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Guardians of the fragrance:Uncovering the genetics behind citrus oil glands

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Plant Communications 2024年第5期5卷 97-99页

作者： sunil kumar sahu Muhammad Imran State Key Laboratory of Agricultural Genomics Key Laboratory of GenomicsMinistry of AgricultureBGI ResearchShenzhen 518083China BGI Research Wuhan 430074China State Key Laboratory for Conservation and Utilization of Subtropical AgroBioresources College of AgricultureSouth China Agriculture UniversityGuangzhou 510642China Center for Plant Biology School of Life SciencesTsinghua UniversityBeijing 100084China

The colorful,nutrient-rich peels of citrus fruits have long been valued for their tangy flavors and aromatic *** oils are produced and stored in special secretory structures called oil glands,which are prevalent across citrus varieties(Knight et al.,2001).Oil glands serve as"reservoirs"for diverse metabolites such as terpenes and flavonoids that give citrus fruits their characteristic aroma(Mahato et al.,2019;Voo et al.,2012;Xian et al.,2022).Many of these compounds also act as chemical defenses against pest and pathogens(Fisher and Phillips,2008).

关键词： citrus Guard reservoirs

Haplotype-resolved and chromosome-scale genomes provide insights into co-adaptation between the Amur tiger and Amur leopard

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Zoological Research 2024年第3期45卷 464-467页

作者： Hai-Meng Li Bo-Yang Liu Min-Hui Shi Le Zhang Shang-Chen Yang sunil kumar sahu Liang-Yu Cui Shan-Lin Liu Nicolas Dussex Yue Ma Dan Liu Wei-Yao Kong Hao-Rong Lu Yue Zhao Love Dalén Huan Liu Tian-Ming Lan Guang-Shun Jiang Yan-Chun Xu College of Wildlife and Protected Area Northeast Forestry UniversityHarbinHeilongjiang 150040China State Key Laboratory of Agricultural Genomics BGI ResearchShenzhenGuangdong 518083China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China College of Life Sciences Zhejiang UniversityHangzhouZhejiang 310058China BGI Research WuhanHubei 430074China Department of Entomology College of Plant ProtectionChina Agricultural UniversityBeijing 100193China Centre for Palaeogenetics Svante Arrhenius väg 20CStockholm 10691Sweden Department of Zoology Stockholm UniversityStockholm 10691Sweden Department of Bioinformatics and Genetics Swedish Museum of Natural HistoryStockholm 10691Sweden Heilongjiang Siberian Tiger Park HarbinHeilongjiang 150000China Jinlin Provincial Academy of Forestry Science ChangchunJilin 130033China China National GeneBank BGI ResearchShenzhenGuangdong 518120China Guangdong Provincial Key Laboratory of Genome Read and Write BGI ResearchShenzhenGuangdong 518083China BGI Life Science Joint Research Center Northeast Forestry UniversityHarbinHeilongjiang 150040China Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected AreaNortheast Forestry UniversityHarbinHeilongjiang 150040China National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization HarbinHeilongjiang 150040China

DEAR EDITOR,Big cats,such as Amur tigers(Panthera tigris altaica)and Amur leopards(*** orientalis),are apex predator and have evolved specialized traits for hunting and carnivory(Moya et al.,2022),thus playing a crucial role in maintaining biodiversity and ecosystem integrity by regulating prey-predator ***,human-induced pressures,habitat fragmentation,and environmental alterations have restricted these species in small and isolated ***,all extant big cats are categorized as endangered or threatened according to their conservation *** tigers and Amur leopards share overlapping geographic ranges,habitats,and certain prey species in the forests of Northeast Asia(Jiang et al.,2015).To reduce interspecies conflict,these carnivores exhibit differentiated dietary and temporal *** tigers predominantly prey on large ungulates,while Amur leopards hunt small to medium-sized animals(Sugimoto et al.,2016).Additionally,they occupy different temporal niches,with tigers being active at night and leopards more active during the *** spatial and temporal niche partitioning,interspecific competition between these two species is ***,benefiting from their greater size,have a competitive advantage over leopards,which can manifest in occasional leopard predation by tigers and declines in leopard populations with increasing tiger density(Jiang et al.,2015).Tigers also displace leopards from marginal habitats in nature reserves where they coexist.

关键词： habitat Panthera resolved

Long-read sequencing(method of the year 2022):The way forward for plant omics research

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Molecular Plant 2023年第5期16卷 791-793页

作者： sunil kumar sahu Huan Liu State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhen 518083China College of Life Sciences University of Chinese Academy of SciencesBejing 100049China

Long-read sequencing(LRS)technology along with the recent development of computational tools,crowned the“method of the year 2022”(Marx,2023),have made it possible to sequence and assemble the genomes of practically every representative species(Kovaka et al.,2023).By considering its immense role and potential in advancing scientific research,the LRS market was valued at$1.35 billion in 2021 and is anticipated to reach$4.4 billion by 2031,growing at a compound annual growth rate of 14.4%from 2022 to 2031(***).Here,we discuss the current state and advantages of LRS technologies,the successful cases and novel discoveries with LRS,potential broad applications in plant genomics research,and the challenges that still need to be overcome in the future.

