Chicken Journal club (Bible hour)

Paper Schedule 2013

(for Vintage Literature click here)

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon.

Tuesday, March 8th, 2016 - Madeleine

Ze X, Duncan SH, Louis P, Flint HJ.
ISME J. 2012 Aug;6(8):1535-43. doi: 10.1038/ismej.2012.4. Epub 2012 Feb 16.

PubMed

Functional specialization of gut CD103+ dendritic cells in the regulation of tissue-selective T cell homing

Tuesday, Feburary 23rd, 2016 - Stephanie

Johansson-Lindbom B, Svensson M, Pabst O, Palmqvist C, Marquez G, Förster R, Agace WW.
J Exp Med. 2005 Oct 17;202(8):1063-73. Epub 2005 Oct 10.

PubMed

AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification

Tuesday, January 26th, 2016 - Sandra

Petersen-Mahrt SK, Harris RS, Neuberger MS.
Nature. 2002 Jul 4;418(6893):99-103.

PubMed

ß-adrenergic stimulation increases macrophage CD14 expression and E. coli phagocytosis through PKA signaling mechanisms

Tuesday, January 12th, 2016 - Marcel

Muthu K, He LK, Szilagyi A, Strotmon P, Gamelli RL, Shankar R
J Leukoc Biol. 2010 Oct;88(4):715-24. doi: 10.1189/jlb.0410186. Epub 2010 Jul 19.

PubMed

The lymph nodes draining the small intestine and colon are anatomically separate and immunologically distinct

Tuesday, November 17th, 2015 - Anna

Houston SA, Cerovic V, Thomson C, Brewer J, Mowat AM, Milling S.
Mucosal Immunol. 2015 Sep 2. doi: 10.1038/mi.2015.77. [Epub ahead of print]

PubMed

CRISPR-Cas systems for editing, regulating and targeting genomes

Tuesday, November 3rd, 2015 - Yasu

Sander JD, Joung JK.
Nat Biotechnol. 2014 Apr;32(4):347-55. doi: 10.1038/nbt.2842. Epub 2014 Mar 2.

PubMed

Passenger Mutations Confound Interpretation of All Genetically Modified Congenic Mice.

Tuesday, October 20th, 2015 - Francesca

Vanden Berghe T, Hulpiau P, Martens L, Vandenbroucke RE, Van Wonterghem E, Perry SW, Bruggeman I, Divert T, Choi SM, Vuylsteke M, Shestopalov VI, Libert C, Vandenabeele P.
Immunity. 2015 Jul 21;43(1):200-9. doi: 10.1016/j.immuni.2015.06.011. Epub 2015 Jul 7.

PubMed

Flow cytometry APC-tandem dyes are degraded through a cell-dependent mechanism

Tuesday, September 24th, 2015 - Mercedes

Le Roy C, Varin-Blank N, Ajchenbaum-Cymbalista F, Letestu R.
Cytometry A. 2009 Oct;75(10):882-90. doi: 10.1002/cyto.a.20774.

PubMed

Symbiotic bacteria direct expression of an intestinal bactericidal lectin.

Tuesday, September 8th, 2015 - Stephanie

Cash HL, Whitham CV, Behrendt CL, Hooper LV.
Science. 2006 Aug 25;313(5790):1126-30.

PubMed

A direct PCR approach to accelerate analyses of human-associated microbial communities

Tuesday, June 16th, 2015 - Madeleine

Flores GE, Henley JB, Fierer N.
APLoS One. 2012;7(9):e44563. doi: 10.1371/journal.pone.0044563. Epub 2012 Sep 4.

PubMed

Age, microbiota, and T cells shape diverse individual IgA repertoires in the intestine

Tuesday, June 2nd, 2015 - Sandra

Lindner C, Wahl B, Föhse L, Suerbaum S, Macpherson AJ, Prinz I, Pabst O.
J Exp Med. 2012 Feb 13;209(2):365-77. doi: 10.1084/jem.20111980. Epub 2012 Jan 16.

PubMed

Direct secretory effect of interleukin-1 via type I receptors in human colonic mucous epithelial cells (HT29-C1.16E)

Tuesday, May 12th, 2015 - Marcel

Jarry A, Vallette G, Branka JE, Laboisse C.
Gut. 1996 Feb;38(2):240-2.

