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1.  Drag force acting on a neuromast in the fish lateral line trunk canal. I. Numerical modelling of external–internal flow coupling 
Fishes use a complex, multi-branched, mechanoreceptive organ called the lateral line to detect the motion of water in their immediate surroundings. This study is concerned with a subset of that organ referred to as the lateral line trunk canal (LLTC). The LLTC consists of a long tube no more than a few millimetres in diameter embedded immediately under the skin of the fish on each side of its body. In most fishes, pore-like openings are regularly distributed along the LLTC, and a minute sensor enveloped in a gelatinous cupula, referred to as a neuromast, is located between each pair of pores. Drag forces resulting from fluid motions induced inside the LLTC by pressure fluctuations in the external flow stimulate the neuromasts. This study, Part I of a two-part sequence, investigates the motion-sensing characteristics of the LLTC and how it may be used by fishes to detect wakes. To this end, an idealized geometrical/dynamical situation is examined that retains the essential problem physics. A two-level numerical model is developed that couples the vortical flow outside the LLTC to the flow stimulating the neuromasts within it. First, using a Navier–Stokes solver, we calculate the unsteady flow past an elongated rectangular prism and a fish downstream of it, with both objects moving at the same speed. By construction, the prism generates a clean, periodic vortex street in its wake. Then, also using the Navier–Stokes solver, the pressure field associated with this external flow is used to calculate the unsteady flow inside the LLTC of the fish, which creates the drag forces acting on the neuromast cupula. Although idealized, this external–internal coupled flow model allows an investigation of the filtering properties and performance characteristics of the LLTC for a range of frequencies of biological interest. The results obtained here and in Part II show that the LLTC acts as a low-pass filter, preferentially damping high-frequency pressure gradient oscillations, and hence high-frequency accelerations, associated with the external flow.
doi:10.1098/rsif.2008.0291
PMCID: PMC2696135  PMID: 18926967
fish lateral line; wake vortices; mathematical modelling
2.  Sensory integration in the hydrodynamic world of rainbow trout. 
Water movements, of both abiotic and biotic origin, provide a wealth of information for fishes. They detect these water movements by arrays of hydrodynamic sensors located on the surface of the body as superficial neuromasts and embedded in subdermal lateral line canals. Recently, the anatomical dichotomy between superficial and canal neuromasts has been matched by demonstrations of a corresponding functional dichotomy. Superficial neuromasts are sensitive to water flows over the surface of the fish and are the sub-modality that participates in orientation to water currents, a behaviour known as rheotaxis. The canal neuromasts are sensitive to water vibration and it is this sub-modality that determines the localization of artificial prey. Recently, however, it has been shown that the complex behaviour of natural prey capture in the dark requires input from both lateral line sensory submodalities and here we show that the ability of trout to hold station behind a stationary object in fast flowing water also requires integration of information from both sub-modalities.
doi:10.1098/rsbl.2003.0052
PMCID: PMC1809957  PMID: 14667381
3.  A review of fish swimming mechanics and behaviour in altered flows 
Fishes suspended in water are subject to the complex nature of three-dimensional flows. Often, these flows are the result of abiotic and biotic sources that alter otherwise uniform flows, which then have the potential to perturb the swimming motions of fishes. The goal of this review is to highlight key studies that have contributed to a mechanistic and behavioural understanding of how perturbing flows affect fish. Most of our understanding of fish behaviour in turbulence comes from observations of natural conditions in the field and laboratory studies employing controlled perturbations, such as vortices generated in the wake behind simple geometric objects. Laboratory studies have employed motion analysis, flow visualization, electromyography, respirometry and sensory deprecation techniques to evaluate the mechanisms and physiological costs of swimming in altered flows. Studies show that flows which display chaotic and wide fluctuations in velocity can repel fishes, while flows that have a component of predictability can attract fishes. The ability to maintain stability in three-dimensional flows, either actively with powered movements or passively using the posture and intrinsic compliance of the body and fins, plays a large role in whether fish seek out or avoid turbulence. Fish in schools or current-swept habitats can benefit from altered flows using two distinct though not mutually exclusive mechanisms: flow refuging (exploiting regions of reduced flow relative to the earth frame of reference) and vortex capture (harnessing the energy of environmental vortices). Integrating how the physical environment affects organismal biomechanics with the more complex issue of behavioural choice requires consideration beyond simple body motions or metabolic costs. A fundamental link between these two ways of thinking about animal behaviour is how organisms sense and process information from the environment, which determines when locomotor behaviour is initiated and modulated. New data are presented here which show that behaviour changes in altered flows when either the lateral line or vision is blocked, showing that fish rely on multi-modal sensory inputs to negotiate complex flow environments. Integrating biomechanics and sensory biology to understand how fish swim in turbulent flow at the organismal level is necessary to better address population-level questions in the fields of fisheries management and ecology.
