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

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† Flu R01 <br>
† Flu R01 <br>
* Do std curve without carrier RNA. Compare with ASB data. <br>
* <br>
* Integration: Spec? On chip? Jane will look into it. <br>
* <br>
'''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''' <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. Cutter plotter? Faunhofer Chip serpentine channel. "QQ Needs to know how to make valves." <br>  
* RNA extraction troubleshooting. Do deinhibition of monolith components. Test those with the Ambion RNAse kit. <br>
* RNA extraction troubleshooting. <br>
* <br>
* Try clean fabrication of chips and monoliths.<br>
* <br>
* Try RNAseH wash through. <br>
* A primers look good at this point. Van Elden 2001. '''(C.L. Ward 2004 primers works best for PCR)'''<br>
* Jessie should learn SEM. <br>
'''* Need to update IBC to include rDNA work. <br>'''
'''* Need to update IBC to include rDNA work. <br>'''
* Virus concentration. Volume collection issues at this time. Where is the loss? <br>
* '''Alexa Fluo-488 succinimidyl ester (Molecular Probes) stains the flu virus fluorescent. <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>'''
'''My question about the this module of the integrated chip include: <br>'''
'''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? <br>
'''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.<br>'''
'''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. <br> '''


† Virus concentration (upstream from the assay.) <br>
† Coulter Flu Fraunhofer Project (minor item on new agenda)
* How to read? Color, sensitivity?  Alignment. Check with JD. <br>
'''Alexa Fluo-488 succinimidyl ester (Molecular Probes) stains the flu virus fluorescent. <br>
''''''The problem is not how to visualize virus right now, because the design is clearly not optimized for collecting all the samples are the outlet. The major loss is from sample handling instead of from non specific binding to the material. <br>
My question about the this module of the integrated chip include: <br>
1. 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? <br>
2. 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 vacuum in the liquid layer.<br>
3. The chip should be made of COP, Teflon membrane, and Teflon film, so as to integrate well with the other modules. Therefore, the fixture needs to be redesigned. <br> ''''''
 
† Coulter Flu Fraunhofer Project
* IBC for Fraun flu. approved. <br>
* IBC for Fraun flu. approved. <br>
* Meeting time will have to move <br>
<br>
† Agilent Automated Sample Preparation
* With Straws in Parallel at this point. Speeding up the assay. <br>
* Waiting for the machine. <br>
<br>
<br>
† Agilent Meetings
* With Straws in Parallel at this point. <br>
* <br>
† COBRA <br>  
† COBRA <br>  
* Update on concentration of live bugs? MSSA? <br>
* Update on concentration of live bugs? MSSA? <br>
* Evap system (JD and JZ)<br>
* Virus concentration (dialyzed against PBS, no SERS signal, dialyze against water now). <br>
<br>
* paper 1: Evap with Sol Gel substrate. Not integrated. MSSA, E coli. <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>
<br>
† Biointerfaces group <br>
† Biointerfaces group <br>
Line 60: Line 48:
* took SEM images of parallelized designs, will show them if possible in the meeting. <br>
* took SEM images of parallelized designs, will show them if possible in the meeting. <br>
* Through SEM images, we found the smallest feature size is 1.2 um. <br>
* Through SEM images, we found the smallest feature size is 1.2 um. <br>
   
  * set up 2 week check in meeting with team. <br>
<br>
<br>
† CIMIT- Colson Grant<br>
† CIMIT- Sepsis<br>
* IRB approved. <br>
* IRB approved. <br>
* Cathie submitted the companion BU IRB form for exemption. <br>
* Cathie submitted the companion BU IRB form for exemption. <br>
<br>
<br>
† PCR <br>
† PCR (will get absorbed into the Flu agenda item at the top) <br>
* QQ: PCR 2 paper draft. <br>
* CMK: PCR 2 paper draft. <br>
* CMK: PCR 1 draft <br>
* CMK: PCR 1 draft. Analytical Chem. <br>
'''* on-chip PCR on a series of diluted lambda phage DNA.'''
'''* on-chip PCR on a series of diluted lambda phage DNA.'''
  ''' the detect limitation for ABI is 10<sup>-9</sup>g/ul
  ''' the detect limitation for ABI is 10<sup>-9</sup>g/ul
   on-chip PCR have the same sensitivity.'''
   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.'''
'''* 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>
 
* New primers? <br>
* Double PCR on chip. <br>
<br>
† RCA/HDA<br>
† RCA/HDA<br>
* Start planning R01 for Submission on 10/5/09. MM, JD, CMK. <br>
* Start planning R01 for Submission on 2/5/10. MM, JD, CMK. <br>
* Getting solution back out is still an issue. <br>
* JD working on paper. Will deliver to MM this week. <br>
* Integrated chip worked (19th). Accumulating multiple runs. (Check into primer lifetime) <br>
* Figures discussion. <br>
* Evaporation problems near edges. Maybe design change? <br>
<br>
* Teflon issue with the enzyme? Check into it. <br>
* PATH Grant <br>
* Frank J.
* 12 mos, 24 mos. working prototypes of SNAP. <br>
<br>
<br>
† Silica Optimization (Lambda): <br>
† Silica Optimization (Lambda): (get absorbed into the flu agenda item at top) <br>
*  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 08:14, 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



  • QQ will work on the initial integration steps of SPE + RT (resevoir)+ PCR.
  • RNA extraction troubleshooting. Do deinhibition of monolith components. Test those with the Ambion RNAse kit.


* Need to update IBC to include rDNA work.

  • Virus concentration. Volume collection issues at this time. Where is the loss?
  • 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 (minor item on new agenda)

  • IBC for Fraun flu. approved.
  • Meeting time will have to move


† Agilent Automated Sample Preparation

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


† COBRA

  • Update on concentration of live bugs? MSSA?
  • 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

  • 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. 
* set up 2 week check in meeting with team.


† CIMIT- Sepsis

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


† PCR (will get absorbed into the Flu agenda item at the top)

  • CMK: PCR 2 paper draft.
  • CMK: PCR 1 draft. Analytical Chem.

* 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.

  • New primers?
  • Double PCR on chip.


† RCA/HDA

  • Start planning R01 for Submission on 2/5/10. MM, JD, CMK.
  • JD working on paper. Will deliver to MM this week.
  • Figures discussion.


  • PATH Grant
  • Frank J.
  • 12 mos, 24 mos. working prototypes of SNAP.


† Silica Optimization (Lambda): (get absorbed into the flu agenda item at top)

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



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