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| =August 2014=
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| ==06.08.2014==
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| * revive bacteria from glycerol stock (see [[Christian Niederauer/Notebook/RacingBacteria/Protocols#Reviving_Bacteria_from_Glycerol_Stock | Glycerol Protocol]])
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| ==08.08.2014==
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| [[Christian_Niederauer/Notebook/RacingBacteria/Protocols/Microfluidics/PDMS | PDMS Duplicate Protocol]]<br>
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| [[Christian_Niederauer/Notebook/RacingBacteria/Protocols/Microfluidics/Plasma_Cleaning | Plasma Cleaning Protocol]]
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| Problems encountered with creating PDMS stamps:<br>
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| * oven is not entirely flat
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| * the "coring tool" is a cut glass pipette which continues to break and creates jagged holes
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| * device is prone to leakage if the holes are placed near the edge of the stamp
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| * devices are very thin and making it bigger by sticking additional pdms layer is tedious
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| -> build [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Stock#Leveling_Petri_Dish leveling device], order coring tool, try cutting stamp so that the device is not near an edge, make deep araldite molds (thick stamp is hard to achieve with silicon wafer, as ideally the surface tension of the PDMS should keep the fluid on the wafer. If you add to much fluid, it will break surface tension and spread over the whole petri dish. Silicon wafer is too delicate to experiment with some ring-shaped devices to keep PDMS on the wafer.)
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| ==11.08.2014 Checking for Motility==
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| * make suspension of one colony in eppi with 1mL PBS by picking it up with a micropipette tip and suspend tip into eppi
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| * cut window in double sided tape and put onto slide
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| * add a drop of bacteria suspension (3µL) and put coverslide onto slide
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| Result: bacteria from the big colony are motile, whereas bacteria from the small colony were not<br>
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| -> reinoculate bacteria from one or more big colonies of the master plate into liquid LB medium over night<br>
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| As a comparison: 1µm latex beads on same coverslip-slide arrangement in 1:1000 dilution<br>
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| Data: E:\12-08-rp437\ and E:\12-08-beads\
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|
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| ==12.08.2014 Reinoculate motile colony==
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| * put 5ml LB broth into falcon tube
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| * pick up one big colony with pipette tip and discard the tip in falcon tube
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| * incubate ON
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| * dip sterile inoculate ring into liquid colony and [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Protocols#Streaking_Bacteria_onto_Agar_Plate streak] on agar plate the next day
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| * incubate plate over night => this is the new [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Stock#Master_Plate master plate]
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|
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| ==25.08.2014 Araldite Replica from PDMS & COMSOL==
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| '''COMSOL Multiphysics'''<br>
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| Downloading COMSOL Multiphysics 4.3b 64-bit at the fedora linux machine in the dry lab.
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| '''Araldite Replica'''<br>
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| According to the [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Protocols#How_to_create_a_Araldite_Mold_of_PDMS_Stamp_for_PDMS_Stamp Araldite Replica Protocol], 9g (5g of part A-resin and 4g of part B-hardener) are prepared, degassed and should have been poured after ~30 minutes. The break during the introduction course about the new microscope was after 1 hour. By then, the epoxy already was beginning to solidify. In addition to that, it seemed that the amount of epoxy mixed should be increased for easier pouring and handling (solidifies more slowly, more tolerance in terms of weight ratio).<br>
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| Manufacturing of replicas is postponed to 26.08.2014.
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|
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| ==26.08.2014 ACTUAL Araldite Replica from PDMS & COMSOL==
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| '''Araldite Replica'''<br>
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| Using [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Protocols#How_to_create_a_Araldite_Mold_of_PDMS_Stamp_for_PDMS_Stamp Araldite Protocol]: Mixing 10g part A and 8g part B of Araldite and pouring onto the [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Stock#H-Pattern_PDMS_stamps H-Pattern PDMS stamp] from 20.08.<br>
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| The replica will be called [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Stock#Araldite_Molds Araldite Replica I].<br>
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| Another Araldite replica is made with a pre-cut [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Stock#H-Pattern_PDMS_stamps PDMS stamp made on 22.08.].<br>
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| An extra layer of PDMS is added below the stamp to achieve a deeper mold in the end. It is called [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Stock#Araldite_Molds Araldite Replica II].<br>
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| '''Comsol Multiphysics'''<br>
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| Always change into usr folder with ''cd ../''<br>
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| Mount .iso with<br>
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| ''sudo mount -r -t iso9660 -o loop COMSOL43b_dvd.iso /media''<br>
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| ''cd media/''<br>
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| ''sudo sh setup''<br>
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| Start License Server manually:<br>
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| ''cd local/comsol43b/license/glnxa64/''<br>
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| ''./lmgrd -c ../license.dat -l ../comsol44.log''
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| Run Comsol in ''local/comsol43b/bin/glnxa64/'' -> comsol<br>
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| Gives error:<br>
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| <gallery>Image:RaBa_comsolerror.png</gallery>
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|
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| ==27.08.2014 PDMS from Araldite & Liquid Colony==
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| * with [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Protocols#Preparation_of_PDMS_membrane PDMS-Protocol]: create PDMS from [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Stock#Araldite_Molds Araldite Replica II] and compare with [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Stock#H-Pattern_PDMS_stamps original entire-pattern stamp from 20.08.].
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| * [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Protocols#Inoculating_Bacteria_into_Liquid_Colony Liquid Colony is created] under hood with some left over sterile LB medium by discarding pipette tip into that tube after picking up a few colonys from the [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Stock#Master_Plate Master Plate].
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| * coring tools are too big (orange: 2.5mm, green: 3mm), have to wait for the right ones
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| Plan: punch holes into the [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Stock#H-Pattern_PDMS_stamps PDMS from Araldite II], plasma clean with coverslip and attach tubings, then insert [http://en.wikipedia.org/wiki/Safranin safranin]. If it works properly, insert [http://openwetware.org/wiki/Christian_Niederauer/Notebook/RacingBacteria/Stock#Liquid_Colony bacteria suspension]
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|
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| ==28.08.2014==
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| ==29.08.2014==
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|
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| =September 2014=
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| ==01.09.2014==
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| ==02.09.2014==
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| ==03.09.2014==
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| ==04.09.2014==
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| ==05.09.2014==
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| ==08.09.2014==
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| ==09.09.2014==
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| ==10.09.2014==
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| ==11.09.2014==
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| ==12.09.2014==
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| ==15.09.2014==
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| ==16.09.2014==
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| ==17.09.2014==
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| ==18.09.2014==
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| ==19.09.2014==
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| ==22.09.2014==
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| ==23.09.2014==
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| ==24.09.2014==
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| ==25.09.2014==
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| ==26.09.2014==
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| ==29.09.2014==
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| ==30.09.2014==
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|
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| =October 2014=
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| ==01.10.2014==
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| ==02.10.2014==
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| ==03.10.2014==
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| ==06.10.2014==
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| ==07.10.2014==
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| ==08.10.2014==
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| ==09.10.2014==
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| ==10.10.2014==
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