Team:AUC TURKEY/Notebook
From 2013hs.igem.org
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+ | <h1>Notebook</h1> | ||
+ | <div>Use arrow keys to turn notebook's pages.</div><br/><br/> | ||
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- | <div> | + | <div><h3>25 March</h3> |
+ | Today, we finally constructed a system. In this system, the RNA thermometer will be activated forcing the production of the urease enzyme serving the purpose of “bactocooling”.<br/> | ||
+ | This is the clearified system.<br/> | ||
+ | We also designed the parts that we will be adding to the registry.<br/> | ||
+ | <h3>29 March</h3> | ||
+ | Something so unpleasant became apparent to us today. Mustafa realized that the Brown Stanford 2008 Team had not submitted the sequence of the urease BioBrick to the parts registry. So basically, we cannot use the part in comfort as we now are not sure if the urease part will work or not. | ||
+ | So we had to prepare a new work plan to desigante what we should do from now on. | ||
+ | <ol><li>Today we submitted the <b>Project Description</b> which was due for Sunday.</li> | ||
+ | <li>We need to clarify the part design for our project.</li> | ||
+ | </ol> | ||
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<div> | <div> | ||
+ | <ol start="3"> | ||
+ | <li>We need to somehow obtain the base sequence for urease or we will be forced to thrust the iGEM Kit.</li> | ||
+ | <li>We must complete the human practices before the heavy workload begins.</li> | ||
+ | </ol> | ||
+ | For the construction <br/> | ||
+ | So now we have to decide what we will do with the urease part.<br/> | ||
+ | There is also the project description.<br/> | ||
+ | <b>Project Description:</b> “In Jamboree 2013, we hope to present you the bactocooler that we have started to design. We shall add a part to our system which shall detect “thermal stimuli”. This may be a system that will be activated at a certain temperature. | ||
+ | As a result of our thermal stimuli, we want our cooler system to be activated. To decrease the temperature, we are thinking of breaking down an organic compound with an endothermic reaction. | ||
+ | Overall, we can state that we intend to make a synthetic cooler which will be activated after a specific temperature”. | ||
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+ | <h2>April</h2> | ||
</div> | </div> | ||
+ | <div></div> | ||
<div> | <div> | ||
+ | <h3>1 April</h3> | ||
+ | Today, we focused on mainly human practices. | ||
+ | As a result of a meeting, we have specified the human practices we will be doing. | ||
+ | <ul><li><b>Board Game/ PC Game:</b> Furkan Sacit, Fatih, Alperen, Alihan</li> | ||
+ | <li><b>Advertisements:</b> Abdulkadir</li> | ||
+ | <li><b>iGEMan:</b> Fatih</li> | ||
+ | <li><b>iGEM cookies:</b> Cemal</li> | ||
+ | <li><b>Spreading iGEM around:</b> İbrahim, Abdulkadir</li> | ||
+ | <li><b>TRT Documentary:</b> Fatih Sacit</li> | ||
+ | <li><b>Day with the firefighters:</b> Alperen</li> | ||
+ | <li><b>Parody Videos:</b> Fatih</li> | ||
+ | <li><b>iGEMism:</b> Alperen, Cemal | ||
+ | <ol type="a"><li>Socialogic articles</li> | ||
+ | <li>Propaganda posters</li> | ||
+ | <li>Videos</li> | ||
+ | </ol></li> | ||
+ | </ul> | ||
</div> | </div> | ||
<div> | <div> | ||
+ | <h3>8 April</h3> | ||
+ | In the university, we designated the deadlines for the human practices with our instructor. | ||
+ | <ul> | ||
+ | <li><b>Documentary (Furkan Sacit)</b>; If he can get approved from TRT, if he cannot, we won’t.</li> | ||
+ | <li><b>Introduction of iGEM (Abdulkadir, İbrahim)</b>; The deadline is 29 April 2013 <b>Schools:</b> TED, Bilkent, Arı, MEV</li> | ||
+ | <li><b>A day with the firefighters (Alperen, Fatih)</b>; The deadline is 29 April 2013</li> | ||
+ | <li><b>iGEMism</b>s | ||
+ | <ul><li><b>iGEMan (General Mascot)</b></li> | ||
+ | <li><b>Cookies (Our Mothers)</b></li> | ||
+ | <li><b>Poster (Fatih)</b>; deadline is 29 April</li> | ||
+ | <li><b>Videos (Fatih)</b></li> | ||
+ | <li><b>PC Game (Alihan)</b>; deadline is 15 May</li> | ||
+ | </ul> | ||
+ | <li><b>Collaboration</b></li> | ||
+ | </ul> | ||
</div> | </div> | ||
<div> | <div> | ||
+ | <h3>12 April</h3> | ||
