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| - | |style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> General Lab Meeting </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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| - | =9 August 2010 Lab Meeting=
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| - | '''‡ Announcements'''<br>
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| - | * No presentation.<br>
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| - | ""* EVERYONE bring summary slides (1-3 only). <br>'''
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| - | *Lab meeting same time fall M 1-3pm <br>
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| - | '''†Trapping Mycobacteria (Jason)'''<br>
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| - | * Can trap and induce cells every time, and watch them turn off after switching to non-inducing media.
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| - | * Having trouble achieving a second induction (On/Off/On). Concerns about 'health' of cells after 5-6 hours in device.
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| - | * Cells at 37C, but I don't see cell division even though experiment lasts for 2 doubling times.
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| - | * Ordered a standard Invitrogen live-dead assay kit to help figure out what's going on.
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| - | * --> Has anyone in the room tried doing the live/dead on-chip before? I don't think it will be too difficult to do.
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| - | <u> Old summary slides for Jason (from 8/2):</u> [[Image:JasonSlidesModified.ppt|JasonSlidesModified.ppt]]<br>
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| - | <br>
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| - | '''†Wave 80 project (Andy/Jane)'''<br>
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| - | *Did 1 baseline run in parallel for intact particles, RNA from SPE, and RNA from Qiagen.
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| - | *Will start making plasmid templates for extraction process monitoring using real-time PCR (backup to using only bDNA assay strips)
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| - | '''‡ Flu R01:Integration''' <br>
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| - | '''* Weekly meetings Tuesday 3-4 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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| - | ** 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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| - | * SPE yield is much lower compared with Qiagen only in conc sample but not in PBS wash.
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| - | * Patient sample run in preparation: making new chips to solve nanoport problem <br>
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| - | <br>
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| - | '''† SPE Column Optimization for DNA/RNA. (Lead: Jessie)''' <br>
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| - | * Patient samples: <10^4 cp/mL, ~10^6 cp/mL, and >10^5 cp/mL detection limit with SPE.
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| - | * RNA ladder: elute RNA length of 200 to 1500 bases, but not beyond (up to 6000 bases).
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| - | * Chitosan modified silica yielded <10% while regular channel yielded ~50% when purified flu RNA (from Qiagen extraction) is loaded.
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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. <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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| - | *Chip HDA reaction: Cloning successful with Patient #30 - derived HDA chip reactions w/ pGEM vector
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| - | *send SH the HDA in a cup paper draft from JD.(CMK) <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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| - | * Meetings Fridays/every other <br>
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| - | <br>
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| - | '''‡ Automated Sample Preparation (Lead: Alex)'''<br>
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| - | * Paper on HotDog - with CMK/ASB. 7/2
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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 - accepted! <br>
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| - | * Cathie corrections today 8/2. <br>
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| - | <br>
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| - | '''‡ Biointerfaces<br>
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| - | '''* Latest draft with Cathie.<br>'''
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| - | <br>
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| - | '''‡ CIMIT- Sepsis (Lead:Cathie, Team: Alex)'''<br>
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| - | * Had meeting with Prof. Hauser (7/9) and worked with Kiyo and Tolga in Harvard Lab on extracting DNA from Plasma with Qiagen kit. <br>
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| - | * Preparing experimental plan for next steps. <br>
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| - | * Got introduction to procedures for 720 and PCR room by Sonali. <br>
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| - | * Things to clarify: -safety issues and regulations related to transport and work on human samples. <br>
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| - | <br>
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| - | '''‡ PATH Grant (Lead:Cathie, Team:Jake, Samantha)<br>
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| - | * new flow rate data for altered polymer formulation <br>
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| - | * RNA extraction using altered polymer formulation - SPE 0 vs SPE 100 (it works!!!) <br>
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| - | * upcoming experiments <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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