Team:Osaka/Notebook
From 2012.igem.org
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==Weekly Summaries== | ==Weekly Summaries== | ||
<h4>Week 1</h4> | <h4>Week 1</h4> | ||
- | <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 2012 Spring distribution plates, transformed and amplified the DNA for future use.</p> | + | <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 2012 Spring distribution plates, transformed and amplified the DNA for future use.DNA extraction & purification (miniprep) of transformed parts, & gel runs to confirm lengths. Ligations to put together some common combinations (eg promoter + RBS).</p> |
+ | <p>We transfered redioresistance parts from one vector(pSB1C3) to another vector(pSB1A3) and transformed plasmid DNA into Rosetta E.coli. | ||
+ | </p> | ||
<h4>Week 2</h4> | <h4>Week 2</h4> | ||
- | <p> | + | <p>We run the SDS-PAGE gel to check the expression of the gene products at the protein level. The result of DNA sequencing demonstrated that there is a mutation in PprA(Silent mutation).</p> |
<h4>Week 3</h4> | <h4>Week 3</h4> | ||
<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> | <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> | ||
+ | <p>Completion of radioresistance parts and drafting of damage tolerance assay protocol.</p> | ||
+ | |||
+ | <h4>Week 4</h4> | ||
+ | <p>We were going to assemble a promoter evaluation device utilizing firefly and renilla luciferase, but did not make much progress due to low transformation efficiency(?). | ||
+ | </p> | ||
+ | |||
+ | <h4>Week 5</h4> | ||
+ | <p>Preliminary test (damage tolerance, Mitomycin C).</p> | ||
+ | <p>We were going to assemble a promoter evaluation device utilizing firefly and renilla luciferase, but did not make much progress due to low transformation efficiency(?). | ||
+ | </p> | ||
+ | |||
+ | <h4>Week 6</h4> | ||
+ | <p> | ||
+ | Damage tolerance assay (Mitomycin C): transformed cells were exposed to DNA damaging agents 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> | ||
+ | |||
+ | <h4>Week 7</h4> | ||
+ | <p> | ||
+ | Damage tolerance assay (Mitomycin C)</p> | ||
+ | <p> | ||
+ | Preliminary test (damage tolerance, Hydrogen peroxide) | ||
+ | </p> | ||
+ | |||
+ | <h4>Week 8</h4> | ||
+ | Damage tolerance assay (Hydrogen peroxide) | ||
+ | |||
+ | <h4>Week 9</h4> | ||
+ | Damage tolerance assay (Hydrogen peroxide) | ||
==Logbook Entries== | ==Logbook Entries== | ||
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|<span style>[[Team:Osaka/week1|week1]]</span> | |<span style>[[Team:Osaka/week1|week1]]</span> | ||
|<span style></span> | |<span style></span> | ||
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- | | | + | |<span style></span> |
- | |[[Team:Osaka/week1#August | + | |[[Team:Osaka/week1#August 1 (Wed)|1]]<span style={{{s1|"color:{{{c1|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week1#August | + | |[[Team:Osaka/week1#August 2 (Thu)|2]]<span style={{{s2|"color:{{{c2|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week1#August | + | |[[Team:Osaka/week1#August 3 (Fri)|3]]<span style={{{s3|"color:{{{c3|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week1#August | + | |[[Team:Osaka/week1#August 4 (Sat)|4]]<span style={{{s4|"color:{{{c4|deepskyblue}}};"}}}></span> |
|- | |- | ||
|<span style>[[Team:Osaka/week2|week2]]</span> | |<span style>[[Team:Osaka/week2|week2]]</span> | ||
- | |[[Team:Osaka/week2#August | + | |[[Team:Osaka/week2#August 5 (Sun)|5]]<span style={{{s5|"color:{{{c5|red}}};"}}}></span> |
- | |[[Team:Osaka/week2#August | + | |[[Team:Osaka/week2#August 6 (Mon)|6]]<span style={{{s6|"color:{{{c6|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week2#August | + | |[[Team:Osaka/week2#August 7 (Tue)|7]]<span style={{{s7|"color:{{{c7|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week2#August | + | |[[Team:Osaka/week2#August 8 (Wed)|8]]<span style={{{s8|"color:{{{c8|inherit}}};"}}}></span> |
- | |<span style={{{ | + | |[[Team:Osaka/week3#August 9 (Thu)|9]]<span style={{{s9|"color:{{{c9|inherit}}};"}}}></span> |
- | |<span style={{{ | + | |[[Team:Osaka/week3#August 10 (Fri)|10]]<span style={{{s10|"color:{{{c10|inherit}}};"}}}></span> |
