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Isobaric enzymatic assays reveal depth-dependent variation in microbial ectoenzyme activities in the deepest ocean on Earth

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Science China Earth Sciences 2025年第1期68卷 185-194页

作者： Junwei CAO Jiahua WANG Hongge ZHANG Junhao DENG Binbin PAN Jiawang CHEN Li ZHANG Jiasong FANG College of Oceanography and Ecological Science Shanghai Ocean University Ocean College Zhejiang University laboratory for marine biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology

Microbial ectoenzymes play essential roles in the transformation and mineralization of organic matter in the ***, conventional methods for measuring microbial ectoenzyme activities(MEAs) in the deep ocean under atmospheric conditions can misrepresent the metabolic activities of indigenous microbial communities. To overcome this limitation, we measured the activities of three microbial ectoenzymes(aminopeptidase, α-glucosidase, and β-glucosidase) under both atmospheric and in situ pressure conditions in seawater collected using pressure-retaining and non-pressure-retaining samplers in the Challenger Deep, Mariana Trench. In the case of aminopeptidase and α-glucosidase, the highest isobaric MEAs were observed in the surface layer(50 m), followed by those at abyssopelagic depths(4,000–6,000 m) for aminopeptidase, hadal realm(10,903 m)for α-glucosidase, while β-glucosidase activity exhibited the highest value at 10,903 m. Furthermore, the isobaric MEAs in hadal waters were commonly found to be higher than the decompressed counterparts, highlighting the importance of pressure-retaining sampling and isobaric enzymatic assays. The half-saturation constant(Km) showed a general decreasing trend with depth,suggesting that the deep ocean microbes might have adapted to the high-pressure and oligotrophic environment by increasing their ectoenzyme's affinity to substrate. Furthermore, particle-free MEAs contribute more to the total MEAs in the deep ocean than particle-associated MEAs, suggesting the significance of cell-associated and dissolved ectoenzymes in ocean *** study provides a foundation for future investigations of MEAs in the ocean and has important implications for understanding the dynamics of microbially mediated biogeochemical cycling in marine ecosystems.

关键词： Pressure-retaining sampling Microbial ectoenzyme activity Deep-sea microbes High pressure Mariana Trench

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Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

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Science China Life Sciences 2025年第1期68卷 232-248页

作者： Yaohan Jiang Xiao Chen Chundi Wang Liping Lyu Saleh A.Al-Farraj Naomi A.Stover Feng Gao Key laboratory of Evolution & marine Biodiversity (Ministry of Education) and Institute of Evolution & marine Biodiversity Ocean University of China marine College Shandong University Zoology Department College of ScienceKing Saud University Department of biology Bradley University laboratory for marine biology and Biotechnology Qingdao Marine Science and Technology Center

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all *** protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages(three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication,transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase Ⅱ and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR,which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely t

关键词： sexual reproduction transcriptomic proteomic genome rearrangement PIWI NHEJ

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Advances in genotypic antimicrobialresistance testing: a comprehensive review

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Science China Life Sciences 2025年第1期68卷 130-143页

作者： Boheng Duan Xianjun Zeng Junping Peng Huan Kui College of Nanchang University Department of Imaging The Second Affiliated Hospital of Nanchang University NHC Key laboratory of Systems biology of Pathogens National Institute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical College Key laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical Sciences & Peking Union Medical College Key laboratory of Pathogen Infection Prevention and Control (Ministry of Education) State Key Laboratory of Respiratory Health and MultimorbidityNational Institute of Pathogen BiologyChinese Academy of Medical Sciences & Peking Union Medical College

