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KoNA:Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data

Genomics, Proteomics & Bioinformatics 2024年第1期22卷 161-167页

作者： Gunhwan Ko Jae Ho Lee Young Mi Sim Wangho Song Byung-Ha Yoon Iksu Byeon Bang Hyuck Lee Sang-Ok Kim Jinhyuk Choi Insoo Jang Hyerin Kim Jin Ok Yang Kiwon Jang Sora Kim Jong-Hwan Kim Jongbum Jeon Jaeeun Jung Seungwoo Hwang Ji-Hwan Park Pan-Gyu Kim Seon-Young Kim Byungwook Lee Korea Bioinformation Center Korea Research Institute of Bioscience&BiotechnologyDaejeon 34141Republic of Korea

During the last decade,the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges,including access to human data,as well as transfer,storage,and sharing of enormous amounts of *** promote data-driven biological research,the Korean government announced that all biological data generated from government-funded research projects should be deposited at the Korea BioData Station(K-BDS),which consists of multiple databases for individual data ***,we introduce the Korean Nucleotide Archive(KoNA),a repository of nucleotide sequence *** of July 2022,the Korean Read Archive in KoNA has collected over 477 TB of raw next-generation sequencing data from national genome *** ensure data quality and prepare for international alignment,a standard operating procedure was adopted,which is similar to that of the International Nucleotide Sequence Database *** standard operating procedure includes quality control processes for submitted data and metadata using an automated pipeline,followed by manual *** ensure fast and stable data transfer,a high-speed transmission system called GBox is used in ***,the data uploaded to or downloaded from KoNA through GBox can be readily processed using a cloud computing service called *** seamless coupling of KoNA,GBox,and Bio-Express enhances the data experience,including submission,access,and analysis of raw nucleotide *** not only satisfies the unmet needs for a national sequence repository in Korea but also provides datasets to researchers globally and contributes to advances in *** KoNA is available at https://***/kona/.

关键词： Korea BioData Station Nucleotide sequence Next-generation sequencing repository Genomics Deposition and access of big data

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Magnetic Fields Reduce Apoptosis by Suppressing Phase Separation of Tau-441

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research 2024年第1期2023卷 181-197页

作者： Wen-Juan Lin Wen-Pu Shi Wan-Yi Ge Liang-Liang Chen Wei-Hong Guo Peng Shang Da-Chuan Yin Key laboratory for Space bioscience and Biotechnology School of Life SciencesNorthwestern Polytechnical University127 Youyixi RoadXi'an 710072ShaanxiPR China

The biological effects of magnetic fields(MFs)have been a controversial ***,in recent years,there has been increasing evidence that MFs do affect biological ***,the physical mechanism remains ***,we show that MFs(16 T)reduce apoptosis in cell lines by inhibiting liquid–liquid phase separation(LLPS)of Tau-441,suggesting that the MF effect on LLPS may be one of the mechanisms for understanding the“mysterious”magnetobiological *** LLPS of Tau-441 occurred in the cytoplasm after induction with *** phase-separated droplets of Tau-441 recruited hexokinase(HK),resulting in a decrease in the amount of free HK in the *** cells,HK and Bax compete to bind to the voltage-dependent anion channel(VDAC I)on the mitochondrial membrane.A decrease in the number of free HK molecules increased the chance of Bax binding to VDAC I,leading to increased Bax-mediated *** the presence of a static MF,LLPS was marked inhibited and HK recruitment was reduced,resulting in an increased probability of HK binding to VDAC I and a decreased probability of Bax binding to VDAC I,thus reducing Bax-mediated *** findings revealed a new physical mechanism for understanding magnetobiological effects from the perspective of *** addition,these results show the potential applications of physical environments,such as MFs in this study,in the treatment of LLPS-related diseases.

关键词： inhibited Apoptosis finding

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Property evolution and service life prediction of novel metallic materials for future lunar bases

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Rare Metals 2024年第10期43卷 5318-5331页

作者： Sen-Kuan Meng Rui-Song Zhu Hong-Liang Zheng Tong Gao Shi-Hao Jiang Wen-Hao Wang Shu-Hao Zhang Zi-Yuan Zhao Xuan Ge Wei-Min Wang Li-Na Hu Zheng Wang Key laboratory for Liquid-Solid Structural Evolution and Processing of Materials (Ministry of Education) School of Materials Science and EngineeringShandong University Department of Chemistry and bioscience Aalborg University

While lunar bases have been a focus of development in recent years, the complex and extreme environment of the lunar surface remains a considerable challenge for lunar exploration. Unlike those on Earth,lunar day and night temperature variations cause the properties of materials, especially metallic materials, to evolve in completely different manners. In this study, we investigated the property evolution of nine typical highperformance metallic materials using laboratory simulations of the extremely long-period lunar temperature environment. While lunation treatment improves the properties of all metallic materials, the microscopic mechanisms vary for amorphous and crystalline alloys with different structures. The treatment reduces both the loosely packed regions and heterogeneity in amorphous alloys while causing significant phase changes in crystalline alloys. Furthermore, a conservative prediction of the service life of metallic materials on lunar bases is provided based on analyzing microplastic events, followed by the practical material selection recommendations in various lunar application scenarios.

