Team:Osaka/Notebook

From 2011.igem.org

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==Weekly Summaries==
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<h4>Week 1</h4>
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<p>Went through basic molecular biology lab skills and techniques with the new members. Extracted most of the existing parts required for our project from the iGEM 2011 Spring distribution plates, transformed and amplified the DNA for future use.</p>
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<h4>Week 2</h4>
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<p>DNA extraction & purification (miniprep) of last week's transformed parts, & gel runs to confirm lengths. Sequencer was broken so we could not confirm sequence, but most parts' lengths turned out ok. Ligations to put together some common combinations (eg promoter + RBS).</p>
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<h4>Week 3</h4>
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<p>Extraction & amplification of more basic parts from the distribution plates, plus ligation of a few more parts. Not much progress due to lab being closed for Obon holidays.</p>
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<h4>Week 4</h4>
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<p>Original plan was to use GFP as a reporter but spectrofluorometer was broken, so we amplified luciferase parts as a possible alternative. Tetracycline-resistance plasmid backbone was also amplified to enable more options during 3A assembly.</p>
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<h4>Week 5</h4>
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<p>Some of us attended iGEM Japan Meet-Up at Kyoto University. Did more ligations to start putting together lycopene biosynthesis gene cluster (CrtE, CrtB, CrtI) in case the 2009 Cambridge part BBa_K274100 doesn't work.</p>
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<h4>Week 6</h4>
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<p>Finally got our primers after 3 weeks' wait! PCR to amplify PprI, PprA, PprM and RecA from <i>Deinococcus radiodurans</i> genomic DNA. Preliminary trial of DNA damage detector using (<i>E. coli</i> RecA) promoter with lycopene biosynthesis (CrtEBI) as reporter. Results were a little disappointing, perhaps the RecA promoter doesn't work well in the &Delta;<i>RecA</i> strain that we used. Ordered a new batch of competent cells (different strain).</p>
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<h4>Week 7</h4>
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<p>Ligations of <i>D. radiodurans</i> genes to promoters, RBS, etc. Also, ligations to combine radioresistance parts: PprI-PprA, and PprI-PprA-PprM-PprM.</p>
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<h4>Week 8</h4>
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<p>Completion of radioresistance parts & drafting of radioresistance assay protocol.</p>
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<h4>Week 9</h4>
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<p>DNA repair/radioresistance assays: transformed cells were irradiated with UV light and then incubated on agar plates, and viability relative to control used as an evaluation of the abilities of PprI, PprA, PprM, RecA to confer resistance to radiation-induced DNA damage.</p>
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<h4>Week 10</h4>
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<p>Competent cells finally arrived, DNA damage detection assay! Also, wiki updating before the freeze!</p>
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<br>
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==Logbook Entries==
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Click on any day in the calendar below to display detailed logbook entry.
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==Notebook==
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{| class="toccolours" style="float:{{{float|left}}}; width:{{{width|240px}}}; text-align:center;"
{| class="toccolours" style="float:{{{float|left}}}; width:{{{width|240px}}}; text-align:center;"
|- style="background:{{{color1|#ccccff}}};"
|- style="background:{{{color1|#ccccff}}};"
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|colspan="8"|{{{header|July / August}}}
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|colspan="8"|{{{header|August}}}
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|-
|- style="background:{{{color2|#eeeeff}}};"
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|<span style>[[Team:Osaka/week1|week1]]</span>
|<span style>[[Team:Osaka/week1|week1]]</span>
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|<span style={{{s1|"color:{{{c1|red}}};"}}}>31</span>
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|<span style></span>
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|[[Team:Osaka/week1#August 1 (Mon)|1]]<span style={{{s2|"color:{{{c2|inherit}}};"}}}></span>
