Team:ZJU-China/Notebook/August

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Labnote

Biobrick group | Biofilm group

This group...........

May&June

In the two months we discussed some new ideas and finally decided our project
>> Click to see our brainstorm

July

In this month we......
>>Click to see

Week5

Day

Note

Aug.1st Monday

•Fusion PCR Vgb+YFP+tetR, NirB+RFP+tetR,

•PCR: NirB, Vgb

Aug.2nd Tuesday

•Cut: 13K+10I, 22M+10I

• Purify: 13K+10I, 22M+10I
• Ligation: Pvgb+22M+10I, Pnirb+13K+10I

• PCR backbones
• Electrophresis

• Gel excision and purification

Aug.3rd Wednesday

• Make Phusion Buffer, 5×isothermel buffer

• colony PCR: 20H, 20J, 22B

Aug.4th Thursday

• Cut: 10I+22M, 10I+13; and purification

• Ligation: Pvgb+22M+10I, Pnirb+13K+10I,
• colony PCR: 13K+10I

• Culture: 20H, 20J, 22B, 1K, 1I,3C, 5E, 7C

• Transform: 1G, 3A, 5A, 7A from the distribution plate

Aug.5th Friday

• Check the plates. Contamination, or no positive colonies

• Miniprep: 5 backbones, 22B-1, 22B-3

• PCR: nirB from 13K+10I+nirB to firm the ligation. One positive result.

• Culture the positive colony.

Aug.6th Saturday

Aug.7th Sunday

• Cut: 22M,13K with E & S

• Culture the red colonies from plate of pSB1C3

• PCR: 5 backbones
• Cut the PCR products with P+E and run the gel to confirm.

Week6

Day

Note

Aut.8th Monday

• The gel results of 5 backbones are right.

• Miniprep: pSB1C3, vgb+22M+10I

• Culture vgb+22M+1oI in hypoxia
•PCR pSB1C3

Aug.9th Tuesday

• Run the PCR product

• PCR pSB1C3 again

• Run the product, results are good.

Aug.10th Wednesday

• Culture: 20H, 20J
• Transform 13K from plate 3

• Miniprep: 20H-1, 20J-1

• Cut: the 20H-1, 20J-1, 22B-1, 22B-3 with E+P

Aug.11th Thursday

• Run the digestion results. Bands are confirmed right.

• Colony PCR vgb+22M+10I

• Cut the plasmid of vgb+22M+10I

Aug.12th Friday

• Make new stock of competent cells

• Ligation: 13K+10I
• Cut the PCR results and 22M with E+P

• Sequence: nirB, vgbL, 12I, 20H, 20J, 22B

• Transform 13K+10I+pSB1K3
• Cut 13K to validate. Results are right.

Aug.13th Saturday

• Colony PCR: 13K+10I+pSB1K3

• Culture: vgb+22M+10I in 5ml(shaking), 5ml(water bath), 10ml(water bath), 15(water bath).

• Check the YFP expression of 5ml(shaking) and 15ml(water bath). No yellow fluorescent cells,

Aug.14th Sunday

• Transform: the Gibson assembly results.

• Miniprep: 13K+10I
• Cut: 13K+10I

• Purification: the digestion results.
• Ligation: nirB+13K+10I

Week7

Day

Note

Aug.15th Monday

• Plate: nirB+13K+10I

• Colony PCR: vgb+YFP+tetR +terminater

• Gibson PCR

Aug.16th Tuesday

• Colony PCR: vgb+22M+10I, nirB+13K+10I

• No bands of 13K; 22M confirmed

Aut.17th Wednesday

• Miniprep: 22M
• Cut: 22M

• Check CFP expression. No fluorescence.

Aug.18th Thursday

• Transform: 13K, 10I, 22M, 12I, 18P

Aug.19th Friday

• Miniprep: 13K, 10I, 22M, 12I, 18P

• Cut: 13K, 10I, 22M, 12I, 18P

• Run the gel

Aug.20th Saturday

• Ligate 13K+10I, 22M+10I

Aug.21st Sunday

• Transform: the Gibson assembly results.