+ | We finally got to put together the urease missing parts.<br/> | ||
+ | We used computer program to configure the binding sites. There were no exceptions in the base sequence.<br/> | ||
+ | <b>Also, we discussed some of the poster ideas for iGEMism:</b> | ||
+ | <ul><li>A poster with two bacteria shaking hands.</li> | ||
+ | <li>Uncle Sam like <b>iGEM Needs You</b> poster.</li> | ||
+ | <li><b>We must interact</b> poster.</li> | ||
+ | <li>A poster that a bacteria grabs a falling man.</li> | ||
+ | </ul> | ||
+ | <b>Another idea was thought out by Fatih:</b><br/> | ||
+ | A page in the wiki in which you add properties to your bacteria and visually experience it. | ||
</div> | </div> | ||
<div> | <div> | ||
+ | <h3>16 April</h3> | ||
+ | We were planning to prepare on this school-free day but sadly, the required equipment were still not available. | ||
+ | So as a result, we prepared things for iGEMism and gave people their duties: | ||
+ | <ul><li><b>Abstract:</b> İbrahim</li> | ||
+ | <li><b>Data Page:</b> Lashynbek</li> | ||
+ | <li><b>Human Practice:</b> Abdulkadir</li> | ||
+ | <li><b>RNA Thermometer:</b> Fatih</li> | ||
+ | <li><b>Urease:</b> Alperen</li> | ||
+ | <li><b>Parts:</b> Furkan Sacit</li> | ||
+ | <li><b>Overview:</b> Cemal</li> | ||
+ | <li><b>Notebook:</b> Fatih</li> | ||
+ | </ul> | ||
</div> | </div> | ||
<div> | <div> | ||
+ | <h3>19 April</h3> | ||
+ | We were planning to prepare competent cells today but we learned that we had no liquid nitrogen to prepare it.<br/> | ||
+ | We hope to order it soon and finally start doing our lab experiments. | ||
+ | <h3>24 April</h3> | ||
+ | We still did not have liquified Nitrogen, so we instead used other competent cells to do transformation.<br/> | ||
+ | We did our first experiment of the year.<br/> | ||
+ | Also, we had a “kermes” in the morning to fundraise for our project. | ||
+ | <h3>25 April</h3> | ||
+ | Today was the second day of our “kermes”. Through the purehases and the big help from our teachers, we acquired <b>700 TL</b>. We want to thank everyone for their wonderful support.<br/> | ||
+ | Sadly, yesterdays transformation was not successful. | ||
</div> | </div> | ||
<div> | <div> | ||
+ | <h3>30 April</h3> | ||
+ | Today, we did the transformation of 2 RFP plates. | ||
+ | Both of the plates had yield but 1 had only 3 colonies and the other one had only 1. | ||
</div> | </div> | ||
+ | <div></div> | ||
+ | <div></div> | ||
<div> | <div> | ||
+ | <h2>May</h2> | ||
</div> | </div> | ||
+ | <div></div> | ||
<div> | <div> | ||
+ | <h3>4 May</h3> | ||
+ | Today, we prepared liquid culture. Hope it is successful. | ||
+ | <h3>5 May</h3> | ||
+ | We did experiments from the morning the evening. Almost all of them were successful with the exception of ligestion. We realized that the plasmid were not cut during electrophoresis. At least the nanodrop results showed that it was ok. | ||
+ | <h3>11 May</h3> | ||
+ | Today was a long day. From 1.p.m to 10.30 p.m, we prepared compatent cells. At least it was worth the effort, the compatent cells have great efficiency. | ||
+ | <h3>12 May</h3> | ||
+ | E-BIKO | ||
+ | <h3>18 May</h3> | ||
+ | Just as a safety measure, we wanted to learn if whether our compatents were as effcient as we thought isolation. | ||
</div> | </div> | ||
<div> | <div> | ||
+ | <h3>21 May</h3> | ||
+ | We had a meeting in the school. Everybody was assigned their jobs. Also we prepared certain things for the wiki such as the graphics and writings. | ||
</div> | </div> | ||
+ | <div></div> | ||
+ | <div></div> | ||
<div> | <div> | ||
+ | <h2>June</h2> | ||
+ | </div><div></div> | ||
+ | <div> | ||
+ | <h3>1 June</h3> | ||
+ | We searched for plane tickets and found several. 2 of the team members bought their tickets. | ||
+ | Also, we prepared a draft for the RNA Thermometer text we will put into our wiki. | ||
+ | <h3>3 June</h3> | ||
+ | A big part of the rest of the group got their plane tickets today. | ||
+ | Also RNA Thermometer was edited. | ||
+ | <h3>4 June</h3> | ||
+ | Alihan started to make the flash game. He writed some of the code. | ||
+ | Also, we prepared the story of our comics today. | ||
+ | <h3>5 June</h3> | ||
+ | Photos for the comics were taken. | ||