关键词： overcome crown method

Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges

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Journal of Genetics and Genomics 2023年第9期50卷 625-640页

作者： Mengnan Cheng Yujia Jiang Jiangshan Xu Alexios-Fotios AMentis Shuai Wang Huiwen Zheng sunil kumar sahu Longqi Liu Xun Xu BGI-Hangzhou HangzhouZhejiang 310012China BGI-Shenzhen ShenzhenGuangdong 518103China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhenGuangdong 518083China Guangdong Provincial Key Laboratory of Genome Read and Write ShenzhenGuangdong 518120China

The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology,from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing,by which the scientific community has been able to visualize life at an unprecedented *** recently,the Spatially Resolved Transcriptomics(SRT)technologies have filled the gap in probing the spatial or even three-dimensional organization of the molecular foundation behind the molecular mysteries of life,including the origin of different cellular populations developed from totipotent cells and human *** this review,we introduce recent progresses and challenges on SRT from the perspectives of technologies and bioinformatic tools,as well as the representative SRT *** the currently fast-moving progress of the SRT technologies and promising results from early adopted research projects,we can foresee the bright future of such new tools in understanding life at the most profound analytical level.

关键词： Spatially resolved transcriptomics Bioinformatic tools Spatial single-cell Cell communications Tissue dissection Three-dimensional organ

AI/ML Enabled Automation System for Software Defined Disaggregated Open Radio Access Networks:Transforming Telecommunication Business

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Big Data Mining and Analytics 2024年第2期7卷 271-293页

作者： sunil kumar Institute for Communication Systems University of SurreyGuildfordGU27XHUK

Open Air Interface(OAI)alliance recently introduced a new disaggregated Open Radio Access Networks(O-RAN)framework for next generation telecommunications and *** disaggregated architecture is open,automated,software defined,virtual,and supports the latest advanced technologies like Artificial Intelligence(AI)Machine Learning(AI/ML).This novel intelligent architecture enables programmers to design and customize automated applications according to the business needs and to improve quality of service in fifth generation(5G)and Beyond 5G(B5G).Its disaggregated and multivendor nature gives the opportunity to new startups and small vendors to participate and provide cheap hardware software solutions to keep the market *** paper presents the disaggregated and programmable O-RAN architecture focused on automation,AI/ML services,and applications with Flexible Radio access network Intelligent Controller(FRIC).We schematically demonstrate the reinforcement learning,external applications(xApps),and automation steps to implement this disaggregated O-RAN *** idea of this research paper is to implement an AI/ML enabled automation system for software defined disaggregated O-RAN,which monitors,manages,and performs AI/ML-related services,including the model deployment,optimization,inference,and training.

关键词： Artificial Intelligence(AI) Reinforcement Learning(RL) Open Radio Access Networks(O-RAN) Flexible Radio access network Intelligent Controller(FRIC) external Applications(xApps) Machine Learning(ML),sixth generation(6G)

A Cocktail of Natural Compounds Holds Promise for New Immunotherapeutic Potential in Head and Neck Cancer

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Chinese Journal of Integrative Medicine 2024年第1期30卷 42-51页

作者： sunil kumar Asmita Das Department of Biotechnology Delhi Technological UniversityDelhi(110042)India

Objective: To obtain detailed understanding on the gene regulation of natural compounds in altering prognosis of head and neck squamous cell carcinomas(HNSC). Methods: Gene expression data of HNSC samples and peripheral blood mononuclear cells(PBMCs) of HNSC patients were collected from Gene Expression Omnibus(GEO). Differential gene expression analysis of GEO datasets were achieved by the GEO2R tool. Common differentially expressed gerres(DEGs) were screened by comparing DEGs of HNSC with those of PBMCs. The combination was further analyzed for regulating pathways and biological processes that were affected. Results: Totally 110 DEGs were retrieved and identified to be involved in biological processes related to tumor regulation. Then 102 natural compounds were screened for a combination such that the expressions of all 110 commonly DEGs were altered. A combination of salidroside, ginsenoside Rd, oridonin, britanin, and scutellarein was chosen. A multifaceted, multi-dimensional tumor regression was showed by altering autophagy, apoptosis, inhibiting cell proliferation, angiogenesis, metastasis and inflammatory cytokines production. Conclusions: This study has helped develop a unique combination of natural compounds that will markedly reduce the propensity of development of drug resistance in tumors and immune evasion by tumors. The result is crucial to developing a combinatorial natural therapeutic cocktail with accentuated immunotherapeutic potential.

