ZFIN ID: ZDB-LAB-060628-2
Rawls Lab
PI/Director: Rawls, John F.
Contact Person: Rawls, John F.
Email: john.rawls@duke.edu
URL: http://sites.duke.edu/rawlslab/
Address: Department of Molecular Genetics & Microbiology Duke University Medical Center 213 Research Drive 327 CARL Building, Box 3580 Durham, NC 27710
Country: United States
Phone: (919) 660-0894; (919) 660-0893
Fax: (919) 684-2790
Line Designation: rdu


GENOMIC FEATURES ORIGINATING FROM THIS LAB
Show first 50 of 77 genomic features


STATEMENT OF RESEARCH INTERESTS
Animal physiology is directed by complex interactions between factors encoded in the animal's genome and those encountered in its environment. The impact of these interactions on animal health is most evident in the intestine, where digestion and absorption of dietary nutrients occur in the presence of complex communities of microorganisms (microbiota). Interactions between diet, microbiota, and animal hosts regulate immune and metabolic homeostasis and also contribute to a spectrum of human diseases including inflammatory bowel disease, obesity, and malnutrition. Our research interests are focused on understanding how environmental factors such as the intestinal microbiota and diet interact with host genome-encoded processes to influence host physiology and pathophysiology. We are using the zebrafish as a vertebrate model system for this research. The small size and optical transparency of the zebrafish facilitate high-resolution in vivo imaging as well as genetic and chemical manipulations that complement the technical limitations of mammalian models. Extensive anatomic, physiologic, and genomic homologies between zebrafish and mammals permit translation of insights gained in zebrafish into advances in human medicine. To facilitate our research, we have developed methods for rearing zebrafish under germ-free conditions and for introducing selected microbial communities and sterile diets into germ-free fish. We are currently using zebrafish and mouse models to investigate how microbial communities are assembled in the intestine and how bacteria and dietary nutrients regulate host metabolism and immunity. We have also established methods for in vivo analysis of adipose tissues in zebrafish, and we are using that experimental platform to elucidate the mechanisms underlying adipose tissue physiology and obesity-associated metabolic disease. The overall objective of our work is to improve our understanding of vertebrate physiology as a complex and dynamic integration of genome-encoded and environmental factors, which is expected to yield new strategies for promoting health in humans and other animals.


LAB MEMBERS
Heppert, Jennifer Post-Doc Wen, Jia Post-Doc Ye, Lihua Post-Doc
Espenschied, Scott "Ted" Graduate Student Jawahar, Jay Graduate Student Kelly, Cecelia Graduate Student
Mercado, Gilberto Padilla Graduate Student Murdoch, Caitlin Graduate Student Lickwar, Colin Research Staff
McCann, Jessica Research Staff Lu, Hsiu Yi "Justice" Fish Facility Staff


ZEBRAFISH PUBLICATIONS OF LAB MEMBERS
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
Ye, L., Robertson, M.A., Mastracci, T.L., Anderson, R.M. (2016) An insulin signaling feedback loop regulates pancreas progenitor cell differentiation during islet development and regeneration. Developmental Biology. 409(2):354-69
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
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
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
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
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
Minchin, J.E., and Rawls, J.F. (2011) In vivo Analysis of White Adipose Tissue in Zebrafish. Methods in cell biology. 105:63-86
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