Pub Date : 2026-01-01DOI: 10.1016/j.fmre.2024.10.014
Lei Shi , Meng Wang , Xiu-Jie Wang
The fast advancement of artificial intelligence (AI) technologies in recent years, especially the deep learning algorithm and transformer neural network, has brought great impacts on scientific researches. As a displine focusing on curation and analysis of life science data, bioinformatics has experienced remarkable changes under the impetus of AI technologies, not only in nowadays, but also throughout its history. In this review, we firstly summarize the historical events of computer-assisted life science data analysis, then assess the features, contributions and changes of AI methods in life science research by using bibliometric analysis, and discuss the future challenges for AI methods from the life science research aspects. There is no doubt that AI technologies will continuously accelerate and revolutionize life science research in the future, in the meanwhile, the development of new AI methods more suitable for life science data is also in great needs.
{"title":"Application of artificial intelligence in life science: Historical review and future perspectives","authors":"Lei Shi , Meng Wang , Xiu-Jie Wang","doi":"10.1016/j.fmre.2024.10.014","DOIUrl":"10.1016/j.fmre.2024.10.014","url":null,"abstract":"<div><div>The fast advancement of artificial intelligence (AI) technologies in recent years, especially the deep learning algorithm and transformer neural network, has brought great impacts on scientific researches. As a displine focusing on curation and analysis of life science data, bioinformatics has experienced remarkable changes under the impetus of AI technologies, not only in nowadays, but also throughout its history. In this review, we firstly summarize the historical events of computer-assisted life science data analysis, then assess the features, contributions and changes of AI methods in life science research by using bibliometric analysis, and discuss the future challenges for AI methods from the life science research aspects. There is no doubt that AI technologies will continuously accelerate and revolutionize life science research in the future, in the meanwhile, the development of new AI methods more suitable for life science data is also in great needs.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 20-27"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.fmre.2024.02.003
Xuewen Wang , Song Hong , Guirong Tang , Chengshu Wang
Filamentous fungi frequently degenerate during subculturing, which manifests as the reduction or loss of conidiation, sexuality, secondary metabolite production, and/or virulence against hosts. The underlying mechanism of spontaneous fungal degeneration is still elusive. In this study, the fluffy mycelium-type sector variants formed by three ascomycete fungi were transferred and found to show the typical features of culture degeneration. The variant cells were evidenced with the accumulation of reactive oxygen species (ROS), and the ROS-associated formation of hyphal coils. Genome resequencing of these sector cultures identified substantial random mutation sites in each variant in a trend associated with fungal reproduction style. The high bias towards transversions over transitions was similarly detected in degenerate genomes. Otherwise, a higher number of mutations were accumulated in the intergenic regions of the Metarhizium robertsii and Cordyceps militaris sector genomes, whereas the exonic regions of the Aspergillus nidulans variant genes were detected with a higher mutation rate. Unexpectedly, none of those mutated genes had orthologous relationships among the three sectors, while only a few of them were shared between two fungi. A few transcription factor genes with frameshift mutations in sectors were selected for deletions in parental strains, and the null mutants demonstrated the varied degrees of degenerate phenotypes. In addition to reasoning the causal mechanism of fungal degeneration, our data provide insights to better maintain and monitor fungal culture stability.