关键词： natural compounds chemopreventive gene expression head and neck cancer immunomodulator salidroside ginsenoside Rd oridonin britanin scutellarein

Dissecting the genome of star fruit(Averrhoa carambola L.)

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Horticulture Research 2020年第1期7卷 1626-1635页

作者： Yannan Fan sunil kumar sahu Ting Yang Weixue Mu Jinpu Wei Le Cheng Jinlong Yang Ranchang Mu Jie Liu Jianming Zhao Yuxian Zhao Xun Xu Xin Liu Huan Liu State Key Laboratory of Agricultural Genomics China National GeneBankBGIShenzhen518120 ShenzhenChina BGI-Yunnan BGI-Shenzhen650106 KunmingChina Forestry Bureau of Ruili Yunnan Dehong678600 RuiliChina Chinese Academy of Forestry BeijingChina Guangdong Provincial Key Laboratory of Genome Read and Write 518120 ShenzhenChina BGI-Fuyang BGI-Shenzhen236009 FuyangChina Department of Biology University of CopenhagenCopenhagenDenmark

Averrhoa carambola is commonly known as star fruit because of its peculiar shape,and its fruit is a rich source of minerals and *** is also used in traditional medicines in countries such as India,China,the Philippines,and Brazil for treating various ailments,including fever,diarrhea,vomiting,and skin ***,we present the first draft genome of the Oxalidaceae family,with an assembled genome size of 470.51 *** total,24,726 protein-coding genes were identified,and 16,490 genes were annotated using various well-known *** phylogenomic analysis confirmed the evolutionary position of the Oxalidaceae *** on the gene functional annotations,we also identified enzymes that may be involved in important nutritional pathways in the star fruit ***,the data from this first sequenced genome in the Oxalidaceae family provide an essential resource for nutritional,medicinal,and cultivational studies of the economically important star-fruit plant.

关键词： vitamin Brazil cultivation

Bile acid metabolism and signaling in health and disease:molecular mechanisms and therapeutic targets

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Signal Transduction and Targeted Therapy 2024年第5期9卷 2014-2064页

作者： Joshua S.Fleishman sunil kumar Department of Pharmaceutical Sciences College of Pharmacy and Health SciencesSt.John’s UniversityQueensNYUSA

Bile acids,once considered mere dietary surfactants,now emerge as critical modulators of macronutrient(lipid,carbohydrate,protein)metabolism and the systemic pro-inflammatory/anti-inflammatory *** acid metabolism and signaling pathways play a crucial role in protecting against,or if aberrant,inducing cardiometabolic,inflammatory,and neoplastic conditions,strongly influencing health and *** curative treatment exists for any bile acid influenced disease,while the most promising and well-developed bile acid therapeutic was recently rejected by the ***,we provide a bottom-up approach on bile acids,mechanistically explaining their biochemistry,physiology,and pharmacology at canonical and non-canonical *** this mechanistic model of bile acids,we explain how abnormal bile acid physiology drives disease pathogenesis,emphasizing how ceramide synthesis may serve as a unifying pathogenic feature for cardiometabolic *** provide an in-depth summary on pre-existing bile acid receptor modulators,explain their shortcomings,and propose solutions for how they may be ***,we rationalize novel targets for further translational drug discovery and provide future *** than dismissing bile acid therapeutics due to recent setbacks,we believe that there is immense clinical potential and a high likelihood for the future success of bile acid therapeutics.

关键词： metabolism rejected shortcomings

Polyunsaturated fatty acid-producing marine thraustochytrids:A potential source for antimicrobials

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Journal of Coastal Life Medicine 2015年第11期 848-851页

作者： Kaliyamoorthy Kalidasan sunil kumar sahu Kasinathan Kayalvizhi Kandasamy Kathiresan Centre of Advanced Study in Marine Biology Faculty of Marine SciencesAnnamalai UniversityParangipettai-608502Tamil NaduIndia

Objective:To evaluate the antimicrobial activity of marine thraustochytrids extracted from different ***:Crude extracts were derived from marine thraustochytrids,isolated from decaying mangrove leaf *** extracts were tested for antibacterial activity by using agar disc diffusion method against 10 clinical bacterial *** extracts were also analysed for presence of functional chemical groups by using Fourier transform infrared ***:Thraustochytrid extracts exhibited potent antibacterial activity against both Gramnegative and-positive *** antibacterial activity was observed prominently in butanol extract,followed by petroleum ether,methanol and chloroform *** antibacterial activity was maximum[(21.33±1.52)mm]against Staphylococcus aureus and minimum[(7.00±2.00)]mm against Klebsiella pneumonia and Salmonella ***:Thraustochytrids isolated from decaying mangrove leaf litter are potential sources of antibacterial compounds against clinical pathogens,which are called for further investigation of thraustochytrids as natural antibiotics.

关键词： Mangrove Leaf litter Thraustochytrids Polyunsaturated fatty acid Antibacterial activity