Klapperich Lab:Notebook/Lab Meeting Notes/2009/10/13: Difference between revisions

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'''‡ Announcements'''<br>
'''‡ Announcements'''<br>
* No group meeting 10/6. <br>
* <br>
* Invited speaker at group meeting on 10/13 - PLEASE Do NOT MISS  - Dr. Qian Mei, post doc applicant. <br>
* Invited speaker at group meeting on 10/20 - PLEASE Do NOT MISS  - Dr. Tushar Bansal, post doc applicant. <br>
* '''PAPERS Drafted before MicroTAS''' <br>
* '''PAPERS Drafted before MicroTAS''' <br>
* '''Posters for MicroTAS Due to CMK by 10/15'''<br>
* '''Posters for MicroTAS Due to CMK by 10/15'''<br>
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<br>
<br>
† Sample Concentration (Lead: Jane, Team: Jaephil) <br>
† Sample Concentration (Lead: Jane, Team: Jaephil) <br>
* Up to 10^8 for positive control. <br>
* Up to high 10^7 for positive control. Silver substrate no signal. <br>
* Jane working on the cell lysate control. <br>
* Jane working on the cell lysate control: plan to have Cassidy's help on plaque assay while I'm away. <br>
* Main loss is at the outlet/sample collection. <br>
* New cell passage from frozen - the old one is beyond passage 30. <br>
* Alexa Fluor-488 succinimidyl ester (Molecular Probes) stains the flu virus fluorescent. <br>
* Main loss is at the outlet/sample collection: tangential filtration design in drawing stage. <br>
* 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. <br>
* Contacted EC Shaw about rubber stamp mold for new design for evaporation. <br>
* Jane is thinking outside the box. New chip design. Bacteria design is not working. <br>
* Set up COMSOL and StarCD, look for governing equations for simulation of evaporation. <br>
* Committee meeting setup <br>
<br>
<br>
† 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. Jessie this week. <br>
* Design three straight channels. A: std channel we already use. B: widest channel possible, C: something in between. Deliver CAD drawings for these for photomasks by Friday 10/16, functional chips to be delivered by 10/26 [Hussam/Jessie]
*Team met last week to plan experiments. <br>
* Silica free SPE, and SPE free channel experiment to be repeated. Control was old didn't take pressure, report back on 10/15.<br>
*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>
* Load DNA in a straw of 50ul SPE, quick test of hypothesis more SPE = more DNA, report back 10/16. <br>
*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>
<br>
<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>
* QQ: Paper back to QQ 9/29. <br>
* PCR2 Paper formatted for LOAC this week. <br>
* CMK: PCR 1 draft. Analytical Chem. MCK is running more simulations. <br>
* CMK: PCR 1 draft. Analytical Chem. MCK is running more simulations. <br>
*  made 40 cycle chip. <br>
* Success with 30 cycles, Qiagen Kit. Look at annealing temperature as per Alexis. <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>
* Start planning R01 for Submission on 2/5/10. MM, JD, CMK. <br>
* Start planning R01 for Submission on 2/5/10. MM, JD, CMK. <br>
* JD will train QQ how to make HDA chips. This may entail moving from cutter plotter to embossing steps. JD and QQ to meet ASAP to plan the tech transfer. <br>
* Paper submitted 10/6. <br>
* Paper submitted 10/6. <br>
<br>
<br>
'''‡C. diff Project''' (Cathie, Sonali, Satish Singh, His post doc )<br>
'''‡C. diff Project''' (Cathie, Sonali, Satish Singh, Lisa J., His post doc )<br>
* Sonali to train Lisa on SPE. <br>
* Sonali to train Lisa on SPE. <br>
* QQ to run test PCR on chip with genomic DNA and Toxin B primers.  <br>
* QQ to run test PCR on chip with genomic DNA and Toxin B primers.  <br>
<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)'''  
* Meeting 9am Monday 9/14 (every other week) <br>
* Meeting 9am Monday (every other week) <br>
<br>
<br>
'''‡ Agilent Automated Sample Preparation (Lead: Alex)'''<br>
'''‡ Agilent Automated Sample Preparation (Lead: Alex)'''<br>
* With Straws in Parallel at this point. Speeding up the assay. <br>
* With Straws in Parallel at this point. Speeding up the assay. <br>
* Waiting for the machine. <br>
* Alex will have drafts this week. <br>
* Alex drafting abstracts. <br>
<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>'''  
* Integration discussion on the meeting (9.23)<br>
* Metal piece modification for the integration - Parts distored and is begin fixed.<br>
* Virus concentration (dialyzed against PBS, no SERS signal, dialyze against water now). <br>
* paper 1: Evap with Sol Gel substrate.  Not integrated. MSSA, E coli. <br>
* paper 1: Evap with Sol Gel substrate.  Not integrated. MSSA, E coli. <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>
* New experiments happening now. <br>
* New experiments happening now. <br>
* Cathie will submit paper inquiry.<br>
<br>
<br>
'''‡ CIMIT- Sepsis (Lead:Cathie, Team:TBA)'''<br>
'''‡ CIMIT- Sepsis (Lead:Cathie, Team:TBA)'''<br>
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<br>
'''‡ PATH Grant (Lead:Cathie, Team:Frank, Sean, Mark, Jake Trueb (ME), Suma)''' <br>
'''‡ PATH Grant (Lead:Cathie, Team:Frank, Sean, Mark, Jake Trueb (ME), Suma)''' <br>
* Phone meeting with PATH this week. <br>
* Phone meeting with PATH this week. 10/13. <br>
* Training on straw making concluded. <br>
* Training on straw making concluded. <br>
* UGs purchasing parts for straw machine for 709. <br>