• Miniprep: 13K+10I
• Cut: 13K+10I

• Purification: the digestion results.
• Ligation: nirB+13K+10I

Week8

Day

Note

Aug. 22nd Monday

• Transform 13K+10I, 22M+10I

• Test new primers.
• PCR: 22M+10I, 13K+10I

• Run the PCR products.
• Cut the PCR products.

Aug. 23rd Tuesday

• Test primers: CS/CP, VF/VR, pSB1_f/r

• Cut: 11P, 1F, 22M
• Run the cut results.1F-1/2/3 are right.

• Mix the 1F-1/2 purification products

• Cut: 1F-1+1F-2(E+S), 22M-3(X+P), pSB1C3(E+P)

Aug. 24th Wednesday

Aug. 25th Thursday

Aug. 26th Friday

• Amplify: vgb, 1C3

Aug.27th Saturday

• Digest: Vgb, 1C3, fdfhF, 22M+10I, 13K+10I

Aug.28th Sunday

• Ligate: vgb+22M+10I, fdfhF+13K+10I

• Transform the ligation results.

1st August

Freeze slicing of about 50μm. Observe under natural light microscope and can see red florescence. The thickness is about 130μm

4th August

Repeat the last experiment with silicone tube. 6rpm/s results in a flowing speed of 68ml/day

6th August

Similar to the last time. Did not use freeze slicing.

15th August

Cultured E.coli in 5ml LB for 12h.

16th August

Substituting a part of silicone tube with glass tube in silicone tube biofilm formation sets. Culture in 37℃

17th August

Add 50ml LB and culture with circular culture.

18th August

12.00 found one free-flow pump stopped. Cooled for 15 minutes and turned on again. Could be over heated. Can see some bacteria on the bottom of the vessel and tube. When the pump started again, the bacteria was washed away.

19th August

Can observe obvious white biofilm where the silicone tube joins the tube but cannot see red florescence, suspect contamination. No biofilm is observed on the glass tube under microscope.

21st, August

Biofilm formation with large test tubes. Inoculate with 1% e.coli. Rubber tubes are attached to air pump with filter between air pump and the tube to prevent entrance of germs. Two sets use MSM +glucose medium and two sets use LB.
Retry with glass tube biofilm formation set.

24th, August

Terminate biofilm formation, the glass slide left in the drawer to dry. Can see obvious rod like structure under 400 magnification. (spheres in MSM+glucose culture) No red florescence is seen. Most of the surface is covered by single layer cells but some part of it has thick bump like structure.
No biofilm observed on the glass tube.