Antimicrobial resistance(AMR) represents a substantial threat to global public health, complicating the treatment of common infections and leading to prolonged illness and escalated healthcare expenses. To effectively combat AMR, timely and accurate detection is crucial for AMR surveillance and individual-based therapy. Phenotypic antibiotic resistance testing(AST) has long been considered the gold standard in clinical applications, serving as the foundation for clinical AMR diagnosis and optimized therapy. It has significantly contributed to ensuring patients′ health and the development of novel antimicrobials. Despite advancements in automated culture-based AST technologies,inherent limitations impede the widespread use of phenotypic AST in AMR surveillance. Genotypic AST technologies offer a promising alternative option, exhibiting advantages of rapidity, high sensitivity, and specificity. With the continuous advancement and expanding applications of genotypic AST technologies, such as microfluidics, mass spectrometry, and high-resolution melting curve analysis, new vigor has been injected into the development and clinical implementation of genotypic AST technologies. In this narrative review, we discuss the principles, applications, and advancements of emerging genotypic AST methods in clinical settings. The comprehensive review aims to highlight the significant scientific potential of emerging genotypic AST technologies in clinical AMR diagnosis, providing insights to enhance existing methods and explore novel approaches.

关键词： antimicrobial resistance (AMR) genotypic antibiotic resistance testing (AST) AST technologies review

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Cobalamin-dependent radical S-adenosyl-L-methionine protein functions with a partner to successively methylate tricyclic indole alkaloid for chuangxinmycin maturation and derivatization

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Science China Chemistry 2025年第1期68卷 308-316页

作者： Sili Wang Jiancheng Huang Yanan Du Wei Huang Yufeng Xue Xiaokun Xu Guannan Zhong Yuanyuan Shi Bin Hong Xiaoying Bian Wen Liu State Key laboratory of Chemical biology Shanghai Institute of Organic Chemistry University of Chinese Academy of SciencesChinese Academy of Sciences State Key laboratory of Microbial Technology Shandong University National Health Commission (NHC) Key laboratory of Biotechnology for Microbial Drugs Institute of Medicinal BiotechnologyChinese Academy of Medical Science & Peking Union Medical College

Cobalamin(Cbl)-dependent radical S-adenosyl-L-methionine(SAM) proteins constitute the largest collection of the radical SAM superfamily that has hundreds of thousands of individual members. Many of these proteins are involved in the biosynthesis of pharmaceutically important natural products to catalyze chemically demanding reactions. In the biosynthetic pathway of chuangxinmycin(CXM), a unique indole alkaloid antibiotic with potent anti-infective activity, functionalization of the characteristic thiopyrano[4,3,2-cd]indole scaffold by regio-and stereoselective C3-methylation is believed to rely on a Cbl-dependent radical process, which, however, remained to be reconstituted biochemically. We here report the dissection of this enzymatic process, which requires the incorporation of Cxm8, a Cbl-dependent radical SAM protein, with Cxm9, a DUF5825family protein that shares no homology to any proteins of known functions. Cxm8 and Cxm9 function together by forming an unexpected heterodimeric complex that selectively catalyzes C3-methylation of the tricyclic indole-S-hetero ring system in a successive manner, achieving CXM and a recently identified, C3-dimethylated congener. Detailed biochemical characterization,isotope labeling, structural simulation and bioinformatics analysis rationalized the catalysis of the Cxm8/Cxm9 complex and particularly the necessity of the DUF5825 protein for C3-methylase activity. This is the first example that a Cbl-dependent protein acts with a partner to exhibit radical SAM activity.

关键词： cbl-dependent radical SAM protein biosynthesis chuangxinmycin stereoselective methylation

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Small heat shock protein B8:from cell functions to its involvement in diseases and potential therapeutic applications

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Neural Regeneration Research 2025年第10期20卷 2872-2886页

作者： Marta Chierichetti Riccardo Cristofani Valeria Crippa Veronica Ferrari Marta Cozzi Elena Casarotto Paola Pramaggiore Laura Cornaggia Guglielmo Patelli Ali Mohamed Margherita Piccolella Mariarita Galbiati Paola Rusmini Barbara Tedesco Angelo Poletti laboratory of Experimental biology Dipartimento di Scienze Farmacologiche e Biomolecolari“Rodolfo Paoletti”(DiSFeB)Universitàdegli Studi di MilanoMilanItaly

