Klapperich Lab:Notebook/Lab Meeting Notes/2010/02/04: Difference between revisions
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=4 February 2010 Lab Meeting= | |||
Qingqing Prospectus Practice Presentation. | |||
'''‡ Announcements'''<br> | |||
* Oakridge deadline is Confusing. The website says something different from the email. Have one from QQ- Anyone else? <br> | |||
* Shichu Huang is here - WELCOME! <br> | |||
<br> | |||
'''‡ Flu R01:Integration''' <br> | |||
* meetings every other M 1-3pm. 705. <br> | |||
† HDA (Lead: Jaephil, Team:Sonali)<br> | |||
* Start planning R01 for Submission on '''6/5/10.''' MM, JD, CMK. <br> | |||
* HDA mix in dried form - Cathie found it<br> | |||
* LOD tests HDA in a cup - barely amplified at 3pg/mL<br> | |||
* HDA negative water reactions all have primer dimers/non-specific band at 70bp for c diff HDA (MM)<br> | |||
* 2nd HDA design - "microSPE" + "Flu primer" + "HDA in a cup" + "Detection kit from Biohelix"<br> | |||
† Sample Concentration (Lead: Jane, Team: Jaephil) <br> | |||
* New design transfer to COP | |||
* Air resistance in the air channel is too large, redesign channel to reduce air resistance: now testing with cutter plotter | |||
* Leakage through the air channel from the fluid channel: now moving air pots farther from fluid channel | |||
* Set up COMSOL and StarCD, look for governing equations for simulation of evaporation: registered for COMSOL course Feb 25 <br> | |||
† SPE Column Optimization for DNA/RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan) <br> | |||
* Sonali put out a new RNA protocol (correct SPE batter, homemade buffers, less ethanol washing, RNA Secure) before break. <br> | |||
* Protocol tested with 10ng, 1ng, 0.1ng Stratagene purified human RNA (MM) and 100 uL of 1:64 dilution ATCC MDCK sup Flu A/PR/8/34 (JC) <br> | |||
* Human Total RNA see % yields at 50% and fraction 1 + fraction 2 = 4-5ng RNA out of 10ng with all changes. With high vol *ethanol wash but other protocol improvements, see 40% yield at all other concentrations. <br> | |||
*For Flu virus see improved Ct value by 7 cycles in fraction 1 from multiple channels <br> | |||
*Also detecting 1.4 logs more of virus at 1:64 JC virus prep than before. <br> | |||
*Switching from lambda phage DNA to TaqMan RNase P detection [update] <br> | |||
* Hussam Runs chip with RNA (confirm procedure is correct) [update]<br> | |||
* Jessie will run chips with serial virus dilutions from 1:1 to 1:1,000,000 to re-do previous dilution experimnent with WHO SYBR green assay on chip.<br> | |||
* Jessie will test 2mm wide channels with 4uL SPE with Black Beauty for efficiency. <br> | |||
* Sonali will assay BIDMC virus sample with newest protocol with 0.7uM Silica and compare with Qiagen RNA extraction with CDC PCR assay <br> | |||
† integrated chip for flu(SPE+RT+PCR) (Lead: Qingqing) <br> | |||
* integrated chip works with ATCC flu virus <br> | |||
* working on improving the efficiency | |||
* testing real patient sample | |||
* PCR1 Paper back to MCK this week. <br> | |||
* CMK: PCR 1 draft. Analytical Chem. <br> | |||
<br> | |||
'''‡C. diff Project''' (Cathie, Sonali, Satish Singh, Lisa J., His post doc )<br> | |||
* See email notes. | |||
† PCR of C.Difficile DNA (Qingqing)<br> | |||
* ATCC C.dif DNA with Negative patient sample works on chip | |||
* Another positive patient sample was tested on chip | |||
-wrong size products(55bp). | |||
-no designed size product. | |||
<br> | |||
'''‡ Coulter Flu Fraunhofer Project (Lead: Sonali, Team: Sonali, Jessie, Cathie, CMI Folks, Qingqing)''' | |||
* New meeting time, T, 9:30 am every other week. <br> | |||
* Will be done by next Tuesday - PCR with 3 different kits of same serial dilution RNA sample (Invitrogen - SuperscriptIII Platinum, Ambion - AgPath-ID, Qiagen - OneStep RT-PCR Kit)<br> | |||
<br> | |||
'''‡ Agilent Automated Sample Preparation (Lead: Alex)'''<br> | |||
* Paper on HotDog in progress. <br> | |||
'''‡ COBRA (Lead: Jaephil, Team: Cathie, Jane for virus only, PHO folks)<br>''' | |||
* Evap paper - Additional experiment for Fig 3. <br> | |||
<br> | |||
'''‡ Biointerfaces group (Lead: MinCheol, Team: Cathie, MCK, Wong and Meller folks)'''<br> | |||
'''* Cathie will submit paper inquiry.<br>''' | |||
<br> | |||
'''‡ CIMIT- Sepsis (Lead:Cathie, Team:TBA)'''<br> | |||
* First samples collected. <br> | |||
<br> | |||
'''‡ PATH Grant (Lead:Cathie, Team:Frank, Sean, Mark, Jake Trueb (ME))''' <br> | |||
* Submitted Gantt Document to PATH 11/25. <br> | |||
* Frank: Repeating 1-week stabilized extractions today (4 Feb).<br> | |||
* Sean: Started making straws for the new experiments we talked about (DNA weights of 1ng, 10ng, and 100ng through 700nm at SPE 100 monolith at 0-day time point). Have contacted the physics department shop floor to check the progress of the Blackbird pieces I ordered on Monday. <br> | |||
* Mark: as of 4 Feb. has loaded 6 and 4 month trials with 10ng/straw. Results of the 1ng/straw 0-day trial inconclusive, redo possible. Sticking with 10ng/straw for remaining tests. Loaded 2 month trial on Tuesday. Will load shorter time periods next week (i.e. 3-day, 1 week). Straw fabrication ongoing.<br> | |||
<br> | |||
'''‡ IIH Senior Project.'''<br> | |||
* ELISA kits have been delivered | |||
* Protocol written for using cutter plotter. Will post to share drive | |||
* Made "test" chips from 100 micron COP but cuts are sloppy | |||
** Will change settings on cutter to clean up cuts | |||
*** First thought is to slow down speed | |||
* Started acquiring images of the 100 micron "test" chips | |||
Revision as of 12:28, 4 February 2010
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4 February 2010 Lab MeetingQingqing Prospectus Practice Presentation. ‡ Announcements
† HDA (Lead: Jaephil, Team:Sonali)
† Sample Concentration (Lead: Jane, Team: Jaephil)
† SPE Column Optimization for DNA/RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan)
† integrated chip for flu(SPE+RT+PCR) (Lead: Qingqing)
† PCR of C.Difficile DNA (Qingqing)
-wrong size products(55bp). -no designed size product.
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