@@ Line 51: / Line 51: @@
 <div class="main">
 <div  class="pagetitle" id="nbook">
-       <table style="background-color:transparent;" width="750" border="0" cellspacing="0" cellpadding="1">
+       <table style="background-color:transparent;" width="750" border="0" cellspacing="1" cellpadding="1">
    <tr>
      <td ><h3>Labnote</h3></td>
@@ Line 68: / Line 68: @@
       <div id="leftul"><div class="leftul">
                   <div id="accordion">
+  <h4>May&June</h4>
+<div class="pane" style="height:140px;"><a href="https://2011.igem.org/Team:ZJU-China/Notebook/Brainstorm">In the two months we discussed some new ideas and finally decided our project<br/>>> Click to see our brainstorm</a></div>
 	<h4 >July</h4>
@@ Line 95: / Line 96: @@
 	</div>
+	<h4>Protocol</h4>
+        <div class="pane"><a href="https://2011.igem.org/Team:ZJU-China/Protocol">>>Click to see our lab protocol about biofilm formation</a></div>
   </div>
@@ Line 121: / Line 123: @@
 </div>
-   <div class="bigblock">
+   <div class="bigblock"><div class="inner" id="n_biobrick">
 <div class="block" id="nsheet">
-<h3>Week1</h3><hr/>
+<h3>Week5</h3><hr/>
-<table id="notesheet" width="650" border="1" cellspacing="0" cellpadding="1">
+<table id="notesheet" width="650" border="1" cellspacing="1" cellpadding="1">
    <tr><td width="76">Day</td><td width="349">Note</td></tr>
    <tr>
-     <td id="sheetleft">Jul.4th Monday</td>
+     <td id="sheetleft">Aug.1st
-     <td><table id="intable" width="328" border="0" cellspacing="0" cellpadding="1">
+Monday
+</td>
+     <td><table id="intable" width="541" border="0" cellspacing="1" cellpadding="1">
-     <td width="128">• Aerobic cultivation of DH5α</td>
+     <td width="286">•Fusion PCR
+Vgb+YFP+tetR, NirB+RFP+tetR,
+</td>
-     <td width="196">• Preparation of apparatus for the formation of biofilm</td>
+     <td width="251" >•PCR: NirB, Vgb</td>
 </table></td>
    </tr>
    <tr>
-     <td id="sheetleft">Jul 5th Tuesday
+     <td id="sheetleft">Aug.2nd
+Tuesday
 </td>
-     <td>&nbsp;</td>
+     <td><table id="intable" width="615" border="0" cellspacing="1" cellpadding="1">
+      <td width="140"> •Cut: 13K+10I, 22M+10I
+</td>
+    <td width="181" > • Purify: 13K+10I, 22M+10I<br/>
+• Ligation: Pvgb+22M+10I, Pnirb+13K+10I
+</td>
+  <td width="142">• PCR backbones<br/>
+• Electrophresis
+</td>
+  <td width="144">• Gel excision and purification</td>
+</table></td>
    </tr>
    <tr>
-     <td id="sheetleft">Jul.6th
+     <td id="sheetleft">Aug.3rd
 Wednesday
 </td>
-     <td><table width="217" border="0" cellspacing="0" cellpadding="1">
+     <td><table width="640" border="0" cellspacing="1" cellpadding="1">
    <tr>
-     <td width="215">•Receiving  primers ordered previously</td>
+     <td width="170">• Make Phusion Buffer, 5×isothermel buffer
+</td>
+     <td width="184">• colony PCR: 20H, 20J, 22B
+</td>
    </tr>
 </table>
@@ Line 157: / Line 182: @@
    </tr>
    <tr>
-     <td id="sheetleft">Jul.7th
+     <td id="sheetleft">Aug.4th
 Thursday
 </td>
-     <td><table width="238" border="0" cellspacing="0" cellpadding="1">
+     <td><table width="618" border="0" cellspacing="1" cellpadding="1">
    <tr>
-     <td width="200">• Preparation of the aliquot of the primers</td>
+     <td >• Cut: 10I+22M, 10I+13; and purification