PubMed

Bacterial translocation from the gastrointestinal tract of athymic (nu/nu) mice

Tuesday, May 5th, 2015 - William

Owens WE, Berg RD.
Infect Immun. 1980 Feb;27(2):461-7.

PubMed

Graphical Perception: Theory, Experimentation, and Application to the Development of Graphical Methods

Tuesday, April 14th, 2015 - Yasu

William S. Cleveland and Robert McGill
Journal of the American Statistical Association
Vol. 79, No. 387 (Sep., 1984), pp. 531-554

Journal website

Graphical perception and graphical methods for analyzing scientific data

Tuesday, April 14th, 2015 - Yasu

Cleveland WS, McGill R.
Science. 1985 Aug 30;229(4716):828-33.

PubMed

CX3CR1-mediated dendritic cell access to the intestinal lumen and bacterial clearance

Tuesday, March 31st, 2015 - Anna

Niess JH, Brand S, Gu X, Landsman L, Jung S, McCormick BA, Vyas JM, Boes M, Ploegh HL, Fox JG, Littman DR, Reinecker HC.
Science. 2005 Jan 14;307(5707):254-8.

PubMed

Generation of gut-homing IgA-secreting B cells by intestinal dendritic cells

Tuesday, March 24th, 2015 - Li Hai

Mora JR, Iwata M, Eksteen B, Song SY, Junt T, Senman B, Otipoby KL, Yokota A, Takeuchi H, Ricciardi-Castagnoli P, Rajewsky K, Adams DH, von Andrian UH.
Science. 2006 Nov 17;314(5802):1157-60.

PubMed

Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity

Tuesday, March 3rd, 2015 - Francesca

Markle JG, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, von Bergen M, McCoy KD, Macpherson AJ, Danska JS.
Science. 2013 Mar 1;339(6123):1084-8. doi: 10.1126/science.1233521. Epub 2013 Jan 17.

PubMed

Characterization of diet-dependent metabolic serotypes: analytical and biological variability issues in rats

Tuesday, Febrary 3rd, 2015 - Mercedes

Vigneau-Callahan KE1, Shestopalov AI, Milbury PE, Matson WR, Kristal BS.
J Nutr. 2001 Mar;131(3):924S-932S.

PubMed

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

Tuesday, January 20th, 2015 - Kathleen

Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW.
BMC Biol. 2014 Nov 12;12:87. doi: 10.1186/s12915-014-0087-z.

PubMed

Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site

Tuesday, December 16th, 2014 - Sandra

Bostrom J, Yu SF, Kan D, Appleton BA, Lee CV, Billeci K, Man W, Peale F, Ross S, Wiesmann C, Fuh G.
Science. 2009 Mar 20;323(5921):1610-4. doi: 10.1126/science.1165480.

PubMed

Differential secretion of cytokines

Tuesday, December 2nd, 2014 - Yasmin

Moqbel R, Coughlin JJ.
Sci STKE. 2006 Jun 6;2006(338):pe26.

PubMed

Protection from lethal gram-negative bacterial sepsis by targeting Toll-like receptor 4

Tuesday, November 18th, 2014 - William

Roger T, Froidevaux C, Le Roy D, Reymond MK, Chanson AL, Mauri D, Burns K, Riederer BM, Akira S, Calandra T.
Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2348-52. doi: 10.1073/pnas.0808146106. Epub 2009 Jan 30.

PubMed

Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5

Wednesday, November 5th, 2014 - Yasuhiro

Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, Sitaraman SV, Knight R, Ley RE, Gewirtz AT.
Science. 2010 Apr 9;328(5975):228-31. doi: 10.1126/science.1179721. Epub 2010 Mar 4.

PubMed

Molecular analysis of commensal host-microbial relationships in the intestine

Tuesday, September 30th, 2014 - Li Hai

Hooper LV1, Wong MH, Thelin A, Hansson L, Falk PG, Gordon JI.
Science. 2001 Feb 2;291(5505):881-4.

