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Water Biology and Security 2025年

作者： Wang, Junhao Tang, Lei Yu, Xinzi Yu, Chenggong Tang, Xianghai Wang, Dongmei Kong, Fanna Du, Guoying Mao, Yunxiang MOE Key Laboratory of Marine Genetics and Breeding & Key Laboratory of Marine Seed Industry of Shandong Province College of Marine Life Sciences Qingdao 266003 China Key Laboratory of Tropical Aquatic Germplasm of Hainan Province Sanya Oceanographic Institution Ocean University of China Sanya 572024 China MOE Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource & Yazhou Bay Innovation Institute Hainan Tropical Ocean University Sanya 572025 China Qingdao Institute of Blue Seed Industry (Qingdao Institute of Maritime Silk Road) Ocean University of China Qingdao 266073 China Laboratory for Marine Biology and Biotechnology Qingdao Marine Science and Technology Center Qingdao 266063 China

Pyropia yezoensis, a vital intertidal seaweed, plays a crucial role in the preservation of marine biodiversity. In recent years, the rapid expansion of its cultivation has raised concerns regarding the sustainability of seaweed aquaculture practices. However, research on gene exchange among P. yezoensis populations remains limited. In this study, we conducted a comprehensive analysis of gene flow using 228 whole-genome resequencing samples from key wild and cultivated P. yezoensis populations in China, as well as populations from Japan. We identified seven potential gene flow events, with gene flow regions encompassing 0.3%–25.43% of the genome. Genetic analysis revealed that these genomic regions were characterized by high genetic diversity, low genetic differentiation, and increased coding DNA sequence (CDS) density and guanine-cytosine (GC) content. Moreover, 53% of these regions contain at least one signal of selection, with genes involved in RNA and protein processing, transport, cellular homeostasis, and stress response functions associated with thallus growth, development, and stress resistance suggesting a role in environmental adaptability and artificial selection. Notably, we found that the genetic load in cultivated populations was significantly higher than in wild populations;fortunately, gene flow was not the primary factor driving this phenomenon. On the contrary, we found that gene flow events in two trios significantly reduced the genetic load caused by loss-of-function mutations. These findings enhance our understanding of intraspecific gene flow in seaweeds and provide valuable insights for the sustainable cultivation of seaweed aquaculture. © 2025 The Authors

关键词： Gene flow Genetic load Pyropia yezoensis Whole-genome resequencing

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Fluorescence microarrays for enzyme-free DNA detection based on web hybrid chain reaction

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Biosensors and Bioelectronics: X 2022年 11卷

作者： Jin, Furui Ta, La Liu, Min Sun, Yanyan Pan, Yipu Li, Zhoumin Xu, Danke State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University Nanjing210023 China Nanjing University Jinling College Nanjing210089 China Nanjing Xiangzhong Biological Technology Co. Ltd Nanjing210022 China Tianjin Institute for Food Safety Inspection Technology Tianjin300308 China

The diagnosis of pathogenic microorganism infection mainly relies on molecular detection of nucleic acids or proteins, and the nucleic acid detection is the gold standard for the pathogen detection. The viral genome mutates quickly, and the genome of the host cell usually binds to multiple sites in the viral genome, leading to patient infections. Therefore, rapid nucleic acid detection methods with high specificity are essential for controlling the spread of viruses and maintaining human health. In this study, Cy3-labeled DNA probes were obtained based on a convenient and enzyme-free web hybridization chain reaction (wHCR) and used for DNA diagnosis of hepatitis B virus (HBV) in an isothermal platform. In this microarray platform, the target DNA is directly captured on the microarray and identified by the aggregated DNA probes to amplify the fluorescence signal. After fluorescence scanning analysis, the detection limit of HBV DNA fragments on this DNA microarray is 84 fM. In addition, this method not only specifically distinguishes single-base mismatched sequences, but also obtains the quantitative detection of HBV DNA in serum samples. Compared with the enzymatic amplification reaction in which the target nucleic acids are used as the amplification template, this method effectively avoids cross-contamination. Furthermore, compared to enzymatic reactions, the requirements for reaction conditions such as temperature and pH are relatively lenient. This method is user-friendly and suitable for molecular detection of infectious diseases under limited resource conditions. © 2022 The Authors

