Klapperich Lab:Notebook/Lab Meeting Notes/2010/04/15: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
No edit summary
(4 intermediate revisions by 4 users not shown)
Line 15: Line 15:
'''‡ Flu R01:Integration''' <br>
'''‡ Flu R01:Integration''' <br>
* meetings every other M 1-3pm. 705.  <br>
* meetings every other M 1-3pm. 705.  <br>
** SEQUENCING WORK<br>
* for PCR just do more reactions, pool and etoh precipitate. <br>
** For HDA, we need to explore cloning. <br>


† HDA (Lead: Jaephil, Team:Sonali)<br>
† HDA (Lead: Jaephil, Team:Sonali)<br>
* IBC Approval or 720 to work with real C.diff samples. <br>
* Patient Samples - dilution experiments (MM/SH) <br>
* Patient Samples - dilution experiments (MM/SH) <br>
* Start planning R01 for Submission on '''6/5/10.''' MM, CMK. <br>
* Start planning R01 for Submission on '''10/5/10.''' MM, CMK. <br>
* HDA mix in dried form - Expecting it from BH -- ON HOLD. <br>
* HDA mix in dried form - Expecting it from BH -- ON HOLD. <br>
* warm start here <br>
* warm start here (Give some to Lisa)<br>
* QQ preliminary chip work <br>
* QQ preliminary chip work <br>
* Sequence all output <br>
* Sequence all output <br>
Line 26: Line 32:
<br>
<br>
† Sample Concentration (Lead: Jane, Team: Jaephil) <br>
† Sample Concentration (Lead: Jane, Team: Jaephil) <br>
* Straight channel adhesion test PCR result expected. Longer time more retention. <br>  
* Straight channel adhesion test PCR result expected. From 4/6 result, PDMS 4mm wide channel doesn't show decrease in output RNA over time <br>
* Straight 1mm and 4mm PDMS-Teflon channel adhesion test pending PCR result. <br>
* Try collection vs dilutions, collection vs time, need binding constant to quantify results. <br>
* Try collection vs dilutions, collection vs time, need binding constant to quantify results. <br>
* New multi-channel chip mold is ready for making chips <br>
* Samples expected from Fauchet group. Contact today. ???  - CMK will check again. <br>
* Samples expected from Fauchet group. Contact today. <br>
<br>
<br>
† SPE Column Optimization for DNA/RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan) <br>
† SPE Column Optimization for DNA/RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan) <br>
Line 35: Line 41:
* http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN%2F5155018 <br>
* http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN%2F5155018 <br>


* (In progress) Jessie will run chips with serial virus dilutions from 1:1 to 1:1,000,000 to re-do previous dilution experimnent with WHO SYBR green assay on chip.<br>
* (Almost done) Jessie will run chips with serial virus dilutions from 1:1 to 1:1,000,000 to re-do previous dilution experimnent with WHO SYBR green assay on chip.<br>
* Less input sample (same concentration, 37.5uL sample vs 100uL sample). From raw data (from 30uL extracted RNA), less sample gives significantly(p-value = 0.0005) less copies.  If normalized to per mL of sample input, copies/mL are comparable between two sample inputs (p-value = 0.5094).(JC) <br>
* <br>
* Plaque assay on patient samples for QQ's paper. <br>
* Casein in human serum experiments ongoing. (HM) <br>
<br>
<br>
† Integrated chip for flu(SPE+RT+PCR) (Lead: Qingqing) <br>
† Integrated chip for flu(SPE+RT+PCR) (Lead: Qingqing) <br>
Line 67: Line 71:
<br>
<br>
'''‡ PATH Grant (Lead:Cathie, Team:Frank, Sean, Mark, Jake Trueb (ME))''' <br>
'''‡ PATH Grant (Lead:Cathie, Team:Frank, Sean, Mark, Jake Trueb (ME))''' <br>
* Phone call with PATH 3/22. Frank has class 2-4 but will come ASAP.<br>
*.<br>
* Frank: Two- and three-week storage experiments completed.  Four-week to be done next Wed.  Longer-term (2, 3, 4-month) in storage.  +/- carrier RNA not yet completed.  Currently writing up final report.<br>
* Frank: Two- and three-week storage experiments completed.  Four-week to be done next Wed.  Longer-term (2, 3, 4-month) in storage.  +/- carrier RNA not yet completed.  Currently writing up final report.<br>
* Sean: First set of data is in (for the 700 nm silica straws). Today (4/15) I will finish the straws for the 150 nm silica and the SPE batters for the 14 nm silica.  Tomorrow I plan on running and PCR'ing samples for the 150 nm silica straws as well as making the straws for the 14 nm silica.  On Saturday I will run and PCR samples for the last set of straws. <br>
* Sean: First set of data is in (for the 700 nm silica straws). Today (4/15) I will finish the straws for the 150 nm silica and the SPE batters for the 14 nm silica.  Tomorrow I plan on running and PCR'ing samples for the 150 nm silica straws as well as making the straws for the 14 nm silica.  On Saturday I will run and PCR samples for the last set of straws. <br>
* Mark: as of 3/17/10 up to 10% recovery from 10 ng input sample with water elution.  Also up to 13% recovery with 100ng/straw.  Loaded two sample groups for multiple temperatures for 1-week and 2-week/1-month time points.  1-week trial completed as of 3/24. Results peak at 20% (-70C) and decrease with temperature.  Next to test straws with Qiagen buffer.<br>
* Mark: as of 4/15/10 up to 30% recovery from 10 ng input sample with water elution.  Also up to 13% recovery with 100ng/straw.  1-week trial completed as of 3/24. Results peak at 20% (-70C) and decrease with temperature.  2-month and 1-month trials complete, resulting in further degradation than in the 1-week trial. 4- and 6-month trials still in storage.<br>
<br>
<br>
'''‡ IIH Senior Project.'''<br>
'''‡ IIH Senior Project.'''<br>
* Progress Report 2  due today
* ELISA done, Talking to Phil Allen about proper imaging
* Finished image and data analysis of 100 micrometer films. <br>
* Writing report
* Working on 44 micron films. <br>
* Drafting ELISA. <br>


