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Commensal Microbiota Regulate Vertebrate Innate Immunity-Insights From the Zebrafish.

Murdoch CC, Rawls JF.

Front Immunol. 2019 Sep 6;10:2100. doi: 10.3389/fimmu.2019.02100. eCollection 2019. Review.


Lysosome-Rich Enterocytes Mediate Protein Absorption in the Vertebrate Gut.

Park J, Levic DS, Sumigray KD, Bagwell J, Eroglu O, Block CL, Eroglu C, Barry R, Lickwar CR, Rawls JF, Watts SA, Lechler T, Bagnat M.

Dev Cell. 2019 Oct 7;51(1):7-20.e6. doi: 10.1016/j.devcel.2019.08.001. Epub 2019 Aug 29.


Commensal Bacteria Regulate Gene Expression and Differentiation in Vertebrate Olfactory Systems Through Transcription Factor REST.

Casadei E, Tacchi L, Lickwar CR, Espenschied ST, Davison JM, Muñoz P, Rawls JF, Salinas I.

Chem Senses. 2019 Oct 17;44(8):615-630. doi: 10.1093/chemse/bjz050.


Epithelial delamination is protective during pharmaceutical-induced enteropathy.

Espenschied ST, Cronan MR, Matty MA, Mueller O, Redinbo MR, Tobin DM, Rawls JF.

Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):16961-16970. doi: 10.1073/pnas.1902596116. Epub 2019 Aug 7.


Disrupted Maturation of the Microbiota and Metabolome among Extremely Preterm Infants with Postnatal Growth Failure.

Younge NE, Newgard CB, Cotten CM, Goldberg RN, Muehlbauer MJ, Bain JR, Stevens RD, O'Connell TM, Rawls JF, Seed PC, Ashley PL.

Sci Rep. 2019 Jun 3;9(1):8167. doi: 10.1038/s41598-019-44547-y.


Visualizing Engrafted Human Cancer and Therapy Responses in Immunodeficient Zebrafish.

Yan C, Brunson DC, Tang Q, Do D, Iftimia NA, Moore JC, Hayes MN, Welker AM, Garcia EG, Dubash TD, Hong X, Drapkin BJ, Myers DT, Phat S, Volorio A, Marvin DL, Ligorio M, Dershowitz L, McCarthy KM, Karabacak MN, Fletcher JA, Sgroi DC, Iafrate JA, Maheswaran S, Dyson NJ, Haber DA, Rawls JF, Langenau DM.

Cell. 2019 Jun 13;177(7):1903-1914.e14. doi: 10.1016/j.cell.2019.04.004. Epub 2019 Apr 25.


Intestinal Serum amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization.

Murdoch CC, Espenschied ST, Matty MA, Mueller O, Tobin DM, Rawls JF.

PLoS Pathog. 2019 Mar 7;15(3):e1007381. doi: 10.1371/journal.ppat.1007381. eCollection 2019 Mar.


An explant technique for high-resolution imaging and manipulation of mycobacterial granulomas.

Cronan MR, Matty MA, Rosenberg AF, Blanc L, Pyle CJ, Espenschied ST, Rawls JF, Dartois V, Tobin DM.

Nat Methods. 2018 Dec;15(12):1098-1107. doi: 10.1038/s41592-018-0215-8. Epub 2018 Nov 30.


Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana.

Kelly MS, Surette MG, Smieja M, Rossi L, Luinstra K, Steenhoff AP, Goldfarb DM, Pernica JM, Arscott-Mills T, Boiditswe S, Mazhani T, Rawls JF, Cunningham CK, Shah SS, Feemster KA, Seed PC.

Pediatr Infect Dis J. 2018 Nov;37(11):1176-1183. doi: 10.1097/INF.0000000000002174.


A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology.

Williamson IA, Arnold JW, Samsa LA, Gaynor L, DiSalvo M, Cocchiaro JL, Carroll I, Azcarate-Peril MA, Rawls JF, Allbritton NL, Magness ST.

