ZFIN Person: Rawls, John F.

ZFIN ID: ZDB-PERS-980202-13

ZFIN ID: ZDB-PERS-980202-13

Rawls, John F.

Email:	john.rawls@duke.edu
URL:	https://sites.duke.edu/rawlslab/
Affiliation:	Rawls Lab
Address:	Department of Molecular Genetics & Microbiology Duke Microbiome Center Duke University School of Medicine 213 Research Drive 323 CARL Building, Box 3580 Durham, NC 27710 USA
Country:
Phone:	(919) 613-7212
Fax:	(919) 684-2790
ORCID ID:	0000-0002-5976-5206

BIOGRAPHY AND RESEARCH INTERESTS

I grew up in Lexington KY, received my undergraduate education at Emory University, then pursued my Ph.D. in developmental biology at Washington University in the lab of Dr. Stephen Johnson. I stayed at Washington University for my postdoctoral training in gastroenterology and host-microbiota interactions in the lab of Dr. Jeffrey Gordon. I started my independent laboratory in 2006 at the University of North Carolina at Chapel Hill, then relocated my lab to Duke University in 2013.

PUBLICATIONS

Heppert, J.K., Lickwar, C.R., Tillman, M.C., Davis, B.R., Davison, J.M., Lu, H.Y., Chen, W., Busch-Nentwich, E.M., Corcoran, D.L., Rawls, J.F. (2022) Conserved roles for Hnf4 family transcription factors in zebrafish development and intestinal function. Genetics. 222(4):

Jawahar, J., McCumber, A.W., Lickwar, C.R., Amoroso, C.R., de la Torre Canny, S.G., Wong, S., Morash, M., Thierer, J.H., Farber, S.A., Bohannan, B.J.M., Guillemin, K., Rawls, J.F. (2022) Starvation causes changes in the intestinal transcriptome and microbiome that are reversed upon refeeding. BMC Genomics. 23:225

Yan, C., Yang, Q., Zhang, S., Millar, D.G., Alpert, E.J., Do, D., Veloso, A., Brunson, D.C., Drapkin, B.J., Stanzione, M., Scarfò, I., Moore, J.C., Iyer, S., Qin, Q., Wei, Y., McCarthy, K.M., Rawls, J.F., Dyson, N.J., Cobbold, M., Maus, M.V., Langenau, D.M. (2021) Single-cell imaging of T cell immunotherapy responses in vivo. The Journal of experimental medicine. 218(10):

Wen, J., Mercado, G.P., Volland, A., Doden, H.L., Lickwar, C.R., Crooks, T., Kakiyama, G., Kelly, C., Cocchiaro, J.L., Ridlon, J.M., Rawls, J.F. (2021) Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine. Science advances. 7(30)

Chen, C., Gu, Y., Philippe, J., Zhang, P., Bachman, H., Zhang, J., Mai, J., Rufo, J., Rawls, J.F., Davis, E.E., Katsanis, N., Huang, T.J. (2021) Acoustofluidic rotational tweezing enables high-speed contactless morphological phenotyping of zebrafish larvae. Nature communications. 12:1118

Heppert, J.K., Davison, J.M., Kelly, C., Mercado, G.P., Lickwar, C.R., Rawls, J.F. (2021) Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium. Nature reviews. Gastroenterology & hepatology. 18:7-23

Ye, L., Bae, M., Cassilly, C.D., Jabba, S.V., Thorpe, D.W., Martin, A.M., Lu, H.Y., Wang, J., Thompson, J.D., Lickwar, C.R., Poss, K.D., Keating, D.J., Jordt, S.E., Clardy, J., Liddle, R.A., Rawls, J.F. (2020) Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways. Cell Host & Microbe. 29(2):179-196.e9

Cholan, P.M., Han, A., Woodie, B.R., Watchon, M., Kurz, A.R., Laird, A.S., Britton, W.J., Ye, L., Holmes, Z.C., McCann, J.R., David, L.A., Rawls, J.F., Oehlers, S.H. (2020) Conserved anti-inflammatory effects and sensing of butyrate in zebrafish. Gut microbes. 12:1-11

