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Revealing Tissue Heterogeneity and Spatial Dark Genes from Spatially Resolved Transcriptomics by Multiview Graph Networks

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Research 2024年第2期6卷 629-645页

作者： Ying Li Yuejing Lu Chen Kang Peiluan Li Luonan Chen School of Mathematics and Statistics Henan University of Science and TechnologyLuoyang471023China Longmen Laboratory LuoyangHenan471003China Key Laboratory of Systems Biology Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai201100China Key Laboratory of Systems Health Science of Zhejang Province Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310000China School of Life Science and Technology ShanghaiTech UniversityShanghai201100.China

Spatially resolved transcriptomics(SRT)is capable of comprehensively characterizing gene expression patterns and providing an unbiased image of spatial *** fully understand the organizational complexity and tumor immune escape mechanism,we propose stMGATF,a multiview graph attention fusion model that integrates gene expression,histological images,spatial location,and gene *** better extract information,stMGATF exploits SimCLRv2 for visual feature exaction and employs edge feature enhanced graph attention networks for the learning potential embedding of each view.A global attention mechanism is used to adaptively integrate 3 views to obtain low-dimensional *** to diverse SRT datasets,stMGATF is robust and outperforms other methods in detecting spatial domains and denoising data even with different resolutions and *** particular,stMGATF contributes to the elucidation of tissue heterogeneity and extraction of 3-dimensional expression ***,considering the associations between genes in tumors,stMGATF can identify the spatial dark genes ignored by traditional methods,which can be used to predict tumor-driving transcription factors and reveal tumor immune escape mechanisms,providing theoretical evidence for the development of new immunotherapeutic strategies.

关键词： Spatial integrate driving

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The UDP-glycosyltransferase OsUGT706D2 positively regulates cold and submergence stress tolerance in rice

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The Crop Journal 2024年第3期12卷 732-742页

作者： Qing Liu Lanlan Zhang Shuwei Lyu Hang Yu Wenjie Huang Liqun Jiang Jing Zhang Bingrui Sun Xingxue Mao Pingli Chen Junlian Xing Wenfeng Chen Zhilan Fan Shijuan Yan Chen Li Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory/Key Laboratory of Genetics and Breeding of High Quality Rice in Southern china(Co-construction by Ministry and Province) Ministry of Agriculture and Rural AffairsRice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization Agro-biological Gene Research CenterGuangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina

In a genome-wide association study,we identified a rice UDP-glycosyltransferase gene,OsUGT706D2,whose transcription was activated in response to cold and submergence stress and to exogenous abscisic acid(ABA).OsUGT706D2 positively regulated the biosynthesis of tricin-4’-O-(syringyl alcohol)ether-7-O-glucoside at both the transcriptional and metabolic ***706D2 mediated cold and submergence tolerance by modulating the expression of stress-responsive genes as well as the abscisic acid(ABA)signaling *** of function of OsUGT706D2 increased cold and submergence tolerance and loss of function of OsUGT706D2 reduced cold *** positively regulated OsUGT706D2-mediated cold tolerance but reduced submergence *** findings suggest the potential use of OsUGT706D2 for improving abiotic stress tolerance in rice.

关键词： UDP-glycosyltransferase Rice Cold tolerance Submergence tolerance ABA

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Prevalence and risk factors of cardiovascular diseases and psychological distress among female scientists and technicians

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2022年第12期23卷 1057-1064页

作者： Lijun ZHANG Yanping BAO Guo LI Shuhui TAO Meiyan LIU Department of Psycho-Cardiology Beijing Anzhen HospitalCapital Medical UniversityBejing 100029China national Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence Peking UniversityBeijing 100191China School of Public Health Peking UniversityBejing 100191China Henan Medical School Henan UniversityKaifeng 475001China

