Automated Reconstruction of Three-Dimensional Fish Motion,Forces, and Torques

Fish can move freely through the water column and make complex three-dimensional motions to explore their environment, escape or feed. Nevertheless, the majority of swimming studies is currently limited to two-dimensional analyses. Accurate experimental quantification of changes in body shape, position and orientation (swimming kinematics) in three dimensions is therefore essential to advance biomechanical research of fish swimming. Here, we present a validated method that automatically tracks a swimming fish in three dimensions from multi-camera high-speed video. We use an optimisation procedure to fit a parameterised, morphology-based fish model to each set of video images. This results in a time sequence of position, orientation and body curvature. We post-process this data to derive additional kinematic parameters (e.g. velocities, accelerations) and propose an inverse-dynamics method to compute the resultant forces and torques during swimming. The presented method for quantifying 3D fish motion paves the way for future analyses of swimming biomechanics.     

Function of dorsal fins in bamboo shark during steady swimming

To gain insight into the function of the dorsal fins in white-spotted bamboo sharks (Orectolobiformes: Hemiscyillidae) during steady swimming, data on three-dimensional kinematics and electromyographic recordings were collected. Bamboo sharks were induced to swim at 0.5 and 0.75 body lengths per second in a laminar flow tank. Displacement, lag and angles were analyzed from high-speed video images. Onset, offset, duration, duty cycle and asynchrony index were calculated from three muscle implants on each side of each dorsal fin. The dorsal fins were displaced more laterally than the undulating body. In addition, the dorsal tips had larger lateral displacement than the trailing edges. Increased speed was accompanied by an increase in tail beat frequency with constant tail beat amplitude. However, lateral displacement of the fins and duration of muscle bursts remained relatively constant with increased speed. The range of lateral motion was greater for the second dorsal fin (mean 33.3°) than for the first dorsal fin (mean 28.4°). Bending within the fin was greater for the second dorsal fin (mean 43.8°) than for the first dorsal fin (mean 30.8°). Muscle onset and offset among implants on the same side of each dorsal fin was similar. Three-dimensional conformation of the dorsal fins was caused by interactions between muscle activity, material properties, and incident flow. Alternating bilateral activity occurred in both dorsal fins, further supporting the active role of these hydrofoils in thrust production during steady swimming. The dorsal fins in bamboo sharks are capable of thrust production during steady swimming and do not appear to function as stabilizing structures.     

Biological Inspiration: From Carangiform Fish to Multi-Joint Robotic Fish

This paper presents a novel approach to modelling carangiform fish-like swimming motion for multi-joint robotic fish so that they can obtain fish-like behaviours and mimic the body motion of carangiform fish. A given body motion function of fish swimming is firstly converted to a tail motion function which describes the tail motion relative to the head. Then, the tail motion function is discretized into a series of tail postures over time. Thirdly, a digital approximation method calculates the taming angles of joints in the tail to approximate each tail posture; and finally, these angles are grouped into a look-up table, or re-gressed to a time-dependent function, for practically controlling the tail motors in a multi-joint robotic fish. The paper made three contributions: tail motion relative to the head, an error function for digital approximation and regressing a look-up table for online optimization. To prove the feasibility of the proposed methodology, two basic swimming motion patterns, cruise straight and C-shape sharp turning, are modelled and implemented in our robotic fish. The experimental results show that the relative tail motion and the approximation error function are good choices and the proposed method is feasible.     

Unexpected Regularity in Swimming Behavior of Clausocalanus furcatus Revealed by a Telecentric 3D Computer Vision System

Planktonic copepods display a large repertoire of motion behaviors in a three-dimensional environment. Two-dimensional video observations demonstrated that the small copepod Clausocalanus furcatus, one the most widely distributed calanoids at low to medium latitudes, presented a unique swimming behavior that was continuous and fast and followed notably convoluted trajectories. Furthermore, previous observations indicated that the motion of C. furcatus resembled a random process. We characterized the swimming behavior of this species in three-dimensional space using a video system equipped with telecentric lenses, which allow tracking of zooplankton without the distortion errors inherent in common lenses. Our observations revealed unexpected regularities in the behavior of C. furcatus that appear primarily in the horizontal plane and could not have been identified in previous observations based on lateral views. Our results indicate that the swimming behavior of C. furcatus is based on a limited repertoire of basic kinematic modules but exhibits greater plasticity than previously thought.     

