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href="https://2011.igem.org/Team:ZJU-China/August.html">August<br />
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</a> <a href="https://2011.igem.org/Team:ZJU-China/September.html">September<br />
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<p></p>
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<h1>Lab Notes - July</h1>
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<!--importantcontainer-->
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<div id="page1">
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<h1>Week1</h1>
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<table id="notesheet" width="650" border="1" cellspacing="0"
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cellpadding="1" style="vertical-align: middle">
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<tr>
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<td width="76"><strong>Day</strong></td>
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-
<td width="349"><strong>Note</strong></td>
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-
</tr>
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-
 
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<tr>
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<td id="sheetleft">Jul.4th Monday</td>
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-
<td>
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-
<table id="intable" width="328" border="0" cellspacing="0"
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cellpadding="1">
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<td width="128">鈥?Aerobic cultivation of DH5伪</td>
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-
 
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<td width="196">鈥?Preparation of apparatus for the formation of
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biofilm</td>
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-
 
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</table>
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</td>
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-
</tr>
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<tr>
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<td id="sheetleft">Jul 5th Tuesday</td>
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<td>&nbsp;</td>
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</tr>
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<tr>
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<td id="sheetleft">Jul.6th Wednesday</td>
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<td>
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-
<table width="217" border="0" cellspacing="0" cellpadding="1">
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<tr>
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<td width="215">鈥eceiving primers ordered previously</td>
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+
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</tr>
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-
</table>
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-
</td>
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-
</tr>
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<tr>
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<td id="sheetleft">Jul.7th Thursday</td>
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-
<td>
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-
<table width="238" border="0" cellspacing="0" cellpadding="1">
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-
<tr>
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-
<td width="200">鈥?Preparation of the aliquot of the primers</td>
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<td width="200">鈥?Something wrong with a shaking incubator</td>
+
-
</tr>
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-
</table>
+
-
</td>
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-
</tr>
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-
<tr>
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<td id="sheetleft">Jul.8th Friday</td>
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<td>
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-
<table width="222" border="0" cellspacing="0" cellpadding="1">
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<tr>
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<td width="155">鈥?Preparation of culture plates for the
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transformations</td>
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-
</tr>
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-
</table>
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</td>
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</tr>
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<tr>
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<td id="sheetleft">Jul.9th Saturday</td>
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-
<td>
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-
<table width="313" border="0" cellspacing="0" cellpadding="1">
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-
<tr>
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<td width="127">鈥?Preparation of culture plates for the
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transformations</td>
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<td width="182">鈥?protocols of transformation</td>
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-
</tr>
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-
</table>
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-
</td>
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-
</tr>
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-
<tr>
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-
<td id="sheetleft">Jul.10th Sunday</td>
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-
<td>
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-
<table width="246" border="0" cellspacing="0" cellpadding="1">
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<tr>
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-
<td>鈥?Several colonies were picked up and cultivated in 5mL LB
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medium. 鈥ryosectioning of biofilm</td>
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
 
+
-
</table>
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-
</p>
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-
<h1>Week2</h1>
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-
<table id="notesheet" width="650" border="1" cellspacing="0"
+
-
cellpadding="1">
+
-
<tr>
+
-
<td width="76"><strong>Day</strong></td>
+
-
<td width="349"><strong>Note</strong></td>
+
-
</tr>
+
-
 
+
-
<tr>
+
-
<td id="sheetleft">Jul.11th Monday</td>
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-
<td>
+
-
<table id="intable" width="541" border="0" cellspacing="0"
+
-
cellpadding="1">
+
-
 
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-
<td width="128">鈥?Set up new LB culture plates with ampicillin
+
-
and kanamycin
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-
</p>
+
-
</td>
+
-
 
+
-
 
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-
<td width="196">鈥?路Sterilization of Glycerol and <br />
+
-
路Preparation of 25mg/mL kanamycin</td>
+
-
<td>鈥ransformation of the parts mentioned on Jul.9th for the
+
-
second time</td>
+
-
<td>鈥bservation 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">鈥?Pick two colonies of each parts and cultivate
+
-
them in LB medium</td>
+
-
 
