Team:Sevilla/Week2

From 2011.igem.org

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$("#fridayProtocols").hide();
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<img src="https://lh4.googleusercontent.com/-mWdHbQ0QAs4/TiWW7ODKTII/AAAAAAAAARg/SuDg9gxMM5M/s288/IMG_4656.JPG" style="padding-left:200px;"height="192" width="288" />
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<input type="button" value="Show Monday protocols" id="mondayBP">
<input type="button" value="Show Monday protocols" id="mondayBP">
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<p>In. Mid vel vel elementum, placerat tincidunt, vut lacus purus nunc massa a habitasse? Ac pid elementum aliquam, natoque! Porttitor facilisis amet lacus, ridiculus nascetur! Sociis vel aenean natoque penatibus aliquam in, augue mauris, dictumst, nunc mid platea a! Massa? Vut dis purus. Odio magna nec. Lorem ut turpis adipiscing scelerisque dis, scelerisque. Sed quis, porttitor et pulvinar in. Massa sit, porta urna nunc auctor non elementum! Augue dolor cum sociis, dignissim elementum. Integer. Penatibus. Phasellus et porta nec! Hac in nec porttitor ridiculus rhoncus. Hac natoque mid est nunc platea nisi sed habitasse! Amet nec placerat ultricies egestas.
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<p> Miniprep Protocol:
 +
<p>We use the Miniprep Protocol giving in the kit of Favorgen biotech corp.:</p>
 +
<p>1. Transfer 2 ml of well-grown bacteria culture to a microcentrifuge tube.</p>
 +
<p>2. Descend the bacteria by centrifuging at 10.000 rpm for 1 minute and discard the supernatant completely.</p>
 +
<p>3. Add 250 μl of FAPD1 Buffer to the pellet and resuspend the cells completely by pipetting.</p>
 +
<p>4. Add 250 μl of FAPD2 Buffer and gently invert the tube 5 times to lyse the cells and incubate at room temperature for 2 min.</p>
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<p>5. Add 350 μl of FAPD3 Buffer and invert the tube 5 times</p>
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<p>6. Centrifuge for 10 min at 14.000 rpm</p>
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<p>7. Transfer the suspernatant carefully to FAPD Column. Centrifuge for 1 min and then discard the flow-through.</p>
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<p>8. Add 400 μl of W1 Buffer to FAPD Column. Centrifuge for 1 min then discard the flow-through.</p>
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<p>9. Add 750 μl of Wash Buffer to FAPD Column. Centrifuge for 1 min then discard the flow-through.</p>
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<p>10. Centrifuge for an additional 3 min to dry the column.</p>
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<p>11. Place FAPD Column to a new 1,5 ml microcentrifuge tube.</p>
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<p>12. Add 30 μl of ddH2O to the membrane center of FAPD Column. Stand the column for 2 min.</p>
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<p>13. Centrifuge for 2 min at 14.000 rpm to elute plasmid DNA. </p>
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</br>
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Vel cum diam, lorem integer et montes, nec placerat, turpis lacus nec placerat, rhoncus rhoncus, a porta augue ac! Et aliquet. Porttitor diam egestas, non vut etiam montes, aliquet? Pellentesque. Dolor nascetur amet. Adipiscing sed pulvinar cursus! Urna in, in turpis duis in sit placerat, vut non aliquam? Mattis habitasse augue mus. Pulvinar auctor natoque est lacus porta sagittis! A in massa lundium? In non, lundium nisi magna proin elementum sed porttitor sed amet risus a aliquet mid a? Proin turpis, ac magna, dictumst lorem tincidunt penatibus sociis rhoncus? Duis cursus sit diam amet nisi mattis egestas habitasse diam.
 