The fish tail motion forms an attached leading edge vortex

The tail (caudal fin) is one of the most prominent characteristics of fishes, and the analysis of the flow pattern it creates is fundamental to understanding how its motion generates locomotor forces. A mechanism that is known to greatly enhance locomotor forces in insect and bird flight is the leading edge vortex (LEV) reattachment, i.e. a vortex (separation bubble) that stays attached at the leading edge of a wing. However, this mechanism has not been reported in fish-like swimming probably owing to the overemphasis on the trailing wake, and the fact that the flow does not separate along the body of undulating swimmers. We provide, to our knowledge, the first evidence of the vortex reattachment at the leading edge of the fish tail using three-dimensional high-resolution numerical simulations of self-propelled virtual swimmers with different tail shapes. We show that at Strouhal numbers (a measure of lateral velocity to the axial velocity) at which most fish swim in nature (approx. 0.25) an attached LEV is formed, whereas at a higher Strouhal number of approximately 0.6 the LEV does not reattach. We show that the evolution of the LEV drastically alters the pressure distribution on the tail and the force it generates. We also show that the tail''s delta shape is not necessary for the LEV reattachment and fish-like kinematics is capable of stabilising the LEV. Our results suggest the need for a paradigm shift in fish-like swimming research to turn the focus from the trailing edge to the leading edge of the tail.     

Pathogenesis of acute viral disease induced in fish by carp interstitial nephritis and gill necrosis virus

A lethal disease of koi and common carp (species Cyprinus carpio) has afflicted many fish farms worldwide since 1998, causing severe financial losses. Morbidity and mortality are restricted to common carp and koi and appear in spring and autumn, when water temperatures are 18 to 28 degrees C. We have isolated the virus causing the disease from sick fish, propagated it in koi fin cell culture, and shown that virus from a single clone causes lethal disease in carp and koi upon infection. Intraperitoneal virus injection or bathing the fish in virus-containing water kills 85 to 100% of the fish within 7 to 21 days. This virus is similar to the previously reported koi herpesvirus; however, it has characteristics inconsistent with the herpesvirus family, and thus we have called it carp interstitial nephritis and gill necrosis virus. We examined the pathobiology of this disease in carp by using immunohistochemistry and PCR. We found large amounts of the virus in the kidneys of sick fish and smaller amounts in liver and brain. A rapid increase in the viral load in the kidneys was detected by using both immunofluorescence and semiquantitative PCR. Histological analyses of fish at various times after infection revealed signs of interstitial nephritis as early as 2 days postinfection, which increased in severity up to 10 days postinfection. There was severe gill disease evidenced by loss of villi with accompanying inflammation in the gill rakers. Minimal focal inflammation was noted in livers and brains. This report describes the etiology and pathology of a recently described viral agent in fish.     

Ciliary beating in three dimensions: Steps of a quantitative description

We document a novel approach for quantitative assessment of ciliary activity, exemplified in rapid three-dimensional cyclic motion of the frontal cirri of Stylonychia. Cells held under voltage-clamp control are stimulated by step pulses to elicit reproducible hyperpolarization- or depolarization-induced ciliary motor responses. High-speed video recording at 200 fields per second is used for imaging ciliary organelles of the same cell in two perspectives: the axial view and, following cell rotation by 90 degrees, the lateral view. From video sequences of typically 1 s, the contours of the cirral images are determined and digitized. Computer programs are established to (1) reduce an observed image to a "ciliary axis", (2) sort series of axes by template to generate an averaged ciliary cycle in 2D-projection, and (3) to associate the generalized axial and lateral 2D-images for generation of a sequence of three-dimensional images, which quantitatively represent the cycle in space and time. The method allows us to produce predetermined perspectives of images selected from the ciliary cycle, and to generate stereo views for graphical representation of ciliary motion. The approach includes a potential for extraction of the complete microtubular sliding program of a cilium under reproducible electric stimulation of the ciliary membrane.     

