Difference between revisions of "Klapperich Lab:Notebook/Lab Meeting Notes/2009/08/25"

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(25 August 2009 Lab Meeting)
(25 August 2009 Lab Meeting)
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*  August-18-presentation [http://openwetware.org/wiki/Image:Aug_18_09_presentation.ppt]
*  August-18-presentation [http://openwetware.org/wiki/Image:Aug_18_09_presentation.ppt]
*  Results Summary of Aug-18-09 [http://openwetware.org/wiki/Image:Results_Summary_Aug-18-09.xls] <br>
*  Results Summary of Aug-18-09 [http://openwetware.org/wiki/Image:Results_Summary_Aug-18-09.xls] <br>
*  Amorphous Chip results [http://openwetware.org/wiki/Image:Aug_25_09_slides_.ppt]

Revision as of 07:18, 25 August 2009

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25 August 2009 Lab Meeting

  • Attending:
  • Missing:
  • Presentation: Jaephil: Chip Integration FLU

† Announcements

  • Lab lunch today after meeting.

† Flu R01

  • Do std curve without carrier RNA. Compare with ASB data.
  • Integration: Spec? On chip? Jane will look into it.

Are we still looking to do this on chip? For on chip, we need to fabricate mirrors such that light can access assays in channels. For off chip, we need to look into OEM light source, fiber optices, fluorescence spectrometer, and detectors. They are pricey. such as this one: http://www.oceanoptics.com/products/usb4000fl.asp

  • QQ will work on the initial integration steps of SPE + RT (resevoir)+ PCR. Cutter plotter? Faunhofer Chip serpentine channel. "QQ Needs to know how to make valves."
  • RNA extraction troubleshooting.
  • Try clean fabrication of chips and monoliths.
  • Try RNAseH wash through.
  • A primers look good at this point. Van Elden 2001. (C.L. Ward 2004 primers works best for PCR)
  • Jessie should learn SEM.

* Need to update IBC to include rDNA work.

† Virus concentration (upstream from the assay.)

  • How to read? Color, sensitivity? Alignment. Check with JD.

Alexa Fluo-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.
My question about the this module of the integrated chip include:
1. Fluid handling capacity. How much is the input fluid volume? As far as I heard, it makes more sense to concentrate mL's of patient sample to 100's uL, instead of from 100's uL to a few uL's. Is this true?
2. Channel re-design. My major concern is the difficulty in fluid manipulation with pressure in the evaporation chip. ie. we cannot push the fluid with syringe pump, or collect the fluid with pipette in the liquid layer. Redesign of the channels involves incorporation of valves and direct flow of concentrated sample to the SPE module to minimize loss.
3. Materials. The chip should be made of COP, Teflon membrane, and Teflon film, so as to integrate well with the other modules. Therefore, the air flow channel needs to be redesigned to make multi-layer fluid flow possible.

† Coulter Flu Fraunhofer Project

  • IBC for Fraun flu. approved.

† Agilent Meetings

  • With Straws in Parallel at this point.


  • Update on concentration of live bugs? MSSA?
  • 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

  • New fabrcation in process.
  • took SEM images of parallelized designs, will show them if possible in the meeting.
  • Through SEM images, we found the smallest feature size is 1.2 um.

† CIMIT- Colson Grant

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


  • QQ: PCR 2 paper draft.
  • CMK: PCR 1 draft

* on-chip PCR on a series of diluted lambda phage DNA.

 the detect limitation for ABI is 10-9g/ul
 on-chip PCR have the same sensitivity.

* 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.


  • 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):

  • August-18-presentation [1]
  • Results Summary of Aug-18-09 [2]
  • Amorphous Chip results [3]