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<img src="https://lh5.googleusercontent.com/-xkIfQD6E3Ok/TiWXB1_8s2I/AAAAAAAAASc/vEdT33by8WM/s288/IMG_4670.JPG" style=padding-left:300px;"height="192" width="288" />
<img src="https://lh5.googleusercontent.com/-xkIfQD6E3Ok/TiWXB1_8s2I/AAAAAAAAASc/vEdT33by8WM/s288/IMG_4670.JPG" style=padding-left:300px;"height="192" width="288" />
<p>
<p>
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</br>
After deciding how we'll build each BioBrick, and counting all the ligations we need to
After deciding how we'll build each BioBrick, and counting all the ligations we need to
do, we finally tackle the digestions with the different restriction enzymes. Mastermix
do, we finally tackle the digestions with the different restriction enzymes. Mastermix
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</br>
</br>
</div>
</div>
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<p>In. Mid vel vel elementum, placerat tincidunt, vut lacus purus nunc massa a habitasse? Ac pid elementum aliquam, natoque! Porttitor facilisis amet lacus, ridiculus nascetur! Sociis vel aenean natoque penatibus aliquam in, augue mauris, dictumst, nunc mid platea a! Massa? Vut dis purus. Odio magna nec. Lorem ut turpis adipiscing scelerisque dis, scelerisque. Sed quis, porttitor et pulvinar in. Massa sit, porta urna nunc auctor non elementum! Augue dolor cum sociis, dignissim elementum. Integer. Penatibus. Phasellus et porta nec! Hac in nec porttitor ridiculus rhoncus. Hac natoque mid est nunc platea nisi sed habitasse! Amet nec placerat ultricies egestas.
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<p><strong>Células competentes II</strong></p>
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<p>1)Incubate a bacterial colony in 3 mL LB, 37ºC with agitation all night.</p>
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Vel cum diam, lorem integer et montes, nec placerat, turpis lacus nec placerat, rhoncus rhoncus, a porta augue ac! Et aliquet. Porttitor diam egestas, non vut etiam montes, aliquet? Pellentesque. Dolor nascetur amet. Adipiscing sed pulvinar cursus! Urna in, in turpis duis in sit placerat, vut non aliquam? Mattis habitasse augue mus. Pulvinar auctor natoque est lacus porta sagittis! A in massa lundium? In non, lundium nisi magna proin elementum sed porttitor sed amet risus a aliquet mid a? Proin turpis, ac magna, dictumst lorem tincidunt penatibus sociis rhoncus? Duis cursus sit diam amet nisi mattis egestas habitasse diam.
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<p>2)Take 300 μL from this LB and put it into another 30 mL LB medium  at 37ºC until reaching an optical density of 0’35 – 0’6 at 600 wavelength </p>
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<p>3)Take away 1 mL and cool on ice for 5 minutes.</p>
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</p>
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<p>4)Centrifuge for 30 seconds at 15000g, discard the supernatant and resuspend the pellet in 75 μL of cold LB and keep it in ice for 5 min.</p>
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<p>5)Add 75 μL Solution TSS 2x, mix everything and keep it in ice for 5 min. Cells now can be used inmediately o freeze them at -80ºC.</p>
 +
<p><strong>Solution TSS</strong> contains:
 +
Triptone 8g/l, yeast extract 5 g/L, NaCl 5g/L, Polietilenglicol (PEG) 8000 200 g/L, DMSO 10% (v/v), 100ml/L MgSO4 1M. Add 700 mL of water and calibrate the pH to 6,5. Finally, fill it until reach 1L.</p>
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</br>
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</p>
</p>
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<img src="https://lh5.googleusercontent.com/-GXrWkcwPJPU/TibGABAC11I/AAAAAAAAAVs/jg8cex8tdHk/s288/IMG_4711.JPG" style=padding-left:200px;"height="288" width="192" /> <img src="https://lh5.googleusercontent.com/-KRWFbZ4F2Ms/Tif3xgtvNaI/AAAAAAAAAY8/H2PLNUHJnDY/s400/IMG_4755.JPG" height="267" width="400" />
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<img id="gato" src="https://lh5.googleusercontent.com/-GXrWkcwPJPU/TibGABAC11I/AAAAAAAAAVs/jg8cex8tdHk/s288/IMG_4711.JPG" style=padding-left:200px;"height="288" width="192" />  
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<img src="https://lh5.googleusercontent.com/-KRWFbZ4F2Ms/Tif3xgtvNaI/AAAAAAAAAY8/H2PLNUHJnDY/s400/IMG_4755.JPG" height="267" width="400" />
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</br>
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<p>
More mini-preps and frozen samples. But we're also trying something new! Our first
More mini-preps and frozen samples. But we're also trying something new! Our first
electrophoresis to see how the digestions and the mini-preps go. We're examining the
electrophoresis to see how the digestions and the mini-preps go. We're examining the
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</p>
</p>
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<img src="https://lh4.googleusercontent.com/-uUiZzK1cigA/TibGGJ_VofI/AAAAAAAAAWQ/Ft4hghUuDLo/s288/IMG_4701.JPG" style=padding-left:200px;"height="192" width="288" /> <img src="https://lh5.googleusercontent.com/-Ps2bY8XQNMs/TibGFrv0PhI/AAAAAAAAAWM/8a8phy0tthY/s288/IMG_4702.JPG" style=padding-left:20px;"height="192" width="288" />
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<img src="https://lh4.googleusercontent.com/-uUiZzK1cigA/TibGGJ_VofI/AAAAAAAAAWQ/Ft4hghUuDLo/s288/IMG_4701.JPG" style=padding-left:200px;"height="192" width="288" />  
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<img src="https://lh5.googleusercontent.com/-Ps2bY8XQNMs/TibGFrv0PhI/AAAAAAAAAWM/8a8phy0tthY/s288/IMG_4702.JPG" style=padding-left:20px;"height="192" width="288" />
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</br>
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<p>
 
