Klapperich Lab:Notebook/Lab Meeting Notes/2009/10/27: Difference between revisions
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==27 October 2009 Lab Meeting== | |||
* Attending: <br> | |||
* Missing:<br> | |||
* Presentation:Special Guest. Dr.Jonathan Simon. Cathie will present for 15 min. '''2pm, PLEASE BE ON TIME.''' <br> | |||
<br> | |||
'''‡ Announcements'''<br> | |||
* No meeting on 11/3 <br> | |||
* Dr. Shichu Huang from Auburn talking on 11/10. ''Need folks to have lunch with her at 12pm and also for lab tours and chatting at 4-5pm.''<br> | |||
* Oakridge deadline is 1 Feb 2010. <br> | |||
* '''PAPERS Drafted before MicroTAS''' Are we done with this? 1st draft by Thur <br> | |||
* '''Posters for MicroTAS''' Can Jaephil take them all? Yes. Give me a tube <br> | |||
<br> | |||
'''‡ Flu R01:Integration''' <br> | |||
* New design - address evaporation loss, Reagent delivery and storage solution. Consider marginating flows? <br> | |||
* New design sent to make Rubber mold <br> | |||
<br> | |||
† Sample Concentration (Lead: Jane, Team: Jaephil) <br> | |||
* MDCK Cells are not propagating. Try troubleshooting efforts. Sonali will do on Monday. <br> | |||
* Cassidy needs to see plaque assay again - so when cells are up, she needs training. <br> | |||
* Up to high 10^7 for positive control. Silver substrate no signal. <br> | |||
* Jane working on the cell lysate control. <br> | |||
* Main loss is at the outlet/sample collection: tangential filtration design in drawing stage. <br> | |||
* Contacted EC Shaw about rubber stamp mold for new design for evaporation. <br> | |||
* Set up COMSOL and StarCD, look for governing equations for simulation of evaporation. <br> | |||
* Committee meeting setup <br> | |||
<br> | |||
† SPE Column Optimization for RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan) <br> | |||
*Video with two color dyes and [red(primer) then blue, green, water+tween] | |||
*repeat experiment reported on 10/27 with 700nm Silica 3X. | |||
* controls for these: empties, non-silica monolith and full silica monolith, std. recipe. <br> | |||
* Load DNA in a straw of 5,50,100ul SPE, quick test of hypothesis: more SPE = more DNA, <i>To be repeated with Alex and Mark </i> <br> | |||
*'' Look into modifying Alex's pneumatic setup for the PATH guys. Instead of building the straw array over here NOTE: Sean'' <br> | |||
*PLanning net silica per channel experiments. with 700nm, 3x possible. Deliver around 11/5/09.<br> | |||
<br> | |||
* New virus prep (JC, 6/11/09), getting Ct's of 27 for 1:16 dilution and 28 for 1:64 dilution. Use more diluted sample for future optimization experiments? Channels were 700nm silica/1X. pfu/ml is 10^6. <br> | |||
* Tried 2 more chips with 3X 0.15um Silica. Chips are breaking b/c of no crosslinking. SPE was coming out even at 2ml/hr flow rate.<br> | |||
* Running no silica and no SPE chips with virus. (JC/RNA) - No Silica channels grab comparable amounts of RNA with the channels with silica, lower with no SPE.<br> | |||
* PCR is running on the samples from the new channel design. Will compare results with Hussam after the meeting and report back if significantly different.<br> | |||
<br> | |||
† PCR - CMI (Lead: Qingqing) <br> | |||
* QQ will work on the initial integration steps of SPE + RT (reservoir)+ PCR. <br> | |||
* new design has been tested <br> | |||
It solved some problems, however bubbles were still created at the <br> high-temperature section at slow flow rate. And they grow up to big <br> bubbles and did not move along the channel, which affect the moving of <br> reagent. | |||
- some new method will be tested this week to solve this problem. | |||
* PCR of C.Difficile DNA | |||
- primer for toxin A. | |||
a.300nM did not amplify on real-time machine.nothing was detected by bio-analyzer | |||
b.700nM had a ct value of 27.A small peak (0.63ng/ul) was detected on bio-analyzer | |||