基于视频跟踪的竖缝式鱼道内鱼类运动行为分析

竖缝式鱼道过鱼对象运动行为与鱼道池室内水力条件是否相适应是进行鱼道设计的关键。研究通过视频跟踪法对竖缝式鱼道中目标鱼的运动轨迹进行实时跟踪, 获取鱼的运动加速度、运动速度, 并和人工手动跟踪的鱼类运动轨迹进行对比, 证明基于视频跟踪法的鱼类运动分析程序既能较好的应用于竖缝式鱼道中, 获取鱼类运动行为, 又可减少大量的人工操作, 有助于为竖缝式鱼道设计提供重要基础数据。     

A comparative study on innate immune parameters in the epidermal mucus of various fish species

Fish epidermal mucus and its components provide the first line of defense against pathogens. Little is known about the role of epidermal mucus enzymes in the innate immune system of fish species such as Arctic char (Salvelinus alpinus), brook trout (S. fontinalis), koi carp(Cyprinus carpio), striped bass (Morone saxatilis), haddock, (Melanogrammus aeglefinus), Atlantic cod (Gadus morhua) and hagfish (Myxine glutinosa). The epidermal mucus samples from these fish were analysed for the specific activities of various hydrolytic enzymes including lysozyme, alkaline phosphatase, cathepsin B and proteases and the enzyme levels were compared among the fish species. Of all the species hagfish mucus showed a high activity for lysozyme and proteases and koi carp mucus had the highest levels of alkaline phosphatase and cathepsin B. A wide variation in enzyme activities was observed among the seven species and also between species of same family such as Arctic char and brook trout (salmonidae), haddock and cod (gadidae). Only lysozyme levels showed a marked variation with salinity where seawater fish showed approximately two times higher lysozyme activity than freshwater-reared fish species. Characterization of proteases with specific inhibitors showed Arctic char, brook trout, haddock and cod having higher levels of serine over metalloproteases whereas koi carp and striped bass had higher levels of metalloproteases over serine proteases. In contrast, hagfish had almost equal proportion of both serine and metalloproteases. This study demonstrates variation in the level of hydrolytic enzymes in the epidermal mucus of fish. These results provide preliminary information for a better understanding of the role of epidermal mucus and its components in the fish innate immune system.     

基于Matlab的鱼类游泳动力学分析

鱼类游泳动力学分析研究对解决鱼道等工程应用中水力学设计方面的关键问题有着重要的意义,利用计算机技术对鱼类游泳动力学进行分析有助于研究目标鱼类的生理特性、游泳能力及其与水力环境因子的响应关系。基于MATLAB软件对我国特有鱼类鲢幼鱼进行游泳动力学分析,借助鲢幼鱼游泳时的摆尾行为,得到不同水流速度下鲢幼鱼的摆尾频率、摆尾幅度、游泳速度和加速度;对比人工计数和手动跟踪分析方法,从实际操作复杂程度和实验数据准确性的角度,分析各数据采集方法的优劣性。结果表明基于Matlab软件采用跟踪鱼的身体中线的思路能更高效的获取大量的运动参数,比如摆尾频率、摆尾幅度、游泳速度和加速度等指标。文章介绍了一种基于Matlab开发的鱼类游泳动力学分析方法,有助于为以后鱼类游泳动力学研究提供依据。     

Detection of carp interstitial nephritis and gill necrosis virus in fish droppings

Carp interstitial nephritis and gill necrosis virus (CNGV) is an unclassified large DNA virus that morphologically resembles members of the Herpesviridae but contains a large (ca. approximately 280-kbp) linear double-stranded DNA. This virus has also been named koi herpesvirus, koi herpes-like virus, and cyprinid herpesvirus 3. CNGV is the cause of a lethal disease that afflicts common carp and koi. By using immunohistochemistry, molecular analysis, and electron microscopy we previously demonstrated that this virus is present mainly in the intestine and kidney of infected fish. Based on these observations, we postulated that viruses and/or viral components may appear in droppings of infected carp. Here we report that (i) by using PCR we demonstrated that fish droppings contain viral DNA, (ii) fish droppings contain viral antigens which are useful for CNGV diagnosis, and (iii) fish droppings contain active virus which can infect cultured common carp brain cells and induce the disease in na?ve fish following inoculation. Thus, our findings show that CNGV can be identified by using droppings without taking biopsies or killing fish and that infectious CNGV is present in the stools of sick fish. The possibility that fish droppings preserve viable CNGV during the nonpermissive seasons is discussed.     