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Out of the lab before 19.00. What a record!
 
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<input type="button" value="Show Wednesday protocols" id="wednesdayBP">
<input type="button" value="Show Wednesday protocols" id="wednesdayBP">
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</br>
</br>
</div>
</div>
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<p>In. Mid vel vel elementum, placerat tincidunt, vut lacus purus nunc massa a habitasse? Ac pid elementum aliquam, natoque! Porttitor facilisis amet lacus, ridiculus nascetur! Sociis vel aenean natoque penatibus aliquam in, augue mauris, dictumst, nunc mid platea a! Massa? Vut dis purus. Odio magna nec. Lorem ut turpis adipiscing scelerisque dis, scelerisque. Sed quis, porttitor et pulvinar in. Massa sit, porta urna nunc auctor non elementum! Augue dolor cum sociis, dignissim elementum. Integer. Penatibus. Phasellus et porta nec! Hac in nec porttitor ridiculus rhoncus. Hac natoque mid est nunc platea nisi sed habitasse! Amet nec placerat ultricies egestas.
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<p><strong>Digestion</strong></p>
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Vel cum diam, lorem integer et montes, nec placerat, turpis lacus nec placerat, rhoncus rhoncus, a porta augue ac! Et aliquet. Porttitor diam egestas, non vut etiam montes, aliquet? Pellentesque. Dolor nascetur amet. Adipiscing sed pulvinar cursus! Urna in, in turpis duis in sit placerat, vut non aliquam? Mattis habitasse augue mus. Pulvinar auctor natoque est lacus porta sagittis! A in massa lundium? In non, lundium nisi magna proin elementum sed porttitor sed amet risus a aliquet mid a? Proin turpis, ac magna, dictumst lorem tincidunt penatibus sociis rhoncus? Duis cursus sit diam amet nisi mattis egestas habitasse diam.
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<p>1.Make the following master mix:</p>
 +
<p>-1 μl enzyme 1</p>
 +
<p>-1 μl enzyme 2</p>
 +
<p>-3 μl enzyme buffer</p>
 +
<p>-15 μl ddH2O</p>
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<p>2.Add 20 μl of master mix to 10 μl of DNA</p>
 +
<p>3.Incubate this mix 3 hours in a bath at 37ºC </p>
 +
<p>4.Make a heat shock at 80 ºC for 20 min</p>
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<p>5.Store the eppendorfs at 4ºC</p>
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Coffee break while we run one more electrophoresis...
Coffee break while we run one more electrophoresis...
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<img src="https://lh3.googleusercontent.com/-S90vyEr0ke8/Tif3HI93rhI/AAAAAAAAAXg/LSvK9aosDRA/s400/IMG_4732.JPG" style=padding-left:300px;" height="267" width="400" />
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</br>
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<p>
<p>
We have a nice visit today! Lauren, from the team of Pennsylvania, is here to tell us
We have a nice visit today! Lauren, from the team of Pennsylvania, is here to tell us
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on kinetics with her while Marta struggles to design the primers we'll need for the PCR
on kinetics with her while Marta struggles to design the primers we'll need for the PCR
reactions next week. There's no way to get them exactly right, what a nightmare!
reactions next week. There's no way to get them exactly right, what a nightmare!
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<p>Thursday Protocols</p>
 