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|[[Team:Osaka/week1#August 1 (Mon)|1]]<span style={{{s1|"color:{{{c1|inherit}}};"}}}></span>
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|[[Team:Osaka/week1#August 2 (Tue)|2]]<span style={{{s3|"color:{{{c3|inherit}}};"}}}></span>
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|[[Team:Osaka/week1#August 2 (Tue)|2]]<span style={{{s2|"color:{{{c2|inherit}}};"}}}></span>
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|[[Team:Osaka/week1#August 3 (Wed)|3]]<span style={{{s4|"color:{{{c4|inherit}}};"}}}></span>
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|[[Team:Osaka/week1#August 3 (Wed)|3]]<span style={{{s3|"color:{{{c3|inherit}}};"}}}></span>
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|[[Team:Osaka/week1#August 4 (Thu)|4]]<span style={{{s5|"color:{{{c5|inherit}}};"}}}></span>
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|[[Team:Osaka/week1#August 4 (Thu)|4]]<span style={{{s4|"color:{{{c4|inherit}}};"}}}></span>
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|[[Team:Osaka/week1#August 5 (Fri)|5]]<span style={{{s6|"color:{{{c6|inherit}}};"}}}></span>
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|[[Team:Osaka/week1#August 5 (Fri)|5]]<span style={{{s5|"color:{{{c5|inherit}}};"}}}></span>
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|-
|-
|<span style>[[Team:Osaka/week2|week2]]</span>
|<span style>[[Team:Osaka/week2|week2]]</span>
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|[[Team:Osaka/week2#August 7 (Sun)|7]]<span style={{{s8|"color:{{{c8|red}}};"}}}></span>
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|[[Team:Osaka/week2#August 7 (Sun)|7]]<span style={{{s7|"color:{{{c7|red}}};"}}}></span>
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|[[Team:Osaka/week2#August 8 (Mon)|8]]<span style={{{s9|"color:{{{c9|inherit}}};"}}}></span>
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|[[Team:Osaka/week2#August 8 (Mon)|8]]<span style={{{s8|"color:{{{c8|inherit}}};"}}}></span>
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|[[Team:Osaka/week2#August 9 (Tue)|9]]<span style={{{s10|"color:{{{c10|inherit}}};"}}}></span>
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|[[Team:Osaka/week2#August 9 (Tue)|9]]<span style={{{s9|"color:{{{c9|inherit}}};"}}}></span>
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|[[Team:Osaka/week2#August 10 (Wed)|10]]<span style={{{s11|"color:{{{c11|inherit}}};"}}}></span>
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|[[Team:Osaka/week2#August 10 (Wed)|10]]<span style={{{s10|"color:{{{c10|inherit}}};"}}}></span>
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|<span style={{{s12|"color:{{{c12|red}}};"}}}>11</span>
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|<span style={{{s11|"color:{{{c11|red}}};"}}}>11</span>
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|<span style={{{s13|"color:{{{c13|red}}};"}}}>12</span>
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|<span style={{{s12|"color:{{{c12|red}}};"}}}>12</span>
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|<span style={{{s14|"color:{{{c14|red}}};"}}}>13</span>
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|<span style={{{s13|"color:{{{c13|red}}};"}}}>13</span>
|-
|-
|<span style>[[Team:Osaka/week3|week3]]</span>
|<span style>[[Team:Osaka/week3|week3]]</span>
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|<span style={{{s15|"color:{{{c15|red}}};"}}}>14</span>
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|<span style={{{s14|"color:{{{c14|red}}};"}}}>14</span>
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|[[Team:Osaka/week3#August 15 (Mon)|15]]<span style={{{s16|"color:{{{c16|red}}};"}}}></span>
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|<span style={{{s15|"color:{{{c15|red}}};"}}}>15</span>
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|[[Team:Osaka/week3#August 16 (Tue)|16]]<span style={{{s17|"color:{{{c17|inherit}}};"}}}></span>
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|[[Team:Osaka/week3#August 16 (Tue)|16]]<span style={{{s16|"color:{{{c16|inherit}}};"}}}></span>
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|-
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|<span style>[[Team:Osaka/week4|week4]]</span>
|<span style>[[Team:Osaka/week4|week4]]</span>
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|<span style>[[Team:Osaka/week5|week5]]</span>
|<span style>[[Team:Osaka/week5|week5]]</span>
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|<span style>[[Team:Osaka/week5|week5]]</span>
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|<span style>[[Team:Osaka/week6|week6]]</span>
|<span style>[[Team:Osaka/week6|week6]]</span>
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|[[Team:Osaka/week5#September 4 (Sun)|4]]<span style={{{s4|"color:{{{c4|deepskyblue}}};"}}}></span>
