Klapperich Lab:Notebook/Lab Meeting Notes/2008/09/30: Difference between revisions

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* Will do RTPCR and not anti sera assays - Cathie told Chris et al. 9/29.<br>
* Will do RTPCR and not anti sera assays - Cathie told Chris et al. 9/29.<br>
* More sample back? Can we put in 1.5 ml saline, collect in 3ml VTM tube directly?  Can we amend - Cathie emailed on 9/29. <br>
* More sample back? Can we put in 1.5 ml saline, collect in 3ml VTM tube directly?  Can we amend - Cathie emailed on 9/29. <br>
* Plaque assay status? <br>
* Plaque assay status. Agar overlay problem is solved. Data later. <br>
* Cathie has to submit the progress report to INSPIR. <br>
* Cathie STILL has to submit the progress report to INSPIR. <br>
<br>
<br>
† SEPSIS Project/'''Chip Bonding Issues''' <br>
† SEPSIS Project - CIMIT Bird Flu <br>
* ZEONEX 690R, Tg, we measured it 141 C <br>
* Sample (raw pellets and film) from Ticona COC ordered. <br>
* http://www.zeonex.com/datasheets.asp <br>
* B sub in blood is done. Lets talk about comepleting the gram positive plots so they "match." <br>
* Toluene method. Why didn't we use it? (QQ, AG)<br>
* PCR Pipettes bought...no one uses them for non-PCR use!!!!!!!! <br>
* DO NOT CHANGE THE PROTOCOL W/OUT TALKING TO ME OR JAEPHIL<br>
* E coli in pee/blood done. <br>
* Fixture for Sonali (HM).<br>
* SEM image analysis of pore size. Jane did preliminary analysis. Can Jane finish this up for the paper? Ongoing. Images from Hussam. Thresholding is an issue in the image processing. More planar images. <br>
* Buy Ticona COC materials (JD). <br>
* Sonali finished EF data in blood. <br>
* B Sub data in blood extracted redo PCR/contaminated water. <br>
* PCR Pipettes must buy...no one uses them for non-PCR use!!!!!!!! <br>
* E coli in pee/blood? This week. <br>
* SEM image analysis of pore size? - We have images. We need to do thresholding, and avg. pore size measurement. Jessica's MATLAB Code. Send her code to JANE to look at. <br>
* Analytical calculations for pore size?  D'arcy's law is off by orders of magnitude. Next steps? MinCheol's model (randomly generated monolith) Min-Cheol and Jane working on it.<br>
<br>
<br>
†RNA project
†RNA project
* Sonali will teach Stephanie Jurkat Culture. <br>
* Sonali will teach Stephanie Jurkat Culture. <br>
* Jeff Braman will visit in early Dec. <br>
* Jeff Braman will visit in early Dec. <br>
* We can think about building our own straw system like Fraunhofer's.<br>
* We have Anirban's protocol and system etc. Issues resolved.<br>
* Discuss Anirban's protocol and system etc. What gets shared. What gets Used. (Cathie)<br>
* Stephanie working with Paul to make more straws. <br>
* SM and AC will do first experiment on Friday. <br>
  <br>
  <br>
† COBRA <br>
† COBRA <br>
* Mark finish control circuit (Temp, humidity, pressure) design and ordered parts <br>  
* Mark finish control circuit (Temp, humidity, pressure) design and ordered parts <br>  
* Evaporation fixture will be picked up during this week, and assembled after comeback <br>  
* Fluorescence microscopy available from 720. Try beads experiment. <br>
* HELEN says:  Jaephil should take a representative sample of what Alexis proposed to be your input: 100 uL of DI water with bacteria (MSSA should be our bacteria)
* Cutter plotter ordered to make new fluidic layer <br>
  And demonstrate ability to deliver the specified amount from the microfluidics.<br>
* Jane, Cathie, Larry, Ranjith will meet soon to discuss scale up of sol gel in chip process.  <br>
* Discuss dispensing from evap chip in a real world way. <br>
* Current design gives E.coli signal, clotting is still a problem <br>
* Change of design: funnel-shaped wells, smooth hole, make samples in pipette tips? <br>
* Jane working on CIMIT fellowship presentation and future plans for THESIS! <br>
* Jane working on CIMIT fellowship presentation and future plans for THESIS! <br>
<br>
<br>
† Valve Array/Valve building (FJ) <br>
† Valve Array/Valve building (FJ) <br>
* Waiting for fixture still from Melissa <br>
* Waiting for fixture still from Melissa. Hopefully this week. <br>
* Got drawings and preliminary info from Pennarthur group at UCSB.<br>
* Update: Monday 29 Sept Frank contacted Shane Conran of Superior Fluid Solutions (referred by Jess from UCSB).  Will draw up preliminary design and send to us for evaluation. <br>
* Waiting for further contact.<br>
* Update: Monday 6 Oct Haven't heard anything from Shane yet.  Attempting to contact again, so far without success.<br>
* Update: Monday 29 Sept Frank contacted Shane Conran of Superior Fluid Solutions (referred by Jess from UCSB).  Will draw up preliminary design and send to us for evaluation.<br>
<br>
<br>
† Fraunhofer: LOAC <br>
† Fraunhofer: LOAC <br>
* Still Still Still troubleshooting <br>
* Alex working with Paul. (something called personal lubricant)<br>
* Alex working on more toluene bonding issues. <br>
* Try Ticona material. (HM, JD, AG) <br>
* Still Still Still troubleshooting '''??'''<br>
<br>
<br>
† Biointerfaces group <br>
† Biointerfaces group <br>
* Preliminary bead trapping DEMONSTRATED. <br>
* Make a mold for Brett this week. When mask is made. <br>
* Mask writer down. Make a CR mask on Friday.<br>
* Make a mold for Brett next week. <br>
* Do preliminary E. coli experiment soon. <br>
* Do preliminary E. coli experiment soon. <br>
* Making a CR mask Tuesday afternoon. <br>
<br>
<br>
† CIMIT- Colson Grant<br>
† CIMIT- Colson Grant<br>
Line 68: Line 66:
<br>
<br>
† PCR <br>
† PCR <br>
* QQ Model has 30 cycles. MinCheol made the computational model. Star-CD program has been upgraded by Dan Kamalic. <br>
* PCR areas defined. Protocols reviewed. Contamination issues discussed.... <br>
* PHD2000.ordered very expensive....respect it!<br>
* QQ tested Taqman assays. Two probe sets. One set is better than the other. <br>
* QQ  designed a TaqMan Assay for the lambda phage PCR <br>
* '''Contamination. Make an internal control on the chip.''' <br>  
* PEG results are good but we need to get rid of the primer-dimers before publication -- update "primer-dimer" features appear in the pre cycled gel lanes. Why?? Not primer dimers, contamination. (SM will consult)<br>
* Only 1/5 chips are good at the hot embossing step. The vaccum chuck will be checked and o-rings changed (JD) <br>
* Contamination. Make an internal control on the chip. <br>  
* Fixuture for PCR chip. The heater and the thermocouples would be on the fixture. <br>
* What is the time consuming step on using a new chip every time? (QQ)<br>
* MinCheol is making Four simple PCR models to optimize temperature distribution along to the channel. Will do another model with the insulation on the bottom. <br>
* MinCheol is making three simple PCR models to optimize temperature distribution along to the channel. <br>
* MinCheol is simulating DNA's Residence Time for simple PCR models. The DNA particles need to be much smaller. Also, consult the Lab on Chip paper that JD mentioned. <br>


