Team:AUC TURKEY/Notebook

From 2013hs.igem.org

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<h1>Notebook</h1>
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<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>
</div>
</div>
<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”.
</div>
</div>
<div>
<div>
</div>
</div>
<div>
<div>
 +
<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!
 +
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Latest revision as of 05:04, 22 June 2013



Notebook

Use arrow keys to turn notebook's pages.


AUC TURKEY
iGEM 2013 HS
NOTEBOOK

March

1 March

  • Today marks the official start of our 2013 iGEM adventure. We hope that today becomes a start for the many great things to come.
  • The reason why today was the "official" start is because our first trip to Turgut Ozal University for this year was today. We met with Mustafa Semih Elitok, our advisor, to discuss the current situation and our project ideas.
  • The 2 new members of the team got acquinted with our advisor.
  • Out of today's discussions, we have decided to work on the following project ideas:
    • Cyanide Disposing Bacteria: Cemal and Abdulkadir will work on this idea.
    • Miner Bacteria: Alperen and Furkan Sacit will work on this idea.
    • Thermobacter: Fatih will work on this idea.
    • Musilage Bacter: İbrahim and Lashynbek will work on this idea.

8 March

  • We continued discussing our project ideas.
  • As a result of the improvising, we decided to conduct research on only these 3 ideas for now:
    • Electrocortecoli
      The E.coli that we plan to produce will be negatively charged. Combined with an adesion molecule, the E.coli will bind to a specific cell thus creating an overall negatively charged system. This system can then be easily destroyed in the presence of a charged unit. Through this, sepcific cells can be targeted with E.coli and then be easily destroyed. The list of the research required for us to do is as follows:
      • Finding the sequence of an adesion molecule which can be implantabled to E.coli
      • Finding a way to electrocharge our E.coli
      • Searching iGEM to see if something which could be of use was done before
  • Thermobacter
    The thermobacter will be able to sense temperature and react to it through producing urease which will cause the urea we add into the environment to be converted to uric acid. This reaction is endothermic and will result in the environment cooling down. Through this system, an automatic cooler through bacteria will be formed. The list of the research required for us to do is as follows:
    • Searching to see if this project was don before or if there is anything in iGEM that could be of use
    • Finding the sequence for urease enzyme
    • Designating several ententities of the RNA Thermometer which can be of use
  • Mineral-Fuser Bacter

14 March

Today we discussed:
  • Project Ideas
  • Sponsorship
  • Our Previous iGEM Experience
Project Ideas
  • Electrocortecoli: We were not able to discuss much about it as we hadn't been successful in finding information. We know the existence of an adhesion molecule for mammal cells in iGEM called cadherin but it is for mammal cells. Also, we still have no clue on how to electrocharge our E.coli.
  • Thermobacter: This project looks like it is in the bag. The parts are already in iGEM (RNA Thermometer and urease enzyme). We won't have to worry much about the research for the RNA Thermometer.
  • Mineral-Fuser Bacter: The research we conducted over the last week showed that it will be extremely difficult to do this as a project as there is already a lack of information on this matter. The only thing that we could find was that a certain type of bacteria has this property but scientists haven't identified how they do it.
  • A Revival of our old Idea Stone Miner: In a multiple choice question of an exam, Furkan Beştepe read about a type of coral called "Lithophaga". This coral was found in Naples and had been designated as the cause of the degrading of historical buildings. This coral can eat through stone!

15 March

  • The discussions we had in school yesterday were pretty much carried out but this time with our advisor.
  • Also, we did our new tradition once more. What is this you may ask. Well it is 2 minutes of random idea burst without reasoning. Here are the results: Neurobacter, Painkiller, Writer, Clock-o-Bacter, Methanecoli, Rust Eater, Decayer, Tooth Paste, Tooth Filling, Balloon Inflator, CO Filter, Imnosia Bacter, SleepingBactuety, Photosynthetic, Fire Figther, Quartz Watch, Tire Repair, Anti-Bacterial-Bacter, UV to Visible Light Converter, Barocoli, Cooler, Optic Glass, Virus Detector, Infrared Bacter, Jammer, Psychic Bacter, Crystalecoli, Balance, Sewing Bacter, MRBacter, Pixellence, Glass Eater, Asphalt 4, Vacuum, Sun Lotion, Painter, Hemoglobin Detector, PCR, Anti-Radioctivity Bacter, Bactomembrane, Glue Bacter, Plastic Eater, Paper Consumer

22 March

  • As of today, considering the time and difficulty, we decided to focus only on Thermobacter. To improve thermobacter, we realized that we had add at least one part to iGEM. As a new part we could do:
    1. A New Type of RNA Thermometer
    2. Another addition to the project
  • With the remaining time, we came up with human practice ideas:
    • Visiting schools
    • Visiting businessmen
    • Visiting corporations
    • Conducting surveys
    • Preparing handouts
    • Doing advertisements
    • iGEMan
    • Making a board game
    • Making a computer game
    • Preparing Canvas Times 2
    • Doing Videos

25 March

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”.
This is the clearified system.
We also designed the parts that we will be adding to the registry.