Yan, C., Do, D., Yang, Q., Brunson, D.C., Rawls, J.F., Langenau, D.M. (2020) Single-cell imaging of human cancer xenografts using adult immunodeficient zebrafish. Nature Protocols. 15(9):3105-3128

Loh, N.Y., Minchin, J.E.N., Pinnick, K.E., Verma, M., Todorčević, M., Denton, N., Moustafa, J.E., Kemp, J.P., Gregson, C.L., Evans, D.M., Neville, M.J., Small, K.S., McCarthy, M.I., Mahajan, A., Rawls, J.F., Karpe, F., Christodoulides, C. (2020) RSPO3 impacts body fat distribution and regulates adipose cell biology in vitro. Nature communications. 11:2797

Ye, L., Mueller, O., Bagwell, J., Bagnat, M., Liddle, R.A., Rawls, J.F. (2019) High fat diet induces microbiota-dependent silencing of enteroendocrine cells. eLIFE. 8:

Murdoch, C.C., Rawls, J.F. (2019) Commensal Microbiota Regulate Vertebrate Innate Immunity-Insights From the Zebrafish. Frontiers in immunology. 10:2100

Park, J., Levic, D.S., Sumigray, K.D., Bagwell, J., Eroglu, O., Block, C.L., Eroglu, C., Barry, R., Lickwar, C.R., Rawls, J.F., Watts, S.A., Lechler, T., Bagnat, M. (2019) Lysosome-Rich Enterocytes Mediate Protein Absorption in the Vertebrate Gut. Developmental Cell. 51(1):7-20.e6

Casadei, E., Tacchi, L., Lickwar, C.R., Espenschied, S.T., Davison, J.M., Muñoz, P., Rawls, J.F., Salinas, I. (2019) Commensal bacteria regulate gene expression and differentiation in vertebrate olfactory systems through transcription factor REST. Chemical senses. 44(8):615-630

Espenschied, S.T., Cronan, M.R., Matty, M.A., Mueller, O., Redinbo, M.R., Tobin, D.M., Rawls, J.F. (2019) Epithelial delamination is protective during pharmaceutical-induced enteropathy. Proceedings of the National Academy of Sciences of the United States of America. 116(34):16961-16970

Yan, C., Brunson, D.C., Tang, Q., Do, D., Iftimia, N.A., Moore, J.C., Hayes, M.N., Welker, A.M., Garcia, E.G., Dubash, T.D., Hong, X., Drapkin, B.J., Myers, D.T., Phat, S., Volorio, A., Marvin, D.L., Ligorio, M., Dershowitz, L., McCarthy, K.M., Karabacak, M.N., Fletcher, J.A., Sgroi, D.C., Iafrate, J.A., Maheswaran, S., Dyson, N.J., Haber, D.A., Rawls, J.F., Langenau, D.M. (2019) Visualizing Engrafted Human Cancer and Therapy Responses in Immunodeficient Zebrafish. Cell. 177(7):1903-1914.e14

Murdoch, C.C., Espenschied, S.T., Matty, M.A., Mueller, O., Tobin, D.M., Rawls, J.F. (2019) Intestinal Serum amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization. PLoS pathogens. 15:e1007381

Cronan, M.R., Matty, M.A., Rosenberg, A.F., Blanc, L., Pyle, C.J., Espenschied, S.T., Rawls, J.F., Dartois, V., Tobin, D.M. (2018) An explant technique for high-resolution imaging and manipulation of mycobacterial granulomas. Nature Methods. 15:1098-1107

Minchin, J.E.N., Scahill, C.M., Staudt, N., Busch-Nentwich, E.M., Rawls, J.F. (2018) Deep phenotyping in zebrafish reveals genetic and diet-induced adiposity changes that may inform disease risk. Journal of Lipid Research. 59(8):1536-1545

King, J., Foster, J., Davison, J.M., Rawls, J.F., Breton, G. (2017) Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation. Zebrafish. 15(2):202-205

Phelps, D., Brinkman, N.E., Keely, S.P., Anneken, E.M., Catron, T.R., Betancourt, D., Wood, C.E., Espenschied, S.T., Rawls, J.F., Tal, T. (2017) Microbial colonization is required for normal neurobehavioral development in zebrafish. Scientific Reports. 7:11244

