Journal of The Royal Society Interface最新文献_第2页

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, Bemisia tabaci. 基于温度驱动种群模型和害虫监测数据的首次田间入侵初始条件和时间估算：在木薯粉虱、烟粉虱中的应用

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-07 DOI: 10.1098/rsif.2025.0059

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, Bemisia tabaci.","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":"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 Bemisia tabaci 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.","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}

引用次数: 0

Reconstructing hammerstone size flake by flake: an experimental approach. 逐层重建锤石尺寸：一种实验方法。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-14 DOI: 10.1098/rsif.2024.0879

Li Li, Shannon P McPherron

{"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":"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.","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}

引用次数: 0

Applicability of spatial early warning signals to complex network dynamics. 空间预警信号在复杂网络动力学中的适用性。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-07 DOI: 10.1098/rsif.2024.0696

Neil G MacLaren, Kazuyuki Aihara, Naoki Masuda

{"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":"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.","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}

引用次数: 0

Settling aerodynamics is a driver of symmetry in deciduous tree leaves. 沉降空气动力学是落叶树叶对称的驱动因素。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-07 DOI: 10.1098/rsif.2024.0654

Matthew Dominic Biviano, Kaare Hartvig Jensen

{"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":"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 Arabidopsis mutant asymmetric leaves1 (as1) fell 15% slower than the wild-type. Applying the as1-digital 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 fast-leaf hypothesis: deciduous leaves are symmetric and relatively unlobed partly because this maximizes their settling speed and concomitant nutrient retention.","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}

引用次数: 0

A parametric finite element model of leg campaniform sensilla in Drosophila to study campaniform sensilla location and arrangement. 建立果蝇腿部钟形感受器的参数化有限元模型，研究钟形感受器的位置和排列。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-07 DOI: 10.1098/rsif.2024.0559

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 Drosophila 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":"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 Drosophila 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 in vivo-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.","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}

引用次数: 0

Automated analysis of bird head motion in unconstrained settings: a foundational study on semicircular canal evolution in archosaurs. 无约束环境下鸟类头部运动的自动分析：始祖恐龙半规管进化的基础研究。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-28 DOI: 10.1098/rsif.2024.0919

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":"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.","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}

引用次数: 0

Wear-coping mechanisms and functional morphology of the radular teeth of Vittina turrita (Neritimorpha, Gastropoda). 腹足目黑齿鱼（Vittina turrita, Neritimorpha, Gastropoda）齿状齿的抗磨损机制和功能形态。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-28 DOI: 10.1098/rsif.2025.0016

Wencke Krings, Ellen Schulz-Kornas, Stanislav N Gorb

{"title":"Wear-coping mechanisms and functional morphology of the radular teeth of Vittina turrita (Neritimorpha, Gastropoda).","authors":"Wencke Krings, Ellen Schulz-Kornas, Stanislav N Gorb","doi":"10.1098/rsif.2025.0016","DOIUrl":"10.1098/rsif.2025.0016","url":null,"abstract":"In most molluscan species, the food is manipulated and taken in by the radula, a chitinous structure exhibiting diverse morphologies and compositions. The teeth of Patellogastropoda and Polyplacophora are well studied, with heavy mineralization reducing wear and failure. However, some gastropod taxa possess unmineralized teeth, even though they forage from rocks. This study characterizes the teeth of the gastropod Vittina turrita as representative neritid species. Using a combination of techniques-scanning electron microscopy, confocal laser scanning microscopy, nanoindentation and energy-dispersive X-ray spectroscopy -the biomechanical and compositional properties of the teeth were examined. The heterogeneous presence of compositional gradients, together with previous wear analyses, renders the teeth to have different functions. Some teeth are involved in loosening food, collecting food particles or, as joints, spanning the radula in a certain configuration. A key finding was the presence of tooth coatings enriched with calcium (Ca) in regions prone to abrasion. The study also identified heterogeneities in autofluorescence patterns, which were directly associated with the distribution of Ca within the coatings and the degree of tanning. This study broadens our understanding of mechanical adaptation in gastropod feeding structures, showing that feeding from solid surfaces is also possible with partial and targeted reinforcement instead of full tooth mineralization-and that structure-function relationships are more diverse than previously thought.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20250016"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144159567","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}

引用次数: 0

Targeting NSCLC drug resistance: Systems biology insights into the MALAT1/miR-145-5p axis and Wip1 in regulating ferroptosis and apoptosis. 靶向NSCLC耐药：MALAT1/miR-145-5p轴和Wip1调控铁凋亡和细胞凋亡的系统生物学见解

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-05-01 Epub Date: 2025-05-28 DOI: 10.1098/rsif.2024.0852

