Klapperich Lab:Notebook/Lab Meeting Notes/2009/07/07: Difference between revisions

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== 7 July 2009 Lab Meeting==
* Attending:  <br>
*  Presentation: ?? <br>
<br>
† Announcements<br>
*<br>
<br>
† Flu R01 <br>
* Signed CDC MTA. <br>
* Integration: Spec? On chip? Jane will look into it. <br>
* QQ will work on the initial integration steps of SPE + RT (resevoir)+ PCR. Cutter plotter? Faunhofer Chip serpentine channel. <br>
* RNA extraction troubleshooting. <br>
* Try clean fabrication of chips and monoliths.<br>
* Try RNAseH wash through. <br>
* Absolute Quantification assays: <br>
* A primers look good at this point. Van Elden 2001. <br>
* Jessie should learn SEM. <br>


† Virus concentration (upstream from the assay.) <br>
* QQ - HM - JZ - Chip Integration. <br>
* How to read? Color, sensitivity?  Alignment. Check with JD. <br>
<br>
† Coulter Flu Fraunhofer Project
* Fraun folks coming to get trained next week. RNA isolation. Safety issues. English. <br>
* IBC for Fraun flu. waiting? <br>
* Brendan can come to Fraun Flu meetings if he wants....as primer design goes. <br>
* Ajani should come to Fraun Flu meetings to learn how to make straws. Alex will train him. <br>
<br>
'''† SEPSIS Project <br>
* Published! <br>'''
* <br>
†RNA project
* Call Natalia. <br>
* <br>
† COBRA <br>
* Update on concentration of live bugs? <br>
* Evap system (JD and JZ)<br>
<br>
** Let's get this to a point where we can publish and move on
paper 1: Evap with Sol Gel substrate.  <br>
paper 2: Covap with PMA, Rhodamine, PS beads?...virus...?<br>
- Rhodamine experiments done <br>
- Signals are similar between with and without GNP <br>
- Rhodamine binds poorly to gold <br>
- try GNP-pMA next. R6G-silver NP.
- Need to redefine hypothesis
<br>
<br>
† Biointerfaces group <br>
* fabricated SU-8 mold with Herringbone grooves. <br>
* Brett took a photo of the device for the paper, but will repeat <br>
* Jason coated thin gold on the surface of the PDMS mold, and will take SEM images for the sieves. --->SEM down<br>
* draft paper2 for the submission to "Biophysical Journal" has been started. <br>
* Will repeat trapping experiments this Friday to obtain good quality images for the Fig. 2 in the paper. <br>
<br>
† CIMIT- Colson Grant<br>
* IRB submitted.<br>
* Cathie working on the companion BU IRB form for exemption. <br>
<br>
† PCR <br>
* QQ: PCR 2 paper draft. <br>
* CMK: PCR 1 draft <br>
* DONE with PEG attempts. <br>
* PEG-coating protocol developed - TROUBLESHOOTING. <br>
* on-chip experiment with blank chip without PEG,BSA. It works with expected lower efficiency <br> 
* on-chip experiment with PEG-coated chip without PEG,BSA in reagent. It does not work, or the product is under the detection limitation of bioanalyzer.
* QQ : write protocol for PEG graft. <br>
  it has been uploaded in the share driver.
* QQ: Try changing heater and thermocouple. <br>
  done
* QQ: Try running PCR after plasma treatment and water wash only. <br>
  done
* QQ and MM: look back at flu PCR. Recall the repeatability. Decide course of action with Sonali. See what you can do to do "real" samples soon.  One pot? Two steps necessary instead? <br>
  the repeatebility has been comfirmed.
<br>
† RCA/HDA<br>
* Start planning R01 for Submission on 10/5/09. MM, JD, CMK. <br>
* Getting solution back out is still an issue. <br>
* Integrated chip worked (19th). Accumulating multiple runs. (Check into primer lifetime) <br>
* Evaporation problems near edges. Maybe design change? <br>
* Teflon issue with the enzyme? Check into it. <br>
† Silica Optimization (Lambda): <br>
*  Do absolute quant assay. Mass Spec data suggests junk is polymer. Pursue GPC later.  <br>
* '''Get lower Bioan. Kit.''' <br>


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7 July 2009 Lab Meeting

  • Attending:
  • Presentation: ??