关键词： Enzymes

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Further efforts in climate change adaptation and mitigation are indispensable

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Innovation 2025年

作者： Su, Buda Dong, Wenjie Jiang, Tong Kundzewicz, Zbigniew W. State Key Laboratory of Climate System Prediction and Risk Management Nanjing University of Information Science & Technology Nanjing210044 China School of Atmospheric Sciences Sun Yat-sen University Zhuhai519082 China Laboratory for Climate Risk and Urban-Rural Smart Governance School of Geography Jiangsu Second Normal University Nanjing210013 China Department of Hydrology Meteorology and Water Management Warsaw University of Life Sciences Warsaw02-787 Poland

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Single-chromosome Yeast Models Reveal the Configuration Robustness of Functional Eukaryotic Genomes

Single-chromosome Yeast Models Reveal the Configuration Robu...

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2022生物物理大会

作者： Xin Gu Tiantian Ye Xiao-Ran Zhang Lingyun Nie Huan Wang Wei Li Rui Lu Chuanhai Fu Li-Lin Du Jin-Qiu Zhou The State Key Laboratory of Molecular Biology CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell Biology National Institute of Biological Sciences School of Life Sciences University of Science and Technology of China Frasergen Bioinformatics Co. Ltd

Chromosomes in eukaryote nucleus carry genes, and are responsible for passing genetic information from parents to offspring. Different organisms usually contain different numbers of chromosomes. Whether the organization and/or number of chromosomes that have evolved in a particular species contribute to speciation reamins unclear. Here we have successfully established several single-chromosome fission yeast Schizosaccharomyces pombe models,

关键词： Single-chromosome Yeast Models Reveal the Configuration Robustness of Functional Eukaryotic Genomes

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Combination of two multiplex genome-edited soybean varieties enables customization of protein functional properties

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Molecular Plant 2022年第7期15卷 1081-1083页

作者： Mengyan Bai Cuicui Yuan Huaqin Kuang Qian Sun Xinchen Hu Luning Cui Wenxin Lin Chunyan Peng Peng Yue Shikui Song Zebin Guo Yuefeng Guan College of Life Sciences Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China FAFU-UCR Joint Center for Horticultural Biology and Metabolomics Haixia Institute of Science and TechnologyFujian Agriculture and Forestry UniversityFuzhou 350002China Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006China College of Food Sciences Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China Shofine Seeds Co. Ltd.JiningShandong 272400China College of Resources and Environment Fujian Agriculture and Forestry UniversityFuzhouFujian 350002China

Dear Editor,Soybean(Glycine max)is a major source of plant-based protein for people worldwide,providing a healthy,affordable,and environmentally friendly alternative to animal-based protein(Montgomery,2003).It has been estimated that there are currently over 12000 food products that contain soy protein(Montgomery,2003).Different food applications of soy protein require distinct properties that affect its function and sensory *** instance,the sensory quality of soymilk is significantly affected by protein emulsibility,whereas tofu quality is determined by protein-gelling ability(Kinsella,1979).

关键词： Montgomery enable soybean

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Parallel screening and cheminformatics modeling of flavonoid activated aptasensors

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Synthetic and Systems Biotechnology 2022年第4期7卷 1148-1158页

作者： Yu Xiu Ni Zhang Pranesha Prabhakaran Sungho Jang Qipeng Yuan Curt MBreneman Gyoo Yeol Jung Wanwipa Vongsangnak Mattheos A.G.Koffas Beijing Key Laboratory of Bioactive Substances and Functional Food Beijing Union UniversityBeijing100029China Department of Chemical and Biological Engineering Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic InstituteTroyNY12180USA State Key Laboratory of Chemical Resource Engineering Beijing University of Chemical TechnologyBeijing100029China Department of Chemistry and Chemical Biology Rensselaer Polytechnic InstituteTroyNY12180USA Interdisciplinary Graduate Programs in Bioscience Faculty of ScienceKasetsart UniversityBangkok10900Thailand Omics Center for Agriculture BioresourcesFoodand HealthKasetsart University(OmiKU)BangkokThailand Division of Bioengineering College of Life Sciences and BioengineeringIncheon National University119 Academy-roYeonsu-guIncheon22012South Korea Department of Bioengineering and Nano-Bioengineering Incheon National University119 Academy-roYeonsu-guIncheon22012South Korea Research Center for Bio Materials&Process Development Incheon National University119 Academy-roYeonsu-guIncheon22012South Korea Department of Chemical Engineering Pohang University of Science and Technology77 Cheongam-roNam-guPohangGyeongbuk37673South Korea School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology77 Cheongam-roNam-guPohangGyeongbuk37673South Korea Department of Zoology Faculty of ScienceKasetsart UniversityBangkok10900Thailand