PubMed

Autoantigen recognition is required for recruitment of IGRP(206-214)-autoreactive CD8+ T cells but is dispensable for tolerance

Tuesday, September 16th, 2014 - Francesca

Wang J, Tsai S, Han B, Tailor P, Santamaria P.
J Immunol. 2012 Sep 15;189(6):2975-84. doi: 10.4049/jimmunol.1201787. Epub 2012 Aug 20.

PubMed

Simultaneous amplification and detection of specific DNA sequences

Tuesday, August 12th, 2014 - Anna

Higuchi R1, Dollinger G, Walsh PS, Griffith R.
Biotechnology (N Y). 1992 Apr;10(4):413-7.

PubMed

Systems biology: a brief overview

Tuesday, July 22th, 2014 - Julien

Kitano H.
Science. 2002 Mar 1;295(5560):1662-4.

PubMed

Spectrophotometer: new instrument for ultrarapid cell analysis

Tuesday, July 8th, 2014 - Mercedes

Kamentsky LA, Melamed MR, Derman H.
Science. 1965 Oct 29;150(3696):630-1.

PubMed

High-throughput sequencing of the zebrafish antibody repertoire

Tuesday, June 17th, 2014 - Sandra

Weinstein JA1, Jiang N, White RA 3rd, Fisher DS, Quake SR.
Science. 2009 May 8;324(5928):807-10. doi: 10.1126/science.1170020.

PubMed - PDF

Requirement for RORgamma in thymocyte survival and lymphoid organ development.

Tuesday, June 10th, 2014 - Stephanie

Sun Z, Unutmaz D, Zou YR, Sunshine MJ, Pierani A, Brenner-Morton S, Mebius RE, Littman DR.
Science. 2000 Jun 30;288(5475):2369-73.

PubMed - PDF

Unresponsiveness of MyD88-deficient mice to endotoxin

Tuesday, May 27th, 2014 - Yasmin

Kawai T, Adachi O, Ogawa T, Takeda K, Akira S.
Immunity. 1999 Jul;11(1):115-22.

PubMed - PDF

Interleukin-6: possible biological roles during exercise

Tuesday, May 27th, 2014 - Yasmin

Reihmane D, Dela F.
Eur J Sport Sci. 2014;14(3):242-50. doi: 10.1080/17461391.2013.776640. Epub 2013 Mar 11.

PubMed - PDF

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

Tuesday, May 13th, 2014 - William

Maslowski KM, Vieira AT, Ng A, Kranich J, Sierro F, Yu D, Schilter HC, Rolph MS, Mackay F, Artis D, Xavier RJ, Teixeira MM, Mackay CR.
Nature. 2009 Oct 29;461(7268):1282-6. doi: 10.1038/nature08530.

PubMed - PDF

Requirement for lymphoid tissue-inducer cells in isolated follicle formation and T cell-independent immunoglobulin A generation in the gut

Tuesday, April 22nd, 2014 - Li Hai

Tsuji M, Suzuki K, Kitamura H, Maruya M, Kinoshita K, Ivanov II, Itoh K, Littman DR, Fagarasan S.
Immunity. 2008 Aug 15;29(2):261-71. doi: 10.1016/j.immuni.2008.05.014. Epub 2008 Jul 24.

PubMed - PDF

Rapid secretion of interleukin-1beta by microvesicle shedding

Tuesday, March 25th, 2014 - Francesca

MacKenzie A, Wilson HL, Kiss-Toth E, Dower SK, North RA, Surprenant A.
Immunity. 2001 Nov;15(5):825-35.

PubMed - PDF

Points of significance: Power and sample size

Tuesday, March 4th, 2014 - Yasuhiro

Martin Krzywinski  & Naomi Altman
Nature Methods 10, 1139–1140 (2013) doi:10.1038/nmeth.2738
(Pubmed is not yet uploaded)

Salmonella gut invasion involves TTSS-2-dependent epithelial traversal, basolateral exit, and uptake by epithelium-sampling lamina propria phagocytes

Tuesday, January 28th, 2014 - Mercedes

Müller AJ, Kaiser P, Dittmar KE, Weber TC, Haueter S, Endt K, Songhet P, Zellweger C, Kremer M, Fehling HJ, Hardt WD.
Cell Host Microbe. 2012 Jan 19;11(1):19-32. doi: 10.1016/j.chom.2011.11.013.

