Scholars@Duke
Michel Bagnat

Michel Bagnat

Nanaline Duke Distinguished Professor
Cell Biology
m.bagnat@cellbio.duke.edu
Duke Box 3709, Durham, NC 27710
333B Nanaline Duke Building, Durham, NC 27710

Selected Publications

Notochord segmentation in zebrafish controlled by iterative mechanical signaling.

Journal Article Dev Cell · July 22, 2024 In bony fishes, patterning of the vertebral column, or spine, is guided by a metameric blueprint established in the notochord sheath. Notochord segmentation begins days after somitogenesis concludes and can occur in its absence. However, somite patterning ... Full text Link to item Cite

Protein absorption in the zebrafish gut is regulated by interactions between lysosome rich enterocytes and the microbiome.

Journal Article bioRxiv · June 11, 2024 Dietary protein absorption in neonatal mammals and fishes relies on the function of a specialized and conserved population of highly absorptive lysosome rich enterocytes (LREs). The gut microbiome has been shown to enhance absorption of nutrients, such as ... Full text Link to item Cite

TNF Promoter Hypomethylation Is Associated With Mucosal Inflammation in IBD and Anti-TNF Response.

Journal Article Gastro Hep Adv · 2024 BACKGROUND AND AIMS: Inflammatory bowel diseases (IBDs) are chronic inflammatory conditions influenced heavily by environmental factors. DNA methylation is a form of epigenetic regulation linking environmental stimuli to gene expression changes and inflamm ... Full text Link to item Cite

Dynamic BMP signaling mediates notochord segmentation in zebrafish.

Journal Article Curr Biol · June 19, 2023 The vertebrate spine is a metameric structure composed of alternating vertebral bodies (centra) and intervertebral discs.1 Recent studies in zebrafish have shown that the epithelial sheath surrounding the notochord differentiates into alternating cartilage ... Full text Link to item Cite

Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second.

Journal Article Nat Photonics · May 2023 Wide field of view microscopy that can resolve 3D information at high speed and spatial resolution is highly desirable for studying the behaviour of freely moving model organisms. However, it is challenging to design an optical instrument that optimises al ... Full text Open Access Link to item Cite

Axial segmentation by iterative mechanical signaling.

Journal Article bioRxiv · March 28, 2023 In bony fishes, formation of the vertebral column, or spine, is guided by a metameric blueprint established in the epithelial sheath of the notochord. Generation of the notochord template begins days after somitogenesis and even occurs in the absence of so ... Full text Link to item Cite

Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second.

Journal Article ArXiv · January 19, 2023 To study the behavior of freely moving model organisms such as zebrafish (Danio rerio) and fruit flies (Drosophila) across multiple spatial scales, it would be ideal to use a light microscope that can resolve 3D information over a wide field of view (FOV) ... Link to item Cite

Polarized transport of membrane and secreted proteins during lumen morphogenesis.

Journal Article Semin Cell Dev Biol · January 15, 2023 A ubiquitous feature of animal development is the formation of fluid-filled cavities or lumina, which transport gases and fluids across tissues and organs. Among different species, lumina vary drastically in size, scale, and complexity. However, all lumen ... Full text Link to item Cite

Morphogenetic Roles of Hydrostatic Pressure in Animal Development.

Journal Article Annu Rev Cell Dev Biol · October 6, 2022 During organismal development, organs and systems are built following a genetic blueprint that produces structures capable of performing specific physiological functions. Interestingly, we have learned that the physiological activities of developing tissue ... Full text Link to item Cite

Self-organization of apical membrane protein sorting in epithelial cells.

Journal Article FEBS J · February 2022 Polarized epithelial cells are characterized by the asymmetric distribution of proteins between apical and basolateral domains of the plasma membrane. This asymmetry is highly conserved and is fundamental to epithelial cell physiology, development, and hom ... Full text Link to item Cite

Knock-in tagging in zebrafish facilitated by insertion into non-coding regions.