{"title":"Accumulation of the spontaneous and random mutations is causative of fungal culture degeneration","authors":"Xuewen Wang , Song Hong , Guirong Tang , Chengshu Wang","doi":"10.1016/j.fmre.2024.02.003","DOIUrl":"10.1016/j.fmre.2024.02.003","url":null,"abstract":"<div><div>Filamentous fungi frequently degenerate during subculturing, which manifests as the reduction or loss of conidiation, sexuality, secondary metabolite production, and/or virulence against hosts. The underlying mechanism of spontaneous fungal degeneration is still elusive. In this study, the fluffy mycelium-type sector variants formed by three ascomycete fungi were transferred and found to show the typical features of culture degeneration. The variant cells were evidenced with the accumulation of reactive oxygen species (ROS), and the ROS-associated formation of hyphal coils. Genome resequencing of these sector cultures identified substantial random mutation sites in each variant in a trend associated with fungal reproduction style. The high bias towards transversions over transitions was similarly detected in degenerate genomes. Otherwise, a higher number of mutations were accumulated in the intergenic regions of the <em>Metarhizium robertsii</em> and <em>Cordyceps militaris</em> sector genomes, whereas the exonic regions of the <em>Aspergillus nidulans</em> variant genes were detected with a higher mutation rate. Unexpectedly, none of those mutated genes had orthologous relationships among the three sectors, while only a few of them were shared between two fungi. A few transcription factor genes with frameshift mutations in sectors were selected for deletions in parental strains, and the null mutants demonstrated the varied degrees of degenerate phenotypes. In addition to reasoning the causal mechanism of fungal degeneration, our data provide insights to better maintain and monitor fungal culture stability.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 260-269"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139879674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.fmre.2024.01.019
Yang Guo , Jianmei Li , Ruifen Dou , Haitao Ye , Changzhi Gu
Quantum defects in solid materials, such as nitrogen-vacancy color centers in diamond, have been extensively studied and successfully demonstrated as single photon emitters and potential qubits for quantum computers. However, a major challenge has always been positioning these quantum defects near the sample surface for measuring or sensing purposes. The emergence of quantum defects in two-dimensional (2D) van der Waals (vdW) materials open up new opportunities for overcoming these limitations. These materials possess unique properties, including vdW interlayer coupling and clean surfaces without unsaturated dangling bonds, which provide greater advantages for manufacturing multi-qubit systems. In this review, we present the research progress on quantum defects in 2D vdW materials, covering quantum guidelines for spin defects in solid state, the latest demonstrations of quantum defects, the unique methods and techniques for generating and modulating defects in 2D vdW materials.
{"title":"Quantum defects in two-dimensional van der Waals materials","authors":"Yang Guo , Jianmei Li , Ruifen Dou , Haitao Ye , Changzhi Gu","doi":"10.1016/j.fmre.2024.01.019","DOIUrl":"10.1016/j.fmre.2024.01.019","url":null,"abstract":"<div><div>Quantum defects in solid materials, such as nitrogen-vacancy color centers in diamond, have been extensively studied and successfully demonstrated as single photon emitters and potential qubits for quantum computers. However, a major challenge has always been positioning these quantum defects near the sample surface for measuring or sensing purposes. The emergence of quantum defects in two-dimensional (2D) van der Waals (vdW) materials open up new opportunities for overcoming these limitations. These materials possess unique properties, including vdW interlayer coupling and clean surfaces without unsaturated dangling bonds, which provide greater advantages for manufacturing multi-qubit systems. In this review, we present the research progress on quantum defects in 2D vdW materials, covering quantum guidelines for spin defects in solid state, the latest demonstrations of quantum defects, the unique methods and techniques for generating and modulating defects in 2D vdW materials.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 126-140"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139893107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.fmre.2024.03.003
Jiayi Cheng , Bowen Zhang , Wenjun Cai , Siqing Zhao , Xiaoyun Deng , Baofeng Wang , Xiaohua Zhu , Yingying Lv , Wenzhen Zhu , Xiaoqing Zhang , Hong Chen , Ling Liu
Advanced technologies of targeted differentiation and genetic engineering in pluripotent stem cells (PSCs) offer production of purposefully designed cells for transplantation. Here, we engineer rhesus monkey PSCs (rhPSCs) to produce safe and functional neural progenitors and neurons, which could be noninvasively surveyed and controlled after brain transplantation. RhPSCs expressing hM3Dq-mCherry exhibited normal karyotype and had the ability to equally self-renew and differentiate into functional neurons as that of the mCherry expressing control. After allotransplantation into monkey prefrontal cortex, the hM3Dq-mCherry expressing rhPSC-derived cortical progenitors survived and matured gradually, which could be long-termly surveyed by [18F]-fluorodeoxyglucose positron emission tomography ([18F]FDG-PET) and electroencephalogram (EEG) following clozapine-N-oxide (CNO) administration. Remote activation of transplanted neurons caused increased [18F]-fluorodeoxyglucose uptake started at 3 months and reached a plateau 9–12 months post-transplantation. EEG analysis revealed a decrease in the high delta spectrum power while an increase in the beta power after CNO delivery. Notably, no seizure-like spikes were observed even after repeated CNO exposure. Magnetic resonance (MR) imaging found no overgrowth in all allografts. Expression of herpes simplex virus thymidine kinase (HSVtk), a Ganciclovir (GCV)-induced suicide gene in rhPSCs further assured the safety without sacrificing the functional outcome of brain grafts. Our study offers a feasible strategy for long-term noninvasive survey and remote control of brain-grafted neurons.