关键词： Lunar exploration Metallic glass Metallic material Property evolution

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Glutamate oxidase-integrated biomimetic Fe_(3)O_(4) hybrids as cascade nanozymes for glutamate detection

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Particuology 2024年第5期88卷 192-200页

作者： Peikun Li Yanchao Wang Xiuyan Luo Zixin Geng Jiahui Jia Ruirui Wang Jiandong Cui Hongjie Bian Shiru Jia State Key laboratory of Food Nutrition and Safety Laboratory of Industrial Fermentation MicrobiologyMinistry of EducationTianjin University of Science and TechnologyTianjin300457China Sports Department Hebei University of Science and TechnologyShijiazhang050000China research Center for Fermentation Engineering of Hebei College of Bioscience and BioengineeringHebei University of Science and TechnologyShijiazhang050000China

Herein,a new nanozyme/natural enzyme hybrid biosensor was established for ultrasensitive l-glutamic acid(L-Glu)*** Fe_(3)O_(4) nanoparticles with peroxidase-like activity and stability was used as a nanozyme and carrier for immobilizing l-Glutamate oxidase(GLOD)through Schiffff base reaction to construct a chem-enzyme cascade *** resultant Fe_(3)O_(4)-GOLD exhibited a wide linear range(10−500μM)and a low detection limit of 6.03μM for L-Glu ***,the Fe_(3)O_(4)-GOLD exhibited excellent pH stability,thermal stability,reusability and storage *** repeated nine cycles,Fe_(3)O_(4)-GOLD still retained 70%of its initial ***,Fe_(3)O_(4)-GOLD maintained 50%of its initial activity after storage for 20 days,while free GLOD only retained 20%of its initial *** strategy of integrating biomimetic Fe 3 O4 and natural enzymes for cascade catalysis makes it possible to design an efficient and stable chemo-enzyme composite catalysts,which are promising for applications in biosensing and biomimetic catalysis.

关键词： Fe_(3)O_(4) nanozyme GLOD Chemo-enzymes Glutamate detection

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Dietary nutrition, intestinal microbiota dysbiosis and post-weaning diarrhea in piglets

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Animal Nutrition 2024年第2期17卷 188-207页

作者： Xuebing Han Xiangdong Hu Wei Jin Gang Liu Department of Urology Shengjing Hospital of China Medical University College of bioscience and Biotechnology Hunan Agricultural University Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry State Key laboratory of Subtropical Silviculture Zhejiang A&F University

Weaning is a critical transitional point in the life cycle of piglets. Early weaning can lead to post-weaning syndrome, destroy the intestinal barrier function and microbiota homeostasis, cause diarrhea and threaten the health of piglets. The nutritional components of milk and solid foods consumed by newborn animals can affect the diversity and structure of their intestinal microbiota, and regulate post-weaning diarrhea in piglets. Therefore, this paper reviews the effects and mechanisms of different nutrients,including protein, dietary fiber, dietary fatty acids and dietary electrolyte balance, on diarrhea and health of piglets by regulating intestinal function. Protein is an essential nutrient for the growth of piglets;however, excessive intake will cause many harmful effects, such as allergic reactions, intestinal barrier dysfunction and pathogenic growth, eventually aggravating piglet diarrhea. Dietary fiber is a nutrient that alleviates post-weaning diarrhea in piglets, which is related to its promotion of intestinal epithelial integrity, microbial homeostasis and the production of short-chain fatty acids. In addition, dietary fatty acids and dietary electrolyte balance can also facilitate the growth, function and health of piglets by regulating intestinal epithelial function, immune system and microbiota. Thus, a targeted control of dietary components to promote the establishment of a healthy bacterial community is a significant method for preventing nutritional diarrhea in weaned piglets.

