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| - | |style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Project name</span>
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| - | |style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html> </html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
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| - | <!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
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| - | =14 June 2010 Lab Meeting=
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| - | '''‡ Announcements'''<br>
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| - | * No presentation - Agenda items only - BRING DATA to discuss. <br>
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| - | * Lab meeting weekly M 1-3pm Room 705.
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| - | '''†Trapping Mycobacteria (Jason)'''<br>
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| - | *No new data this week (Jason has quals).
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| - | *Revised Grant Proposal: JUNE 21<br>
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| - | *Can successfully trap mycobacteria in device.<br>
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| - | *Optimizing things like cell concentration, Tween concentration to get best trapping.<br>
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| - | *Waiting on oscillating strains to test induction.<br>
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| - | *Cells stick to "ceiling" and "floor" of all channels. Seems like truly hydrodynamic trapping isn't really necessary. Want to try making a simple straight-channel device and test its performance (after June 21).<br>
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| - | <br>
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| - | '''†Wave 80 project (Andy)'''<br>
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| - | *IBC protocol meeting 6/14 (Mon) 3-4pm with EHS before the main meeting on Tues.
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| - | '''‡ Flu R01:Integration''' <br>
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| - | '''* Weekly meetings Tuesday 1-2 pm. <br>'''
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| - | * List people required to attend meeting: MM, JC, Brendan, Ahjegannie, Chris? Send notes to QQ, MM will brief her when she's back <br>
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| - | * 1) 73 (+) and 73 (-) samples(Cathie)<br>
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| - | * 2) Key pieces of data needed for each sample:PFU/ml for a subset of samples, tube PCR & copy #/ml all, chip PCR all, TC all <br>
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| - | * 3) Jessie will input the inventory (# samples from BUMC, #samples from BIDMC, break down by the number of aliquots per sample) <br>
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| - | * 4) Use BIDMC samples based on ones Nira P. has culture/PCR data for.
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| - | * 5) JC -- PFU/ml, copy number PCR; MM -- culture and RNA extractions for JC copy# PCR; BC, QQ, AS, CH -- chip PCR
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| - | * 6) Set timelines for each task for each person
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| - | ** SEQUENCING WORK<br>
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| - | * for PCR just do more reactions, pool and etoh precipitate. <br>
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| - | ** For HDA, re-try with min-elute PCR purification kit to concentrate product, remove dimers for TOPO TA (MM). <br>
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| - | ** Andy started training Shichu for cloning, To be continued as needed. <br>
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| - | ** Warm start enzyme -- less dimers but waters always come up positive for E.coli. Go back to regularly sold enzyme IsoAmp II. Get dimers, but difference in size (50-70 bp) allows for distinguishing from products (113bp)on gels. <br>
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| - | ** Warm start enzyme is causing false positives -- New primers, New water, new kit, RNA hood in BL2 lab used with RNA pipets <br>
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| - | ** Use on bleached cut chips, with 2X enzyme amount and 0.05% BSA blocking on dry bath <br>
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| - | ** Dry heat bath, thermal conductive tape, insulator and styrofoam box on chip to set temp at 65C +/- 0.5 after 20 min. <br>
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| - | **
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| - | * Check other methods of heating (SH). <br>
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| - | '''† HDA (Lead:Sonali)'''<br>
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| - | * Start planning R01 for Submission on '''10/5/10.''' MM, CMK. <br>
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| - | * HDA mix in dried form - Expecting it from BH -- ON HOLD. <br>
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| - | * <br>
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| - | * QQ preliminary chip work <br>
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| - | * Sequence all output -- see cloning section above <br>
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| - | * 2nd HDA design - "microSPE" + "Flu primer" + "HDA in a cup" + "Detection kit from Biohelix"<br>
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| - | <br>
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| - | '''† Sample Concentration (Lead: Jane)''' <br>
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| - | * New design integrating evap + SPE in progress. Cut chip with valve is good at fluid handling. <br>
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| - | * Baby aspirator helps with sample collection for off chip mixing <br>
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| - | * Multilayer design transfer sequence: cut PCR plate cover (polyolefin or polyester) - PDMS inverse mold - treat with HPMC - PDMS mold - epoxy mold - hot emboss onto COP chip <br>
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| - | <br>
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| - | '''† SPE Column Optimization for DNA/RNA. (Lead: Jessie)''' <br>
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| - | * Combined dilution experiment data
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| - | * SPE with and without silica - chips ran but don't have enough PCR reagents.<br>
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| - | <br>
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| - | '''† Integrated chip for flu(SPE+RT+PCR) (Lead: Qingqing)''' <br>
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| - | * 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. <br>
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| - | * REVISIT the % recovery number. <br>
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| - | * QQ tried: more enzyme, Tween 20, BSA amounts. <br>
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| - | * integrated flu chip paper has been send to cathie, wait for revision.
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| - | <br>
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| - | * PCR1 will combine with PCR2 (CMK)<br>
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| - | <br>
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| - | '''‡C. diff Project''' (Cathie, Sonali, Satish Singh, Lisa J., His post doc )'''<br>
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| - | * TOPO-cloning of reference PCR products from geonomic C.diff and patient-specific (#30) sample needs to be redone with normal Taq / dNTP; will not clone with dUTP-modified master mix from Applied Biosystems.
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| - | * 6/23 next meeting. <br>
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| - | <br>
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| - | '''‡ Coulter Flu Fraunhofer Project (Lead: Sonali, Team: Sonali, Jessie, Cathie, CMI Folks, Qingqing)'''
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| - | *
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| - | <br>
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| - | '''‡ Agilent Automated Sample Preparation (Lead: Alex)'''<br>
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| - | * Paper on HotDog - with CMK/ASB. still 5/17 <br>
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| - | <br>
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| - | '''‡ COBRA (Lead: Jaephil, Team: Cathie, Jane for virus only, PHO folks)<br>'''
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| - | * Evap paper - submitted. <br>
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| - | <br>
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| - | '''‡ Biointerfaces group (Lead: MinCheol, Team: Cathie, MCK, Wong and Meller folks)'''<br>
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| - | '''* Latest draft with Cathie.<br>'''
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| - | <br>
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| - | '''‡ CIMIT- Sepsis (Lead:Cathie, Team:TBA)'''<br>
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| - | * <br>
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| - | <br>
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| - | '''‡ PATH Grant (Lead:Cathie, Team:Jake, Samantha)<br>
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| - | * Set up meeting with Jeff Blander. <br>
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| - | * <br>
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| - | <!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
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| - | |}
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| - | __NOTOC__
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