多能干细胞（PSCs）的靶向分化和基因工程的先进技术提供了有目的设计的移植细胞的生产。在这里，我们设计恒河猴PSCs （rhPSCs）来产生安全和功能性的神经祖细胞和神经元，这些神经祖细胞和神经元可以在脑移植后进行无创调查和控制。表达hM3Dq-mCherry的RhPSCs表现出正常的核型，并且与表达mCherry的对照细胞一样具有自我更新和分化为功能神经元的能力。同种异体移植到猴前额皮质后，表达rhpsc衍生皮质祖细胞的hM3Dq-mCherry存活并逐渐成熟，可通过[18F]-氟脱氧葡萄糖正电子发射断层扫描（[18F]FDG-PET）和氯氮平- n -氧化物（CNO）给药后的脑电图（EEG）进行长期观察。移植神经元的远程激活导致氟脱氧葡萄糖摄取增加[18F]-从3个月开始，并在移植后9-12个月达到平台期。脑电图分析显示，CNO输送后高δ谱功率下降，而β谱功率增加。值得注意的是，即使在反复暴露CNO后，也没有观察到类似癫痫发作的尖峰。所有同种异体移植物均未见过度生长。单纯疱疹病毒胸苷激酶（HSVtk），一种更昔洛韦（GCV）诱导的自杀基因在rhPSCs中的表达进一步确保了安全性，而不会牺牲脑移植物的功能结果。本研究为脑移植神经元的长期无创监测和远程控制提供了一种可行的策略。
{"title":"Engineering of rhesus monkey pluripotent stem cells for noninvasive survey and remote control after brain allotransplantation","authors":"Jiayi Cheng , Bowen Zhang , Wenjun Cai , Siqing Zhao , Xiaoyun Deng , Baofeng Wang , Xiaohua Zhu , Yingying Lv , Wenzhen Zhu , Xiaoqing Zhang , Hong Chen , Ling Liu","doi":"10.1016/j.fmre.2024.03.003","DOIUrl":"10.1016/j.fmre.2024.03.003","url":null,"abstract":"<div><div>Advanced technologies of targeted differentiation and genetic engineering in pluripotent stem cells (PSCs) offer production of purposefully designed cells for transplantation. Here, we engineer rhesus monkey PSCs (rhPSCs) to produce safe and functional neural progenitors and neurons, which could be noninvasively surveyed and controlled after brain transplantation. RhPSCs expressing hM3Dq-mCherry exhibited normal karyotype and had the ability to equally self-renew and differentiate into functional neurons as that of the mCherry expressing control. After allotransplantation into monkey prefrontal cortex, the hM3Dq-mCherry expressing rhPSC-derived cortical progenitors survived and matured gradually, which could be long-termly surveyed by [<sup>18</sup>F]-fluorodeoxyglucose positron emission tomography ([<sup>18</sup>F]FDG-PET) and electroencephalogram (EEG) following clozapine-N-oxide (CNO) administration. Remote activation of transplanted neurons caused increased [<sup>18</sup>F]-fluorodeoxyglucose uptake started at 3 months and reached a plateau 9–12 months post-transplantation. EEG analysis revealed a decrease in the high delta spectrum power while an increase in the beta power after CNO delivery. Notably, no seizure-like spikes were observed even after repeated CNO exposure. Magnetic resonance (MR) imaging found no overgrowth in all allografts. Expression of herpes simplex virus thymidine kinase (HSVtk), a Ganciclovir (GCV)-induced suicide gene in rhPSCs further assured the safety without sacrificing the functional outcome of brain grafts. Our study offers a feasible strategy for long-term noninvasive survey and remote control of brain-grafted neurons.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 521-534"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140273104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.fmre.2024.07.009
Jiaojiao Zhang , Jing Liu , Wen Hu , Xue Jiang , Long Zhou , Yumin Tang , Zhong Lin Wang , Rusen Yang
Piezoelectric biomaterials have shown good energy conversion capability and promising future for biomedical applications. However, their performance is still limited by their relatively low piezoelectric constant, and increasing the power by connecting multiple devices is restricted by the challenge of synchronizing all individual devices. Herein, we develop double-layer FF peptide microrods arrays with independently controlled polarization in each layer. The resultant piezoelectric nanogenerator showed much enhanced performance because the synchronous deformation and the appropriate polarization directions of microrods in each individual layer enable the constructive contribution of voltage and current output from all microrods. The nanogenerator generated an open circuit voltage of 2.05 V in a serial connection mode, which doubles the output from a single-layer device. When two layers are connected in parallel and the polarization is in a head-to-head configuration, a twofold increase in the current output is also achieved. This work provides a new strategy to design integrated devices with much improved performance for wearable technology and therapeutic systems.
