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DMF-scMT-seq linking methylome and transcriptome within single cells with digital microfluidics

Science China Chemistry 2024年第6期67卷 2070-2078页

作者： Xing Xu Xi Zeng Xin lin Shiyan lin Shanshan Liang Tian Tian rui Su Jia Song Chaoyong Yang Collaborative Innovation Center of Chemistry for Energy Materials The MOE Key Laboratory of Spectrochemical Analysis and InstrumentationState Key Laboratory of Physical Chemistry of Solid SurfacesDepartment of Chemical BiologyCollege of Chemistry and Chemical EngineeringThe First Affiliated Hospital of Xiamen UniversityXiamen UniversityXiamen361005China Institute of Molecular Medicine Renji HospitalShanghai Jiao Tong University School of MedicineShanghai200127China Chemistry and Materials Science College Shanghai Normal UniversityShanghai200234China Chemistry and Biomedicine Innovation Center(ChemBIC) School of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China

Single-cell joint analysis of methylome and transcriptome reveals how the methylation regulates the transcriptional ***,traditional bench-top protocols for single-cell DNA methylation and RNA transcription co-detection are laborintensive,cost-ineffective and ***,we establish the DMF-sc MT-seq,a highly-efficient and cost-effective method to simultaneously analyze single-cell DNA methylation and transcriptional activity based on digital *** MT-seq automates the workflow of single-cell isolation,cellular hypotonic lysis,nucleic acid separation and methylome/transcriptome library construction in a contactless and addressable *** system ensures high accuracy(R>0.85),high gene detection ability(14,697 genes per cell at 4 million sequencing depth),and high CpG coverage(677,198 CpG sites per cell at 1million sequencing depth).By using DMF-sc MT-seq,the relationship of DNA methylation and RNA transcription under different genomic contexts is *** further apply DMF-sc MT-seq to study the dynamics of transcription regulation with methylation-inhibiting anti-tumor Decitabine,and identify the methylated promoter/gene body driven genes in response to Decitabine ***-sc MT-seq facilitates the construction of the correlation of DNA methylation and transcriptional activity at the single-cell level in a flexible,sensitive and accurate way,which is anticipated to be a powerful tool in studying single-cell biological systems.

关键词： single-cell analysis digital microfluidics methylome sequencing transcriptome sequencing

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Heat stress induced hepatocyte apoptosis in largemouth bass Micropterus salmoides via IRE1α/TRAF2/ASK1/JNK pathway

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Journal of Oceanology and Limnology 2024年第3期42卷 988-1000页

作者： Xuqian zhao Wenjia MAO Zijie lin Qufei linG School of Biology and Basic Medical Sciences Suzhou Medical College of Soochow UniversitySuzhou 215000China

Heat stress(HS)has been shown to adversely affect fish livers and can lead to extensive *** investigate the relationship between endoplasmic reticulum(ER)stress and HS-induced apoptosis in fish livers,we isolated and cultured primary hepatocytes of largemouth bass,Micropterus salmoides by trypsin method,then established an in-vitro model of liver cells under HS(35℃).The contents of lactic dehydrogenase(LDH)and hydrogen peroxide(H2O2)were determined to evaluate the effects of HS on hepatocyte injury and oxidative ***-qPCR was performed to discover the key genes in unfolded protein response(UPR)pathways involved at different HS *** inhibitor 4-PBA and IRE1αinhibitor 4μ8C were used to further investigate the effects of HS on IRE1αapoptosis pathway in *** show that HS led to significant increases in the release of LDH,the content of H2O2,and the expressions of oxidative protein folding genes(ero1αand pdi)under HS,suggesting severe hepatocyte injury and oxidative stress happened in heat-stressed largemouth bass *** continuous activation of IRE1αpathway genes(grp78,grp94,atf6,perk,eif2a,atf4,chop,ire1α,traf2,ask1,jnk1,and jnk2)indicated that HS led significantly to ER *** particular,the mRNA expression levels of ER stress-related genes(grp78,grp94,atf6,perk,ire1α,chop,jnk1,and jnk2)in the high temperature(HT)+4-PBA group and the HT+4μ8C group were significantly down-regulated under *** 4μ8C treatment,the expression levels of apoptosis-related genes(caspase-2,caspase-3,caspase-6,caspase-7,caspase-8,caspase-9,and caspase-10)and LDH content were significantly decreased,whereas the cell survival rate was significantly increased when given 4-PBA or 4μ8C *** findings demonstrate that HS could induce liver apoptosis of largemouth bass through the IRE1αpathway,which may act as a key switch mediating liver apoptosis of largemouth bass under HS.

