检索结果-内蒙古大学图书馆

Integrating computational and experimental insights into osmolyte-driven activation of Geobacillus kaustophilus L-asparaginase for acrylamide mitigation

引用

Journal of Molecular Liquids 2025年 423卷

作者： Özdemir, F.İnci Servili, Burak Demirtaş, Özge Şükür, Gözde Tülek, Ahmet Yildirim, Deniz Gebze Technical University Department of Molecular Biology and Genetics Kocaeli Gebze41400 Turkey Kadir Has University of Science and Engineering Bioinformatics and Genetics Program İstanbul Fatih35430 Turkey Iğdır University Postgraduate Education Institute Department of Bioengineering and Sciences Iğdır Merkez76000 Turkey Cukurova University Faculty of Ceyhan Engineering Department of Chemical Engineering Adana Ceyhan01950 Turkey

Osmolytes play a critical role in enhancing the stability and activity of enzymes for industrial applications. This study systematically investigated the effects of various osmolytes on the activity, optimal pH, temperature, stability, metal ion effects, storage, and acrylamide mitigation performance of L-asparaginase from the thermophilic Geobacillus kaustophilus (GkASNase). The experimental findings were further supported by computationally integrated tools such as homology modeling, docking, and molecular dynamics (MD) simulations. Among the selected osmolytes (maltose, sorbitol, trehalose, glycine, and sucrose), GkASNase showed the highest stability during 30 days of storage in the presence of maltose and arginine. Maltose increased GkASNase activity approximately 2-fold at 37 °C and 55 °C. In the presence of osmolytes, the Km values of GkASNase decreased and the Vmax values increased compared to controls at 37 °C and 55 °C. In the presence of osmolytes, the acrylamide mitigation performance of GkASNase increased by 1.7-fold in a 15 min reaction. The computational analysis indicates that L-asparagine as substrate enhances protein compactness and stability, while arginine as osmolyte increases flexibility and optimizes water distribution around the enzyme. These findings provide novel insights into enzyme stabilization that have implications for therapeutic and biotechnological applications. © 2025 Elsevier B.V.

关键词： Maltose

来源：评论

学校读者我要写书评

暂无评论

Enabling technology and core theory of synthetic biology

引用

Science China(Life Sciences) 2023年第8期66卷 1742-1785页

作者： Xian-En Zhang Chenli Liu Junbiao Dai Yingjin Yuan Caixia Gao Yan Feng Bian Wu Ping Wei Chun You Xiaowo Wang Tong Si Faculty of Synthetic Biology Shenzhen Institute of Advanced TechnologyShenzhen 518055China Institute of Synthetic Biology Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Microbial Metabolism Shanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Tianjin Institute of Industrial Biotechnology Chinese Academy of SciencesTianjin 300308China Ministry of Education Key Laboratory of Bioinformatics Center for Synthetic and Systems BiologyBioinformatics DivisionBeijing National Research Center for Information Science and TechnologyDepartment of AutomationTsinghua UniversityBeijing 100084China

Synthetic biology provides a new paradigm for life science research(“build to learn”)and opens the future journey of biotechnology(“build to use”).Here,we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology,including synthesis and assembly of a genome,DNA storage,gene editing,molecular evolution and de novo design of function proteins,cell and gene circuit engineering,cell-free synthetic biology,artificial intelligence(AI)-aided synthetic biology,as well as *** also introduce the concept of quantitative synthetic biology,which is guiding synthetic biology towards increased accuracy and predictability or the real rational *** conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.

