{"title":"Bayesian networks for network inference in biology.","authors":"James Hammond, V Anne Smith","doi":"10.1098/rsif.2024.0893","DOIUrl":"https://doi.org/10.1098/rsif.2024.0893","url":null,"abstract":"<p><p>Bayesian networks (BNs) have been used for reconstructing interactions from biological data, in disciplines ranging from molecular biology to ecology and neuroscience. BNs learn conditional dependencies between variables, which best 'explain' the data, represented as a directed graph which approximates the relationships between variables. In the 2000s, BNs were a popular method that promised an approach capable of inferring biological networks from data. Here, we review the use of BNs applied to biological data over the past two decades and evaluate their efficacy. We find that BNs are successful in inferring biological networks, frequently identifying novel interactions or network components missed by previous analyses. We suggest that as false positive results are underreported, it is difficult to assess the accuracy of BNs in inferring biological networks. BN learning appears most successful for small numbers of variables with high-quality datasets that either discretize the data into few states or include perturbative data. We suggest that BNs have failed to live up to the promise of the 2000s but that this is most likely due to experimental constraints on datasets, and the success of BNs at inferring networks in a variety of biological contexts suggests they are a powerful tool for biologists.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240893"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12055290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144017267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Dynamic clamping induces rotation-to-beating transition of pinned filaments in gliding assays.","authors":"Amir Khosravanizadeh, Serge Dmitrieff","doi":"10.1098/rsif.2024.0859","DOIUrl":"https://doi.org/10.1098/rsif.2024.0859","url":null,"abstract":"<p><p>We used numerical simulations to investigate how properties of motor proteins control the dynamical behaviour of driven flexible filaments. A filament on top of a patch of anchored motor proteins is pinned at one end, a setup referred to as a spiral gliding assay. There exists a variety of motor proteins with different properties. We found that when these properties are changed, this system generally can show three different regimes: (i) fluctuation, where the filament undergoes random fluctuations because the motors are unable to bend it, (ii) rotation, in which the filament bends and then moves continuously in one direction, and (iii) beating, where the filament rotation direction changes over time. We found that the transition between fluctuation and rotation occurs when motors exert a force sufficient to buckle the filament. The threshold force coincides with the second buckling mode of a filament undergoing a continuously distributed load. Moreover, we showed that when motors near the pinning point work close to their stall force, they cause dynamic clamping, leading to the beating regime. Rather than being imposed by experimental conditions, this clamping is transient and results from the coupling between filament mechanics and the collective behaviour of motors.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240859"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12056559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143971065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jacques Fries, Javier Diaz, Marie Jardat, Ignacio Pagonabarraga, Pierre Illien, Vincent Dahirel
{"title":"Active droplets controlled by enzymatic reactions.","authors":"Jacques Fries, Javier Diaz, Marie Jardat, Ignacio Pagonabarraga, Pierre Illien, Vincent Dahirel","doi":"10.1098/rsif.2024.0803","DOIUrl":"https://doi.org/10.1098/rsif.2024.0803","url":null,"abstract":"<p><p>The formation of condensates is now considered a major organizing principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple generic model to study the interplay between two enzyme populations and a two-state protein. In one state, the protein forms condensed droplets through attractive interactions, while in the other state, the proteins remain dispersed. Each enzyme catalyses the production of one of these two protein states only when reactants are in its vicinity. A key feature of our model is the explicit representation of enzyme trajectories, capturing the fluctuations in their local concentrations. The spatially dependent growth rate of droplets naturally arises from the stochastic motion of these explicitly modelled enzymes. Using two complementary numerical methods-(i) Brownian dynamics simulations and (ii) a hybrid method combining Cahn-Hilliard-Cook diffusion equations with Brownian dynamics for the enzymes-we investigate how enzyme concentration and dynamics influence the evolution with time and the steady-state number and size of droplets. Our results show that the concentration and diffusion coefficient of enzymes govern the formation and size-selection of biocondensates.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240803"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12056557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144010739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dries Marzougui, Riddhi Das, Barbara Mazzolai, Dominique Adriaens, Francis Wyffels