{"title":"Development of double-layer FF peptide microrod arrays for high performance piezoelectric nanogenerators","authors":"Jiaojiao Zhang , Jing Liu , Wen Hu , Xue Jiang , Long Zhou , Yumin Tang , Zhong Lin Wang , Rusen Yang","doi":"10.1016/j.fmre.2024.07.009","DOIUrl":"10.1016/j.fmre.2024.07.009","url":null,"abstract":"<div><div>Piezoelectric biomaterials have shown good energy conversion capability and promising future for biomedical applications. However, their performance is still limited by their relatively low piezoelectric constant, and increasing the power by connecting multiple devices is restricted by the challenge of synchronizing all individual devices. Herein, we develop double-layer FF peptide microrods arrays with independently controlled polarization in each layer. The resultant piezoelectric nanogenerator showed much enhanced performance because the synchronous deformation and the appropriate polarization directions of microrods in each individual layer enable the constructive contribution of voltage and current output from all microrods. The nanogenerator generated an open circuit voltage of 2.05 V in a serial connection mode, which doubles the output from a single-layer device. When two layers are connected in parallel and the polarization is in a head-to-head configuration, a twofold increase in the current output is also achieved. This work provides a new strategy to design integrated devices with much improved performance for wearable technology and therapeutic systems.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 416-422"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.fmre.2024.10.001
Jing-Xian Li , Zhi-Chao Wang , Zheng Liu , Yin Yao
Chronic rhinosinusitis (CRS) represents one of the most common chronic conditions occurring in the nasal cavity and sinuses, affecting approximately 10% of the global population and imposing a significant socioeconomic burden. The introduction of novel methodologies, notably single-cell sequencing, has unveiled the extensive heterogeneity of structural cells and immune cells, significantly enhanced our understanding of CRS pathogenesis and facilitated the development of more precise diagnostic and therapeutic approaches. Dysfunction of the epithelial barrier, inflammatory memory stored within the epithelium, and the heightened interactions between epithelial cells and immune cells have been implicated in playing pivotal roles in CRS pathogenesis. Emerging evidence highlights the critical role of local immunoglobulin overproduction in CRS. Within ectopic lymphoid tissues (eLTs), a dynamic interplay exists where follicular helper T (Tfh) cells facilitate, while follicular regulatory T (Tfr) cells inhibit, the production of immunoglobulins. Conversely, PD-1highCXCR5– T cells are capable of promoting immunoglobulin production independent of eLTs. Importantly, the ongoing immunoglobulin class-switch recombination to IgE has been observed in polyp tissues. Additionally, accumulating evidence has highlighted the significant contributions of macrophages and mast cells in driving type 2 immunity in eosinophilic CRS, positioning these cells as potential therapeutic targets. The enhanced understanding of structural and immune cell dynamics in CRS not only sheds light on the intricate pathophysiological mechanisms underlying the condition but also inspires the pursuit of innovative treatments aimed at recalibrating the complex interactions within the immune landscape of CRS patients.
