Team:ZJU-China/August.html

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<title>Notebook - August</title>
<title>Notebook - August</title>
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<tr>
<tr>
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<td width="286">鈥usion PCR Vgb+YFP+tetR, NirB+RFP+tetR,</td>
+
<td width="286">▪Fusion PCR Vgb+YFP+tetR, NirB+RFP+tetR,</td>
-
<td width="251">鈥CR: NirB, Vgb</td>
+
<td width="251">▪PCR: NirB, Vgb</td>
</tr>
</tr>
</table>
</table>
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<tr>
<tr>
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<td width="124">鈥ut: 13K+10I, 22M+10I</td>
+
<td width="124">▪Cut: 13K+10I, 22M+10I</td>
-
<td width="180">鈥?Purify: 13K+10I, 22M+10I<br />
+
<td width="180">▪Purify: 13K+10I, 22M+10I<br />
-
鈥?Ligation: Pvgb+22M+10I, Pnirb+13K+10I</td>
+
▪Ligation: Pvgb+22M+10I, Pnirb+13K+10I</td>
-
<td width="154">鈥?PCR backbones<br />
+
<td width="154">▪PCR backbones<br />
-
鈥?Electrophresis</td>
+
▪Electrophresis</td>
-
<td width="136">鈥?Gel excision and purification</td>
+
<td width="136">▪Gel excision and purification</td>
</tr>
</tr>
</table>
</table>
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<table width="611" border="0" cellspacing="1" cellpadding="1">
<table width="611" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
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<td width="304">鈥?Make Phusion Buffer, 5脳isothermel buffer</td>
+
<td width="304">▪Make Phusion Buffer, isothermel buffer</td>
-
<td width="300">鈥?colony PCR: 20H, 20J, 22B</td>
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<td width="300">▪colony PCR: 20H, 20J, 22B</td>
</tr>
</tr>
</table>
</table>
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<table width="618" border="0" cellspacing="1" cellpadding="1">
<table width="618" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
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<td>鈥?Cut: 10I+22M, 10I+13; and purification</td>
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<td>▪Cut: 10I+22M, 10I+13; and purification</td>
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<td>鈥?Ligation: Pvgb+22M+10I, Pnirb+13K+10I,<br />
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<td>▪Ligation: Pvgb+22M+10I, Pnirb+13K+10I,<br />
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鈥?colony PCR: 13K+10I</td>
+
▪colony PCR: 13K+10I</td>
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<td>鈥?Culture: 20H, 20J, 22B, 1K, 1I,3C, 5E, 7C</td>
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<td>▪Culture: 20H, 20J, 22B, 1K, 1I,3C, 5E, 7C</td>
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<td>鈥?Transform: 1G, 3A, 5A, 7A from the distribution plate</td>
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<td>▪Transform: 1G, 3A, 5A, 7A from the distribution plate</td>
</tr>
</tr>
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<table width="612" border="0" cellspacing="1" cellpadding="1">
<table width="612" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
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<td width="188">鈥?Check the plates. Contamination, or no
+
<td width="188">▪Check the plates. Contamination, or no
positive colonies</td>
positive colonies</td>
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<td width="121">鈥?Miniprep: 5 backbones, 22B-1, 22B-3</td>
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<td width="121">▪Miniprep: 5 backbones, 22B-1, 22B-3</td>
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<td width="197">鈥?PCR: nirB from 13K+10I+nirB to firm the
+
<td width="197">▪PCR: nirB from 13K+10I+nirB to firm the
ligation. One positive result.</td>
ligation. One positive result.</td>
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<td width="93">鈥?Culture the positive colony.</td>
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<td width="93">▪Culture the positive colony.</td>
</tr>
</tr>
</table>
</table>
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<table width="610" border="0" cellspacing="1" cellpadding="1">
<table width="610" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
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<td width="244">鈥?Cut: 22M,13K with E &amp; S</td>
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<td width="244">▪Cut: 22M,13K with E &amp; S</td>
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<td width="164">鈥?Culture the red colonies from plate of pSB1C3</td>