New Data on Axial Locomotion in Fishes: How Speed Affects Diversity of Kinematics and Motor Patterns

Despite considerable recent progress in understanding the functionof the axial muscles and skeleton in fishes, generalizing fromthese results has been hindered by the great phylogenetic diversityof taxa, the lack of quantitative morphometric data on axialmusculoskeletal structure, and limited analysis of the fullrange of locomotor behaviors exhibited within any one taxon.This paper reviews novel results from our studies of two taxawithin a single monophyletic clade, the sunfish family Centrarchidae.Integrated analyses of lateral displacement, lateral bending,and axial muscle activity reveal widespread effects of swimmingspeed both within a particular mode of swimming and among differentbehavioral modes. The longitudinal position along the body ofthe fish also commonly affects kinematics, muscle activity andthe timing of electromyograms (EMGs) relative to kinematics.EMGs and kinematic events propagate from head to tail for bothsteady and kick and glide swimming. In contrast, during theescape response, the onset of EMGs forms a standing wave pattern,whereas kinematic events are propagated. Several novel featuresof the axial motor pattern are summarized for the kick and glidemode of unsteady swimming. For example, the onset of white fiberEMGs lags significantly behind that of the red fibers at thesame longitudinal position, and red fibers are inactivated athigher unsteady swimming speeds. Muscle activity propagatesposteriorly via the sequential activation of myomeres, but thereare statistically significant differences in the timing of EMGsfrom the contractile tissue opposite a single vertebra. Duringrelatively slow kick and glide swimming, the extreme dorsaland ventral portions of myomeres are not active. Estimates ofthe longitudinal extent of the fish with simultaneous muscleactivity indicate that EMGs from an individual myomere usuallyhave temporal overlap with more than 20 neighboring myomereson the same side of the fish. Consequently, the functional unitsfor axial locomotion of fishes do not correspond simply to theanatomical units of individual myomeres. Rather the in vivomotor pattern is a primary determinant of the functional unitsinvolved in swimming.     

Center of mass motion in swimming fish: effects of speed and locomotor mode during undulatory propulsion

Studies of center of mass (COM) motion are fundamental to understanding the dynamics of animal movement, and have been carried out extensively for terrestrial and aerial locomotion. But despite a large amount of literature describing different body movement patterns in fishes, analyses of how the center of mass moves during undulatory propulsion are not available. These data would be valuable for understanding the dynamics of different body movement patterns and the effect of differing body shapes on locomotor force production. In the present study, we analyzed the magnitude and frequency components of COM motion in three dimensions (x: surge, y: sway, z: heave) in three fish species (eel, bluegill sunfish, and clown knifefish) swimming with four locomotor modes at three speeds using high-speed video, and used an image cross-correlation technique to estimate COM motion, thus enabling untethered and unrestrained locomotion. Anguilliform swimming by eels shows reduced COM surge oscillation magnitude relative to carangiform swimming, but not compared to knifefish using a gymnotiform locomotor style. Labriform swimming (bluegill at 0.5 body lengths/s) displays reduced COM sway oscillation relative to swimming in a carangiform style at higher speeds. Oscillation frequency of the COM in the surge direction occurs at twice the tail beat frequency for carangiform and anguilliform swimming, but at the same frequency as the tail beat for gymnotiform locomotion in clown knifefish. Scaling analysis of COM heave oscillation for terrestrial locomotion suggests that COM heave motion scales with positive allometry, and that fish have relatively low COM oscillations for their body size.     

Description of an as yet unclassified DNA virus from diseased Cyprinus carpio species

