Journal of The Royal Society Interface最新文献_第5页

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

Principles of in vitro selection of ribozymes from random sequence libraries. 从随机序列文库中体外选择核酶的原则。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-16 DOI: 10.1098/rsif.2024.0878

Paul G Higgs, Ulrich F Muller

{"title":"Principles of in vitro selection of ribozymes from random sequence libraries.","authors":"Paul G Higgs, Ulrich F Muller","doi":"10.1098/rsif.2024.0878","DOIUrl":"https://doi.org/10.1098/rsif.2024.0878","url":null,"abstract":"In vitro selection methods are used to identify catalytic RNAs from pools of random sequences. We discuss the central concepts using experimental data and computational models. Experiments proceed in multiple rounds, each with a reaction step and a step in which reacted sequences are recovered. Sequences are enriched each round by a factor depending on combined reaction and recovery probability. In the first round, there are few functional sequences, and it is necessary to minimize the probability of losing these. In later rounds, the loss probability is negligible, and the procedure can be optimized to maximize the enrichment factor. Clusters of related sequences emerge which descend from separate sequences in the initial pool. The fitness of an RNA depends on how well it matches a structure with specified sequence and base-pair constraints. Sequences that exactly match the constraints may be rare, but sequences a few mutations away are much more common; hence it is likely that clusters descend from suboptimal sequences. There is a high probability that beneficial mutations arise during the experiment. This explains the experimental observation that there is little correlation between cluster frequencies and fitnesses, whereas correlation between enrichment factors and fitnesses is strong.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240878"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11999736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144016583","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

Emerging frontiers in protein structure prediction following the AlphaFold revolution. AlphaFold革命后蛋白质结构预测的新领域。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-16 DOI: 10.1098/rsif.2024.0886

Martin Luke Rennie, Michael R Oliver

引用次数: 0

Competition between elasticity and adhesion in caterpillar locomotion. 履带运动中弹性与附着力的竞争。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-23 DOI: 10.1098/rsif.2024.0703

Mario Argenziano, Massimiliano Zingales, Arsenio Cutolo, Emanuela Bologna, Massimiliano Fraldi

{"title":"Competition between elasticity and adhesion in caterpillar locomotion.","authors":"Mario Argenziano, Massimiliano Zingales, Arsenio Cutolo, Emanuela Bologna, Massimiliano Fraldi","doi":"10.1098/rsif.2024.0703","DOIUrl":"https://doi.org/10.1098/rsif.2024.0703","url":null,"abstract":"In recent years, there has been a growing interest in understanding animals' locomotion mechanisms for developing bio-inspired micro- or nano-robots capable of overcoming obstacles and navigating in confined environments. Among non-pedal crawlers, caterpillars exhibit one of the most stable and efficient gait strategies, utilizing muscle contractions and substrate grip. Although several approaches have been proposed to model their locomotion, little is known about the competition between body elasticity and adhesion, which we demonstrate playing a central role in crawling gait. Preliminarily, experimental observations and measurements were performed on Pieris brassicae larvae, gaining insights into fundamental features characterizing caterpillar locomotion and estimating key geometrical and mechanical parameters. A minimal but effective one-dimensional discrete model was thus conceived to capture all the relevant aspects of the movement. Inter-mass springs model the deformable body units, Winkler-like constraints with an adhesion threshold reproduce elastic interactions and attaching/detaching events at prolegs-substrate interface, and a triggering muscle contraction initiates the larva's crawling cycle, generating the observed travelling wave. After demonstrating theoretically that caterpillars move obeying quasi-static laws, we proved robustness of the proposed approach by showing very good agreement between theoretical outcomes and experimental evidence, so paving the way for new optimization strategies in soft robotics.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240703"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12015574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006225","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

Alcids-like flapping wing for exploring the role of wing folding in underwater locomotion. 探索翼折叠在水下运动中的作用。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-30 DOI: 10.1098/rsif.2024.0830