-    <td width="200">• Something wrong with a shaking incubator</td>
+</td>
+<td>• Ligation: Pvgb+22M+10I, Pnirb+13K+10I,<br/>
+• colony PCR: 13K+10I
+</td>
+<td>• Culture: 20H, 20J, 22B, 1K, 1I,3C, 5E, 7C</td>
+<td>• Transform: 1G, 3A, 5A, 7A from the distribution plate</td>
    </tr>
 </table>
@@ Line 169: / Line 202: @@
    </tr>
    <tr>
-     <td id="sheetleft">Jul.8th
+     <td id="sheetleft">Aug.5th
 Friday
 </td>
-     <td><table width="222" border="0" cellspacing="0" cellpadding="1">
+     <td><table width="627" border="0" cellspacing="1" cellpadding="1">
        <tr>
-        <td width="155">• Preparation of culture plates for the transformations</td>
+       <td >• Check the plates. Contamination, or no positive colonies</td>
+       <td>• Miniprep: 5 backbones, 22B-1, 22B-3</td>
+       <td>• PCR: nirB from 13K+10I+nirB to firm the ligation. One positive result.</td>
+       <td>• Culture the positive colony.</td>
        </tr>
      </table></td>
    </tr>
    <tr>
-     <td id="sheetleft">Jul.9th
+     <td id="sheetleft">Aug.6th
 Saturday
 </td>
-     <td><table width="313" border="0" cellspacing="0" cellpadding="1">
+     <td><table width="620" border="0" cellspacing="1" cellpadding="1">
    <tr>
-     <td width="127">• Preparation of culture plates for the transformations</td>
-    <td width="182">• protocols of transformation</td>
    </tr>
 </table>
@@ Line 191: / Line 229: @@
    </tr>
    <tr>
-     <td id="sheetleft">Jul.10th
+     <td id="sheetleft">Aug.7th
 Sunday
 </td>
-     <td><table width="246" border="0" cellspacing="0" cellpadding="1">
+     <td><table width="620" border="0" cellspacing="1" cellpadding="1">
        <tr>
-         <td>• Several colonies were picked up and cultivated in  5mL LB medium.
+         <td width="244">• Cut: 22M,13K with E &amp; S
-•Cryosectioning of biofilm
+</td>
+<td width="164">• Culture the red colonies from plate of pSB1C3</td>
+<td>• PCR: 5 backbones<br/>
+• Cut the PCR products with P+E and run the gel to confirm.
 </td>
        </tr>
@@ Line 204: / Line 246: @@
 </table>
-<p>&nbsp;</p>
+ <p>&nbsp;</p>
 </div>
 <div class="block" id="nsheet">
-<h3>Week2</h3><hr/>
+<h3>Week6</h3><hr/>
-<table id="notesheet" width="650" border="1" cellspacing="0" cellpadding="1">
-   <tr><td width="76">Day</td><td width="349">Note</td></tr>
+<table id="notesheet" width="650" border="1" cellspacing="0" cellpadding="1">
+   <tr><td width="76">Day</td><td width="349">Note</td></tr>
    <tr>
-     <td id="sheetleft">Jul.11th Monday</td>
+     <td id="sheetleft">Aut.8th
-     <td><table id="intable" width="541" border="0" cellspacing="0" cellpadding="1">
+Monday
+</td>
+     <td><table id="intable" width="100%" border="0" cellspacing="0" cellpadding="1">
-     <td width="128">•  Set up new LB culture plates with ampicillin and kanamycin</p></td>
+     <td width="191">• The gel results of 5 backbones are right.
+</td>
-     <td width="196">•
+     <td width="249" >• Miniprep: pSB1C3, vgb+22M+10I</td><br />
-      ·Sterilization of Glycerol and <br />
+<td width="157">• Culture vgb+22M+1oI in hypoxia<br/>
-        ·Preparation of 25mg/mL kanamycin</td>
+•PCR pSB1C3
-  <td>•Transformation of the parts mentioned on Jul.9th for the second time</td>
+</td>
