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TaxDiff: taxonomic-guided diffusion model for protein sequence generation

Science China(Information Sciences) 2025年第4期68卷 385-386页

作者： Zongying LIN Hao LI Liuzhenghao LV Yu WANG Bin LIN Junwu ZHANG Zijun CHEN Calvin Yu-Chian CHEN Li YUAN Yonghong TIAN School of Electronic and Computer Engineering Peking University AI for Science (AI4S)-Preferred Program Peking University Shenzhen Graduate School Peng Cheng Laboratory School of Chemical Biology and Biotechnology Peking University

Protein design aims to generate protein variants with targeted biological functions, which is significant in multiple biological areas, including enzyme reaction catalysis, vaccine design, and fluorescence intensity. Protein design contains two paradigms: sequence generation and structure generation. Recently, EvoDiff [1] proposed a universal designing paradigm, combining structure and sequence generation using the diffusion framework, which improves the protein design efficiency.

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Robust temporal knowledge inference via pathway snapshots with liquid neural network

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Methods 2025年 241卷 24-32页

作者： Han, Peifu Wang, Jianmin Liu, Dayan Liu, Lin Song, Tao College of Computer Science and Technology China University of Petroleum Qingdao 266580 China The Interdisciplinary Graduate Program in Integrative Biotechnology Yonsei University Incheon 21983 South Korea Department of Stomatology The First Medical Center Chinese PLA General Hospital Beijing 100853 China

Static graphs play a pivotal role in modeling and analyzing biological and biomedical data. However, many real-world scenarios—such as disease progression and drug pharmacokinetic processes—exhibit dynamic behaviors. Consequently, static graph methods often struggle to robustly address new environments characterized by complex and previously unseen relationship changes. Here, we propose a method for constructing temporal knowledge inference agents tailored to disease pathways, enabling effective relation reasoning beyond their training environment under complex shifts. To achieve this, we developed an imitation learning framework using liquid neural networks, a class of continuous-time neural models inspired by the brain function that are causal and adaptable to changing conditions. Our findings indicate that liquid agents can distill the essential tasks from knowledge graph inputs while accounting temporal evolution, thereby enabling the transfer of temporal skills to novel time nodes. Compared to state-of-the-art deep reinforcement learning agents, experiments demonstrate that temporal robustness in decision-making emerges uniquely in liquid networks. © 2025

关键词： Disease Pathways Liquid Neural Networks Relation Reasoning Robust Decision-Making Temporal Knowledge Inference

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A systematic literature review on adsorption of potentially toxic elements from aquatic systems by sugarcane and corn residues

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Adsorption 2025年第5期31卷 1-29页

作者： de Almeida Ribeiro Carvalho, Mayara Goveia, Danielle Botero, Wander Gustavo de Oliveira, Luciana Camargo Graduate Program in Biotechnology and Environmental Monitoring Federal University of São Carlos Sorocaba Campus São Paulo Brazil Institute of Sciences and Engineering Paulista State University Itapeva Campus São Paulo Brazil Graduate Program in Chemistry and Biotechnology Federal University of Alagoas A. C. Simões Campus Alagoas Brazil

Potentially toxic elements (PTE) pose environmental concerns due to their persistence, toxicity, and accumulation in living organisms. Their effective removal from waters and effluents is crucial for preserving aquatic ecosystems, human health, and biodiversity. Conventional treatment methods face challenges like waste generation and harmful substances. In this context, adsorption using agro-industrial residues emerges as a sustainable, low-cost, and environmentally friendly alternative. This is especially relevant in countries like Brazil, the United States, India, China, Argentina, and Thailand, where sugarcane and corn residues are abundantly available. This systematic literature review aims to provide a comprehensive overview of the adsorption of PTE from aquatic systems using sugarcane and corn residues, contributing to the identification of trends, gaps, and future directions in this field. Sugarcane bagasse and corncobs are highlighted as the most commonly used residues. The most frequently reported experimental conditions include grinding as treatment, batch mode adsorption, adsorbate concentration of 50 mg L−1, adsorbent concentration of 10 mg L−1, temperature of 25 °C, and a contact time of 60 min. Specific details such as particle size (0.25 mm for sugarcane, 0.15 mm for corn), main PTE (Pb for sugarcane, Cd for corn), and optimal pH (5 for sugarcane, 6 for corn) were also identified. However, research gaps remain, such as the use of sugarcane and corn leaves, the biological modification of residues, and the study of less-explored PTEs like Fe and Mn. These gaps provide opportunities for future investigations and advances in water treatment technologies.