doi:10.1098/rstb.2007.2082
PMCID: PMC2442850  PMID: 17472925
turbulence; vortices; kinematics; lateral line; muscle activity; flow visualization
4.  Drag force acting on a neuromast in the fish lateral line trunk canal. II. Analytical modelling of parameter dependencies 
In Part I of this two-part study, the coupled flows external and internal to the fish lateral line trunk canal were consecutively calculated by solving the Navier–Stokes (N–S) equations numerically in each domain. With the external flow known, the solution for the internal flow was obtained using a parallelepiped to simulate the neuromast cupula present between a pair of consecutive pores, allowing the calculation of the drag force acting on the neuromast cupula. While physically rigorous and accurate, the numerical approach is tedious and inefficient since it does not readily reveal the parameter dependencies of the drag force. In Part II of this work we present an analytically based physical–mathematical model for rapidly calculating the drag force acting on a neuromast cupula. The cupula is well approximated as an immobile sphere located inside a tube-shaped canal segment of circular cross section containing a constant property fluid in a steady-periodic oscillating state of motion. The analytical expression derived for the dimensionless drag force is of the form |FN|/(|PL−PR|π(D/2)2)=f(d/D,Lt/D,ωD*), where |FN| is the amplitude of the drag force; |PL−PR| is the amplitude of the pressure difference driving the flow in the interpore tube segment; d/D is the ratio of sphere diameter to tube diameter; Lt/D is the ratio of interpore tube segment length to tube diameter; and ωD*=ω(D/2)2/ν is the oscillating flow kinetic Reynolds number (a dimensionless frequency). Present results show that the dimensionless drag force amplitude increases with decreasing Lt/D and maximizes in the range 0.65≤d/D≤0.85, depending on the values of Lt/D and ωD*. It is also found that in the biologically relevant range of dimensionless frequencies 1≤ωD*≤20 and segment lengths 4≤Lt/D≤16, the sphere tube (neuromast–canal) system acts as a low-pass filter for values d/D≤0.75, approximately. For larger values of d/D the system is equally sensitive to all frequencies, but the drag force is significantly decreased. Comparisons with N–S calculations of the drag force show good agreement with the analytical model results. By revealing the parameter dependencies of the drag force, the model serves to guide biological understanding and the optimized design of corresponding bioinspired artificial sensors.
doi:10.1098/rsif.2008.0293
PMCID: PMC2696136  PMID: 18926966
neuromast drag force; analytical modelling; parameter dependencies
5.  Vortex-induced vibrations of two cylinders in tandem arrangement in the proximity–wake interference region 
Journal of fluid mechanics  2009;621:321-364.
We investigate numerically vortex-induced vibrations (VIV) of two identical two-dimensional elastically mounted cylinders in tandem in the proximity–wake interference regime at Reynolds number Re = 200 for systems having both one (transverse vibrations) and two (transverse and in-line) degrees of freedom (1-DOF and 2-DOF, respectively). For the 1-DOF system the computed results are in good qualitative agreement with available experiments at higher Reynolds numbers. Similar to these experiments our simulations reveal: (1) larger amplitudes of motion and a wider lock-in region for the tandem arrangement when compared with an isolated cylinder; (2) that at low reduced velocities the vibration amplitude of the front cylinder exceeds that of the rear cylinder; and (3) that above a threshold reduced velocity, large-amplitude VIV are excited for the rear cylinder with amplitudes significantly larger than those of the front cylinder. By analysing the simulated flow patterns we identify the VIV excitation mechanisms that lead to such complex responses and elucidate the near-wake vorticity dynamics and vortex-shedding modes excited in each case. We show that at low reduced velocities vortex shedding provides the initial excitation mechanism, which gives rise to a vertical separation between the two cylinders. When this vertical separation exceeds one cylinder diameter, however, a significant portion of the incoming flow is able to pass through the gap between the two cylinders and the gap-flow mechanism starts to dominate the VIV dynamics. The gap flow is able to periodically force either the top or the bottom shear layer of the front cylinder into the gap region, setting off a series of very complex vortex-to-vortex and vortex-to-cylinder interactions, which induces pressure gradients that result in a large oscillatory force in phase with the vortex shedding and lead to the experimentally observed larger vibration amplitudes. When the vortex shedding is the dominant mechanism the front cylinder vibration amplitude is larger than that of the rear cylinder. The reversing of this trend above a threshold reduced velocity is associated with the onset of the gap flow. The important role of the gap flow is further illustrated via a series of simulations for the 2-DOF system. We show that when the gap-flow mechanism is triggered, the 2-DOF system can develop and sustain large VIV amplitudes comparable to those observed in the corresponding (same reduced velocity) 1-DOF system. For sufficiently high reduced velocities, however, the two cylinders in the 2-DOF system approach each other, thus significantly reducing the size of the gap region. In such cases the gap flow is entirely eliminated, and the two cylinders vibrate together as a single body with vibration amplitudes up to 50% lower than the amplitudes of the corresponding 1-DOF in which the gap flow is active. Three-dimensional simulations are also carried out to examine the adequacy of two-dimensional simulations for describing the dynamic response of the tandem system at Re = 200. It is shown that even though the wake transitions to a weakly three-dimensional state when the gap flow is active, the three-dimensional modes are too weak to affect the dynamic response of the system, which is found to be identical to that obtained from the two-dimensional computations.
doi:10.1017/S0022112008004850
PMCID: PMC2728241  PMID: 19693281
6.  Zebrafish Larvae Exhibit Rheotaxis and Can Escape a Continuous Suction Source Using Their Lateral Line 
PLoS ONE  2012;7(5):e36661.