A parallel screening of 27 different flavonoids and chalcones was conducted using 6 artificial naringenin-activated riboswitches(M1,M2,M3,O,L and H).A quantitative structure-property relationship approach was applied to understand the physicochemical properties of the flavonoid structures resulting in specificity differences relied on the fluorescence intensity of a green fluorescent protein *** models of riboswitches M1,M2 and O that had good predictive power were constructed with descriptors selected for their high *** electronegativity and hydrophilicity of the flavonoids structures were identified as two properties that increased binding affinity to RNA *** groups at the C-3′and C-4’positions of the flavonoid molecule were strictly required for ligand-activation with riboswitches M1 and *** O and L preferred multi-hydroxylated flavones as *** on the A ring of the flavonoid molecule were not important in the molecular recognition process.O-glycosylated derivatives were not recognized by any of the riboswitches,presumably due to steric *** the challenges of detecting RNA conformational change after ligand binding,the resulting models elucidate important physicochemical features in the ligands for conformational structural studies of artificial aptamer complexes and for design of ligands having higher binding specificity.

关键词： Riboswitch RNA device Flavonoids Structure-property relationships Physicochemical properties

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A Robust Sers Sensing Platform for Analyzing Circulating Mirnas by Integrating Nucleic Acid Amplification with Nano-Aggregation

SSRN

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SSRN 2022年

作者： Sun, Yudie Fang, La Yi, Yang Feng, Aobo Zhang, Kui Xu, Jing-Juan School of Chemistry and Chemical Engineering Anhui University of Technology Anhui Maanshan243032 China State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nan-jing University Nanjing210023 China

Circulating miRNAs in the blood can regulate disease development and thus indicate dis-ease states via their various expression levels. For these reasons, circulating miRNAs consti-tute useful biomarkers, and an approach to the accurate detection of circulating miRNAs is attractive in the diagnosis and treatment of diseases. However, methods for detecting circulating miRNA that take into account both sensitivity and practicality are not currently available. Therefore, we aimed herein to solve some inherent problems in the actual detec-tion using a robust surface-enhanced Raman scattering (SERS) platform with integrated nucleic acid amplification and nanoparticle aggregation to detect circulating miRNAs. After target recognition and initial signal amplification by DNA walker, we observed that release triggered an open hairpin DNA on gold nanoparticles (AuNPs), which then promote AuNP aggregation, causing the accumulation of a large number of SERS hot spots. The SERS bio-sensor achieved a better performance than the sandwich-type separation detection, with a low detection limit (0.37 fM) and a broad linear range (1 fM-10 nM) in liquids. This SERS platform can be used as a powerful tool for the detection of circulating miRNAs, and it can be used to improve the sensitivity and accuracy of various clinical-disease diagnoses. © 2022, The Authors. All rights reserved.

关键词： DNA

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Influence of Slope Angle on Deposit Morphology and Propagation of laboratory Landslides

arXiv

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arXiv 2023年

作者： Wu, Yan-Bin Duan, Zhao Peng, Jian-Bing Zhang, Qing Pähtz, Thomas Ocean College Zhejiang University Zhoushan316021 China College of Geology and Environment Xi'an University of Science and Technology Xi'An710054 China Shaanxi Provincial Key Laboratory of Geological Support for Coal Green Exploitation Xi'An710055 China School of geology engineering and Geomatics Chang'an University Xi'An710054 China Key Laboratory of western Mineral Resources and Geological Engineering of Ministry of Education Chang'an University Xi'An710054 China Donghai Lab Zhoushan316021 China

