Klapperich Lab:Notebook/Lab Meeting Notes/2010/02/25: Difference between revisions
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† HDA (Lead: Jaephil, Team:Sonali)<br> | † HDA (Lead: Jaephil, Team:Sonali)<br> | ||
* Patient Samples - dilution experiments (MM/SH/JD) <br> | |||
* Start planning R01 for Submission on '''6/5/10.''' MM, JD, CMK. <br> | * Start planning R01 for Submission on '''6/5/10.''' MM, JD, CMK. <br> | ||
* HDA mix in dried form - Expecting it from BH. <br> | * HDA mix in dried form - Expecting it from BH. <br> | ||
* | * warm start on the way <br> | ||
* HDA negative water reactions all have primer dimers/non-specific band at 70bp for c diff HDA (MM)<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> | * 2nd HDA design - "microSPE" + "Flu primer" + "HDA in a cup" + "Detection kit from Biohelix"<br> | ||
<br> | |||
† Sample Concentration (Lead: Jane, Team: Jaephil) <br> | † Sample Concentration (Lead: Jane, Team: Jaephil) <br> | ||
* Air resistance in the air channel is too large. <br> | |||
* Air resistance in the air channel is too large | ** New branched "membrane" chip design #1 in lithography stage. <br> | ||
** | ** New "tube" chip design in drawing stage. Obtained more porous PTFE tubing samples <br> | ||
* | * Samples expected from Fauchet group. <br> | ||
<br> | |||
† SPE Column Optimization for DNA/RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan) <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> | * Sonali put out a new RNA protocol (correct SPE batter, homemade buffers, less ethanol washing, RNA Secure) before break. <br> | ||
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* Sonali completed 5 total patients (BUMC and BIDMC) extracted and RT-PCR'd successfully using new RNA protocol and small SPE channel chips. All samples selected based on Qiagen kit extractions having low Cts at 15-20 cycles <br> | * Sonali completed 5 total patients (BUMC and BIDMC) extracted and RT-PCR'd successfully using new RNA protocol and small SPE channel chips. All samples selected based on Qiagen kit extractions having low Cts at 15-20 cycles <br> | ||
* Sonali gave Qingqing 3 of these patient RNAs extracted on chip SPE for testing on-chip RT-PCR with SuperScript vs Qiagen one-Step kit. <br> | * Sonali gave Qingqing 3 of these patient RNAs extracted on chip SPE for testing on-chip RT-PCR with SuperScript vs Qiagen one-Step kit. <br> | ||
<br> | |||
† | † Integrated chip for flu(SPE+RT+PCR) (Lead: Qingqing) <br> | ||
* integrated chip works with ATCC flu virus <br> | * integrated chip works with ATCC flu virus <br> | ||
* working on improving the efficiency | * working on improving the efficiency | ||
* testing real patient sample | * testing real patient sample <br> | ||
** talk about PCR improvements BEFORE we use new patient samples. <br> | |||
* PCR1 will combine with PCR2 if PCR2 comes back for revisions. (CMK)<br> | * PCR1 will combine with PCR2 if PCR2 comes back for revisions. (CMK)<br> | ||
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* See email notes. <br> | * See email notes. <br> | ||
* See HDA notes above for styrofoam cup/chip work (MM) | * See HDA notes above for styrofoam cup/chip work (MM) | ||
<br> | |||
† PCR of C.Difficile DNA (Qingqing)<br> | † PCR of C.Difficile DNA (Qingqing)<br> | ||
* ATCC C.dif DNA with Negative patient sample works on chip | * ATCC C.dif DNA with Negative patient sample works on chip | ||
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'''‡ Coulter Flu Fraunhofer Project (Lead: Sonali, Team: Sonali, Jessie, Cathie, CMI Folks, Qingqing)''' | '''‡ Coulter Flu Fraunhofer Project (Lead: Sonali, Team: Sonali, Jessie, Cathie, CMI Folks, Qingqing)''' | ||
* New meeting time, T, 9:30 am every other week. MEETINGS CANCELLED THIS WEEK. <br> | * New meeting time, T, 9:30 am every other week. MEETINGS CANCELLED THIS 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) | * 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) -- DONE 2/25 br> | ||
<br> | <br> | ||
'''‡ Agilent Automated Sample Preparation (Lead: Alex)'''<br> | '''‡ Agilent Automated Sample Preparation (Lead: Alex)'''<br> | ||
* Paper on HotDog | * Paper on HotDog - with CMK/ASB <br> | ||
<br> | |||
'''‡ COBRA (Lead: Jaephil, Team: Cathie, Jane for virus only, PHO folks)<br>''' | '''‡ COBRA (Lead: Jaephil, Team: Cathie, Jane for virus only, PHO folks)<br>''' | ||
* Evap paper - Additional experiment for Fig 3. <br> | * Evap paper - Additional experiment for Fig 3. By 3/15. <br> | ||
<br> | <br> | ||
'''‡ Biointerfaces group (Lead: MinCheol, Team: Cathie, MCK, Wong and Meller folks)'''<br> | '''‡ Biointerfaces group (Lead: MinCheol, Team: Cathie, MCK, Wong and Meller folks)'''<br> | ||
'''* Cathie will submit paper | '''* Cathie will submit paper.<br>''' | ||
<br> | <br> | ||
'''‡ CIMIT- Sepsis (Lead:Cathie, Team:TBA)'''<br> | '''‡ CIMIT- Sepsis (Lead:Cathie, Team:TBA)'''<br> | ||
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'''‡ PATH Grant (Lead:Cathie, Team:Frank, Sean, Mark, Jake Trueb (ME))''' <br> | '''‡ PATH Grant (Lead:Cathie, Team:Frank, Sean, Mark, Jake Trueb (ME))''' <br> | ||
* Submitted Gantt Document to PATH 11/25. <br> | * Submitted Gantt Document to PATH 11/25. <br> | ||
* Frank: | * Frank: One zero-time 6-straw set run with 5-25% efficiency. Second set in progress (24 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). | * 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). Testing has been very slow-going due to an excess amount of other school work/tests. <br> | ||
* Mark: as of | * Mark: as of 25 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 2/2. 1-week trial eluted Monday 2/15 again inconclusive - most likely there was a problem with the straws, a bad lot (same lot as the 1ng/straw test). To redo 1-week trial in the future with new lot of straws. Also troubleshooting with smaller wash volumes (down to 50uL) with results on 2/25. Straw fabrication ongoing.<br> | ||
<br> | <br> | ||
'''‡ IIH Senior Project.'''<br> | '''‡ IIH Senior Project.'''<br> | ||
* Progress Report 1 completed | * Progress Report 1 completed | ||
Revision as of 13:15, 25 February 2010
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25 February 2010 Lab MeetingAlex Presentation. ‡ Announcements ‡ Flu R01:Integration
† HDA (Lead: Jaephil, Team:Sonali)
* wrong size products(55bp). * no designed size product.
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