Biology subjects

Kawabata, Y.

Publications and source records attributed to Kawabata, Y..

13 recordsLinked to original sources

bioRxiv2025

Evolution of sideways locomotion in crabs

The evolutionary change in the mode of locomotion is often a major evolutionary event, triggering diversification. Sideways locomotion is a defining feature of true crabs (Brachyura) and may have contributed to their ecological success. Yet, the evolutionary origin of this unique behavior remains unknown. Here we show that the prevalence of sideways locomotion in true crabs reflects a single evolutionary origin from a forward-moving ancestor. Our behavioral analysis of 50 live crab species indicates that crab locomotion can be broadly separated into two predominant modes, sideways and forward locomotion. The phylogenetic comparative analysis revealed a single origin of sideways locomotion, with multiple independent reversions to forward locomotion in ecologically specialized groups. The species richness data show that the lineage in which sideways locomotion originated is far more diverse than its nearest outgroups. These results are consistent with the idea that sideways locomotion acted as a key innovation contributing to the evolutionary diversification of true crabs. Such a rare but innovative behavioral trait provides a framework for understanding how locomotor modes shape evolutionary diversification in animals.

evolutionary biology↗

bioRxiv2025

Development of a 24-Channel 3T Phased-Array Coil for fMRI in Awake Monkeys - Mitigating Spatiotemporal Artifacts in Ferumoxytol-Weighted Functional Connectivity Estimation

Functional magnetic resonance imaging (fMRI) of awake macaque monkeys holds promise for advancing our understanding of primate brain organization, including humans. However, estimating functional connectivity in awake animals is challenging due to the limited duration of imaging sessions and the relatively low sensitivity to neural activity. To overcome these challenges, we developed a 24-channel 3T receive radiofrequency (RF) coil optimized for parallel imaging of awake macaques. This enabled the acquisition of multiband and GRAPPA-accelerated ferumoxytol-weighted resting-state fMRI. The Human Connectome Project-style data processing pipelines were adapted to address the unique preprocessing demands of cerebral blood volume-weighted (CBVw) imaging, including motion correction, functional-to-structural image co-registration, and training a multi-run independent component analysis-based X-noiseifier (ICA-FIX) classifier for removal of structured artifacts. Our CBVw fMRI approach resulted in an elevated contrast-to-noise ratio compared to blood oxygenation level dependent (BOLD) imaging in anesthetized macaques. However, structured imaging artifacts still contributed more variance to the functional timeseries than neural activity. By applying the ICA-FIX classifier, we achieved highly reproducible parcellated functional connectivity at the single-subject level. At the group-level, we identified dense functional networks with spatial features homologous to those observed in humans. The developed RF receive coil, image acquisition protocols, and data analysis pipelines are publicly available, providing the broader scientific community with tools to leverage these advances for further research.

neuroscience↗

bioRxiv2024

Analysis of oogenesis defects in Dyro mutant of Drosophila melanogaster.

Dyro mutant is female sterile, and oogenesis is aborted during stage8-9 of oogenesis. We investigated detail of the oogenesis defect of Dyro mutant. At first, we confirmed loss of Dyro caused female sterility by genetic rescue experiment. Then, we performed genetic mosaic analysis and found Dyro expression in germ cell is important for oogenesis. In Dyro mutant, inhibition of programmed cell death suppressed cell death of germ cells during oogenesis but failed to rescue fertility. It indicates that abortion of oogenesis is not because of mis-regulation of cell death signal but there is oogenesis defect which activates Caspase signaling pathway. Then, we observed Dyro mutant and looking for defects which may trigger cell death of germ cells in Dyro mutant. We found oogenesis abortion timing is similar to yolk protein mutant but different from amino acid starvation. It suggests that nutrient signal defect does not triggers cell death in Dyro mutant. We carefully observed the defect of Dyro mutant ovaries and found abnormal morphology of nucleolus and chromosome in nurse cells. It seems chromosome in Dyro mutant is thick and nucleolus is limited in small space between thick chromosomes in Dyro mutant nurse cells. Other defect we found is aggregated protein accumulation in germ cells. These data suggest that Dyro has important role in mid-oogenesis stage germ cell and loss of Dyro causes defect in nuclear of nurse cells which may leads to abortion of oogenesis.

developmental biology↗

bioRxiv2023

Automated escape system: identifying prey's kinematic and behavioral features critical for predator evasion