29 March

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.
  1. Today we submitted the Project Description which was due for Sunday.
  2. We need to clarify the part design for our project.
  1. We need to somehow obtain the base sequence for urease or we will be forced to thrust the iGEM Kit.
  2. We must complete the human practices before the heavy workload begins.
For the construction
So now we have to decide what we will do with the urease part.
There is also the project description.
Project Description: “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”.

April

1 April

Today, we focused on mainly human practices. As a result of a meeting, we have specified the human practices we will be doing.
  • Board Game/ PC Game: Furkan Sacit, Fatih, Alperen, Alihan
  • Advertisements: Abdulkadir
  • iGEMan: Fatih
  • iGEM cookies: Cemal
  • Spreading iGEM around: İbrahim, Abdulkadir
  • TRT Documentary: Fatih Sacit
  • Day with the firefighters: Alperen
  • Parody Videos: Fatih
  • iGEMism: Alperen, Cemal
    1. Socialogic articles
    2. Propaganda posters
    3. Videos

8 April

In the university, we designated the deadlines for the human practices with our instructor.
  • Documentary (Furkan Sacit); If he can get approved from TRT, if he cannot, we won’t.
  • Introduction of iGEM (Abdulkadir, İbrahim); The deadline is 29 April 2013 Schools: TED, Bilkent, Arı, MEV
  • A day with the firefighters (Alperen, Fatih); The deadline is 29 April 2013
  • iGEMisms
    • iGEMan (General Mascot)
    • Cookies (Our Mothers)
    • Poster (Fatih); deadline is 29 April
    • Videos (Fatih)
    • PC Game (Alihan); deadline is 15 May
  • Collaboration

12 April

We finally got to put together the urease missing parts.
We used computer program to configure the binding sites. There were no exceptions in the base sequence.
Also, we discussed some of the poster ideas for iGEMism:
  • A poster with two bacteria shaking hands.
  • Uncle Sam like iGEM Needs You poster.
  • We must interact poster.
  • A poster that a bacteria grabs a falling man.
Another idea was thought out by Fatih:
A page in the wiki in which you add properties to your bacteria and visually experience it.

16 April

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:
  • Abstract: İbrahim
  • Data Page: Lashynbek
  • Human Practice: Abdulkadir
  • RNA Thermometer: Fatih
  • Urease: Alperen
  • Parts: Furkan Sacit
  • Overview: Cemal
  • Notebook: Fatih

19 April

We were planning to prepare competent cells today but we learned that we had no liquid nitrogen to prepare it.
We hope to order it soon and finally start doing our lab experiments.

24 April

We still did not have liquified Nitrogen, so we instead used other competent cells to do transformation.
We did our first experiment of the year.
Also, we had a “kermes” in the morning to fundraise for our project.

25 April

Today was the second day of our “kermes”. Through the purehases and the big help from our teachers, we acquired 700 TL. We want to thank everyone for their wonderful support.
Sadly, yesterdays transformation was not successful.

30 April

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.

May

4 May

Today, we prepared liquid culture. Hope it is successful.

5 May

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.

11 May

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.

12 May

E-BIKO

18 May

Just as a safety measure, we wanted to learn if whether our compatents were as effcient as we thought isolation.

21 May

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.

June

1 June

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.

3 June

A big part of the rest of the group got their plane tickets today. Also RNA Thermometer was edited.

4 June

Alihan started to make the flash game. He writed some of the code. Also, we prepared the story of our comics today.

5 June

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.

6 June

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.

7 June

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.

8 June

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.

9 June

RFP-IbpB-ROSE Isolation RFP-IbpB-ROSE Digestion RFP-IbpB-ROSE Electrophoresis Also we continued to do the comics and did more Photoshopping.

10 June

We did spectrophotometer calculations with 0,6 OD. There was RFP produced as a result and we dropped the OD to 0.3.

11 June

Spectrophotometer again with 0.3 OD

12 June

Spectrophotometer again with 0.3 OD

13 June

Spectrophotometer again with 0.3 OD IbpB Isolation, Digestion and Electrophoresis RFP-1C Liquid Culture Preparation

14 June

Spectrophotometer again with 0.3 OD RFP-1C Isolation, Digestion and Electrophoresis Liquid Culture of IbpB and ROSE

15 June

IbpB – ROSE Isolation, Digestion and Electrophoresis

17 June

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.

18 June

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.
The plasmid named as 500 has been digested and electrophorised. However, fortunately for us base length was correct.

We did ligestion of IbpB and 500 parts. We cultivated in plate which antibiotic is chloramfenicol.

We took ROSE’s liquid culture and their pellets were white. But it theoretically should be red. We did isolation,digestion and electrophoresis.

19 June

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.

We were going to measure them with the plate reader but it’s filter was broken. We couldn’t do it.

Also, we looked at the specimens we took from the IbpB and RFP under the fluorescent microscope.

20 June

Our transformation didn’t work out again. We left them for over-night incubation once more.

We tried to fix our bacteria in the fluorescent microscope once more.

21 June

Microscope again

Ligation and Transformation Again

21-22 June

Wiki Freeze!

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