Zebrafish larvae show a robust behavior called rheotaxis, whereby they use their lateral line system to orient upstream in the presence of a steady current. At 5 days post fertilization, rheotactic larvae can detect and initiate a swimming burst away from a continuous point-source of suction. Burst distance and velocity increase when fish initiate bursts closer to the suction source where flow velocity is higher. We suggest that either the magnitude of the burst reflects the initial flow stimulus, or fish may continually sense flow during the burst to determine where to stop. By removing specific neuromasts of the posterior lateral line along the body, we show how the location and number of flow sensors play a role in detecting a continuous suction source. We show that the burst response critically depends on the presence of neuromasts on the tail. Flow information relayed by neuromasts appears to be involved in the selection of appropriate behavioral responses. We hypothesize that caudally located neuromasts may be preferentially connected to fast swimming spinal motor networks while rostrally located neuromasts are connected to slow swimming motor networks at an early age.
doi:10.1371/journal.pone.0036661
PMCID: PMC3343021  PMID: 22570735
7.  Heterochrony, modularity, and the functional evolution of the mechanosensory lateral line canal system of fishes 
EvoDevo  2014;5:21.
Background
The canals of the mechanosensory lateral line system are components of the dermatocranium, and demonstrate phenotypic variation in bony fishes. Widened lateral line canals evolved convergently in a limited number of families of teleost fishes and it had been hypothesized that they evolved from narrow canals via heterochrony and explore modularity in the lateral line system. Two species of cichlids with different canal phenotypes were used to test a hypothesis of heterochrony. Histological material prepared from ontogenetic series of Aulonocara stuartgranti (widened canals) and Tramitichromis sp. (narrow canals) was analyzed using ANCOVA to determine rates of increase in canal diameter and neuromast size (length, width) and to compare the timing of onset of critical stages in canal morphogenesis (enclosure, ossification).
Results
A faster rate of increase in canal diameter and neuromast width (but not length), and a delay in onset of canal morphogenesis were found in Aulonocara relative to Tramitichromis. However, rates of increase in canal diameter and neuromast size among canals, among canal portions and among canals segments reveal similar trends within both species.
Conclusion
The evolution of widened lateral line canals is the result of dissociated heterochrony - acceleration in the rate of increase of both canal diameter and neuromast size, and delay in the onset of canal morphogenesis, in Aulonocara (widened canals) relative to Tramitichromis (narrow canals). Common rates of increase in canal diameter and neuromast size among canal portions in different dermatocranial bones and among canal segments reflect the absence of local heterochronies, and suggest modular integration among canals in each species. Thus, canal and neuromast morphology are more strongly influenced by their identities as features of the lateral line system than by the attributes of the dermatocranial bones in which the canals are found. Rate heterochrony manifested during the larval stage ensures that the widened canal phenotype, known to be associated with benthic prey detection in adult Aulonocara, is already present before feeding commences. Heterochrony can likely explain the convergent evolution of widened lateral line canals among diverse taxa. The lateral line system provides a valuable context for novel analyses of the relationship between developmental processes and the evolution of behaviorally and ecologically relevant phenotypes in fishes.
doi:10.1186/2041-9139-5-21
PMCID: PMC4066827  PMID: 24959342
Aulonocara; Tramitichromis; Cichlidae; Neuromast; Dermatocranium; Heterochrony; Modularity; Lateral line
8.  The Nogo-C2/Nogo Receptor Complex Regulates the Morphogenesis of Zebrafish Lateral Line Primordium through Modulating the Expression of dkk1b, a Wnt Signal Inhibitor 
PLoS ONE  2014;9(1):e86345.
The fish lateral line (LL) is a mechanosensory system closely related to the hearing system of higher vertebrates, and it is composed of several neuromasts located on the surface of the fish. These neuromasts can detect changes in external water flow, to assist fish in maintaining a stationary position in a stream. In the present study, we identified a novel function of Nogo/Nogo receptor signaling in the formation of zebrafish neuromasts. Nogo signaling in zebrafish, like that in mammals, involves three ligands and four receptors, as well as three co-receptors (TROY, p75, and LINGO-1). We first demonstrated that Nogo-C2, NgRH1a, p75, and TROY are able to form a Nogo-C2 complex, and that disintegration of this complex causes defective neuromast formation in zebrafish. Time-lapse recording of the CldnB::lynEGFP transgenic line revealed that functional obstruction of the Nogo-C2 complex causes disordered morphogenesis, and reduces rosette formation in the posterior LL (PLL) primordium during migration. Consistent with these findings, hair-cell progenitors were lost from the PLL primordium in p75, TROY, and Nogo-C2/NgRH1a morphants. Notably, the expression levels of pea3, a downstream marker of Fgf signaling, and dkk1b, a Wnt signaling inhibitor, were both decreased in p75, TROY, and Nogo-C2/NgRH1a morphants; moreover, dkk1b mRNA injection could rescue the defects in neuromast formation resulting from knockdown of p75 or TROY. We thus suggest that a novel Nogo-C2 complex, consisting of Nogo-C2, NgRH1a, p75, and TROY, regulates Fgf signaling and dkk1b expression, thereby ensuring stable organization of the PLL primordium.
doi:10.1371/journal.pone.0086345
PMCID: PMC3897714  PMID: 24466042
9.  Gene miles-apart is required for formation of otic vesicle and hair cells in zebrafish 
Cell Death & Disease  2013;4(10):e900-.