Yayi Shen, Zijia Zhao, Hiroto Tanaka, Bai Chen, Zhong Huang

{"title":"Alcids-like flapping wing for exploring the role of wing folding in underwater locomotion.","authors":"Yayi Shen, Zijia Zhao, Hiroto Tanaka, Bai Chen, Zhong Huang","doi":"10.1098/rsif.2024.0830","DOIUrl":"https://doi.org/10.1098/rsif.2024.0830","url":null,"abstract":"Alcids showcase excellent aerial-aquatic locomotion abilities benefitting from the morphing wing. In the aerial environment, alcids fully extend their wings, while underwater, they partly fold the wings. In this article, we mimicked the wing morphology of the alcids family to explore the hydrodynamic advantage of the folded configuration in the aquatic environment and four three-dimensional-printed wings including any combination of with feather or without feather, and extended or folded were created. The steady-state experiment reveals that the extended wings of alcids double the lift, counteracting gravity, while folding the wings halves the drag and reduces unnecessary lift, with configurations maintaining a similar lift-to-drag ratio. We investigated the alcid wing kinematics and designed an electronic wing mechanism with flapping and pitching motions to mimic the wing motion of the alcid. Quasi-steady estimation confirmed the presence of an active upstroke during diving in alcids. The experimental results validate the estimation, showing good agreement in force trends and average forward force. Additionally, the flapping wing experiment also demonstrates that pitch motion improves thrust generation, reduces lateral vibrations and increases mechanical efficiency. Under identical kinematics, extended models performed best, but alcids may prefer folded wings underwater for their highest thrust at the same Strouhal number and lower power needs.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240830"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143971156","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 systematic evaluation of the language-of-viral-escape model using multiple machine learning frameworks. 使用多个机器学习框架对病毒逃逸语言模型进行系统评估。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-30 DOI: 10.1098/rsif.2024.0598

Brent E Allman, Luiz Vieira, Daniel J Diaz, Claus O Wilke

{"title":"A systematic evaluation of the language-of-viral-escape model using multiple machine learning frameworks.","authors":"Brent E Allman, Luiz Vieira, Daniel J Diaz, Claus O Wilke","doi":"10.1098/rsif.2024.0598","DOIUrl":"https://doi.org/10.1098/rsif.2024.0598","url":null,"abstract":"Predicting the evolutionary patterns of emerging and endemic viruses is key for mitigating their spread. In particular, it is critical to rapidly identify mutations with the potential for immune escape or increased disease burden. Knowing which circulating mutations pose a concern can inform treatment or mitigation strategies such as alternative vaccines or targeted social distancing. In 2021, Hie B, Zhong ED, Berger B, Bryson B. 2021 Learning the language of viral evolution and escape. Science 371, 284-288. (doi:10.1126/science.abd7331) proposed that variants of concern can be identified using two quantities extracted from protein language models, grammaticality and semantic change. These quantities are defined by analogy to concepts from natural language processing. Grammaticality is intended to be a measure of whether a variant viral protein is viable, and semantic change is intended to be a measure of potential for immune escape. Here, we systematically test this hypothesis, taking advantage of several high-throughput datasets that have become available, and also comparing this model with several more recently published machine learning models. We find that grammaticality can be a measure of protein viability, though methods that are trained explicitly to predict mutational effects appear to be more effective. By contrast, we do not find compelling evidence that semantic change is a useful tool for identifying immune escape mutations.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240598"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144027190","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

Resolving the kinetics of an ensemble of muscle myosin motors via a temperature-dependent fitting procedure. 通过温度相关拟合程序解决肌球蛋白马达整体动力学问题。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-30 DOI: 10.1098/rsif.2025.0040

Valentina Buonfiglio, Niccolò Zagli, Irene Pertici, Vincenzo Lombardi, Pasquale Bianco, Duccio Fanelli

引用次数: 0