquito PBAN is activated during spreading wings when the mosquito emerges from its pupa. Initially, the mosquito wings are all living cells and when its PBAN regulates some hormones to make some cells apoptosis, just leaving few cells alive on its bone of wings, it finally forms transparent wings. This explanation about mosquito PBAN gave us a deeper realization about PBAN.
 +
<p></p>
 +
 +
'''Take a Look at Their Mosquito Breeding Cage and Insect Light Trap ：'''<br>
 +
　Dr. Tzeng let us take a look at Culex pipiens molestus (the underground house mosquito) breeding cage, and also introduced the behavior of many kinds of mosquito. This mosquito breeding cage inspired us many new ideas about our insects testing box. In fact, we mimicked the same concept of mosquito breeding cage to test our PBAN effect simply.
 +
<p></p>
 +
 +
<div class=BOX>　　 
 +
<table border=0  width=90% >
 +
<td align=center>[[File:NCTU_Formosa_2014_HP_7.jpg|300px|thumb|center]]</td>
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<td align=center>[[File:NCTU_Formosa_2014_HP_8.jpg|300px|thumb|center]]</td>
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</table>
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</div>
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 +
<p></p>
 +
'''Further Discussion about our project：''' <br>
 +
[[File:NCTU_Formosa_2014_HP_10.jpg|300px|thumb|center]]
 +
　Dr. Tzeng have enthusiasm on discussing our project. To prevent any problem from happening, Dr. Tzeng and we inspected all the probability which may cause our project failed like PBAN degeadation in insects’ intestine ( whether we have to use little thuricide to cause some holes on insects’ intestine to make it absorb our PBAN easily ) and the restriction of our project ( we have to capture the first “female” insect in our device, and actually our project work. ). In the discussing process, we inspected many problems again, and also get many suggestion from Dr. Tzeng. We hoped we can overcome all the problems, and improve our project.
 +
<p></p>
 +
 +
'''Advantages Discussion of Our Device：'''<br>
 +
　Referring to our project, we use PBAN to make the harmful insects produce pheromone for us to help us attract many same kinds of insects. Dr. Tzeng was very interested in our project, and thought compared to the common use (Pheromone Trap & Pesticide ) in the market, our main idea have no dug resistance problem ( PBAN is insects’ physiologically natural substance ) and have no worry about the problem of running off our PBAN ( PBAN can be mass produced from our E.coli. ). It is a very user-friendly、eco-friendly and perfect project.
 +
<p></p>
 +
　In briefly conclusion, our team and Dr. Tzeng had deep discussion in this visitation. Not only experience sharing but also project inspection made us learn much and got many new ideas which let us realize how to make use of our project to achieve the best effect.
 +
</div></div>
</div></div>
 +
 +
 +
 +
<div class="li"><div class="card">
<div class="li"><div class="card">
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===Futurework===
 +
<p></p>
 +
</div></div>
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===E.colightuner Simulation===
 
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<p>We have all the modeling of each single unit . Now, we want to combine each unit to make a stimulation to the E.colightuner. </p>
 
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[[File:Figure1_NCTU_Formosa.png|300px|center|Figure 10.The overall constituent of E.colightuner ]]
 
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<p>Figure 10 shows the essential constituent of our E. colightuner. To save our efforts experimenting with this essential engine of E. colightuner, we built '''a model beforehand to help us evaluate its practicability.''' Our model is consisted of four components A, B, C, and D</p>
 
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[[File:Figure2_NCTU_Formosa.png|300px|center|Figure 11. component A ]]
 
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<p>Figure 11 is the overall picture of our component A. Notice that component A is built from similar biobricks as our E.colightuner. The only difference between the two is the promoters used. '''Both P<sub>red</sub> of E.colightuner are substituted with P<sub>cons</sub> in component A.''' With that said, by taking the difference in the strength between P<sub>red</sub> and P<sub>cons</sub>, into calculations, we would be able to model out E. colightuner with component A. Before that, however, we would have to first build a model for component A. </p>
 
-
[[File:Figure3_NCTU_Formosa.png|300px|center|Figure 12. component B ]]
 
-
<P>To build a model for component A, we combined component B and C. As you can see in component B shown in Figure 12, it does not include P<sub>lux</sub> and luxR like component A. By assuming that when luxR is expressed, P<sub>lux</sub> would immediately reach its full strength, however, we can consider luxR and P<sub>lux</sub> pair as simply a Pcons,that is constitutively activated. From this perspective, component A and B are the same, except that component A is also effected by the translation efficiency of 37<sup>o</sup>C RBS. Component C is the model for 37<sup>o</sup>C RBS which was shown in the Single Unit part above. So '''by multiplying component C and component B, we would be able to obtain a model for component A.'''</p>
 
-
<p>In order to increase the accuracy of our component A model,''' we used ANFIS to fit our modeling result with the actual experimental data of our component A.''' By doing this, we obtained a new modeling curve for component that is more precise and accurate, shown in Figure 13. </p>
 
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[[File:NCTU_A-value.jpg|center|Figure 13. using ANFIS to modified the simulated data by experimental data to obtain a more accurate result .]]
 