This study aimed to explore the prevalence and risk factors of cardiovascular disease(CVD)and psychological distress among female scientists and technicians in ***,we included scientists and technicians from representative research institutions,medical institutions,colleges,universities,and businesses in china,and the data were collected from July 1,2019 to March 31,2021 via online *** parameters evaluated in this study included age,sex,marital status,educational background,monthly income,sleep hours,sleep problems,smoking,alcohol consumption,work-related stress,work burnout,cardiovascular symptoms,CVD,family history,and depressive and anxiety symptoms.A total of 14530 scientists and technicians were included,comprising 7144 men and 7386 *** found 34.9%men and 16.6%women with CVD,35.1%men and 21.4%women with depressive symptoms,28.7%men and 13.8%women with anxiety symptoms,and 22.0%men and9.5%women with CVD combined with depressive or anxiety *** study focused on the details of *** women(age≤35 years)had the highest prevalence of depressive symptoms(24.9%),anxiety symptoms(16.2%),and comorbidity(11.2%).It was established that,despite traditional risk factors,unmanageable work burnout,depressive symptoms,and anxiety symptoms were associated with a higher risk of CVD in women;insomnia,overwhelming work stress,unmanageable work burnout,and CVD were linked to a higher risk of depressive symptoms and anxiety;insomnia,overwhelming work stress,and unmanageable work burnout were related to CVD combined with depressive or anxiety symptoms.A bidirectional relationship was noted between CVD and depression or anxiety in female scientists and technicians,and insomnia and overwhelming work stress were positively associated with *** is suggested that effective measures should be taken to protect female scientists and technicians from CVD and psychological distress.

关键词： Female scientist and technician Depressive symptom Anxiety Insomnia Cardiovascular disease(CVD)

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Through-polymer,via technology-enabled,flexible,lightweight,and integrated devices for implantable neural probes

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Microsystems & Nanoengineering 2024年第2期10卷 279-291页

作者： Cunkai Zhou Ye Tian Gen Li Yifei Ye Lusha Gao Jiazhi Li Ziwei Liu Haoyang Su Yunxiao Lu Meng Li Zhitao Zhou Xiaoling Wei Lunming Qin Tiger H.Tao Liuyang Sun College of Electronics and Information Engineering Shanghai University of Electric PowerShanghaiChina 2020 X-Lab Shanghai Institute of Microsystem and Information TechnologyChinese Academy of SciencesShanghaiChina School of Graduate Study University of Chinese Academy of SciencesBeijingChina State Key Laboratory of Transducer Technology Shanghai Institute of Microsystem and Information TechnologyChinese Academy of SciencesShanghaiChina Center of Materials Science and Optoelectronics Engineering University of Chinese Academy of SciencesBeijingChina School of Physical Science and Technology ShanghaiTech UniversityShanghaiChina Center for Excellence in Brain Science and Intelligence Technology Chinese Academy of SciencesShanghaiChina Neuroxess Co. Ltd.(Jiangxi)NanchangJiangxiChina Guangdong Institute of Intelligence Science and Technology HengqinZhuhaiGuangdongChina Tianqiao and Chrissy Chen Institute for Translational Research ShanghaiChina

In implantable electrophysiological recording systems,the headstage typically comprises neural probes that interface with brain tissue and integrated circuit chips for signal *** advancements in MEMS and CMOS technology have significantly improved these components,their interconnection still relies on conventional printed circuit boards and sophisticated *** conventional approach adds considerable weight and volume to the package,especially for high channel count *** address this issue,we developed a through-polymer via(TPV)method inspired by the through-silicon via(TSV)technique in advanced three-dimensional *** innovation enables the vertical integration of flexible probes,amplifier chips,and PCBs,realizing a flexible,lightweight,and integrated device(FLID).The total weight of the FLIDis only 25%that of its conventional counterparts relying on adapters,which significantly increased the activity levels of animals wearing the FLIDs to nearly match the levels of control animals without ***,by incorporating a platinum-iridium alloy as the top layer material for electrical contact,the FLID realizes exceptional electrical performance,enabling in vivo measurements of both local field potentials and individual neuron action *** findings showcase the potential of FLIDs in scaling up implantable neural recording systems and mark a significant advancement in the field of neurotechnology.