† Announcements



† Flu R01

  • Signed CDC MTA.
  • Integration: Spec? On chip? Jane will look into it.
  • QQ will work on the initial integration steps of SPE + RT (resevoir)+ PCR. Cutter plotter? Faunhofer Chip serpentine channel.
  • RNA extraction troubleshooting.
  • Try clean fabrication of chips and monoliths.
  • Try RNAseH wash through.
  • Absolute Quantification assays:
  • A primers look good at this point. Van Elden 2001.
  • Jessie should learn SEM.

† Virus concentration (upstream from the assay.)

  • QQ - HM - JZ - Chip Integration.
  • How to read? Color, sensitivity? Alignment. Check with JD.


† Coulter Flu Fraunhofer Project

  • Fraun folks coming to get trained next week. RNA isolation. Safety issues. English.
  • IBC for Fraun flu. waiting?
  • Brendan can come to Fraun Flu meetings if he wants....as primer design goes.
  • Ajani should come to Fraun Flu meetings to learn how to make straws. Alex will train him.


† SEPSIS Project

  • Published!

†RNA project

  • Call Natalia.

† COBRA

  • Update on concentration of live bugs?
  • Evap system (JD and JZ)


    • Let's get this to a point where we can publish and move on

paper 1: Evap with Sol Gel substrate.
paper 2: Covap with PMA, Rhodamine, PS beads?...virus...?
- Rhodamine experiments done
- Signals are similar between with and without GNP
- Rhodamine binds poorly to gold
- try GNP-pMA next. R6G-silver NP. - Need to redefine hypothesis

† Biointerfaces group

  • fabricated SU-8 mold with Herringbone grooves.
  • Brett took a photo of the device for the paper, but will repeat
  • Jason coated thin gold on the surface of the PDMS mold, and will take SEM images for the sieves. --->SEM down
  • draft paper2 for the submission to "Biophysical Journal" has been started.
  • Will repeat trapping experiments this Friday to obtain good quality images for the Fig. 2 in the paper.


† CIMIT- Colson Grant

  • IRB submitted.
  • Cathie working on the companion BU IRB form for exemption.


† PCR

  • QQ: PCR 2 paper draft.
  • CMK: PCR 1 draft
  • DONE with PEG attempts.
  • PEG-coating protocol developed - TROUBLESHOOTING.
  • on-chip experiment with blank chip without PEG,BSA. It works with expected lower efficiency
  • on-chip experiment with PEG-coated chip without PEG,BSA in reagent. It does not work, or the product is under the detection limitation of bioanalyzer.
  • QQ : write protocol for PEG graft. 
  it has been uploaded in the share driver.
  • QQ: Try changing heater and thermocouple. 
  done
  • QQ: Try running PCR after plasma treatment and water wash only. 
  done
  • QQ and MM: look back at flu PCR. Recall the repeatability. Decide course of action with Sonali. See what you can do to do "real" samples soon. One pot? Two steps necessary instead? 
 the repeatebility has been comfirmed.


† RCA/HDA

  • Start planning R01 for Submission on 10/5/09. MM, JD, CMK.
  • Getting solution back out is still an issue.
  • Integrated chip worked (19th). Accumulating multiple runs. (Check into primer lifetime)
  • Evaporation problems near edges. Maybe design change?
  • Teflon issue with the enzyme? Check into it.

† Silica Optimization (Lambda):

  • Do absolute quant assay. Mass Spec data suggests junk is polymer. Pursue GPC later.
  • Get lower Bioan. Kit.


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