Klapperich Lab:Notebook/Lab Meeting Notes/2009/09/22: Difference between revisions

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† SPE Column Optimization for RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan) <br>
† SPE Column Optimization for RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan) <br>
* RNA extraction troubleshooting. Do deinhibition of monolith components. Test those with the Ambion RNAse kit. <br>
* RNA extraction troubleshooting. Do deinhibition of monolith components. Test those with the Ambion RNAse kit. Jessie this week. <br>
*Team met last week to plan experiments. <br>
*Team met last week to plan experiments. <br>
*New Designs of bigger channels are made, 35 to 70 μl total volume (MinCheol was Consulted)
*New Designs of bigger channels are made, 35 to 70 μl total volume (MinCheol was Consulted). Downside here is the time to extract. Hussam to make spreadsheet of channel type vs. times for lysis, extraction, and elution. <br>
*Silica free SPE , and SPE free channel experiment were ran , to be PCR'ed  
*Silica free SPE, and SPE free channel experiment were run, to be PCR'ed.Lambda phage assay.<br>
* Jessie worked with plasmid. Good std. curve. Not good predictor of the real sample amount. J will redo math with Sonali and Hussam to check.<br>
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<br>
† PCR - CMI  (Lead: Qingqing) <br>
† PCR - CMI  (Lead: Qingqing) <br>
* QQ will work on the initial integration steps of SPE + RT (resevoir)+ PCR. <br>
* QQ will work on the initial integration steps of SPE + RT (resevoir)+ PCR. <br>
* CMK: PCR 2 paper draft. <br>
* QQ: Paper back to QQ 9/22. <br>
* CMK: PCR 1 draft. Analytical Chem. <br>
* CMK: PCR 1 draft. Analytical Chem. MCK is running more simulations. <br>
* With new syring and tubing, on-chip PCR for the patient sample does not have detectable amplified product. however, the postitive control on the thermal cycle works good. <br>
* made 40 cycle chip. <br>
* New primers? <br>
* Success with 30 cycles, Qiagen Kit. Look at annealing temperature as per Alexis. <br>
* Double PCR on chip. <br>
* Integration chip for Qiagen RT-PCR one tube reaction. Control sample first, patient sample second. <br>
<br>
<br>
† HDA (Lead: Jaephil, Team:Sonali)<br>
† HDA (Lead: Jaephil, Team:Sonali)<br>

Revision as of 12:27, 22 September 2009

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22 September 2009 Lab Meeting

  • Attending:
  • Missing: Sonali, MinCheol
  • Presentation:


‡ Announcements

  • PAPERS Drafted before MicroTAS
  • Posters for MicroTAS Due to CMK by 10/15

‡ Flu R01:Integration
* Need to update IBC to include rDNA work.

  • New design - address evaporation loss, Reagent delivery and storage solution


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

  • Up to 10^8 for positive control.
  • Jane working on the cell lysate control.
  • Main loss is at the outlet/sample collection.
  • Alexa Fluor-488 succinimidyl ester (Molecular Probes) stains the flu virus fluorescent.
  • The current problem is not how to visualize virus right now, because the design is clearly not optimized for collecting all the samples at the outlet. The major loss is from sample handling instead of from non specific binding to the material.
  • Jane is thinking outside the box. New chip design. Bacteria design is not working.


† SPE Column Optimization for RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan)

  • RNA extraction troubleshooting. Do deinhibition of monolith components. Test those with the Ambion RNAse kit. Jessie this week.
  • Team met last week to plan experiments.
  • New Designs of bigger channels are made, 35 to 70 μl total volume (MinCheol was Consulted). Downside here is the time to extract. Hussam to make spreadsheet of channel type vs. times for lysis, extraction, and elution.
  • Silica free SPE, and SPE free channel experiment were run, to be PCR'ed.Lambda phage assay.
  • Jessie worked with plasmid. Good std. curve. Not good predictor of the real sample amount. J will redo math with Sonali and Hussam to check.


† PCR - CMI (Lead: Qingqing)

  • QQ will work on the initial integration steps of SPE + RT (resevoir)+ PCR.
  • QQ: Paper back to QQ 9/22.
  • CMK: PCR 1 draft. Analytical Chem. MCK is running more simulations.
  • made 40 cycle chip.
  • Success with 30 cycles, Qiagen Kit. Look at annealing temperature as per Alexis.
  • Integration chip for Qiagen RT-PCR one tube reaction. Control sample first, patient sample second.


† HDA (Lead: Jaephil, Team:Sonali)

  • Start planning R01 for Submission on 2/5/10. MM, JD, CMK.
  • Sonali works on a paper draft.
  • Figures discussion.


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

  • Meeting 12:30-1:30pm every other Wed. in my office.
  • This week meeting at 10:15 AM my office Wednesday.


‡ Coulter Flu Fraunhofer Project (Lead: Sonali, Team: Sonali, Jessie, Cathie, CMI Folks, Qingqing)

  • Meeting 9am Monday 9/14 (every other week)


‡ Agilent Automated Sample Preparation (Lead: Alex)

  • With Straws in Parallel at this point. Speeding up the assay.
  • Waiting for the machine.
  • Alex drafting abstracts.


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

  • Integration discussion on the meeting (9.23)
  • Virus concentration (dialyzed against PBS, no SERS signal, dialyze against water now).
  • paper 1: Evap with Sol Gel substrate. Not integrated. MSSA, E coli.


‡ Biointerfaces group (Lead: MinCheol, Team: Cathie, MCK, Wong and Meller folks)

  • New experiments happening now.


‡ CIMIT- Sepsis (Lead:Cathie, Team:TBA)

  • IRB approved.
  • Cathie submitted the companion BU IRB form for exemption.


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

  • 12 mos, 24 mos. working prototypes of SNAP.




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