PubMed - PDF

Independent control of immunoglobulin switch recombination at individual switch regions evidenced through Cre-loxP-mediated gene targeting

Tuesday, January 14th, 2014 - Sandra

Gu H, Zou YR, Rajewsky K.
Cell. 1993 Jun 18;73(6):1155-64.

PubMed - PDF

Adaptive immune features of natural killer cells

Tuesday, December 10th, 2013 - Stephanie

Sun JC, Beilke JN, Lanier LL.
Nature. 2009 Jan 29;457(7229):557-61. doi: 10.1038/nature07665. Epub 2009 Jan 11.

PubMed - PDF

The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota

Tuesday, November 26th, 2013 - William

Round JL, Lee SM, Li J, Tran G, Jabri B, Chatila TA, Mazmanian SK.
Science. 2011 May 20;332(6032):974-7. doi: 10.1126/science.1206095. Epub 2011 Apr 21.

PubMed - PDF

Microbiota-mediated colonization resistance against intestinal pathogens

Tuesday, November 19th, 2013 - Yasmin

Buffie CG, Pamer EG.
Nat Rev Immunol. 2013 Nov;13(11):790-801. doi: 10.1038/nri3535. Epub 2013 Oct 7.

PubMed

B cell antigen receptor specificity and surface density together determine B-1 versus B-2 cell development

Tuesday, November 5th, 2013 - Melissa

Lam KP, Rajewsky K.
J Exp Med. 1999 Aug 16;190(4):471-7.

PubMed

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria

Tuesday, October 15th, 2013 - Li Hai

Johansson ME, Phillipson M, Petersson J, Velcich A, Holm L, Hansson GC.
Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):15064-9. doi: 10.1073/pnas.0803124105. Epub 2008 Sep 19.

PubMed

The adaptor MAVS promotes NLRP3 mitochondrial localization and inflammasome activation

Tuesday, October 1st, 2013 - Francesca

Subramanian N, Natarajan K, Clatworthy MR, Wang Z, Germain RN.
Cell. 2013 Apr 11;153(2):348-61. doi: 10.1016/j.cell.2013.02.054.

PubMed

Crohn's disease

Tuesday, September 17th, 2013 - Peter

Baumgart DC, Sandborn WJ.
Lancet. 2012 Nov 3;380(9853):1590-605. doi: 10.1016/S0140-6736(12)60026-9. Epub 2012 Aug 20.

PubMed

Cytotoxic T-cell memory without antigen

Tuesday, September 3rd, 2013 - Jamie

Lau LL, Jamieson BD, Somasundaram T, Ahmed R.
Nature. 1994 Jun 23;369(6482):648-52.

PubMed

T cells express a phagocyte-type NADPH oxidase that is activated after T cell receptor stimulation

Tuesday, September 3rd, 2013 - Jamie

Jackson SH, Devadas S, Kwon J, Pinto LA, Williams MS.
Nat Immunol. 2004 Aug;5(8):818-27. Epub 2004 Jul 18.

PubMed

A primitive T cell-independent mechanism of intestinal mucosal IgA responses to commensal bacteria

Tuesday, August 20th, 2013 - Yasuhiro

Macpherson AJ, Gatto D, Sainsbury E, Harriman GR, Hengartner H, Zinkernagel RM.
Science. 2000 Jun 23;288(5474):2222-6.

PubMed

Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria

Tuesday, August 20th, 2013 - Yasuhiro

Macpherson AJ, Uhr T.
Science. 2004 Mar 12;303(5664):1662-5.

PubMed

Retinoic acid imprints gut-homing specificity on T cells

Tuesday, July 9th, 2013 - William

Iwata M, Hirakiyama A, Eshima Y, Kagechika H, Kato C, Song SY.
Immunity. 2004 Oct;21(4):527-38.

PubMed

The role of the immune system in governing host-microbe interactions in the intestine

Tuesday, June 25th, 2013 - Yasmin

Brown EM, Sadarangani M, Finlay BB.
Nat Immunol. 2013 Jun 18;14(7):660-7. doi: 10.1038/ni.2611.

PubMed

Commensal bacteria at the interface of host metabolism and the immune system

Tuesday, June 25th, 2013 - Yasmin

Brestoff JR, Artis D.
Nat Immunol. 2013 Jun 18;14(7):676-84. doi: 10.1038/ni.2640.