Landslide deposits often exhibit surface features, such as transverse ridges and X-shaped conjugate troughs, whose physical formation origins are not well understood. To study the deposit morphology, laboratory studies typically focus on the simplest landslide geometry: an inclined plane accelerating the sliding mass immediately followed by its deceleration on a horizontal plane. However, existing experiments have been conducted only for a limited range of the slope angle θ. Here, we study the effect of θ on the kinematics and deposit morphology of laboratory landslides along a low-friction base, measured using an advanced 3D scanner. At low θ (30°-35°), we find transverse ridges formed by overthrusting on the landslide deposits. At moderate θ (40°-55°), conjugate troughs form. A Mohr-Coulomb failure model predicts the angle enclosed by the X-shaped troughs as 90°-φ, with φ the internal friction angle, in agreement with our experiments and a natural landslide. This supports the speculation that conjugate troughs form due to failure associated with a triaxial shear stress. At high θ (60°-85°), a double-upheaval morphology forms because the rear of the sliding mass impacts the front during the transition from the slope to the horizontal plane. The overall surface area of the landslides increases during their downslope motion and then decreases during their runout. Copyright © 2023, The Authors. All rights reserved.

关键词： Landslides

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An attention-enhanced deep learning framework for Designing alkaline anion exchange membranes

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Journal of Membrane science 2025年 733卷

作者： Ye Hu Zijun Xiao Deming Xia Bo Pang Xiaoming Yan Xuemei Wu Wanting Chen Gaohong He State Key Laboratory of Fine Chemicals Frontier Science Center for Smart Materials School of Chemical Engineering Dalian University of Technology Dalian 116024 China Key Laboratory of Industrial Ecology and Environmental Engineering (MOE) Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology School of Environmental Science and Technology Dalian University of Technology Dalian 116024 China School of Chemical Engineering Ocean and Life Dalian University of Technology Panjin 124221 China

Alkaline anion exchange membranes (AEMs) are crucial for electrochemical devices, such as fuel cells and water electrolyzers, demanding both high conductivity and alkaline stability. However, their development relied on labor-intensive trial-and-error methods. Here, a computational refinement and yielding system for top-class AEMs (CRYSTAL) was developed. This system generates novel AEM structures, which are then refined using prediction models, enabling an integrated and intelligent design process. Utilizing a Transformer-based architecture with multi-head self-attention mechanism, CRYSTAL effectively analyzes structural sequences, extracting high-dimensional molecular features and contextual relationships. This attention-enhanced framework ensures efficient and reliable structural generation while maintaining high-precision predictive performance ( R 2 > 0.9). Ultimately, CRYSTAL screened over 10 million potential AEM candidates, identifying 1629 structures with hydroxide conductivity exceeding 175 mS/cm and providing ten representative high-performance structures. This framework demonstrates transformative potential, significantly accelerating the discovery of advanced AEMs and establishing a scalable pathway for next-generation polymer technologies.

关键词： Anion exchange membranes Computational materials design High-throughput screening Machine learning Transformer

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Resonance Effects in Neuronal-Astrocyte Model with Ion Channel Blockage

SSRN

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SSRN 2022年

作者： Xiao, Fangli Fu, Ziying Jia, Ya Yang, Lijian College of Physical Science and Technology Central China Normal University Wuhan430079 China Hubei Key Laboratory of Genetic Regulation and Integrative Biology School of Life Sciences Central China Normal University Wuhan430079 China

The blockage of specific ion channels has important implications for neuronal dynamics. The effects of ion channel blockage and astrocyte responses to subthreshold periodic signals of different frequencies were investigated in a stochastic extended Hodgkin-Huxley model. We demonstrated that the neuronal response to weak signals is directly weakened by sodium channel blockage: the stronger the ion channel blockage is, the more serious the weakening will be. Conversely, the neuron’s response to external signals is improved by modulating the degree of potassium channel blockage. There is a certain value of potassium channel blocking intensity, corresponding to the optimal response output, that is, the system has reached the resonance state. The occurrence of the resonance phenomenon is related to the frequency of the external stimulus. Besides, the effect of ion channel blockage and the astrocyte on neurons was considered simultaneously. We observed that the system’s response to weak stimuli of different frequencies is enhanced compared to when astrocyte or potassium channel blockage acts separately. Furthermore, we noted the phenomenon of "frequency selection" of the system’s response to weak signals: at low frequencies, potassium channel blockage improves the response, whereas the astrocyte can modulate the neuronal response to external stimuli in the higher frequency range. © 2022, The Authors. All rights reserved.

关键词： Neurons

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