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Enhancement of menaquinone- 7 production through immobilization with hydrogel-based porous membranes

Applied Microbiology and Biotechnology 2025年第1期109卷 1-11页

作者： Zhang, Qiu-Hua Wang, Zheng Wang, Yao-Qiang Liu, Man-Lu Su, Hai-Jia Beijing Key Laboratory of Bioprocess and Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing100029 China Brother Research Center Jiangxi Brother Pharmaceutical Co.LTD Jiujiang332700 China

Abstract: The industrial production of menaquinone-7 (MK-7) by Bacillus subtilis has been historically constrained by significant challenges in bioprocess efficiency. To address these limitations, we explored an innovative immobilization strategy utilizing a porous thin-film hydrogel system. Specifically, we developed a novel porous thin-film PVA + B@Ca hydrogel immobilization method that fundamentally transforms cell encapsulation and fermentation dynamics. The comparison between PVA + B@Ca hydrogel immobilized cells and free cells in fermentation demonstrated a significant increase in MK-7 yield from 32.76 ± 1.92 to 48.33 ± 2.92 mg/L, as well as a reduction of the fermentation duration from 48 to 24 h. Additionally, the immobilized cells demonstrated good stability during continuous fermentation, resulting in a space–time yield of MK-7 that increased to 2.0 mg/L·h, which was five times higher than that achieved with free-cell fermentation. Mechanistic insights revealed through microscopic analysis highlight the transformative nature of the hydrogel immobilization: The PVA + B@Ca hydrogel’s porous structure creates a protective microenvironment that mitigates cellular stress and maintains optimal metabolic conditions. These findings represent a paradigm shift in understanding cellular immobilization, demonstrating how strategic encapsulation can fundamentally enhance MK-7 fermentation biotechnology. Key points: • A novel hydrogel immobilization method was developed for MK- 7 production. • The use of immobilized cells gave a fivefold improvement in the space–time yield. © The Author(s) 2025.

关键词： Bacteriology

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Transient chemical-mediated epigenetic modulation confers unrestricted lineage potential on human primed pluripotent stem cells

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Science China(Life Sciences) 2025年第4期68卷 1084-1101页

作者： Shi Chen Yuanyuan He Lejun Lv Bei Liu Cheng Li Hongkui Deng Jun Xu Department of Cell Biology School of Basic Medical SciencesPeking University Stem Cell Research CenterPeking University Health Science CenterPeking UniversityBeijing100191China Academy of Advanced Interdisciplinary Studies Peking UniversityBeijing100871China BeiCell Therapeutics Beijing100094China School of Life Sciences Center for BioinformaticsCenter for Statistical SciencePeking UniversityBeijing100871China MOE Engineering Research Center of Regenerative Medicine School of Basic Medical SciencesState Key Laboratory of Natural and Biomimetic DrugsPeking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and DifferentiationCollege of Life SciencesPeking-Tsinghua Center for Life SciencesPeking UniversityBeijing100871China

Human primed pluripotent stem cells are capable of generating all the embryonic ***,their extraembryonic trophectoderm potentials are *** remains unclear how to expand their developmental potential to trophectoderm *** we show that transient treatment with a cocktail of small molecule epigenetic modulators imparts trophectoderm lineage potentials to human primed pluripotent stem cells while preserving their embryonic *** chemically treated cells can generate trophectoderm-like cells and downstream trophoblast stem cells,diverging into syncytiotrophoblast and extravillous trophoblast *** and CUT&Tag analyses reveal that these induced cells share transcriptional profiles with in vivo trophectoderm and cytotrophoblast,and exhibit reduced H3K27me3 modification at gene loci specific to trophoblast lineages compared with primed pluripotent *** exploration highlighted the critical roles of epigenetic modulators HDAC2,EZH1/2,and KDM5s in the activation of trophoblast lineage *** findings demonstrate that transient epigenetic resetting activates unrestricted lineage potential in human primed pluripotent stem cells,and offer new mechanistic insights into human trophoblast lineage specification and in vitro models for studying placental development and related disorders.

