Klapperich Lab:Notebook/Lab Meeting Notes/2009/10/27

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27 October 2009 Lab Meeting
‡ Announcements ‡ Flu R01:Integration † Sample Concentration (Lead: Jane, Team: Jaephil)
 * Attending:
 * Missing:
 * Presentation:Special Guest. Dr.Jonathan Simon. Cathie will present for 15 min. 2pm, PLEASE BE ON TIME.
 * No meeting on 11/3
 * 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.
 * Oakridge deadline is 1 Feb 2010.
 * PAPERS Drafted before MicroTAS Are we done with this? 1st draft by Thur
 * Posters for MicroTAS Can Jaephil take them all? Yes. Give me a tube
 * New design - address evaporation loss, Reagent delivery and storage solution. Consider marginating flows?
 * New design sent to make Rubber mold
 * MDCK Cells are not propagating. Try troubleshooting efforts. Sonali will do on Monday.
 * Cassidy needs to see plaque assay again - so when cells are up, she needs training.
 * Up to high 10^7 for positive control. Silver substrate no signal.
 * Jane working on the cell lysate control.
 * Main loss is at the outlet/sample collection: tangential filtration design in drawing stage.
 * Contacted EC Shaw about rubber stamp mold for new design for evaporation.
 * Set up COMSOL and StarCD, look for governing equations for simulation of evaporation.
 * Committee meeting setup

† SPE Column Optimization for RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan) † PCR - CMI (Lead: Qingqing) * new design has been tested It solved some problems, however bubbles were still created at the high-temperature section at slow flow rate. And they grow up to big bubbles and did not move along the channel, which affect the moving of reagent. - some new method will be tested this week to solve this problem. - 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 detected by bio-analyzer.
 * 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.
 * Load DNA in a straw of 5,50,100ul SPE, quick test of hypothesis: more SPE = more DNA, To be repeated with Alex and Mark 
 *  Look into modifying Alex's pneumatic setup for the PATH guys. Instead of building the straw array over here NOTE: Sean
 * PLanning net silica per channel experiments. with 700nm, 3x possible. Deliver around 11/5/09.
 * 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.
 * 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.
 * 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.
 * 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.
 * QQ will work on the initial integration steps of SPE + RT (reservoir)+ PCR.
 * PCR of C.Difficile DNA

need to get back from Cathie † HDA (Lead: Jaephil, Team:Sonali) '''‡C. diff Project''' (Cathie, Sonali, Satish Singh, Lisa J., His post doc ) ‡ Coulter Flu Fraunhofer Project (Lead: Sonali, Team: Sonali, Jessie, Cathie, CMI Folks, Qingqing) ‡ Agilent Automated Sample Preparation (Lead: Alex)
 * PCR2 Paper formatted for LOAC this week.
 * CMK: PCR 1 draft. Analytical Chem. MCK is running more simulations.
 * Start planning R01 for Submission on 2/5/10. MM, JD, CMK.
 * HDA chip fabrication training will be after new process settled (comeback from mTAS).
 * Two methods, Hot embossing and cutter plotting will be combined to reduce whole process time. New mold design sent.
 * Paper submitted 10/6.
 * Sonali to train Lisa on SPE.
 * QQ to run test PCR on chip with genomic DNA and Toxin B primers.
 * Meeting 9am Monday (every other week)
 * 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.
 * First Feedback on Draft Paper (Lysis of Yeast Cells) from Anirban. Work ongoing.
 * Nano-C: CNT coated PEEK Samples received. Manufactured first straws with integrated PEEK.

‡ COBRA (Lead: Jaephil, Team: Cathie, Jane for virus only, PHO folks)  ‡ Biointerfaces group (Lead: MinCheol, Team: Cathie, MCK, Wong and Meller folks) ‡ CIMIT- Sepsis (Lead:Cathie, Team:TBA) ‡ PATH Grant (Lead:Cathie, Team:Frank, Sean, Mark, Jake Trueb (ME), Suma)
 * Metal piece modification for the integration - Fix did not turned out good. Make new or try fix again?
 * paper 1, 1st draft by Thu(10.29): Evap with Sol Gel substrate. Not integrated. MSSA, E coli.
 * New experiments happening now.
 * Cathie will submit paper inquiry.
 * IRB approved.
 * Cathie submitted the companion BU IRB form for exemption. Revised, still still waiting.
 * Phone meeting with PATH this week. 10/13.
 * UGs purchasing parts for straw machine for 709.
 * UGs purchasing reagents for running extraction experiments and doing PCR.
 * Frank to start running extractions this week.
 * Frank contacted Biomatrica (RNAstable) last Thursday via phone and email; has not heard anything back yet.
 * Sean is currently working on designing a straw-holding piece for the new fixture in 709.
 * 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.


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