Biology subjects

Yoda, K.

Publications and source records attributed to Yoda, K..

10 recordsLinked to original sources

bioRxiv2026

PhaB-independent poly(3-hydroxybutyrate) production in the thermophilic hydrogen-oxidizing bacterium Hydrogenophilus thermoluteolus

Hydrogenophilus thermoluteolus TH-1 is a thermophilic hydrogen-oxidizing bacterium capable of producing poly(3-hydroxybutyrate) (PHB) from CO2. To redirect carbon flux for producing other useful biomaterials, we disrupted the acetoacetyl-CoA reductase genes (phaB1 and phaB2), which are central to the primary PHB synthesis pathway. Unexpectedly, the resulting {Delta}phaB1B2 mutant still accumulated PHB under autotrophic conditions, reaching approximately 25-35 % of the wild-type level. Furthermore, PHB accumulation in the mutant was significantly restored when fatty acids (butyrate and oleate) were used as carbon sources, whereas acetate and malate resulted in reduced accumulation. These results suggest the existence of a PhaB-independent PHB synthesis pathway. We propose that intermediates from the {beta}-oxidation of fatty acids are converted to (R)-3-hydroxybutyryl-CoA, bypassing the disrupted PhaB enzymes. Additionally, the basal PHB production from non-fatty acid sources implies the involvement of a reverse {beta}-oxidation pathway. This study highlights the metabolic versatility of strain TH-1 for future metabolic engineering.

microbiology↗

bioRxiv2026

Dorsal fins are not universal stabilizers in cetaceans: limited yaw effects and flipper-coupled roll stability

Cetacean dorsal fins are traditionally regarded as vertical stabilizers for yaw and roll, yet marked variation in fin area and position suggests that this function is not universal. We combined computational fluid dynamics simulations of five cetacean species with comparative analyses of dorsal fin and flipper morphology across 81 species to test whether variation in dorsal fin morphology reflects the evolution of hydrodynamic stabilization. Yaw-destabilizing moments were dominated by the trunk regardless of flipper posture, whereas dorsal fins were generally too small and too close to the center of rotation to provide substantial static yaw restoration. In contrast, dorsal fins influenced roll stability in concert with extended anhedral flippers. Although dorsal fins were likely present in the common ancestor of extant cetaceans, strong dorsal fin-mediated roll stabilization was largely restricted to oceanic bite-feeding delphinids, in which rapid evolutionary enlargement of the dorsal fin and persistently extended anhedral flippers likely enhanced roll stability. In most other lineages, roll stability could be maintained by flipper posture alone despite small dorsal fins. These results recast the cetacean dorsal fin not as a universal stabilizer, but as a lineage-specific roll stabilizing structure whose function emerges through mechanical coupling with the flippers.

evolutionary biology↗

bioRxiv2026

Integration of UAS-based spatial surveys and bio-logging tracking enhances precision in population size estimation

Accurately estimating wildlife population sizes, essential for ecological theory and conservation management, yet remains challenging. Although unmanned aerial systems (UASs) combined with machine learning, have revolutionized population estimation, they face limitations in addressing the hierarchical population processes from individual behavior to colony-and population-level dynamics. To overcome this limitation, we developed a data integration framework that jointly analyzes multiple datasets, representing different scales of the same underlying process, were jointly analyzed. Using a seabird colony as a model system, we integrated UAS-based count data in the colony with bio-logging-based tracking data to estimate population size by quantifying both the number of individuals present and the proportion absent from the surveyed area. These complementary datasets were linked using state-space models allowing accurate population estimates with explicit uncertainty quantification. Furthermore, we evaluated the robustness of the estimations with respect to sample size. Sub-sampling simulations revealed that estimation uncertainty was more sensitive to sample size in bio-logging-based tracking data than in UAS-based count data. This finding highlights the importance of understanding dataset-specific properties when designing effective investigations. Overall, our resource-efficient framework is broadly applicable across species and populations and demonstrates how integrating complementary observation methods can improve population estimates and inform conservation practice.

ecology↗

bioRxiv2024

Magellanic penguins balance navigation with foraging opportunities in complex current regimes