Hearing loss is a serious burden to physical and mental health worldwide. Aberrant development and damage of hearing organs are recognized as the causes of hearing loss, the molecular mechanisms underlining these pathological processes remain elusive. Investigation of new molecular mechanisms involved in proliferation, differentiation, migration and maintenance of neuromast primordium and hair cells will contribute to better understanding of hearing loss pathology. This knowledge will enable the development of protective agents and mechanism study of drug ototoxicity. In this study, we demonstrate that the zebrafish gene miles-apart, a homolog of sphingosine-1-phosphate receptor 2 (s1pr2) in mammals, has an important role in the development of otic vesicle, neuromasts and survival of hair cells. Whole-mount in situ hybridization of embryos showed that miles-apart expression occurred mainly in the encephalic region and the somites at 24 h.p.f. (hour post fertilization), in the midbrain/hindbrain boundary, the brainstem and the pre-neuromast of lateral line at 48 h.p.f. in a strict spatiotemporal regulation. Both up- and downregulation of miles-apart led to abnormal otoliths and semicircular canals, excess or few hair cells and neuromasts, and their disarranged depositions in the lateral lines. Miles-apart (Mil) dysregulation also caused abnormal expression of hearing-associated genes, including hmx2, fgf3, fgf8a, foxi1, otop1, pax2.1 and tmieb during zebrafish organogenesis. Moreover, in larvae miles-apart gene knockdown significantly upregulated proapoptotic gene zBax2 and downregulated prosurvival gene zMcl1b; in contrast, the level of zBax2 was decreased and of zMcl1b enhanced by miles-apart overexpression. Collectively, Mil activity is linked to organization and number decision of hair cells within a neuromast, also to deposition of neuromasts and formation of otic vesicle during zebrafish organogenesis. At the larva stage, Mil as an upstream regulator of bcl-2 gene family has a role in protection of hair cells against apoptosis by promoting expression of prosurvival gene zMcl1b and suppressing proapoptotic gene zBax2.
doi:10.1038/cddis.2013.432
PMCID: PMC3920936  PMID: 24176858
miles-apart; hair cells; neuromast; otoliths; hearing-associated genes; apoptosis
10.  Electrosensory ampullary organs are lateral line placode-derived in bony fishes 
Nature communications  2011;2:496.
Electroreception is an ancient subdivision of the lateral line sensory system, found in all major vertebrate groups (though lost in frogs, amniotes, and most ray-finned fishes). Electroreception is mediated by “hair cells” in ampullary organs, distributed in fields flanking lines of mechanosensory hair cell-containing neuromasts that detect local water movement. Neuromasts, and afferent neurons for both neuromasts and ampullary organs, develop from lateral line placodes. Although ampullary organs in the axolotl (a representative of the lobe-finned clade of bony fishes) are lateral line placode-derived, non-placodal origins have been proposed for electroreceptors in other taxa. Here we show morphological and molecular data describing lateral line system development in the basal ray-finned fish Polyodon spathula, and present fate-mapping data that conclusively demonstrate a lateral line placode origin for ampullary organs and neuromasts. Together with the axolotl data, this confirms that ampullary organs are ancestrally lateral line placode-derived in bony fishes.
doi:10.1038/ncomms1502
PMCID: PMC4212271  PMID: 21988912
paddlefish; lateral line; electroreceptors; neuromasts; ampullary organs; placodes; hair cells
11.  Phoenix Is Required for Mechanosensory Hair Cell Regeneration in the Zebrafish Lateral Line 
PLoS Genetics  2009;5(4):e1000455.
In humans, the absence or irreversible loss of hair cells, the sensory mechanoreceptors in the cochlea, accounts for a large majority of acquired and congenital hearing disorders. In the auditory and vestibular neuroepithelia of the inner ear, hair cells are accompanied by another cell type called supporting cells. This second cell population has been described as having stem cell-like properties, allowing efficient hair cell replacement during embryonic and larval/fetal development of all vertebrates. However, mammals lose their regenerative capacity in most inner ear neuroepithelia in postnatal life. Remarkably, reptiles, birds, amphibians, and fish are different in that they can regenerate hair cells throughout their lifespan. The lateral line in amphibians and in fish is an additional sensory organ, which is used to detect water movements and is comprised of neuroepithelial patches, called neuromasts. These are similar in ultra-structure to the inner ear's neuroepithelia and they share the expression of various molecular markers. We examined the regeneration process in hair cells of the lateral line of zebrafish larvae carrying a retroviral integration in a previously uncharacterized gene, phoenix (pho). Phoenix mutant larvae develop normally and display a morphologically intact lateral line. However, after ablation of hair cells with copper or neomycin, their regeneration in pho mutants is severely impaired. We show that proliferation in the supporting cells is strongly decreased after damage to hair cells and correlates with the reduction of newly formed hair cells in the regenerating phoenix mutant neuromasts. The retroviral integration linked to the phenotype is in a novel gene with no known homologs showing high expression in neuromast supporting cells. Whereas its role during early development of the lateral line remains to be addressed, in later larval stages phoenix defines a new class of proteins implicated in hair cell regeneration.