<br>
<br>
† RCA <br>
† RCA <br>
* Cathie Working on Whitepaper <br>
* Cathie Still Working on Whitepaper almost done! <br>
* Send PAs to Sonali and Jaephil for sending RCA grant on to someplace else. <br>
<br>
<br>
† Senior project <br>
† Senior project <br>
* New student recruited. Theodore. <br>
* Megan ordering oligos and primers for the RCA. Quote. Check with Heiko on his sources. <br>
* Megan works on micro membrane valve and pump development as sr project. <br>
* Haven't seen Teddy yet. <br>
<br>
<br>
<br>
† F31: Cochlea <br>
† F31: Cochlea <br>
* ARO Abstract due October 1st. <br>
* ARO Abstract due October 1st. <br>
* Raw data late this week. <br>
* Data summary focusing on the fundamental biological questions for next week. <br>
*
 
<br>
<br>
† Silica Optimization (Lambda): <br>
† Silica Optimization (Lambda): <br>
* Ongoing <br>
* Ongoing. More concentrations. Forged chips. <br>
* Pressure testing on these channels when they are flowing. <br>
 
[http://openwetware.org/wiki/Image:Progress_9-22_to_9-28.doc hussam's update] <br>
 
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__NOTOC__
__NOTOC__

Revision as of 04:13, 7 October 2008

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30 September 2008 Lab Meeting Agenda

† No research report today.