关键词： alloy neural recording

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Stay-Green Panicle Branches Improve Processing Quality of Elite Rice Cultivars

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Rice science 2023年第1期30卷 11-14页

作者： CHEN Yibo ZHAO Lei WANG Chongrong LI Hong HUANG Daoqiang WANG Zhidong ZHOU Degui PAN Yangyang GONG Rong ZHOU Shaochuan Rice Research Institute Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou 510640China

Rice panicle branches are key routes for transportation of photo synthetic products to *** senescence is an important trait that the breeders considered when breeding elite rice cultivars in South ***,little is known about the mechanisms underlying the contributions of stay-green panicle branches to rice yield and ***,we reported stay-green branches that continuously maintained transportation function and provided carbohydrates for basal grain development at the late stages of rice *** ensured the coordination of development between apical and basal grains,and further improved the processing quality of elite *** findings provided strategies for improving the fullness and quality of rice grains and presented an important basis for cultivating elite rice.

关键词： elite breeding cultivar

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Time effects of rice straw and engineered bacteria on reduction of exogenous Cu mobility in three typical Chinese soils

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Pedosphere 2022年第5期32卷 665-672页

作者： Hanzhi SHI Dian WEN Yongdong HUANG Shoujun XU Tenghaobo DENG Furong LI Zhichao WU Xu WANG Peihua ZHAO Fuhua WANG Ruiying DU Institute of Quality Standard and Monitoring Technology for Agro-Products Guangdong Academy of Agricultural SciencesGuangzhou 510640(China) Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality Ministry of Agriculture and Rural AffairsGuangzhou 510640(China) Guangdong Provincial Key Laboratory of Quality&Safety Risk Assessment for Agro-Products Guangzhou 510640(China)

Globally,copper(Cu)accumulation in soils is a major environmental *** organic waste and some bacterial species can readily absorb metals in an eco-friendly manner,and thus are commonly used in metal-contaminated soil *** study investigates the change in Cu fractions during the aging process and the time effects of rice straw(RS)and engineered bacteria(EB)(Pseudomonas putida X4/pIME)on reduction of Cu *** typical Chinese soils(red,cinnamon,and black soils)were incubated with RS or RS+EB in the presence of exogenous Cu for 24 *** soil physicochemical properties,reactive soil components,Cu fractions,and Cu mobility were determined over *** Cu mobility factor(MF)values were the lowest in the black soil(6.4-9.2)because of its high organic carbon and clay *** additions of both RS and RS+EB accelerated Cu stabilization during the aging process in all three *** Cu MF values decreased with time during the initial 20 months;however,the MF values increased thereafter in all soils,which might be due to the reduction of humic substances and amorphous iron oxides and the increase in iron oxides complexed on the organic *** reduction rates of Cu MF were similar after 16,24,and more than 24 months in the red,cinnamon,and black soils,respectively,indicating that RS and RS+EB could limit Cu mobility at different times in various *** RS treatment showed the greatest efficiency in reducing Cu mobility in the red,cinnamon,and black soils after 12,12,and 8 months of incubation,*** RS+EB treatment was more efficient than the RS treatment in the red soil during the initial 8 months of the incubation *** study provides theoretical support for Cu risk assessments and RS supplementation for Cu remediation in different soils.