{"title":"Exploring the evolutionary adaptations of the unique seahorse tail's muscle architecture through <i>in silico</i> modelling and robotic prototyping.","authors":"Dries Marzougui, Riddhi Das, Barbara Mazzolai, Dominique Adriaens, Francis Wyffels","doi":"10.1098/rsif.2024.0876","DOIUrl":"https://doi.org/10.1098/rsif.2024.0876","url":null,"abstract":"<p><p>Seahorses possess a unique tail muscle architecture that enables efficient grasping and anchoring onto objects. This prehensile ability is crucial for their survival, as it allows them to resist currents, cling to mates during reproduction and remain camouflaged to avoid predators. Unlike in any other fish, the muscles of the seahorse tail form long, parallel sheets that can span up to 11 vertebral segments. This study investigates how this distinctive muscle arrangement influences the mechanics of prehension. Through <i>in silico</i> simulations validated by a three-dimensional-printed prototype, we reveal the complementary roles of these elongated muscles alongside shorter, intersegmental muscles. Furthermore, we show that muscles spanning more segments allow greater contractile forces and provide more efficient force-to-torque transmissions. Our findings confirm that the elongated muscle-tendon organization in the seahorse tail provides a functional advantage for grasping, offering insights into the evolutionary adaptations of this unique tail structure.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240876"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12055296/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143989067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frank Thomas Ndjomatchoua, Richard Olaf James Hamilton Stutt, Ritter A Guimapi, Luca Rossini, Christopher A Gilligan
{"title":"Integration of temperature-driven population model and pest monitoring data to estimate initial conditions and timing of first field invasion: application to the cassava whitefly, <i>Bemisia tabaci</i>.","authors":"Frank Thomas Ndjomatchoua, Richard Olaf James Hamilton Stutt, Ritter A Guimapi, Luca Rossini, Christopher A Gilligan","doi":"10.1098/rsif.2025.0059","DOIUrl":"https://doi.org/10.1098/rsif.2025.0059","url":null,"abstract":"<p><p>Empirical field data and simulation models are often used separately to monitor and analyse the dynamics of insect pest populations over time. Greater insight may be achieved when field data are used directly to parametrize population dynamic models. In this paper, we use a differential evolution algorithm to integrate mechanistic physiological-based population models and monitoring data to estimate the population density and the physiological age of the first cohort at the start of the field monitoring. We introduce an ad hoc temperature-driven life-cycle model of <i>Bemisia tabaci</i> in conjunction with field monitoring data. The likely date of local whitefly invasion is estimated, with a subsequent improvement of the model's predictive accuracy. The method allows computation of the likely date of the first field incursion by the pest and demonstrates that the initial physiological age somewhat neglected in prior studies can improve the accuracy of model simulations. Given the increasing availability of monitoring data and models describing terrestrial arthropods, the integration of monitoring data and simulation models to improve model prediction and pioneer invasion date estimate will lead to better decision-making in pest management.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20250059"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12056672/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144008739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Reconstructing hammerstone size flake by flake: an experimental approach.","authors":"Li Li, Shannon P McPherron","doi":"10.1098/rsif.2024.0879","DOIUrl":"10.1098/rsif.2024.0879","url":null,"abstract":"<p><p>Understanding force application in flake production is essential for reconstructing hominin behaviour, technological advancements and biomechanics. Extensive research has examined stone tool production, focusing on the intended material outcomes such as the cores, tools and flakes. Analyzing force application in this process requires knowledge of hammerstone selection and use. Despite progress made in understanding hammerstone selection and use, linking specific knapping outcomes to hammerstone use remains challenging. This difficulty stems from the complex relationship between fracture mechanics and material signatures in lithic artifacts. Key variables related to hammerstone use and their influence on flaking outcomes remain poorly understood. We draw on fracture mechanics to explore factors driving flake ring crack size-the circular region where the Hertzian cone, a feature of conchoidal flaking, intersects with the platform. Our experiment systematically examines how hammerstone size, velocity and strike angle-factors influencing strike force-affect ring crack and flake size under controlled conditions. We validate our findings with previously reported controlled and replicative experiments. Results show that flake ring crack size can estimate hammerstone size. Our findings mean that we can reconstruct the flaking process and particularly variability in the application of force at a level of detail previously unavailable.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240879"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12074805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144002218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Applicability of spatial early warning signals to complex network dynamics.","authors":"Neil G MacLaren, Kazuyuki Aihara, Naoki Masuda","doi":"10.1098/rsif.2024.0696","DOIUrl":"https://doi.org/10.1098/rsif.2024.0696","url":null,"abstract":"<p><p>Early warning signals (EWSs) for complex dynamical systems aim to anticipate tipping points before they occur. While signals computed from time-series data, such as temporal variance, are useful for this task, they are costly to obtain in practice because they need many samples over time to calculate. Spatial EWSs use just a single sample per spatial location and aggregate the samples over space rather than time to try to mitigate this limitation. However, although many complex systems in nature and society form diverse networks, the performance of spatial EWSs is mostly unknown for general networks because the vast majority of studies of spatial EWSs have been on regular lattice networks. Therefore, we have carried out a comprehensive investigation of six major spatial EWSs on various networks. We find that the winning EWS depends on tipping scenarios, although the coefficient of variation and spatial skewness tend to outperform alternative EWSs. We also find that spatial EWSs behave in a drastically different manner between the square lattice and complex networks and tend to be more reliable for the latter than the former. The present results encourage further studies of spatial EWSs on complex networks.