{"title":"Flipons enable genomes to learn by intermediating the exchange of energy for information.","authors":"Alan Herbert","doi":"10.1098/rsif.2025.0049","DOIUrl":"10.1098/rsif.2025.0049","url":null,"abstract":"<p><p>Recent findings have confirmed the long-held belief that alternative DNA conformations encoded by genetic elements called flipons have important biological roles. Many of these alternative structures are formed by sequences originally spread throughout the human genome by endogenous retroelements (ERE) that captured 50% of the territory before being disarmed. Only 2.6% of the remaining DNA codes for proteins. Other organisms have instead streamlined their genomes by eliminating invasive retroelements and other repeat elements. The question arises, why retain any ERE at all? A new synthesis suggests that flipons enable genomes to learn and programme the context-specific readout of information by altering the transcripts produced. The exchange of energy for information is mediated through changes in DNA topology. Here I provide a formulation for how genomes learn and describe the underlying p-bit algorithm through which flipons are tuned. The framework suggests new strategies for the therapeutic reprogramming of cells.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20250049"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937930/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710409","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":"Efficiency and control trade-offs and work loop characteristics of flapping-wing systems with synchronous and asynchronous muscles.","authors":"Suyash Agrawal, Christopher Rahn, Bo Cheng","doi":"10.1098/rsif.2024.0660","DOIUrl":"10.1098/rsif.2024.0660","url":null,"abstract":"<p><p>Natural fliers with flapping wings face the dual challenges of energy efficiency and active control of wing motion for achieving diverse modes of flight. It is hypothesized that flapping-wing systems use resonance to improve muscle mechanical output energy efficiency, a principle often followed in bioinspired flapping-wing robots. However, resonance can limit the degree of active control, a trade-off rooted in the dynamics of wing motor systems and can be potentially reflected in muscle work loops. To systematically investigate how energy efficiency trades off with active control of wingbeat frequency and amplitude, here we developed a parsimonious model of the wing motor system with either synchronous or asynchronous power muscles. We then non-dimensionalized the model and performed simulations to examine model characteristics as functions of Weis-Fogh number and dimensionless flapping frequency. For synchronous power muscles, our model predicts that energy efficiency trades off with frequency control rather than amplitude control at high Weis-Fogh numbers; however, no such trade-off was found for models with asynchronous power muscles. The work loops alone are insufficient to fully capture wing motor characteristics, and therefore fail to directly reflect the trade-offs. Finally, using simulation results, we predict that natural fliers function at Weis-Fogh numbers close to 1.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240660"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657545","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}
Qingrui Song, Tianci Chen, Wei Sun, Mingjian Huang, Yuhang Guo, Yunlong Jiao, Kun Liu, Jiaxin Ye
{"title":"Tribological metamaterial: how feathers reduce drag and friction through hidden energy dissipation structures.","authors":"Qingrui Song, Tianci Chen, Wei Sun, Mingjian Huang, Yuhang Guo, Yunlong Jiao, Kun Liu, Jiaxin Ye","doi":"10.1098/rsif.2024.0751","DOIUrl":"10.1098/rsif.2024.0751","url":null,"abstract":"<p><p>The lateral moving resistance of a liquid droplet on a solid surface generally increases with velocity and is dominated by the non-viscous wetting line friction. Many superhydrophobic man-made and biological surfaces have minimal, nevertheless speed-sensitive, water droplet friction, limiting their potential to reduce drag at high speeds in natural situations. Using an <i>in situ</i> surface force apparatus, we demonstrated low and remarkably speed-insensitive (over 300-fold) water bridge sliding friction on a goose feather vane. Detailed analyses suggest a dominant, hidden energy dissipation channel probably related to the deformation and elastic recovery of feather's characteristic metamaterial-like structure, which also results in feather's speed insensitive (from 0.1 to 1 mm s<sup>-1</sup>) ultra-low dry sliding friction coefficient observed in this study (approx. 0.07). The new insights gained have the potential to motivate novel approaches to the design of all-weather and speed-insensitive low-friction surfaces with practical applications in aviation and lubrication technology.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240751"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897818/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605349","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}
Humeyra Betul Yekeler, Ilke Kabaoglu, Ece Guler, Manuel Pedro F Graça, Oguzhan Gunduz, Deepak M Kalaskar, Muhammet Emin Cam