+
-
 
+
-
<td width="203">鈥ransformation of three parts(20J,20H.22B from
+
-
Kit plates of 2011 Distribution ) which are related to the
+
-
degradation of Cellulose</td>
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-
<td width="91">鈥⒙稭ini prep to isolate 10I,12I and 22M</td>
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-
<td width="130">鈥onservation of 10I,12I,22M and 11P</td>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.13th Wednesday</td>
+
-
<td>
+
-
<table width="618" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td width="104">鈥?Place the culture plate of 20J,20H and 22B in
+
-
the fridge.</td>
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-
<td width="102">鈥in prep to isolate 13K 鈥onservation of 13K</td>
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-
<td width="163">鈥estriction digest of the
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-
parts(12I,10I,22M,13K) with EcoRI and PstI</td>
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-
<td width="111">鈥el electrophoresis to analyse restriction
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-
fragments</td>
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-
<td width="128">鈥est the Tm of Primers CP1&amp;CS,NP&amp;NS
+
-
with 13K. The result of Gel electrophoresis shows that 60.2鈩?is the
+
-
Tm of NS and NP, and 57.4鈩?is the Tm of CS and CP1.</td>
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.14th Thursday</td>
+
-
<td>
+
-
<table width="618" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td>鈥?Test the Tm of the YFP,RFP,tetR,Vgb and nirB primers.
+
-
The result of Gel electrophoresis shows that the Tm for the primers
+
-
of Vgb is 54鈩?and the Tm for the primers of nirB is 55鈩?The RCR of
+
-
YFP,RFP and tetR failed.</td>
+
-
 
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.15th Friday</td>
+
-
<td>
+
-
<table width="600" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td width="155">鈥?PCR(Phusion)<br />
+
-
鈥?Digest 10I, 22M, 13K 鈥?Used wrong cutter, digestion again.</td>
+
-
<td>鈥?Run the results of PCR and the first digestion. The
+
-
annealing temperature of YFP needed change. The digestion results
+
-
confirmed</td>
+
-
<td>鈥?Run the digestion results of second time. The bands are
+
-
confirmed.</td>
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.16th Saturday</td>
+
-
<td>
+
-
<table width="620" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td width="127">鈥?Cut the linearized pSB1k3 with E+P</td>
+
-
<td width="123">鈥?Purify the digestion results of 22M, 13K, 10I</td>
+
-
<td width="133">鈥?Confirm digestion of pSB1k3 by
+
-
electrophoresis, then purification</td>
+
-
<td width="113">鈥?Test Tm of YFP<br />
+
-
鈥?ligation: 22M+10I, 13K+10I</td>
+
-
<td width="114">鈥?Tm of YFP is 54 degree 鈥?transform the
+
-
ligation results.</td>
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.17th Sunday</td>
+
-
<td>
+
-
<table width="620" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td>鈥?PCR 22M<br />
+
-
鈥?purify Vgb, RFP, RFP-tetR, YFP-tetR. Gibson PCR.</td>
+
-
<td>鈥?ligation the purified the fragments in yesterday.</td>
+
-
<td>鈥?22M PCR<br />
+
-
鈥?Transform the ligation results.</td>
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
 
+
-
</table>
+
-
 
+
-
<p>&nbsp;</p>
+
-
<h1>Week3</h1>
+
-
<table id="notesheet" width="713" border="1" cellspacing="0"
+
-
cellpadding="1">
+
-
<tr>
+
-
<td width="87"><strong>Day</strong></td>
+
-
<td width="616"><strong>Note</strong></td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.18th Monday</td>
+
-
<td>
+
-
<table id="intable" width="541" border="0" cellspacing="0"
+
-
cellpadding="1">
+
-
 
+
-
<td width="128">鈥?Genome extraction of E.coli</td>
+
-
 
+
-
 
+
-
<td width="196">鈥?PCR of NirB<br />
+
-
鈥?cut 10I with X+P, cut 22M, 13K with E+S, cut pSB1k3 with E+P</td>
+
-
<td>鈥?Ligate: 10I+13K, 10I+22M <br />
+
-
鈥?Repeat NirB PCR</td>
+
-
<td>
+
-
<p align="left">鈥?Culture 11P<br />
+
-
鈥?Miniprep 10I, 22M, 13K</p>
+
-
</td>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul 19th Tuesday</td>
+
-
<td>
+
-
<table id="intable" width="615" border="0" cellspacing="0"
+
-
cellpadding="1">
+
-
 
