Team:Osaka/Notebook

From 2011.igem.org

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<!-- *** What falls between these lines is the Alert Box!  You can remove it from your pages once you have read and understood the alert *** -->
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{{Osaka}}
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__NOTOC__
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<div class="padding">
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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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<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;">
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This is a template page. READ THESE INSTRUCTIONS.
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</div>
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<div id="instructions" style="text-align: center; font-weight: normal; font-size: small; color: #f6f6f6; padding: 5px;">
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You are provided with this team page template with which to start the iGEM season. You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
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</div>
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<div id="warning" style="text-align: center; font-weight: bold; font-size: small; color: #f6f6f6; padding: 5px;">
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You <strong>MUST</strong> have a team description page, a project abstract, a complete project description, a lab notebook, and a safety page.  PLEASE keep all of your pages within your teams namespace. 
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<!-- *** End of the alert box *** -->
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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>
 +
<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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{|align="justify"
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<h4>Week 5</h4>
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|You can write a background of your team here.  Give us a background of your team, the members, etc. Or tell us more about something of your choosing.
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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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|[[Image:Osaka_logo.png|200px|right|frame]]
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|-
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|
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''Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)''
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|[[Image:Osaka_team.png|right|frame|Your team picture]]
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|-
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|align="center"|[[Team:Osaka | Team Example]]
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|}
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<!--- The Mission, Experiments --->
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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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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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<h4>Week 7</h4>
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!align="center"|[[Team:Osaka|Home]]
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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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!align="center"|[[Team:Osaka/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=Osaka Official Team Profile]
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!align="center"|[[Team:Osaka/Project|Project]]
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!align="center"|[[Team:Osaka/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:Osaka/Modeling|Modeling]]
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!align="center"|[[Team:Osaka/Notebook|Notebook]]
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!align="center"|[[Team:Osaka/Safety|Safety]]
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!align="center"|[[Team:Osaka/Attributions|Attributions]]
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|}
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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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==Notebook==
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<h4>Week 9</h4>
 +
<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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You should make use of the calendar feature on the wiki and start a lab notebook.  This may be looked at by the judges to see how your work progressed throughout the summer.  It is a very useful organizational tool as well.
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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>
 +
<br>
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==Logbook Entries==
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<p>
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Click on any day in the calendar below to display detailed logbook entry.
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</p>
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{| class="toccolours" style="float:{{{float|left}}}; width:{{{width|240px}}}; text-align:center;"
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|- style="background:{{{color1|#ccccff}}};"
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|colspan="8"|{{{header|August}}}
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|-
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|- style="background:{{{color2|#eeeeff}}};"
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|width=100px|Week
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|width="14%"|<span style="color:red;">S</span>