{"title":"A comparison of electrospinning and pressurized gyration: Production of empagliflozin-loaded polylactic acid/polycaprolactone fibrous patches.","authors":"Humeyra Betul Yekeler, Ilke Kabaoglu, Ece Guler, Manuel Pedro F Graça, Oguzhan Gunduz, Deepak M Kalaskar, Muhammet Emin Cam","doi":"10.1098/rsif.2024.0635","DOIUrl":"10.1098/rsif.2024.0635","url":null,"abstract":"<p><p>Novel therapeutic strategies are essential for enhancing efficacy and accelerating the treatment of diabetes mellitus. This investigation focused on incorporating empagliflozin into a composite of polylactic acid and polycaprolactone, resulting in the fabrication of drug-loaded fibrous patches (DFPs) for transdermal application, both by electrospinning (ES) and by pressurized gyration (PG). Scanning electron microscopy results revealed that DFPs generated through the PG method exhibited smaller diameters and a larger surface area than ES. Fourier-transform infrared spectroscopy and X-ray powder diffraction analyses confirmed the successful encapsulation of the drug in both DFPs. DFPs/PG exhibited a controlled release of 98.7 ± 1.3% of the total drug over 14 days, while DFPs/ES released 98.1 ± 2.1% in 12 days, according to <i>in vitro</i> drug release studies. This study underscores that the PG method can generate DFPs with extended controlled release. 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyl tetrazolium bromide test results validate the biocompatibility of DFPs, affirming their lack of adverse effects on human dermal fibroblast cell viability. Consequently, DFPs can be manufactured for transdermal administration using PG, exhibiting similar characteristics to ES but with the added advantage of mass production capability.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240635"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605312","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}
Abbie Evans, William Hart, Stefano Longobardi, Rajat Desikan, Anna Sher, Robin Thompson
{"title":"Reducing transmission in multiple settings is required to eliminate the risk of major Ebola outbreaks: a mathematical modelling study.","authors":"Abbie Evans, William Hart, Stefano Longobardi, Rajat Desikan, Anna Sher, Robin Thompson","doi":"10.1098/rsif.2024.0765","DOIUrl":"10.1098/rsif.2024.0765","url":null,"abstract":"<p><p>The Ebola virus (EV) persists in animal populations, with zoonotic transmission to humans occurring every few months or years. When zoonotic transmission arises, it is important to understand which interventions are most effective at preventing a major outbreak driven by human-to-human transmission. Here, we analyse a mathematical model of EV transmission and calculate the probability of a major outbreak starting from a single introduced case. We consider community, funeral and healthcare facility transmission and conduct sensitivity analyses to explore the effects of non-pharmaceutical interventions (NPIs) that influence these transmission routes. We find that, if the index case is treated in the community, then the elimination of transmission at funerals reduces the probability of a major outbreak substantially (from 0.410 to 0.066 under our baseline model parametrization). However, eliminating the risk of major outbreaks entirely requires combinations of measures that limit transmission in different settings, such as community engagement to promote safe burial practices and implementation of barrier nursing in healthcare facilities. In addition to generating insights into the drivers of Ebola outbreaks, this research provides a modelling framework for assessing the effectiveness of interventions at mitigating outbreaks of other infectious diseases with transmission in multiple settings.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240765"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919492/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657548","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":"Scaling COVID-19 rates with population size in the United States.","authors":"Austin R Cruz, Brian J Enquist, Joseph R Burger","doi":"10.1098/rsif.2024.0839","DOIUrl":"10.1098/rsif.2024.0839","url":null,"abstract":"<p><p>Using county-level data from the United States, we assessed allometric scaling relationships of coronavirus disease (COVID-19) cases, deaths and age structure within and across the first four major waves of the pandemic (wild-type, alpha, delta, omicron). Results generally indicate that the burden of cases disproportionately impacted larger-sized counties, while the burden of deaths disproportionately impacted smaller counties. This may be partially due to multiple interacting social mechanisms, including a higher proportion of older adults who live in smaller counties. Moreover, these likely social mechanisms interacting with vaccinations and virus waves created a dynamic pattern whereby the rate and magnitude of infections and deaths were population- and time-dependent. Our results offer a novel perspective on the scaling dynamics of infectious diseases, highlighting how both the rate and magnitude of COVID-19 cases and deaths scale differently across counties. Population size and age structure are key factors in predicting disease burden. Our findings have practical implications, suggesting that scaling-informed public health policies could more effectively allocate resources and interventions to mitigate the impact of future epidemics across heterogeneous populations.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240839"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710411","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}
Judith A Müller, Gerlinde Schwake, Anita Reiser, Daniel Woschée, Zahra Alirezaeizanjani, Joachim O Rädler, Sophia Rudorf
{"title":"Less is more: slow-codon windows enhance eGFP mRNA resilience against RNA interference.","authors":"Judith A Müller, Gerlinde Schwake, Anita Reiser, Daniel Woschée, Zahra Alirezaeizanjani, Joachim O Rädler, Sophia Rudorf","doi":"10.1098/rsif.2024.0582","DOIUrl":"10.1098/rsif.2024.0582","url":null,"abstract":"<p><p>Extensive efforts have been devoted to enhancing the translation efficiency of mRNA delivered to mammalian cells via codon optimization. However, the impact of codon choice on mRNA stability remains underexplored. In this study, we investigated the influence of codon usage on mRNA degradation kinetics in cultured human cell lines using live-cell imaging on single-cell arrays. By measuring mRNA lifetimes at the single-cell level for synthetic mRNA constructs, we confirmed that mRNAs containing slowly translated codon windows have shorter lifetimes. Unexpectedly, these mRNAs did not exhibit decreased stability in the presence of small interfering RNA (siRNA) compared with the unmutated sequence, suggesting an interference of different concurrent degradation mechanisms. We employed stochastic simulations to predict ribosome density along the open reading frame, revealing that the ribosome densities correlated with mRNA stability in a cell-type- and codon-position-specific manner. In summary, our results suggest that the effect of codon choice and its influence on mRNA lifetime is context-dependent with respect to cell type, codon position and RNA interference.