关键词： aging Cu distribution mobility factor sequential extraction soil incubation

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Temporal-spatial analysis of cyromazine in cowpea using liquid chromatography–mass spectrometry coupled with mass spectrometry imaging

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Food Quality and Safety 2023年第3期7卷 466-473页

作者： Xuemei Tang Congling Huang Jianxiang Huang Jiale Wang Zhiting Chen Yan Chen Zemiao Xiao Kai Wan Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong academy of Agricultural Sciences Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality(Guangzhou)Ministry of Agriculture and Rural AffairsNational Reference Laboratory for Agricultural Testing(Pesticide Residues)GuangzhouChina

Background:Cowpea(Vigna unguiculata ***.)is an economically important *** is nutritious and popular with ***,it has been listed as one of the agricultural products of critical concern about safety in china and cyromazine is the major risk ***:This study analyzed the dissipation and permeation kinetics of cyromazine residue in cowpea,to offer a scientific basis for the rational use of pesticide and ensure the safety of agricultural *** and methods:The dissipation and residue level of the systemic insecticide cyromazine on cowpea under field and stored conditions were ***,the spatial distribution of cyromazine was studied using mass spectrometry imaging to visualize the dynamic processes of permeation and migration in the tissues post pesticide ***:The dissipation processing of cyromazine in cowpea was shown to follow the first-order kinetics and half-life was 7.76 d in the *** cowpea,the permeation and migration rate of cyromazine was faster than that in kidney beans and accumulation was mainly in the *** is not safe to apply cyromazine to cowpeas with reference to the application method on kidney ***:These findings present vital data for the determination of risks linked with cowpea consumption and pesticide intake.

关键词： Cyromazine cowpea mass spectrometry imaging pesticide residue

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Comparisons of Metabolic Profiles for Carbohydrates,Amino Acids,Lipids,Fragrance and Flavones During Grain Development in indica Rice Cultivars

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Rice science 2022年第2期29卷 155-165页

作者： CHEN Yibo WANG Zhidong WANG Chongrong LI Hong HUANG Daoqiang ZHOU Degui ZHAO Lei PAN Yangyang GONG Rong ZHOU Shaochuan Guangdong academy of Agricultural Sciences Rice Research Institute/Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhou 510640China

We used a widely targeted metabolomics approach to examine the metabolic changes in three pedigreed indica cultivars(Meixiangzhan 2,Meisizhan and Qixinzhan),with different eating qualities,at 8,15 and 30 d after flowering(DAF)to explore the formation mechanism of rice eating and nutritional qualities at a global metabolic level.A total of 623 metabolites were identified,and results showed that metabolic variations among rice cultivars decreased with grain developmental stage,suggesting that sufficient carbohydrate and amino acid supply during grain development may contribute to excellent rice eating and nutritional quality *** 19:0 and 16:1 were beneficial for excellent eating quality formation during grain *** fragrance was attributed mainly to spermidine andγ-aminobutyric *** cultivars with excellent eating quality at 15-30 DAF had relatively higher flavone content,possibly because they had adequate carbohydrate and amino acid contents during grain *** results provided insight into the mechanisms for establishing rice eating and nutritional qualities during grain formation at a global metabolic level,and can be applied towards improving rice quality.

关键词： eating quality metabolomics nutritional quality high-quality rice grain development

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Anti-infection effects of heparin on SARS-CoV-2 in a diabetic mouse model

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Zoological Research 2023年第6期44卷 1003-1014页

作者： Zhongyun Zhang Ning Zhang Xuancheng Lu Min Zhou Xiaoxiang Yan Weiqiong Gu Jingru Yang Qin Zhang Cheng Zhang Yuhuan Gong Mingjun Jia Xiaoyu Zhang Peng Ning Mei Liu Xiaoyan Li Xiaomeng Shi Wenjun Liu George FGao Guang Ning Jiqiu Wang Yuhai Bi Department of Endocrinology and Metabolism Shanghai Institute of Endocrine and Metabolic DiseasesRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai 200025China Shanghai national Clinical Research Center for Metabolic Diseases Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR ChinaShanghai National Center for Translational MedicineShanghai 200025China CAS Key Laboratory of Pathogen Microbiology and Immunology Institute of MicrobiologyCenter for Influenza Research and Early-warning(CASCIRE)CAS-TWAS Center of Excellence for Emerging Infectious Diseases(CEEID)Chinese Academy of SciencesBeijing 100101China Laboratory Animal Center Chinese Center for Disease Control and Prevention(China CDC)Beijing 102206China Department of Respiratory and Critical Care Medicine Institute of Respiratory DiseasesRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai 200025China Department of Cardiology Institute of Cardiovascular DiseasesRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai 200025China School of Laboratory Medicine and Life Sciences Wenzhou Medical UniversityWenzhouZhejiang 325000China University of Chinese academy of Sciences Beijing 100049China