Heat shock protein family B(small)member 8(HSPB8)is a 22 kDa ubiquitously expressed protein belonging to the family of small heat shock ***8 is involved in various cellular mechanisms mainly related to proteotoxic stress response and in other processes such as inflammation,cell division,and ***8 binds misfolded clients to prevent their aggregation by assisting protein refolding or degradation through chaperone-assisted selective *** line with this function,the pro-degradative activity of HSPB8 has been found protective in several neurodegenerative and neuromuscular diseases characterized by protein misfolding and *** cancer,HSPB8 has a dual role being capable of exerting either a pro-or an anti-tumoral activity depending on the pathways and factors expressed by the model of cancer under ***,HSPB8 exerts a protective function in different diseases by modulating the inflammatory response,which characterizes not only neurodegenerative diseases,but also other chronic or acute conditions affecting the nervous system,such as multiple sclerosis and intracerebellar *** note,HSPB8 modulation may represent a therapeutic approach in other neurological conditions that develop as a secondary consequence of other *** is the case of cognitive impairment related to diabetes mellitus,in which HSPB8 exerts a protective activity by assuring mitochondrial *** review aims to summarize the diverse and multiple functions of HSPB8 in different pathological conditions,focusing on the beneficial effects of its ***-based and alternative therapeutic approaches targeting HSPB8 and its regulated pathways will be discussed,emphasizing how new strategies for cell and tissue-specific delivery represent an avenue to advance in disease treatments.

关键词： aggregation autophagy cancer chaperone chaperone-assisted selective autophagy cognitive impairment HSPB8 neuroinflammation neuromuscular diseases therapy

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Deciphering fungal metabolon coupling tandem inverse-electrondemand Diels-Alder reaction and semipinacol rearrangement for the biosynthesis of spiro polycyclic alkaloids

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Science China Chemistry 2025年第1期68卷 288-296页

作者： Shuai Liu Wen-Qiang Xu Ying-Tong Di Man-Cheng Tang Ding-Kang Chen Ming-Ming Cao Yao-Wen Chang Hong-Yu Tang Chun-Mao Yuan Jun-Bo Yang Zhi-Li Zuo Han Guo Zi-Fei Xu Ying Zeng Yun-Dong Wu Xiao-Jiang Hao Key laboratory of Phytochemistry and Natural Medicines (Chinese Academy of Sciences) Kunming Institute of Botany Chinese Academy of Sciences University of Chinese Academy of Sciences Lab of Computational Chemistry and Drug Design State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Shenzhen Bay laboratory State Key laboratory of Microbial Metabolism School of Life Sciences & Biotechnology Shanghai Jiao Tong University State Key laboratory of Functions and Applications of Medicinal Plants Guizhou Medical University Molecular biology Experimental Center Germplasm Bank of Wild Species in Southwest China Kunming Institute of Botany Chinese Academy of Sciences Yunnan Key laboratory for Wild Plant Resources Kunming Institute of Botany Chinese Academy of Sciences Research Unit of Chemical biology of Natural Anti-Virus Products Chinese Academy of Medical Sciences

In the intricate process of natural product biosynthesis, a metabolon can enhance metabolic flux by associating sequential enzymes. A fungal metabolon, comprising of flavin-dependent monooxygenase Spe F and P450 monooxygenase Spe G, is identified in the biosynthesis of spiro polycyclic alkaloids(+)-notoamide B and its diastereomer(+)-versicolamide B. Using notoamide E as a substance, Spe F/Spe G metabolon can control the stereoselectivity of its 2,3-epoxidation, followed by hydrogen atom ion at C-17 to generate reactive epoxide tau-m A with dienyl iminium unit. Subsequently,(+)-notoamide B and(+)-versicolamide B are produced via tandem nonenzymatic inverse-electron-demand Diels-Alder reaction and semipinacol rearrangement. This provides the first example of metabolon in the biosynthesis of spiro-prenylated indole alkaloids.