Animals navigating in fluid environments often face lateral forces from wind or water currents that challenge travel efficiency and route accuracy. We investigated how 27 Magellanic penguins (Spheniscus magellanicus) adapt their navigation strategies to return to their colony amid regional tidal ocean currents. Using GPS-enhanced dead-reckoning loggers and high-resolution ocean current data, we reconstructed penguin travel vectors during foraging trips to assess their responses to variable currents during their colony-bound movements. By integrating estimates of energy costs and prey pursuits, we found that birds balanced direct navigation with current-driven drift: in calm currents, they maintained precise line-of-sight headings to their colony. In stronger currents, they aligned their return with lateral flows, which increased travel distance, but at minimal energy costs, and provided them with increased foraging opportunities. Since the lateral tidal currents always reversed direction over the course of return paths, the penguins return paths were consistently S-shaped but still resulted in the birds returning efficiently to their colonies. These findings suggest that Magellanic penguins can sense current drift and use it to optimize energy expenditure by maintaining overall directional accuracy while capitalizing on foraging opportunities.

animal behavior and cognition↗

bioRxiv2024

Self-organized acoustic behavior in bats arises from simple rules

Although self-organized behavior has been extensively studied in the movement of group-behaving animals, such as fish or birds, far less attention has been paid to vocal behavior in animal groups, especially in mammals. Here, by testing the vocal response of echolocating bats (Miniopterus fuliginosus) to the playback of jamming stimuli in the lab, we discovered a mathematical model that can well describe vocal frequency control by bats in response to jamming stimuli mimicking echolocation sounds emitted in a group of bats. We then extended the model to a group of flying bats and observed frequency-adjusting behavior by which the frequency differences for the group increased overall, similar to a previous observation on group-flying bats. Further, we showed the frequency-adjusting behavior led to less potential misdetections by echolocation in a group. Our findings suggest this frequency-adjusting behavior is a self-organized vocal behavior that mitigates conflicts within a group, one achieved via simple behavioral rules, as in other types of collective animal behavior.

animal behavior and cognition↗

bioRxiv2022

Albatrosses employ orientation and routing strategies similar to yacht racers

The way goal-oriented birds adjust their travel direction and route in response to wind significantly affects their travel costs. This is expected to be particularly pronounced in pelagic seabirds, which utilize a wind-dependent flight style called dynamic soaring. Dynamic soaring seabirds in situations without a definite goal, e.g. searching for prey, are known to preferentially fly with tail-to-side winds to increase the speed and search area, and reduce travel costs. However, little is known about their reaction to wind when heading to a definite goal, such as homing. Homing tracks of wandering albatrosses (Diomedea exulans) vary from beelines to zigzags, which are similar to those of sailboats. Here, given that both albatrosses and sailboats travel slower in headwinds and tailwinds, we tested whether the time-minimizing strategies used by yacht racers can be compared to the locomotion patterns of wandering albatrosses. We predicted that when the goal is located upwind or downwind, albatrosses should deviate their travel directions from the goal on the microscale and increase the number of turns on the macroscale. Both hypotheses were supported by track data from albatrosses and racing yachts in the Southern Ocean confirming that albatrosses qualitatively employ the same strategy as yacht racers. Nevertheless, albatrosses did not strictly minimize their travel time, likely making their flight robust against wind fluctuations to reduce flight costs. Our study provides the first empirical evidence of tacking in albatrosses and demonstrates that man-made movement strategies provide a new perspective on the laws underlying wildlife movement.

animal behavior and cognition↗

bioRxiv2022

The role of wingbeat frequency and amplitude in flight power

Body-mounted accelerometers provide a new prospect for estimating power use in flying birds, as the signal varies with the two major kinematic determinants of aerodynamic power: wingbeat frequency and amplitude. Yet wingbeat frequency is sometimes used as a proxy for power output in isolation. There is therefore a need to understand which kinematic parameter birds vary and whether this is predicted by flight mode (e.g., accelerating, ascending/descending flight), speed or morphology. We investigate this using high-frequency acceleration data from (i) 14 species flying in the wild, (ii) two species flying in controlled conditions in a wind tunnel and (iii) a review of experimental and field studies. While wingbeat frequency and amplitude were positively correlated, R2 values were generally low, supporting the idea that parameters can vary independently. Indeed, birds were more likely to modulate wingbeat amplitude for more energy-demanding flight modes, including climbing and take-off. Nonetheless, the striking variability even within species and flight types, highlights the complexity of describing the kinematic relationships, which appear sensitive to both the biological and physical context. Notwithstanding this acceleration metrics that incorporate both kinematic parameters should be more robust proxies for power than wingbeat frequency alone.