+
-
<td width="140">鈥?mini-prep: 10I+13K, 10I+22M</td>
+
-
 
+
-
 
+
-
<td width="213">鈥nsert 10I+13K, 10I+22M into pSB1k3</td>
+
-
<td width="110">鈥ransform: 5E, 3C, 7C, 1K, 1I from the
+
-
distribution plate</td>
+
-
<td width="144">鈥ransform 10I+22M, 10I+13K</td>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.20th Wednesday</td>
+
-
<td>
+
-
<table width="610" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td width="170">鈥olonies of 22M+10I, 13K+10I, 5E, 3C, 7C, 1K,
+
-
1I confirmed</td>
+
-
<td width="102">鈥?Gibson PCR</td>
+
-
<td width="250">鈥olony PCR 22M+10I, 13K+10I, 5E, 3C, 7C, 1K,
+
-
1I</td>
+
-
<td width="80">鈥CR NirB</td>
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.21th Thursday</td>
+
-
<td>
+
-
<table width="618" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td>鈥CR verification of 22M+10I, 13K+10I, 5E, 3C, 7C, 1K, 1I
+
-
</td>
+
-
<td>鈥?Gibson PCR 鈥?Run the results of PCR verification. Bands
+
-
confirmed.</td>
+
-
<td>鈥?Culture the 22M+10I, 13K+10I, 5E, 3C, 7C, 1K, 1I 鈥?
+
-
Purification of Gibson PCR results</td>
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.22th Friday</td>
+
-
<td>
+
-
<table width="618" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td width="117">鈥?PCR amplification of Gibson assembly results
+
-
</td>
+
-
<td width="144">鈥?Mini prep: 22M+10I, 22.Presever in -20<br />
+
-
鈥?Medi prep: 1K,1I,3C,5E,7C<br />
+
-
鈥?Gibson Assembly fail.</td>
+
-
<td width="164">鈥?PCR NirB by Phusion<br />
+
-
鈥epeat PCR by changing Pnibr to Gnirbr<br />
+
-
鈥ut the mini and medi prep results with E</td>
+
-
<td width="185">鈥un the results of PCR and digestion. Fail in
+
-
PCR of NirB, succeed in 10I+3K and 10I+22M ligation.</td>
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.23th Saturday</td>
+
-
<td>
+
-
<table width="613" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td width="237">鈥ouble digestion of 13K+10I, 22M+10I, pSB1c3
+
-
 
+
-
</td>
+
-
<td width="169">鈥?Fail in purification of Medi prep</td>
+
-
<td width="201">鈥?PCR NirB<br />
+
-
鈥?Ligate NirB+13K+10I, Vgb+22M+10I</td>
+
-
 
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.24th Sunday</td>
+
-
<td>
+
-
<table width="608" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td width="244">鈥?Gibson assembly: NirB+RFP+tetR<br />
+
-
鈥?Cut results of Gibson assembly and pSB1c3.</td>
+
-
<td width="164">鈥?Purify the ligation results in yesterday</td>
+
-
<td width="194">鈥?ligate with backbone 鈥?Culture 1I, 1K, 3C,
+
-
5E, 7C, 11P</td>
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
 
+
-
</table>
+
-
<p>&nbsp;</p>
+
-
<h1>Week4</h1>
+
-
<table id="notesheet" width="691" border="1" cellspacing="0"
+
-
cellpadding="1">
+
-
<tr>
+
-
<td width="63"><strong>Day</strong></td>
+
-
<td width="630"><strong>Note</strong></td>
+
-
</tr>
+
-
 
+
-
<tr>
+
-
<td id="sheetleft">Jul.25th Monday</td>
+
-
<td>
+
-
<table id="intable" width="541" border="0" cellspacing="0"
+
-
cellpadding="1">
+
-
 
+
-
<td width="128">鈥?Transform Pnirb+13k+10I+pSBK3-2</td>
+
-
 
+
-
 
+
-
<td>鈥?Place the culture in 4 degree</td>
+
-
<td>鈥?Medi-and mini-prep of five cultre</td>
+
-
<td>鈥ibson Assembly confirmation by gel</td>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul. 26th Tuesday</td>
+
-
<td>
+
-
<table id="intable" width="610" border="0" cellspacing="0"
+
-
cellpadding="1">
+
-
 