关键词： Sugar cane

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HYBRID QUANTUM NEURAL NETWORKS WITH VARIATIONAL QUANTUM REGRESSOR FOR ENHANCING QSPR MODELING OF CO2-CAPTURING AMINE

arXiv

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arXiv 2025年

作者： Cho, Hyein Kim, Jeonghoon Lim, Hocheol The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine Yonsei University Incheon Korea Republic of Incheon Korea Republic of

Accurate amine property prediction is essential for optimizing CO2 capture efficiency in postcombustion processes. Quantum machine learning (QML) can enhance predictive modeling by leveraging superposition, entanglement, and interference to capture complex correlations. In this study, we developed hybrid quantum neural networks (HQNN) to improve quantitative structure-property relationship modeling for CO2-capturing amines. By integrating variational quantum regressors with classical multi-layer perceptrons and graph neural networks, quantum advantages were explored in physicochemical property prediction under noiseless conditions and robustness was evaluated against quantum hardware noise using IBM quantum systems. Our results showed that HQNNs improve predictive accuracy for key solvent properties, including basicity, viscosity, boiling point, melting point, and vapor pressure. The fine-tuned and frozen pre-trained HQNN models with 9 qubits consistently achieved the highest rankings, highlighting the benefits of integrating quantum layers with pretrained classical models. Furthermore, simulations under hardware noise confirmed the robustness of HQNNs, maintaining predictive performance. Overall, these findings emphasize the potential of hybrid quantum-classical architectures in molecular modeling. As quantum hardware and QML algorithms continue to advance, practical quantum benefits in QSPR modeling and materials discovery are expected to become increasingly attainable, driven by improvements in quantum circuit design, noise mitigation, and scalable architectures. © 2025, CC BY-NC-ND.

关键词： Quantum entanglement

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SAGE-Amine: Generative Amine Design with Multi-Property Optimization for Efficient CO2 Capture

arXiv

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arXiv 2025年

作者： Lim, Hocheol Cho, Hyein Kim, Jeonghoon Incheon21983 Korea Republic of The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine Yonsei University Incheon21983 Korea Republic of

Efficient CO2 capture is vital for mitigating climate change, with amine-based solvents being widely used due to their strong reactivity with CO2. However, optimizing key properties such as basicity, viscosity, and absorption capacity remains challenging, as traditional methods rely on labor-intensive experimentation and predefined chemical databases, limiting the exploration of novel solutions. Here, SAGE-Amine was introduced, a generative modeling approach that integrates Scoring-Assisted Generative Exploration (SAGE) with quantitative structure-property relationship models to design new amines tailored for CO2 capture. Unlike conventional virtual screening restricted to existing compounds, SAGE-Amine generates novel amines by leveraging autoregressive natural language processing models trained on amine datasets. SAGE-Amine identified known amines for CO2 capture from scratch and successfully performed single-property optimization, increasing basicity or reducing viscosity or vapor pressure. Furthermore, it facilitated multi-property optimization, simultaneously achieving high basicity with low viscosity and vapor pressure. The 10 top-ranked amines were suggested using SAGE-Amine and their thermodynamic properties were further assessed using COSMO-RS simulations, confirming their potential for CO2 capture. These results highlight the potential of generative modeling in accelerating the discovery of amine solvents and expanding the possibilities for industrial CO2 capture applications. © 2025, CC BY-NC-ND.