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<td width="164">▪Culture the red colonies from plate of pSB1C3</td>
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<td width="192">鈥?PCR: 5 backbones<br />
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<td width="192">▪PCR: 5 backbones<br />
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鈥?Cut the PCR products with P+E and run the gel to confirm.</td>
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▪Cut the PCR products with P+E and run the gel to confirm.</td>
</tr>
</tr>
</table>
</table>
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<tr>
<tr>
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<td width="191">鈥?The gel results of 5 backbones are right.</td>
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<td width="191">▪The gel results of 5 backbones are right.</td>
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<td width="249">鈥?Miniprep: pSB1C3, vgb+22M+10I</td>
+
<td width="249">▪Miniprep: pSB1C3, vgb+22M+10I</td>
-
<td width="157">鈥?Culture vgb+22M+1oI in hypoxia<br />
+
<td width="157">▪Culture vgb+22M+1oI in hypoxia<br />
-
鈥CR pSB1C3</td>
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▪CR pSB1C3</td>
</tr>
</tr>
</table>
</table>
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<tr>
<tr>
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<td width="33%">鈥?Run the PCR product</td>
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<td width="33%">▪Run the PCR product</td>
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<td width="33%">鈥?PCR pSB1C3 again</td>
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<td width="33%">▪PCR pSB1C3 again</td>
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<td width="33%">鈥?Run the product, results are good.</td>
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<td width="33%">▪Run the product, results are good.</td>
</tr>
</tr>
</table>
</table>
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<table width="100%" border="0" cellspacing="0" cellpadding="1">
<table width="100%" border="0" cellspacing="0" cellpadding="1">
<tr>
<tr>
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<td width="170">鈥?Culture: 20H, 20J<br />
+
<td width="170">▪Culture: 20H, 20J<br />
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鈥?Transform 13K from plate 3</td>
+
▪Transform 13K from plate 3</td>
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<td width="184">鈥?Miniprep: 20H-1, 20J-1</td>
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<td width="184">▪Miniprep: 20H-1, 20J-1</td>
-
<td>鈥?Cut: the 20H-1, 20J-1, 22B-1, 22B-3 with E+P</td>
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<td>▪Cut: the 20H-1, 20J-1, 22B-1, 22B-3 with E+P</td>
</tr>
</tr>
</table>
</table>
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<table width="100%" border="0" cellspacing="0" cellpadding="1">
<table width="100%" border="0" cellspacing="0" cellpadding="1">
<tr>
<tr>
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<td>鈥?Run the digestion results. Bands are confirmed right.</td>
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<td>▪Run the digestion results. Bands are confirmed right.</td>
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<td>鈥?Colony PCR vgb+22M+10I</td>
+
<td>▪Colony PCR vgb+22M+10I</td>
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<td>鈥?Cut the plasmid of vgb+22M+10I</td>
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<td>▪Cut the plasmid of vgb+22M+10I</td>
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<table width="100%" border="0" cellspacing="0" cellpadding="1">
<table width="100%" border="0" cellspacing="0" cellpadding="1">
<tr>
<tr>
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<td>鈥?Make new stock of competent cells</td>
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<td>▪Make new stock of competent cells</td>
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<td>鈥?Ligation: 13K+10I<br />
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<td>▪Ligation: 13K+10I<br />
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鈥?Cut the PCR results and 22M with E+P</td>
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▪Cut the PCR results and 22M with E+P</td>
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<td>鈥?Sequence: nirB, vgbL, 12I, 20H, 20J, 22B</td>
+