Journal Article Development (Cambridge, England) · October 2021 Zebrafish provide an excellent model for in vivo cell biology studies because of their amenability to live imaging. Protein visualization in zebrafish has traditionally relied on overexpression of fluorescently tagged proteins from heterologous promoters, ... Full text Cite

Smoothelin-like 2 Inhibits Coronin-1B to Stabilize the Apical Actin Cortex during Epithelial Morphogenesis.

Journal Article Curr Biol · February 22, 2021 The actin cortex is involved in many biological processes and needs to be significantly remodeled during cell differentiation. Developing epithelial cells construct a dense apical actin cortex to carry out their barrier and exchange functions. The apical c ... Full text Link to item Cite

Development of a straight vertebrate body axis.

Journal Article Development (Cambridge, England) · October 2020 The vertebrate body plan is characterized by the presence of a segmented spine along its main axis. Here, we examine the current understanding of how the axial tissues that are formed during embryonic development give rise to the adult spine and summarize ... Full text Cite

Notochordal Signals Establish Phylogenetic Identity of the Teleost Spine.

Journal Article Curr Biol · July 20, 2020 The spine is a defining feature of the vertebrate body plan. However, broad differences in vertebral structures and morphogenetic strategies occur across vertebrate groups, clouding the homology between their developmental programs. Analysis of a zebrafish ... Full text Link to item Cite

Distinct roles for luminal acidification in apical protein sorting and trafficking in zebrafish.

Journal Article J Cell Biol · April 6, 2020 Epithelial cell physiology critically depends on the asymmetric distribution of channels and transporters. However, the mechanisms targeting membrane proteins to the apical surface are still poorly understood. Here, we performed a visual forward genetic sc ... Full text Link to item Cite

Notochord vacuoles absorb compressive bone growth during zebrafish spine formation.

Journal Article Elife · January 29, 2020 The vertebral column or spine assembles around the notochord rod which contains a core made of large vacuolated cells. Each vacuolated cell possesses a single fluid-filled vacuole, and loss or fragmentation of these vacuoles in zebrafish leads to spine kinki ... Full text Link to item Cite

High fat diet induces microbiota-dependent silencing of enteroendocrine cells.

Journal Article Elife · December 3, 2019 Enteroendocrine cells (EECs) are specialized sensory cells in the intestinal epithelium that sense and transduce nutrient information. Consumption of dietary fat contributes to metabolic disorders, but EEC adaptations to high fat feeding were unknown. Here ... Full text Link to item Cite

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

Journal Article Dev Cell · October 7, 2019 The guts of neonatal mammals and stomachless fish have a limited capacity for luminal protein digestion, which allows oral acquisition of antibodies and antigens. However, how dietary protein is absorbed during critical developmental stages when the gut is ... Full text Link to item Cite

Tissue self-organization underlies morphogenesis of the notochord.

Journal Article Philos Trans R Soc Lond B Biol Sci · September 24, 2018 The notochord is a conserved axial structure that in vertebrates serves as a hydrostatic scaffold for embryonic axis elongation and, later on, for proper spine assembly. It consists of a core of large fluid-filled vacuolated cells surrounded by an epitheli ... Full text Open Access Link to item Cite

Spine Patterning Is Guided by Segmentation of the Notochord Sheath.

Journal Article Cell Rep · February 20, 2018 The spine is a segmented axial structure made of alternating vertebral bodies (centra) and intervertebral discs (IVDs) assembled around the notochord. Here, we show that, prior to centra formation, the outer epithelial cell layer of the zebrafish notochord ... Full text Link to item Cite

Mecp2 regulates tnfa during zebrafish embryonic development and acute inflammation.

Journal Article Dis Model Mech · December 19, 2017 Mutations in MECP2 cause Rett syndrome, a severe neurological disorder with autism-like features. Duplication of MECP2 also causes severe neuropathology. Both diseases display immunological abnormalities that suggest a role for MECP2 in controlling immune ... Full text Link to item Cite

Bleb Expansion in Migrating Cells Depends on Supply of Membrane from Cell Surface Invaginations.