-  <td>•Observation the sections</td>
-</table></td>
-  </tr>
-  <tr>
-    <td id="sheetleft">Jul 12th Tuesday
-</td>
-    <td><table id="intable" width="560" border="0" cellspacing="0" cellpadding="1">
-     <td width="128">• Pick two colonies of each parts and cultivate them in LB medium</td>
+</table></td>
+  </tr>
+  <tr>
+     <td id="sheetleft">Aug.9th
+Tuesday
+</td>
+    <td><table id="intable" width="100%" border="0" cellspacing="0" cellpadding="1">
+      <td width="33%"> • Run the PCR product
+</td>
-     <td width="203"> •Transformation of three parts(20J,20H.22B from Kit plates of 2011 Distribution ) which are related to the degradation of Cellulose </td>
-   <td width="91">•·Mini  prep to isolate 10I,12I and 22M</td>
+     <td width="33%" > • PCR pSB1C3 again
-  <td width="130">•Conservation of 10I,12I,22M and 11P</td>
+</td>
-</table></td>
+   <td width="33%">• Run the product, results are good.
-   </tr>
+</td>
-   <tr>
-     <td id="sheetleft">Jul.13th
+</table></td>
+   </tr>
+   <tr>
+     <td id="sheetleft">Aug.10th
 Wednesday
-</td>
-     <td><table width="640" border="0" cellspacing="0" cellpadding="1">
-   <tr>
+</td>
-     <td width="120">• Place the culture plate of 20J,20H and 22B in the fridge.</td>
+     <td><table width="100%" border="0" cellspacing="0" cellpadding="1">
-    <td width="102">•Min prep to isolate 13K
+   <tr>
-•Conservation of 13K
+     <td width="170">• Culture: 20H, 20J<br/>
-</td>
+• Transform 13K from plate 3
-<td width="156">•Restriction digest of the parts(12I,10I,22M,13K) with EcoRI and PstI</td>
-<td width="95">•Gel electrophoresis to analyse restriction fragments</td>
+</td>
-<td width="157">•Test the Tm of Primers CP1&amp;CS,NP&amp;NS with 13K. The result of Gel electrophoresis shows that 60.2℃ is the Tm of NS and NP, and 57.4℃ is the Tm of CS and CP1.</td>
+    <td width="184">• Miniprep: 20H-1, 20J-1
-   </tr>
+</td>
-</table>
+<td>• Cut: the 20H-1, 20J-1, 22B-1, 22B-3 with E+P</td>
-</td>
+   </tr>
-   </tr>
+</table>
-   <tr>
+</td>
-     <td id="sheetleft">Jul.14th
+   </tr>
+   <tr>
+     <td id="sheetleft">Aug.11th
 Thursday
-</td>
-     <td><table width="618" border="0" cellspacing="0" cellpadding="1">
-   <tr>
+</td>
-     <td >• Test the Tm of the YFP,RFP,tetR,Vgb and nirB primers.
+     <td><table width="100%" border="0" cellspacing="0" cellpadding="1">
-The result of Gel electrophoresis shows that the Tm for the primers of Vgb is 54℃ and the Tm for the primers of nirB is 55℃.The RCR of YFP,RFP and tetR failed.
+   <tr>
-</td>
+     <td >• Run the digestion results. Bands are confirmed right.
+</td>
-   </tr>
+<td>• Colony PCR vgb+22M+10I
-</table>
+</td>
-</td>
+<td>• Cut the plasmid of vgb+22M+10I
-   </tr>
-   <tr>
+</td>
-     <td id="sheetleft">Jul.15th
+   </tr>
+</table>
+</td>
+   </tr>
+   <tr>
+     <td id="sheetleft">Aug.12th
 Friday
-</td>
-     <td><table width="600" border="0" cellspacing="0" cellpadding="1">
-       <tr>
+</td>
-        <td width="155"> • PCR(Phusion)<br/>
+     <td><table width="100%" border="0" cellspacing="0" cellpadding="1">
-• Digest 10I, 22M, 13K
+       <tr>
-• Used wrong cutter, digestion again.
+       <td >• Make new stock of competent cells</td>
-</td>
+       <td>• Ligation: 13K+10I<br/>
