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Food Science and Human Wellness 2024年第2期13卷 801-812页

作者： Cui Li shuhui song Yanan He Haijie Liu College of Food Science and Nutritional Engineering China Agricultural UniversityBeijing 100083China Institute of Agri-food Processing and Nutrition Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China

Glucosinolates are important phytochemicals in Brassicaceae.We investigated the effect of CaCl_(2)-HCl electrolyzed water(CHEW)on glucosinolates biosynthesis in broccoli sprouts.The results showed that CHEW treatment significantly decreased reactive oxygen species(ROS)and malondialdeh yde(MDA)contents in broccoli sprouts.On the the 8^(th)day,compared to tap water treatment,the the total glucosinolate content of broccoli sprouts with CHEW treatment increased by 10.6%and calcium content was dramatically enhanced from 14.4 mg/g DW to 22.7 mg/g DW.Comparative transcriptome and metabolome analyses revealed that CHEW treatment activated ROS and calcium signaling transduction pathways in broccoli sprouts and they interacted through MAPK cascades.Besides,CHEW treatment not only promoted the biosynthesis of amino acids,but also enhanced the expression of structural genes in glucosinolate synthesis through transcription factors(MYBs,bHLHs,WRKYs,etc.).The results of this study provided new insights into the regulatory network of glucosinolates biosynthesis in broccoli sprouts under CHEW treatment.

关键词： Broccoli sprouts CaCl_(2)-HCl electrolyzed water Glucosinolates Transcriptomics Metabolomics

Plant genomic resources at National Genomics Data Center:assisting in data-driven breeding applications

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aBIOTECH 2024年第1期5卷 94-106页

作者： Dongmei Tian Tianyi Xu Hailong Kang Hong Luo Yanqing Wang Meili Chen Rujiao Li Lina Ma Zhonghuang Wang Lili Hao Bixia Tang Dong Zou Jingfa Xiao Wenming Zhao Yiming Bao Zhang Zhang shuhui song National Genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems,including the constituent elements within and among species.Through various efforts in genomic data archiving,integrative analysis and value-added curation,the National Genomics Data Center(NGDC),which is a part of the China National Center for Bioinformation(CNCB),has successfully established and currently maintains a vast amount of database resources.This dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research efforts.Here,we present a comprehensive overview of central repositories dedicated to archiving,presenting,and sharing plant omics data,introduce knowledgebases focused on variants or gene-based functional insights,highlight species-specific multiple omics database resources,and briefly review the online application tools.We intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

关键词： Plant-omics data Data repositories Data integration Knowledgebase Plant genomics

Progress in oncolytic viruses modified with nanomaterials for intravenous application

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维普期刊数据库

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Cancer Biology & Medicine 2023年第11期20卷 830-855页

作者： Liting Chen Zhijun Ma Chen Xu Youbang Xie Defang Ouyang shuhui song Xiao Zhao Funan Liu Department of Surgical Oncology and General Surgery Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal TumorsMinistry of EducationThe First Affiliated Hospital of China Medical UniversityShenyang 110001China Phase IClinical Trials Center Ministry of EducationThe First Affiliated Hospital of China Medical UniversityShenyang 110102China CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety CAS Center for Excellence in NanoscienceNational Center for Nanoscience and TechnologyBejing 100190China Department of General Surgery Panjin People's HospitalPanjin 124221China Department of Hematology and Rheumatology Qinghai Provincial People's HospitalXining 810007China State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical Sciences(ICMS)University of MacaoMacao 999078China Center of Materials Science and Optoelectronics Engineering University of Chinese Academy of SciencesBejing 100049China IGDB-NCNST Joint Research Center Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

In oncolytic virus(OV)therapy,a critical component of tumor immunotherapy,viruses selectively infect,replicate within,and eventually destroy tumor cells.Simultaneously,this therapy activates immune responses and mobilizes immune cells,thereby eliminating residual or distant cancer cells.However,because of OVs’high immunogenicity and immune clearance during circulation,their clinical applications are currently limited to intratumoral injections,and their use is severely restricted.In recent years,numerous studies have used nanomaterials to modify OVs to decrease virulence and increase safety for intravenous injection.The most commonly used nanomaterials for modifying OVs are liposomes,polymers,and albumin,because of their biosafety,practicability,and effectiveness.The aim of this review is to summarize progress in the use of these nanomaterials in preclinical experiments to modify OVs and to discuss the challenges encountered from basic research to clinical application.