<td>▪Sequence: nirB, vgbL, 12I, 20H, 20J, 22B</td>
-
<td>鈥?Transform 13K+10I+pSB1K3<br />
+
<td>▪Transform 13K+10I+pSB1K3<br />
-
鈥?Cut 13K to validate. Results are right.</td>
+
▪Cut 13K to validate. Results are right.</td>
</tr>
</tr>
</table>
</table>
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<table width="620" border="0" cellspacing="0" cellpadding="1">
<table width="620" border="0" cellspacing="0" cellpadding="1">
<tr>
<tr>
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<td>鈥?Colony PCR: 13K+10I+pSB1K3</td>
+
<td>▪Colony PCR: 13K+10I+pSB1K3</td>
-
<td>鈥?Culture: vgb+22M+10I in 5ml(shaking), 5ml(water bath),
+
<td>▪Culture: vgb+22M+10I in 5ml(shaking), 5ml(water bath),
10ml(water bath), 15(water bath).</td>
10ml(water bath), 15(water bath).</td>
-
<td>鈥?Check the YFP expression of 5ml(shaking) and 15ml(water
+
<td>▪Check the YFP expression of 5ml(shaking) and 15ml(water
bath). No yellow fluorescent cells,</td>
bath). No yellow fluorescent cells,</td>
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<table width="620" border="0" cellspacing="0" cellpadding="1">
<table width="620" border="0" cellspacing="0" cellpadding="1">
<tr>
<tr>
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<td width="244">鈥?Transform: the Gibson assembly results.</td>
+
<td width="244">▪Transform: the Gibson assembly results.</td>
-
<td width="164">鈥?Miniprep: 13K+10I<br />
+
<td width="164">▪Miniprep: 13K+10I<br />
-
鈥?Cut: 13K+10I</td>
+
▪Cut: 13K+10I</td>
-
<td>鈥?Purification: the digestion results.<br />
+
<td>▪Purification: the digestion results.<br />
-
鈥?Ligation: nirB+13K+10I</td>
+
▪Ligation: nirB+13K+10I</td>
</tr>
</tr>
</table>
</table>
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<tr>
<tr>
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<td width="191">鈥?Plate: nirB+13K+10I</td>
+
<td width="191">▪Plate: nirB+13K+10I</td>
-
<td width="249">鈥?Colony PCR: vgb+YFP+tetR +terminater</td>
+
<td width="249">▪Colony PCR: vgb+YFP+tetR +terminater</td>
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<td width="157">鈥?Gibson PCR</td>
+
<td width="157">▪Gibson PCR</td>
</tr>
</tr>
</table>
</table>
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<tr>
<tr>
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<td width="140">鈥?Colony PCR: vgb+22M+10I, nirB+13K+10I</td>
+
<td width="140">▪Colony PCR: vgb+22M+10I, nirB+13K+10I</td>
-
<td width="181">鈥?No bands of 13K; 22M confirmed</td>
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<td width="181">▪No bands of 13K; 22M confirmed</td>
</tr>
</tr>
</table>
</table>
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<table width="609" border="0" cellspacing="1" cellpadding="1">
<table width="609" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
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<td width="304">鈥?Miniprep: 22M<br />
+
<td width="304">▪Miniprep: 22M<br />
-
鈥?Cut: 22M</td>
+
▪Cut: 22M</td>
-
<td width="298">鈥?Check CFP expression. No fluorescence.</td>
+
<td width="298">▪Check CFP expression. No fluorescence.</td>
</tr>
</tr>
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<table width="618" border="0" cellspacing="1" cellpadding="1">
<table width="618" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
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<td>鈥?Transform: 13K, 10I, 22M, 12I, 18P</td>
+
<td>▪Transform: 13K, 10I, 22M, 12I, 18P</td>
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<table width="609" border="0" cellspacing="1" cellpadding="1">
<table width="609" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
-
<td width="277">鈥?Miniprep: 13K, 10I, 22M, 12I, 18P</td>
+
<td width="277">▪Miniprep: 13K, 10I, 22M, 12I, 18P</td>
-
<td width="227">鈥?Cut: 13K, 10I, 22M, 12I, 18P</td>
+
<td width="227">▪Cut: 13K, 10I, 22M, 12I, 18P</td>
-
<td width="95">鈥?Run the gel</td>
+
<td width="95">▪Run the gel</td>
</tr>
</tr>
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<table width="620" border="0" cellspacing="1" cellpadding="1">
<table width="620" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
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<td>鈥?Ligate 13K+10I, 22M+10I</td>
+
<td>▪Ligate 13K+10I, 22M+10I</td>
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<table width="620" border="0" cellspacing="1" cellpadding="1">
<table width="620" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
-
<td width="244">鈥?Transform: the Gibson assembly results.</td>