关键词： trophectoderm lineages human primed pluripotent stem cells epigenetic regulation small molecules

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SpaGRA:Graph augmentation facilitates domain identification for spatially resolved transcriptomics

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Journal of Genetics and Genomics 2025年第1期52卷 93-104页

作者： Xue Sun Wei Zhang Wenrui Li Na Yu Daoliang Zhang Qi Zou Qiongye Dong Xianglin Zhang Zhiping Liu Zhiyuan Yuan Rui Gao Center of Intelligent Medicine School of Control Science and EngineeringShandong UniversityJinanShandong 250061China MOE Key Lab of Bioinformatics and Bioinformatics Division of BNRIST Department of AutomationTsinghua UniversityBeijing 100084China Institute of Precision Medicine Peking University Shenzhen HospitalShenzhenGuangdong 518036China Department of Clinical Laboratory The Second HospitalCheeloo College of MedicineShandong UniversityJinanShandong 250033China Institute of Science and Technology for Brain-Inspired Intelligence Center for Medical Research and InnovationShanghai Pudong HospitalFudan University Pudong Medical CenterFudan UniversityShanghai 200433China

Recent advances in spatially resolved transcriptomics(SRT)have provided new opportunities for characterizing spatial structures of various ***-based geometric deep learning has gained widespread adoption for spatial domain identification ***,most methods define adjacency relation between cells or spots by their spatial distance in SRT data,which overlooks key biological interactions like gene expression similarities,and leads to inaccuracies in spatial domain *** tackle this challenge,we propose a novel method,SpaGRA(https://***/sunxue-yy/SpaGRA),for automatic multi-relationship construction based on graph *** uses spatial distance as prior knowledge and dynamically adjusts edge weights with multi-head graph attention networks(GATs).This helps SpaGRA to uncover diverse node relationships and enhance message passing in geometric contrastive ***,SpaGRA uses these multi-view relationships to construct negative samples,addressing sampling bias posed by random *** results show that SpaGRA presents superior domain identification performance on multiple datasets generated from different *** SpaGRA,we analyze the functional regions in the mouse hypothalamus,identify key genes related to heart development in mouse embryos,and observe cancer-associated fibroblasts enveloping cancer cells in the latest Visium HD ***,SpaGRA can effectively characterize spatial structures across diverse SRT datasets.

关键词： Spatial domain identification Spatially resolved transcriptomics Multi-head graph attention networks Graph augmentation Geometric contrastive learning

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Programmable scanning diffuse speckle contrast imaging of cerebral blood flow

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Neurophotonics 2025年第1期12卷 015006页

作者： Akbari, Faezeh Liu, Xuhui Hamedi, Fatemeh Mohtasebi, Mehrana Chen, Li Chen, Lei Yu, Guoqiang University of Kentucky Department of Biomedical Engineering LexingtonKY United States University of Kentucky Biostatistics and Bioinformatics Shared Resource Facility Markey Cancer Center LexingtonKY United States University of Kentucky Spinal Cord and Brain Injury Research Center Department of Physiology LexingtonKY United States

Significance: Cerebral blood flow (CBF) imaging is crucial for diagnosing cerebrovascular diseases. However, existing large neuroimaging techniques with high cost, low sampling rate, and poor mobility make them unsuitable for continuous and longitudinal CBF monitoring at the bedside. Aim: We aimed to develop a low-cost, portable, programmable scanning diffuse speckle contrast imaging (PS-DSCI) technology for fast, high-density, and depth-sensitive imaging of CBF in rodents. Approach: The PS-DSCI employed a programmable digital micromirror device (DMD) for remote line-shaped laser (785 nm) scanning on tissue surface and synchronized a 2D camera for capturing boundary diffuse laser speckle contrasts. New algorithms were developed to address deformations of line-shaped scanning, thus minimizing CBF reconstruction artifacts. The PS-DSCI was examined in head-simulating phantoms and adult mice. Results: The PS-DSCI enables resolving intralipid particle flow contrasts at different tissue depths. In vivo experiments in adult mice demonstrated the capability of PS-DSCI to image global/regional CBF variations induced by 8% CO2 inhalation and transient carotid artery ligations. Conclusions: Compared with conventional point scanning, line scanning in PS-DSCI significantly increases spatiotemporal resolution. The high sampling rate of PS-DSCI is crucial for capturing rapid CBF changes while high spatial resolution is important for visualizing brain vasculature. © The Authors. Published by SPIE under a Creative Commons Attribution 4.0 International License.