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240582"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657547","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":"Role of layered architecture in marine sponge root fibres: new lessons from nature for the design of tension cables.","authors":"Sayaka Kochiyama, Haneesh Kesari","doi":"10.1098/rsif.2024.0252","DOIUrl":"10.1098/rsif.2024.0252","url":null,"abstract":"<p><p>Patterns found in structural materials of biological origin are an excellent source of inspiration for engineers. The root fibres (basalia spicules) of the marine sponge <i>Euplectella aspergillum</i> anchor it to the ocean floor and exhibit a lamellar architecture. It is generally thought that the spicule's architecture contributes to the spicule's fracture toughness. However, in recent experiments, the spicules' architecture did not contribute to their fracture toughness in a statistically significant way, with their fracture initiation toughness being similar to that of synthetic glass. In this article, we present a mechanics model and show that the spicule's architecture could be contributing to its strength, potentially benefiting the sponge's survival. When a spicule forms a loop, we find that its layers can increase the spicule's strength by reducing the bending stress induced by the tensile load transmitted along its length.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240252"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657611","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}
Yanhong Wang, Ettore Barbieri, Yi Zhang, Nick Terrill, Himadri Shikhar Gupta
{"title":"Integrating ultrastructural diffraction imaging and multiscale modelling to unveil the nanoscale mechanics of arthropod cuticle in bending.","authors":"Yanhong Wang, Ettore Barbieri, Yi Zhang, Nick Terrill, Himadri Shikhar Gupta","doi":"10.1098/rsif.2024.0601","DOIUrl":"10.1098/rsif.2024.0601","url":null,"abstract":"<p><p>Determining the mechano-structural relations in biological materials with hierarchical structure is crucial to understanding natural optimization strategies and designing functional bioinspired composites. However, measuring the nanoscale mechanics and dynamic response is challenging when the specimen geometry and loading environment are physiologically complex. To overcome this challenge, we develop a combination of synchrotron X-ray diffraction testing and analytical modelling to explore the mechano-structural changes during bending loads on stomatopod cuticle. Stomatopod cuticle is an example of a hierarchical biomaterial optimized for high impact and bending resistance. Using models for large deformations of elastic continua, we measure cuticle strains from macroscopic deformations and combine diffraction-based fibril strains with stresses to quantify the local elastic moduli and nanoscale strain concentration factors, which are found to vary across cuticle sub-regions and under different flexion loading modes. This approach has the advantage of identifying constituent biomaterial properties and mechanisms <i>in situ</i> and is also suitable for studying time-dependent changes, such as concurrent strains of the nanofibrous phase that occur during physiological loading.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240601"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143657546","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}
Lorenzo Carré, Francesca Natali, Giuseppe Zaccai, Vaitson Çumaku, Bruno Franzetti
{"title":"Determination of <i>in cellulo</i> proteome molecular dynamics in different halophilic Archaea.","authors":"Lorenzo Carré, Francesca Natali, Giuseppe Zaccai, Vaitson Çumaku, Bruno Franzetti","doi":"10.1098/rsif.2024.0630","DOIUrl":"10.1098/rsif.2024.0630","url":null,"abstract":"<p><p>While biophysical studies have unravelled properties of specific proteins <i>in vitro</i>, characterizing globally their native state within the cell remains a challenge. In particular, protein adaptation to harsh intracellular physical and chemical conditions is poorly understood. Extremophiles, which thrive in severe environments, are good models for the study of such adaptation. Five haloarchaeal species, isolated from hypersaline environments, were used to assess correlations between intracellular salt concentrations and molecular dynamics properties. <i>In cellulo</i> protein stability was measured using nano differential scanning fluorimetry, and neutron spectrometry was used to determine molecular dynamics resilience and global flexibility. It was found that high intracellular accumulation of Mg<sup>2+</sup> and low intracellular accumulation of K<sup>+</sup> were correlated with higher stability and resilience. Sequence traits associated with mean proteome halophilicity, such as decreased hydrophobicity and increased acidity, weighted by the relative abundance of each protein, were also correlated with stability and resilience. <i>Haloferax mediterranei</i>, however, was found to be an exception as its proteome showed the highest <i>in cellulo</i> molecular stability and resilience associated with fewest sequence traits related to halophilicity, highlighting the significance of the intracellular salt environment in determining proteome biophysical properties.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240630"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11896700/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605317","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}