关键词： synthetic biology quantitative synthetic biology genome synthesis and assembly DNA storage molecular evolution de novo design computer-aided design cell engineering gene circuit chassis cell artificial intelligent(AI) biofoundry

来源：评论

学校读者我要写书评

暂无评论

MIXL1 activation in endoderm differentiation of human induced pluripotent stem cells

引用

Stem Cell Reports 2025年第5期20卷

作者： Osteil, Pierre Withey, Sarah Santucci, Nicole Aryamanesh, Nader Pang, Ignatius Salehin, Nazmus Sun, Jane Qin, Annie Su, Jiayi Knowles, Hilary Li, Xiucheng Bella Cai, Simon Wolvetang, Ernst Tam, Patrick P.L. Embryology Research Unit Children's Medical Research Institute University of Sydney Sydney Australia School of Medical Sciences Faculty of Medicine and Health University of Sydney Sydney Australia Australian Institute for Bioengineering and Nanotechnology University of Queensland Brisbane Australia Bioinformatics Group Children's Medical Research Institute University of Sydney Sydney Australia

Human induced pluripotent stem cells (hiPSCs) possess the ability to differentiate into a multitude of cell and tissue types but display heterogeneous propensity of differentiation into specific lineage. Characterization of the transcriptome of 11 hiPSC lines showed that activation of MIXL1 at the early stage of stem cell differentiation correlated with higher efficacy in generating definitive endoderm and advancing differentiation and maturation of endoderm derivatives. Enforced expression of MIXL1 in the endoderm-inefficient hiPSCs enhanced the propensity of endoderm differentiation, suggesting that modulation of key drivers of lineage differentiation can re-wire hiPSC to the desired lineage propensity to generate the requisite stem cell products. © 2025 The Author(s)

关键词： 2D gastruloids differentiation endoderm human induced pluripotent stem cells MIXL1 scRNA-seq

来源：评论

学校读者我要写书评

暂无评论

A Novel Approach Based on Voronoï Cells to Classify Spectrogram Zeros of Multicomponent Signals

A Novel Approach Based on Voronoï Cells to Classify Spectro...

引用

International Conference on Acoustics, Speech, and Signal Processing (ICASSP)

作者： N. Laurent S. Meignen M. A. Colominas J. M. Miramont F. Auger LJK University of Grenoble-Alpes and CNRS UMR 5224 Grenoble France Faculty of Engineering (UNER) Oro Verde Institute for Research and Development in Bioengineering and Bioinformatics (IBB UNER - CONICET) Entre Rios Argentina Institut de Recherche en Énergie Électrique de Nantes Atlantique (IREENA UR 4642) Nantes Université Saint-Nazaire France

In this paper, we propose a novel approach to classify the spectrogram zeros (SZs) of multicomponent signals based on the analysis of the Voronoï cells associated with these zeros. More precisely, the characterization of the distribution of the spectrogram maxima of a complex white Gaussian noise along the edges of the Voronoï cells associated with SZs enables us to derive an algorithm to classify the different types of zeros present in the spectrogram of a multicomponent signal. Numerical applications on simulated signals confirm the relevance of the proposed classification algorithm, and an illustration on a real signal concludes the paper.

关键词： Time-frequency analysis Gaussian noise Signal processing algorithms Interference Acoustics Classification algorithms Noise measurement

来源：评论

学校读者我要写书评

暂无评论

Utilizing ATeam Fluorescent Proteins for Assessing ATP Synthesis and Hydrolysis In Vitro and in Isolated Yeast Mitochondria

引用

Biochimica et Biophysica Acta (BBA) - Bioenergetics 2024年 1865卷

作者： Anna S. Lapashina Danila O. Tretyakov Kseniia V. Galkina Olga V. Markova Dmitry A. Knorre Boris A. Feniouk A.N.Belozersky Institute Lomonosov Moscow State University Moscow Russian Federation Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russian Federation

来源：评论

学校读者我要写书评

暂无评论

Erratum to: Pharmacological Doses of Thiamine Benefit Patients with the Charcot-Marie-Tooth Neuropathy by Changing Thiamine Diphosphate Levels and Affecting Regulation of Thiamine-Dependent Enzymes