Author Summary
By screening for regeneration deficient zebrafish mutations, we identified a zebrafish mutant line deficient in a highly specific regeneration process, the renewal of hair cells in the lateral line. Although this organ is specific to fish and amphibians, it contains essentially the same mechanosensory cells (the hair cells) that function in the ear for sound and balance detection in all vertebrates. Mammals are unusual vertebrates in that they have lost the ability to regenerate functional hair cells after damage by sound or chemical exposure. All other vertebrates retain their ability to regenerate their hair cells after damage, but this process is not well understood at the molecular level. The retroviral insertion linked to the phoenix mutation is in a new gene family class that is specifically required for the supporting cells to enter into mitosis after hair cell damage. What is particularly unusual about this mutation is that it appears not to affect the normal development and differentiation pathways, but only seems to affect the cells' post-differentiation regeneration.
doi:10.1371/journal.pgen.1000455
PMCID: PMC2662414  PMID: 19381250
12.  Sensory processing of water currents by fishes. 
Water currents are extremely important in the aquatic environment and play a very significant role in the lives of fishes. Sensory processing of water currents involves a number of sensory modalities including the inner ear, vision, tactile sense and the mechanosensory lateral line. The inner ear will detect whole-body accelerations generated by changes in flow, or by turbulence, whereas visual and tactile inputs will signal translational movement with respect to an external visual or tactile reference frame. The superficial neuromasts of the mechanosensory lateral line detect flow over the surface of the body and have the appropriate anatomical distribution and physiological properties to signal the strength and the direction of flow and, hence, contribute to the detection of regional differences in flow over different parts of the body.
PMCID: PMC1692841  PMID: 11079424
13.  Vortical Flow Field During Phonation in an Excised Canine Larynx Model 
Objectives
To more fully understand the mechanisms of vocal fold vibration and sound production, we studied the velocity flow fields above the folds. Such velocity fields during phonation have not been reported in the literature.
Methods
Using the particle image velocimetry method for 3 excised canine larynges, we obtained the velocity fields in the mid-membranous coronal plane during different phases of phonation. The velocity field was determined synchronously with the vocal fold motion recorded by high-speed videography.
Results
The results show that vortices occur immediately above the vocal folds and that the location and shape of the vortices depend on the phase of the phonation cycle. Consistent vortical structures found included starting vortices, Kelvin-Helmholtz vortices, entrainment vortices, and vortices directly above the folds during the divergent glottal stage.
Conclusions
These vortical structures were consistently found during specific phases of the glottal cycle for 3 canine larynges that significantly varied in size. This consistent behavior suggests that the vortices may be important for both vibration and sound production; however, further study is needed to prove this. The clinical significance of these vortices is discussed.
PMCID: PMC2586301  PMID: 17419527
laryngeal disease; larynx; phonation; voice disorder
14.  Lateral line-mediated rheotactic behavior in tadpoles of the African clawed frog (Xenopus laevis) 
Tadpoles (Xenopus laevis) have a lateral line system whose anatomical structure has been described, but whose functional significance has not been closely examined. These experiments tested the hypothesis that the lateral line system is involved in rheotaxis. Tadpoles in developmental stages 47–56 oriented toward the source of a water current. Orientation was less precise after treatment with cobalt chloride or streptomycin, but was similar to that of untreated animals after exposure to gentamicin. In no current conditions, tadpoles exhibited a characteristic head-down posture by which they held themselves in the water column at an angle around 45°. This body posture became significantly less tilted in the presence of water current. Treatment with cobalt chloride or streptomycin increased the angle of tilt close to that seen in no current conditions, while gentamicin treatment tended to decrease tilt angle. The data are consistent with anatomical and physiological findings that tadpole neuromasts are similar to superficial, but not canal, neuromasts in fishes, and they suggest that the lateral line system is involved in both directional current detection and current-related postural adjustments in Xenopus.
doi:10.1007/s00359-004-0534-3
PMCID: PMC1193646  PMID: 15300386
African clawed frog; Lateral line; Rheotaxis; Tadpole; Xenopus
15.  Rheotaxis in Larval Zebrafish Is Mediated by Lateral Line Mechanosensory Hair Cells 
PLoS ONE  2012;7(2):e29727.
The lateral line sensory system, found in fish and amphibians, is used in prey detection, predator avoidance and schooling behavior. This system includes cell clusters, called superficial neuromasts, located on the surface of head and trunk of developing larvae. Mechanosensory hair cells in the center of each neuromast respond to disturbances in the water and convey information to the brain via the lateral line ganglia. The convenient location of mechanosensory hair cells on the body surface has made the lateral line a valuable system in which to study hair cell damage and regeneration. One way to measure hair cell survival and recovery is to assay behaviors that depend on their function. We built a system in which orientation against constant water flow, positive rheotaxis, can be quantitatively assessed. We found that zebrafish larvae perform positive rheotaxis and that, similar to adult fish, larvae use both visual and lateral line input to perform this behavior. Disruption or damage of hair cells in the absence of vision leads to a marked decrease in rheotaxis that recovers upon hair cell repair or regeneration.
doi:10.1371/journal.pone.0029727
PMCID: PMC3281009  PMID: 22359538
16.  Using Particle Imaging Velocimetry to Measure Anterior-Posterior Velocity Gradients in the Excised Canine Larynx Model 
Objectives
To quantify the anterior-posterior velocity gradient, we studied the velocity flow fields above the vocal folds in both the midcoronal and midsagittal planes. It was also our purpose to use these fields to deduce the mechanisms that cause the anterior-posterior gradient and to determine whether the vortical structures are highly 3-dimensional.