 +
|width="14%"|M
 +
|width="14%"|T
 +
|width="14%"|W
 +
|width="14%"|T
 +
|width="14%"|F
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|width="14%"|<span style="color:deepskyblue;">S</span>
 +
|-
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|<span style>[[Team:Osaka/week1|week1]]</span>
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|<span style></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={{{s2|"color:{{{c2|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={{{s4|"color:{{{c4|inherit}}};"}}}></span>
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|[[Team:Osaka/week1#August 5 (Fri)|5]]<span style={{{s5|"color:{{{c5|inherit}}};"}}}></span>
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|[[Team:Osaka/week1#August 6 (Sat)|6]]<span style={{{s6|"color:{{{c6|deepskyblue}}};"}}}></span>
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|-
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|<span style>[[Team:Osaka/week2|week2]]</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={{{s8|"color:{{{c8|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={{{s10|"color:{{{c10|inherit}}};"}}}></span>
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|<span style={{{s11|"color:{{{c11|red}}};"}}}>11</span>
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|<span style={{{s12|"color:{{{c12|red}}};"}}}>12</span>
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|<span style={{{s13|"color:{{{c13|red}}};"}}}>13</span>
 +
|-
 +
|<span style>[[Team:Osaka/week3|week3]]</span>
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|<span style={{{s14|"color:{{{c14|red}}};"}}}>14</span>
 +
|<span style={{{s15|"color:{{{c15|red}}};"}}}>15</span>
 +
|[[Team:Osaka/week3#August 16 (Tue)|16]]<span style={{{s16|"color:{{{c16|inherit}}};"}}}></span>
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|[[Team:Osaka/week3#August 17 (Wed)|17]]<span style={{{s17|"color:{{{c17|inherit}}};"}}}></span>
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|[[Team:Osaka/week3#August 18 (Thu)|18]]<span style={{{s18|"color:{{{c18|inherit}}};"}}}></span>
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|[[Team:Osaka/week3#August 19 (Fri)|19]]<span style={{{s19|"color:{{{c19|inherit}}};"}}}></span>
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|[[Team:Osaka/week3#August 20 (Sat)|20]]<span style={{{s20|"color:{{{c20|deepskyblue}}};"}}}></span>
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|-
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|<span style>[[Team:Osaka/week4|week4]]</span>
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|[[Team:Osaka/week4#August 21 (Sun)|21]]<span style={{{s21|"color:{{{c21|red}}};"}}}></span>
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|[[Team:Osaka/week4#August 22 (Mon)|22]]<span style={{{s22|"color:{{{c22|inherit}}};"}}}></span>
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|[[Team:Osaka/week4#August 23 (Tue)|23]]<span style={{{s23|"color:{{{c23|inherit}}};"}}}></span>
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|[[Team:Osaka/week4#August 24 (Wed)|24]]<span style={{{s24|"color:{{{c24|inherit}}};"}}}></span>
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|[[Team:Osaka/week4#August 25 (Thu)|25]]<span style={{{s25|"color:{{{c25|inherit}}};"}}}></span>
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|[[Team:Osaka/week4#August 26 (Fri)|26]]<span style={{{s26|"color:{{{c26|inherit}}};"}}}></span>
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|[[Team:Osaka/week4#August 27 (Sat)|27]]<span style={{{s27|"color:{{{c27|deepskyblue}}};"}}}></span>
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|-
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|<span style>[[Team:Osaka/week5|week5]]</span>
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|[[Team:Osaka/week5#August 28 (Sun)|28]]<span style={{{s28|"color:{{{c28|red}}};"}}}></span>
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|[[Team:Osaka/week5#August 29 (Mon)|29]]<span style={{{s29|"color:{{{c29|red}}};"}}}></span>
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|[[Team:Osaka/week5#August 30 (Tue)|30]]<span style={{{s30|"color:{{{c30|inherit}}};"}}}></span>
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|[[Team:Osaka/week5#August 31 (Wed)|31]]<span style={{{s31|"color:{{{c31|inherit}}};"}}}></span>
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|colspan="4"|
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|- style="background:{{{color3|#eeeeff}}};"
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|colspan="7"|{{{footer|}}}
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|}<noinclude>
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{| class="toccolours" style="float:{{{float|left}}}; width:{{{width|240px}}}; text-align:center;"
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|- style="background:{{{color1|#ccccff}}};"
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|colspan="8"|{{{header|September}}}
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|-
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|- style="background:{{{color2|#eeeeff}}};"
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|width=100px|Week
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|width="14%"|<span style="color:red;">S</span>
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|width="14%"|M
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|width="14%"|T
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|width="14%"|W
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|width="14%"|T
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|width="14%"|F
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|width="14%"|<span style="color:deepskyblue;">S</span>
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|-
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|<span style>[[Team:Osaka/week5|week5]]</span>
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|<span style></span>
