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Widespread and active piezotolerant microorganisms mediate phenolic compound degradation under high hydrostatic pressure in hadal trenches

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marine Life Science & Technology 2024年第2期6卷 331-348页

作者： Hao Ling Yongxin Lv Yu Zhang Ning‑Yi Zhou Ying Xu state Key laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China School of Oceanography Shanghai Jiao Tong UniversityShanghai 200240China state Key of laboratory of Ocean engineering Shanghai Jiao Tong UniversityShanghai 200240China

Phenolic compounds,as well as other aromatic compounds,have been reported to be abundant in hadal trenches.Although high-throughput sequencing studies have hinted at the potential of hadal microbes to degrade these compounds,direct microbiological,genetic and biochemical evidence under in situ pressures remain absent.Here,a microbial consortium and a pure culture of Pseudomonas,newly isolated from Mariana Trench sediments,efficiently degraded phenol under pressures up to 70 and 60 MPa,respectively,with concomitant increase in biomass.By analyzing a high-pressure(70 MPa)culture metatranscriptome,not only was the entire range of metabolic processes under high pressure generated,but also genes encod-ing complete phenol degradation via ortho-and meta-cleavage pathways were revealed.The isolate of Pseudomonas also contained genes encoding the complete degradation pathway.Six transcribed genes(dmpKLMNOP_(sed))were functionally identified to encode a multicomponent hydroxylase catalyzing the hydroxylation of phenol and its methylated derivatives by heterogeneous expression.In addition,key catabolic genes identified in the metatranscriptome of the high-pressure cultures and genomes of bacterial isolates were found to be all widely distributed in 22 published hadal microbial metagenomes.At microbiological,genetic,bioinformatics,and biochemical levels,this study found that microorganisms widely found in hadal trenches were able to effectively drive phenolic compound degradation under high hydrostatic pressures.This information will bridge a knowledge gap concerning the microbial aromatics degradation within hadal trenches.

关键词： Hadal trench High hydrostatic pressure Phenolic compounds degradation Piezotolerant microorganisms Widespread distribution

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A novel flow electrode capacitive deionization device with spindle-shaped desalting chamber

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Frontiers of Environmental Science & engineering 2024年第4期18卷 1-4页

作者： Yunke Li Junjun Ma Chenxu Yang Jianrui Niu Yonghuan Bian Ruicheng Chen Puming Zhang Jing Zhang Chun Liu College of Environmental Science and engineering Hebei University of Science and TechnologyShijiazhuang 050018China Pollution Prevention biotechnology laboratory of Hebei province Shijiazhuang 050018China

Flow-electrode capacitive deionization(FCDI)is an innovative technology in which an intermediate chamber plays an important role in the desalination process.However,relatively few studies have been conducted on the structures of these intermediate chambers.In this study,we propose a novel flow-electrode capacitive deionization device with a spindle-shaped inlet chamber(S-FCDI).The desalination rate of the S-FCDI under optimal operating conditions was 36%higher than that of the FCDI device with a conventional rectangular chamber(R-FCDI).The spindle-shaped chamber transferred 1.2μmol more ions than the rectangular chamber,based on energy per joule.Additionally,we performed a detailed analysis of different inlet chamber shapes using computational fluid dynamics software.We concluded that S-FCDI has a relatively low flow resistance and almost no stagnation zone.This provides unique insights into the development of intermediate chambers.This study may contribute to the improvement of the desalination performance in industrial applications of FCDI.