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240696"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12055298/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144010741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Settling aerodynamics is a driver of symmetry in deciduous tree leaves.","authors":"Matthew Dominic Biviano, Kaare Hartvig Jensen","doi":"10.1098/rsif.2024.0654","DOIUrl":"https://doi.org/10.1098/rsif.2024.0654","url":null,"abstract":"<p><p>Leaves shed by deciduous trees contain 40% of the annually sequestered carbon and include nutrients vital to the expansion and health of forest ecosystems. To achieve this, leaves must fall quickly to land near the parent tree-otherwise, they are lost to the wind, like pollen or gliding seeds. However, the link between leaf shape and sedimentation speed remains unclear. To gauge the relative performance of extant leaves, we developed an automated sedimentation apparatus capable of performing approximately 100 free-fall experiments per day on biomimetic paper leaves. The majority of 25 representative leaves settle at rates similar to our control (a circular disc). Strikingly, the <i>Arabidopsis</i> mutant asymmetric leaves1 (<i>as1</i>) fell 15% slower than the wild-type. Applying the <i>as1-digital</i> mutation to deciduous tree leaves revealed a similar speed reduction. Data correlating shape and settling across a broad range of natural, mutated and artificial leaves support the <i>fast-leaf hypothesis</i>: deciduous leaves are symmetric and relatively unlobed partly because this maximizes their settling speed and concomitant nutrient retention.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240654"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12055283/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Brian D Saltin, Clarus Goldsmith, Moritz Haustein, Ansgar Büschges, Nicholas S Szczecinski, Alexander Blanke
{"title":"A parametric finite element model of leg campaniform sensilla in <i>Drosophila</i> to study campaniform sensilla location and arrangement.","authors":"Brian D Saltin, Clarus Goldsmith, Moritz Haustein, Ansgar Büschges, Nicholas S Szczecinski, Alexander Blanke","doi":"10.1098/rsif.2024.0559","DOIUrl":"https://doi.org/10.1098/rsif.2024.0559","url":null,"abstract":"<p><p>Campaniform sensilla (CS) are mechanosensors embedded in the cuticle of insects. They are often found at locations near the joints of leg segments. On legs, CS are generally considered to respond directionally to cuticle bending during legged locomotion. It is currently unclear how CS locations affect strain levels at the CS, but this information is crucial for understanding how CS respond to stimuli. Here we present a parametric finite element model of the femoral CS field for <i>Drosophila</i> hind legs with 12 general and seven CS-specific parameters each. This model allows testing how changes in CS location, orientation and material property affect strain levels at each CS. We used experimentally acquired kinematic data and computed ground reaction forces to simulate <i>in vivo</i>-like forward stepping. The displacements found in this study at the physiological CS field location near the trochanter-femur joint are smaller than those necessary for conformation changes of ion channels involved in signal elicitation. Also, variation of material properties of the CS had little influence on displacement magnitudes at the CS cap where the sensory neuron attaches. Thus, our results indicate that ground reaction forces alone are unlikely to serve CS field activation during forward walking.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240559"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12056673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144008736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marco Santos-Lopes, Ricardo Araújo, Romain David, Paulo L Correia
{"title":"Automated analysis of bird head motion in unconstrained settings: a foundational study on semicircular canal evolution in archosaurs.","authors":"Marco Santos-Lopes, Ricardo Araújo, Romain David, Paulo L Correia","doi":"10.1098/rsif.2024.0919","DOIUrl":"10.1098/rsif.2024.0919","url":null,"abstract":"<p><p>This study presents a framework to automatically analyse head motion in birds from videos of natural behaviours. The process involves detecting birds, identifying key points on their heads and tracking changes in their positions over time. Bird detection and key point extraction were trained on publicly available datasets, featuring videos and images of diverse bird species in uncontrolled settings. Initial challenges with complex video backgrounds causing misidentifications and inaccurate key points were addressed through validation, refinement, filtering and smoothing. Head angular velocities and rotation frequencies were computed from the refined key points. The algorithm performed well at moderate speeds but was limited by the 30 Hz frame rate of most videos, which constrained measurable angular velocities and frequencies and caused motion blur, affecting key point detection. Our findings suggest that the framework may provide plausible estimates of head motion but also emphasize the importance of high frame-rate videos in future research, including extensive comparisons against ground truth data, to fully characterize bird head movements. Importantly, this work is a foundational effort to understand the evolutionary drivers of the semicircular canals, the biosensor that monitors head rotations, for both extinct and extant tetrapods.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240919"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12115815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144159438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}