O_LIIdentifying the kinematic and behavioral variables of prey that influence the evasion from predator attacks is essential not only for comprehending the determinants of successful predator evasion but also for shedding light on the evolution of specific traits and the dynamics of predator-prey relationships on a larger scale. However, quantifying the relationship between these variables and the success or failure of predator evasion is challenging, particularly for variables with small variations within prey species. One promising approach to address this challenge is the use of a simulated prey system, which allows us to manipulate the kinematic and behavioral features of prey and expose them to real predators. Nevertheless, creating a system that moves comparably to real prey animals remains difficult, especially for invertebrate and lower vertebrate species that respond quickly to predators and escape rapidly. C_LIO_LIIn this study, we have developed an automated escape system that is comparable to real prey species, responding to a predator within tens of milliseconds and escaping at over 1.0 m/s. The system automatically detects an approaching predator and pulls the prey away from the predator once the predator reaches a predetermined threshold distance. Reaction distance, response latency, as well as escaping speed, duration, and direction can be adjusted in the system. C_LIO_LIBy repeatedly measuring the response latency and escaping speed of the system, we demonstrated the systems ability to exhibit fast and rapid responses while maintaining consistency across successive trials. As a case study, we manipulated the escape speed and reaction distance of the prey to expose them to a predatory fish, Coreoperca kawamebari. The results show that both variables significantly affect the outcome of predator-prey interactions. C_LIO_LIThese findings indicate that the developed escape system is useful for identifying kinematic and behavioral features of prey that are critical for predator evasion. Moreover, due to its relatively low cost and customizability, we propose that this system can be applied to investigate various aspects of animal behaviors (e.g., eliciting escape responses by artificial stimuli) in different animal species. C_LI

animal behavior and cognition↗

bioRxiv2021

Idea Paper: Effects of gonad type and body mass on the time required for sex change in fishes

Sex change is a well-known phenomenon in teleost fishes, and it takes several days to a few months depending on the species and direction of sex change. However, the underlying factors influencing the time required for sex change (TS) remain unclear. Given that the time for producing a new gonad largely determines TS, the gonad type (i.e., whether fish retain the gonad of opposite sex or not [delimited or non-delimited]) and metabolic rate are the ultimate determinants of TS. This study sought to test two hypotheses: (1) the delimited gonad shortens TS; and (2) TS scales with mass0.1-0.2, because the metabolic scaling exponent ({beta}) in fishes is 0.8-0.9 and biological times scale with mass1-{beta} in general. We compiled data on TS for 12 female-to-male and 14 male-to-female sex-changing species from the literature. Results of individual examinations of the effects of gonad type and mass were consistent with our hypotheses. However, upon simultaneous examination of the effects of gonad type and mass, these effects became unclear because of their strong multicollinearity. The compiled data for delimited and non-delimited gonads were biased toward the smaller and larger species, respectively, precluding us from being able to statistically distinguish between these effects. Small species with non-delimited gonads and large species with delimited gonads exist; however, their TS has not been measured with high temporal resolution thus far. Therefore, additional experiments on these species are required to statistically distinguish between, as well as to better understand, the effects of gonad type and mass on TS.

animal behavior and cognition↗

bioRxiv2021

Escaping from multiple visual threats: Modulation of escape responses in Pacific staghorn sculpin (Leptocottus armatus).

Fish perform rapid escape responses to avoid sudden predatory attacks. During escape responses, fish bend their bodies into a C-shape and quickly turn away from the predator and accelerate. The escape trajectory is determined by the initial turn (Stage 1) and a contralateral bend (Stage 2). Previous studies have used a single threat or model predator as a stimulus. In nature, however, multiple predators may attack from different directions simultaneously or in close succession. It is unknown whether fish are able to change the course of their escape response when startled by multiple stimuli at various time intervals. Pacific staghorn sculpin (Leptocottus armatus) were startled with a left and right visual stimulus in close succession. By varying the timing of the second stimulus, we were able to determine when and how a second stimulus could affect the escape response direction. Four treatments were used: a single visual stimulus (control); or two stimuli coming from opposite sides separated by a 0 ms (simultaneous treatment); a 33 ms; or a 83 ms time interval. The 33 ms and 83 ms time intervals were chosen to occur shortly before and after a predicted 60 ms visual escape latency (i.e. during Stage 1). The 0 ms and 33 ms treatments influenced both the escape trajectory and the Stage 1 turning angle, compared to a single stimulation, whereas the 83 ms treatment had no effect on the escape response. We conclude that Pacific staghorn sculpin can modulate their escape response only between stimulation and the onset of the response, but that escape responses are ballistic after the body motion has started. SUMMARY STATEMENTUsing double stimulation from opposite sides at different time intervals to simulate coordinated predatory attacks, Pacific staghorn sculpin escape away from the first stimulus, but were unable to turn away from the second stimulus while the escape response was in progress.

