29 November 2010 Lab Meeting

‡ Announcements

• 2-4pm
  
• SONALI is up to talk.
  
• Jake and Sam next week.
  
• 
  

†Trapping Mycobacteria (Jason)

• Can induce cells multiple times ("triple peak")
  
• Trapping monolayer is hard due to device architecture
  
• Making new device and doing more induction expts
  

†Nanomedicine

• Sunil
  

†Wave 80 project (Andy/Jane)

• Optimization for eliminating non-specific PCR products after 1st-strand synthesis : A) Increasing annealing temperature to 65 C helps, and B) Treating 1st-strand products with RNaseA helps (AF)
  
• Will try time-course on full pol ssDNA synthesis to minimize E. coli lysis during M13 transfection (AF)
  
• Ran Boom buffer through monolith only straws. Will bDNA the eluent this week.(JZ)
  
• Process flow throughs. (JZ)
  
• Chentian - Figuring out a way to do silica channels. First pass: making plug with monolith.
  
• ABI Taqman for HIV. Waiting for that to arrive. For LTR instead of gag. (MM)
  
• Currently doing "hourly" extractions of pure RNA with and without stablizer. (SAB)
  
• Uploaded pictures of blackbird fixture to central desktop for Wave 80 team. (SAB)
  

‡ Flu R01:Integration

• Paper for chip with Cathie.
  

 need to make an outline 

• paper for biostatistics. Thinking phase Sonali.
  
• Sequence 10 more products - for weekly QC.
  

 done

• Run weekly negative gels.
  

 done

† HDA (Lead:Sonali)

• Start planning R01 for Submission on 2/5/11. MM, CMK.
  
• 
  

† Sample Concentration (Lead: Jane)

• Qiagen and SPE done in parallel on original and concentrated samples.
  
• 3 new fixtures made. Tried and worked. Need deburring.
  
• New mask and mold made. New chip in progress.
  
• Ran exp at Connor lab with current chip and new fixture on fluorescent VSV, plaque assay and imaging results pending.
  

† SPE Column Optimization for DNA (Sam and Sonali)

• Sr project working on DNA extraction using glycogen ppt method.
  

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

• HDA in tube to test extracted "ELISA negative samples", the result is different from real-time PCR
  
• Run gel to check real-time PCR products, product bands are really faint (different from before)
  
• In the process of cloning HDA positive samples to check whether they are true positive
  
• Run regular PCR with Sara’s old primers, results are inconsistent with HDA and real-time PCR
  

‡ Coulter Flu Fraunhofer Project (Sonali)

• They still need RNA from us.
  

‡ Automated Sample Preparation (Lead: Alex)

‡ Biointerfaces
* submitted.

‡ CIMIT- Sepsis (Lead:Cathie, Team: Alex)

• negative control problem in the 16s assay. TaqMan?
  

‡ PATH Grant (Lead:Cathie, Team:Jake, Samantha)

• Need to order more straws.
  
• Working on new blood lysis procedure with Tween 20, proteinase K and GuSCN.
  
• Working on NCIIA Grant, due Dec. 3rd.
  
• Starting extractions on actual devices.
  
• RNA and DNA extractions with varied lysis buffers using glycogen ppt method.
  
• Altering check valve on device air accumulator.