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Cryptotanshinone Suppresses the STAT3/BCL-2 Pathway to Provoke Human Bladder Urothelial Carcinoma Cell Death

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Environmental Toxicology 2025年第4期40卷 624-635页

作者： Tung, Min-Che Chang, Ge-Man Dai, Wen-Chyi Hsu, Chen-Hsuan Chang, Hsiang-Chun Yang, Wei-Ting Ho, Yann-Jen Lu, Chien-Hsing Chen, Yi-Hsin Chang, Chia-Che Division of Urology Department of Surgery Tungs' Taichung MetroHarbor Hospital Taichung Taiwan Graduate Institute of Biomedical Sciences National Chung Hsing University Taichung Taiwan Doctoral Program in Biotechnology Industrial Innovation and Management National Chung Hsing University Taichung Taiwan Department of Life Sciences National Chung Hsing University Taichung Taiwan Department of Obstetrics and Gynecology Taichung Veterans General Hospital Taichung Taiwan Doctoral Program in Translational Medicine National Chung Hsing University Taichung Taiwan Department of Nephrology Taichung Tzu Chi Hospital Buddhist Tzu chi Medical Foundation Taichung Taiwan School of Medicine Tzu Chi University Hualein Taiwan Department of Artificial Intelligence and Data Science National Chung Hsing University Taichung Taiwan Master Program in Precision Health Rong Hsing Research Center for Translational Medicine The iEGG and Animal Biotechnology Research Center National Chung Hsing University Taichung Taiwan Department of Medical Laboratory Science and Biotechnology Asia University Taichung Taiwan Department of Medical Research China Medical University Hospital Taichung Taiwan

Bladder cancer is one of the most common human malignancies worldwide. Aberrant activation of signal transducer and activator of transcription 3 (STAT3) is crucial to driving malignant progression and predicting poor prognosis of multiple human cancers, including bladder cancer, making STAT3 a promising target of cancer therapeutics. Cryptotanshinone (CTS) is an anticancer ingredient of Danshen (Salvia miltiorrhiza), a top-graded Chinese medicinal herb. However, whether CTS targets STAT3 to exert its cytotoxic effect on human bladder cancer remains unknown. Herein, we demonstrated that CTS is cytotoxic to multiple human urinary bladder transitional cell carcinoma (TCC) cell lines while sparing normal human urothelial cells. CTS provoked apoptosis-dependent bladder TCC cytotoxicity, as apoptosis blockage by z-VAD-fmk markedly rescued the clonogenicity of CTS-treated cells. Besides, CTS was found to suppress constitutive and interleukin 6-inducible activation of STAT3, evidenced by the downregulation of STAT3 tyrosine 705 phosphorylation and BCL2, a recognized STAT3 transcriptional target. Notably, ectopic expression of a dominant-active STAT3 mutant (STAT3-C) or BCL-2 alleviated CTS-induced apoptosis and clonogenicity inhibition, thus confirming STAT3 blockade as a pivotal mechanism of CTS's cytotoxic action on bladder TCC cells. Lastly, immunoblotting revealed that CTS lowered the levels of active JAK2, an upstream kinase that mediates STAT3 tyrosine 705 phosphorylation. Altogether, we conclude that the blockade of the JAK2/STAT3/BCL-2 antiapoptotic signaling axis is a vital mechanism whereby CTS provokes bladder cancer cytotoxicity. The current evidence implicates CTS's potential to be translated into a bladder cancer therapeutic agent. © 2024 Wiley Periodicals LLC.