Cell Mol Gastroenterol Hepatol. 2018 May 22;6(3):301-319. doi: 10.1016/j.jcmgh.2018.05.004. eCollection 2018.


Deep phenotyping in zebrafish reveals genetic and diet-induced adiposity changes that may inform disease risk.

Minchin JEN, Scahill CM, Staudt N, Busch-Nentwich EM, Rawls JF.

J Lipid Res. 2018 Aug;59(8):1536-1545. doi: 10.1194/jlr.D084525. Epub 2018 May 23.


Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation.

King J, Foster J, Davison JM, Rawls JF, Breton G.

Zebrafish. 2018 Apr;15(2):202-205. doi: 10.1089/zeb.2017.1486. Epub 2017 Nov 27.


Microbial colonization is required for normal neurobehavioral development in zebrafish.

Phelps D, Brinkman NE, Keely SP, Anneken EM, Catron TR, Betancourt D, Wood CE, Espenschied ST, Rawls JF, Tal T.

Sci Rep. 2017 Sep 11;7(1):11244. doi: 10.1038/s41598-017-10517-5.


Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells.

Lickwar CR, Camp JG, Weiser M, Cocchiaro JL, Kingsley DM, Furey TS, Sheikh SZ, Rawls JF.

PLoS Biol. 2017 Aug 29;15(8):e2002054. doi: 10.1371/journal.pbio.2002054. eCollection 2017 Aug.


Elucidating the role of plexin D1 in body fat distribution and susceptibility to metabolic disease using a zebrafish model system.

Minchin JEN, Rawls JF.

Adipocyte. 2017 Oct 2;6(4):277-283. doi: 10.1080/21623945.2017.1356504. Epub 2017 Aug 9.


The Nasopharyngeal Microbiota of Children With Respiratory Infections in Botswana.

Kelly MS, Surette MG, Smieja M, Pernica JM, Rossi L, Luinstra K, Steenhoff AP, Feemster KA, Goldfarb DM, Arscott-Mills T, Boiditswe S, Rulaganyang I, Muthoga C, Gaofiwe L, Mazhani T, Rawls JF, Cunningham CK, Shah SS, Seed PC.

Pediatr Infect Dis J. 2017 Sep;36(9):e211-e218. doi: 10.1097/INF.0000000000001607.


Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha.

Davison JM, Lickwar CR, Song L, Breton G, Crawford GE, Rawls JF.

Genome Res. 2017 Jul;27(7):1195-1206. doi: 10.1101/gr.220111.116. Epub 2017 Apr 6.


A classification system for zebrafish adipose tissues.

Minchin JEN, Rawls JF.

Dis Model Mech. 2017 Jun 1;10(6):797-809. doi: 10.1242/dmm.025759. Epub 2017 Mar 27.


Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health.

Leulier F, MacNeil LT, Lee WJ, Rawls JF, Cani PD, Schwarzer M, Zhao L, Simpson SJ.

Cell Metab. 2017 Mar 7;25(3):522-534. doi: 10.1016/j.cmet.2017.02.001. Review.


Best practices for germ-free derivation and gnotobiotic zebrafish husbandry.

Melancon E, Gomez De La Torre Canny S, Sichel S, Kelly M, Wiles TJ, Rawls JF, Eisen JS, Guillemin K.

Methods Cell Biol. 2017;138:61-100. doi: 10.1016/bs.mcb.2016.11.005. Review.


In vivo imaging and quantification of regional adiposity in zebrafish.

Minchin JE, Rawls JF.

Methods Cell Biol. 2017;138:3-27. doi: 10.1016/bs.mcb.2016.11.010. Epub 2016 Dec 26. Review.


Genomic sequencing-based mutational enrichment analysis identifies motility genes in a genetically intractable gut microbe.

Bae S, Mueller O, Wong S, Rawls JF, Valdivia RH.

Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):14127-14132. Epub 2016 Nov 23.


Baby, It's Cold Outside: Host-Microbiota Relationships Drive Temperature Adaptations.

Gomez de la Torre Canny S, Rawls JF.