{"title":"Progress in cellular mechanisms of chronic rhinosinusitis","authors":"Jing-Xian Li , Zhi-Chao Wang , Zheng Liu , Yin Yao","doi":"10.1016/j.fmre.2024.10.001","DOIUrl":"10.1016/j.fmre.2024.10.001","url":null,"abstract":"<div><div>Chronic rhinosinusitis (CRS) represents one of the most common chronic conditions occurring in the nasal cavity and sinuses, affecting approximately 10% of the global population and imposing a significant socioeconomic burden. The introduction of novel methodologies, notably single-cell sequencing, has unveiled the extensive heterogeneity of structural cells and immune cells, significantly enhanced our understanding of CRS pathogenesis and facilitated the development of more precise diagnostic and therapeutic approaches. Dysfunction of the epithelial barrier, inflammatory memory stored within the epithelium, and the heightened interactions between epithelial cells and immune cells have been implicated in playing pivotal roles in CRS pathogenesis. Emerging evidence highlights the critical role of local immunoglobulin overproduction in CRS. Within ectopic lymphoid tissues (eLTs), a dynamic interplay exists where follicular helper T (Tfh) cells facilitate, while follicular regulatory T (Tfr) cells inhibit, the production of immunoglobulins. Conversely, PD-1<sup>high</sup>CXCR5<sup>–</sup> T cells are capable of promoting immunoglobulin production independent of eLTs. Importantly, the ongoing immunoglobulin class-switch recombination to IgE has been observed in polyp tissues. Additionally, accumulating evidence has highlighted the significant contributions of macrophages and mast cells in driving type 2 immunity in eosinophilic CRS, positioning these cells as potential therapeutic targets. The enhanced understanding of structural and immune cell dynamics in CRS not only sheds light on the intricate pathophysiological mechanisms underlying the condition but also inspires the pursuit of innovative treatments aimed at recalibrating the complex interactions within the immune landscape of CRS patients.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 477-488"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nowadays, magnesium (Mg) alloys are increasingly being considered as a promising lightweight structural material because of their inherent low density and high specific strength. However, the broad application of most Mg alloys is limited by their poor strong-ductility trade-off at room temperature. At present, tailoring the bimodal grain structure (BGS) has the potential to concurrently enhance strength and ductility. Therefore, in order to achieve controllable preparation of BGS, recent research on the formation of Mg alloy with BGS was evaluated from the perspectives of alloy design, initial microstructure of billets, and process parameter. In addition to summarizing the role of BGS in synergistically improving strength and ductility, the influence of BGS on other properties of Mg alloys was also summarized, such as tension-compression yield asymmetry, corrosion resistance, fatigue performance, and fracture toughness. The research progress in controlling BGS provides valuable insights into the design and production of high-performance Mg alloys.
{"title":"Recent progress in preparation of bimodal grain structure and improvement of mechanical and corrosion properties of magnesium alloys","authors":"Jing Zuo , Taiki Nakata , Chao Xu , Lin Geng , Shigeharu Kamado","doi":"10.1016/j.fmre.2024.08.001","DOIUrl":"10.1016/j.fmre.2024.08.001","url":null,"abstract":"<div><div>Nowadays, magnesium (Mg) alloys are increasingly being considered as a promising lightweight structural material because of their inherent low density and high specific strength. However, the broad application of most Mg alloys is limited by their poor strong-ductility trade-off at room temperature. At present, tailoring the bimodal grain structure (BGS) has the potential to concurrently enhance strength and ductility. Therefore, in order to achieve controllable preparation of BGS, recent research on the formation of Mg alloy with BGS was evaluated from the perspectives of alloy design, initial microstructure of billets, and process parameter. In addition to summarizing the role of BGS in synergistically improving strength and ductility, the influence of BGS on other properties of Mg alloys was also summarized, such as tension-compression yield asymmetry, corrosion resistance, fatigue performance, and fracture toughness. The research progress in controlling BGS provides valuable insights into the design and production of high-performance Mg alloys.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 383-399"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.fmre.2024.05.003
Chunxiang Peng , Xiaogen Zhou , Jun Liu , Minghua Hou , Stan Z. Li , Guijun Zhang
With the breakthrough of AlphaFold2, nearly all single-domain protein structures can be built at experimental resolution. However, accurate modelling of full-chain structures of multidomain proteins, particularly all relevant conformations for those with multiple states remain challenging. In this study, we develop a multidomain protein assembly method, M-SADA, for assembling multiple conformational states. In M-SADA, a multiple population-based evolutionary algorithm is proposed to sample multiple conformational states under the guidance of multiple energy functions constructed by combining homologous and analogous templates with inter-domain distances predicted by deep learning. On a developed benchmark dataset containing 72 multidomain proteins with multiple conformational states, the performance of M-SADA is significantly better than that of AlphaFold2 on multiple conformational states modelling, where 29/72 (40.3%) of proteins can be assembled with a TM-score > 0.90 for two highly distinct conformational states with M-SADA. Furthermore, M-SADA is tested on a developed benchmark dataset containing 296 multidomain proteins with single conformational state, and results show that the average TM-score of M-SADA on the best models is 0.913, which is 5.2% higher than that of AlphaFold2 models (0.868). Results on CASP15 multidomain targets also show that M-SADA can predict new domain arrangements when individual domain structures are correct.