- DNA template dilution experiments has been done. | |||
- Primer for toxin B did not work on real-time machine. No result was<br> detected by bio-analyzer. | |||
* PCR2 Paper formatted for LOAC this week. <br> | |||
need to get back from Cathie | |||
* CMK: PCR 1 draft. Analytical Chem. MCK is running more simulations. <br> | |||
<br> | |||
† HDA (Lead: Jaephil, Team:Sonali)<br> | |||
* Start planning R01 for Submission on 2/5/10. MM, JD, CMK. <br> | |||
* HDA chip fabrication training will be after new process settled (comeback from mTAS). <br> | |||
* Two methods, Hot embossing and cutter plotting will be combined to reduce whole process time. New mold design sent. <br> | |||
* Paper submitted 10/6. <br> | |||
<br> | |||
'''‡C. diff Project''' (Cathie, Sonali, Satish Singh, Lisa J., His post doc )<br> | |||
* Sonali to train Lisa on SPE. <br> | |||
* QQ to run test PCR on chip with genomic DNA and Toxin B primers. <br> | |||
<br> | |||
'''‡ Coulter Flu Fraunhofer Project (Lead: Sonali, Team: Sonali, Jessie, Cathie, CMI Folks, Qingqing)''' | |||
* Meeting 9am Monday (every other week) <br> | |||
<br> | |||
'''‡ Agilent Automated Sample Preparation (Lead: Alex)'''<br> | |||
* Machine is now "ready to go". Bacillus subtilis gDNA will be tested this Wednesday (10/28). Bacillus subtilis cells will follow next. Then Hot Dog samples. Quantification through Nano-Drop and RT-PCR. <br> | |||
* First Feedback on Draft Paper (Lysis of Yeast Cells) from Anirban. Work ongoing.<br> | |||
* Nano-C: CNT coated PEEK Samples received. Manufactured first straws with integrated PEEK. <br> | |||
'''‡ COBRA (Lead: Jaephil, Team: Cathie, Jane for virus only, PHO folks)<br>''' | |||
* Metal piece modification for the integration - Fix did not turned out good. Make new or try fix again?<br> | |||
* paper 1, 1st draft by Thu(10.29): Evap with Sol Gel substrate. Not integrated. MSSA, E coli. <br> | |||
<br> | |||
'''‡ Biointerfaces group (Lead: MinCheol, Team: Cathie, MCK, Wong and Meller folks)'''<br> | |||
* New experiments happening now. <br> | |||
* Cathie will submit paper inquiry.<br> | |||
<br> | |||
'''‡ CIMIT- Sepsis (Lead:Cathie, Team:TBA)'''<br> | |||
* IRB approved. <br> | |||
* Cathie submitted the companion BU IRB form for exemption. Revised, still still waiting. <br> | |||
<br> | |||
'''‡ PATH Grant (Lead:Cathie, Team:Frank, Sean, Mark, Jake Trueb (ME), Suma)''' <br> | |||
* Phone meeting with PATH this week. 10/13. <br> | |||
* UGs purchasing parts for straw machine for 709. <br> | |||
* UGs purchasing reagents for running extraction experiments and doing PCR. <br> | |||
* Frank to start running extractions this week. <br> | |||
* Frank contacted Biomatrica (RNAstable) last Thursday via phone and email; has not heard anything back yet. <br> | |||
* Sean is currently working on designing a straw-holding piece for the new fixture in 709. <br> | |||
* Sean met with Alex for an integration of straws on black machine. They sketched a design. Sean will make a professional drawing and create a required parts list. Alex will supervise the design. Before handing in the job to the shop floor, the design will be presented to Cathie. <br> | |||
Revision as of 12:40, 27 October 2009
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27 October 2009 Lab Meeting
† SPE Column Optimization for RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan)
* new design has been tested
- primer for toxin A. a.300nM did not amplify on real-time machine.nothing was detected by bio-analyzer b.700nM had a ct value of 27.A small peak (0.63ng/ul) was detected on bio-analyzer - DNA template dilution experiments has been done. - Primer for toxin B did not work on real-time machine. No result was
need to get back from Cathie
‡ COBRA (Lead: Jaephil, Team: Cathie, Jane for virus only, PHO folks)
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