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<p>In. Mid vel vel elementum, placerat tincidunt, vut lacus purus nunc massa a habitasse? Ac pid elementum aliquam, natoque! Porttitor facilisis amet lacus, ridiculus nascetur! Sociis vel aenean natoque penatibus aliquam in, augue mauris, dictumst, nunc mid platea a! Massa? Vut dis purus. Odio magna nec. Lorem ut turpis adipiscing scelerisque dis, scelerisque. Sed quis, porttitor et pulvinar in. Massa sit, porta urna nunc auctor non elementum! Augue dolor cum sociis, dignissim elementum. Integer. Penatibus. Phasellus et porta nec! Hac in nec porttitor ridiculus rhoncus. Hac natoque mid est nunc platea nisi sed habitasse! Amet nec placerat ultricies egestas.
 
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Vel cum diam, lorem integer et montes, nec placerat, turpis lacus nec placerat, rhoncus rhoncus, a porta augue ac! Et aliquet. Porttitor diam egestas, non vut etiam montes, aliquet? Pellentesque. Dolor nascetur amet. Adipiscing sed pulvinar cursus! Urna in, in turpis duis in sit placerat, vut non aliquam? Mattis habitasse augue mus. Pulvinar auctor natoque est lacus porta sagittis! A in massa lundium? In non, lundium nisi magna proin elementum sed porttitor sed amet risus a aliquet mid a? Proin turpis, ac magna, dictumst lorem tincidunt penatibus sociis rhoncus? Duis cursus sit diam amet nisi mattis egestas habitasse diam.
 
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<div class="summary">
<div class="summary">
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<p>It seems nothing's gone right so far except for the transformations. We'll have to start over...BUT WE HAVEN'T SAID OUR LAST WORD YET! [To be continued...]
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<p>It seems nothing's gone right so far except for the transformations. We'll have to start again...BUT IT ISN'T OVER 'TIL THE FAT LADY SINGS! [To be continued...]
 +
 
</p>
</p>
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<input type="button" value="Show Friday protocols" id="fridayBP">
 
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<p>Friday Protocols</p>
 
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<div class="summary">
<div class="summary">
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<p> Blondie and little Rosidito didn't appear in the lab these two days so our bacterial cultures died and we have to lose time on Monday making new bacterial cultures. The rest of the group are starting to hate both clumsy girls.
+
<p> Blondie and little Rosidito didn't appear in the lab over the last two days so our bacterial cultures died and we have to waste time on Monday making new ones. The rest of the group are starting to hate both clumsy girls.
-
[Just kidding, we love them: they're the best, efficient and the most beautiful]
+
[Just kidding, we love them: they're the best, so efficient and the most beautiful creatures]
 +
 
</p>
</p>
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<input type="button" value="Show weekend protocols" id="weekendBP">
 