+
<td width="244">▪Transform: the Gibson assembly results.</td>
-
<td width="164">鈥?Miniprep: 13K+10I<br />
+
<td width="164">▪Miniprep: 13K+10I<br />
-
鈥?Cut: 13K+10I</td>
+
▪Cut: 13K+10I</td>
-
<td>鈥?Purification: the digestion results.<br />
+
<td>▪Purification: the digestion results.<br />
-
鈥?Ligation: nirB+13K+10I</td>
+
▪Ligation: nirB+13K+10I</td>
</tr>
</tr>
</table>
</table>
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cellpadding="1">
cellpadding="1">
<tr>
<tr>
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<td width="191">鈥?Transform 13K+10I, 22M+10I</td>
+
<td width="191">▪Transform 13K+10I, 22M+10I</td>
-
<td width="249">鈥?Test new primers.<br />
+
<td width="249">▪Test new primers.<br />
-
鈥?PCR: 22M+10I, 13K+10I</td>
+
▪PCR: 22M+10I, 13K+10I</td>
-
<td width="157">鈥?Run the PCR products.<br />
+
<td width="157">▪Run the PCR products.<br />
-
鈥?Cut the PCR products.</td>
+
▪Cut the PCR products.</td>
</tr>
</tr>
</table>
</table>
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cellpadding="1">
cellpadding="1">
<tr>
<tr>
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<td width="140">鈥?Test primers: CS/CP, VF/VR, pSB1_f/r</td>
+
<td width="140">▪Test primers: CS/CP, VF/VR, pSB1_f/r</td>
-
<td width="181">鈥?Cut: 11P, 1F, 22M<br />
+
<td width="181">▪Cut: 11P, 1F, 22M<br />
-
鈥?Run the cut results.1F-1/2/3 are right.</td>
+
▪Run the cut results.1F-1/2/3 are right.</td>
-
<td width="126">鈥?Mix the 1F-1/2 purification products</td>
+
<td width="126">▪Mix the 1F-1/2 purification products</td>
-
<td width="145">鈥?Cut: 1F-1+1F-2(E+S), 22M-3(X+P), pSB1C3(E+P)</td>
+
<td width="145">▪Cut: 1F-1+1F-2(E+S), 22M-3(X+P), pSB1C3(E+P)</td>
</tr>
</tr>
</table>
</table>
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<table width="594" border="0" cellspacing="1" cellpadding="1">
<table width="594" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
-
<td width="590">鈥?Amplify: vgb, 1C3</td>
+
<td width="590">▪Amplify: vgb, 1C3</td>
</tr>
</tr>
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<table width="606" border="0" cellspacing="1" cellpadding="1">
<table width="606" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
-
<td width="602">鈥?Digest: Vgb, 1C3, fdfhF, 22M+10I, 13K+10I</td>
+
<td width="602">▪Digest: Vgb, 1C3, fdfhF, 22M+10I, 13K+10I</td>
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<table width="608" border="0" cellspacing="1" cellpadding="1">
<table width="608" border="0" cellspacing="1" cellpadding="1">
<tr>
<tr>
-
<td width="366">鈥?Ligate: vgb+22M+10I, fdfhF+13K+10I</td>
+
<td width="366">▪Ligate: vgb+22M+10I, fdfhF+13K+10I</td>
-
<td width="235">鈥?Transform the ligation results.</td>
+
<td width="235">▪Transform the ligation results.</td>
</tr>
</tr>
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<h1>1st August</h1>
<h1>1st August</h1>
-
<p>Freeze slicing of about 50渭m. Observe under natural light
+
<p>Freeze slicing of about 50μm. Observe under natural light
-
microscope and can see red florescence. The thickness is about 130渭m</p>
+
microscope and can see red florescence. The thickness is about 130μm</p>
</div>
</div>
<div class="block" id="nsheet">
<div class="block" id="nsheet">
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<h1>16th August</h1>
<h1>16th August</h1>
<p>Substituting a part of silicone tube with glass tube in silicone
<p>Substituting a part of silicone tube with glass tube in silicone
-
tube biofilm formation sets. Culture in 37鈩?/p>
+
tube biofilm formation sets. Culture in 37℃/p>
</div>
</div>
<div class="block" id="nsheet">
<div class="block" id="nsheet">
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Revision as of 09:28, 17 October 2011

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> Notebook - August

Lab Notes

July August
 September

Protocol

Protocol

Brainstorm

Brainstorm

Lab Notes - August

Biobrick Group

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, 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
Aug.8th Monday
▪The gel results of 5 backbones are right. ▪Miniprep: pSB1C3, vgb+22M+10I ▪Culture vgb+22M+1oI in hypoxia
▪CR 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
Aug.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.


Biofilm Group

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℃/p>

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.

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