关键词： Cell death

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Inhibitory effect of standardized Kaempferia parviflora extract on sarcopenia by improving protein metabolism pathways in aged C57BL/6J mice

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Journal of Traditional and Complementary Medicine 2025年

作者： Kim, Changhee Kang, Minseong Kim, Yeeun Hwang, Jae-Kwan Department of Biotechnology Yonsei University Seoul South Korea Graduate Program in Bioindustrial Engineering Yonsei University Seoul South Korea

Background: Sarcopenia is a muscle disease typically characterized by an age-related loss of muscle mass and function, leading to the deterioration of health in older adults. The current study aimed to investigate the therapeutic potential of standardized Kaempferia parviflora extract (KPE) on sarcopenia and elucidate its underlying molecular mechanisms. Methods: To assess the inhibitory effects of KPE on sarcopenia, 18-month-old C57BL/6J mice were employed as an aged model. The mice were orally administered 100 and 200 mg/kg KPE daily for 8 weeks. Results: KPE improved age-reduced grip strength and exercise endurance. It not only increased hindlimb muscle weight, volume, and myofiber cross-sectional area but also decreased abdominal fat volume and adipose tissue weight. KPE downregulated the mRNA expression of tumor necrosis factor alpha and interleukin-6 by inactivating nuclear factor kappa B protein expression and increasing the mRNA expression of anti-oxidant enzymes. Moreover, it significantly reduced the mRNA expression of muscle ring finger-1 and muscle atrophy F-box for proteolysis and stimulated the mammalian target of rapamycin pathway for protein translation by stimulating the phosphatidylinositol 3-kinase/Akt pathway. KPE also increased the relative mitochondrial DNA content by upregulating peroxisome proliferator-activated receptor gamma coactivator 1 alpha, nuclear respiratory factor 1, and mitochondrial transcription factor A mRNA expression. Conclusion: This study's findings demonstrate that KPE improves age-induced sarcopenia by regulating protein turnover and mitochondrial homeostasis. Therefore, KPE is potentially useful as a functional ingredient that inhibits or decelerates sarcopenia. © 2025 Center for Food and Biomolecules, National Taiwan University

关键词： Kaempferia parviflora Mitochondrial homeostasis Protein turnover Sarcopenia

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Decoding microRNA arm switching: a key to evolutionary innovation and gene regulation

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Cellular and Molecular Life Sciences 2025年第1期82卷 1-23页

作者： Pinhal, Danillo Gonçalves, Leandro de B. Campos, Vinícius F. Patton, James G. Genomics and Molecular Evolution Laboratory Department of Chemical and Biological Sciences Institute of Biosciences DCQB IBB UNESP SP Botucatu CEP 18618-689 Brazil Structural Genomics Laboratory Graduate Program in Biotechnology Technological Development Center Federal University of Pelotas RS Pelotas Brazil Department of Biological Sciences Vanderbilt University Nashville 37232 TN United States

miRNA arm switching is a pivotal regulatory mechanism that allows organisms to fine-tune gene expression by selectively utilizing either the 5p or 3p strand of a miRNA duplex. This process, conserved across species, facilitates adaptive responses to developmental cues, environmental changes, and disease states. By dynamically altering strand selection, arm switching reshapes gene regulatory networks, contributing to phenotypic diversity and evolutionary innovation. Despite its growing recognition, the mechanisms driving arm switching—such as thermodynamic properties and enzyme-mediated processing—remain incompletely understood. This review synthesizes current findings, highlighting arm switching as a highly conserved mechanism with profound implications for the evolution of regulatory networks. We explore how this phenomenon expands miRNA functionality, drives phenotypic plasticity, and co-evolves with miRNA gene duplications to fuel the diversification of biological functions across taxa. © The Author(s) 2025.