关键词： Spindle-shaped chamber Desalination performance Flow electrode capacitive deionization

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Identification of an immune-related gene signature for predicting prognosis and immunotherapy efficacy in liver cancer via cell-cell communication

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World Journal of Gastroenterology 2024年第11期30卷 1609-1620页

作者： Jun-Tao Li Hong-Mei Zhang Wei Wang Dong-Qing Wei College of Mathematics and Information Science Henan Normal UniversityXinxiang 453007Henan ProvinceChina College of Computer and Information engineering Henan Normal UniversityXinxiang 453007Henan ProvinceChina state Key laboratory of Microbial Metabolism and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China

BACKGROUND Liver cancer is one of the deadliest malignant tumors worldwide.Immunotherapy has provided hope to patients with advanced liver cancer,but only a small fraction of patients benefit from this treatment due to individual differences.Identifying immune-related gene signatures in liver cancer patients not only aids physicians in cancer diagnosis but also offers personalized treatment strategies,thereby improving patient survival rates.Although several methods have been developed to predict the prognosis and immunotherapeutic efficacy in patients with liver cancer,the impact of cell-cell interactions in the tumor microenvir-onment has not been adequately considered.AIM To identify immune-related gene signals for predicting liver cancer prognosis and immunotherapy efficacy.METHODS Cell grouping and cell-cell communication analysis were performed on single-cell RNA-sequencing data to identify highly active cell groups in immune-related pathways.Highly active immune cells were identified by intersecting the highly active cell groups with B cells and T cells.The significantly differentially expressed genes between highly active immune cells and other cells were subsequently selected as features,and a least absolute shrinkage and selection operator(LASSO)regression model was constructed to screen for diagnostic-related features.Fourteen genes that were selected more than 5 times in 10 LASSO regression experiments were included in a multivariable Cox regression model.Finally,3 genes(stathmin 1,cofilin 1,and C-C chemokine ligand 5)significantly associated with survival were identified and used to construct an immune-related gene signature.RESULTS The immune-related gene signature composed of stathmin 1,cofilin 1,and C-C chemokine ligand 5 was identified through cell-cell communication.The effectiveness of the identified gene signature was validated based on experi-mental results of predictive immunotherapy response,tumor mutation burden analysis,immune cell infiltration analysis,survival analysis,and expression an

关键词： Liver cancer Cell-cell communication Gene signature Prognosis Immunotherapy Single-cell RNA sequencing

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Dynamic shielding of bacterial outer membrane vesicles for safe and efficient chemo-immunotherapy against tumors

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Nano Research 2024年第2期17卷 836-847页

作者： Shuping Li Xin Li Jiaqi Meng Weier Bao Shuang Wang Peng Ye Xiao-Dong Gao Wei Wei Key laboratory of Carbohydrate Chemistry and biotechnology Ministry of Education School of BiotechnologyJiangnan UniversityWuxi 214122China state Key laboratory of Biochemical engineering Institute of Process EngineeringChinese Academy of SciencesBeijing 100190China School of Chemical engineering University of Chinese Academy of SciencesBeijing 100049China

Bacterial outer membrane vesicles(OMVs)are potent immunostimulants of regulating the tumor microenvironment(TME)for immunotherapy,and can be used to deliver drugs.However,the severe systemic inflammatory response triggered by OMVs upon intravenous(i.v.)injection has limited their application.Here,we developed a safe and effective strategy by conjugating doxorubicin-loaded serum albumin(SA-DOX,AD)onto the surface of OMVs using a matrix metalloproteinase(MMP)-cleavable peptide linker(cL).This approach enabled the dynamic shielding of OMVs to reduce the systemic side effects while simultaneously enhancing the anti-tumor effects through chemo-immunotherapy.Specifically,the resulting OMV-cL-AD formulation exhibited significantly enhanced accumulation at the tumor site after i.***.administration,facilitated by the SA decoration on the OMVs surface.Subsequently,the shield on the OMV-cL-AD was cleaved by the over-expressed MMP in the TME,leading to the release of both OMVs and AD.This process provided OMV-induced immunotherapy and DOX-induced chemotherapy,resulting in synergistic tumor inhibition.In conclusion,our work demonstrated the potential of OMV-cL-AD as an effective immunochemotherapy strategy that can prolong the survival time of mice without inducing side effects.