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<p>Weekend Protocols</p>
 
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<p>In. Mid vel vel elementum, placerat tincidunt, vut lacus purus nunc massa a habitasse? Ac pid elementum aliquam, natoque! Porttitor facilisis amet lacus, ridiculus nascetur! Sociis vel aenean natoque penatibus aliquam in, augue mauris, dictumst, nunc mid platea a! Massa? Vut dis purus. Odio magna nec. Lorem ut turpis adipiscing scelerisque dis, scelerisque. Sed quis, porttitor et pulvinar in. Massa sit, porta urna nunc auctor non elementum! Augue dolor cum sociis, dignissim elementum. Integer. Penatibus. Phasellus et porta nec! Hac in nec porttitor ridiculus rhoncus. Hac natoque mid est nunc platea nisi sed habitasse! Amet nec placerat ultricies egestas.
 
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Vel cum diam, lorem integer et montes, nec placerat, turpis lacus nec placerat, rhoncus rhoncus, a porta augue ac! Et aliquet. Porttitor diam egestas, non vut etiam montes, aliquet? Pellentesque. Dolor nascetur amet. Adipiscing sed pulvinar cursus! Urna in, in turpis duis in sit placerat, vut non aliquam? Mattis habitasse augue mus. Pulvinar auctor natoque est lacus porta sagittis! A in massa lundium? In non, lundium nisi magna proin elementum sed porttitor sed amet risus a aliquet mid a? Proin turpis, ac magna, dictumst lorem tincidunt penatibus sociis rhoncus? Duis cursus sit diam amet nisi mattis egestas habitasse diam.
 
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Latest revision as of 01:46, 22 September 2011


Monday 18 July


Our inoculums look pleasantly cloudy, as expected. All except two. We freeze samples of the good ones in glycerol at -80 ºC in a wonderful fridge that could also easily house a corpse (who knows?).

We start studying the protocols of our mini-prep kit to purify the BioBrick plasmids from our transformed cultures. They don't look that complicated but we have to do about 50; shoulders to the wheel!

We receive several BioBricks and the strains we had ordered: vainillin and rhlR BioBricks, two strains of B.subtilis, another strain containing VanM/N genes... people are being quite kind to us! We seed the bacteria and transform them with the BioBricks, depending on the format they come in.

Our mini-preps are ready at last after a hard day’s work, and we are able to leave some inoculums of DH5-a to prepare competent cells tomorrow.

21.30: Lab OFF.



Monday Protocols


Miniprep Protocol:

We use the Miniprep Protocol giving in the kit of Favorgen biotech corp.:

1. Transfer 2 ml of well-grown bacteria culture to a microcentrifuge tube.

2. Descend the bacteria by centrifuging at 10.000 rpm for 1 minute and discard the supernatant completely.

3. Add 250 μl of FAPD1 Buffer to the pellet and resuspend the cells completely by pipetting.

4. Add 250 μl of FAPD2 Buffer and gently invert the tube 5 times to lyse the cells and incubate at room temperature for 2 min.

5. Add 350 μl of FAPD3 Buffer and invert the tube 5 times

6. Centrifuge for 10 min at 14.000 rpm

7. Transfer the suspernatant carefully to FAPD Column. Centrifuge for 1 min and then discard the flow-through.

8. Add 400 μl of W1 Buffer to FAPD Column. Centrifuge for 1 min then discard the flow-through.

9. Add 750 μl of Wash Buffer to FAPD Column. Centrifuge for 1 min then discard the flow-through.

10. Centrifuge for an additional 3 min to dry the column.

11. Place FAPD Column to a new 1,5 ml microcentrifuge tube.

12. Add 30 μl of ddH2O to the membrane center of FAPD Column. Stand the column for 2 min.

13. Centrifuge for 2 min at 14.000 rpm to elute plasmid DNA.



Tuesday 19 July


Materials and chemicals keep appearing in big cardboard boxes full of styro-foam pieces (we're storing it all in the hopes of filling a bath next month and having some fun).