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|[[Team:Osaka/week6#September 4 (Sun)|4]]<span style={{{s4|"color:{{{c4|deepskyblue}}};"}}}></span>
|[[Team:Osaka/week6#September 5 (Mon)|5]]<span style={{{s5|"color:{{{c5|red}}};"}}}></span>
|[[Team:Osaka/week6#September 5 (Mon)|5]]<span style={{{s5|"color:{{{c5|red}}};"}}}></span>
|[[Team:Osaka/week6#September 6 (Tue)|6]]<span style={{{s6|"color:{{{c6|inherit}}};"}}}></span>
|[[Team:Osaka/week6#September 6 (Tue)|6]]<span style={{{s6|"color:{{{c6|inherit}}};"}}}></span>
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|<span style>[[Team:Osaka/week9|week9]]</span>
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|[[Team:Osaka/week10#October 5 (Wed)|5]]<span style={{{s5|"color:{{{c5|inherit}}};"}}}></span>
|[[Team:Osaka/week10#October 5 (Wed)|5]]<span style={{{s5|"color:{{{c5|inherit}}};"}}}></span>
|[[Team:Osaka/week10#October 6 (Thu)|6]]<span style={{{s6|"color:{{{c6|inherit}}};"}}}></span>
|[[Team:Osaka/week10#October 6 (Thu)|6]]<span style={{{s6|"color:{{{c6|inherit}}};"}}}></span>
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|[[Team:Osaka/week10#October 7 (Fri)|7]]<span style={{{s7|"color:{{{c7|inherit}}};"}}}></span>
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|<span style={{{s7|"color:{{{c7|inherit}}};"}}}>7</span>
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|[[Team:Osaka/week10#October 8 (Sat)|8]]<span style={{{s8|"color:{{{c8|inherit}}};"}}}></span>
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|<span style={{{s8|"color:{{{c8|deepskyblue}}};"}}}>8</span>
|-
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|<span style>[[Team:Osaka/week11|week11]]</span>
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|[[Team:Osaka/week11#October 9 (Sun)|9]]<span style={{{s9|"color:{{{c9|deepskyblue}}};"}}}></span>
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|<span style={{{s9|"color:{{{c9|red}}};"}}}>9</span>
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|[[Team:Osaka/week11#October 10 (Mon)|10]]<span style={{{s10|"color:{{{c10|red}}};"}}}></span>
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|<span style={{{s10|"color:{{{c10|inherit}}};"}}}>10</span>
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|[[Team:Osaka/week11#October 11 (Tue)|11]]<span style={{{s11|"color:{{{c11|inherit}}};"}}}></span>
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|<span style={{{s11|"color:{{{c11|inherit}}};"}}}>11</span>
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|[[Team:Osaka/week11#October 12 (Wed)|12]]<span style={{{s12|"color:{{{c12|inherit}}};"}}}></span>
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|<span style={{{s12|"color:{{{c12|inherit}}};"}}}>12</span>
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|[[Team:Osaka/week11#October 13 (Thu)|13]]<span style={{{s13|"color:{{{c13|inherit}}};"}}}></span>
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|<span style={{{s13|"color:{{{c13|inherit}}};"}}}>13</span>
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|[[Team:Osaka/week11#October 14 (Fri)|14]]<span style={{{s14|"color:{{{c14|inherit}}};"}}}></span>
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|<span style={{{s14|"color:{{{c14|inherit}}};"}}}>14</span>
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|[[Team:Osaka/week11#October 15 (Wed)|15]]<span style={{{s15|"color:{{{c15|inherit}}};"}}}></span>
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||[[Team:Osaka/week11#October 15 (Sat)|15]]
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|<span style>[[Team:Osaka/week12|week12]]</span>
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|[[Team:Osaka/week12#October 16 (Sun)|16]]<span style={{{s16|"color:{{{c16|deepskyblue}}};"}}}></span>
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|[[Team:Osaka/week12#October 16 (Sun)|16]]
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|[[Team:Osaka/week12#October 17 (Mon)|17]]<span style={{{s17|"color:{{{c17|red}}};"}}}></span>
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|<span style={{{s17|"color:{{{c17|inherit}}};"}}}>17</span>
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|[[Team:Osaka/week12#October 18 (Tue)|18]]<span style={{{s18|"color:{{{c18|inherit}}};"}}}></span>
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|[[Team:Osaka/week12#October 18 (Tue)|18]]
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|[[Team:Osaka/week12#October 19 (Wed)|19]]<span style={{{s19|"color:{{{c19|inherit}}};"}}}></span>
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|[[Team:Osaka/week12#October 19 (Wed)|19]]
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|[[Team:Osaka/week12#October 20 (Thu)|20]]<span style={{{s20|"color:{{{c20|inherit}}};"}}}></span>
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|[[Team:Osaka/week12#October 22 (Sat)|22]]
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Latest revision as of 10:32, 28 October 2011