{"title":"Multiple conformational states assembly of multidomain proteins using evolutionary algorithm based on structural analogues and sequential homologues","authors":"Chunxiang Peng , Xiaogen Zhou , Jun Liu , Minghua Hou , Stan Z. Li , Guijun Zhang","doi":"10.1016/j.fmre.2024.05.003","DOIUrl":"10.1016/j.fmre.2024.05.003","url":null,"abstract":"<div><div>With the breakthrough of AlphaFold2, nearly all single-domain protein structures can be built at experimental resolution. However, accurate modelling of full-chain structures of multidomain proteins, particularly all relevant conformations for those with multiple states remain challenging. In this study, we develop a multidomain protein assembly method, M-SADA, for assembling multiple conformational states. In M-SADA, a multiple population-based evolutionary algorithm is proposed to sample multiple conformational states under the guidance of multiple energy functions constructed by combining homologous and analogous templates with inter-domain distances predicted by deep learning. On a developed benchmark dataset containing 72 multidomain proteins with multiple conformational states, the performance of M-SADA is significantly better than that of AlphaFold2 on multiple conformational states modelling, where 29/72 (40.3%) of proteins can be assembled with a TM-score > 0.90 for two highly distinct conformational states with M-SADA. Furthermore, M-SADA is tested on a developed benchmark dataset containing 296 multidomain proteins with single conformational state, and results show that the average TM-score of M-SADA on the best models is 0.913, which is 5.2% higher than that of AlphaFold2 models (0.868). Results on CASP15 multidomain targets also show that M-SADA can predict new domain arrangements when individual domain structures are correct.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 77-87"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.fmre.2024.01.008
Q. Yuan , J.-Q. Zhang , Y.-Q. Wei , S.-Q. Dai , P.-D. Li , J. Li , T.-H. Cui , F. Zhou , L. Chen , J. Lin , M. Feng
Heat engines are essential devices in modern industry, converting heat energy into useful mechanical work via their working substances. Here we experimentally simulate the conventional heat engine by employing the vibrational mode of a single trapped ion as the working substance. In contrast to simply employing the ion in thermal motion, we consider coherently stimulating the ion’s vibrational motion as the phonon laser, which helps acquire clearer results by effectively suppressing the thermal fluctuation. As such, we demonstrate in an exact and high signal-to-noise way the standard steps of both the Otto and Carnot cycles in a single ion, and compare their maximum efficiencies by monitoring the amplitude and frequency of the vibration. Our work witnesses an interesting single-atom thermal engine using coherently controlled phonons. It would be the smallest platform for simulating or demonstrating classical thermodynamic laws and phenomena at a single ion scale via optical manipulation techniques for phonon lasers.