+ | Also, Alihan continued to do the flash game. | ||
+ | Plus, 2 iGEMism posters were prepared today. | ||
+ | Also on the side, Urease draft for the wiki was prepared. | ||
+ | </div><div> | ||
+ | <h3>6 June</h3> | ||
+ | We continued to prepare for the comics and flash game. | ||
+ | RNA Thermometer and Urease were edited. | ||
+ | We also sketched out our experiment process for the next 2 weeks. | ||
+ | <h3>7 June</h3> | ||
+ | We continued to prepare the flash game and also discussed the experiments we should do. | ||
+ | Our genes arrived from the company we ordered and we immidiately started transformating them and let them go for overnight incubation. | ||
+ | <h3>8 June</h3> | ||
+ | Liquid Culture for RFP was prepared. | ||
+ | RNA Thermometer text was edited and the flash game was continued. | ||
+ | We did Photoshop and also iGEMism posters today. | ||
+ | <h3>9 June</h3> | ||
+ | RFP-IbpB-ROSE Isolation | ||
+ | RFP-IbpB-ROSE Digestion | ||
+ | RFP-IbpB-ROSE Electrophoresis | ||
+ | Also we continued to do the comics and did more Photoshopping. | ||
+ | </div><div> | ||
+ | <h3>10 June</h3> | ||
+ | We did spectrophotometer calculations with 0,6 OD. There was RFP produced as a result and we dropped the OD to 0.3. | ||
+ | <h3>11 June</h3> | ||
+ | Spectrophotometer again with 0.3 OD | ||
+ | <h3>12 June</h3> | ||
+ | Spectrophotometer again with 0.3 OD | ||
+ | <h3>13 June</h3> | ||
+ | Spectrophotometer again with 0.3 OD | ||
+ | IbpB Isolation, Digestion and Electrophoresis | ||
+ | RFP-1C Liquid Culture Preparation | ||
+ | <h3>14 June</h3> | ||
+ | Spectrophotometer again with 0.3 OD | ||
+ | RFP-1C Isolation, Digestion and Electrophoresis | ||
+ | Liquid Culture of IbpB and ROSE | ||
+ | </div><div> | ||
+ | <h3>15 June</h3> | ||
+ | IbpB – ROSE Isolation, Digestion and Electrophoresis | ||
+ | <h3>17 June</h3> | ||
+ | We have taken IbpB 1, 2, 3 and RFP 1, RFP 2 and RFP 3 liquid cultures and we have done isolation, digestion and electrophoresis. According to the electrophosesis result our genes base length was right but we couldn’t understand why our IbpB liquid culture didn’t show red colour. | ||
+ | <h3>18 June</h3> | ||
+ | At the end of 36 hours incubation,we transferred our Ibpb and RFP liquid culture to 2 ml eppendorves and we centrifuged them.And IbpBs and RFPs which in 42 centigrade incubating.IbpB and RFPs which have been incubating in room temprature RFPs pellets were red.But IbpB’s pellets were white. Because of this we proved our experiment and IbpB thermometer activated in 42 centigrade but IbpB thermometer didn’t activate in room temperature. | ||
+ | </div><div> | ||
+ | The plasmid named as 500 has been digested and electrophorised. However, fortunately for us base length was correct.<br/><br/> | ||
+ | We did ligestion of IbpB and 500 parts. We cultivated in plate which antibiotic is chloramfenicol.<br/><br/> | ||
+ | We took ROSE’s liquid culture and their pellets were white. But it theoretically should be red. We did isolation,digestion and electrophoresis. | ||
+ | <h3>19 June</h3> | ||
+ | The transformation which we had done in yesterday was failed.We repeated the transformation again. We calculated the OD of the RFP and IbpB’s at 27 C and 37 C. According to their OD values, we diluted them. We then transferred them to the 96 well plate.<br/><br/> | ||
+ | We were going to measure them with the plate reader but it’s filter was broken. We couldn’t do it.<br/><br/> | ||
+ | Also, we looked at the specimens we took from the IbpB and RFP under the fluorescent microscope. | ||
+ | </div><div> | ||
+ | <h3>20 June</h3> | ||
+ | Our transformation didn’t work out again. We left them for over-night incubation once more.<br/><br/> | ||
+ | We tried to fix our bacteria in the fluorescent microscope once more. | ||
+ | <h3>21 June</h3> | ||
+ | Microscope again<br/><br/> | ||
+ | Ligation and Transformation Again | ||
+ | <h3>21-22 June</h3> | ||
+ | Wiki Freeze! | ||
+ | </div><div> | ||
+ | <center> | ||
+ | <img src="https://static.igem.org/mediawiki/2013hs/e/e1/AUC_Turkey_iGEM_Blue.png" style="margin-top:135px" /> | ||
+ | </center> | ||
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Latest revision as of 05:04, 22 June 2013