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RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages

Virologica Sinica 2024年第1期39卷 156-168页

作者： Changqiao You Shuai Jiang Yunyun Ding Shunxing Ye Xiaoxiao Zou Hongming Zhang Zeqi Li Fenglin Chen Yongliang Li Xingyi Ge Xinhong Guo college of Biology Hunan UniversityChangsha410082China college of bioscience and biotechnology Hunan Agricultural UniversityChangsha410128China

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the pathogen responsible for coronavirus disease 2019(COVID-19),continues to evolve,giving rise to more variants and global *** research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related *** this study,we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples,including human coronaviruses(HCoVs)and SARSr-CoV-2 *** sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets,encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 *** genetic-level species testing,we validated the accuracy and reliability of the barcode segments for identifying ***,75 main and subordinate species-specific barcode segments for SARS-CoV-2,located in ORF1ab,S,E,ORF7a,and N coding sequences,were intercepted and screened based on single-nucleotide polymorphism sites and weighted ***-testing,these segments exhibited high recall rates(nearly 100%),specificity(almost 30%at the nucleotide level),and precision(100%)performance on *** were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database(http://***/).The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism ***,this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.

关键词： RNA barcode segments SARS-CoV-2 variants and related lineages HCoVs Genetic tests Complete genome sequences

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

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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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Is it now possible to transition from laparoscopic liver resection to robotic liver resection?

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Hepatobiliary Surgery and Nutrition 2024年第3期13卷 557-559页

作者： Kyeong Sik Kim Dae Won Jun Department of General Surgery College of MedicineHanyang UniversitySeoulKorea Department of Internal Medicine College of MedicineHanyang UniversitySeoulKorea Hanyang Institute of bioscience and biotechnology Hanyang UniversitySeoulKorea

Minimally invasive surgery(MIS)has significantly progressed and emerged as the preferred approach for various gastrointestinal procedures,including gastrectomy,cholecystectomy,and various colorectal surgeries(1).However,the widespread acceptance of robotic surgery in liver resection has encountered obstacles,attributed to factors such as the lack of appropriate surgical instruments,the intricate learning curve,and safety ***,the utilization of MIS in liver resection is linked to decreased blood loss,reduced post-operative pain,shorter hospital stays,and lower morbidity rates compared to both open and laparoscopic liver resection procedures(2).

关键词： Laparoscopic liver resection robotic liver resection minimally invasive surgery(MIS)

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Molecular mechanisms underlying the negative effects of transient heatwaves on crop fertility

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Plant Communications 2024年第9期5卷 101-115页

作者： Qian Yao Ping Li Xin Wang Shuhua Liao Pu Wang Shoubing Huang college of Agronomy and biotechnology China Agricultural UniversityBeijing 100193China

Transient heatwaves occurring more frequently as the climate warms,yet their impacts on crop yield are severely underestimated and even *** lasting only a few days or even hours during sensitive stages,such as microgametogenesis and flowering,can significantly reduce crop yield by disrupting plant *** advances in multi-omics and GWAS analysis have shed light on the specific organs(e.g.,pollen,lodicule,style),key metabolic pathways(sugar and reactive oxygen species metabolism,Ca2+homeostasis),and essential genes that are involved in crop responses to transient heatwaves during sensitive *** review therefore places particular emphasis on heat-sensitive stages,with pollen development,floret opening,pollination,and fertilization as the central narrative *** multifaceted effects of transient heatwaves and their molecular basis are systematically reviewed,with a focus on key structures such as the lodicule and tapetum.A number of heat-tolerance genes associated with these processes have been identified in major crops like maize and *** mechanisms and key heat-tolerance genes shared among different stages may facilitate the more precise improvement of heat-tolerant crops.

关键词： heat stress floret fertility pollen pollen tube growth seed set molecular mechanism

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Higher levels of the lipophilic antioxidants coenzyme Q_(10) and vitamin E in long-lived termite queens than in short-lived workers

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Insect Science 2024年第1期31卷 201-210页

作者： Eisuke Tasaki Yorihiro Yamamoto Yoshihito Iuchi Department of Biological Chemistry Graduate School of Sciences and Technology for InnovationYamaguchi UniversityYamaguchiJapan School of bioscience and biotechnology Tokyo University of TechnologyHachiojiTokyoJapan