关键词： outer membrane vesicles doxorubicin tumor microenvironment immunotherapy chemotherapy

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A chitosan-based antibacterial hydrogel with injectable and self-healing capabilities

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marine Life Science & Technology 2024年第1期6卷 115-125页

作者： Rui Chen Yanan Hao Secundo Francesco Xiangzhao Mao Wen-Can Huang state Key laboratory of marine Food Processing and Safety Control College of Food Science and EngineeringOcean University of ChinaQingdao 266404China laboratory for marine Drugs and Bioproducts of Qingdao National laboratory for marine Science and Technology Qingdao 266237China Qingdao Key laboratory of Food biotechnology Qingdao 266404China Key laboratory of Biological Processing of Aquatic Products China National Light IndustryQingdao 266404China Istituto di Scienze e Tecnologie Chimiche“Giulio Natta” Consiglio Nazionale delle Ricerche via Mario Bianco 920131 MilanItaly

The presence of bacteria directly affects wound healing.Chitosan-based hydrogel biomaterials are a solution as they offer advantages for wound-healing applications due to their strong antimicrobial properties.Here,a double-cross-linking chitosanbased hydrogel with antibacterial,self-healing,and injectable properties is reported.Thiolated chitosan was successfully prepared,and the thiolated chitosan molecules were cross-linked by Ag-S coordination to form a supramolecular hydrogel.Subsequently,the amine groups in the thiolated chitosan covalently cross-linked with genipin to further promote hydrogel formation.In vitro experimental results indicate that hydrogel can release Ag^(+)over an extended time,achieving an antibacterial rate of over 99% against Escherichia coli and Staphylococcus aureus.Due to the reversible and dynamic feature of Ag-S coordination,an antibacterial hydrogel exhibited injectable and self-healing capabilities.Additionally,the hydrogel showed excellent biocompatibility and biodegradability.

关键词： Hydrogel Chitosan Silver ion Cross-linking Antibacterial

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Aptasensing biosynthesized phosphatidylserine with a AuNPs nanozyme-based colorimetric aptasensor

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Food Science and Human Wellness 2024年第2期13卷 823-829页

作者： Sai Wang Rui Ma Chengqiang Li Ling Zhang Haiyang Zhang Xuehan Li Xiangzhao Mao Qingdao Key laboratory of Food biotechnology College of Food Science and EngineeringOcean University of ChinaQingdao 266404China Key laboratory of Biological Processing of Aquatic Products China National Light IndustryQingdao 266404China laboratory for marine Drugs and Bioproducts of Qingdao National laboratory for marine Science and Technology Qingdao 266237China

Sensitive monitoring of the target products during the biosynthesis process is crucial,and facile analytical approaches are urgently needed.Herein,phosphatidylserine(PS)was chosen as the model target,a colorimetric aptasensor was developed for the rapid quantitation in biosynthesis samples.A chimeric aptamer was constructed with two homogeneous original PS aptamers.Specific recognition between the chimeric aptamer and PS results in the desorption of aptamer from the surface of the AuNPs nanozyme,and the peroxidase-like enzymatic activity of the AuNPs nanozyme was weakened in a relationship with the different concentrations.The developed aptasensor performed well when applied for analyzing PS in biosynthesis samples.The aptasensor offers good sensitivity and selectivity,under optimal conditions,achieving monitoring and quantitation of PS in the range of 2.5-80.0μmol/L,with a limit of detection at 536.2 nmol/L.Moreover,the aptasensor provides good accuracy,with comparison rates of 98.17%-106.40%,when compared with the HPLC-ELSD.This study provides a good reference for monitoring other biosynthesized products and promoting the development of aptamers and aptasensors in real-world applications.

关键词： Phosphatidylserine Chimeric aptamer AuNPs nanozyme Colorimetric aptasensor

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Flow Field Characteristics of Multi-Trophic Artificial Reef Based on Computation Fluid Dynamics

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Journal of Ocean University of China 2024年第2期23卷 317-327页

作者： HUANG Junlin LI Jiao LI Yan GONG Pihai GUAN Changtao XIA Xu School of engineering Ocean University of ChinaQingdao 266100China Yellow Sea Fisheries Research Institute Chinese Academy of Fishery SciencesKey Laboratory of Sustainable Development of Marine FisheriesMinistry of Agriculture and Rural AffairsQingdao Key Laboratory for Marine Fish Breeding and BiotechnologyQingdao 266071China laboratory for marine Fisheries Science and Food Production Processes Pilot National Laboratory for Marine Science and Technology(Qingdao)Qingdao 266071China