Lickwar, C.R., Camp, J.G., Weiser, M., Cocchiaro, J.L., Kingsley, D.M., Furey, T.S., Sheikh, S.Z., Rawls, J.F. (2017) Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells. PLoS Biology. 15:e2002054

Minchin, J.E.N., Rawls, J.F. (2017) Elucidating the role of plexin D1 in body fat distribution and susceptibility to metabolic disease using a zebrafish model system. Adipocyte. 6(4):277-283

Davison, J.M., Lickwar, C.R., Song, L., Breton, G., Crawford, G.E., Rawls, J.F. (2017) Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha. Genome research. 27(7):1195-1206

Minchin, J.E., Rawls, J.F. (2017) A classification system for zebrafish adipose tissues. Disease models & mechanisms. 10(6):797-809

Melancon, E., Gomez De La Torre Canny, S., Sichel, S., Kelly, M., Wiles, T.J., Rawls, J.F., Eisen, J.S., Guillemin, K. (2017) Best practices for germ-free derivation and gnotobiotic zebrafish husbandry. Methods in cell biology. 138:61-100

Minchin, J.E., Rawls, J.F. (2017) In vivo imaging and quantification of regional adiposity in zebrafish. Methods in cell biology. 138:3-27

Bae, S., Mueller, O., Wong, S., Rawls, J.F., Valdivia, R.H. (2016) Genomic sequencing-based mutational enrichment analysis identifies motility genes in a genetically intractable gut microbe. Proceedings of the National Academy of Sciences of the United States of America. 113:14127-14132

Burns, A.R., Zac Stephens, W., Stagaman, K., Wong, S., Rawls, J.F., Guillemin, K., Bohannan, B.J. (2016) Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. The ISME Journal. 10(3):655-64

Wong, S., Stephens, W.Z., Burns, A.R., Stagaman, K., David, L.A., Bohannan, B.J., Guillemin, K., Rawls, J.F. (2015) Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut. mBio. 6(5):e00687-15

Wang, L., Oehlers, S.H., Espenschied, S.T., Rawls, J.F., Tobin, D.M., Ko, D.C. (2015) CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation. Genome biology. 16:190

Minchin, J.E., Dahlman, I., Harvey, C.J., Mejhert, N., Singh, M.K., Epstein, J.A., Arner, P., Torres-Vazquez, J., Rawls, J.F. (2015) Plexin D1 determines body fat distribution by regulating the type V collagen microenvironment in visceral adipose tissue. Proceedings of the National Academy of Sciences of the United States of America. 112(14):4363-8

Marjoram, L., Alvers, A., Deerhake, M.E., Bagwell, J., Mankiewicz, J., Cocchiaro, J.L., Beerman, R.W., Willer, J., Sumigray, K.D., Katsanis, N., Tobin, D.M., Rawls, J.F., Goll, M.G., Bagnat, M. (2015) Epigenetic control of intestinal barrier function and inflammation in zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 112(9):2770-5

Kanther, M., Tomkovich, S., Xiaolun, S., Grosser, M.R., Koo, J., Flynn, E.J., Jobin, C., and Rawls, J.F. (2014) Commensal microbiota stimulate systemic neutrophil migration through induction of Serum amyloid A. Cellular Microbiology. 16(7):1053-67

Gratacap, R.L., Rawls, J.F., and Wheeler, R.T. (2013) Mucosal candidiasis elicits NF-κB activation, proinflammatory gene expression and localized neutrophilia in zebrafish. Disease models & mechanisms. 6(5):1260-70

Minchin, J.E., Williams, V.C., Hinits, Y., Low, S., Tandon, P., Fan, C.M., Rawls, J.F., and Hughes, S.M. (2013) Oesophageal and sternohyal muscle fibres are novel Pax3-dependent migratory somite derivatives essential for ingestion. Development (Cambridge, England). 140(14):2972-2984

Sadler, K.C., Rawls, J.F., and Farber, S.A. (2013) Getting the inside tract: new frontiers in zebrafish digestive system biology. Zebrafish. 10(2):129-131

Onyiah, J.C., Sheikh, S.Z., Maharshak, N., Steinbach, E.C., Russo, S.M., Kobayashi, T., Mackey, L.C., Hansen, J.J., Moeser, A.J., Rawls, J.F., Borst, L.B., Otterbein, L.E., and Plevy, S.E. (2013) Carbon Monoxide and Heme Oxygenase-1 Prevent Intestinal Inflammation in Mice by Promoting Bacterial Clearance. Gastroenterology. 144(4):789-798