关键词： heat stress Micropterus salmoides endoplasmic reticulum stress apoptosis oxidative stress

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Precipitation and anthropogenic activities regulate the changes of NDVI in Zhegucuo Valley on the southern Tibetan Plateau

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Journal of Mountain Science 2024年第2期21卷 607-618页

作者： zhao Wanglin WANG Hengying ZHANG Huifang ZHANG lin School of Ecology and Environment Tibet UniversityLhasa 850000China Institute of Tibetan Plateau Research Chinese Academy of SciencesBeijing 100101China Southwest Survey and Planning Institute of National Forestry and Grassland Administration Kunming 650000China Monitoring Center for Ecological Environment of Xizang Autonomous Region Lhasa 850000China

Whether climate change or anthropogenic activities play a more pivotal role in regulating vegetation growth on the Tibetan Plateau is still controversial.A better understanding on grassland changes at a fine scale may provide important guidance for local government policy and grassland *** two of the most reliable satellite NDVI products(MODIS NDVI and SPOT NDVI),we evaluated the dynamic of grasslands in the Zhegucuo valley on the southern Tibetan Plateau from 2000 to 2020,and analyzed its driving factors and relative influences of climate change and anthropogenic ***,the key indicators of climate change were assumed to be precipitation and *** main results were:(1)the grassland NDVI in Zhegucuo valley did not reflect a significant temporal change during the last 21 *** variation of precipitation during the early growing season(GSP)resembled that of NDVI,and the GSP was positively correlated with *** the pixel level,the partial correlation analysis showed that 37.79%of the pixels depicted a positive relationship between GSP and NDVI,while 11.32%of the pixels showed a negative relationship between temperature during the early growing season(GST)and NDVI.(2)In view of the spatial distribution,the areas mainly controlled by GSP were generally distributed in the southern part,while those affected by GST stood in the eastern part,mainly around the Zhegucuo lake where most population in Cuomei County settled down.(3)Decreasing NDVI trends were mainly occurred in alpine steppe at lower elevations rather than alpine meadow at higher elevations.(4)The residual trend(RESTREND)analysis further indicated that the anthropogenic activities played a more pivotal role in regulating the annual changes of NDVI rather than climate factors in this *** studies should pay more attention on climate extremes rather than the simple temporal ***,the influence of human activities on alpine grassland needs to be accessed and fully

关键词： Anthropogenic activities Climate change Precipitation Fencing Vegetation degradation

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Muti-locus phylogeny and divergence time analyses of Russula from China

Muti-locus phylogeny and divergence time analyses of Russula...

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中国菌物学会2016年学术年会

作者： Guo Jie Li Hua An Wen Fu Cheng lin rui lin zhao State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of Sciences State Key Laboratory of Rice Biology Institute of BiotechnologyZhejiang University

The genus Russula is a group containing more than 760 species in the world,including many species of edible,medicinal and other economic *** of Russula form symbiotic association of mycorrhizae with roots of various species of shrubs and both coniferous and deciduous trees,playing an important role in *** genus is split into 11 subgenera in the current taxonomic systems of Russula,which are mainly based on morphological characteristics,such as pileus color,context taste,color of spore print,presence of dermatocystidia and primordial hyphae,and size of basidia and *** quite limited molecular phylogeny works are only based on ITS and LSU sequences analyses from several subgenera *** existence of huge number of species,highly variable phenotype and deficient phylogenetic study results Russula is becoming a difficult group in systematic *** this study,a comprehensive phylogenetic analyses based on ITS,n LSU,tef-1α,mt SSU,rpb1 and rpb2 sequences（all are newly generated from this research） derived from 256 Russula specimens in China which represent 161 species from all known 11 subgenera and 26 sections are *** clock dating analysis using BEAST v1.8.3 based on those 6 genes reveal the divergence times of Russula and related subgenera and *** divergence time is introduced as one of universal standardized criteria in taxa ranking as those of previous study in *** research shows the known subgenera Brevipes,Ingratula,Malodora,Russula and Tenellula are generally monophyletic groups,subgenera Coccinula,Compacta,Heterophyllidia,Incrustatula,Insidiosula and Polychromidia are obviously *** order to accommodation those new discoveries,a revised taxonomic system of Rususla is proposed,which composed of 5 new subgenera,sections Amethystina,Indolenta,Maculata,Rosea and Virdanta are raised into subgenera level,and along with 35 new ***,the revised taxonomic system of genus Russu

关键词： Russulaceae divergence times multigene phylogenetics systematics taxonomy

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Offspring analysis using two CAPS markers in the edible mushroom Agaricus sinodeliciosus

Offspring analysis using two CAPS markers in the edible mush...