Journal Article Dev Cell · December 4, 2017 Cell migration is essential for morphogenesis, organ formation, and homeostasis, with relevance for clinical conditions. The migration of primordial germ cells (PGCs) is a useful model for studying this process in the context of the developing embryo. Zebr ... Full text Link to item Cite

Sheath Cell Invasion and Trans-differentiation Repair Mechanical Damage Caused by Loss of Caveolae in the Zebrafish Notochord.

Journal Article Curr Biol · July 10, 2017 The notochord, a conserved axial structure required for embryonic axis elongation and spine development, consists of giant vacuolated cells surrounded by an epithelial sheath [1-3]. During morphogenesis, vacuolated cells maintain their structural integrity ... Full text Link to item Cite

TNFa/TNFR2 signaling is required for glial ensheathment at the dorsal root entry zone.

Journal Article PLoS Genet · April 2017 Somatosensory information from the periphery is routed to the spinal cord through centrally-projecting sensory axons that cross into the central nervous system (CNS) via the dorsal root entry zone (DREZ). The glial cells that ensheath these axons ensure ra ... Full text Link to item Cite

Single epicardial cell transcriptome sequencing identifies Caveolin 1 as an essential factor in zebrafish heart regeneration.

Journal Article Development · January 15, 2016 In contrast to mammals, adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of cardiomyocytes spared from damage. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration th ... Full text Link to item Cite

Developing pressures: fluid forces driving morphogenesis.

Journal Article Curr Opin Genet Dev · June 2015 Over several decades genetic studies have unraveled many molecular mechanisms that underlie the signaling networks guiding morphogenesis, but the mechanical forces at work remain much less well understood. Accumulation of fluid within a luminal space can g ... Full text Link to item Cite

Infection, Inflammation and Healing in Zebrafish: Intestinal Inflammation.

Journal Article Curr Pathobiol Rep · June 1, 2015 Inflammatory bowel diseases (IBD), which include Crohn's disease and ulcerative colitis, contribute to significant morbidity and mortality globally. Despite an increase in incidence, IBD onset is still poorly understood. Mouse models of IBD recapitulate se ... Full text Link to item Cite

Loss of cftr function leads to pancreatic destruction in larval zebrafish.

Journal Article Dev Biol · March 15, 2015 The development and function of many internal organs requires precisely regulated fluid secretion. A key regulator of vertebrate fluid secretion is an anion channel, the cystic fibrosis transmembrane conductance regulator (CFTR). Loss of CFTR function lead ... Full text Link to item Cite

Epigenetic control of intestinal barrier function and inflammation in zebrafish.

Journal Article Proc Natl Acad Sci U S A · March 3, 2015 The intestinal epithelium forms a barrier protecting the organism from microbes and other proinflammatory stimuli. The integrity of this barrier and the proper response to infection requires precise regulation of powerful immune homing signals such as tumo ... Full text Link to item Cite

Developmental regulation of apical endocytosis controls epithelial patterning in vertebrate tubular organs.

Journal Article Nat Cell Biol · March 2015 Epithelial organs develop through tightly coordinated events of cell proliferation and differentiation in which endocytosis plays a major role. Despite recent advances, how endocytosis regulates the development of vertebrate organs is still unknown. Here w ... Full text Link to item Cite

Apicobasal polarity and lumen formation during development

Chapter · January 1, 2015 Networks of interconnected tubes form the basic structural element of many organs. Tubes are composed of polarized epithelia that enclose a lumen. During organogenesis, lumens form by several distinct mechanisms, ranging from wrapping of an epithelial shee ... Full text Cite

Single continuous lumen formation in the zebrafish gut is mediated by smoothened-dependent tissue remodeling.

Journal Article Development · March 2014 The formation of a single lumen during tubulogenesis is crucial for the development and function of many organs. Although 3D cell culture models have identified molecular mechanisms controlling lumen formation in vitro, their function during vertebrate org ... Full text Link to item Cite

Loss of col8a1a function during zebrafish embryogenesis results in congenital vertebral malformations.

Journal Article Dev Biol · February 1, 2014 Congenital vertebral malformations (CVM) occur in 1 in 1000 live births and in many cases can cause spinal deformities, such as scoliosis, and result in disability and distress of affected individuals. Many severe forms of the disease, such as spondylocost ... Full text Link to item Cite

Directing traffic into the future.