PubMed

DCs induce CD40-independent immunoglobulin class switching through BLyS and APRIL

Tuesday, June 11th, 2013 - Melissa

Litinskiy MB, Nardelli B, Hilbert DM, He B, Schaffer A, Casali P, Cerutti A.
Nat Immunol. 2002 Sep;3(9):822-9. Epub 2002 Aug 5.

PubMed - News & Views 

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota

Tuesday, May 28th, 2013 - Li Hai

Stecher B, Robbiani R, Walker AW, Westendorf AM, Barthel M, Kremer M, Chaffron S, Macpherson AJ, Buer J, Parkhill J, Dougan G, von Mering C, Hardt WD.
PLoS Biol. 2007 Oct;5(10):2177-89.

PubMed

Differential activation of the inflammasome by caspase-1 adaptors ASC and Ipaf.

Tuesday, May 14th, 2013 - Francesca

Mariathasan S, Newton K, Monack DM, Vucic D, French DM, Lee WP, Roose-Girma M, Erickson S, Dixit VM.
Nature. 2004 Jul 8;430(6996):213-8. Epub 2004 Jun 9.

PubMed
 

Control of early viral and bacterial distribution and disease by natural antibodies

Tuesday, April 30th, 2013 - Yasuhiro

Ochsenbein AF, Fehr T, Lutz C, Suter M, Brombacher F, Hengartner H, Zinkernagel RM.
Science. 1999 Dec 10;286(5447):2156-9.

PubMed

Sequencing technologies - the next generation

Tuesday, April 16th, 2013 - Sandra

Metzker ML.
Nat Rev Genet. 2010 Jan;11(1):31-46. doi: 10.1038/nrg2626. Epub 2009 Dec 8.

PubMed
 

Microbial flora drives interleukin 22 production in intestinal NKp46+ cells that provide innate mucosal immune defense

Tuesday, April 2nd, 2013 - Julia

Satoh-Takayama N, Vosshenrich CA, Lesjean-Pottier S, Sawa S, Lochner M, Rattis F, Mention JJ, Thiam K, Cerf-Bensussan N, Mandelboim O, Eberl G, Di Santo JP.
Immunity. 2008 Dec 19;29(6):958-70. doi: 10.1016/j.immuni.2008.11.001. Epub 2008 Dec 11.

PubMed - supplementary material

Eosinophils: changing perspectives in health and disease

Tuesday, March 19th, 2013 - Yasmin

Rosenberg HF, Dyer KD, Foster PS.
Nat Rev Immunol. 2013 Jan;13(1):9-22. doi: 10.1038/nri3341. Epub 2012 Nov 16.

PubMed

Acquisition of a multifunctional IgA+ plasma cell phenotype in the gut

Tuesday, March 12th, 2013 - William

Fritz JH, Rojas OL, Simard N, McCarthy DD, Hapfelmeier S, Rubino S, Robertson SJ, Larijani M, Gosselin J, Ivanov II, Martin A, Casellas R, Philpott DJ, Girardin SE, McCoy KD, Macpherson AJ, Paige CJ, Gommerman JL.
Nature. 2011 Dec 11;481(7380):199-203. doi: 10.1038/nature10698.

PubMed

Enterotypes of the human gut microbiome

Tuesday, February 26th, 2013 - Melissa

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J; MetaHIT Consortium, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P.
Nature. 2011 May 12;473(7346):174-80. doi: 10.1038/nature09944. Epub 2011 Apr 20.

PubMed 

Non-haemolytic beta-amino-acid oligomers

Tuesday, February 5th, 2013 - Li Hai

Porter EA, Wang X, Lee HS, Weisblum B, Gellman SH.
Nature. 2000 Apr 6;404(6778):565. No abstract available. Erratum in: Nature 2000 May 18;405(6784):298.

PubMed
 

Detection of intracytoplasmic cytokine using flow cytometry and directly conjugated anti-cytokine antibodies

Tuesday, January 22nd, 2013 - Mercedes

Prussin C, Metcalfe DD.
J Immunol Methods. 1995 Dec 15;188(1):117-28.

PubMed