-<td>• Run the results of PCR and the first digestion. The annealing temperature of YFP needed change. The digestion results confirmed</td>
+• Cut the PCR results and 22M with E+P
-<td>• Run the digestion results of second time. The bands are confirmed.</td>
+</td>
-       </tr>
+       <td>• Sequence: nirB, vgbL, 12I, 20H, 20J, 22B</td>
-     </table></td>
+       <td>• Transform 13K+10I+pSB1K3<br/>
-   </tr>
+• Cut 13K to validate. Results are right.
-   <tr>
+</td>
-     <td id="sheetleft">Jul.16th
+       </tr>
+     </table></td>
+   </tr>
+   <tr>
+     <td id="sheetleft">Aug.13th
 Saturday
-</td>
-     <td><table width="620" border="0" cellspacing="0" cellpadding="1">
-   <tr>
+</td>
-     <td width="127">• Cut the linearized pSB1k3 with E+P</td>
+     <td><table width="620" border="0" cellspacing="0" cellpadding="1">
-     <td width="123">• Purify the digestion results of 22M, 13K, 10I</td>
+   <tr>
-    <td width="133">• Confirm digestion of pSB1k3 by electrophoresis, then purification</td>
+     <td>• Colony PCR: 13K+10I+pSB1K3</td>
-     <td width="113">• Test Tm of YFP<br/>
+     <td>• Culture: vgb+22M+10I in 5ml(shaking), 5ml(water bath), 10ml(water bath), 15(water bath).</td>
-• ligation: 22M+10I, 13K+10I
+     <td>• Check the YFP expression of 5ml(shaking) and 15ml(water bath). No yellow fluorescent cells,</td>
-</td>
-<td width="114">• Tm of YFP is 54 degree
+   </tr>
-• transform the ligation results.
+</table>
 </td>
    </tr>
-</table>
+   <tr>
-</td>
+     <td id="sheetleft">Aug.14th
-   </tr>
-   <tr>
-     <td id="sheetleft">Jul.17th
 Sunday
-</td>
-     <td><table width="620" border="0" cellspacing="0" cellpadding="1">
+</td>
-       <tr>
+     <td><table width="620" border="0" cellspacing="0" cellpadding="1">
-         <td>• PCR 22M<br/>
+       <tr>
-• purify Vgb, RFP, RFP-tetR, YFP-tetR. Gibson PCR.
+         <td width="244">• Transform: the  Gibson assembly results.
-</td>
-<td>• ligation the purified the fragments in yesterday.</td>
+</td>
-<td>• 22M PCR<br/>
+<td width="164">• Miniprep: 13K+10I<br/>
-• Transform the ligation results.
+• Cut: 13K+10I
 </td>
-      </tr>
+<td>• Purification: the digestion results.<br/>
-     </table></td>
+• Ligation: nirB+13K+10I
-   </tr>
+</td>
+      </tr>
+    </table></td>
+  </tr>
+</table>
+<p>&nbsp;</p>
+</div>
+<div class="block" id="nsheet">
+<h3>Week7</h3><hr/>
+<table id="notesheet" width="650" border="1" cellspacing="1" cellpadding="1">
+  <tr><td width="76">Day</td><td width="349">Note</td></tr>
+  <tr>
+    <td id="sheetleft">Aug.15th
+Monday
+</td>
+    <td><table id="intable" width="603" border="0" cellspacing="1" cellpadding="1">
+    <td width="191">• Plate: nirB+13K+10I
+</td>
+    <td width="249" >• Colony PCR: vgb+YFP+tetR +terminater</td><br />
+<td width="157">• Gibson PCR
+</td>
+</table></td>
+  </tr>
+  <tr>
+     <td id="sheetleft">Aug.16th
+Tuesday
+</td>
+    <td><table id="intable" width="615" border="0" cellspacing="1" cellpadding="1">
+      <td width="140"> • Colony PCR: vgb+22M+10I, nirB+13K+10I
+</td>
+    <td width="181" > • No bands of 13K; 22M confirmed
+</td>
+</table></td>
+  </tr>
+  <tr>
+    <td id="sheetleft">Aut.17th
+Wednesday
+</td>
+    <td><table width="640" border="0" cellspacing="1" cellpadding="1">
+  <tr>
+    <td width="170">• Miniprep: 22M<br/>
