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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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| - | =17 May 2010 Lab Meeting=
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| - | '''‡ Announcements'''<br>
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| - | * New people: Ajeghannie, Andy, Samantha(next week). <br>
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| - | * Lab meeting weekly M 1-3pm Room 705.
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| - | '''†Bacteria Trapping work (Jason K)'''<br>
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| - | '''†Wave 80 project (Andy)'''<br>
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| - | '''‡ Flu R01:Integration''' <br>
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| - | * Need new meeting time.
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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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| - | * MM's agenda requested for meeting 1) The number of positive and negative samples to be analyzed for the grant (Cathie)<br>
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| - | * 2) Key pieces of data needed for each sample (PFU/ml, copy #/ml, chip PCR, tube PCR, TC)? (Cathie, MM) <br>
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| - | * 3) Jessie will describe our inventory (# samples from BUMC, #samples from BIDMC, break down by the number of aliquots per sample) -- handle on what samples are available to complete item 2) above <br>
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| - | * 4) Decide what samples we will use to acheive item 2 above -- what QQ's team will use for on-chip experiments
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| - | * 5) Decide who will accomplish what in item 2) above -- what each person is responsible for
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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, clone with TOPO TA when cleared for cloning in 720 (MM). <br>
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| - | ** Shichu needs to be trained for cloning <br>
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| - | ** dxs PCR primers worked for HDA in tube. Positive results on chip with 0.05% BSA blocking and 2X warm start enzyme. <br>
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| - | ** dxs HDA -- need to repeat to confirm -- stock primer tubes contaminated. New primers arriving today. Set up in virus or RNA extraction hood <br>
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| - | ** did not evaluate Isoamp II enzyme yet with BSA and 2X. Also did not evaluate 4X ISoampII or III enzyme. <br>
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| - | ** Temp problem solved: chip dxs HDA -- using dry heat bath, insulator and styrofoam box on chip to set temp at 65C +/- 0.5-1C <br>
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| - | ** Temp -- Try QQ's thermal conductive tape between chip and heat block surface to see if <0.5-1C variation (MM) <br>
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| - | ** Chip ladders solved: chip dxs HDA -- ladders from degraded gDNA prevented by 10% bleach for 20 min <br>
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| - | ** Summary dxs hda: Cannot fabricate nuclease free chips in 709. Cleaning chips post-production is critical. Cleaning protocol for HDA chips is 10% bleach 20 min, 300ul water, heat at 95C 5 min on PCR room dry bath, vacuum aspirate condensation to dry. Use bleached containers to soak chips (stored in PCR room). Do all this in the PCR room on fabrication bench. Store clean chips in PCR room. Load with reaction in PCR room. Amplify outside PCR room.
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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 <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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| - | * Straight channel adhesion test PCR result from PDMS-PDMS, PDMS-Teflon channels reported: in a shorter time (<1hr), more collection from Teflon channel, regardless of wide/narror. In a long time up to 5 hr, Teflon or PDMS, narrow or wide didn't have difference <br>
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| - | * Now making COP test chips for testing COP-Teflon channel adhesion. The same method will be followed <br>
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| - | * New design integrating evap + SPE in progress. Will cut to test prototype.
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| - | <br>
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| - | '''† SPE Column Optimization for DNA/RNA. (Lead: Jessie)''' <br>
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| - | * (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>
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| - | * <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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| - | * Shichu to learn Qiagen extractions and then teach to one or two undergrads. <br>
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| - | * Shichu to learn stool sample prep for use on-chip from Lisa with Ahjegannie. <br>
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| - | * Shichu to use prepped sample for on-chip integrated extraction and PCR with QQ's chip (learn from QQ). <br>
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| - | '''‡ Coulter Flu Fraunhofer Project (Lead: Sonali, Team: Sonali, Jessie, Cathie, CMI Folks, Qingqing)'''
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| - | * Meeting this week at 9:30am in Fraunhofer <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 - Cathie almost ready to submit. <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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| - | * Sample collection ongoing. <br>
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| - | <br>
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| - | '''‡ PATH Grant (Lead:Cathie, Team:Jake, Samantha)<br>
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| - | * Samantha Byrnes will start in one week.
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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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