Cell Host Microbe. 2015 Dec 9;18(6):635-6. doi: 10.1016/j.chom.2015.11.009.


The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota.

Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, Guy CD, Seed PC, Rawls JF, David LA, Hunault G, Oberti F, Calès P, Diehl AM.

Hepatology. 2016 Mar;63(3):764-75. doi: 10.1002/hep.28356. Epub 2016 Jan 13.


Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut.

Wong S, Stephens WZ, Burns AR, Stagaman K, David LA, Bohannan BJ, Guillemin K, Rawls JF.

MBio. 2015 Sep 29;6(5):e00687-15. doi: 10.1128/mBio.00687-15.


CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation.

Wang L, Oehlers SH, Espenschied ST, Rawls JF, Tobin DM, Ko DC.

Genome Biol. 2015 Sep 15;16:190. doi: 10.1186/s13059-015-0722-1.


The composition of the zebrafish intestinal microbial community varies across development.

Stephens WZ, Burns AR, Stagaman K, Wong S, Rawls JF, Guillemin K, Bohannan BJ.

ISME J. 2016 Mar;10(3):644-54. doi: 10.1038/ismej.2015.140. Epub 2015 Sep 4.


Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development.

Burns AR, Stephens WZ, Stagaman K, Wong S, Rawls JF, Guillemin K, Bohannan BJ.

ISME J. 2016 Mar;10(3):655-64. doi: 10.1038/ismej.2015.142. Epub 2015 Aug 21.


Got worms? Perinatal exposure to helminths prevents persistent immune sensitization and cognitive dysfunction induced by early-life infection.

Williamson LL, McKenney EA, Holzknecht ZE, Belliveau C, Rawls JF, Poulton S, Parker W, Bilbo SD.

Brain Behav Immun. 2016 Jan;51:14-28. doi: 10.1016/j.bbi.2015.07.006. Epub 2015 Jul 7.


Alteration of the rat cecal microbiome during colonization with the helminth Hymenolepis diminuta.

McKenney EA, Williamson L, Yoder AD, Rawls JF, Bilbo SD, Parker W.

Gut Microbes. 2015;6(3):182-93. doi: 10.1080/19490976.2015.1047128.


Plexin D1 determines body fat distribution by regulating the type V collagen microenvironment in visceral adipose tissue.

Minchin JE, Dahlman I, Harvey CJ, Mejhert N, Singh MK, Epstein JA, Arner P, Torres-Vázquez J, Rawls JF.

Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):4363-8. doi: 10.1073/pnas.1416412112. Epub 2015 Mar 23.


Epigenetic control of intestinal barrier function and inflammation in zebrafish.

Marjoram L, Alvers A, Deerhake ME, Bagwell J, Mankiewicz J, Cocchiaro JL, Beerman RW, Willer J, Sumigray KD, Katsanis N, Tobin DM, Rawls JF, Goll MG, Bagnat M.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2770-5. doi: 10.1073/pnas.1424089112. Epub 2015 Feb 17.


Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape.

Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF.

Genome Res. 2014 Sep;24(9):1504-16. doi: 10.1101/gr.165845.113. Epub 2014 Jun 24.


Commensal microbiota stimulate systemic neutrophil migration through induction of serum amyloid A.

Kanther M, Tomkovich S, Xiaolun S, Grosser MR, Koo J, Flynn EJ 3rd, Jobin C, Rawls JF.

Cell Microbiol. 2014 Jul;16(7):1053-67. doi: 10.1111/cmi.12257. Epub 2014 Jan 24.


Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density.

Wong S, Waldrop T, Summerfelt S, Davidson J, Barrows F, Kenney PB, Welch T, Wiens GD, Snekvik K, Rawls JF, Good C.

Appl Environ Microbiol. 2013 Aug;79(16):4974-84. doi: 10.1128/AEM.00924-13. Epub 2013 Jun 14.


Oesophageal and sternohyal muscle fibres are novel Pax3-dependent migratory somite derivatives essential for ingestion.

Minchin JE, Williams VC, Hinits Y, Low S, Tandon P, Fan CM, Rawls JF, Hughes SM.