关键词： Oncolytic virus nanomaterials drug delivery tumor treatment intravenous application

RCoV19:A One-stop Hub for SARS-CoV-2 Genome Data Integration,Variant Monitoring,and Risk Pre-warning

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Genomics, Proteomics & Bioinformatics 2023年第5期21卷 1066-1079页

作者： Cuiping Li Lina Ma Dong Zou Rongqin Zhang Xue Bai Lun Li Gangao Wu Tianhao Huang Wei Zhao Enhui Jin Yiming Bao shuhui song National Genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Sino-Danish College University of Chinese Academy of SciencesBeijing 100049China

The Resource for Coronavirus 2019(RCoV19)is an open-access information resource dedicated to providing valuable data on the genomes,mutations,and variants of the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).In this updated implementation of RCoV19,we have made significant improvements and advancements over the previous version.Firstly,we have implemented a highly refined genome data curation model.This model now features an automated integration pipeline and optimized curation rules,enabling efficient daily updates of data in RCoV19.Secondly,we have developed a global and regional lineage evolution monitoring platform,alongside an outbreak risk pre-warning system.These additions provide a comprehensive understanding of SARS-CoV-2 evolution and transmission patterns,enabling better preparedness and response strategies.Thirdly,we have developed a powerful interactive mutation spectrum comparison module.This module allows users to compare and analyze mutation patterns,assisting in the detection of potential new lineages.Furthermore,we have incorporated a comprehensive knowledgebase on mutation effects.This knowledgebase serves as a valuable resource for retrieving information on the functional implications of specific mutations.In summary,RCoV19 serves as a vital scientific resource,providing access to valuable data,relevant information,and technical support in the global fight against COVID-19.The complete contents of RCoV19 are available to the public at https://***/ncov/.

关键词： SARS-CoV-2 Mutation Variants Surveillance Pre-warning

Database Resources in BIG Data Center:Submission, Archiving, and Integration of Big Data in Plant Science

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维普期刊数据库

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Molecular Plant 2019年第3期12卷 279-281页

作者： shuhui song Zhang Zhang BIG Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

With the rapid advancement of sequencing technologies and the growing volume of omics data in plants, there is much anticipation in digging out the treasure from such big data and accordingly refining the current agricultural practice to be applied in the near future. Toward this end, database resources that deliver web services for plant omics data submission, archiving, and integration are urgently needed. As a part of Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences (CAS), BIG Data Center (http://***) provides open access to a suite of database resources (Table 1), with the aim of supporting plant research activities for domestic and international users in both academia and industry to translate big data into big discoveries (BIG Data Center Members, 2017;BIG Data Center Members, 2018;BIG Data Center Members, 2019). Here, we give a brief introduction of plant-related database resources in BIG Data Center and appeal to plant research com丒 munities to make full use of these resources for plant data submission, archiving, and integration.

关键词： Database Resources BIG Data Center

SoyOmics:A deeply integrated database on soybean multi-omics

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维普期刊数据库

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Molecular Plant 2023年第5期16卷 794-797页

作者： Yucheng Liu Yang Zhang Xiaonan Liu Yanting Shen Dongmei Tian Xiaoyue Yang Shulin Liu Lingbin Ni Zhang Zhang shuhui song Zhixi Tian State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China National Genomics Data Center&CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China China National Center for Bioinformation Beijing 100101China University of Chinese Academy of Sciences Beijing 100039China

Dear Editor,As one of the most important crops to supply the majority of plant oil and protein for the whole world,soybean is facing an increasing global demand.The reference genome of accession"Williams82"opened the gate of genomics research in soybean(Schmutz et al.,2010).After that,vast multi-omics data were generated,thereby providing valuable resources for functional study and molecular breeding.Parts of these data have been collected in different soybean databases(see details in Supplemental Table 1),such as Soybase(Grant et al.,2010)and SoyKB(Joshi et al.,2012),which made valuable efforts to facilitate the wide utility of these data.Nevertheless,these existing databases poorly tackled multi-omics data integration and interactivity for soybean,provoking tremendous challenges for researchers to deal with these big omics data,particularly considering the unprecedented rate of data growth(Yang et al.,2021).Thus,constructing an integrated multi-omics database for soybean that provides a one-stop solution for big data mining with friendly interactivity is highly desired.