More good news: our transformed cultures have grown as expected, as have the B. subtilis strains. At the end of the day we make inoculums of them all so that they grow o/n and tomorrow we can freeze samples and do yet more mini-preps (we have only just started and we're already sick and tired of that kit...)

We need to discuss which assembling method we'll use with the BioBricks. It takes us some hours, and in the meantime, Andrés faces the personal challenge of making competent cells from the DH5-a inoculum with the new protocol. Tomorrow we'll see who has won the battle...

And Pedro isn't wasting any time at all, he's just found out these racks are stackable, like Lego. This discovery has changed his life, look how happy he is!


After deciding how we'll build each BioBrick, and counting all the ligations we need to do, we finally tackle the digestions with the different restriction enzymes. Mastermix kits this time. More protocols. GREAT.


Tuesday Protocols


Células competentes II

1)Incubate a bacterial colony in 3 mL LB, 37ºC with agitation all night.

2)Take 300 μL from this LB and put it into another 30 mL LB medium at 37ºC until reaching an optical density of 0’35 – 0’6 at 600 wavelength

3)Take away 1 mL and cool on ice for 5 minutes.

4)Centrifuge for 30 seconds at 15000g, discard the supernatant and resuspend the pellet in 75 μL of cold LB and keep it in ice for 5 min.

5)Add 75 μL Solution TSS 2x, mix everything and keep it in ice for 5 min. Cells now can be used inmediately o freeze them at -80ºC.

Solution TSS contains: Triptone 8g/l, yeast extract 5 g/L, NaCl 5g/L, Polietilenglicol (PEG) 8000 200 g/L, DMSO 10% (v/v), 100ml/L MgSO4 1M. Add 700 mL of water and calibrate the pH to 6,5. Finally, fill it until reach 1L.



Wednesday 20 July


AT LAST our official mascot is here! Say hello to Mr. Gibbs! Rocío had him held captive in her house, but to make up for that, she's brought a WONDERFUL Disney princess clock to cheer our lab up! It gives the lab that homely touch. We have also brought a coffee machine - we need caffeine in industrial amounts to work here for so many hours a day.


More mini-preps and frozen samples. But we're also trying something new! Our first electrophoresis to see how the digestions and the mini-preps go. We're examining the results. It's ok for the first time, but there's a long way to go yet...

Marta is in charge of our first ligations, tomorrow we'll see how they went.

...and how did the great battle end? Andrés 1 - E.coli 0. We have competent cells!

Out of the lab before 19.00. What a record!



Wednesday Protocols


Digestion

1.Make the following master mix:

-1 μl enzyme 1

-1 μl enzyme 2

-3 μl enzyme buffer

-15 μl ddH2O

2.Add 20 μl of master mix to 10 μl of DNA

3.Incubate this mix 3 hours in a bath at 37ºC

4.Make a heat shock at 80 ºC for 20 min

5.Store the eppendorfs at 4ºC



Thursday 21 July


We run an electrophoresis of the digestions we made yesterday, but it hasn't worked properly, it seems the process still needs some fine-tuning.

We spend some time preparing the rewards for those who gave us money for the project through the crowd-funding platform. Letters, funny badges, videos...

Coffee break while we run one more electrophoresis...


We have a nice visit today! Lauren, from the team of Pennsylvania, is here to tell us about her project, and learn a bit more about ours. Carlos is having an intense discussion on kinetics with her while Marta struggles to design the primers we'll need for the PCR reactions next week. There's no way to get them exactly right, what a nightmare!


Friday 22 July


It seems nothing's gone right so far except for the transformations. We'll have to start again...BUT IT ISN'T OVER 'TIL THE FAT LADY SINGS! [To be continued...]


Weekend


Blondie and little Rosidito didn't appear in the lab over the last two days so our bacterial cultures died and we have to waste time on Monday making new ones. The rest of the group are starting to hate both clumsy girls. [Just kidding, we love them: they're the best, so efficient and the most beautiful creatures]

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