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中国菌物学会2018年学术年会

作者： Zhi-lin ling Hui-Jun Wang Philippe Callac rui-lin zhao State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of Sciences College of Life Sciences University of Chinese Academy of Sciences INRA UR1264 MycSAMycologie et sécurité des aliments

Agaricus sinodeliciosus is an edible and wild mushroom from Northwest China, and belongs to Agaricus section Bivelares which includes several famous cultivated species, such as A. bisporus. Agaricus species present diverse types of life cycles, which strongly impact breeding programs. The main objective of this study was to identify the different categories of spores produced by this potentially cultivated species. Using a morphological approach based on the number of sterigmata per basidium;and a genetic approach based on the genotypes of the progeny at two loci, the rate of heterokaryotic spores was estimated to 6% and 16%, *** codominant markers were chosen in the gene MIP and the ITS region. Genotypic analysis and mating tests confirmed that in A. sinodeliciosus like in A. bisporus and A. subrufescens, the marker MIP is centromere-linked and tightly linked to the mating type locus, while the marker ITS is not linked to MIP nor to a centromere. We concluded that A. sinodeliciosus has a unifactoriel system of sexual incompatibility, an amphithallic life cycle predominantly heterothallic, and that its homothallism follows a non-random model with non-sister postmeiotic nuclei paired in the same spore. This method using two informative markers is reliable not only to select the homokaryotic offspring but also to classify the homokaryons in two breeding stocks according to their mating type alleles.

关键词： Amphithallic heterokaryons homokaryons sexual system

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Design of pH-responsive antimicrobial peptide melittin analog-camptothecin conjugates for tumor therapy

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Asian Journal of Pharmaceutical Sciences 2024年第1期19卷 135-146页

作者： Sujie Huang Yuxuan Gao ling Ma Bo Jia Wenhao zhao Yufan Yao Wenyuan Li Tongyi lin rui Wang Jingjing Song Wei Zhang Institute of Pharmacology School of Basic Medical SciencesLanzhou UniversityLanzhou 730000China Key Laboratory of Preclinical Study for New Drugs of Gansu Province School of Basic Medical Sciences&Research Unit of Peptide ScienceChinese Academy of Medical SciencesLanzhou UniversityLanzhou 730000China State Key Laboratory of Veterinary Etiological Biology College of Veterinary MedicineLanzhou UniversityLanzhou 730000China Lanzhou University Second Hospital Lanzhou UniversityLanzhou 730000China

Melittin,a classical antimicrobial peptide,is a highly potent antitumor ***,its significant toxicity seriously hampers its application in tumor *** this study,we developed novel melittin analogs with pH-responsive,cell-penetrating and membranelytic activities by replacing arginine and lysine with *** conjugation with camptothecin(CPT),CPT-AAM-1 and CPT-AAM-2 were capable of killing tumor cells by releasing CPT at low concentrations and disrupting cell membranes at high concentrations under acidic ***,we found that the C-terminus of the melittin analogs was more suitable for drug conjugation than the ***-AAM-1 significantly suppressed melanoma growth in vivo with relatively low ***,the present study demonstrates that the development of antitumor drugs based on pH-responsive antimicrobial peptide-drug conjugates is a promising strategy.

关键词： Antimicrobial peptide Peptide-drug conjugate Cell-penetrating activity Membrane disruption Antitumor activity

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Weather-Driven Solar Power Forecasting Using D-Informer:Enhancing Predictions with Climate Variables

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Energy Engineering 2024年第5期121卷 1245-1261页

作者： Chenglian Ma rui Han zhao An Tianyu Hu Meizhu Jin School of Electrical Engineering Northeast Electric Power UniversityJilin132013China Shenzhen Institute of Advanced Technology Chinese Academy of SciencesShenzhen518055China

Precise forecasting of solar power is crucial for the development of sustainable energy *** forecasting approaches often fail to adequately consider the crucial role of weather factors in photovoltaic(PV)power generation and encounter issues such as gradient explosion or disappearance when dealing with extensive time-series *** overcome these challenges,this research presents a cutting-edge,multi-stage forecasting method called *** method skillfully merges the differential transformation algorithm with the Informer model,leveraging a detailed array of meteorological variables and historical PV power generation *** D-Informer model exhibits remarkable superiority over competing models across multiple performance metrics,achieving on average a 67.64%reduction in mean squared error(MSE),a 49.58%decrease in mean absolute error(MAE),and a 43.43%reduction in root mean square error(RMSE).Moreover,it attained an R2 value as high as 0.9917 during the winter season,highlighting its precision and *** significant advancement can be primarily attributed to the incorporation of a multi-head self-attention mechanism,which greatly enhances the model’s ability to identify complex interactions among diverse input variables,and the inclusion of weather variables,enriching the model’s input data and strengthening its predictive accuracy in time series ***,the experimental results confirm the effectiveness of the proposed approach.