Methods
Using the particle imaging velocimetry method for 5 excised canine larynges. we obtained phase-averaged velocity fields in the midcoronal and midsagittal planes for 30 phases of phonation. The velocity fields were determined synchronously with the vocal fold motion recorded by high-speed videography.
Results
The results show that immediately above the folds, there is no significant anterior-posterior velocity gradient. However, as the flow travels downstream, the laryngeal jet tends to narrow in width and skew toward the anterior commissure. Vortices are seen at the anterior and posterior edges of the flow.
Conclusions
The downstream narrowing in the midsagittal plane is consistent with and is probably due to a phenomenon known as axis switching. Axis switching also involves vortices in the sagittal and coronal planes bending in the axial plane. This results in highly 3-dimensional, complex vortical structures. However, there is remarkable cyclic repeatability of these vortices during a phonation cycle.
PMCID: PMC2586298  PMID: 18357838
anterior-posterior velocity gradient; particle imaging velocimetry; phonation. vocal fold; voice production; vortex
17.  Neomycin-Induced Hair Cell Death and Rapid Regeneration in the Lateral Line of Zebrafish (Danio rerio)  
Mechanoreceptive hair cells are extremely sensitive to aminoglycoside antibiotics, including neomycin. Hair cell survival was assessed in larval wild-type zebrafish lateral line neuromasts 4 h after initial exposure to a range of neomycin concentrations for 1 h. Each of the lateral line neuromasts was scored in live fish for the presence or absence of hair cells using the fluorescent vital dye DASPEI to selectively label hair cells. All neuromasts were devoid of DASPEI-labeled hair cells 4 h after 500 µM neomycin exposure. Vital DASPEI staining was proportional to the number of hair cells per neuromast identified in fixed larvae using immunocytochemistry for acetylated tubulin and phalloidin labeling. The time course of hair cell regeneration in the lateral line neuromasts was also analyzed following neomycin-induced damage. Regenerated hair cells were first observed using live DASPEI staining 12 and 24 h following neomycin treatment. The potential role of proliferation in regenerating hair cells was analyzed. A 1 h pulse-fix protocol using bromodeoxyuridine (BrdU) incorporation was used to identify S-phase cells in neuromasts. BrdU incorporation in neomycin-damaged neuromasts did not differ from control neuromasts 4 h after drug exposure but was dramatically upregulated after 12 h. The proliferative cells identified during a 1 h period at 12 h after neomycin treatment were able to give rise to new hair cells by 24–48 h after drug treatment. The results presented here provide a standardized preparation for studying and identifying genes that influence vertebrate hair cell death, survival, and regeneration following ototoxic insults.
doi:10.1007/s10162-002-3022-x
PMCID: PMC3202713  PMID: 12943374
hair cell death; lateral line; aminoglycosides; hair cell regeneration; zebrafish; genetic screening
18.  Three dimensional flow in the human left atrium 
Heart  2001;86(4):448-455.
BACKGROUND—Abnormal flow patterns in the left atrium in atrial fibrillation or mitral stenosis are associated with an increased risk of thrombosis and systemic embolisation; the characteristics of normal atrial flow that avoid stasis have not been well defined.
OBJECTIVES—To present a three dimensional particle trace visualisation of normal left atrial flow in vivo, constructed from flow velocities in three dimensional space.
METHODS—Particle trace visualisation of time resolved three dimensional magnetic resonance imaging velocity measurements was used to provide a display of intracardiac flow without the limitations of angle sensitivity or restriction to imaging planes. Global flow patterns of the left atrium were studied in 11 healthy volunteers.
RESULTS—In all subjects vortical flow was observed in the atrium during systole and diastolic diastasis (mean (SD) duration of systolic vortex, 280 (77) ms; and of diastolic vortex, 256 (118) ms). The volume incorporated and recirculated within the vortices originated predominantly from the left pulmonary veins. Inflow from the right veins passed along the vortex periphery, constrained between the vortex and the atrial wall.
CONCLUSIONS—Global left atrial flow in the normal human heart comprises consistent patterns specific to the phase of the cardiac cycle. Separate paths of left and right pulmonary venous inflow and vortex formation may have beneficial effects in avoiding left atrial stasis in the normal subject in sinus rhythm.


Keywords: atrium; blood flow; magnetic resonance imaging; haemodynamics
doi:10.1136/heart.86.4.448
PMCID: PMC1729920  PMID: 11559688
19.  On the spacing of Langmuir circulation in strong shear 
Journal of fluid mechanics  2005;525:215-236.
The inviscid instability of O(ε) two-dimensional free-surface gravity waves propagating along an O(1) parallel shear flow is considered. The modes of instability involve spanwise-periodic longitudinal vortices resembling oceanic Langmuir circulation. Here, not only are wave-induced mean effects important but also wave modulation, caused by velocity anomalies which develop in the streamwise direction. The former are described by a generalized Lagrangian-mean formulation and the latter by a modified Rayleigh equation. Since both effects are essential, the instability may be called ‘generalized’ Craik–Leibovich (CLg). Of specific interest is whether spanwise distortion of the wave field, both at the free surface and in the interior, acts to enhance or inhibit instability to longitudinal vortices. Also of interest is whether the instability gives rise to a preferred spacing for the vortices and whether that spacing concurs well or poorly with experiment. The layer depth is varied from much less than the e-folding depth of the O(ε) wave motion to infinity. Relative to an identical shear flow with rigid though wavy top boundary, it is found, inter alia, that wave modulation acts in concert with the free surface, at some wavenumbers, to increase the maximum growth rate of the instability. Indeed, two preferred spanwise spacings occur, one which gives rise to longitudinal vortices through a convective oscillatory bifurcation and a second, at higher wavenumber and growth rate, through a stationary bifurcation. The preferred spacings set by the stationary bifurcation concur well with those observed in laboratory experiments, with the implication that the instability acting in the experiments is very likely to be CLg.