McMenamin, S.K., Minchin, J.E., Gordon, T.N., Rawls, J.F., and Parichy, D.M. (2013) Dwarfism and Increased Adiposity in the gh1 Mutant Zebrafish vizzini. Endocrinology. 154(4):1476-87

Cocchiaro, J.L., and Rawls, J.F. (2013) Microgavage of zebrafish larvae. Journal of visualized experiments : JoVE. (72):e4434

Goldsmith, J.R., Cocchiaro, J.L., Rawls, J.F., and Jobin, C. (2013) Zebrafish glafenine-intestinal injury is ameliorated by mu-opioid signaling via enhancement of Atf6-dependent cellular stress responses. Disease models & mechanisms. 6(1):146-159

Semova, I., Carten, J.D., Stombaugh, J., Mackey, L.C., Knight, R., Farber, S.A., and Rawls, J.F. (2012) Microbiota regulate intestinal absorption and metabolism of Fatty acids in the zebrafish. Cell Host & Microbe. 12(3):277-288

Camp, J.G., Jazwa, A.L., Trent, C.M., and Rawls, J.F. (2012) Intronic Cis-Regulatory Modules Mediate Tissue-Specific and Microbial Control of angptl4/fiaf Transcription. PLoS Genetics. 8(3):e1002585

Roeselers, G., Mittge, E.K., Stephens, W.Z., Parichy, D.M., Cavanaugh, C.M., Guillemin, K., and Rawls, J.F. (2011) Evidence for a core gut microbiota in the zebrafish. The ISME Journal. 5(10):1595-608

Kanther, M., Sun, X., Mühlbauer, M., Mackey, L.C., Flynn, E.J., Bagnat, M., Jobin, C., and Rawls, J.F. (2011) Microbial colonization induces dynamic temporal and spatial patterns of NF-kappaB activation in the zebrafish digestive tract. Gastroenterology. 141(1):197-207

Minchin, J.E., and Rawls, J.F. (2011) In vivo Analysis of White Adipose Tissue in Zebrafish. Methods in cell biology. 105:63-86

Milligan-Myhre, K., Charette, J.R., Phennicie, R.T., Stephens, W.Z., Rawls, J.F., Guillemin, K., and Kim, C.H. (2011) Study of host-microbe interactions in zebrafish. Methods in cell biology. 105:87-116

Kanther, M., and Rawls, J.F. (2010) Host-microbe interactions in the developing zebrafish. Current opinion in immunology. 22(1):10-19

Volkman, H.E., Pozos, T.C., Zheng, J., Davis, J.M., Rawls, J.F., and Ramakrishnan, L. (2010) Tuberculous Granuloma Induction via Interaction of a Bacterial Secreted Protein with Host Epithelium. Science (New York, N.Y.). 327(5964):466-469

Flynn, E.J. 3rd, Trent, C.M., and Rawls, J.F. (2009) Ontogeny and nutritional control of adipogenesis in zebrafish (Danio rerio). Journal of Lipid Research. 50(8):1641-1652

Camp, J.G., Kanther, M., Semova, I., and Rawls, J.F. (2009) Patterns and scales in gastrointestinal microbial ecology. Gastroenterology. 136(6):1989-2002

Pham, L.N., Kanther, M., Semova, I., and Rawls, J.F. (2008) Methods for generating and colonizing gnotobiotic zebrafish. Nature Protocols. 3(12):1862-1875

Rawls, J.F., Mahowald, M.A., Goodman, A.L., Trent, C.M., and Gordon, J.I. (2007) In vivo imaging and genetic analysis link bacterial motility and symbiosis in the zebrafish gut. Proceedings of the National Academy of Sciences of the United States of America. 104(18):7622-7627

Rawls, J.F., Mahowald, M.A., Ley, R.E., and Gordon, J.I. (2006) Reciprocal Gut Microbiota Transplants from Zebrafish and Mice to Germ-free Recipients Reveal Host Habitat Selection. Cell. 127(20:423-433