关键词： metabolon Diels-Alder reaction semipinacol rearrangement biosynthesis notoamides spiro polycyclic alkaloids

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Prospects on mangrove knowledge services in the smart era: From plant atlas to knowledge graphs

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Science China Earth Sciences 2025年第1期68卷 111-127页

作者： Zhi-Wei HOU Wenlong JING Cheng-Zhi QIN Ji YANG Qing XIA Xiaoling YIN Key laboratory of Guangdong for Utilization of Remote Sensing and Geographical Information System Guangdong Open Laboratory of Geospatial Information Technology and Application Guangzhou Institute of Geography Guangdong Academy of Sciences Southern marine Science and Engineering Guangdong laboratory (Guangzhou) State Key laboratory of Resources and Environmental Information System Institute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences College of Resources and Environment University of Chinese Academy of Sciences School of Traffic & Transportation Engineering Changsha University of Science and Technology

Mangroves are crucial to the ecological security of the Earth and human well-being. Their management, conservation, and restoration are of great importance and necessitate the support of spatio-temporal information and multidisciplinary knowledge such as biology and ecology. Traditional knowledge services such as plant atlas provide illustrated textual knowledge of mangroves. However, this kind of service is oriented to information retrieval and is incapable of effectively mining and utilizing fragmented knowledge from multi-source heterogeneous data, facing the problem of “massive data, rare knowledge”. Knowledge graphs are capable of extracting, organizing, and fusing the knowledge contained in massive data into semantic networks that can be understood and computed by computers. They provide a solution for the realization of intelligent knowledge services. Focusing on the urgent need for mangrove knowledge acquisition, formal representation, and intelligent services, this paper proposes a research prospect on mangrove knowledge graphs and knowledge services. We first analyze the similarities and differences between various domain-specific concepts of Tupu. On this basis, we define the mangrove knowledge graph as a large-scale knowledge base that integrates multi-disciplinary knowledge and spatio-temporal information with mangrove ecosystems as the core. Then, we propose a research framework for mangrove knowledge services that can realize the transformation from multi-modal data to intelligent knowledge services, including multiple research levels such as ubiquitous data sensing and aggregation, knowledge organization and graph construction, and intelligent mangrove knowledge services. Subsequently, the methods and workflow for constructing mangrove knowledge graphs are introduced. Finally, we discuss the challenges and possible future directions of mangrove knowledge services in the smart era, including the construction of a mangrove knowledge system that integra

关键词： Mangrove Tupu Knowledge graph Multi-modal Knowledge service

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Prolonged intermittent theta burst stimulation restores the balance between A_(2A)R-and A_(1)R-mediated adenosine signaling in the 6-hydroxidopamine model of Parkinson's disease

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Neural Regeneration Research 2025年第7期20卷 2053-2067页

作者： Milica Zeljkovic Jovanovic Jelena Stanojevic Ivana Stevanovic Milica Ninkovic Tihomir V.Ilic Nadezda Nedeljkovic Milorad Dragic laboratory for Neurobiology Department of General Physiology and BiophysicsFaculty of BiologyUniversity of BelgradeBelgradeSerbia Medical Faculty of Military Medical Academy University of DefenceBelgradeSerbia

An imbalance in adenosine-mediated signaling,particularly the increased A_(2A)R-mediated signaling,plays a role in the pathogenesis of Parkinson's *** therapeutic approaches fail to alter disease progression,demonstrating the need for novel approaches in *** transcranial magnetic stimulation is a non-invasive approach that has been shown to improve motor and non-motor symptoms of Parkinson's ***,the underlying mechanisms of the beneficial effects of repetitive transcranial magnetic stimulation remain *** purpose of this study is to investigate the extent to which the beneficial effects of prolonged intermittent theta burst stimulation in the 6-hydroxydopamine model of experimental parkinsonism are based on modulation of adenosine-mediated *** with unilateral 6-hydroxydopamine lesions underwent intermittent theta burst stimulation for 3 weeks and were tested for motor skills using the Rotarod ***,quantitative reverse transcription polymerase chain reaction,immunohistochemistry,and biochemical analysis of components of adenosine-mediated signaling were performed on the synaptosomal fraction of the lesioned caudate *** intermittent theta burst stimulation improved motor symptoms in 6-hydroxydopamine-lesioned animals.A 6-hydroxydopamine lesion resulted in progressive loss of dopaminergic neurons in the caudate *** with intermittent theta burst stimulation began 7 days after the lesion,coinciding with the onset of motor *** treatment with prolonged intermittent theta burst stimulation,complete motor recovery was *** improvement was accompanied by downregulation of the e N/CD73-A_(2A)R pathway and a return to physiological levels of A_(1)R-adenosine deaminase 1 after 3 weeks of intermittent theta burst *** results demonstrated that 6-hydroxydopamine-induced degeneration reduced the expression of A_(1)R and elevated the expression of A_(2A)***