doi:10.1017/S0022112004002654
PMCID: PMC2405900  PMID: 18516246
20.  Pleiotropic effects of a single gene on skeletal development and sensory system patterning in sticklebacks 
EvoDevo  2014;5:5.
Background
Adaptation to a new environment can be facilitated by co-inheritance of a suite of phenotypes that are all advantageous in the new habitat. Although experimental evidence demonstrates that multiple phenotypes often map to the same genomic regions, it is challenging to determine whether phenotypes are associated due to pleiotropic effects of a single gene or to multiple tightly linked genes. In the threespine stickleback fish (Gasterosteus aculeatus), multiple phenotypes are associated with a genomic region around the gene Ectodysplasin (Eda), but only the presence of bony lateral plates has been conclusively shown to be caused by Eda.
Results
Here, we ask whether pleiotropy or linkage is responsible for the association between lateral plates and the distribution of the neuromasts of the lateral line. We first identify a strong correlation between plate appearance and changes in the spatial distribution of neuromasts through development. We then use an Eda transgene to induce the formation of ectopic plates in low plated fish, which also results in alterations to neuromast distribution. Our results also show that other loci may modify the effects of Eda on plate formation and neuromast distribution.
Conclusions
Together, these results demonstrate that Eda has pleiotropic effects on at least two phenotypes, highlighting the role of pleiotropy in the genetic basis of adaptation.
doi:10.1186/2041-9139-5-5
PMCID: PMC3976036  PMID: 24499504
Pleiotropy; Genetics of adaptation; Lateral line; Neuromast; Dermal skeleton
21.  Heterogeneity and Dynamics of Lateral Line Afferent Innervation During Development in Zebrafish (Danio rerio) 
The Journal of comparative neurology  2012;520(7):1376-1386.
The lateral line system of larval zebrafish is emerging as a model to study a range of topics in neurobiology, from hair cell regeneration to sensory processing. However, despite numerous studies detailing the patterning and development of lateral line neuromasts, little is known about the organization of their connections to afferent neurons and targets in the hindbrain. We found that as fish grow and neuromasts proliferate over the body surface, the number of afferent neurons increases linearly. The number of afferents innervating certain neuromasts increases over time, while it decreases for other neuromasts. The ratio of afferent neurons to neuromasts differs between the anterior and posterior lateral line system, suggesting potential differences in sensitivity threshold or spatial resolution. A single afferent neuron routinely contacts a group of neuromasts, suggesting that different afferent neurons can convey information about receptive fields along the body. When afferent projections are traced into the hindbrain, where a distinct somatotopy has been previously described, we find that this general organization is absent at the Mauthner cell. We speculate that directional input from the lateral line is less important at an early age, whereas the speed of the escape response is paramount, and that directional responses arise later in development. By quantifying morphological connections in the lateral line system, this study provides a detailed foundation to understand how hydrodynamic information is processed and ultimately translated into appropriate motor behaviors.
doi:10.1002/cne.22798
PMCID: PMC3377011  PMID: 22102005
afferent neuron; Mauthner cell; neuromast; plasticity; somatotopy
22.  Evolution of electrosensory ampullary organs: conservation of Eya4 expression during lateral line development in jawed vertebrates 
Evolution & development  2012;14(3):277-285.
SUMMARY
The lateral line system of fishes and amphibians comprises two ancient sensory systems: mechanoreception and electroreception. Electroreception is found in all major vertebrate groups (i.e., jawless fishes, cartilaginous fishes and bony fishes); however, it was lost in several groups including anuran amphibians (frogs) and amniotes (reptiles, birds and mammals), as well as in the lineage leading to the neopterygian clade of bony fishes (bowfins, gars and teleosts). Electroreception is mediated by modified ‘hair cells’, which are collected in ampullary organs that flank lines of mechanosensory hair cell-containing neuromasts. In the axolotl (a urodele amphibian), grafting and ablation studies have shown a lateral line placode origin for both mechanosensory neuromasts and electrosensory ampullary organs (and the neurons that innervate them). However, little is known at the molecular level about the development of the amphibian lateral line system in general and electrosensory ampullary organs in particular. Previously, we identified Eya4 as a marker for lateral line (and otic) placodes, neuromasts and ampullary organs in a shark (a cartilaginous fish) and a paddlefish (a basal ray-finned fish). Here, we show that Eya4 is similarly expressed during otic and lateral line placode development in the axolotl (a representative of the lobe-finned fish clade). Furthermore, Eya4 expression is specifically restricted to hair cells in both neuromasts and ampullary organs, as identified by co-expression with the calcium-buffering protein Parvalbumin3. As well as identifying new molecular markers for amphibian mechanosensory and electrosensory hair cells, these data demonstrate that Eya4 is a conserved marker for lateral line placodes and their derivatives in all jawed vertebrates.