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<p>As mentioned above, we needed to take the effect of P<sub>red</sub> into account before we could a model of E.colightuner based on component A. Component D has the model of P<sub>red</sub> built in a similar way as component A model which was shown before, too. We first built a model for P<sub>red</sub> and fitted it into the actual experimental data. </p>
 
-
<p>Having both precise model for component A and component D, we simply had to multiple them to obtain the final model for our E.Colightuner in Figure 14. </p>
 
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[[File:Figure7_NCTU_Formosa.png|300px|center|Figure 14. the final model for E.colightuner . A = Figure2. B = Figure3. C = 37 degree celsius RBS , D = red promoter]]
 
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Using the single unit to predict the project we simplify like Figure 10, we got Figure 15. The predictive curve is under red light and at 37<sup>o</sup>C. Due to the sRNA repression, the expression rate of mGFP is really low. This phenomenon is reasonable and interpretable. Thus, '''this modeling method can accurately predict the expression trend of a new biobrick.''' Applying this modeling system maturely, we can use computers to control our E.colightuner in the future.
 
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[[File:Nctu_model_whole_project.jpg|800px|center|Figure 15. The Figure 14 predicted tendency.]]
 
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===Surveys===
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<p></p>
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{{:Team:NCTU Formosa/source/card-end}}
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     <p>Cover image credit: <a href="http://www.dvq.co.nz/" target="_blank">DVQ</a></p>
     <p>Cover image credit: <a href="http://www.dvq.co.nz/" target="_blank">DVQ</a></p>
     </div> </div>
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Latest revision as of 15:05, 17 October 2014

Human Practice

Change the font size right here

Contents

團隊交流

This is an animated dialog which is useful for displaying information. The dialog window can be moved, resized and closed with the 'x' icon.

Open Dialog


111
222

This is an animated dialog which is useful for displaying information. The dialog window can be moved, resized and closed with the 'x' icon.

Open Dialog

NCTU Formosa 2014 HP 1.jpg

We invited Mingdao High school iGEM team to exchange ideas with us. We also held a pizza party to enhance more fun in this event.

NCTU Formosa 2014 HP 2.jpg

We asked Mingdao high school to give a brief introduction to their project－Odor Let It Die. It’s really an interesting and creative idea. Although they are just high school students, their English presenters clearly explained what problems they want to solve. In the discussion section, we gave them several feedback and suggestions to perfect their project.

NCTU Formosa 2014 HP 3.jpg

As for our presenting section, we successfully caught their eyes with our creative project－Operation Debug, which is to attract pests in the farm with PBAN. After our amazing presentation, we believed they not only learned more knowledge about synthetic biology but also impressed by the future development potential of this field.

NCTU Formosa 2014 HP 4.jpg

Because some high school students are pretty curious about our laboratory, so we guided them to pay a visit to lab at the end of this event. We introduce the equipment we usually use in the process of DNA synthesis.

Video conferencing with Xiamen University

We had a video conferencing with the iGEM team of Xiamen University, China, in May. As both teams just started their own research projects at that time, the main topics of this video conferencing only consisted of a brief description or introduction of the protocols for each other’s project, how the research team was established and organized. According to this short conferencing, we knew the Xiamen team mainly consists of sophomores or juniors, whereas they were surprised to learn that almost 90% of our team members are freshmen.


Every paragraph will be affected by the style.

Me too!

And me!

<style> body { 

   background: #ffffff url("NCTU_Formosa_2014_HP_1.jpg") no-repeat right top;
   margin-right: 200px;

} </style> </html>

戶外考察

Dinning Together in Feng Wu

Experience Sharing of Capturing Bloodsucking Flies in the farm：
　Dr. Tzeng told us the livestock farmers used to borrow the Insect light trap from them to capture the Bloodsucking Flies. To our surprise, he said the light trap can capture thousands of insects at just one night. Aditionally, they also had some cooperation program with livestock farmers. At that time, they used many different interesting approaches, like colors & light to test the behavior of Bloodsucking Flies. This experience sharing made us learn some basic methods of testing insects’ behavior.