- | |<span style={{{ | + | |[[Team:Osaka/week3#August 11 (Sat)|11]]<span style={{{s11|"color:{{{c11|deepskyblue}}};"}}}></span> |
|- | |- | ||
|<span style>[[Team:Osaka/week3|week3]]</span> | |<span style>[[Team:Osaka/week3|week3]]</span> | ||
+ | |[[Team:Osaka/week3#August 12 (Sun)|12]]<span style={{{s12|"color:{{{c12|red}}};"}}}></span> | ||
+ | |<span style={{{s13|"color:{{{c13|red}}};"}}}>13</span> | ||
|<span style={{{s14|"color:{{{c14|red}}};"}}}>14</span> | |<span style={{{s14|"color:{{{c14|red}}};"}}}>14</span> | ||
|<span style={{{s15|"color:{{{c15|red}}};"}}}>15</span> | |<span style={{{s15|"color:{{{c15|red}}};"}}}>15</span> | ||
- | |[[Team:Osaka/week3#August 16 ( | + | |[[Team:Osaka/week3#August 16 (Thu)|16]]<span style={{{s16|"color:{{{c16|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week3#August 17 ( | + | |[[Team:Osaka/week3#August 17 (Fri)|17]]<span style={{{s17|"color:{{{c17|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week3#August 18 ( | + | |[[Team:Osaka/week3#August 18 (Sat)|18]]<span style={{{s18|"color:{{{c18|deepskyblue}}};"}}}></span> |
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|<span style>[[Team:Osaka/week4|week4]]</span> | |<span style>[[Team:Osaka/week4|week4]]</span> | ||
- | |[[Team:Osaka/week4#August | + | |[[Team:Osaka/week4#August 19 (Sun)|19]]<span style={{{s19|"color:{{{c19|red}}};"}}}></span> |
- | |[[Team:Osaka/week4#August | + | |[[Team:Osaka/week4#August 20 (Mon)|20]]<span style={{{s20|"color:{{{c20|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week4#August | + | |[[Team:Osaka/week4#August 21 (Tue)|21]]<span style={{{s21|"color:{{{c21|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week4#August | + | |[[Team:Osaka/week4#August 22 (Wed)|22]]<span style={{{s22|"color:{{{c22|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week4#August | + | |[[Team:Osaka/week4#August 23 (Thu)|23]]<span style={{{s23|"color:{{{c23|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week4#August | + | |[[Team:Osaka/week4#August 24 (Fri)|24]]<span style={{{s24|"color:{{{c24|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week4#August | + | |[[Team:Osaka/week4#August 25 (Sat)|25]]<span style={{{s25|"color:{{{c25|deepskyblue}}};"}}}></span> |
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|<span style>[[Team:Osaka/week5|week5]]</span> | |<span style>[[Team:Osaka/week5|week5]]</span> | ||
- | |[[Team:Osaka/week5#August | + | |[[Team:Osaka/week5#August 26 (Sun)|26]]<span style={{{s26|"color:{{{c26|red}}};"}}}></span> |
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- | |[[Team:Osaka/week5#August 31 ( | + | |[[Team:Osaka/week5#August 29 (Wed)|29]]<span style={{{s29|"color:{{{c29|inherit}}};"}}}></span> |
+ | |[[Team:Osaka/week5#August 30 (Thu)|30]]<span style={{{s30|"color:{{{c30|inherit}}};"}}}></span> | ||
+ | |[[Team:Osaka/week5#August 31 (Fri)|31]]<span style={{{s31|"color:{{{c31|inherit}}};"}}}></span> | ||
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- | |[[Team:Osaka/week5#September | + | |[[Team:Osaka/week5#September 1 (Sat)|1]]<span style={{{s1|"color:{{{c1|inherit}}};"}}}></span> |
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|<span style>[[Team:Osaka/week6|week6]]</span> | |<span style>[[Team:Osaka/week6|week6]]</span> | ||
- | |[[Team:Osaka/week6#September | + | |[[Team:Osaka/week6#September 2 (Sun)|2]]<span style={{{s2|"color:{{{c2|deepskyblue}}};"}}}></span> |
- | |[[Team:Osaka/week6#September | + | |[[Team:Osaka/week6#September 3 (Mon)|3]]<span style={{{s3|"color:{{{c3|red}}};"}}}></span> |
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- | |[[Team:Osaka/week6#September | + | |[[Team:Osaka/week6#September 7 (Fri)|7]]<span style={{{s7|"color:{{{c7|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week6#September | + | |[[Team:Osaka/week6#September 8 (Sat)|8]]<span style={{{s8|"color:{{{c8|inherit}}};"}}}></span> |
|- | |- | ||
|<span style>[[Team:Osaka/week7|week7]]</span> | |<span style>[[Team:Osaka/week7|week7]]</span> | ||
- | |[[Team:Osaka/week7#September | + | |[[Team:Osaka/week7#September 9 (Sun)|9]]<span style={{{s9|"color:{{{c9|deepskyblue}}};"}}}></span> |
