Biomod/2011/TeamJapan/Tokyo/Notebook/Lab.notebook

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<div id="navigation"> <div id="menu" style="position:static"> <ul> <li><a class="aMain" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo">Home</a></li> <li><a class="aTeam" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Team/Students">Team</a></li> <li><a class="aProject" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Project</a> <!-- <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project">Overview</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/introduction">Introduction</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Model">Model</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Devices">Devices</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Modes">Modes</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Results</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> </ul> --> <li><font color="#ffffff">Results</font> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results">Experiments</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Design</a></li> </ul></li> <!-- <li><a class="Simulation" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Simulations">Simulations</a></li> <li><a class="DNA design" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices">DNA Designs</a></li> --> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Achievements">Achievements</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Future_works">Future works</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Protocols">Protocols</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Notebook/Lab.notebook">Notes</a></li> <li><a class="aNotebook" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sponsors/">Sponsors</a></li> <li><a class="aSitemap" href="http://openwetware.org/wiki/Biomod/2011/TeamJapan/Tokyo/Sitemap">Sitemap</a></li>

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Lab.notebook

25.May ・Had a brainstorming.
・Excluded the ideas that clearly unfeasible and categorized rest feasible idea.
13.June ・Narrowed each category of ideas down to a shortlist of projects. Finally, we selected 4 projects.
・By the next meeting, we researched and formed each project
17.June ・Dr.Takinoue gave us lecture of molecular robotics.
21.June ・Adopted controlling micro object by using DNA as our project.
・Discussed the methods of how to control micro object by DNA, and narrowed them down 5 ideas: using light, heat, electric field, magnetic field and tubelin.
・By the next meeting, we researched each of the ideas.
28.June ・Presented the ideas we had researched in detail to each other.
・Considering the presentations, we decided to develop light controlling device. We thought we can use ultraviolet rays, photoligation. or azobenzene as the controlling device.
・As a former step of the controlling, we discussed how to move micro object by DNAs.
29.June ・Came up the idea of moving the object like DNA spider.
・Discussed how attach many DNA to micro object and slide glass as a track of this molecular robot.
5.July ・Discussed the detail of experiments in this summer.
12.July ・Discussed the name of our project.
22.July ・The start of our experiments.
・Designed DNA sequence of DNA cilia.
・Fixed fluoresceinated oligonucleotide DNA probes to slide glass in a circle.
24.July ・Discussed the name of our project.
・Produced documents for sponsors.
25.July ・Fixed fluoresceinated oligonucleotide DNA probes to 40um glass beads.
・Processed polyascetal-resin and made a mold of 100um　width of micro-channel.
26.July ・Made a PDMS-mold of micro-channel by using polyascetal-mold.
・Discussed the sponsors.
27.July ・Improved the making of polyascetal-mold.
・Checked the detection limit of the concentration of DNA solution by urea-PAGE stained with ethidium bromide.
1.August ・Made the brace of PDMS-mold and slide glass.
・Checked the detection limit of the concentration of DNA solution by urea-PAGE stained with SYBR gold.
2.August ・Wrote protocols in English.
・Designed DNA sequence of DNA tracks.
3.August ・Fixed fluoresceinated oligonucleotide DNA probes to 2um polystyrene beads, but the beads was melted.
・Drained ink on slide glass into PDMS-mold to check the micro-channel.
・Improved the making of the brace of PDMS-mold and slide glass.
5.August ・Fixed fluoresceinated oligonucleotide DNA probes to 2um polystyrene beads, but the beads were clumped.
・Tested the activity of deoxyribozyme we designed as DNA cilia, but it didn’t work.
・Checked there were a leak or not when drained silane into PDMS-mold. Because of leaks of silane, we increase the thickness of PDMS-mold to fix the mold and slide glass tightly.
8.August ・Fixed deoxyribozyme DNA probes to 2um polystyrene beads, but the beads was a little clumped.
・Adjusted pH of deoxyribozyme solution buffer and retested the activity of deoxyribozyme, but it worked without divalent metal ions.
・Developed 50um width of micro-channel.
9.August ・Fixed deoxyribozyme DNA proves to 40um glass beads.
・Tested the activity of deoxyribozyme on 40um glass beads by urea-PAGE, but it didn’t worked.
・Tried to find the best condition of draining DNA solution into PDMS-mold.
10.August ・Fixed deoxyribozyme DNA proves to 1um polystyrene beads. Tried to find the condition of not being clumping.
・Drained fluoresceinated DNA solution into PDMS-mold fixed on silanized and DSS treated slide glass, but we couldn’t observe fluoresceinated DNA on the glass.
15.August ・Tested the activity of deoxyribozyme on 1um polystyrene beads by urea-PAGE, but the positive control didn’t work.
・Tried to find the best condition of fixing DNA to slide glass.
18.August ・Fixed deoxyribozyme DNA proves to 1um polystyrene beads and 70 um glass beads.
・Tested which buffer deoxyribozyme works in. Decided to use SSC buffer.
・Tried to find the best condition of fixing DNA to slide glass.
19.August ・Tested the activity of deoxyribozyme on 1um polystyrene beads by urea-PAGE, but it didn’t worked.
・Tried to find the best condition of fixing DNA to slide glass.
21.August ・Prepared our presentation on 26 AUG, BIOMOD TeamJapan Midterm Meeting.
22.August ・Prepared our presentation on 26 AUG, BIOMOD TeamJapan Midterm Meeting.
23.August ・Prepared our presentation on 26 AUG, BIOMOD TeamJapan Midterm Meeting.
・Tested the activity of deoxyribozyme on 1um polystyrene beads by urea-PAGE, but it didn’t worked.
24.August ・Prepared our presentation on 26 AUG, BIOMOD TeamJapan Midterm Meeting.
・Tested the activity of deoxyribozyme on 1um polystyrene beads by urea-PAGE. It worked a little.
25.August ・Prepared our presentation on 26 AUG, BIOMOD TeamJapan Midterm Meeting.
26.August ・BIOMOD TeamJapan Midterm meeting
29.August ・Discussed the plan by Jamboree based on indications from TeamJapan Midterm meeting.
30.August ・Tried to find the best condition of fixing deoxyribozyme DNA proves to 1um polystyrene beads.
・Tried to find the best condition of fixing DNA to slide glass.
31.August ・Tested the activity of deoxyribozyme on 1um polystyrene beads we made yesterday by urea-PAGE. It worked clearly.
・Made various shape of micro-channel.
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