biophysics↗

bioRxiv2022

Pelagic seabirds reduce risk by flying into the eye of the storm

Cyclones can cause mass mortality of seabirds, sometimes wrecking thousands of individuals. The few studies to track pelagic seabirds during cyclones show they tend to circumnavigate the strongest winds. We tracked adult shearwaters in the Sea of Japan over 11 years and find that the response to cyclones varied according to the wind speed and direction. In strong winds, birds that were sandwiched between the storm and mainland Japan flew away from land and towards the eye of the storm, flying within [≤] 30 km of the eye and tracking it for up to 8 hours. This exposed shearwaters to some of the highest wind speeds near the eye wall ([≤] 21 m s-1), but enabled them to avoid strong onshore winds in the storms wake. Extreme winds may therefore become a threat when an inability to compensate for drift could lead to forced landings and collisions. Birds may need to know where land is in order to avoid it. This provides additional selective pressure for a map sense and could explain why juvenile shearwaters, which lack a map sense, instead navigating using a compass heading, are susceptible to being wrecked. We suggest that the ability to respond to storms is influenced by both flight and navigational capacities. This may become increasingly pertinent due to changes in extreme weather patterns. Significance StatementCyclones can cause billions of dollars of damage and loss of human life. They can also cause mass mortality and strandings in seabirds. We used GPS tracking data from streaked shearwaters breeding in the worlds most active cyclone basin to understand how seabirds respond to these systems. Birds varied their response according to the wind speed and direction, generally flying towards the eye of the cyclone in strong winds. This surprising strategy enables dynamic soaring birds to control their exposure to risky wind vectors that could drift them onshore. Nonetheless, birds may need to know where land is in order to avoid it. Juveniles lack this "map sense", making them susceptible to wrecking in some scenarios.

ecology↗

bioRxiv2020

Soaring styles of extinct giant birds and pterosaurs

The largest extinct volant birds (Pelagornis sandersi and Argentavis magnificens) and pterosaurs (Pteranodon and Quetzalcoatlus) are thought to have used wind-dependent soaring flight, similar to modern large birds. There are two types of soaring: thermal soaring, used by condors and frigatebirds, which involves the use of updrafts to ascend and then glide horizontally over the land or the sea; and dynamic soaring, used by albatrosses, which involves the use of wind speed differences with height above the sea surface. Previous studies have suggested that Pelagornis sandersi used dynamic soaring, while Argenthavis magnificens, Pteranodon, and Quetzalcoatlus used thermal soaring. However, the performance and wind speed requirements of dynamic and thermal soaring for these species have not yet been quantified comprehensively. We quantified these values using aerodynamic models and compared them with that of extant birds. For dynamic soaring, we quantified maximum flight speeds and maximum upwind flight speeds. For thermal soaring, we quantified the animals sinking speed circling at a given radius and how far it could glide losing a given height. Our results confirmed those from previous studies that Pteranodon and Argentavis magnificens used thermal soaring. Conversely, the results for Pelagornis sandersi and Quetzalcoatlus were contrary to those from previous studies. Pelagornis sandersi used thermal soaring, and Quetzalcoatlus had a poor ability both in dynamic and thermal soaring. Our results demonstrate the need for comprehensive assessments of performance and required wind conditions when estimating soaring styles of extinct flying species.

animal behavior and cognition↗

bioRxiv2019

AI on animals: AI-assisted animal-borne logger never misses the moments that biologists want

Animal-borne data loggers, i.e., biologgers, allow researchers to record a variety of sensor data from animals in their natural environments (Hussey et al. 2015; Kays et al. 2015). This data allows biologists to observe many aspects of the animals lives, including their behavior, physiology, social interactions, and external environment. However, the need to limit the size of these devices to a small fraction of the animals size imposes strict limits on the devices hardware and battery capacities (Kays et al. 2015). Here we show how AI can be leveraged on board these devices to intelligently control their activation of costly sensors, e.g., video cameras, allowing them to make the most of their limited resources during long deployment periods. Our method goes beyond previous works that have proposed controlling such costly sensors using simple threshold-based triggers, e.g., depth-based (Watanuki et al. 2007; Volpov et al. 2015) and acceleration-based (Nishiumi et al. 2018; Brown et al. 2012) triggers. Using AI-assisted biologgers, biologists can focus their data collection on specific complex target behaviors such as foraging activities, allowing them to automatically record video that captures only the moments they want to see. By doing so, the biologger can reserve its battery power for recording only those target activities. We anticipate our work will provide motivation for more widespread adoption of AI techniques on biologgers, both for intelligent sensor control and intelligent onboard data processing. Such techniques can not only be used to control what is collected by such devices, but also what is transmitted off the devices, such as is done by satellite relay tags (Cox et al. 2018).

ecology↗