+• Cut: 22M
+</td>
+    <td width="184">• Check CFP expression. No fluorescence.
+</td>
+  </tr>
+</table>
+</td>
+  </tr>
+  <tr>
+    <td id="sheetleft">Aug.18th
+Thursday
+</td>
+    <td><table width="618" border="0" cellspacing="1" cellpadding="1">
+  <tr>
+    <td >• Transform: 13K, 10I, 22M, 12I, 18P
+</td>
+  </tr>
+</table>
+</td>
+  </tr>
+  <tr>
+    <td id="sheetleft">Aug.19th
+Friday
+</td>
+    <td><table width="627" border="0" cellspacing="1" cellpadding="1">
+      <tr>
+       <td >• Miniprep: 13K, 10I, 22M, 12I, 18P </td>
+       <td>• Cut: 13K, 10I, 22M, 12I, 18P
+</td>
+       <td>• Run the gel</td>
+      </tr>
+    </table></td>
+  </tr>
+  <tr>
+    <td id="sheetleft">Aug.20th
+Saturday
+</td>
+    <td><table width="620" border="0" cellspacing="1" cellpadding="1">
+  <tr>
+    <td>• Ligate 13K+10I, 22M+10I</td>
+  </tr>
+</table>
+</td>
+  </tr>
+  <tr>
+    <td id="sheetleft">Aug.21st
+Sunday
+</td>
+    <td><table width="620" border="0" cellspacing="1" cellpadding="1">
+      <tr>
+        <td width="244">• Transform: the  Gibson assembly results.
+</td>
+<td width="164">• Miniprep: 13K+10I<br/>
+• Cut: 13K+10I
+</td>
+<td>• Purification: the digestion results.<br/>
+• Ligation: nirB+13K+10I
+</td>
+      </tr>
+    </table></td>
+  </tr>
+</table>
+<p>&nbsp;</p>
+</div>
+<div class="block" id="nsheet">
+<h3>Week8</h3><hr/>
+<table id="notesheet" width="650" border="1" cellspacing="1" cellpadding="1">
+  <tr><td width="76">Day</td><td width="349">Note</td></tr>
+  <tr>
+    <td id="sheetleft">Aug. 22nd
+Monday
+</td>
+    <td><table id="intable" width="603" border="0" cellspacing="1" cellpadding="1">
+    <td width="191">• Transform 13K+10I, 22M+10I
+</td>
+    <td width="249" >• Test new primers.<br />
+• PCR: 22M+10I, 13K+10I
+</td>
+<td width="157">• Run the PCR products.<br />
+• Cut the PCR products.
+</td>
+</table></td>
+  </tr>
+  <tr>
+    <td id="sheetleft">Aug. 23rd
+Tuesday
+</td>
+    <td><table id="intable" width="615" border="0" cellspacing="1" cellpadding="1">
+      <td width="140">• Test primers: CS/CP, VF/VR, pSB1_f/r
+</td>
+    <td width="181" > • Cut: 11P, 1F, 22M<br/>
+• Run the cut results.1F-1/2/3 are right.
+</td>
+<td>• Mix the 1F-1/2 purification products</td>
+<td>• Cut: 1F-1+1F-2(E+S), 22M-3(X+P), pSB1C3(E+P)</td>
+</table></td>
+  </tr>
+  <tr>
+    <td id="sheetleft">Aug. 24th
+Wednesday
+</td>
+    <td><table width="640" border="0" cellspacing="1" cellpadding="1">
+  <tr>
+  </tr>
+</table>
+</td>
+  </tr>
+  <tr>
+    <td id="sheetleft">Aug. 25th
+Thursday
+</td>
+    <td><table width="618" border="0" cellspacing="1" cellpadding="1">
+  <tr>
+  </tr>
+</table>
+</td>
+  </tr>
+  <tr>
+    <td id="sheetleft">Aug. 26th
+Friday
+</td>
+    <td><table width="627" border="0" cellspacing="1" cellpadding="1">
+      <tr>
+       <td >• Amplify: vgb, 1C3</td>
+      </tr>
+    </table></td>
+  </tr>
+  <tr>
+    <td id="sheetleft">Aug.27th
+Saturday
+</td>
+    <td><table width="620" border="0" cellspacing="1" cellpadding="1">
+  <tr>
+    <td>• Digest: Vgb, 1C3, fdfhF, 22M+10I, 13K+10I</td>
+  </tr>
+</table>
+</td>
+  </tr>
+  <tr>
+    <td id="sheetleft">Aug.28th
+Sunday
+</td>
+    <td><table width="620" border="0" cellspacing="1" cellpadding="1">
+      <tr>