Rawls, J.F., Samuel, B.S., and Gordon, J.I. (2004) Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proceedings of the National Academy of Sciences of the United States of America. 101(13):4596-4601

Rawls, J.F. and Johnson, S.L. (2003) Temporal and molecular separation of the kit receptor tyrosine kinase's roles in zebrafish melanocyte migration and survival. Developmental Biology. 262(1):152-161

Rawls, J.F., Frieda, M.R., McAdow, A.R., Gross, J.P., Clayton, C.M., Heyen, C.K., and Johnson, S.L. (2003) Coupled mutagenesis screens and genetic mapping in zebrafish. Genetics. 163(3):997-1009

Rawls, J.F., Mellgren, E.M., and Johnson, S.L. (2001) How the zebrafish gets its stripes. Developmental Biology. 240(2):301-314

Rawls, J.F. and Johnson, S.L. (2001) Requirements for the kit receptor tyrosine kinase during regeneration of zebrafish fin melanocytes. Development (Cambridge, England). 128(11):1943-1949

Rawls, J.F. (2001) Genetic dissection of kit-dependent melanocyte development in zebrafish, Danio rerio. Ph.D. Thesis.

Parichy, D.M., Mellgren, E.M., Rawls, J.F., Lopes, S.S., Kelsh, R.N., and Johnson, S.L. (2000) Mutational analysis of endothelin receptor b1 (rose) during neural crest and pigment pattern development in the zebrafish Danio rerio. Developmental Biology. 227(2):294-306

Rawls, J.F. and Johnson, S.L. (2000) Zebrafish kit mutation reveals primary and secondary regulation of melanocyte development during fin stripe regeneration. Development (Cambridge, England). 127(17):3715-3724

Parichy, D.M., Rawls, J.F., Pratt, S.J., Whitfield, T.T., and Johnson, S.L. (1999) Zebrafish sparse corresponds to an orthologue of c-kit and is required for the morphogenesis of a subpopulation of melanocytes, but is not essential for hematopoiesis or primordial germ cell development. Development (Cambridge, England). 126(15):3425-3436

NON-ZEBRAFISH PUBLICATIONS
Bear, J.E., Rawls, J.F., and Saxe, C.L. III. (1998) SCAR, a WASP-related protein, isolated as a suppressor of receptor defects in late Dictyostelium development. J Cell Biol.142 (5): 1325-1335.

Shen XJ, Rawls JF, Randall T, Burcal L, Mpande CN, Jenkins N, Jovov B, Abdo Z, Sandler RS, Keku TO. (2010) Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. Gut Microbes. 1(3):138-47.

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. (2012)
Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans. ISME J. doi: 10.1038/ismej.2012.43.

McFall-Ngai, M., Hadfield, M., Bosch, T., Carey, H., Domazet-Loso, T., Douglas, A., Dubilier, N., Eberl, G., Fukami, T., Gilbert, S., Hentschel, U., King, N., Kjelleberg, S., Knoll, A., Kremer, N., Mazmanian, S., Metcalf, J., Nealson, K., Pierce, N., Rawls, J., Reid, A., Ruby, N., Rumpho, M., Sanders, J., Tautz, D., and Wernegreen, J. (2013) Animals in a bacterial world: a new imperative for the life sciences. Proc. Natl. Acad. Sci. U.S.A. 110(9): 3229-3236.

Leulier, F., McNeil, L., Lee, W.-J., Rawls, J.F., Cani, P., Schwarzer, M., Zhao, L. and Simpson, S. (2017) Integrative physiology: at the crossroads of nutrition, microbiota and animal physiology. Cell Metabolism 25(3): 522–534.

Martiny, J.B.H., Whiteson, K., Bohannan, B., David, L.A., Hynson, N., McFall-Ngai, M., Rawls, J.F., Schmidt, T., Abdo, Z., Blaser, M., Bordenstein, S., Bréchot, C., Bull, C., Dorrestein, P., Eisen, J., Garcia-Pichel, F., Gilbert, J., Hofmockel, K., Holtz, M., Knight, R., Welch, D.M., McDonald, D., Methe, B., Mouncey, N., Mueller, N., Pfister, C., Proctor, L., and Sachs, J. (2019) The Emergence of Microbiome Centres. Nature Microbiology 5: 2–3.