+
-
<td width="134">鈥?Cut Pnirb, Pvgb,(E+S)<br />
+
-
鈥?Cut 10I+13K, 10I+22M.(X+P)</td>
+
-
 
+
-
 
+
-
<td width="167">鈥?Ligation: vgb+10I+22M, nirB+10I+13K,</td>
+
-
<td width="172">鈥?Ligation: pSBK13+vgb+10I+22M,
+
-
pSBK13+nirB+10I+13K</td>
+
-
<td width="129">鈥?Transform the ligation results.</td>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.27th Wednesday</td>
+
-
<td>
+
-
<table width="608" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td width="170">鈥?No colony on the plate<br />
+
-
鈥?Gibson assembly</td>
+
-
<td width="184">鈥?Run the results of Gibson assembly</td>
+
-
<td width="248">鈥?Excise the bands, the purify the DNA<br />
+
-
鈥?Gibson Assenmly</td>
+
-
 
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.28th Thursday</td>
+
-
<td>
+
-
<table width="609" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td width="607">鈥?011 China Meet-up @ Hefei</td>
+
-
 
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.29th Friday</td>
+
-
<td>
+
-
<table width="607" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td>鈥?011 China Meet-up @ Hefei</td>
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.30th Saturday</td>
+
-
<td>
+
-
<table width="620" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
 
+
-
 
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
<tr>
+
-
<td id="sheetleft">Jul.31th Sunday</td>
+
-
<td>
+
-
<table width="600" border="0" cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td width="368">鈥?Culture 22M+10I, 13K+10I</td>
+
-
<td width="228">鈥?Cut a0H, 20J, 22B</td>
+
-
 
+
-
</tr>
+
-
</table>
+
-
</td>
+
-
</tr>
+
-
 
+
-
</table>
+
-
<br />
+
-
<br />
+
-
</div>
+
-
<!--page1-->
+
-
<div id="importantcontainer">
+
-
<div class="frame" id="important">
+
-
<div class="bgcolors" id="round">
+
-
<h1>Data/Protocol</h1>
+
-
</div>
+
-
</div>
+
-
</div>
+
-
<div id="framecontent">
+
-
<h1>Jul.13th Wednesday</h1>
+
-
 
+
-
<p><strong>Systems of restriction digestion with EcoRI and
+
-
PstI</strong></p>
+
-
<p>
+
-
<table style="margin: 15px;" width="110" height="200" border="1"
+
-
cellspacing="0" cellpadding="1">
+
-
<tr>
+
-
<td>Plasmid</td>
+
-
<td>1渭L (>100ng)</td>
+
-
</tr>
+
-
<tr>
+
-
<td>EcoRI</td>
+
-
<td>1渭L</td>
+
-
</tr>
+
-
<tr>
+
-
<td>PstI</td>
+
-
<td>1渭L</td>
+
-
</tr>
+
-
<tr>
+
-
<td>10脳Buffer Tango</td>
+
-
<td>2渭L</td>
+
-
</tr>
+
-
<tr>
+
-
<td>ddH2O</td>
+
-
<td>15渭L</td>
+
-
</tr>
+
-
</table>
+
-
<img src="https://static.igem.org/mediawiki/2011/c/c3/0713program.png"
+
-
width="200" height="200" /></p>
+
-
<p><strong>Temperature grad</strong><br />
+
-
56鈩?57.4鈩?60.2鈩?62.9鈩?64.3鈩?65.8鈩?/p>
+
-
<div id="framecontent">
+
-
<p>&nbsp;</p>
+
-
 
+
-
<p><strong>PCR system (test the Tm of the primers
+
-
CP1&amp;CS, NP&amp;NS)</strong></p>
+
-
 