关键词： Neuroimaging

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Identifying candidate biomarkers for detecting bronchogenic carcinoma stages using metaheuristic algorithms based on information fusion theory

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Discover Oncology 2025年第1期16卷 1-27页

作者： Khalvati, Bagher Kavousi, Kaveh Keyhanipour, Amir Hosein Arabfard, Masoud Department of Bioinformatics Kish International Campus University of Tehran Kish Iran Laboratory of Complex Biological Systems and Bioinformatics (CBB) Department of Bioinformatics Institute of Biochemistry and Biophysics (IBB) University of Tehran Tehran Iran Computer Engineering Department Faculty of Engineering College of Farabi University of Tehran Tehran Iran Chemical Injuries Research Center Systems Biology and Poisonings Institute Baqiyatallah University of Medical Sciences Tehran Iran

Objective: Invasive lung cancer staging poses significant challenges, often requiring painful and costly biopsy procedures. This study aims to identify non-invasive biomarkers for detecting bronchogenic carcinoma and its various stages by analyzing gene expression data using bioinformatics and machine learning techniques. By leveraging these advanced computational methods, we seek to eliminate the need for surgical intervention in the diagnostic process. Methods: We utilized the TCGA-LUAD dataset, including gene expression data from healthy and cancerous samples. To identify robust biomarkers, we applied eight metaheuristic algorithms for feature selection, combined with four classification methods and two data fusion techniques to optimize performance. Results: Our approach achieved 100% accuracy in distinguishing healthy samples from cancerous ones, outperforming existing methods that reported 97% accuracy. Notably, while prior methods have struggled to separate bronchogenic carcinoma stages effectively, our research achieved an approximate accuracy of 77% in stage classification. Furthermore, using gene enrichment methods, we identified 5, 7, and 16 diagnostic biomarker candidates for stages I, II, III, and IV, respectively. Conclusion: This study demonstrates that integrating bioinformatics, gene set enrichment, and biological pathway analysis can enable non-invasive diagnostics for bronchogenic carcinoma stages. These findings hold promise for developing alternatives to traditional, invasive staging systems, potentially improving patient outcomes and reducing healthcare costs. © The Author(s) 2025.

关键词： Biomarker Bronchogenic carcinoma Feature selection algorithms Information fusion Machine learning

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CRISPR/Cas9 editing of p-COUMAROYL-CoA:MONOLIGNOL TRANSFERASE 1 in maize alters phenolic metabolism, lignin structure, and lignin-first biomass processing

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Trends in Biotechnology 2025年第5期43卷 1166-1195页

作者： Oliveira, Dyoni M. Saleme, Marina de L.S. Smith, Rebecca A. Vangeel, Thijs Lima, Marcelo de F. Chanoca, Alexandra A. Mota, Thatiane R. Vanhevel, Yasmine Coussens, Griet Van Aelst, Korneel Geerts, Jordi Cornet, Iris Vaneechoutte, Dries Vandepoele, Klaas Pauwels, Laurens Goeminne, Geert Morreel, Kris Sels, Bert F. Ralph, John Vanholme, Ruben Boerjan, Wout Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium VIB Center for Plant Systems Biology Ghent Belgium Great Lakes Bioenergy Research Center and the Wisconsin Energy Institute University of Wisconsin-Madison MadisonWI United States Department of Microbial and Molecular Systems Center for Sustainable Catalysis and Engineering KU Leuven–University of Leuven Leuven Belgium Biochemical Wastewater Valorization and Engineering Group University of Antwerp Antwerp Belgium VIB Metabolomics Core Ghent Belgium Department of Biochemistry University of Wisconsin MadisonWI United States

Valorization of lignocellulosic biomass for sustainable production of high-value chemicals is challenged by the complexity of lignin, a phenolic biopolymer. Beyond the classical lignin monomers derived from p-coumaryl, coniferyl, and sinapyl alcohol, grass lignins incorporate substantial amounts of monolignol p-coumarates that are produced by p-COUMAROYL-CoA:MONOLIGNOL TRANSFERASE (PMT). Here, the CRISPR/Cas9-mediated mutation of ZmPMT1 in maize enabled the design of biomass depleted in p-coumaroylated lignin and enriched in guaiacyl lignin. Lignin-first biorefining of stem biomass from zmpmt1 mutants by reductive catalytic fractionation (RCF) generated a lignin oil depleted in carboxylates and enriched in guaiacyl-derived alcohols, which are desirable substrates for bio-based polyurethane synthesis. The reported lignin engineering in maize is a promising strategy for designing a dual-purpose crop, providing both food and feed, along with a renewable feedstock for the production of plant-based chemicals. © 2025 Elsevier Ltd

