Team:Sevilla/Week1

From 2011.igem.org

(Difference between revisions)

Latest revision as of 17:01, 21 September 2011

Week 1
Week 2

Week 3
Week 4

Week 5
Week 6

Week 7
Week 8

Week 9
Week 10

Week 11
Week 12

Monday 11 July

Working in the lab, our first attempt!

After becoming familiar with all the machines, chemicals, pipettes and what seems like thousands of tubes surrounding us, we "tidily" place our own material around the laboratory and set some basic rules for labelling, disposal of waste products and safety stuff. Planning the week is essential, so we spend several hours looking through all the BioBricks we want to use, and working out how we’ll have to mix them to make our bacteria work properly. Restriction enzymes, anti-biotics, promoters, reporters... what wonderful chaos.

Monday Protocols

No protocols used today,but we're gathering some for the next days. Give us some time!

Tuesday 12 July

We prepare the competent cells from the inoculum we made yesterday, following a protocol that seems to be fairly easy and simple. At the same time, some other members of the group shut themselves away in the kitchen to cook up some litres of LB-agar with different antibiotics, and prepare the Petri dishes. Once they're ready, we seed the competent cells.

Tuesday Protocols

Competent cells:

1. Grow cells in tubes with 3 ml of LB o/n at 37ºC with agitation

2. Transfer the cultures to 50 ml of LB and let grow until it reaches an OD of 0,5

3. Cool it in ice for 10 min

4. Transfer 12 ml to steril tubes

5. Centrifuge at 3000rpm for 10 min and remove the supernatant

6. Resuspend cells in CaCl2 100mM (add 5ml to each tube)

7. Add 7ml of CaCl2 100mM (4ºC) to each tube so that the final volume is 12 ml

8. Incubate in ice for 30 min and centrifuge at 4000rpm for 5 min. Remove supernatant.

9. Resuspend all the collected cells in 5 ml of CaCl2: add 5 ml to the first tube, resuspend and put it into the second tube, and so on until all the pellets are contained in the final tube with 5 ml.

10. Store with glycerol at -80ºC (30ul glycerol + 170 ul cell culture)

Wednesday 13 July

To test our competent cells we split into three groups to transform bacteria with all the BioBricks we have, following the enclosed protocol. We seed the transformed bacteria in dishes with the appropriate antibiotic and let them grow overnight. We keep talking about the best way to assemble the BioBricks once we get them. So many things to take into account and so many materials that haven't arrived yet...

Wednesday Protocols

Transformation

1.Let defrost the competent cells in ice.

2.Add 2 μL DNA to 50 μL competents cells while working in ice.

3.Incubate the cells in ice for 30 min

4.Immerse the cells in a bath of 42 ºC for 80 seconds

5.Incubate in ice for 5 min

6.Add 1 mL of LB medium without antibiotics and incubate for 90 min at 37ºC with agitation

7.Centrifuge 5 min at 5000 rpm. Remove 700 μl supernatant and resuspend the pellet.

8.Take two culture dishes with LB agar with the correct antibiotic. Put 50 μl and 200 μl of transformed cells in a dish and make a lawn culture.

9.Incubate 12-14 hours at 37ºC

Thursday 14 July

We entered the laboratory and ran over excitedly to see how our transformations had gone only to discover that none of the bacteria had grown. What a disappointment...We go to the Genetics department to cry a little and get some competent cells so we can start over. They also give us their own protocol to try again, and a control plasmid for transformations (S3139). Competent cells in hand, we do the transformations again with the BioBricks and leave to grow overnight at 37ºC. Hope tomorrow there's something other than LB-agar in those dishes...

Friday 15 July

OH YEAH! There they are! It seems our transformation has been a success. But we don't have all the materials needed to use our new protocol to prepare competent cells, so we spend the evening cooking some more LB, preparing LB-agar dishes and trying to understand how the autoclave works (we are currently enjoying a love-hate relationship with that stupid machine).

Weekend 16-17 July

Sunday evening and it’s 38 ºC in Seville; here we are preparing inoculums of all our transformed cultures to keep them growing in LB+antibiotics o/n at 37 ºC. Who said the weekend was a break?