+
-
<table style="margin: 15px;" width="110" border="1" cellspacing="0"
+
-
cellpadding="1">
+
-
<tr>
+
-
<td>10脳Buffer</td>
+
-
<td>2渭L</td>
+
-
</tr>
+
-
<tr>
+
-
<td>dNTPs</td>
+
-
<td>0.5渭L</td>
+
-
</tr>
+
-
<tr>
+
-
<td>primers CP1 (NP)</td>
+
-
<td>1渭L</td>
+
-
</tr>
+
-
<tr>
+
-
<td>primers CS (NS)</td>
+
-
<td>1渭L</td>
+
-
</tr>
+
-
<tr>
+
-
<td>Template</td>
+
-
<td>1渭L</td>
+
-
</tr>
+
-
<tr>
+
-
<td>rTaq</td>
+
-
<td>0.2渭L</td>
+
-
</tr>
+
-
<tr>
+
-
<td>H2O</td>
+
-
<td>14.5渭L</td>
+
-
</tr>
+
-
<tr>
+
-
<td>Total</td>
+
-
<td>20渭L</td>
+
-
</tr>
+
-
</table>
+
-
</p>
+
-
<p>Within each compartment are<strong> components</strong>: include
+
-
different types of biomass ,substrates , products. biomass is often
+
-
divided into active microbial species, inert cells, and extracellular
+
-
polymeric substances(EPS).</p>
+
-
<p>The components can undergo transformation, transport, and
+
-
transfer <strong>processes</strong>. For example, substrate is consumed,
+
-
and this leads to the synthesis of new active biomass.</p>
+
-
<p>All process affecting each component in each compartment are
+
-
mathematically linked together into a<strong> mass balance
+
-
equation</strong> that contains rate terms and parameters for each process.</p>
+
-
<p><strong>Model Selection:</strong>Many kinds of Mathematics models
+
-
have been founded to describe a system of biofilm. Models of different
+
-
dimensions (1d, 2d, 3d) focus on different properties of a biofilm.
+
-
Since we care most about the oxygen concentration gradients
+
-
perpendicular to the substratum, <strong>numerical
+
-
1-dimensional dynamic model(N1)</strong> would be a proper choice for us.</p>
+
-
</div>
+
-
<!--bgcolors--></div>
+
-
<!--important--></div>
+
-
<!--importantcontainer-->
+
-
<p style="clear: both;"></p>
+
-
<div id="page2">
+
-
<div class="block" id="nsheet"><img
+
-
src="http://ung.igem.org/wiki/images/4/42/Biofilmcomp.png" width="640"
+
-
height="464" style="margin: 5px;" />
+
-
<p>&nbsp;</p>
+
-
</div>
+
-
<div class="block" id="nsheet">
+
-
<h1>Early July</h1>
+
-
<p>Pre-experiments with biofilm formation with circular and non
+
-
circular silicone tube, 24 well plate on different support including
+
-
glass, paper, plastic film, rubber. The final material are used based on
+
-
the easiness biofilm form on them and on the easiness to observe under
+
-
microscope.</p>
+
-
<img
+
-
src="https://static.igem.org/mediawiki/2011/b/be/20110711-3nP4100X0877.jpg"
+
-
width="400" style="margin-left: 20px;">
+
-
<p>&nbsp;</p></div>
+
-
<div class="block" id="nsheet">
+
-
<h1>28th July</h1>
+
-
<p>13.30: DH5蓱 11p 5mlX4<br />
+
-
23.00: silicone tube set at 37鈩?/p>
+
-
</div>
+
-
<div class="block" id="nsheet">
+
-
<h1>29th July</h1>
+
-
<p>13.00: LB culture 50ml with circular culture medium. LB culture
+
-
50ml with noncircular culture medium.</p>
+
-
 
+
-
</div>
+
-
<div class="block" id="nsheet">
+
-
<h1>31st July</h1>
+
-
<p>13.00: -80鈩?storing silicone tube. A thick white and loosely bond
+
-
substance is seen on the inner wall of the 5mm silicone tube, and on the
+
-
inner wall of the 1mm silicone tube a flatter and smoother white
+
-
substance. Especially obvious where the tube turns. Possibly because the
+
-
speed of culture flow is slower.</p>
+
-
 
+
-
</div>
+
-
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+
-
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Latest revision as of 17:37, 19 October 2011

  1. REDIRECT Team:ZJU-China/Notebook
Retrieved from "http://2011.igem.org/Team:ZJU-China/Notebook.html"