Termite queens and kings live longer than nonreproductive *** molecular mechanisms contributing to their long lifespan have been investigated;however,the underlying biochemical explanation remains *** Q(CoQ),a component of the mitochondrial electron transport chain,plays an essential role in the lipophilic antioxidant defense *** beneficial effects on health and longevity have been well studied in several ***,we demonstrated that long-lived termite queens have significantly higher levels of the lipophilic antioxidant CoQ_(10) than *** chromatography analysis revealed that the levels of the reduced form of CoQ_(10) were 4 fold higher in the queen's body than in the worker's *** addition,queens showed 7 fold higher levels of vitamin E,which plays a role in antilipid peroxidation along with CoQ,than ***,the oral administration of CoQ_(10) to termites increased the CoQ_(10) redox state in the body and their survival rate under oxidative *** findings suggest that CoQ_(10) acts as an efficient lipophilic antioxidant along with vitamin E in long-lived termite *** study provides essential biochemical and evolutionary insights into the relationship between CoQ_(10) concentrations and termite lifespan extension.

关键词： antioxidant defense system coenzyme Q termite queens vitamin E

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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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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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P-induced electron transfer interaction for enhanced selective hydrogenation rearrangement of furfural to cyclopentanone

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Journal of Energy Chemistry 2024年第5期92卷 43-51页

作者： Weichen Wang Hongke Zhang Yidan Wang Fangyuan Zhou Zhiyu Xiang Wanbin Zhu Hongliang Wang Center of Biomass Engineering College of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China

Optimizing the intrinsic activity of non-noble metal by precisely tailoring electronic structure offers an appealing way to construct cost-effective catalysts for selective biomass ***,we reported a P-doping bifunctional catalyst(Ni-P/mSiO_(2))that achieved 96.6%yield for the hydrogenation rearrangement of furfural to cyclopentanone at mild conditions(1 MPaH_(2),150°C).The turnover frequency of Ni-P/mSiO_(2)was 411.9 h^(-1),which was 3.2-fold than that of Ni/mSiO_(2)(127.2 h^(-1)).Detailed characterizations and differential charge density calculations revealed that the electron-deficient Niδ+species were generated by the electron transfer from Ni to P,which promoted the ring rearrangement *** functional theory calculations illustrated that the presence of P atoms endowed furfural tilted adsorb on the Ni surface by the C=O group and facilitated the desorption of *** work unraveled the connection between the localized electronic structures and the catalytic properties,so as to provide a promising reference for designing advanced catalysts for biomass valorization.

关键词： Furfural Hydrogenation rearrangement P-doping Electron transfer Biomass valorization

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CRISPR/CasRx-mediated resistance to Soybean mosaic virus in soybean

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The Crop Journal 2024年第4期12卷 1093-1101页

作者： Le Gao Lijun Xie Yanmin Xiao Xinge Cheng Ruosi Pu Ziheng Zhang Yu Liu Shaopei Gao Zilong Zhang Haoran Qu Haijian Zhi Kai Li MARA Key Laboratory of Biology and Genetics Improvement of Soybean Zhongshan Biological Breeding Laboratory(ZSBBL)National Innovation Platform for Soybean Breeding and Industry-Education IntegrationState Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjing 210095JiangsuChina Department of Horticulture Beijing Vocational College of AgricultureBeijing 102442China college of Agronomy&biotechnology China Agricultural UniversityBeijing 100193China college of bioscience and biotechnology Shenyang Agricultural UniversityShenyang 110866LiaoningChina

Soybean mosaic virus(SMV),an RNA virus,is the most common and destructive pathogenic virus in soybean *** newly developed CRISPR/Cas immune system has provided a novel strategy for improving plant resistance to viruses;hence,this study aimed to engineer SMV resistance in soybean using this ***,multiple sgRNAs were designed to target positive-and/or negative-sense strands of the SMV HC-Pro ***,the corresponding CRISPR/CasRx vectors were constructed and transformed into *** inoculation with SMV,39.02%,35.77%,and 18.70%of T_(1)plants were confirmed to be highly resistant(HR),resistant(R),and mildly resistant(MR)to SMV,respectively,whereas only 6.50%were identified as susceptible(S).Additionally,qRT-PCR and DAS-ELISA showed that,both at 15 and 30 d post-inoculation(dpi),SMV accumulation significantly decreased or was even undetectable in HR and R plants,followed by MR and S ***,the expression level of the CasRx gene varied in almost all T_(1)plants with different resistance level,both at 15 and 30 ***,when SMV resistance was evaluated in the T_(2)generation,the results were similar to those recorded for the T_(1)*** findings provide new insights into the application of the CRISPR/CasRx system for soybean improvement and offer a promising alternative strategy for breeding for resistance to biotic stress that will contribute to the development of SMV-immune soybean germplasm to accelerate progress towards greater soybean crop productivity.

关键词： Soybean RNA virus Soybean mosaic virus Resistance CRISPR/CasRx

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