{"title":"Exact simulation of classical heat engine cycles using single-ion phonon laser","authors":"Q. Yuan , J.-Q. Zhang , Y.-Q. Wei , S.-Q. Dai , P.-D. Li , J. Li , T.-H. Cui , F. Zhou , L. Chen , J. Lin , M. Feng","doi":"10.1016/j.fmre.2024.01.008","DOIUrl":"10.1016/j.fmre.2024.01.008","url":null,"abstract":"<div><div>Heat engines are essential devices in modern industry, converting heat energy into useful mechanical work via their working substances. Here we experimentally simulate the conventional heat engine by employing the vibrational mode of a single trapped ion as the working substance. In contrast to simply employing the ion in thermal motion, we consider coherently stimulating the ion’s vibrational motion as the phonon laser, which helps acquire clearer results by effectively suppressing the thermal fluctuation. As such, we demonstrate in an exact and high signal-to-noise way the standard steps of both the Otto and Carnot cycles in a single ion, and compare their maximum efficiencies by monitoring the amplitude and frequency of the vibration. Our work witnesses an interesting single-atom thermal engine using coherently controlled phonons. It would be the smallest platform for simulating or demonstrating classical thermodynamic laws and phenomena at a single ion scale via optical manipulation techniques for phonon lasers.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 149-154"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140091722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.fmre.2024.01.013
Chuan Tong , Ji Tan , Min Luo , Jiafang Huang , Shuyao Xiao , Baigui Liu , James T. Morris
Increased nitrogen (N) loading and sea-level rise (SLR) are two dominant drivers of global change that threaten tidal marshes and the ecosystem services they provide, including the sequestration of organic carbon. Nevertheless, the mechanisms through which N loading enrichment, SLR inundation increase, and their combined effects impact the rates and pathways of soil organic carbon (SOC) mineralization in tidal marshes remain poorly understood. We utilized a factorial design in an oligohaline tidal marsh, utilizing in situ weirs to simulate SLR inundation increase by manipulating the duration of flooding with or without nitrogen enrichment as NaNO3 plus NH4Cl or with a combination of increased flood duration and nitrogen. After nearly 2 years, the addition of N increased total SOC mineralization (CMR), soil microbial Fe(III) reduction (FeRR), NO3– reduction (NRR), and SO42– reduction (SRR) but decreased methanogenesis (MGR). The abiotic factor Fe(III)/Fe(II) ratio and dissolved organic carbon (DOC), and the biotic factors, β-glucosidase (BG), and phenol oxidase (PHO) activity explained the increased SOC mineralization rates following N enrichment. Increased flood duration did not change CMR, but increased flooding offset the stimulatory effects of N addition on CMR, FeRR, SRR, NRR and MGR. The contributions of Fe(III) reduction and SO42– reduction pathways to SOC mineralization increased in all experimental treatments, FeRR, SRR, NRR, and MGR were significantly positively correlated with the abundance of Geobacter, dsrA, nrfA, and mcrA. SLR inundation increase did not increase soil carbon loss in this oligohaline marsh and may counteract the simulation of soil C loss due to N enrichment.
{"title":"Inundation counteracts the promoting effect of nitrogen enrichment on soil organic carbon mineralization in a tidal marsh","authors":"Chuan Tong , Ji Tan , Min Luo , Jiafang Huang , Shuyao Xiao , Baigui Liu , James T. Morris","doi":"10.1016/j.fmre.2024.01.013","DOIUrl":"10.1016/j.fmre.2024.01.013","url":null,"abstract":"<div><div>Increased nitrogen (N) loading and sea-level rise (SLR) are two dominant drivers of global change that threaten tidal marshes and the ecosystem services they provide, including the sequestration of organic carbon. Nevertheless, the mechanisms through which N loading enrichment, SLR inundation increase, and their combined effects impact the rates and pathways of soil organic carbon (SOC) mineralization in tidal marshes remain poorly understood. We utilized a factorial design in an oligohaline tidal marsh, utilizing <em>in situ</em> weirs to simulate SLR inundation increase by manipulating the duration of flooding with or without nitrogen enrichment as NaNO<sub>3</sub> plus NH<sub>4</sub>Cl or with a combination of increased flood duration and nitrogen. After nearly 2 years, the addition of N increased total SOC mineralization (CMR), soil microbial Fe(III) reduction (FeRR), NO<sub>3</sub><sup>–</sup> reduction (NRR), and SO<sub>4</sub><sup>2–</sup> reduction (SRR) but decreased methanogenesis (MGR). The abiotic factor Fe(III)/Fe(II) ratio and dissolved organic carbon (DOC), and the biotic factors, β-glucosidase (BG), and phenol oxidase (PHO) activity explained the increased SOC mineralization rates following N enrichment. Increased flood duration did not change CMR, but increased flooding offset the stimulatory effects of N addition on CMR, FeRR, SRR, NRR and MGR. The contributions of Fe(III) reduction and SO<sub>4</sub><sup>2–</sup> reduction pathways to SOC mineralization increased in all experimental treatments, FeRR, SRR, NRR, and MGR were significantly positively correlated with the abundance of <em>Geobacter, dsr</em>A, <em>nrf</em>A, and <em>mcr</em>A. SLR inundation increase did not increase soil carbon loss in this oligohaline marsh and may counteract the simulation of soil C loss due to N enrichment.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 301-312"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139824436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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