Shantanu Gupta, Daner Acunha Silveira, José Carlos Mombach, Ronaldo F Hashimoto

{"title":"Targeting NSCLC drug resistance: Systems biology insights into the MALAT1/miR-145-5p axis and Wip1 in regulating ferroptosis and apoptosis.","authors":"Shantanu Gupta, Daner Acunha Silveira, José Carlos Mombach, Ronaldo F Hashimoto","doi":"10.1098/rsif.2024.0852","DOIUrl":"10.1098/rsif.2024.0852","url":null,"abstract":"The long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (lncRNA MALAT1) and microRNA-145-5p (miR-145) axis play a pivotal role in regulating drug resistance, apoptosis and senescence in non-small cell lung cancer (NSCLC). MALAT1 drives drug resistance by suppressing miR-145 and activating MUC1, thereby inhibiting ferroptosis; however, its precise role in regulating ferroptosis in NSCLC remains unclear. Therefore, we propose a computational modelling approach to unravel the impact of the MALAT1/miR-145 axis on ferroptosis and drug resistance, to identify potential therapeutic strategies that promote ferroptosis. Using Boolean logic and a stochastic updating scheme, we developed and validated a robust regulatory model that encompasses ferroptosis, apoptosis, senescence and drug resistance pathways. The model, based on extensive literature and validated through gain- and loss-of-function perturbations, demonstrated strong alignment with observed clinical data that were not included in its construction. Our analysis identified three previously unreported feedback loops, miR-145/Wip1/p53, miR-145/Myc/MALAT1 and miR-145/MUC1/BMI1, establishing miR-145 as a central regulator in NSCLC. Perturbations targeting MALAT1 and wild-type p53-induced phosphatase 1 (Wip1) revealed potential therapeutic opportunities, with miR-145 activation emerging as a promising strategy to induce ferroptosis and overcome drug resistance. These findings highlight the MALAT1/miR-145 axis as a transformative therapeutic target, presenting a computational foundation to advance NSCLC treatment strategies.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 226","pages":"20240852"},"PeriodicalIF":3.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12115852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144159439","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}

引用次数: 0

Infrared camouflage in leaf-sitting frogs: a cautionary tale on adaptive convergence. 坐叶蛙的红外伪装：一个关于自适应收敛的警示故事。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-09 DOI: 10.1098/rsif.2024.0771

Devi Stuart-Fox, Katrina Joanne Rankin, Madeleine Shah Scott, Lu-Yi Wang, Amanda M Franklin

{"title":"Infrared camouflage in leaf-sitting frogs: a cautionary tale on adaptive convergence.","authors":"Devi Stuart-Fox, Katrina Joanne Rankin, Madeleine Shah Scott, Lu-Yi Wang, Amanda M Franklin","doi":"10.1098/rsif.2024.0771","DOIUrl":"10.1098/rsif.2024.0771","url":null,"abstract":"Many cryptic green animals match leaves in invisible near-infrared (NIR) wavelengths. This observation is an enduring puzzle because animals do not see NIR light, so NIR background matching is unlikely to contribute to visual camouflage. Two alternative explanations have been proposed-infrared camouflage (i.e. matching the temperature of the background) and thermoregulation-but neither hypothesis has been experimentally tested. To test these hypotheses, we developed bilayer coatings that mimicked the reflectivity of green leaf-sitting frogs with high NIR (HNIR) or low NIR (LNIR) reflectance. Under a solar simulator in the laboratory, agar model frogs with LNIR reflectance heated up more quickly and reached higher temperatures than those with HNIR reflectance. However, when placed in a tropical rainforest (natural habitat of leaf-sitting frogs), HNIR and LNIR models did not significantly differ in the similarity of surface temperature to the adjacent leaves or in core temperature, thus failing to support the infrared camouflage and thermoregulation hypotheses, respectively. The lack of difference between treatments is probably due to the limited exposure of frogs to direct solar radiation in their natural habitats. We propose an explanation for NIR background matching based on specific mechanisms underlying green coloration and translucence in frogs and caution against assuming adaptive convergence.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240771"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11978450/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811608","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}

引用次数: 0

Incorporating spatial diffusion into models of bursty stochastic transcription. 将空间扩散纳入突发随机转录模型。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-09 DOI: 10.1098/rsif.2024.0739

Christopher E Miles

{"title":"Incorporating spatial diffusion into models of bursty stochastic transcription.","authors":"Christopher E Miles","doi":"10.1098/rsif.2024.0739","DOIUrl":"10.1098/rsif.2024.0739","url":null,"abstract":"The dynamics of gene expression are stochastic and spatial at the molecular scale, with messenger RNA (mRNA) transcribed at specific nuclear locations and then transported to the nuclear boundary for export. Consequently, the spatial distributions of these molecules encode their underlying dynamics. While mechanistic models for molecular counts have revealed numerous insights into gene expression, they have largely neglected now-available subcellular spatial resolution down to individual molecules. Owing to the technical challenges inherent in spatial stochastic processes, tools for studying these subcellular spatial patterns are still limited. Here, we introduce a spatial stochastic model of nuclear mRNA with two-state (telegraph) transcriptional dynamics. Observations of the model can be concisely described as following a spatial Cox process driven by a stochastically switching partial differential equation. We derive analytical solutions for spatial and demographic moments and validate them with simulations. We show that the distribution of mRNA counts can be accurately approximated by a Poisson-beta distribution with tractable parameters, even with complex spatial dynamics. This observation allows for efficient parameter inference demonstrated on synthetic data. Altogether, our work adds progress towards a new frontier of subcellular spatial resolution in inferring the dynamics of gene expression from static snapshot data.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240739"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11978452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811607","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}

引用次数: 0