doi:10.1111/j.1525-142X.2012.00544.x
PMCID: PMC4224121  PMID: 23017075
23.  Visual perception of axes of head rotation 
Registration of ego-motion is important to accurately navigate through space. Movements of the head and eye relative to space are registered through the vestibular system and optical flow, respectively. Here, we address three questions concerning the visual registration of self-rotation. (1) Eye-in-head movements provide a link between the motion signals received by sensors in the moving eye and sensors in the moving head. How are these signals combined into an ego-rotation percept? We combined optic flow of simulated forward and rotational motion of the eye with different levels of eye-in-head rotation for a stationary head. We dissociated simulated gaze rotation and head rotation by different levels of eye-in-head pursuit. We found that perceived rotation matches simulated head- not gaze-rotation. This rejects a model for perceived self-rotation that relies on the rotation of the gaze line. Rather, eye-in-head signals serve to transform the optic flow's rotation information, that specifies rotation of the scene relative to the eye, into a rotation relative to the head. This suggests that transformed visual self-rotation signals may combine with vestibular signals. (2) Do transformed visual self-rotation signals reflect the arrangement of the semi-circular canals (SCC)? Previously, we found sub-regions within MST and V6+ that respond to the speed of the simulated head rotation. Here, we re-analyzed those Blood oxygenated level-dependent (BOLD) signals for the presence of a spatial dissociation related to the axes of visually simulated head rotation, such as have been found in sub-cortical regions of various animals. Contrary, we found a rather uniform BOLD response to simulated rotation along the three SCC axes. (3) We investigated if subject's sensitivity to the direction of the head rotation axis shows SCC axes specifcity. We found that sensitivity to head rotation is rather uniformly distributed, suggesting that in human cortex, visuo-vestibular integration is not arranged into the SCC frame.
doi:10.3389/fnbeh.2013.00011
PMCID: PMC3573326  PMID: 23919087
optic flow; MST; V3A; V6; motion perception; eye movements; self-rotation; vestibular system
24.  Wake Development behind Paired Wings with Tip and Root Trailing Vortices: Consequences for Animal Flight Force Estimates 
PLoS ONE  2014;9(3):e91040.
Recent experiments on flapping flight in animals have shown that a variety of unrelated species shed a wake behind left and right wings consisting of both tip and root vortices. Here we present an investigation using Particle Image Velocimetry (PIV) of the behaviour and interaction of trailing vortices shed by paired, fixed wings that simplify and mimic the wake of a flying animal with a non-lifting body. We measured flow velocities at five positions downstream of two adjacent NACA 0012 aerofoils and systematically varied aspect ratio, the gap between the wings (corresponding to the width of a non-lifting body), angle of attack, and the Reynolds number. The range of aspect ratios and Reynolds number where chosen to be relevant to natural fliers and swimmers, and insect flight in particular. We show that the wake behind the paired wings deformed as a consequence of the induced flow distribution such that the wingtip vortices convected downwards while the root vortices twist around each other. Vortex interaction and wake deformation became more pronounced further downstream of the wing, so the positioning of PIV measurement planes in experiments on flying animals has an important effect on subsequent force estimates due to rotating induced flow vectors. Wake deformation was most severe behind wings with lower aspect ratios and when the distance between the wings was small, suggesting that animals that match this description constitute high-risk groups in terms of measurement error. Our results, therefore, have significant implications for experimental design where wake measurements are used to estimate forces generated in animal flight. In particular, the downstream distance of the measurement plane should be minimised, notwithstanding the animal welfare constraints when measuring the wake behind flying animals.
doi:10.1371/journal.pone.0091040
PMCID: PMC3954621  PMID: 24632825
25.  Perturbing the developing skull: using laser ablation to investigate the robustness of the infraorbital bones in zebrafish (Danio rerio) 
BMC Developmental Biology  2014;14(1):44.
Background
The development of the craniofacial skeleton from embryonic mesenchyme is a complex process that is not yet completely understood, particularly for intramembranous bones. This study investigates the development of the neural crest derived infraorbital (IO) bones of the zebrafish (Danio rerio) skull. Located under the orbit, the IO bones ossify in a set sequence and are closely associated with the lateral line system. We conducted skeletogenic condensation and neuromast laser ablation experiments followed by shape analyses in order to investigate the relationship between a developing IO bone and the formation of the IO series as well as to investigate the highly debated inductive potential of neuromasts for IO ossification.
Results
We demonstrate that when skeletogenic condensations recover from laser ablation, the resulting bone differs in shape compared to controls. Interestingly, neighbouring IO bones in the bone series are unaffected. In addition, we show that the amount of canal wall mineralization is significantly decreased following neuromast laser ablation at juvenile and larval stages.
Conclusions
These results highlight the developmental robustness of the IO bones and provide direct evidence that canal neuromasts play a role in canal wall development in the head. Furthermore, we provide evidence that the IO bones may be two distinct developmental modules. The mechanisms underlying developmental robustness are rarely investigated and are important to increase our understanding of evolutionary developmental biology of the vertebrate skull.
doi:10.1186/s12861-014-0044-7
PMCID: PMC4282728  PMID: 25516292
Intramembranous ossification; Morphometrics; Robustness; Lateral line canal walls; Craniofacial development

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