The Art of Insect Rearing for Them：
　Dr. Tzeng told us insect rearing is not only a branch of knowledge, but a kind of art. For example, when malaria was a pandemic disease all over the world, some related research had difficulty in obvious progression, because Anopheles gambiae had not been reared successfully at that time. However, since a researcher from United Kingdom had success in rearing Anopheles gambiae in lab, the malaria disease had been completely researched, and the health life of human had been improved. This concept raised a great inspiration for how to do the research of our project.

Suggestion of Our Harmful Insects--Bactrocera dorsalis：
　Dr. Tzeng told us the bactrocera dorsalis is a serious problem for Taiwanese agriculture, which causes 17 billions dollors of loss every year. Our government had used many methods ( like：air drop many non-fertility bactrocera dorsalis to the farm ), trying to solve this problem, but finally failed. Dr. Tzeng suggested Bactrocera dorsalis as the target harmful insect of our project to solve the main problem of Taiwanese agricultural insects damage.

Discussion about Ecological Equilibrium Problem of Our Project：
　As for the ecological equilibrium problem of our project, Dr. Tzeng thought foundamentally we human farm in the area, having caused harm to nature. If you persist in the ecological equilibrium problem, then you have to ask yourself why you do farming and cause harm to the environment？Dr. Tzeng gave us a special view point, highlighting in the beginning, we human who do farming to survive have caused harm to the environment, so we shouldn’t inspect the ecological equilibrium problem of capturing insects.

Experience Sharing of Dengue Fever Prevention and Control：
　Dr. Tzeng shared the interesting experience of his presentation about Dengue Fever Prevention and Control at many town offices and also introduced there are two kinds of dengue fever vector mosquito, one is Aedes albopictus outdoors and the other is aedes aegypti indoors. We not only learned simple knowledge of dengue fever but also realized the feeling of helping people with professional knowledge.


Visitation of their Department Building

　　　　　　　　
NCTU Formosa 2014 HP 5.jpg
NCTU Formosa 2014 HP 6.jpg

Explanation of the Real Function of Mosquito PBAN：
　In fact, the mosquito PBAN is activated during spreading wings when the mosquito emerges from its pupa. Initially, the mosquito wings are all living cells and when its PBAN regulates some hormones to make some cells apoptosis, just leaving few cells alive on its bone of wings, it finally forms transparent wings. This explanation about mosquito PBAN gave us a deeper realization about PBAN.

Take a Look at Their Mosquito Breeding Cage and Insect Light Trap ：
　Dr. Tzeng let us take a look at Culex pipiens molestus (the underground house mosquito) breeding cage, and also introduced the behavior of many kinds of mosquito. This mosquito breeding cage inspired us many new ideas about our insects testing box. In fact, we mimicked the same concept of mosquito breeding cage to test our PBAN effect simply.

　　
NCTU Formosa 2014 HP 7.jpg
NCTU Formosa 2014 HP 8.jpg

Further Discussion about our project：

NCTU Formosa 2014 HP 10.jpg

　Dr. Tzeng have enthusiasm on discussing our project. To prevent any problem from happening, Dr. Tzeng and we inspected all the probability which may cause our project failed like PBAN degeadation in insects’ intestine ( whether we have to use little thuricide to cause some holes on insects’ intestine to make it absorb our PBAN easily ) and the restriction of our project ( we have to capture the first “female” insect in our device, and actually our project work. ). In the discussing process, we inspected many problems again, and also get many suggestion from Dr. Tzeng. We hoped we can overcome all the problems, and improve our project.

Advantages Discussion of Our Device：
　Referring to our project, we use PBAN to make the harmful insects produce pheromone for us to help us attract many same kinds of insects. Dr. Tzeng was very interested in our project, and thought compared to the common use (Pheromone Trap & Pesticide ) in the market, our main idea have no dug resistance problem ( PBAN is insects’ physiologically natural substance ) and have no worry about the problem of running off our PBAN ( PBAN can be mass produced from our E.coli. ). It is a very user-friendly、eco-friendly and perfect project.

　In briefly conclusion, our team and Dr. Tzeng had deep discussion in this visitation. Not only experience sharing but also project inspection made us learn much and got many new ideas which let us realize how to make use of our project to achieve the best effect.



Futurework


Surveys


Retrieved from "http://2014.igem.org/Team:NCTU_Formosa/Test"