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-<p>Monday 11 June</p>
+<p>Monday 11 July</p>
 </html>{{:Team:Sevilla/Templates/hr|colour=#FFB880|class=week1}}<html>
 </br>
@@ Line 169: / Line 172: @@
 <p>
-Working in a lab, first approach!</p>
+Working in the lab, our first attempt!
+</p>
 <p>
-After becoming familiar with all the machines, chemicals, pipettes and the thousands of tubes that surround us, we place "tidily" our own material all over the laboratory and set some basic rules for the labeling, the waste products disposal and safety stuff. Planning the week is essential, so we spend some hours looking through all the BioBricks we want to use and how we have to mix them to make our bacteria work propperly. Restriction enzymes, antiobiotics, promoters, reporters...such a nice chaos. </p>
+After becoming familiar with all the machines, chemicals, pipettes and what seems
+like thousands of tubes surrounding us, we "tidily" place our own material around the
+laboratory and set some basic rules for labelling, disposal of waste products and safety
+stuff. Planning the week is essential, so we spend several hours looking through all the
+BioBricks we want to use, and working out how we’ll have to mix them to make our
+bacteria work properly. Restriction enzymes, anti-biotics, promoters, reporters... what
+wonderful chaos.
+ </p>
@@ Line 178: / Line 189: @@
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+</br>
-<a href="#" class="button">
+<input type="button" value="Show Monday protocols" id="mondayBP" class="prot"/>
-<span class="user">Show Monday protocols</span>
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@@ Line 206: / Line 216: @@
 <div class="day">
 </br>
-<p>Tuesday 12 June</p>
+<p>Tuesday 12 July</p>
 </html>{{:Team:Sevilla/Templates/hr|colour=#FFB880|class=week1}}<html>
 </br>
@@ Line 214: / Line 224: @@
 <p>
-We prepare the competent cells from the inoculum we made yesterday, following a protocol that seems to be quite easy and simple. At the same time, some other members of the group shut theirselves up in the kitchen to cook some litres of LB-agar with different antibiotics and prepare the Petri dishes. Once they're ready, we seed the competent cells.
+We prepare the competent cells from the inoculum we made yesterday, following a protocol that seems to be fairly easy and simple. At the same time, some other members of the group shut themselves away in the kitchen to cook up some litres of LB-agar
+with different antibiotics, and prepare the Petri dishes. Once they're ready, we seed the competent cells.
 </p>
 <img src="https://lh3.googleusercontent.com/-a_vKo81vjUQ/TiWW6K0VE3I/AAAAAAAAARU/2HbyyNM7-ME/s288/IMG_4653.JPG" style="padding-left:300px;"height="192" width="288" />
@@ Line 231: / Line 243: @@
 </div>
-<p>
+<p><strong>
-Competent cells:</p>
+Competent cells:</strong></p>
 <p>
 . Grow cells in tubes with 3 ml of LB o/n at 37ºC with agitation</p>
@@ Line 260: / Line 272: @@
 <div class="day">
 </br>
-<p>Wednesday 13 June</p>
+<p>Wednesday 13 July</p>
 </html>{{:Team:Sevilla/Templates/hr|colour=#FFB880|class=week1}}<html>
 </br>
@@ Line 268: / Line 280: @@
 <p>
-To test our competent cells we split into three groups to transform bacteria with all the BioBricks we have, following the enclosed protocol. We seed the transformed bacteria in dishes with the appropiate antibiotic and let them growing overnight. We keep talking about the better ways to assemble the BioBricks once we get them. So many things to take into account and so many materials haven't come yet...
+To test our competent cells we split into three groups to transform bacteria with all the
+BioBricks we have, following the enclosed protocol. We seed the transformed bacteria
+in dishes with the appropriate antibiotic and let them grow overnight. We keep talking
+about the best way to assemble the BioBricks once we get them. So many things to take
+into account and so many materials that haven't arrived yet...
 </p>
 <img src="https://lh6.googleusercontent.com/-Zb44NXtTPBI/TibF30zA3MI/AAAAAAAAAUk/EBxLjDuCd5I/s288/IMG_4728.JPG" style=padding-left:300px;"height="192" width="288" />
@@ Line 283: / Line 300: @@
 </br>
 </div>
-<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.
+<p><strong>Transformation</strong></p>
+<p>1.Let defrost the competent cells in ice.</p>
-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.
