15 April 2010 Lab Meeting
Jake Presentation.
‡ Announcements
‡ Flu R01:Integration
- meetings every other M 1-3pm. 705.
† HDA (Lead: Jaephil, Team:Sonali)
- Patient Samples - dilution experiments (MM/SH)
- Start planning R01 for Submission on 6/5/10. MM, CMK.
- HDA mix in dried form - Expecting it from BH -- ON HOLD.
- warm start here
- 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. Longer time more retention.
- Try collection vs dilutions, collection vs time, need binding constant to quantify results.
- New multi-channel chip mold is ready for making chips
- Samples expected from Fauchet group. Contact today.
† SPE Column Optimization for DNA/RNA. (Lead: Sonali, Team: Hussam, Jessie, Brendan)
- (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.
- 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)
- Plaque assay on patient samples for QQ's paper.
- Casein in human serum experiments ongoing. (HM)
† 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 )
‡ 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))
- Phone call with PATH 3/22. Frank has class 2-4 but will come ASAP.
- 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 straws is finished (700 nm at varying SPE values, 140 SPE down to 0 SPE in increments fo 20 SPE). Samples to be run tomorrow morning (4.2.10). NB: these straws have only 16ul of monolith in them. This could possibly affect the outcome, but we anticipate that if all straws for all silica sizes are made with the same 16ul amount, the results will be just as reliable as if ~50ul had been used.
- 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.
‡ IIH Senior Project.
- Progress Report 2 due today
- Finished image and data analysis of 100 micrometer films.
- Working on 44 micron films.
- Drafting ELISA.
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