<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->

Revision as of 12:27, 15 April 2010

Project name <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>

15 April 2010 Lab Meeting

Jake Presentation.

‡ Announcements

‡ Flu R01:Integration

  • meetings every other M 1-3pm. 705.


    • SEQUENCING WORK
  • for PCR just do more reactions, pool and etoh precipitate.
    • For HDA, we need to explore cloning.

† HDA (Lead: Jaephil, Team:Sonali)

  • IBC Approval or 720 to work with real C.diff samples.
  • Patient Samples - dilution experiments (MM/SH)
  • Start planning R01 for Submission on 10/5/10. MM, CMK.
  • HDA mix in dried form - Expecting it from BH -- ON HOLD.
  • warm start here (Give some to Lisa)
  • QQ preliminary chip work
  • Sequence all output
  • 2nd HDA design - "microSPE" + "Flu primer" + "HDA in a cup" + "Detection kit from Biohelix"


† Sample Concentration (Lead: Jane, Team: Jaephil)

  • Straight channel adhesion test PCR result expected. From 4/6 result, PDMS 4mm wide channel doesn't show decrease in output RNA over time
  • Straight 1mm and 4mm PDMS-Teflon channel adhesion test pending PCR result.
  • Try collection vs dilutions, collection vs time, need binding constant to quantify results.
  • Samples expected from Fauchet group. Contact today. ??? - CMK will check again.


† SPE Column Optimization for DNA/RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan)
  • (Almost done) Jessie will run chips with serial virus dilutions from 1:1 to 1:1,000,000 to re-do previous dilution experimnent with WHO SYBR green assay on chip.


† Integrated chip for flu(SPE+RT+PCR) (Lead: Qingqing)

  • Real copy number of previous human samples. So QQ is working with the higher concentration samples. Range is 10^6-10^8 of copy number/ml.
  • REVISIT the % recovery number.
  • QQ tried: more enzyme, Tween 20, BSA amounts.
  • integrated flu chip paper has been send to cathie, wait for revision.
  • PCR1 will combine with PCR2, waitting for revision (CMK)


‡C. diff Project (Cathie, Sonali, Satish Singh, Lisa J., His post doc )

  • See email notes.


‡ Coulter Flu Fraunhofer Project (Lead: Sonali, Team: Sonali, Jessie, Cathie, CMI Folks, Qingqing)

  • New meeting time, T, 9:30 am every other week. MEETINGS CANCELLED NEXT WEEK (4/20).


‡ Agilent Automated Sample Preparation (Lead: Alex)

  • Paper on HotDog - with CMK/ASB


‡ COBRA (Lead: Jaephil, Team: Cathie, Jane for virus only, PHO folks)

  • Evap paper - Additional experiment for Fig 3. JD says will send by Friday (4/16).


‡ Biointerfaces group (Lead: MinCheol, Team: Cathie, MCK, Wong and Meller folks)
* Cathie will submit paper.
‡ CIMIT- Sepsis (Lead:Cathie, Team:TBA)

  • Sample collection ongoing.


‡ PATH Grant (Lead:Cathie, Team:Frank, Sean, Mark, Jake Trueb (ME))

  • .
  • Frank: Two- and three-week storage experiments completed. Four-week to be done next Wed. Longer-term (2, 3, 4-month) in storage. +/- carrier RNA not yet completed. Currently writing up final report.
  • Sean: First set of data is in (for the 700 nm silica straws). Today (4/15) I will finish the straws for the 150 nm silica and the SPE batters for the 14 nm silica. Tomorrow I plan on running and PCR'ing samples for the 150 nm silica straws as well as making the straws for the 14 nm silica. On Saturday I will run and PCR samples for the last set of straws.
  • Mark: as of 4/15/10 up to 30% recovery from 10 ng input sample with water elution. Also up to 13% recovery with 100ng/straw. 1-week trial completed as of 3/24. Results peak at 20% (-70C) and decrease with temperature. 2-month and 1-month trials complete, resulting in further degradation than in the 1-week trial. 4- and 6-month trials still in storage.


‡ IIH Senior Project.

  • ELISA done, Talking to Phil Allen about proper imaging
  • Writing report


Retrieved from "https://openwetware.org/mediawiki/index.php?title=Klapperich_Lab:Notebook/Lab_Meeting_Notes/2010/04/15&oldid=407340"