On the basis of computational fluid dynamics,the flow field characteristics of multi-trophic artificial reefs,including the flow field distribution features of a single reef under three different velocities and the effect of spacing between reefs on flow scale and the flow state,were analyzed.Results indicate upwelling,slow flow,and eddy around a single reef.Maximum velocity,height,and volume of upwelling in front of a single reef were positively correlated with inflow velocity.The length and volume of slow flow increased with the increase in inflow velocity.Eddies were present both inside and backward,and vorticity was positively correlated with inflow velocity.Space between reefs had a minor influence on the maximum velocity and height of upwelling.With the increase in space from 0.5 L to 1.5 L(L is the reef lehgth),the length of slow flow in the front and back of the combined reefs increased slightly.When the space was 2.0 L,the length of the slow flow decreased.In four different spaces,eddies were present inside and at the back of each reef.The maximum vorticity was negatively correlated with space from 0.5 L to 1.5 L,but under 2.0 L space,the maximum vorticity was close to the vorticity of a single reef under the same inflow velocity.

关键词： artificial reef flow field characteristics computation fluid dynamics multi-trophic structure

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Enhanced extracellular production of alpha-lactalbumin from Bacillus subtilis through signal peptide and promoter screening

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Food Science and Human Wellness 2024年第4期13卷 2310-2316页

作者： Yuqi Zhu Pengdong Sun Chunjian Li Yu Zhang Yu Wang Jingyuan Li Yanfeng Liu Jian Chen Yang Deng College of Food Science and engineering Qingdao Agricultural UniversityQingdao 266109China Key laboratory of Special Food Processing(Co-construction by Ministry and province) Ministry of Agriculture Rural AffairsQingdao Agricultural UniversityQingdao 266109China Qingdao Special Food Research Institute Qingdao 266109China Science Center for Future Foods Engineering Research Center of Ministry of Education on Food Synthetic BiotechnologyJiangsu Province Engineering Research Center of Food Synthetic BiotechnologyJiangnan UniversityWuxi 214122China Key laboratory of Carbohydrate Chemistry and biotechnology Ministry of EducationSchool of BiotechnologyJiangnan UniversityWuxi 214122China

Alpha-lactalbumin(α-LA)is a major whey protein found in breast milk and plays a crucial role in the growth and development of infants.In this study,Bacillus subtilis RIK1285 harboring AprE signal peptide(SP)was selected as the original strain for the production ofα-LA.It was found thatα-LA was identified in the pellet after ultrasonic disruption and centrifugation instead of in the fermentation supernatant.The original strain most likely only producedα-LA intracellular,but not extracellular.To improve the expression and secretion ofα-LA in RIK1285,a library of 173 homologous SPs from the B.subtilis 168 genome was fused with target LALBA gene in the pBE-S vector and expressed extracellularly in RIK1285.SP YjcN was determined to be the best signal peptide.Bands in supernatant were observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and purified by nickel column to calculate the highest yield signal peptide.In addition,different promoters(P_(aprE),P_(43),and P_(glv))were compared and applied.The results indicated that the strain RIK1285-pBE-P_(glv)-YjcN-LALBA had the highestα-LA yield,reaching 122.04μg/mL.This study demonstrates successful expression and secretion of humanα-LA in B.subtilis and establishes a foundation for simulating breast milk for infant formulas and developing bioengineered milk.