Journal Article Dev Cell · December 9, 2013 Full text Link to item Cite

Rapid identification of kidney cyst mutations by whole exome sequencing in zebrafish.

Journal Article Development · November 2013 Forward genetic approaches in zebrafish have provided invaluable information about developmental processes. However, the relative difficulty of mapping and isolating mutations has limited the number of new genetic screens. Recent improvements in the annota ... Full text Link to item Cite

Cftr controls lumen expansion and function of Kupffer's vesicle in zebrafish.

Journal Article Development · April 2013 Regulated fluid secretion is crucial for the function of most organs. In vertebrates, the chloride channel cystic fibrosis transmembrane conductance regulator (CFTR) is a master regulator of fluid secretion. Although the biophysical properties of CFTR have ... Full text Link to item Cite

Notochord vacuoles are lysosome-related organelles that function in axis and spine morphogenesis.

Journal Article J Cell Biol · March 4, 2013 The notochord plays critical structural and signaling roles during vertebrate development. At the center of the vertebrate notochord is a large fluid-filled organelle, the notochord vacuole. Although these highly conserved intracellular structures have bee ... Full text Link to item Cite

The vacuole within: how cellular organization dictates notochord function.

Journal Article Bioarchitecture · 2013 The notochord is an evolutionarily conserved structure that has long been known to play an important role in patterning during embryogenesis. Structurally, the notochord is composed of two cell layers: an outer epithelial-like sheath, and an inner core of ... Full text Link to item Cite

IDENTIFICATION OF CFTR AND FLUID SECRETION REGULATORS IN ZEBRAFISH

Journal Article PEDIATRIC PULMONOLOGY · September 1, 2012 Link to item Cite

CFTR IS REQUIRED DURING DEVELOPMENT OF THE ZEBRAFISH LIVER AND PANCREAS

Journal Article PEDIATRIC PULMONOLOGY · September 1, 2012 Link to item Cite

Regulation of intrahepatic biliary duct morphogenesis by Claudin 15-like b.

Journal Article Dev Biol · January 1, 2012 The intrahepatic biliary ducts transport bile produced by the hepatocytes out of the liver. Defects in biliary cell differentiation and biliary duct remodeling cause a variety of congenital diseases including Alagille Syndrome and polycystic liver disease. ... Full text Link to item Cite

Microbial colonization induces dynamic temporal and spatial patterns of NF-κB activation in the zebrafish digestive tract.

Journal Article Gastroenterology · July 2011 BACKGROUND & AIMS: The nuclear factor κ-light-chain enhancer of activated B cells (NF-κB) transcription factor pathway is activated in response to diverse microbial stimuli to regulate expression of genes involved in immune responses and tissue homeostasis ... Full text Link to item Cite

Investigating the process of single lumen formation in the zebrafish gut

Conference MOLECULAR BIOLOGY OF THE CELL · January 1, 2011 Link to item Cite

CFTR FUNCTIONS DURING ZEBRAFISH ORGANOGENESIS

Conference PEDIATRIC PULMONOLOGY · January 1, 2011 Link to item Cite

Cse1l is a negative regulator of CFTR-dependent fluid secretion.

Journal Article Curr Biol · October 26, 2010 Transport of chloride through the cystic fibrosis transmembrane conductance regulator (CFTR) channel is a key step in regulating fluid secretion in vertebrates [1, 2]. Loss of CFTR function leads to cystic fibrosis [1, 3, 4], a disease that affects the lun ... Full text Link to item Cite

USING ZEBRAFISH TO STUDY THE ROLE OF CFTR IN ORGANOGENESIS

Conference PEDIATRIC PULMONOLOGY · January 1, 2009 Link to item Cite

Genetic control of single lumen formation in the zebrafish gut.

Journal Article Nat Cell Biol · August 2007 Most organs consist of networks of interconnected tubes that serve as conduits to transport fluid and cells and act as physiological barriers between compartments. Biological tubes are assembled through very diverse developmental processes that generate st ... Full text Link to item Cite

Genetic control of CFTR function in zebrafish

Conference PEDIATRIC PULMONOLOGY · January 1, 2007 Link to item Cite

Plasma membrane polarization during mating in yeast cells.