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|<span style></span>
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|<span style></span>
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|<span style></span>
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|[[Team:Osaka/week5#September 1 (Thu)|1]]<span style={{{s1|"color:{{{c1|inherit}}};"}}}></span>
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|[[Team:Osaka/week5#September 2 (Fri)|2]]<span style={{{s2|"color:{{{c2|inherit}}};"}}}></span>
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|[[Team:Osaka/week5#September 3 (Sat)|3]]<span style={{{s3|"color:{{{c3|inherit}}};"}}}></span>
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|-
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|<span style>[[Team:Osaka/week6|week6]]</span>
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|[[Team:Osaka/week6#September 4 (Sun)|4]]<span style={{{s4|"color:{{{c4|deepskyblue}}};"}}}></span>
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|[[Team:Osaka/week6#September 5 (Mon)|5]]<span style={{{s5|"color:{{{c5|red}}};"}}}></span>
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|[[Team:Osaka/week6#September 6 (Tue)|6]]<span style={{{s6|"color:{{{c6|inherit}}};"}}}></span>
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|[[Team:Osaka/week6#September 7 (Wed)|7]]<span style={{{s7|"color:{{{c7|inherit}}};"}}}></span>
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|[[Team:Osaka/week6#September 8 (Thu)|8]]<span style={{{s8|"color:{{{c8|inherit}}};"}}}></span>
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|[[Team:Osaka/week6#September 9 (Fri)|9]]<span style={{{s9|"color:{{{c9|inherit}}};"}}}></span>
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|[[Team:Osaka/week6#September 10 (Sat)|10]]<span style={{{s10|"color:{{{c10|inherit}}};"}}}></span>
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|-
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|<span style>[[Team:Osaka/week7|week7]]</span>
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|[[Team:Osaka/week7#September 11 (Sun)|11]]<span style={{{s11|"color:{{{c11|deepskyblue}}};"}}}></span>
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|[[Team:Osaka/week7#September 12 (Mon)|12]]<span style={{{s12|"color:{{{c12|red}}};"}}}></span>
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|[[Team:Osaka/week7#September 13 (Tue)|13]]<span style={{{s13|"color:{{{c13|inherit}}};"}}}></span>
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|[[Team:Osaka/week7#September 14 (Wed)|14]]<span style={{{s14|"color:{{{c14|inherit}}};"}}}></span>
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|[[Team:Osaka/week7#September 15 (Thu)|15]]<span style={{{s15|"color:{{{c15|inherit}}};"}}}></span>
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|[[Team:Osaka/week7#September 16 (Fri)|16]]<span style={{{s16|"color:{{{c16|inherit}}};"}}}></span>
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|[[Team:Osaka/week7#September 17 (Sat)|17]]<span style={{{s17|"color:{{{c17|inherit}}};"}}}></span>
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|-
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|<span style>[[Team:Osaka/week8|week8]]</span>
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|[[Team:Osaka/week8#September 18 (Sun)|18]]<span style={{{s18|"color:{{{c18|deepskyblue}}};"}}}></span>
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|[[Team:Osaka/week8#September 19 (Mon)|19]]<span style={{{s19|"color:{{{c19|red}}};"}}}></span>
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|[[Team:Osaka/week8#September 20 (Tue)|20]]<span style={{{s20|"color:{{{c20|inherit}}};"}}}></span>
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|[[Team:Osaka/week8#September 21 (Wed)|21]]<span style={{{s21|"color:{{{c21|inherit}}};"}}}></span>
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|[[Team:Osaka/week8#September 22 (Thu)|22]]<span style={{{s22|"color:{{{c22|inherit}}};"}}}></span>
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|[[Team:Osaka/week8#September 23 (Fri)|23]]<span style={{{s23|"color:{{{c23|inherit}}};"}}}></span>
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|[[Team:Osaka/week8#September 24 (Sat)|24]]<span style={{{s24|"color:{{{c24|inherit}}};"}}}></span>
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|-
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|<span style>[[Team:Osaka/week9|week9]]</span>
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|[[Team:Osaka/week9#September 25 (Sun)|25]]<span style={{{s25|"color:{{{c25|deepskyblue}}};"}}}></span>
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|[[Team:Osaka/week9#September 26 (Mon)|26]]<span style={{{s26|"color:{{{c26|red}}};"}}}></span>
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|[[Team:Osaka/week9#September 27 (Tue)|27]]<span style={{{s27|"color:{{{c27|inherit}}};"}}}></span>
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|[[Team:Osaka/week9#September 28 (Wed)|28]]<span style={{{s28|"color:{{{c28|inherit}}};"}}}></span>
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|[[Team:Osaka/week9#September 29 (Thu)|29]]<span style={{{s29|"color:{{{c29|inherit}}};"}}}></span>
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|[[Team:Osaka/week9#September 30 (Fri)|30]]<span style={{{s30|"color:{{{c30|inherit}}};"}}}></span>
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|colspan="2"|
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|- style="background:{{{color3|#eeeeff}}};"
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|colspan="7"|{{{footer|}}}
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|}<noinclude>
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{| class="toccolours" style="float:{{{float|left}}}; width:{{{width|240px}}}; text-align:center;"
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|- style="background:{{{color1|#ccccff}}};"
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|colspan="8"|{{{header|October}}}
