Klapperich Lab:Notebook/Lab Meeting Notes/2009/05/12: Difference between revisions

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==12 May 2009 Lab Meeting==


† Announcements<br>
* SIGN UP FOR NEW LAB DUTIES WITH SONALI.
*New lab meeting time T 10a-12pm room 705 starting 5/12/2009 <br>
<br>
† Flu R01 <br>
* RNA extraction troubleshooting. <br>
*
*<br>
<br>
† SEPSIS Project <br>
* Revision in process due 5/20 <br>
*  <br>
<br>
†RNA project
* Jeff visiting week of June 1st <br>
* <br>
<br>
† COBRA <br>
* Integration with the glass slide.  <br>
* new air channel design sent to machine shop <br>
* new fluid channel made in PDMS <br>
* making the polyurethane mold had proven challenging as it sticks to the plastic fixture, tried mold release but didn't help <br>
* new cutting plotter carrier sheet ordered <br>
* new air channel mold did not cure well and the PDMS made from it was leaking. need to do it again, mold material ordered. <br>
<br>
* Substrates (JZ)<br>
** Let's get this to a point where we can publish and move on....JZ and CMK to discuss.  <br>
- Making substrate in microwewlls? (motivation? need to implement valves) <br>
- Co-evaporate colloids? (the morphology won't be uniform or consistent each time, signal analysis system non-existent) <br>
- Sol-gel on Teflon? (can serve to study basic material science only) <br>
* Colloid experiment <br>
- Do Rhodamine. Leaked. Need to try again. <br>
- Found the problem. Liquid and air channel widths reversed. Will make new chip and try again. <br>
-Need a size specific positive control. PS beads? charged? <br>
** 1um unmodified, undiluted PS beads give distinctive spectrum on Ranjith's substrate <br>
** try coated PS beads. <br>
<br>
† Virus concentration
* ATCC flu virus grew and harvested
* Plaque assay of harvested virus in progress: learning from Brendan, will try if enough cells
* Concentrator chip design underway
<br>
† Valve Array/Valve building - done. <br>
* Who is in charge of this now that the SP students are gone? Alex? <br>
† Fraunhofer: LOAC <br>
* Paper in revision Yeah!<br>
* Bonding meeting with MIT folks - Alex left some samples with them. Updates? <br>
<br>
† Biointerfaces group <br>
* Final draft with collaborators. <br>
* designing herringbone groove for better trapping (Mask writer down until next Tuesday)<br>
* investigate the stability under different Peclet numbers (ratio of hydrodynamic force and Brownian force).<br>
<br>
† CIMIT- Colson Grant<br>
* IRB still in revision.<br>
*<br>
<br>
† PCR <br>
*<br>
* <br>
* repeated test of the PCR efficiency for different designs of channel.<br>
* test PCR efficiency using smaller DNA size (63bp product). <br>
* analyze PCR product for different temperature using bioanalyzer.<br>
* getting statistical data for the activation energy from 50 particle simulation (Fig. 5-7) <br> 
* Mincheol has written the introduction, results and discussion, and conclusion. <br>
* will develop large scale particle modeling in full PCR model (30 PCR cycles or 20 PCR cycles) <br> <br>
<br>
† RCA/HDA<br>
* Giving up on white paper. Think about other grant outlets. <br>
* Preliminary no-valve design for 25 microliters. <br>
* 20 more test chips to Sonali (AACC poster). <br>
* Sonali try to do 10 microliters in the tube * Updates? <br>
* Jane is working on passive valve characterization: threshold pressure not related to cantilever length or bonding time, try hole size next  <br>
<br>
† Silica Optimization (Lambda): <br>
*Run single PCR product from QQ or Sonali the test with the bioanalyzer<br>


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12 May 2009 Lab Meeting

† Announcements

  • SIGN UP FOR NEW LAB DUTIES WITH SONALI.
  • New lab meeting time T 10a-12pm room 705 starting 5/12/2009


† Flu R01

  • RNA extraction troubleshooting.


† SEPSIS Project

  • Revision in process due 5/20


†RNA project

  • Jeff visiting week of June 1st


† COBRA

  • Integration with the glass slide.
  • new air channel design sent to machine shop
  • new fluid channel made in PDMS
  • making the polyurethane mold had proven challenging as it sticks to the plastic fixture, tried mold release but didn't help
  • new cutting plotter carrier sheet ordered
  • new air channel mold did not cure well and the PDMS made from it was leaking. need to do it again, mold material ordered.


  • Substrates (JZ)
    • Let's get this to a point where we can publish and move on....JZ and CMK to discuss.

- Making substrate in microwewlls? (motivation? need to implement valves)
- Co-evaporate colloids? (the morphology won't be uniform or consistent each time, signal analysis system non-existent)
- Sol-gel on Teflon? (can serve to study basic material science only)

  • Colloid experiment

- Do Rhodamine. Leaked. Need to try again.
- Found the problem. Liquid and air channel widths reversed. Will make new chip and try again.
-Need a size specific positive control. PS beads? charged?

    • 1um unmodified, undiluted PS beads give distinctive spectrum on Ranjith's substrate
    • try coated PS beads.


† Virus concentration

  • ATCC flu virus grew and harvested
  • Plaque assay of harvested virus in progress: learning from Brendan, will try if enough cells
  • Concentrator chip design underway


† Valve Array/Valve building - done.

  • Who is in charge of this now that the SP students are gone? Alex?

† Fraunhofer: LOAC

  • Paper in revision Yeah!
  • Bonding meeting with MIT folks - Alex left some samples with them. Updates?


† Biointerfaces group

  • Final draft with collaborators.
  • designing herringbone groove for better trapping (Mask writer down until next Tuesday)
  • investigate the stability under different Peclet numbers (ratio of hydrodynamic force and Brownian force).


† CIMIT- Colson Grant

  • IRB still in revision.


† PCR



  • repeated test of the PCR efficiency for different designs of channel.
  • test PCR efficiency using smaller DNA size (63bp product).
  • analyze PCR product for different temperature using bioanalyzer.
  • getting statistical data for the activation energy from 50 particle simulation (Fig. 5-7)
  • Mincheol has written the introduction, results and discussion, and conclusion.
  • will develop large scale particle modeling in full PCR model (30 PCR cycles or 20 PCR cycles)


† RCA/HDA

  • Giving up on white paper. Think about other grant outlets.
  • Preliminary no-valve design for 25 microliters.
  • 20 more test chips to Sonali (AACC poster).
  • Sonali try to do 10 microliters in the tube * Updates?
  • Jane is working on passive valve characterization: threshold pressure not related to cantilever length or bonding time, try hole size next



† Silica Optimization (Lambda):

  • Run single PCR product from QQ or Sonali the test with the bioanalyzer


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