animal behavior and cognition↗

bioRxiv2021

Escaping through the predator's gill cleft: A defensive tactic of juvenile eels after capture by predatory fish

Some prey animals can actively escape from predators even after being captured, but knowledge of such behaviors is still limited, especially in vertebrates. Here, we report the unique active escape behavior of Japanese eel Anguilla japonica juveniles through the gill cleft of the predatory fish Odontobutis obscura. Of the 54 A. japonica juveniles captured by the predator, 28 escaped via the predators gill, and most escaped individuals survived afterwards. In all escaped individuals, their tails emerged first from the gill cleft of the predator, and then their whole bodies slipped out in a backward direction from the cleft. These findings indicate that A. japonica juveniles have the specialized antipredator tactic, which provides the basis for further investigation from behavioral, ecological, and evolutionary perspectives.

zoology↗

bioRxiv2020

Geometrical model explains multiple preferred escape trajectories of fish

The escape trajectory (ET) of prey - measured as the angle relative to the predators approach path - plays a major role in avoiding predation. Previous geometric models predict a single ET; however, many species show highly variable ETs with multiple preferred directions. Although such a high ET variability may confer unpredictability to avoid predation, the reasons why animals prefer specific multiple ETs remain unclear. Here, we constructed a novel geometric model that incorporates the time required for prey to turn and the predators position at the end of its attack. The optimal ET was determined by maximizing the time difference of arrival at the edge of the safety zone between the prey and predator. By fitting the model to the experimental data of fish Pagrus major we show that the model can clearly explain the observed multiple preferred ETs. By using the same model, we were able to explain different patterns of ETs empirically observed in other species (e.g., insects and frogs): a single preferred ET and multiple preferred ETs at small (20-50{degrees}) and large (150-180{degrees}) angles from the predator. Our results open new avenues of investigation for understanding how animals choose their ETs from behavioral and neurosensory perspectives.

animal behavior and cognition↗

bioRxiv2020

Effects of dead conspecifics, hunger states, and seasons on the foraging behavior of the purple urchin Heliocidaris crassispina

Trophic cascades exerts a powerful effect between predator and prey relationships in an ecosystem. In aquatic environments, the signals associated with predators and predation are used by prey as a cue to avoid encountering predators when foraging for food. These cues are powerful enough to control prey populations and indirectly protect primary producers. We evaluated the effects of cues associated with predation on the purple urchin, Heliocidaris crassispina and examined effects of hunger state and season using time-lapse photography, we conducted a series of manipulative and in situ behavior experiments to determine foraging behavior patterns which demonstrate behavior modification. The results suggest that starved urchins were less sensitive to predation cues when compared to normally fed urchins. Field experiments indicated that 70% of fed urchins fled when exposed to a predation cue (presence of a dead urchin), whereas all starved urchins remained regardless of the cue, supporting the results from the laboratory using the dead urchin and algae treatment cues. Sea urchin activity and feeding rates were lower in winter-spring than in summer-autumn. We suggest that hunger state has a large influence over the behavioral-response of sea urchins, while also being affected by season due to metabolic control. In general, starvation overrides predator avoidance behaviors and exposes prey species to higher risks of predation.

ecology↗

bioRxiv2019

Towards HCP-Style Macaque Connectomes: 24-Channel 3T Multi-Array Coil, MRI Sequences and Preprocessing

Macaque monkeys are an important model species for understanding cortical organization of primates, yet tools and methods for noninvasive image acquisition (e.g. MRI RF coils and pulse sequence protocols) and image data preprocessing have lagged behind those developed for humans. To resolve the structural and functional characteristics of the relatively thin macaque cortex, high spatial, temporal, and angular resolutions are required while maintaining high signal-to-noise ratio to ensure good image quality. To address these challenges, we developed a macaque 24-channel receive coil for 3-T MRI with parallel imaging capabilities. This coil enabled adaptation of the Human Connectome Project (HCP) image acquisition protocols to the macaque brain. We also adapted HCP preprocessing methods optimized for the macaque brain, including spatial minimal preprocessing of structural, functional MRI (fMRI), and diffusion MRI (dMRI). The coil provided high signal-to-noise ratio and high efficiency in data acquisition, allowing four- and five-fold acceleration for dMRI and fMRI, respectively. Automated parcellation of cortex, reconstruction of cortical surface, removal of artefacts and nuisance signals in fMRI, and distortion correction of dMRI performed well, and the overall quality of basic neurobiological measures was comparable with those for the HCP. The resulting HCP-style in vivo macaque MRI data show considerable promise for analyzing cortical architecture and functional and structural connectivity using advanced methods that have previously only been available for humans.\n\nHighlights[tpltrtarr] 24-channel 3T MR receive coil designed for the smaller macaque brain.\n[tpltrtarr]In vivo macaque imaging protocols adapted according to guidelines from the HCP.\n[tpltrtarr]Parallel imaging yields five- and four-fold acceleration in fMRI and dMRI sampling.\n[tpltrtarr]HCPs minimal preprocessing and denoising pipelines adapted for macaques.\n[tpltrtarr]The multi-modal MRI data show considerable promise for HCP-style analyses.