Numerous deaths of koi and common carp (Cyprinus carpio) were observed on many farms throughout Israel, resulting in severe financial losses. The lethal viral disease observed is highly contagious and extremely virulent, but morbidity and mortality are restricted to koi and common carp populations. Diseased fish exhibit fatigue and gasping movements in shallow water. Infected fish had interstitial nephritis and gill necrosis as well as petechial hemorrhages in the liver and other symptoms that were not consistent with viral disease, suggesting a secondary infection. Here we report the isolation of carp nephritis and gill necrosis virus (CNGV), which is the etiologic agent of this disease. The virus propagates and induces severe cytopathic effects by 5 days postinfection in fresh koi or carp fin cell cultures (KFC and CFC, respectively), but not in epithelioma papillosum cyprini cells. The virus harvested from KFC cultures induced the same clinical signs, with a mortality of 75 to 95%, upon inoculation into naive koi and common carp. Using PCR, we provide final proof that the isolated virus is indeed the etiologic agent of food and ornamental carp mortalities in fish husbandry. Electron microscopy revealed viral cores with icosahedral morphology of 100 to 110 nm that resembled herpesviruses. Electron micrographs of purified pelleted CNGV sections, together with viral sensitivities to ether and Triton X-100, suggested that it is an enveloped virus. However, the genome of the isolated virus is a double-stranded DNA (dsDNA) molecule of 270 to 290 kbp, which is larger than known herpesviruses. The viral DNA seems highly divergent and bears only small fragments (16 to 45 bp) that are similar to the genomes of several DNA viruses. Nevertheless, amino acid sequences encoded by CNGV DNA fragments bear similarities primarily to members of the Poxviridae and Herpesviridae and to other large dsDNA viruses. We suggest, therefore, that the etiologic agent of this disease may represent an as yet unclassified virus species that is endemic in C. carpio (carp).     

Locomotion of free-swimming ghost knifefish: anal fin kinematics during four behaviors

The maneuverability demonstrated by the weakly electric ghost knifefish (Apteronotus albifrons) is a result of its highly flexible ribbon-like anal fin, which extends nearly three-quarters the length of its body and is composed of approximately 150 individual fin rays. To understand how movement of the anal fin controls locomotion we examined kinematics of the whole fin, as well as selected individual fin rays, during four locomotor behaviors executed by free-swimming ghost knifefish: forward swimming, backward swimming, heave (vertical) motion, and hovering. We used high-speed video (1000 fps) to examine the motion of the entire anal fin and we measured the three-dimensional curvature of four adjacent fin rays in the middle of the fin during each behavior to determine how individual fin rays bend along their length during swimming. Canonical discriminant analysis separated all four behaviors on anal fin kinematic variables and showed that forward and backward swimming behaviors contrasted the most: forward behaviors exhibited a large anterior wavelength and posterior amplitude while during backward locomotion the anal fin exhibited both a large posterior wavelength and anterior amplitude. Heave and hover behaviors were defined by similar kinematic variables; however, for each variable, the mean values for heave motions were generally greater than for hovering. Individual fin rays in the middle of the anal fin curved substantially along their length during swimming, and the magnitude of this curvature was nearly twice the previously measured maximum curvature for ray-finned fish fin rays during locomotion. Fin rays were often curved into the direction of motion, indicating active control of fin ray curvature, and not just passive bending in response to fluid loading.     

Locomotion of Gymnarchus Niloticus： Experiment and Kinematics

In addition to forward undulatory swimming, Gymnarchus niloticus can swim via undulations of the dorsal fin while the body axis remains straight; furthermore, it swims forward and backward in a similar way, which indicates that the undulation of the dorsal fin can simultaneously provide bidirectional propulsive and maneuvering forces with the help of the tail fin. A high-resolution Charge-Coupled Device （CCD） imaging camera system is used to record kinematics of steady swimming as well as maneuvering in G. niloticus. Based on experimental data, this paper discusses the kinematics （cruising speed, wave speed, cycle frequency, amplitude, lateral displacement） of forward as well as backward swimming and maneuvering. During forward swimming, the propulsive force is generated mainly by undulations of the dorsal fin while the body axis remains straight. The kinematic parameters （wave speed, wavelength, cycle frequency, amplitude） have statistically significant correlations with cruising speed. In addition, the yaw at the head is minimal during steady swimming. From experimental data, the maximal lateral displacement of head is not more than 1% of the body length, while the maximal lateral displacement of the whole body is not more than 5% of the body length. Another important feature is that G. niloticus swims backwards using an undulatory mechanism that resembles the forward undulatory swimming mechanism. In backward swimming, the increase of lateral displacement of the head is comparatively significant; the amplitude profiles of the propulsive wave along the dorsal fin are significantly different from those in forward swimming. When G. niloticus does fast maneuvering, its body is first bent into either a C shape or an S shape, then it is rapidly unwound in a travelling wave fashion. It rarely maneuvers without the help of the tail fin and body bending.     