引用

Biochemistry. Biokhimiia 2024年第8期89卷 1531-1532页

作者： Artem V Artiukhov Olga N Solovjeva Natalia V Balashova Olga P Sidorova Anastasia V Graf Victoria I Bunik Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University Moscow 119234 Russia. Department of Biochemistry Sechenov University Moscow 119991 Russia. Faculty of Advanced Medicine Vladimirsky Moscow Regional Research and Clinical Institute Moscow 129110 Russia. Faculty of Continuing Medical Education RUDN Medical Institute Moscow 117198 Russia. Department of Neurology Vladimirsky Moscow Regional Research and Clinical Institute Moscow 129110 Russia. Faculty of Biology Lomonosov Moscow State University Moscow 119234 Russia. Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University Moscow 119234 Russia. bunik@belozersky.msu.ru. Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow 119234 Russia.

来源：评论

学校读者我要写书评

暂无评论

Potassium homeostasis and signalling: from the whole plant to the subcellular level

引用

Quantitative Plant Biology 2025年 6卷 e13-e13页

作者： Wegner, Lars H. Pottosin, Igor Dreyer, Ingo Shabala, Sergey International Research Center for Environmental Membrane Biology School of Agriculture and Bioengineering Foshan University Foshan China Centro Universitario de Investigaciones Biomédicas Universidad de Colima Colima Mexico Electrical Signaling in Plants (ESP) Laboratory Center of Bioinformatics Simulation and Modeling (CBSM) Faculty of Engineering Universidad de Talca Talca Chile School of Biological Science University of Western Australia Crawley WA Australia

Potassium is an essential macronutrient required for plant growth and development. Over the recent decade, an important signalling role of K+ has emerged. Here, we discuss some aspects of such signalling at the variou... 详细信息

Potassium is an essential macronutrient required for plant growth and development. Over the recent decade, an important signalling role of K⁺ has emerged. Here, we discuss some aspects of such signalling at the various levels of plant functional organisation. The topic covered include: (1) mechanisms of long-distant K⁺ transport in the xylem and phloem and the molecular identity and regulation of K⁺ loading and unloading into plant vasculature;(2) essentiality and physiological roles of K⁺ cycling between shoots and roots;(3) plant sensing and signalling of low K⁺;(4) maintenance of K⁺ homeostasis at the cellular level;(5) stress-induced modulation of cytosolic K⁺ as a signal in plant adaptive responses to hostile environment;(6) stress-specific K⁺ signatures and mechanisms of their decoding by regulation of purine metabolism and H⁺-ATPase activity;(7) cytosolic K⁺ loss as a metabolic switch and a regulator of autophagy;and (8) vacuolar K⁺ transport and sensing. © 2025 The Author(s). Published by Cambridge University Press in association with John Innes Centre.

关键词： autophagy long-distance transport metabolic switch programmed cell death stress response

来源：评论

学校读者我要写书评

暂无评论

PLUMED Plugin Integration into High Performance Pmemd Program for Enhanced Molecular Dynamics Simulations

Supercomputing Frontiers and Innovations

引用

Supercomputing Frontiers and Innovations 2021年第4期8卷 94-99页

作者： Drobot, Viktor V. Kirilin, Evgeny M. Kopylov, Kirill E. Svedas, Vytas K. Lomonosov Moscow State University Belozersky Institute of Physicochemical Biology Moscow Russia Lomonosov Moscow State University Research Computing Center Moscow Russia Lomonosov Moscow State University Faculty of Bioengineering and Bioinformatics Moscow Russia

Metadynamics as an enhanced sampling procedure of molecular dynamics simulations is an effective tool to simulate complex molecular motions, conformations and reactivity, including enzyme plasticity and catalysis. The classic non-enhanced molecular simulation tools have reached unprecedently high performance utilizing GPU units, however their implementation for enhanced sampling are still on demand. The widespread AMBER (molecular dynamics package) + PLUMED (metadynamics plugin) still does not take advantage of GPU computing or the CPU utilization optimization included in the AMBER pmemd program. In this work we have developed PLUMED binding to pmemd program resolving performance issues within hybrid molecular dynamics/ metadynamics runs. Preliminary checks and test results of the model system have validated this implementation. © The Authors 2021. This paper is published with open access at ***