neuroscience↗

bioRxiv2017

A miniaturized threshold-triggered acceleration data-logger for recording burst movements of aquatic animals

Animal-borne accelerometers are effective tools for quantifying the kinematics of animal behaviors, such as swimming, running, and flying, under natural conditions. However, quantifying burst movements of small and agile aquatic animals (e.g., small teleost fish), such as during predatory behavior, or while fleeing, remains challenging. To capture the details of burst movements, accelerometers need to sample at a very high frequency, which will inevitably shorten the duration of the recording or increase the size of the device. To overcome this problem, we developed a high-frequency acceleration data-logger that can be triggered by a manually-defined acceleration threshold, thus allowing the selective measurement of animal burst movements. We conducted experiments under laboratory and field conditions to examine the performance of the logger. The laboratory experiment using red seabream (Pagrus major) showed that the new logger could measure the kinematics of their escape behaviors (i.e., body beat cycles and maximum acceleration values). The field experiment using free-swimming yellowtail kingfish (Seriola lalandi) showed that the loggers trigger correctly (i.e., of the 18 burst movements, 17 were recorded by the loggers). We suggest that this new logger can be applied to measure the burst movements of various small and agile animals, whose movements may be otherwise difficult to measure.

animal behavior and cognition↗

bioRxiv2017

Stepwise approach to oocyte depletion in Sry mutated XY female mice

Little is known regarding the mechanisms underlying infertility in male-to-female sex-reversed females. To gain a better understanding of germ cell dysfunction in this condition, we produced XYsry--females via the CRISPR/Cas9 system in C57BL/6 inbred strain mice. Mutant mice showed severe attrition of germ cells during foetal development, resulting in depletion of ovarian germ cells before sexual maturation. Comprehensive transcriptome analysis of embryonic day 13.5 primordial germ cells (PGCs) and postnatal day 1 oocytes demonstrated that XYsry--PGCs had already deviated from the developmental process at the mitotic stage. In addition, XYsry--oocytes resulted in meiotic disruption and developmental failure, and the genes related to these processes were significantly changed. This grievous disruption, which caused germ cell deterioration in XYsry--females, was shown to proceed from the germ cells themselves. These results provide novel insight into the germ cell depletion of sex-reversed mice as well as into disorders of sex differentiation in human, such as Swyer syndrome, wherein patients present as typical females albeit with an XY karyotype and infertile.

developmental biology↗

bioRxiv2017

Effect Of Initial Body Orientation On Escape Probability In Prey Fish Escaping From Predators

Since the escape response is crucial to survival and hence to the fitness of species, several studies have attempted to elucidate the kinematic and behavioral components of the response that affect evasion outcome. The preys body orientation relative to a predator at the onset of the escape response (initial orientation) could affect evasion outcome, because the turn angle and its duration before the initiation of escape locomotion would be smaller when the initial orientation is more away from the predator. We tested this hypothesis by recording the escape responses of juvenile red sea bream (Pagrus major) in response to the predatory scorpion fish (Sebastiscus marmoratus) using a high-speed video camera. Our results show that an increased initial orientation (i.e., more away from the predator) increases escape probability. Our results also indicate that an increase in the initial orientation decreases the turn angle and its duration. The flight initiation distance tends to be small when the initial orientation is away from the predator, suggesting that the prey might have a blind zone of sensory perception. These findings highlight the importance of incorporating initial orientation into both empirical and theoretical studies of the kinematics of predator-prey interactions.\n\nSummary statementOur predator-prey experiments reveal that the preys initial body orientation relative to a predator affects the preys turn angle and its duration, and consequently affects escape probability.

animal behavior and cognition↗