关键词： A_(1)R A_(2A)R adenosine receptors adenosine ecto-5′-nucleotidase intermittent theta burst stimulation non-invasive brain stimulation Parkinson's disease purinergic signalling

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Effects of dietary supplementation of Ulva pertusa and non-starch polysaccharide enzymes on gut microbiota of Siganus canaliculatus

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Journal of Oceanology and Limnology 2018年第2期36卷 438-449页

作者： ZHANG Xinxu WU Huijuan LI Zhongzhen LI Yuanyou WANG Shuqi ZHU Dashi WEN Xiaobo LI Shengkang Guangdong Provincial Key laboratory of marine bioteehnology Shantou University Shantou 515063 China marine biology Institute Shantou University Shantou 515063 China

Fishes represent the highest diversity of vertebrates; however, our understanding of the compositions and functions of their gut microbiota is limited. In this study, we provided the first insight into the gut microbiota of the herbivorous fish Siganus eanalieulatus by using three molecular ecology techniques based on the 16S rRNA genes （denaturing gradient gel electrophoresis, clone library construction, and high- throughput Illumina sequencing）, and the Illumina sequencing technique is suggested here due to its higher overall coverage of the total 16S rRNA genes. A core gut microbiota of 29 bacterial groups, covering 〉99.9% of the total bacterial community, was found to be dominated by Proteobacteria and Firmicutes in fish fed three different diets with/without the supplementation of Ulva pertusa and non-starch polysaccharide （NSP） enzymes （cellulase, xylanase, and [3-glucanase）. Diverse potential NSP-degrading bacteria and probiotics （e.g., Ruminococcus, Clostridium and Lachnospiraceae） were detected in the intestine of the fish fed U. pertusa, suggesting that these microorganisms likely participated in the degradation of NSPs derived from U. pertusa. This study supports our previous conclusion that U. pertusa-based diets are suitable for the production ofS. eanaliculatus with lower costs without compromising quality.

关键词： aquaculture gut microbiota Siganus canaliculatus 16S rRNA gene Ulvapertusa

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Nanoscale and hollow inorganic sulfide@porous organic network doped intelligent hydrogels for accelerating diabetes wound therapeutics

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Science China Chemistry 2025年

作者： Yanhong Li Qiang Zhang Quanbo Wang Junping Wang Xiaomei Zhang Caixia Yin School of Chemistry and Chemical Engineering Shandong University Key laboratory of Chemical biology and Molecular Engineering of Ministry of Education Shanxi University

Diabetic wound healing remains a major challenge due to the excess hyperglycemia microenvironment,massively bacterial infections,macrophage dysfunction,and persistent *** comprehensively solve these problems,novel multifunctional materials are highly ***,a versatile and intelligent hydrogel (Cu2S@FePPOPTPM@GOx@Gel) is ***2S@FePPOPTPM@GOx with hollow morphology and controllable size was rationally designed and fabricated by using Cu2S nanocubes as a template,followed by in situ growth of FePPOPTPMand loading glucose oxidase （GOx）,*** infection occurs,the Schiff base bonds in Cu2S@FePPOPTPM@GOx@Gel can controllably release Cu2S@FePPOPTPM@GOx based on its excellent dynamic pH-responsiveness,thereby synergically reducing blood glucose levels and killing bacteria achieved relying on the excellent catalytic activity of GOx towards glucose and its promoted peroxidelike activity of *** experiments on diabetic wound model in vivo demonstrated that Cu2S@FePPOPTPM@GOx@Gel promoted wound healing and skin regeneration,which was attributed to its antibacterial properties,alleviating inflammation,stimulating vascular regeneration,and encouraging M2 polarization of *** work provides a novel strategy for the construction of a microenvironment-responsive and antibiotics-free drug delivery platform to treat diabetic wounds,as well as broad prospects of nanomaterials in the clinical treatment of chronic wounds.

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