关键词： Diarrhea Intestinal barrier Dietary protein Dietary fiber Dietary fatty acid Dietary electrolyte balance

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Leaf Morphology Genes SRL1 and RENL1 Co-Regulate Cellulose Synthesis and Affect Rice Drought Tolerance

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Rice science 2024年第1期31卷 103-117,I0020-I0022页

作者： LIU Dan ZHAO Huibo WANG Zi’an XU Jing LIU Yiting WANG Jiajia CHEN Minmin LIU Xiong ZHANG Zhihai CEN Jiangsu ZHU Li HU Jiang REN Deyong GAO Zhenyu DONG Guojun ZHANG Qiang SHEN Lan LI Qing QIAN Qian HU Songping ZHANG Guangheng State Key laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China research Center of Plant Functional Genes and Tissue Culture Technology College of Bioscience and BioengineeringJiangxi Agricultural UniversityNanchang 330045China Qian Qian Academician Workstation National Nanfan Research Institute(Sanya)Chinese Academy of Agricultural SciencesSanya 572024China

The morphological development of rice(Oryza sativa L.)leaves is closely related to plant architecture,physiological activities,and ***,it is unclear whether there is a co-regulatory relationship between the morphological development of leaves and adaptation to drought *** this study,a drought-sensitive,roll-enhanced,and narrow-leaf mutant(renl1)was induced from a semi-rolled leaf mutant(srl1)by ethyl methane sulfonate(EMS),which was obtained from Nipponbare(NPB)through ***-based cloning and functional validation showed that RENL1 encodes a cellulose synthase,allelic to NRL1/*** RENL1 mutation resulted in reduced vascular bundles,vesicular cells,cellulose,and hemicellulose contents in cell walls,diminishing the water-holding capacity of *** addition,the root system of the renl1 mutant was poorly developed and its ability to scavenge reactive oxygen species(ROS)was decreased,leading to an increase in ROS after drought ***,genetic results showed that RENL1 and SRL1 synergistically regulated cell wall *** results revealed a theoretical basis for further elucidating the molecular regulation mechanism of cellulose on rice drought tolerance,and provided a new genetic resource for enhancing the synergistic regulation network of plant type and stress resistance,thereby realizing simultaneous improvement of multiple traits in rice.

关键词： cellulose cell wall drought tolerance leaf morphology rice

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Deciphering the controlling factors for phase transitions in zeolitic imidazolate frameworks

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National Science Review 2024年第4期11卷 151-163页

作者： Tao Du Shanwu Li Sudheer Ganisetti Mathieu Bauchy Yuanzheng Yue Morten M.Smedskjaer Department of Chemistry and bioscience Aalborg University Department of Mechanical Engineering-Engineering Mechanics Michigan Technological University Physics of Amo Rphous and Inorganic Solids laboratory(PARISlab) Department of Civil and Environmental EngineeringUniversity of CaliforniaLos Angeles

Zeolitic imidazolate frameworks（ZIFs） feature complex phase transitions, including polymorphism,melting, vitrification, and polyamorphism. Experimentally probing their structural evolution during transitions involving amorphous phases is a significant challenge, especially at the medium-range length scale. To overcome this challenge, here we first train a deep learning-based force field to identify the structural characteristics of both crystalline and non-crystalline ZIF phases. This allows us to reproduce the structural evolution trend during the melting of crystals and formation of ZIF glasses at various length scales with an accuracy comparable to that of ab initio molecular dynamics, yet at a much lower computational cost. Based on this approach, we propose a new structural descriptor, namely, the ring orientation index, to capture the propensity for crystallization of ZIF-4(Zn（Im）2, Im = C3H3N2-) glasses, as well as for the formation of ZIF-zni(Zn（Im）2) out of the high-density amorphous phase. This crystal formation process is a result of the reorientation of imidazole rings by sacrificing the order of the structure around the zinc-centered tetrahedra. The outcomes of this work are useful for studying phase transitions in other metal-organic frameworks（MOFs） and may thus guide the development of MOF glasses.

关键词： metal-organic frameworks phase transitions melting glass formation transferable deep learning force field ring orientation

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Linking of Chemical Reactions and Silica Nanoparticle Contact Using Synthetic Helical Molecules

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Chinese Journal of Chemistry 2024年第15期42卷 1781-1796页

作者： Sheng Zhang Ming Bao Mieko Arisawa Masahiko Yamaguchi state Key laboratory of Fine Chemicals Dalian University of TechnologyDalianLiaoning 116024China Department of bioscience and Biotechnology Graduate Schoolof Bioresource and Bioenvironmental SciencesKyushu UniversityFukuoka 819-0395Japan

Biological cells exhibit diverse phenomena induced through linking of chemical reactions of molecules and solid surface *** is then a significant topic in the field of chemistry to study phenomena induced through this linking using synthetic systems,which can promote our understanding of biological phenomena and can be applied to the development of novel *** nanoparticles(sNPs),which are synthetic inorganic materials,are attractive for such purposes,because of their following characteristics:they can adsorb large amounts of molecules on their surfaces,they can aggregate through contact between SNPs as well as contact between molecules and SNPs,and the molecules can be easily removed from solutions by *** contact of sNP surfaces with molecules then affects chemical reactions of molecules and also behaviors of *** article describes systems derived from synthetic helical molecules and sNPs,which exhibit notable phenomena including selective adsorption and molecular recognition,equilibrium shift,step kinetics with induction period,precipitation with flow and sweeping,and disaggregation and desorption by sonication,in which the high affinity of helical molecules with sNP surfaces plays important *** models that explain the phenomena are *** applications are also discussed,including the separation of molecules,capture of intermediates,the storage and release of molecules,equilibrium shift,clocking,and the translation of mechanical stimulations into chemical reactions.