关键词： database details thereby

Rice Genomics: over the Past Two Decades and into the Future

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维普期刊数据库

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Genomics, Proteomics & Bioinformatics 2018年第6期16卷 397-404页

作者： shuhui song Dongmei Tian Zhang Zhang songnian Hu Jun Yu BIG Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Domestic rice(Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct ?eld applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we brie?y review its achievements over the past two decades and present the potential for its bright future.

关键词： Rice genome Genomic diversity Heterosis Domestication

MPoxVR: A comprehensive genomic resource for monkeypox virus variant surveillance

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The Innovation 2022年第5期3卷 31-32页

作者： Yingke Ma Meili Chen Yiming Bao shuhui song MPoxVR Team National Genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Monkeypox is a viral zoonotic disease endemic in Central and West Africa.Since January 1,2022,3413 laboratory-confirmed monkeypox cases and one death have been reported from 50 countries/territories in five WHO regions(as of June 22,2022;https://www.***.int/emergencies/disease-outbreak-news/item/2022-DON396),and 1310 new cases and eight new countries have been reported in the past week.Genomic epidemiology is vital to determine the similarity between viruses and suggest possible links between cases,origins of infection,and transmission dynamics when combined with epidemiological information.However,one of the priority evidence gaps relating to the monkeypox outbreak is genome sequencing and in-host variation analysis.1 So,timely sharing both raw sequence data and consensus genomic data are useful to public health investigators and academic partners undertaking related studies.

关键词： epidemiology similarity monkey

SR4R:An Integrative SNP Resource for Genomic Breeding and Population Research in Rice

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维普期刊数据库

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Genomics, Proteomics & Bioinformatics 2020年第2期18卷 173-185页

作者： Jun Yan Dong Zou Chen Li Zhang Zhang shuhui song Xiangfeng Wang Department of Crop Genomics and Bioinformatics College of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100094China China National Center for Bioinformation Beijing 100101China National Genomics Data Center&CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100101China Rice Research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640China

The information commons for rice(IC4 R)database is a collection of 18 million single nucleotide polymorphisms(SNPs)identified by resequencing of 5152 rice accessions.Although IC4 R offers ultra-high density rice variation map,these raw SNPs are not readily usable for the public.To satisfy different research utilizations of SNPs for population genetics,evolutionary analysis,association studies,and genomic breeding in rice,raw genotypic data of these 18 million SNPs were processed by unified bioinformatics pipelines.The outcomes were used to develop a daughter database of IC4 R-SnpReady for Rice(SR4 R).SR4 R presents four reference SNP panels,including 2,097,405 hapmapSNPs after data filtration and genotype imputation,156,502 tagSNPs selected from linkage disequilibrium-based redundancy removal,1180 fixedSNPs selected from genes exhibiting selective sweep signatures,and 38 barcodeSNPs selected from DNA fingerprinting simulation.SR4 R thus offers a highly efficient rice variation map that combines reduced SNP redundancy with extensive data describing the genetic diversity of rice populations.In addition,SR4 R provides rice researchers with a web interface that enables them to browse all four SNP panels,use online toolkits,as well as retrieve the original data and scripts for a variety of population genetics analyses on local computers.SR4 R is freely available to academic users at http://sr4 r.ic4 ***/.

关键词： Rice SNP Database HapMap Panel

The Elements of Data Sharing

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Genomics, Proteomics & Bioinformatics 2020年第1期18卷 1-4页

作者： Zhang Zhang shuhui song Jun Yu Wenming Zhao Jingfa Xiao Yiming Bao China National Center for Bioinformation Beijing 100101China National Genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100101China

Data and their tailored characteristics are inheritable and longlived,surpassing their analyzed results and conclusions regardless if they are produced by their generators or users.Aside from designing experiments for the new acquisition,scientific researchers always begin with a thorough synthesis of the existing data,especially those that have been demonstrated authentic and timely.

关键词： authentic passing synthesis