Journal Article J Cell Biol · June 19, 2006 The yeast mating cell provides a simple paradigm for analyzing mechanisms underlying the generation of surface polarity. Endocytic recycling and slow diffusion on the plasma membrane were shown to facilitate polarized surface distribution of Snc1p (Valdez- ... Full text Link to item Cite

A genome-wide visual screen reveals a role for sphingolipids and ergosterol in cell surface delivery in yeast.

Journal Article Proc Natl Acad Sci U S A · December 13, 2005 Recently synthesized proteins are sorted at the trans-Golgi network into specialized routes for exocytosis. Surprisingly little is known about the underlying molecular machinery. Here, we present a visual screen to search for proteins involved in cargo sor ... Full text Link to item Cite

O-glycosylation as a sorting determinant for cell surface delivery in yeast.

Journal Article Mol Biol Cell · April 2004 Little is known about the mechanisms that determine localization of proteins to the plasma membrane in Saccharomyces cerevisiae. The length of the transmembrane domains and association of proteins with lipid rafts have been proposed to play a role in sorti ... Full text Link to item Cite

Aberrant processing of the WSC family and Mid2p cell surface sensors results in cell death of Saccharomyces cerevisiae O-mannosylation mutants.

Journal Article Mol Cell Biol · January 2004 Protein O mannosylation is a crucial protein modification in uni- and multicellular eukaryotes. In humans, a lack of O-mannosyl glycans causes congenital muscular dystrophies that are associated with brain abnormalities. In yeast, protein O mannosylation i ... Full text Link to item Cite

Rvs161p and sphingolipids are required for actin repolarization following salt stress.

Journal Article Eukaryot Cell · December 2002 In Saccharomyces cerevisiae, the actin cytoskeleton is depolarized by NaCl stress. In this study, the response was maximal after 30 min, and then actin patches repolarized. Rvs161p was required for actin repolarization because the rvs161delta mutant did no ... Full text Link to item Cite

Cell surface polarization during yeast mating.

Journal Article Proc Natl Acad Sci U S A · October 29, 2002 Exposure to mating pheromone in haploid Saccharomyces cerevisiae cells results in the arrest of the cell cycle, expression of mating-specific genes, and polarized growth toward the mating partner. Proteins involved in signaling, polarization, cell adhesion ... Full text Link to item Cite

Lipid rafts in protein sorting and cell polarity in budding yeast Saccharomyces cerevisiae.

Journal Article Biol Chem · October 2002 Cellular membranes contain many types and species of lipids. One of the most important functional consequences of this heterogeneity is the existence of microdomains within the plane of the membrane. Sphingolipid acyl chains have the ability of forming tig ... Full text Link to item Cite

Plasma membrane proton ATPase Pma1p requires raft association for surface delivery in yeast.

Journal Article Mol Biol Cell · December 2001 Correct sorting of proteins is essential to generate and maintain the identity and function of the different cellular compartments. In this study we demonstrate the role of lipid rafts in biosynthetic delivery of Pma1p, the major plasma membrane proton ATP ... Full text Link to item Cite

Lipid rafts function in biosynthetic delivery of proteins to the cell surface in yeast.

Journal Article Proc Natl Acad Sci U S A · March 28, 2000 Lipid rafts, formed by lateral association of sphingolipids and cholesterol, have been implicated in membrane traffic and cell signaling in mammalian cells. Sphingolipids also have been shown to play a role in protein sorting in yeast. Therefore, we wanted ... Full text Link to item Cite

OP18/stathmin binds near the C-terminus of tubulin and facilitates GTP binding.

Journal Article Eur J Biochem · June 1999 It is has been previously suggested that the protein Op18/stathmin may interact with tubulin via the alpha-tubulin subunit [Larsson, N., Marklund, U., Melander Gradin, H., Brattsand, G. & Gullberg, M. (1997) Mol. Cell. Biol. 17, 5530-5539]. In this study w ... Full text Link to item Cite