title: Quantitative description of fluid flows produced by left-right cilia in zebrafish.
abstract: Motile cilia generate directional flows that move mucus through airways, cerebrospinal fluid through brain ventricles, and oocytes through fallopian tubes. In addition, specialized monocilia beat in a rotational pattern to create asymmetric flows that are involved in establishing the left-right (LR) body axis during embryogenesis. These monocilia, which we refer to as "left-right cilia," produce a leftward flow of extraembryonic fluid in a transient "organ of asymmetry" that directs asymmetric signaling and development of LR asymmetries in the cardiovascular system and gastrointestinal tract. The asymmetric flows are thought to establish a chemical gradient and/or activate mechanosensitive cilia to initiate calcium ion signals and a conserved Nodal (TGFβ) pathway on the left side of the embryo, but the mechanisms underlying this process remain unclear. The zebrafish organ of asymmetry, called Kupffer's vesicle, provides a useful model system for investigating LR cilia and cilia-powered fluid flows. Here, we describe methods to visualize flows in Kupffer's vesicle using fluorescent microspheres and introduce a new and freely available MATLAB particle tracking code to quantitatively describe these flows. Analysis of normal and aberrant flows indicates this approach is useful for characterizing flow properties that impact LR asymmetry and may be more broadly applicable for quantifying other cilia flows.
authors.affiliation: Department of Physics, Syracuse University, Syracuse, NY, USA.
authors.forename: Craig
authors.initials: C
authors.lastname: Fox
authors.affiliation: Department of Physics, Syracuse University, Syracuse, NY, USA; Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY, USA.
authors.forename: M Lisa
authors.initials: ML
authors.lastname: Manning
authors.affiliation: Department of Cell and Developmental Biology, State University of New York, Upstate Medical University, Syracuse, NY, USA.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Amack
mesh_terms: D000818:Animals; D019521:Body Patterning / Q000502:physiology*; D002923:Cilia / Q000502:physiology*; D047108:Embryonic Development / Q000502:physiology; D057446:Hydrodynamics; D008863:Microspheres; D015027:Zebrafish / Q000196:embryology* / Q000502:physiology*; D029961:Zebrafish Proteins / Q000235:genetics
chemical_list: D029961:Zebrafish Proteins; C561793:nephrocystin-4, zebrafish
keywords: Automated particle tracking; Embryonic development; Fluid flows; Kupffer's vesicle; Left–right patterning; MATLAB; Motile cilia; Zebrafish