关键词： Silica nanoparticles Chemical reactions Molecular recognition Linking Nanoparticles Adsorption Chirality Precipitation

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Exploring the modulatory role of bovine lactoferrin on the microbiome and the immune response in healthy and Shiga toxin‑producing *** challenged weaned piglets

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Journal of Animal Science and Biotechnology 2024年第3期15卷 1278-1291页

作者： Matthias Dierick Ruben Ongena Daisy Vanrompay Bert Devriendt Eric Cox laboratory of Immunology Department of Translational PhysiologyInfectiology and Public HealthFaculty of Veterinary MedicineGhent UniversitySalisburylaan 1339820 MerelbekeBelgium laboratory for Immunology and Animal Biotechnology Faculty of Bioscience EngineeringGhent UniversityCoupure links 6539000 GhentBelgium

Background Post-weaned piglets suffer from F18+Escherichia coli(***)infections resulting in post-weaning diar-rhoea or oedema *** used management strategies,including colistin and zinc oxide,have contrib-uted to the emergence and spread of antimicrobial *** antimicrobials capable of directly interacting with pathogens and modulating the host immune responses are being *** has shown promising results against porcine enterotoxigenic *** strains,both in vitro and in *** We investigated the influence of bovine lactoferrin(bLF)on the microbiome of healthy and infected weaned ***,we assessed whether bLF influenced the immune responses upon Shiga toxin-producing ***(STEC)***,2 in vivo trials were conducted:a microbiome trial and a challenge infection trial,using an F18+STEC *** did not affect theα-andβ-***,bLF groups showed a higher relative abundance(RA)for the Actinobacteria phylum and the Bifidobacterium genus in the ileal *** analysing the immune response upon infection,the STEC group exhibited a significant increase in F18-specific IgG serum levels,whereas this response was absent in the bLF *** Taken together,the oral administration of bLF did not have a notable impact on theα-andβ-diversity of the gut microbiome in weaned ***,it did increase the RA of the Actinobacteria phylum and Bifi-dobacterium genus,which have previously been shown to play an important role in maintaining gut ***,bLF administration during STEC infection resulted in the absence of F18-specific serum IgG responses.

关键词： E.coli Immune modulation Lactoferrin Microbiome

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Drosophila X virus-like particles as delivery carriers for improved oral insecticidal efficacy of scorpion Androctonus australis peptide against the invasive fruit fly,Drosophila suzukii

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Insect Science 2024年第3期31卷 847-858页

作者： Qi Xue Luc Swevers Clauvis Nji Tizi Taning Faculty of bioscience Engineering Department of Plants and CropsGhent UniversityGhentBelgium Insect Molecular Genetics and Biotechnology Institute of Biosciences and ApplicationsNational Centre for Scientific Research"Demokritos"AthensGreece

Insect-specific neurotoxic peptides derived from the venoms of scorpions and spiders can cause acute paralysis and death when injected into insects,offering a promising insecticidal component for insect pest ***,effective delivery systems are required to help neurotoxic peptides pass through the gut barrier into the hemolymph,where they can ***,we investigated the potential of a novel nanocarrier,Drosophila X virus-like particle(DXV-VLP),for delivering a neurotoxin from the scorpion Androctonus australis Hector(AaIT)against the invasive pest fruit fly,Drosophila *** results show that the fusion proteins of DXV polyproteins with AalT peptide at their Ctermini could be sufficiently produced in Lepidoptera Hi5 cells in a soluble form using the recombinant baculovirus expression system,and could self-assemble into VLPs with similar particle morphology and size to authentic DXV *** addition,the AalT peptides displayed on DXV-VLPs retained their toxicity,as demonstrated in injection bioassays that resulted in severe mortality(72%)in adults after 72 *** fed to adults,mild mortality was observed in the group treated with DXV-AalT(38%),while no mortality occurred in the group treated with AaIT peptide,thus indicating the significant role of DXV-VLPs in delivering AalT ***,this proof-of-concept study demonstrates for the first time that VLPs can be exploited to enhance oral delivery of insect-specific neurotoxic peptides in the context of pest ***,it provides insights for further improvements and potentially the development of neurotoxin-based bioinsecticides and/or transgenic crops for insect pest control.

关键词： AalT Drosophila suzuki nanocarrier neurotoxic peptides pest control virus-like particle(VLP)

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