Klapperich Lab:Notebook/Lab Meeting Notes/2008/09/23

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(23 September 2008 Lab Meeting Agenda)
(23 September 2008 Lab Meeting Agenda)
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* E coli in pee/blood? This week. <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>
* 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? Min-Cheol and Jane working on it.<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
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† Biointerfaces group <br>
† Biointerfaces group <br>
* Preliminary bead trapping DEMONSTRATED. <br>
* Preliminary bead trapping DEMONSTRATED. <br>
-
* Mask writer down. Friday?<br>
+
* Mask writer down. Make a CR mask on Friday.<br>
* Make a mold for Brett next week. <br>
* Make a mold for Brett next week. <br>
-
* Do preliminary E. coli experiment. <br>
+
* Do preliminary E. coli experiment soon. <br>
<br>
<br>
† CIMIT- Colson Grant<br>
† CIMIT- Colson Grant<br>
Line 78: Line 78:
<br>
<br>
† PCR <br>
† PCR <br>
-
* QQ Model has 30 cycles. MinCheol will try the model. Need to upgrade the Star-CD program. Dan Kamalic has to do this. <br>
+
* QQ Model has 30 cycles. MinCheol made the computational model. Star-CD program has been upgraded by Dan Kamalic. <br>
* PHD2000.ordered very expensive....respect it!<br>
* PHD2000.ordered very expensive....respect it!<br>
* QQ  designed a TaqMan Assay for the lambda phage PCR <br>
* QQ  designed a TaqMan Assay for the lambda phage PCR <br>
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* Contamination. Make an internal control on the chip. <br>  
* Contamination. Make an internal control on the chip. <br>  
* What is the time consuming step on using a new chip every time? (QQ)<br>
* What is the time consuming step on using a new chip every time? (QQ)<br>
 +
* MinCheol is making three simple PCR models to optimize temperature distribution along to the channel. <br>
<br>
<br>

Revision as of 12:12, 25 September 2008

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23 September 2008 Lab Meeting Agenda

† Jaephil's research report.

† Announcements

  • Fall Group Meetings will be on Tuesdays from 12-2pm in room 705
  • Register for CIMIT conference if you want. Irene can reimburse.
  • Register for MRS Boston if you want to.
  • Room 720 needs to be kept clean.
  • Supply costs are out of control! Conserve.


† Flu R01

  • Meeting on 9/12

1. We are not changing the sample collection procedures at this time.
2. We are aiming to get 200 samples this season, starting when flu hits North America as recorded by CDC website.
3. We may collect samples from anther ER location on BUMC campus.
4. We are going to hire a courier to transport the samples on scheduled days!!!
5. They want to know what "confirmed positive" samples we have from anti-sera assays (and we do, too), but I told them we are doing the plaque assay first and will move on to the anti-sera for a subset of the samples that were cytopathic positive starting likely in Nov.

  • Will do RTPCR and not anti sera assays - Cathie will tell Chris.

6. We are still going to split the VTM in our hood and take it over there.

  • More sample back? Can we put in 1.5 ml saline, collect in 3ml VTM tube directly? What is the issue with doing that? Can we amend - Cathie will look into it with them.
  • Plaque assay status. Issue with the overlay.
  • Set up Sonali with Jose Re: Overlay advice.
  • Cathie has to submit the progress report to INSPIR.


† SEPSIS Project/Chip Bonding Issues

  • ZEONEX 690R, Tg, we measured it 141 C
  • http://www.zeonex.com/datasheets.asp
  • Toluene method. Why didn't we use it? (QQ, AG)
  • DO NOT CHANGE THE PROTOCOL W/OUT TALKING TO ME OR JAEPHIL
  • Fixture for Sonali (HM).
  • Buy Ticona COC materials (JD).
  • Sonali finished EF data in blood.
  • B Sub data in blood extracted redo PCR/contaminated water.
  • PCR Pipettes must buy...no one uses them for non-PCR use!!!!!!!!
  • E coli in pee/blood? This week.
  • 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.
  • 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.


†RNA project

  • Sonali will teach Stephanie Jurkat Culture.
  • Jeff Braman will visit in early Dec.
  • We can think about building our own straw system like Fraunhofer's.
  • Discuss Anirban's protocol and system etc. What gets shared. What gets Used. (Cathie)

† COBRA

  • Mark finish control circuit (Temp, humidity, pressure) design and ordered parts
  • Evaporation fixture will be picked up during this week, and assembled after comeback
  • 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)
  And demonstrate ability to deliver the specified amount from the microfluidics.
  • Jane working on CIMIT fellowship presentation and future plans for THESIS!


† Valve Array/Valve building (FJ)

  • Waiting for fixture still from Melissa
  • Got drawings and preliminary info from Pennarthur group at UCSB.
  • Waiting for further contact.


† Fraunhofer: LOAC

  • Still Still Still troubleshooting


† Biointerfaces group

  • Preliminary bead trapping DEMONSTRATED.
  • Mask writer down. Make a CR mask on Friday.
  • Make a mold for Brett next week.
  • Do preliminary E. coli experiment soon.


† CIMIT- Colson Grant

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


† PCR

  • QQ Model has 30 cycles. MinCheol made the computational model. Star-CD program has been upgraded by Dan Kamalic.
  • PHD2000.ordered very expensive....respect it!
  • QQ designed a TaqMan Assay for the lambda phage PCR
  • 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)
  • Contamination. Make an internal control on the chip.
  • What is the time consuming step on using a new chip every time? (QQ)
  • MinCheol is making three simple PCR models to optimize temperature distribution along to the channel.


† RCA

  • Cathie Working on Whitepaper


† Senior project

  • New student recruited. Theodore.
  • Megan works on micro membrane valve and pump development as sr project.


† F31: Cochlea

  • ARO Abstract due October 1st.
  • Raw data late this week.


† Silica Optimization (Lambda):

  • Ongoing

hussam's Update


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