Weekly Summaries

Week 1

Went through basic molecular biology lab skills and techniques with the new members. Extracted most of the existing parts required for our project from the iGEM 2011 Spring distribution plates, transformed and amplified the DNA for future use.

Week 2

DNA extraction & purification (miniprep) of last week's transformed parts, & gel runs to confirm lengths. Sequencer was broken so we could not confirm sequence, but most parts' lengths turned out ok. Ligations to put together some common combinations (eg promoter + RBS).

Week 3

Extraction & amplification of more basic parts from the distribution plates, plus ligation of a few more parts. Not much progress due to lab being closed for Obon holidays.

Week 4

Original plan was to use GFP as a reporter but spectrofluorometer was broken, so we amplified luciferase parts as a possible alternative. Tetracycline-resistance plasmid backbone was also amplified to enable more options during 3A assembly.

Week 5

Some of us attended iGEM Japan Meet-Up at Kyoto University. Did more ligations to start putting together lycopene biosynthesis gene cluster (CrtE, CrtB, CrtI) in case the 2009 Cambridge part BBa_K274100 doesn't work.

Week 6

Finally got our primers after 3 weeks' wait! PCR to amplify PprI, PprA, PprM and RecA from Deinococcus radiodurans genomic DNA. Preliminary trial of DNA damage detector using (E. coli RecA) promoter with lycopene biosynthesis (CrtEBI) as reporter. Results were a little disappointing, perhaps the RecA promoter doesn't work well in the ΔRecA strain that we used. Ordered a new batch of competent cells (different strain).

Week 7

Ligations of D. radiodurans genes to promoters, RBS, etc. Also, ligations to combine radioresistance parts: PprI-PprA, and PprI-PprA-PprM-PprM.

Week 8

Completion of radioresistance parts & drafting of radioresistance assay protocol.

Week 9

DNA repair/radioresistance assays: transformed cells were irradiated with UV light and then incubated on agar plates, and viability relative to control used as an evaluation of the abilities of PprI, PprA, PprM, RecA to confer resistance to radiation-induced DNA damage.

Week 10

Competent cells finally arrived, DNA damage detection assay! Also, wiki updating before the freeze!


Logbook Entries

Click on any day in the calendar below to display detailed logbook entry.

August
Week S M T W T F S
week1 1 2 3 4 5 6
week2 7 8 9 10 11 12 13
week3 14 15 16 17 18 19 20
week4 21 22 23 24 25 26 27
week5 28 29 30 31
September
Week S M T W T F S
week5 1 2 3
week6 4 5 6 7 8 9 10
week7 11 12 13 14 15 16 17
week8 18 19 20 21 22 23 24
week9 25 26 27 28 29 30
October
Week S M T W T F S
week9 1
week10 2 3 4 5 6 7 8
week11 9 10 11 12 13 14 15
week12 16 17 18 19 20 21 22
week13 23 24 25 26 27 28 29
week14 30 31
Retrieved from "http://2011.igem.org/Team:Osaka/Notebook"