Klapperich Lab:Notebook/Lab Meeting Notes/2010/03/04: Difference between revisions

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† Integrated chip for flu(SPE+RT+PCR) (Lead: Qingqing) <br>
† Integrated chip for flu(SPE+RT+PCR) (Lead: Qingqing) <br>
* integrated chip works with ATCC flu virus <br>
* Real copy number of previous human samples. So QQ is working with the higher concentration samples. Range is 10^7-10^9 of copy number/ml.  <br>
* working on improving the efficiency
* REVISIT the % recovery number. <br>
* testing real patient sample <br>
* QQ will try: more enzyme, Tween 20, BSA amounts. <br>
** talk about PCR improvements BEFORE we use new patient samples. <br>
<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>
<br>
<br>
'''‡C. diff Project''' (Cathie, Sonali, Satish Singh, Lisa J., His post doc )<br>
'''‡C. diff Project''' (Cathie, Sonali, Satish Singh, Lisa J., His post doc )<br>
* See email notes. <br>
* See email notes. <br>
* See HDA notes above for styrofoam cup/chip work (MM)
<br>
<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
*
* Another positive patient sample was tested on chip
  * wrong size products(55bp).
  * no designed size product.
<br>
<br>
'''‡ 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) -- DONE 2/25 br>
<br>
<br>
'''‡ Agilent Automated Sample Preparation (Lead: Alex)'''<br>
'''‡ Agilent Automated Sample Preparation (Lead: Alex)'''<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>
* Phone call with PATH 3/22. <br>
* Phone call with PATH 3/22. <br>
* Frank: One zero-time 6-straw set run with 5-25% efficiency. Second set in progress (24 Feb).<br>
* Frank: One week data up 3/5/10..<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). Testing has been very slow-going due to an excess amount of other school work/tests. <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). Testing has been very slow-going due to an excess amount of other school work/tests. <br>
* Mark: as of 3/4/10 up to 10% recovery from 10 ng input sample with water elution.<br>
* Mark: as of 3/4/10 up to 10% recovery from 10 ng input sample with water elution.<br>
<br>
<br>
'''‡ IIH Senior Project.'''<br>
'''‡ IIH Senior Project.'''<br>
* Progress Report 1 completed
* Finished with 100 micrometer films. Registration experiments. "Optimized." <br>
* 44 micron films. COP. This week. <br>
* Elisa Test still on to do list. <br>
 


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Revision as of 13:59, 4 March 2010

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4 March 2010 Lab Meeting

Hussam Presentation.

‡ Announcements

‡ Flu R01:Integration

  • meetings every other M 1-3pm. 705.

† HDA (Lead: Jaephil, Team:Sonali)

  • Patient Samples - dilution experiments (MM/SH/JD)
  • Start planning R01 for Submission on 6/5/10. MM, JD, CMK.
  • HDA mix in dried form - Expecting it from BH.
  • warm start on the way - MTA (CMK)
  • HDA negative water reactions all have primer dimers/non-specific band at 70bp for c diff HDA (MM)
  • 2nd HDA design - "microSPE" + "Flu primer" + "HDA in a cup" + "Detection kit from Biohelix"


† Sample Concentration (Lead: Jane, Team: Jaephil)

  • Air resistance in the air channel is too large.
    • New branched "membrane" chip design #1 in lithography stage.
    • New "tube" chip design in drawing stage. Obtained more porous PTFE tubing samples
  • Samples expected from Fauchet group.


† SPE Column Optimization for DNA/RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan)
  • 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.
  • Less input sample (same concentration). Results to come. (JC)
  • Casein in human serum experiments ongoing. (HM)


† Integrated chip for flu(SPE+RT+PCR) (Lead: Qingqing)

  • Real copy number of previous human samples. So QQ is working with the higher concentration samples. Range is 10^7-10^9 of copy number/ml.
  • REVISIT the % recovery number.
  • QQ will try: more enzyme, Tween 20, BSA amounts.
  • PCR1 will combine with PCR2 if PCR2 comes back for revisions. (CMK)


‡C. diff Project (Cathie, Sonali, Satish Singh, Lisa J., His post doc )

  • See email notes.


† PCR of C.Difficile DNA (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.


‡ Agilent Automated Sample Preparation (Lead: Alex)

  • Paper on HotDog - with CMK/ASB


‡ COBRA (Lead: Jaephil, Team: Cathie, Jane for virus only, PHO folks)

  • Evap paper - Additional experiment for Fig 3. By 3/15.


‡ Biointerfaces group (Lead: MinCheol, Team: Cathie, MCK, Wong and Meller folks)
* Cathie will submit paper.
‡ CIMIT- Sepsis (Lead:Cathie, Team:TBA)

  • Sample collection ongoing.


‡ PATH Grant (Lead:Cathie, Team:Frank, Sean, Mark, Jake Trueb (ME))

  • Phone call with PATH 3/22.
  • Frank: One week data up 3/5/10..
  • 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.
  • Mark: as of 3/4/10 up to 10% recovery from 10 ng input sample with water elution.


‡ IIH Senior Project.

  • Finished with 100 micrometer films. Registration experiments. "Optimized."
  • 44 micron films. COP. This week.
  • Elisa Test still on to do list.



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