+<p>2.Add 2 μL DNA to 50 μL competents cells while working in ice.</p>
+<p>3.Incubate the cells in ice for 30 min</p>
+<p>4.Immerse the cells in a bath of 42 ºC for 80 seconds</p>
+<p>5.Incubate in ice for 5 min</p>
+<p>6.Add 1 mL of LB medium without antibiotics and incubate for 90 min at 37ºC with agitation</p>
+<p>7.Centrifuge 5 min at 5000 rpm. Remove 700 μl supernatant and resuspend the pellet.</p>
+<p>8.Take two culture dishes with LB agar with the correct antibiotic. Put 50 μl and 200 μl of transformed cells in a dish and make a lawn culture.</p>
+<p>9.Incubate 12-14 hours at 37ºC</p>
 </p>
 </div>
@@ Line 294: / Line 317: @@
 <div class="day">
 </br>
-<p>Thursday 14 June</p>
+<p>Thursday 14 July</p>
 </html>{{:Team:Sevilla/Templates/hr|colour=#FFB880|class=week1}}<html>
 </br>
@@ Line 302: / Line 325: @@
 <p>
-We entered the laboratory and ran excitedly to see how our transformations had gone, just to find out none of the bacteria had grown. What a disappointment...We go to the department of Genetics to cry a little and get some competent cells to start over.They also give us their own protocol to try again, and a control plasmid for transformations (S3139). Competent cells in hand, we do the transformations again with the BioBricks and leave growing o/n at 37ºC. Hope tomorrow there's something else than LB-agar in those dishes...
+We entered the laboratory and ran over excitedly to see how our transformations had
+gone only to discover that none of the bacteria had grown. What a disappointment...We
+go to the Genetics department to cry a little and get some competent cells so we can
+start over. They also give us their own protocol to try again, and a control plasmid for
+transformations (S3139). Competent cells in hand, we do the transformations again with
+the BioBricks and leave to grow overnight at 37ºC. Hope tomorrow there's something
+other than LB-agar in those dishes...
 </p>
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-<p>Thursday Protocols</p>
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-</div>
-<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.
-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.
-</p>
-</div>
 </div>
@@ Line 329: / Line 340: @@
 <div class="day">
 </br>
-<p>Friday 15 June</p>
+<p>Friday 15 July</p>
 </html>{{:Team:Sevilla/Templates/hr|colour=#FFB880|class=week1}}<html>
 </br>
@@ Line 337: / Line 348: @@
 <p>
-OH YEAH!There they are!It seems our transformation has been a success. But we don't have all the materials needed to try our new protocol to prepare competent cells, so we spend the evening cooking some more LB, preparing LB-agar dishes and understanding how the autoclave works (we have a love-hate relation with that stupid machine).
+OH YEAH! There they are! It seems our transformation has been a success. But we
+don't have all the materials needed to use our new protocol to prepare competent
+cells, so we spend the evening cooking some more LB, preparing LB-agar dishes and
+trying to understand how the autoclave works (we are currently enjoying a love-hate
+relationship with that stupid machine).
 </p>
 <img src="https://lh5.googleusercontent.com/-TwZrUJijswM/TiWW4_HAK3I/AAAAAAAAARI/yzvogoQmLGM/s288/IMG_4650.JPG"style="padding-left:300px;" height="192" width="288" />
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-<p>Friday Protocols</p>
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-</div>
-<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.
-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.
-</p>
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@@ Line 368: / Line 363: @@
 <div class="day">
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-<p>Weekend 16-17 June</p>
+<p>Weekend 16-17 July</p>
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@@ Line 376: / Line 371: @@
 <p>
-Sunday evening,38ºC in Seville, and here we are preparing inoculums of all our transformed cultures to keep them growing in LB+antibiotics o/n at 37ºC. Who said weekend was a break?
+Sunday evening and it’s 38 ºC in Seville; here we are preparing inoculums of all our
+transformed cultures to keep them growing in LB+antibiotics o/n at 37 ºC. Who said the
+weekend was a break?
 </p>
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-</div>
-<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.
-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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