关键词： Molecular dynamics

来源：评论

学校读者我要写书评

暂无评论

Characterization of conformational flexibility in protein structures by applying artificial intelligence to molecular modeling

引用

Journal of Structural Biology 2025年第2期217卷

作者： Kopylov, Kirill Kirilin, Evgeny Voevodin, Vladimir Švedas, Vytas Lomonosov Moscow State University Research Computing Center Leninskie Gory 1-4 Moscow 119234 Russian Federation Lomonosov Moscow State University Belozersky Institute of Physicochemical Biology Leninskie Gory 1-40 Moscow 119992 Russian Federation Lomonosov Moscow State University Faculty of Bioengineering and Bioinformatics Leninskie Gory 1-73 Moscow 119991 Russian Federation Abu Dhabi United Arab Emirates

Recent AI applications have revolutionized the modeling of structurally unresolved protein regions, thereby complementing traditional computational methods. These state-of-the-art techniques can generate numerous candidate structures, significantly expanding the scope of structural biology. However, to effectively prioritize these models, a physics-based approach is required to assess the energy landscape. Such integration can bridge the gap between rapid model generation and precise determination of functional conformations. To address this challenge, we propose an integrated approach that combines molecular modeling with AI and HPC. Metadynamics simulations in latent space are used to explore potential energy landscapes based on initial approximations of flexible region structures derived from modeling tools such as AlphaFold, RosettaFold, Modeller, SwissModel, etc. The approach was validated by modeling folding of Trp-cage protein and conformational plasticity of ubiquitin. The predominant conformations of previously unresolved mobile regions in the active center of flavin-dependent 2-hydroxybiphenyl-3-monooxygenase (EC 1.14.13.44) were identified, while estimating the energy associated with these conformational changes. © 2025 Elsevier Inc.

关键词： 2-hydroxybiphenyl-3-monooxygenase substrate tunnel Hyperspherical latent space Modelled structure prioritization Protein conformational pathway Unresolved region modelling

来源：评论

学校读者我要写书评

暂无评论

Identification and characterization of conserved miRNAs from Gossypium hirsutum

引用

Ecological Genetics and Genomics 2022年 24卷

作者： Sakthivel, Seethalakshmi Mohideen, Habeeb Shaik Mohamad, Saharuddin Bin Bioinformatics & Entomoinformatics Lab Department of Genetic Engineering School of Bioengineering College of Engineering and Technology SRM Institute of Science and Technology Kattankulathur Chengalpattu 603203 Tamil Nadu India Institute of Biological Sciences. Faculty of Science University of Malaya Kuala Lumpur Malaysia

MicroRNAs (miRNA) are small non-coding RNA molecules of 21–25 nucleotides playing an important role in gene regulation of an organism. Regulatory role of miRNA in cellular and metabolic processes by binding to the target mRNA is reported from different forms of life. In this study, homology search based computational method was used to identify the conserved miRNAs in Gossypium hirsutum species from its EST sequences. We analyzed 337811 EST sequences of G. hirsutum against 8452 known plant miRNAs belonging to 73 plant species available in miRbase database using Blast program. Secondary structure prediction of the precursor sequences was done using MFOLD server. We identified 16 miRNAs from 15 families for which a phylogeny study was performed. Gene Ontology for the predicted miRNAs was done and the identified miRNAs where found to target transcripts having role in biosynthetic process, responses to chemicals, metabolic process regulation and many response related genes. These identified miRNAs can be used as biocontrol markers for plant's defense and its yield under the schema of Integrated Pest Management strategies. © 2022 Elsevier Inc.

关键词： Expressed sequence tag (EST) Gene ontology (GO) Gossypium hirsutum MFOLD MicroRNA (miRNA) Minimum free energy index (MFEI)

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：