关键词： Evolution of gene regulatory networks miRNA strand selection mechanisms Phenotypic plasticity in development Post-transcriptional gene regulation

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Characterization of a new triaxial nanofiber membrane and osteogenic differentiation capacity of human bone marrow mesenchymal stem cells for bone repair

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Journal of Materials Research 2025年 1-18页

作者： Altundag-Erdogan, Özlem Çetinkaya, Hayrullah Çelebi-Saltik, Betül Altun, Belgin Şahin, Mehtap Mağden, Gamze Kara Öteyaka, Mustafa Özgür Department of Stem Cell Sciences Graduate School of Health Sciences and Center for Stem Cell Research and Development Hacettepe University Sihhiye Ankara06100 Turkey Department of Chemical Engineering Eskisehir Osmangazi University Eskişehir26040 Turkey Vocational School Health Services Hacettepe University Sihhiye Ankara06100 Turkey BUGAMED Biotechnology Industry and Trade Inc Eskişehir26380 Turkey Eskişehir Vocational School Electronics and Automation Eskisehir Osmangazi University Mechatronic Program Eskişehir26250 Turkey

A triaxial nanofiber membrane was developed using a custom triaxial nozzle during electrospinning. The membrane consisted of three layers (outer middle (PVA-Collagen Type I-BMP-2), and inner (PVA-nHAP)). TEM revealed the diameters of the outer, middle, and inner layers as 167.5, 142.6, and 119.3 nm, respectively. The triaxial nanofiber membrane exhibited superior tensile strength (36 MPa) and elastic modulus (2.5 GPa), along with a roughness of 359 nm and hydrophilic properties. In addition, it demonstrated a 200% swelling ratio and reduced bacterial colonization by 10.8-fold. Both Calcium deposition and ALP activity were significantly higher and increased expression of BSP (eightfold), OCN (13-fold), and OPN (488-fold) genes were observed in membrane + OST groups (p © The Author(s), under exclusive licence to The Materials Research Society 2025.

关键词： Bone

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Combining Electrospun Nanofibers, Paenibacillus polymyxa Fermented Broth, and Silver Nanoparticles for Enhanced Antimicrobial Materials

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BioNanoScience 2025年第3期15卷 1-13页

作者： Oliveira, Luís F. R. Teodoro, Kelcilene B. R. Andre, Rafaela S. Costa, Vittor P. V. Cavicchioli, Rafael Mercante, Luiza A. de Sousa, Cristina P. Correa, Daniel S. Nanotechnology National Laboratory for Agriculture (LNNA) São Carlos Brazil Graduate Program in Biotechnology (PPGBiotec) Federal University of São Carlos (UFSCar) São Carlos Brazil Institute of Chemistry Federal University of Bahia (UFBA) Salvador Brazil

The World Health Organization has identified antimicrobial resistance as one of the top ten significant threats to global public health. For instance, it is predicted that conventional antibiotics will progressively lose their efficacy, accentuating the urgency to find innovative solutions to combat microorganisms. Efforts to develop novel antimicrobial agents are highly sought, as well as to explore the potential of natural products, such as plant extracts, and microbial secondary metabolites. In this direction, the Paenibacillus polymyxa RNC-D fermented broth (PFB), which is rich in antimicrobial peptides, was tested as component of nanostructured antimicrobial mat. For this, PFB was incorporated into polycaprolactone (PCL) nanofibers produced by electrospinning, which were further modified with silver nanoparticles (AgNPs) to produce enhanced antimicrobial materials. The materials were physicochemically characterized using distinct techniques, while the microbiological studies were carried out using the agar disk diffusion method, microbial penetration test and percentage of bacterial growth inhibition in suspension. The results showed that the incorporation of 25% of the PFB caused a significant improvement in the fiber spinnability, resulting in nanofibers with less surface defects. Moreover, the wettability and hydrophilicity of the mats increased. Antimicrobial studies demonstrated the importance of the PFB to the formulation, which acted synergically, improving the distribution of AgNPs onto the fibers. While the fibrous mats demonstrated a protective effect against environmental microbes, when combined with AgNPs the PCL/PFB mats exhibited an inhibition halo of approximately 11.1 ± 0.4 mm in the agar diffusion test and showed capability of inhibiting the bacterial growth against E. coli. Therefore, our results demonstrate that combining electrospun nanofibers membrane, fermented broth and silver nanoparticles can be an alternative for developing enhanced an

关键词： Antiviral agents

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