Riding the waves: the role of the body wave in undulatory fish swimming

A continuously swimming mullet modulates its thrust productionby changing slip-the ratio between its swimming speed U andthe speed V with which the body wave travels down its body.This variation in thrust is reflected in the wake of the fish.We obtained 2-dimensional impressions of the wake behind a mulletswimming at a slip of 0.7 equivalent to active swimming, ata slip of 0.9 close to free-wheeling, and at a slip of 1.1 whenthe fish is braking. Independent of the slip, vortices are shedat the tail when the tail tip reaches its maximum lateral excursion.The manner in which the wake changes as it decays depends onthe degree of slip: At a slip well below unity, the wake decayswithout any qualitative changes in shape, the medio-frontalcross section of the mature wake consists of a double row ofalternating vortices separated by an undulating jet, and theangle between the jet flow and the mean path of motion is closeto 45°; at a slip above unity, the vortices stretch outlaterally and the mature wake resembles a single row of ovalvortices with two vortex cores, and the jet between the vorticesis almost perpendicular to the mean path of motion; the wakeat slip of 0.9 exhibits a pattern intermediate between the wakesat slips 0.7 and 0.9 with slightly elongate vortices and a jetangle of 61°.     

Spontaneous diploidization of maternal chromosome set in ornamental (koi) carp, Cyprinus carpio L.

An unusually high frequency of spontaneous diploidization in a maternal chromosome set (SDM) was discovered in one ornamental carp (koi) female in an experiment on these fish for induced gynogenesis. Spontaneous appearance of diploid embryos in the gynogenetic offspring (intact eggs × irradiated sperm) and appearance of triploids among control fish (intact eggs × intact sperm) obtained from koi female and males of edible carp indicated spontaneous diploidization of maternal chromosomes (SDM). Possible cytological processes causing this phenomenon are discussed.     

Volumetric imaging of shark tail hydrodynamics reveals a three-dimensional dual-ring vortex wake structure

Understanding how moving organisms generate locomotor forces is fundamental to the analysis of aerodynamic and hydrodynamic flow patterns that are generated during body and appendage oscillation. In the past, this has been accomplished using two-dimensional planar techniques that require reconstruction of three-dimensional flow patterns. We have applied a new, fully three-dimensional, volumetric imaging technique that allows instantaneous capture of wake flow patterns, to a classic problem in functional vertebrate biology: the function of the asymmetrical (heterocercal) tail of swimming sharks to capture the vorticity field within the volume swept by the tail. These data were used to test a previous three-dimensional reconstruction of the shark vortex wake estimated from two-dimensional flow analyses, and show that the volumetric approach reveals a different vortex wake not previously reconstructed from two-dimensional slices. The hydrodynamic wake consists of one set of dual-linked vortex rings produced per half tail beat. In addition, we use a simple passive shark-tail model under robotic control to show that the three-dimensional wake flows of the robotic tail differ from the active tail motion of a live shark, suggesting that active control of kinematics and tail stiffness plays a substantial role in the production of wake vortical patterns.     

An unusual koi herpesvirus associated with a mortality event of common carp Cyprinus carpio in New York State, USA

Koi herpesvirus (KHV), a highly contagious and lethal virus that affects both koi (Cyprinus carpio koi) and common carp (Cyprinus carpio), was isolated in 1998 from two outbreaks of koi suffering mass mortality in New York State, USA, and in Israel. The disease had been described as early as 1996 in Europe. In July 2004, this virus was found associated with a mass mortality event in wild common carp in the Chadakoin River, New York, USA (42 degrees 07' N, 79 degrees W). Affected fish typically showed marked hyperplasia of gill tissues, abdominal adhesions, and severe multifocal to diffuse external hemorrhages. The virus isolated in this outbreak was somewhat unusual in that it initially replicated well in fathead minnow cell cultures, which is typical of spring viremia of carp virus. Testing at the National Veterinary Services Laboratories, Ames, Iowa, USA, confirmed the virus's identity to be KHV. Koi herpesvirus is not currently on the OIE (World Organisation for Animal Health) list of notifiable diseases; however, it is capable of causing mass mortality in susceptible fish at permissive temperatures.