关键词： Bacillus subtilis Alpha-lactalbumin Bioengineering milk Signal peptide Promoter screening

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RebL1 is required for macronuclear structure stability and gametogenesis in Tetrahymena thermophila

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marine Life Science & Technology 2024年第2期6卷 183-197页

作者： Huijuan Hao Yinjie Lian Chenhui Ren Sitong Yang Min Zhao Tao Bo Jing Xu Wei Wang Key laboratory of Chemical Biology and Molecular engineering of Ministry of Education Institute of BiotechnologyShanxi UniversityTaiyuan 030006China School of Life Science Shanxi UniversityTaiyuan 030006China Shanxi Key laboratory of biotechnology Taiyuan 030006China

Histone modification and nucleosome assembly play important roles in chromatin-related processes.Histone chaperones form different complexes and coordinate histone transportation and assembly.Various histone chaperone complexes have been identified in different organisms.The ciliate protozoa(ciliates)have various chromatin structures and different nuclear morphology.However,histone chaperone components and functions of different subunits remain unclear in ciliates.Tet-rahymema thermophila contains a transcriptionally active macronucleus(MAC)and a transcriptionally inactive micronu-cleus(MIC)which exhibit multiple replication and various chromatin remodeling progresses during vegetative growth and sexual developmental stages.Here,we found histone chaperone RebL1 not only localized evenly in the transcriptionally active MAC but also dynamically changed in the MIC during vegetative growth and sexual developmental stages.REBL1 knockdown inhibited cellular proliferation.The macronuclear morphology became bigger in growing mutants.The abnormal macronuclear structure also occurred in the starvation stage.Furthermore,micronuclear meiosis was disturbed during sexual development,leading to a failure to generate new gametic nuclei.RebL1 potentially interacted with various factors involved in histone-modifying complexes and chromatin remodeling complexes in different developmental stages.REBL1 knockdown affected expression levels of the genes involved in chromatin organization and transcription.Taken together,RebL1 plays a vital role in maintaining macronuclear structure stability and gametogenesis in T.thermophila.

关键词： Gametogenesis Histone chaperone Macronuclear structure RebL1 Tetrahymena thermophilaIntroduction

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The emerging roles of lysine-specific demethylase 4A in cancer:Implications in tumorigenesis and therapeutic opportunities

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Genes & Diseases 2024年第2期11卷 645-663页

作者： Guanjun Yang Changyun Li Fan Tao Yanjun Liu Minghui Zhu Yu Du Chenjie Fei Qiusheng She Jiong Chen state Key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products Ningbo UniversityNingboZhejiang 315211China School of Life Science and engineering Henan University of Urban ConstructionPingdingshanHenan 467044China laboratory of Biochemistry and Molecular Biology School of Marine SciencesNingbo UniversityNingboZhejiang 315211China Key laboratory of Aquacultural biotechnology Ministry of Education Ningbo UniversityNingboZhejiang 315211China

Lysine-specific demethylase 4 A(KDM4A,also named JMJD2A,KIA0677,or JHDM3A)is a demethylase that can remove methyl groups from histones H3K9me2/3,H3K36me2/3,and H1.4K26me2/me3.Accumulating evidence suggests that KDM4A is not only involved in body homeostasis(such as cell proliferation,migration and differentiation,and tissue development)but also associated with multiple human diseases,especially cancers.Recently,an increasing number of studies have shown that pharmacological inhibition of KDM4A significantly attenuates tumor progression in vitro and in vivo in a range of solid tumors and acute myeloid leukemia.Although there are several reviews on the roles of the KDM4 subfamily in cancer development and therapy,all of them only briefly introduce the roles of KDM4A in cancer without systematically summarizing the specific mechanisms of KDM4A in various physiological and pathological processes,especially in tumorigenesis,which greatly limits advances in the understanding of the roles of KDM4A in a variety of cancers,discovering targeted selective KDM4A inhibitors,and exploring the adaptive profiles of KDM4A antagonists.Herein,we present the structure and functions of KDM4A,simply outline the functions of KDM4A in homeostasis and non-cancer diseases,summarize the role of KDM4A and its distinct target genes in the development of a variety of cancers,systematically classify KDM4A inhibitors,summarize the difficulties encountered in the research of KDM4A and the discovery of related drugs,and provide the corresponding solutions,which would contribute to understanding the recent research trends on KDM4A and advancing the progression of KDM4A as a drug target in cancer therapy.

关键词： Cancer therapy Drug resistance Histone demethylation JmjC domain KDM4A

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