Revision as of 17:05, 13 October 2009

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13 October 2009 Lab Meeting

  • Attending:
  • Missing:
  • Presentation: Dr. Qian Mei, Post Doc Applicant, 2pm, please BE ON TIME.


‡ Announcements


  • Invited speaker at group meeting on 10/20 - PLEASE Do NOT MISS - Dr. Tushar Bansal, post doc applicant.
  • PAPERS Drafted before MicroTAS
  • Posters for MicroTAS Due to CMK by 10/15


‡ Flu R01:Integration

  • New design - address evaporation loss, Reagent delivery and storage solution. Consider marginating flows?


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

  • Up to high 10^7 for positive control. Silver substrate no signal.
  • Jane working on the cell lysate control: plan to have Cassidy's help on plaque assay while I'm away.
  • New cell passage from frozen - the old one is beyond passage 30.
  • 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)

  • Design three straight channels. A: std channel we already use. B: widest channel possible, C: something in between. Deliver CAD drawings for these for photomasks by Friday 10/16, functional chips to be delivered by 10/26 [Hussam/Jessie]
  • Silica free SPE, and SPE free channel experiment to be repeated. Control was old didn't take pressure, report back on 10/15.
  • Load DNA in a straw of 50ul SPE, quick test of hypothesis more SPE = more DNA, report back 10/16.


† PCR - CMI (Lead: Qingqing)

  • QQ will work on the initial integration steps of SPE + RT (resevoir)+ PCR.
  • PCR2 Paper formatted for LOAC this week.
  • CMK: PCR 1 draft. Analytical Chem. MCK is running more simulations.


† HDA (Lead: Jaephil, Team:Sonali)

  • Start planning R01 for Submission on 2/5/10. MM, JD, CMK.
  • JD will train QQ how to make HDA chips. This may entail moving from cutter plotter to embossing steps. JD and QQ to meet ASAP to plan the tech transfer.
  • Paper submitted 10/6.


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

  • Sonali to train Lisa on SPE.
  • QQ to run test PCR on chip with genomic DNA and Toxin B primers.


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

  • Meeting 9am Monday (every other week)


‡ Agilent Automated Sample Preparation (Lead: Alex)

  • With Straws in Parallel at this point. Speeding up the assay.
  • Alex will have drafts this week.


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

  • Metal piece modification for the integration - Parts distored and is begin fixed.
  • 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.
  • Cathie will submit paper inquiry.


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

  • IRB approved.
  • Cathie submitted the companion BU IRB form for exemption. Revised, still still waiting.


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

  • Phone meeting with PATH this week. 10/13.
  • Training on straw making concluded.
  • UGs purchasing parts for straw machine for 709.



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