关键词： Saccharification

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Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis

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BMC Biology 2025年第1期23卷 1-17页

作者： Wang, Mohan Zheng, Shanshan Zhang, Yan Zhang, Jingwen Lai, Fuming Zhou, Cong Zhou, Qiangwei Li, Xingwang Li, Guoliang National Key Laboratory of Crop Genetic Improvement Hubei Hongshan Laboratory Huazhong Agricultural University Wuhan 430070 China Agricultural Bioinformatics Key Laboratory of Hubei Province Hubei Engineering Technology Research Center of Agricultural Big Data Key Laboratory of Smart Farming Technology for Agricultural Animals 3D Genomics Research Center College of Informatics Huazhong Agricultural University Wuhan 430070 China

Background: Circular RNAs (circRNAs) are a class of non-coding RNAs generated through back splicing. High expression of circRNAs is often associated with numerous abnormal cellular biological processes. However, the regulatory factors of circRNAs are not fully understood. Results: In this study, we identified PTBP1 as a crucial regulator of circRNA biogenesis through a comprehensive analysis of the whole transcriptome profiles across 10 diverse cell lines. Knockdown of PTBP1 led to a significant decrease in circRNA expression, concomitant with a distinct reduction in cell proliferation. To investigate the regulatory mechanism of PTBP1 on circRNA biogenesis, we constructed a minigene reporter based on SPPL3 gene. The results showed that PTBP1 can bind to the flanking introns of circSPPL3, and the mutation of PTBP1 motif impedes the back splicing of circSPPL3. Subsequently, to demonstrate that this observation is not an exception, the comprehensive regulatory effects of PTBP1 on circRNAs were confirmed by miniGFP, reflecting the necessity of the binding site in the flanking introns. Analysis of data from clinical samples showed that both PTBP1 and circRNAs exhibited substantial upregulation in acute myeloid leukemia, further demonstrating a potential role for PTBP1 in promoting circRNA biogenesis under in vivo conditions. Competitive endogenous RNA (ceRNA) network revealed that PTBP1-associated circRNAs participated in biological processes associated with cell proliferation. Conclusions: In summary, our study is the first to identify the regulatory effect of PTBP1 on circRNA biogenesis and indicates a possible link between PTBP1 and circRNA expression in leukemia. © The Author(s) 2025.

关键词： Biogenesis Circular RNAs PTBP1 RNA binding proteins Transcriptome

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Dynamic liquid film nanochannels for adjustable ion and molecule transport

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Nano research 2025年第3期18卷 494-501页

作者： Chunxiao Liang Dianyu Wang Zhe Xu Haitao Deng Fan Xia Ye Tian Key Laboratory of Bioinspired Materials and Interfacial Science Technical Institute of Physics and ChemistryChinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China School of Chemical Engineering Zhengzhou UniversityZhengzhou 450001China State Key Laboratory of Biogeology and Environmental Geology Engineering Research Center of Nano-Geomaterials of Ministry of EducationFaculty of Materials Science and ChemistryChina University of GeosciencesWuhan 430074China Suzhou Institute for Advanced Research University of Science and Technology of ChinaSuzhou 215123China Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of SciencesQingdao 266101China

Gating,a fundamental feature of biological nanochannels,enables the intelligent regulation of ion and molecule transport in response to specific *** by nature,numerous artificial gating systems have been researched through the functionalization of solid-state ***,these gating systems typically allow only two transitions:“open”and“closed”,which makes it challenging to achieve multi-state ***,we construct dynamic liquid film nanochannels(DLFNs)by inserting an oil droplet into a capillary with gradient wettability that is filled with ionic *** liquid film,formed between the oil and the capillary,functions as a nanochannel for ion and molecule transport,with its height dynamically adjusted through the capillary's gradient *** a deeper level,the variations in liquid film thickness are driven by the interfacial water structure,which is mediated by hydrogen bonding ***,unlike traditional solid-state nanochannels,which involve two phases(liquid/solid),the properties of DLFNs are influenced by three phases(oil/water/solid),resulting in distinct performance characteristics,such as reconfigurability,low cost,and ease of *** work provides an avenue for designing dynamic nanofluids and may spark promising applications of DLFNs with multiscale gating properties in drug delivery,microreactors,sieving,biosensing,and other related fields.