Severe acute respiratory syndrome coronavirus 2(SARSCo V-2)infection can result in more severe syndromes and poorer outcomes in patients with diabetes and ***,the precise mechanisms responsible for the combined impact of coronavirus disease 2019(COVID-19)and diabetes have not yet been elucidated,and effective treatment options for SARS-Co V-2-infected diabetic patients remain *** investigate the disease pathogenesis,K18-h ACE2 transgenic(h ACE2^(Tg))mice with a leptin receptor deficiency(h ACE2-Lepr^(-/-))and high-fat diet(h ACE2-HFD)background were *** two mouse models were intranasally infected with a 5×10^(5) median tissue culture infectious dose(TCID_(50))of SARSCo V-2,with serum and lung tissue samples collected at 3days *** h ACE2-Lepr^(-/-)mice were then administered a combination of low-molecular-weight heparin(LMWH)(1 mg/kg or 5 mg/kg)and insulin via subcutaneous injection prior to intranasal infection with1×10^(4) TCID_(50)of SARS-Co *** drug administration continued until the euthanasia of the *** of viral RNA loads,histopathological changes in lung tissue,and inflammation factors were *** demonstrated similar SARS-Co V-2 susceptibility in h ACE2^(Tg)mice under both lean(chow diet)and obese(HFD)***,compared to the h ACE2-Lepr^(+/+)mice,h ACE2-Lepr^(-/-)mice exhibited more severe lung injury,enhanced expression of inflammatory cytokines and hypoxia-inducible factor-1α(HIF-1α),and increased ***,combined LMWH and insulin treatment effectively reduced disease progression and severity,attenuated lung pathological changes,and mitigated inflammatory *** conclusion,preexisting diabetes can lead to more severe lung damage upon SARS-Co V-2 infection,and LMWH may be a valuable therapeutic approach for managing COVID-19patients with diabetes.

关键词： SARS-CoV-2 Diabetes Mouse model Heparin Antiviral therapy

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IMPACTS OF CLIMATE CHANGE ON CROP PRODUCTION, PESTS AND PATHOGENS OF WHEAT AND RICE

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Frontiers of Agricultural Science and Engineering 2022年第1期9卷 4-18页

作者： Bing-Xin WANG Anouschka R.HOF Chun-Sen MA Climate Change Biology Research Group State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China Wildlife Ecology and Conservation Group Wageningen University and Research Centre6708 PBWageningenthe Netherlands Department of Wildlife Fishand Environmental StudiesSwedish University of Agricultural SciencesSE-90736 UmeåSweden

Ongoing climate change is expected to have impacts on crops,insect pests,and plant pathogens and poses considerable threats to sustainable food *** reviews have summarized impacts of a changing climate on agriculture,but the majority of these are presented from an ecological point of view,and scant information is available on specific species in agricultural *** paper provides an overview of impacts of climate change on two staple crops,wheat and ***,the direct effects of climate change on crop growth,yield formation,and geographic distribution of wheat and rice are ***,the effects of climate change on pests and pathogens related with wheat and rice,and their interactions with the crops are ***,potential management strategies to mitigate the direct impacts of climate change on crops,and the indirect impacts on crops through pests and pathogens are *** present overview aims to aid agriculture practitioners and researchers who are interested in wheat and rice to better understand climate change related impacts on the target species.

关键词： climate change pest pathogen food security

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