+        <td width="244">• Ligate: vgb+22M+10I, fdfhF+13K+10I
+</td>
+<td width="164">• Transform the ligation results.
+</td>
+      </tr>
+    </table></td>
+  </tr>
 </table>
 <p>&nbsp;</p>
+</div>
+</div>
 <script type="text/javascript">
 </script>
+<div class="inner" id="biofilm_jul">
+<div class="block" id="nsheet">
+<h3>1st August</h3><hr/>
+<p>Freeze slicing of about 50μm. Observe under natural light microscope and can see red
+florescence. The thickness is about 130μm</p>
+</div>
+<div class="block" id="nsheet">
+<h3>4th August</h3><hr/>
+<p>Repeat the last experiment with silicone tube. 6rpm/s results in a flowing speed of 68ml/day</p>
+</div>
+<div class="block" id="nsheet">
+<h3>6th August</h3><hr/>
+<p>Similar to the last time. Did not use freeze slicing.</p>
+</div>
+<div class="block" id="nsheet">
+<h3>15th August</h3><hr/>
+<p>Cultured E.coli in 5ml LB for 12h.</p>
+</div>
+<div class="block" id="nsheet">
+<h3>16th August</h3><hr/>
+<p>Substituting a part of silicone tube with glass tube in silicone tube biofilm formation sets. Culture in
+℃</p>
+</div>
+<div class="block" id="nsheet">
+<h3>17th August</h3><hr/>
+<p>Add 50ml LB and culture with circular culture.</p>
+</div>
+<div class="block" id="nsheet">
+<h3>18th August</h3><hr>
+<p>12.00 found one free-flow pump stopped. Cooled for 15 minutes and turned on again. Could be
+over heated. Can see some bacteria on the bottom of the vessel and tube. When the pump started
+again, the bacteria was washed away.</p>
+</div>
+<div class="block" id="nsheet">
+<h3>19th August</h3><hr/>
+<p>Can observe obvious white biofilm where the silicone tube joins the tube but cannot see red
+florescence, suspect contamination. No biofilm is observed on the glass tube under microscope.</p>
+</div>
+<div class="block" id="nsheet">
+<h3>21st, August</h3><hr/>
+<p>Biofilm formation with large test tubes. Inoculate with 1% e.coli. Rubber tubes are attached to air
+pump with filter between air pump and the tube to prevent entrance of germs. Two sets use MSM
++glucose medium and two sets use LB.<br/>
+Retry with glass tube biofilm formation set.</p>
+</div>
+<div class="block" id="nsheet">
+<h3>24th, August</h3><hr/>
+<p>Terminate biofilm formation, the glass slide left in the drawer to dry. Can see obvious rod like
+structure under 400 magnification. (spheres in MSM+glucose culture) No red florescence is seen.
+Most of the surface is covered by single layer cells but some part of it has thick bump like
+structure.<br/>
+No biofilm observed on the glass tube.</p>
+</div>
+</div>
+ <script type="text/javascript">
+document.getElementById('p_intro').onclick= function(){
+document.getElementById('biofilm_jul').style.display='none'
+ document.getElementById('n_biobrick').style.display='block'}
+document.getElementById('p_model').onclick= function(){
+document.getElementById('n_biobrick').style.display='none'
+ document.getElementById('biofilm_jul').style.display='block'}
+</script>
 </div>

Team:ZJU-China/Notebook/August

From 2011.igem.org

Latest revision as of 14:51, 3 October 2011

Labnote

May&June

July

August

September

Protocol

Week5

Week6

Week7

Week8

1st August

4th August

6th August

15th August

16th August

17th August

18th August

19th August

21st, August

24th, August