关键词： dynamic liquid film nanochannel gating wettability oil-water-solid interface

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Phase Evolution Extension of Cu₂ZnSn(S,Se)₄ Absorber Boosting the Efficiency of Kesterite Solar Cells to 14.99%

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ACS Energy Letters 2025年 2761-2769页

作者： Yao, Ge Wu, Zucheng Kou, Dongxing Kong, Bingyin Wei, Hao Shao, Zhipeng Zhou, Wenhui Zhou, Zhengji Yuan, Shengjie Qi, Yafang Han, Litao Cui, Guanglei Wu, Sixin Key Lab for Special Functional Materials Ministry of Education National & Local Joint Engineering Research Center for High-Efficiency Display and Lighting Technology School of Nanoscience and Materials Engineering Collaborative Innovation Center of Nano Functional Materials and Applications Henan University Kaifeng 475004 China State Key Laboratory of Photoelectric Conversion and Utilization of Solar Energy Qingdao New Energy Shandong Laboratory Qingdao Industrial Energy Storage Research Institute Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Science Qingdao 266101 China

The presence of secondary phases and a high concentration of deep-level defects led to a large open-circuit voltage deficit (Voc,deficit) for Cu2ZnSn(S,Se)4 (CZTSSe) solar cells. Here we regulate the phase evolution f...

The presence of secondary phases and a high concentration of deep-level defects led to a large open-circuit voltage deficit (V_oc,deficit) for Cu₂ZnSn(S,Se)₄ (CZTSSe) solar cells. Here we regulate the phase evolution from CZTS to CZTSSe in the initial selenization stage to obtain high-quality absorber with minimal defects and secondary phases. By adding the bidentate chelation structured mercaptopropionic acid (MPA) into the air-prepared 2-methoxyethanol (MOE) precursor solution, large CZTS colloidal particles and dense precursor films are prepared. During the initial selenization stage, the reduced nucleation sites can decrease selenium-molecule interactions and extend the phase evolution process. This extension makes the heterogeneous nucleation more controllable, fostering uniform element distribution and enhanced growth of permeating the large-grain layer. These benefits demonstrate a substantial increase in device efficiency up to 14.99% (certified at 14.38%) with a reduced V_oc,deficit of 281.18 mV. The findings are of great significance for further efficiency leaps of kesterite solar cells. © 2025 American Chemical Society.

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Methacrylic acid/Tween 80 engineered amorphous calcium phosphate as an effective bioactive reinforcing nanofillers in dental adhesive

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Dental Materials Journal 2025年第2期44卷 190-200页

作者： Maimansomsuk, Siripatsorn Teangrom, Paremai Teanchai, Chayada Sinthuvanich, Chomdao Ruengket, Pakorn Attarataya, Jakrada Akkarachaneeyakorn, Khrongkhwan Department of Chemistry Faculty of Science Kasetsart University Bangkok10900 Thailand Center of Excellence for Innovation in Chemistry Faculty of Science Kasetsart University Bangkok10900 Thailand Research Center Faculty of Dentistry Mahidol University Bangkok10400 Thailand Department of Biochemistry Faculty of Science Kasetsart University Bangkok Thailand Faculty of Science Kasetsart University Bangkok Thailand Genetic Engineering and Bioinformatics Program Graduate School Kasetsart University Bangkok Thailand Nakhon Ratchasima30000 Thailand

Bioactive fillers in dental adhesives are designed to release beneficial ions, such as calcium and phosphate, to help in remineralization process, and preventing secondary caries. Their incorporation also aims to improve the longevity of dental restorations. Herein, CaP nanoparticles were synthesized through a water-in-oil emulsion method using Tween80 as a surfactant and methacrylic acid (MAA). MAA officiated as a co-surfactant and reduced the size of CaP nanoparticle, including improved compatibility with the components of dental adhesive. The incorporation of 2% T80/CaP/MAA nanofillers into dental adhesive demonstrated increased efficiency, as evidenced by a higher degree of conversion (%DC) and greater micro-tensile bond strength (μTBS). More importantly, T80/CaP/ MAA nanofillers were able to induce remineralization process in the dental structure, which was confirmed by EDX mapping and IR imaging. Finally, a cytotoxicity assessment of the dental adhesive containing T80/CaP/MAA showed no significant adverse effects on human fibroblast cells. © 2025, Japanese Society for Dental Materials and Devices. All rights reserved.

关键词： Stem cells

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