Development. 2013 Jul;140(14):2972-84. doi: 10.1242/dev.090050. Epub 2013 Jun 12. Erratum in: Development. 2013 Oct;140(20):4296.


Getting the inside tract: new frontiers in zebrafish digestive system biology.

Sadler KC, Rawls JF, Farber SA.

Zebrafish. 2013 Jun;10(2):129-31. doi: 10.1089/zeb.2013.1500. No abstract available.


Mucosal candidiasis elicits NF-κB activation, proinflammatory gene expression and localized neutrophilia in zebrafish.

Gratacap RL, Rawls JF, Wheeler RT.

Dis Model Mech. 2013 Sep;6(5):1260-70. doi: 10.1242/dmm.012039. Epub 2013 May 29.


Obese humans with nonalcoholic fatty liver disease display alterations in fecal microbiota and volatile organic compounds.

Boursier J, Rawls JF, Diehl AM.

Clin Gastroenterol Hepatol. 2013 Jul;11(7):876-8. doi: 10.1016/j.cgh.2013.04.016. Epub 2013 Apr 26. No abstract available.


Microgavage of zebrafish larvae.

Cocchiaro JL, Rawls JF.

J Vis Exp. 2013 Feb 20;(72):e4434. doi: 10.3791/4434.


Dwarfism and increased adiposity in the gh1 mutant zebrafish vizzini.

McMenamin SK, Minchin JE, Gordon TN, Rawls JF, Parichy DM.

Endocrinology. 2013 Apr;154(4):1476-87. doi: 10.1210/en.2012-1734. Epub 2013 Mar 1.


Animals in a bacterial world, a new imperative for the life sciences.

McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Lošo T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3229-36. doi: 10.1073/pnas.1218525110. Epub 2013 Feb 7. Review.


Carbon monoxide and heme oxygenase-1 prevent intestinal inflammation in mice by promoting bacterial clearance.

Onyiah JC, Sheikh SZ, Maharshak N, Steinbach EC, Russo SM, Kobayashi T, Mackey LC, Hansen JJ, Moeser AJ, Rawls JF, Borst LB, Otterbein LE, Plevy SE.

Gastroenterology. 2013 Apr;144(4):789-98. doi: 10.1053/j.gastro.2012.12.025. Epub 2012 Dec 22.


Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish.

Semova I, Carten JD, Stombaugh J, Mackey LC, Knight R, Farber SA, Rawls JF.

Cell Host Microbe. 2012 Sep 13;12(3):277-88. doi: 10.1016/j.chom.2012.08.003.


Glafenine-induced intestinal injury in zebrafish is ameliorated by μ-opioid signaling via enhancement of Atf6-dependent cellular stress responses.

Goldsmith JR, Cocchiaro JL, Rawls JF, Jobin C.

Dis Model Mech. 2013 Jan;6(1):146-59. doi: 10.1242/dmm.009852. Epub 2012 Aug 23.


Special issue: gut microbial communities in health and disease.

Rawls JF.

Gut Microbes. 2012 Jul-Aug;3(4):277-8. Epub 2012 Jun 12. No abstract available.


Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans.

Sanapareddy N, Legge RM, Jovov B, McCoy A, Burcal L, Araujo-Perez F, Randall TA, Galanko J, Benson A, Sandler RS, Rawls JF, Abdo Z, Fodor AA, Keku TO.

ISME J. 2012 Oct;6(10):1858-68. doi: 10.1038/ismej.2012.43. Epub 2012 May 24.


Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription.

Camp JG, Jazwa AL, Trent CM, Rawls JF.

PLoS Genet. 2012;8(3):e1002585. doi: 10.1371/journal.pgen.1002585. Epub 2012 Mar 29.


Study of host-microbe interactions in zebrafish.

Milligan-Myhre K, Charette JR, Phennicie RT, Stephens WZ, Rawls JF, Guillemin K, Kim CH.

Methods Cell Biol. 2011;105:87-116. doi: 10.1016/B978-0-12-381320-6.00004-7.

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