Journal club articles -BCM Program in Immunology

Papers presented in Journal Club Program in Immunology Baylor College of Medicine. Please post most recent at top of list.JohnRodgers 20:52, August 5, 2010 (UTC)

9/15/2010 Satoh et al. (2010). The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nature Immunology. Transgenic mice with a diverse human T cell antigen receptor repertoire. Nature Medicine (8 August 2010)
 * 9/22/2010 Schmidt et al. (2010). Crucial role for human toll-like receptor 4 in the development of contact allergy to nickel. Nature Immunology 11 (9), 814-819.
 * 1) what are HUVEC and how are they obtained and prepared?
 * 2) how do we obtain concentrations from an ELISA assay? What is needed to have high confidence is the value obtained?
 * 1) Fig 6ab: How does the ChIP-Seq method work?
 * 2) What is chitin? Is it a well-defined substance? Are there species differences? Why is it sonicated. How is it recognized by cells?
 * 9/8/2010 Gao et al.(2010). Autophagy negatively regulates wnt signalling by promoting dishevelled degradation. Nature cell biology 12 (8), 781-790...
 * 1) How does the TopFlash system work? How fast does it respond to Wnt signaling? What is the half-life of the reporter?
 * 2) Why is DMSO used as the vehicle in the rapamycin experiments? What is the EC50 of rapamycin in this kind of experiment? What is the half-life of rapamycin in culture?
 * 3) In Fig. 1d, how were the fold-changes and their errors calculated?
 * 4) What is correlation? What is the difference between Pearson's r and Spearman's r and why was the latter used in this paper?
 * 9/1/2010 Li et al.(2010)
 * 1) How are yeast artificial chromosomes (YAC) constructed and integrated into a mammalian genome?
 * 2) How was the antibody specific for human Vß5-5 generated and shown to be specific for human Vß5-5?
 * 3) How was the HLA-A*0201-H2-Db-huß2m fusion gene constructed and why is it used in this paper?
 * 4) How was the MelanA26-35 epitope identified?




 * 8/25/2010 Herber et al. 2010. Lipid accumulation and dendritic cell dysfunction in cancerNature Medicine, Vol. 16, No. 8. (11 August 2010), pp. 880-886.
 * 1) BODIPY 493/503. How does it work? How specific is it. Does it stain all membranes? Lipid Rafts? How big is it? Does it extend beyond the “plane” of the membrane? What and where is thefluorescent moiety? How long does is stay in the “lipid” of the cell? Is it metabolized? http://themethodologicalannex.wikia.com/wiki/BODIPY_fluorescent_marker
 * 2) “A low-pressure sort was performed on the BD FACSAria cell sorter with a 100 iμm nozzle.” What does this mean? What is the significance of “low-pressure” and of this particular nozzle? http://themethodologicalannex.wikia.com/wiki/Cell_sorting

'*8/18/2010 Kondilis-Mangum et al. 2010 Transcription-dependent mobilization of nucleosomes at accessible TCR gene segments in vivo.Journal of immunology '184'', No. 12. (15 June 2010), pp. 6970-6977''' * '*[http://www.citeulike.org/group/13793/article/7465836 8/11/2010 Divangahi et al''. (2010) Eicosanoid pathways regulate adaptive immunity to Mycobacterium tuberculosis. Nature Immunology, Vol. 11, No. 8. (11 August 2010), pp. 751-758.]'''
 * 1) How was the TCR Eß enhancer KO made? Please explain in detail
 * 2) How were the nucleosomes isolated? How does the sucrose gradient work? Nucleosome isolation


 * 1) How was the Ptges -/- mouse made? Is the entire gene deleted or only part? Prostaglandin E Synthase (PTGES) Knockout
 * 2) How does the CD11c DTR system work? Is this a knock-in or is it a promoter/cDNA construct? How efficient is the deletion? How specific is the deletion for CD11c+ cells? Diphtheria Toxin Receptor -Transgenic mice
 * 3) How does the Intox nose-only exposure unit work? How “nose-only” is it? Intox nose-only exposure unit
 * 4) Why would one use Dunnett’s post test vs. Bonferroni’s post-test? Multiple Comparisons tests


 * 8/06/2010 Alves-Filho et al. 2010.Interleukin-33 attenuates sepsis by enhancing neutrophil influx to the site of infection. Nature Medicine, Vol. 16, No. 6. (16 June 2010), pp. 708-712.


 * 1) How was the neutrophil chemotaxis assay conducted? Chemotaxis


 * 1) What is myeloperoixdase (MPO) and how is it assayed? Is the assay linear? What is 1 unit of MPO activity?Myeloperoxidase (MPO)
 * 2) "We performed CLP in BALB/c mice, the most relevant animal model for clinical sepsis.” How is this performed in detail, what do the clinical scores mean- how do they relate to human disease, and what makes BALB/c the “most relevant animal model”?  Cecal Ligation and Puncture (CLP)
 * 3) what is GRK2? How specific are the inhibitors? What is the IC50 for the enzyme in solution? What doses are used experimentally? What are the half-lives of the inhibitors in culture? G protein-coupled receptor kinase-2 (GRK2)