Shreffler:Resources

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Protocols

• Bacterial Cell Culture
• Basophil Activation by Flow
  • BioCSI
  • JAX
• CFSE Labeling
• Cell Counting
• Confocal Protocols
• Cryopreserving PBMCs
• EthidiumMonoazideBromide
• FoxP3Intracellular
• Intra-Cellular Staining
• Isolation of PBMCs
• Jurkat Transfection for RA signaling project
• Milk Program Project
• MonocyteDerivedDendriticCells
• MurineBmdcAssay
• Oxidative Burst
• Periodate Treatment of PN extract
• Pervanadate preparation
• ProteinLabeling
• RT-PCR for JAX Project
• Standard_Buffers_Solutions_Media
• Surfacemarker staining for Flow Cytometry
• TcellSkewing_mDC
• TailVeinInjection
• tSyk measurement in basophils
• TregStaining
• attachment:DIG-OVA.doc

Reading List

1. Steinfelder S, Andersen JF, Cannons JL, Feng CG, Joshi M, Dwyer D, Caspar P, Schwartzberg PL, Sher A, and Jankovic D. The major component in schistosome eggs responsible for conditioning dendritic cells for Th2 polarization is a T2 ribonuclease (omega-1). J Exp Med. 2009 Aug 3;206(8):1681-90. DOI:10.1084/jem.20082462 |
2. Everts B, Perona-Wright G, Smits HH, Hokke CH, van der Ham AJ, Fitzsimmons CM, Doenhoff MJ, van der Bosch J, Mohrs K, Haas H, Mohrs M, Yazdanbakhsh M, and Schramm G. Omega-1, a glycoprotein secreted by Schistosoma mansoni eggs, drives Th2 responses. J Exp Med. 2009 Aug 3;206(8):1673-80. DOI:10.1084/jem.20082460 |

   two significant papers on SEA as Th2 adjuvants

3. Suzuki K, Grigorova I, Phan TG, Kelly LM, and Cyster JG. Visualizing B cell capture of cognate antigen from follicular dendritic cells. J Exp Med. 2009 Jul 6;206(7):1485-93. DOI:10.1084/jem.20090209 |

   interesting for methods related to baso confocal project

4. Geiger R, Duhen T, Lanzavecchia A, and Sallusto F. Human naive and memory CD4+ T cell repertoires specific for naturally processed antigens analyzed using libraries of amplified T cells. J Exp Med. 2009 Jul 6;206(7):1525-34. DOI:10.1084/jem.20090504 |

   another methodology paper perhaps for frequency of allergen-specific T cells

5. Campbell JD, Buckland KF, McMillan SJ, Kearley J, Oldfield WL, Stern LJ, Grönlund H, van Hage M, Reynolds CJ, Boyton RJ, Cobbold SP, Kay AB, Altmann DM, Lloyd CM, and Larché M. Peptide immunotherapy in allergic asthma generates IL-10-dependent immunological tolerance associated with linked epitope suppression. J Exp Med. 2009 Jul 6;206(7):1535-47. DOI:10.1084/jem.20082901 |

   madhan's project

6. la Sala A, He J, Laricchia-Robbio L, Gorini S, Iwasaki A, Braun M, Yap GS, Sher A, Ozato K, and Kelsall B. Cholera toxin inhibits IL-12 production and CD8alpha+ dendritic cell differentiation by cAMP-mediated inhibition of IRF8 function. J Exp Med. 2009 Jun 8;206(6):1227-35. DOI:10.1084/jem.20080912 |

   mechanisms of CT

7. Duhen T, Geiger R, Jarrossay D, Lanzavecchia A, and Sallusto F. Production of interleukin 22 but not interleukin 17 by a subset of human skin-homing memory T cells. Nat Immunol. 2009 Aug;10(8):857-63. DOI:10.1038/ni.1767 |

   characterization of a distinct Th subset producing IL-22; relevance to PN adjuvant?, second independent paper also published back-to-back

8. Okamoto M, Van Stry M, Chung L, Koyanagi M, Sun X, Suzuki Y, Ohara O, Kitamura H, Hijikata A, Kubo M, and Bix M. Mina, an Il4 repressor, controls T helper type 2 bias. Nat Immunol. 2009 Aug;10(8):872-9. DOI:10.1038/ni.1747 |

   new transcriptional regulator for Th2 described, could be useful for Th2 phenotyping

Scripts

R analysis

• File:Array flinterman.R
  • script used for Flinterman paper -- one of the first 'BATCH' functions for analysis of multiple data files
• File:Jax pcr.R
  • for analysis of pbmc pcr data in the JAX project -- good use of %in% and grep as well as loops to mash data together from two sources
• File:Milk mash script.R
  • script used by Wayne and Lara to do interim analysis of milk basophil data
• File:AAAAI rCode.R
  • Lara's analysis script for her abstract using data file, 20080818_BaselineBasoDataWithClinicalGroups.csv. Example of 2-way ANOVA.
• File:Duke extract script.R
  • Wayne's analysis of duke peanut mucosal IT data that extracts text files from FlowJo analysis data directory tree and also mashes up baso data with clinical data file and produces time series data with multiple plots using layout for peanut, controls, egg by treatment or placebo

Courses

• R analysis 2009