- | |[[Team:Osaka/week7#September | + | |[[Team:Osaka/week7#September 10 (Mon)|10]]<span style={{{s10|"color:{{{c10|red}}};"}}}></span> |
- | |[[Team:Osaka/week7#September | + | |[[Team:Osaka/week7#September 11 (Tue)|11]]<span style={{{s11|"color:{{{c11|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week7#September | + | |[[Team:Osaka/week7#September 12 (Wed)|12]]<span style={{{s12|"color:{{{c12|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week7#September | + | |[[Team:Osaka/week7#September 13 (Thu)|13]]<span style={{{s13|"color:{{{c13|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week7#September | + | |[[Team:Osaka/week7#September 14 (Fri)|14]]<span style={{{s14|"color:{{{c14|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week7#September | + | |[[Team:Osaka/week7#September 15 (Sat)|15]]<span style={{{s15|"color:{{{c15|inherit}}};"}}}></span> |
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|<span style>[[Team:Osaka/week8|week8]]</span> | |<span style>[[Team:Osaka/week8|week8]]</span> | ||
- | |[[Team:Osaka/week8#September | + | |[[Team:Osaka/week8#September 16 (Sun)|16]]<span style={{{s16|"color:{{{c16|deepskyblue}}};"}}}></span> |
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- | |[[Team:Osaka/week8#September | + | |[[Team:Osaka/week8#September 20 (Thu)|20]]<span style={{{s20|"color:{{{c20|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week8#September | + | |[[Team:Osaka/week8#September 21 (Fri)|21]]<span style={{{s21|"color:{{{c21|inherit}}};"}}}></span> |
- | |[[Team:Osaka/week8#September | + | |[[Team:Osaka/week8#September 22 (Sat)|22]]<span style={{{s22|"color:{{{c22|inherit}}};"}}}></span> |
|- | |- | ||
|<span style>[[Team:Osaka/week9|week9]]</span> | |<span style>[[Team:Osaka/week9|week9]]</span> | ||
- | |[[Team:Osaka/week9#September | + | |[[Team:Osaka/week9#September 23 (Sun)|23]]<span style={{{s23|"color:{{{c23|deepskyblue}}};"}}}></span> |
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Latest revision as of 13:45, 25 September 2012
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 2012 Spring distribution plates, transformed and amplified the DNA for future use.DNA extraction & purification (miniprep) of transformed parts, & gel runs to confirm lengths. Ligations to put together some common combinations (eg promoter + RBS).
We transfered redioresistance parts from one vector(pSB1C3) to another vector(pSB1A3) and transformed plasmid DNA into Rosetta E.coli.
Week 2
We run the SDS-PAGE gel to check the expression of the gene products at the protein level. The result of DNA sequencing demonstrated that there is a mutation in PprA(Silent mutation).
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.
Completion of radioresistance parts and drafting of damage tolerance assay protocol.
Week 4
We were going to assemble a promoter evaluation device utilizing firefly and renilla luciferase, but did not make much progress due to low transformation efficiency(?).
Week 5
Preliminary test (damage tolerance, Mitomycin C).
We were going to assemble a promoter evaluation device utilizing firefly and renilla luciferase, but did not make much progress due to low transformation efficiency(?).
Week 6
Damage tolerance assay (Mitomycin C): transformed cells were exposed to DNA damaging agents 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 7
Damage tolerance assay (Mitomycin C)
Preliminary test (damage tolerance, Hydrogen peroxide)
Week 8
Damage tolerance assay (Hydrogen peroxide)
Week 9
Damage tolerance assay (Hydrogen peroxide)
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 | ||||||
week2 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | |||
week3 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | |||
week4 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | |||
week5 | 26 | 27 | 28 | 29 | 30 | 31 | ||||
September | |||||||||||||
Week | S | M | T | W | T | F | S | ||||||
week5 | 1 | ||||||||||||
week6 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | ||||||
week7 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | ||||||
week8 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | ||||||
week9 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | ||||||