† Announcements

  • A slow migration to 709 can now begin. There will be core equipment entering 720, we will accommodate.
  • Supply costs are out of control! Conserve.


† Flu R01

  • Mark's role outlined this week. He will make fixture for Sonali in near term. Will look at integrated chip in long term.
  • Will do RTPCR and not anti sera assays - Cathie told Chris et al. 9/29.
  • More sample back? Can we put in 1.5 ml saline, collect in 3ml VTM tube directly? Can we amend - Cathie emailed on 9/29.
  • Plaque assay status. Agar overlay problem is solved. Data later.
  • Cathie STILL has to submit the progress report to INSPIR.


† SEPSIS Project - CIMIT Bird Flu

  • Sample (raw pellets and film) from Ticona COC ordered.
  • B sub in blood is done. Lets talk about comepleting the gram positive plots so they "match."
  • PCR Pipettes bought...no one uses them for non-PCR use!!!!!!!!
  • E coli in pee/blood done.
  • SEM image analysis of pore size. Jane did preliminary analysis. Can Jane finish this up for the paper? Ongoing. Images from Hussam. Thresholding is an issue in the image processing. More planar images.


†RNA project

  • Sonali will teach Stephanie Jurkat Culture.
  • Jeff Braman will visit in early Dec.
  • We have Anirban's protocol and system etc. Issues resolved.
  • Stephanie working with Paul to make more straws.
  • SM and AC will do first experiment on Friday.

† COBRA

  • Mark finish control circuit (Temp, humidity, pressure) design and ordered parts
  • Fluorescence microscopy available from 720. Try beads experiment.
  • Cutter plotter ordered to make new fluidic layer
  • Jane, Cathie, Larry, Ranjith will meet soon to discuss scale up of sol gel in chip process.
  • Discuss dispensing from evap chip in a real world way.
  • Current design gives E.coli signal, clotting is still a problem
  • Change of design: funnel-shaped wells, smooth hole, make samples in pipette tips?
  • Jane working on CIMIT fellowship presentation and future plans for THESIS!


† Valve Array/Valve building (FJ)

  • Waiting for fixture still from Melissa. Hopefully this week.
  • Update: Monday 29 Sept Frank contacted Shane Conran of Superior Fluid Solutions (referred by Jess from UCSB). Will draw up preliminary design and send to us for evaluation.
  • Update: Monday 6 Oct Haven't heard anything from Shane yet. Attempting to contact again, so far without success.


† Fraunhofer: LOAC

  • Alex working with Paul. (something called personal lubricant)
  • Alex working on more toluene bonding issues.
  • Try Ticona material. (HM, JD, AG)
  • Still Still Still troubleshooting ??


† Biointerfaces group

  • Make a mold for Brett this week. When mask is made.
  • Do preliminary E. coli experiment soon.
  • Making a CR mask Tuesday afternoon.


† CIMIT- Colson Grant

  • Preliminary plan for IRB submission at Harvard in place. Target date 1/1/09
  • STAR-CD Renewal - January ($2K)


† PCR

  • PCR areas defined. Protocols reviewed. Contamination issues discussed....
  • QQ tested Taqman assays. Two probe sets. One set is better than the other.
  • Contamination. Make an internal control on the chip.
  • Only 1/5 chips are good at the hot embossing step. The vaccum chuck will be checked and o-rings changed (JD)
  • Fixuture for PCR chip. The heater and the thermocouples would be on the fixture.
  • MinCheol is making Four simple PCR models to optimize temperature distribution along to the channel. Will do another model with the insulation on the bottom.
  • MinCheol is simulating DNA's Residence Time for simple PCR models. The DNA particles need to be much smaller. Also, consult the Lab on Chip paper that JD mentioned.


† RCA

  • Cathie Still Working on Whitepaper almost done!
  • Send PAs to Sonali and Jaephil for sending RCA grant on to someplace else.


† Senior project

  • Megan ordering oligos and primers for the RCA. Quote. Check with Heiko on his sources.
  • Haven't seen Teddy yet.



† F31: Cochlea

  • ARO Abstract due October 1st.
  • Data summary focusing on the fundamental biological questions for next week.


† Silica Optimization (Lambda):

  • Ongoing. More concentrations. Forged chips.
  • Pressure testing on these channels when they are flowing.

hussam's update


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