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|-
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|- style="background:{{{color2|#eeeeff}}};"
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|width=100px|Week
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|width="14%"|<span style="color:red;">S</span>
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|width="14%"|M
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|width="14%"|T
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|width="14%"|W
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|width="14%"|T
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|width="14%"|F
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|width="14%"|<span style="color:deepskyblue;">S</span>
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|-
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|<span style>[[Team:Osaka/week9|week9]]</span>
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|<span style></span>
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|<span style></span>
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|<span style></span>
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|<span style></span>
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|<span style></span>
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|<span style></span>
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|[[Team:Osaka/week9#October 1 (Sat)|1]]<span style={{{s1|"color:{{{c1|inherit}}};"}}}></span>
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|-
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|<span style>[[Team:Osaka/week10|week10]]</span>
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|[[Team:Osaka/week10#October 2 (Sun)|2]]<span style={{{s2|"color:{{{c2|deepskyblue}}};"}}}></span>
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|[[Team:Osaka/week10#October 3 (Mon)|3]]<span style={{{s3|"color:{{{c3|red}}};"}}}></span>
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|[[Team:Osaka/week10#October 4 (Tue)|4]]<span style={{{s4|"color:{{{c4|inherit}}};"}}}></span>
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|[[Team:Osaka/week10#October 5 (Wed)|5]]<span style={{{s5|"color:{{{c5|inherit}}};"}}}></span>
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|[[Team:Osaka/week10#October 6 (Thu)|6]]<span style={{{s6|"color:{{{c6|inherit}}};"}}}></span>
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|<span style={{{s7|"color:{{{c7|inherit}}};"}}}>7</span>
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|<span style={{{s8|"color:{{{c8|deepskyblue}}};"}}}>8</span>
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|-
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|<span style>[[Team:Osaka/week11|week11]]</span>
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|<span style={{{s9|"color:{{{c9|red}}};"}}}>9</span>
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|<span style={{{s10|"color:{{{c10|inherit}}};"}}}>10</span>
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|<span style={{{s11|"color:{{{c11|inherit}}};"}}}>11</span>
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|<span style={{{s12|"color:{{{c12|inherit}}};"}}}>12</span>
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|<span style={{{s13|"color:{{{c13|inherit}}};"}}}>13</span>
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|<span style={{{s14|"color:{{{c14|inherit}}};"}}}>14</span>
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||[[Team:Osaka/week11#October 15 (Sat)|15]]
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|-
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|<span style>[[Team:Osaka/week12|week12]]</span>
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|[[Team:Osaka/week12#October 16 (Sun)|16]]
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|<span style={{{s17|"color:{{{c17|inherit}}};"}}}>17</span>
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|[[Team:Osaka/week12#October 18 (Tue)|18]]
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|[[Team:Osaka/week12#October 19 (Wed)|19]]
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|[[Team:Osaka/week12#October 20 (Thu)|20]]
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|[[Team:Osaka/week12#October 21 (Fri)|21]]
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|[[Team:Osaka/week12#October 22 (Sat)|22]]
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|-
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|<span style>[[Team:Osaka/week13|week13]]</span>
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|[[Team:Osaka/week13#October 23 (Sun)|23]]
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|[[Team:Osaka/week13#October 24 (Mon)|24]]
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|[[Team:Osaka/week13#October 25 (Tue)|25]]
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|[[Team:Osaka/week13#October 26 (Wed)|26]]
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|[[Team:Osaka/week13#October 27 (Thu)|27]]
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|[[Team:Osaka/week13#October 28 (Fri)|28]]
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|<span style={{{s29|"color:{{{c29|deepskyblue}}};"}}}>29</span>
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|-
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|<span style>week14</span>
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|<span style={{{s30|"color:{{{c30|red}}};"}}}>30</span>
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|<span style={{{s31|"color:{{{c31|inherit}}};"}}}>31</span>
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|colspan="6"|
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|- style="background:{{{color3|#eeeeff}}};"
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|colspan="7"|{{{footer|}}}
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|}<noinclude>
 +
</div>

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"