关键词： Power forecasting deep learning weather-driven solar power

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Suppression of low-frequency ultrasound broadband vibration using star-shaped single-phase metamaterials

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Defence Technology（防务技术） 2024年第4期34卷 217-224页

作者： rui zhao Jian Zheng Jin Guo Yunbo Shi Hengzhen Feng Jun Tang Jun Liu Science and Technology on Electronic Test&Measurement Laboratory North University of ChinaTaiyuan 030051ShanxiChina School of Mechatronical Engineering Beijing Institute of TechnologyBeijing 100081China

In order to suppress the low-frequency ultrasound vibration in the broadband range of 20 k Hz—100 k Hz,this paper proposes and discusses an acoustic metamaterial with low-frequency ultrasound vibration attenuation properties,which is configured by hybrid arc and sharp-angle convergent star-shaped *** effect of the dispersion relation and the bandgap characteristic for the scatterers in star-shaped are simulated and *** target bandgap width is extended by optimizing the geometry parameters of arc and sharp-angle convergent *** proposed metamaterial configured by optimized hybrid lattices exhibits remarkable broad bandgap characteristics by bandgap complementarity,and the simulation results verify a 99%vibration attenuation amplitude can be obtained in the frequency of20 k Hz—100 k *** the fabrication of the proposed hybrid configurational star-shaped metamaterial by 3D printing technique,the transmission loss experiments are performed,and the experimental results indicate that the fabricated metamaterial has the characteristics of broadband vibration attenuation and an amplitude greater than 85%attenuation for the target *** results demonstrate that the hybrid configurational star-shaped metamaterials can effectively widen the bandgap and realize high efficiency attenuation,which has capability for the vibration attenuation in the application of highprecise equipment.

关键词： Star-shaped metamaterials Broadband Vibration attenuation Low-frequency ultrasound vibration Transmission loss

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Construction of smart propellant with multi-morphologies

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Defence Technology（防务技术） 2024年第3期33卷 180-185页

作者： Weitao Yang Yuchen Gao rui Hu Manman Li Fengqi zhao He Jiang Xuan Zhang Xi’an Modern Chemistry Research Institute Xi’an710065China Northwestern Polytechnical University Xi’an710072China

Smart materials,which exhibit shape memory behavior in response to external stimuli,have shown great potential for use in biomedical *** this study,an energetic composite was fabricated using a UV-assisted DIW 3D printing technique and a shape memory material(SMP)as the *** composite has the ability to reduce the impact of external factors and adjust gun propellant combustion *** composition and 3D printing process were delineated,while the internal structure and shape memory performance of the composite material were *** energetic SMP composite exhibits an angle of reversal of 18 s at 70°,with a maximum elongation typically reaching up to 280% of the original length and a recovery length of approximately 105%during ten ***,thermal decomposition and combustion behavior were also demonstrated for the energetic SMP composite.

关键词： Smart material Gun propellants Multi-morphologies Self-regulation

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A combination of straw incorporation and polymer-coated urea offsets soil ammonia and nitrous oxide emissions in winter wheat fields

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Journal of Integrative Agriculture 2024年第5期23卷 1718-1736页

作者： Xiaoyun Wang Yajie Tian Qianhui Zhang Zhengxin zhao rui Wang Huanjie Cai Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education Northwest A&F UniversityYangling712100China College of Water Resources and Architectural Engineering Northwest A&F UniversityYangling 712100China

The combined effects of straw incorporation(SI)and polymer-coated urea(PCU)application on soil ammonia(NH_(3))and nitrous oxide(N_(2)O)emissions from agricultural fields have not been comprehensively evaluated in Northwest *** conducted a two-year field experiment to assess the effects of combining SI with either uncoated urea(U)or PCU on soil NH_(3)emissions,N_(2)O emissions,winter wheat yields,yield-scaled NH_(3)(/NH_(3)),and yield-scaled N_(2)O(/N_(2)O).Five treatments were investigated,no nitrogen(N)fertilizer(N_(0)),U application at 150 kg N ha-1 with and without SI(SI+U and S_(0)+U),and PCU application at 150 kg N ha^(-1) with and without SI(SI+PCU and S_(0)+PCU).The results showed that the NH_(3);emissions increased by 20.98-34.35%following Sl compared to straw removal,mainly due to increases in soil ammonium(NH_(4)^(+)-N)content and water-flled pore space(WFPS).SI resulted in higher N_(2)O emissions than under the So scenario by 13.31-49.23%due to increases in soil inorganic N(SIN)contents,WFPS,and soil microbial *** contrast,the PCU application reduced the SIN contents compared to the U application,reducing the NH_(3)and N_(2)O emissions by 45.99-58.07 and 18.08-53.04%,***,no significant positive effects of the SI or PCU applications on the winter wheat yield were *** lowest /NH_(3) and /N_(2)O values were observed under the S_(0)+PCU and SI+PCU *** results suggest that single PCU applications and their combination with straw are the optimal agricultural strategies for mitigating gaseous N emissions and maintaining optimal winter wheat yields in Northwest China.

关键词： straw incorporation polymer-coated urea NH_(3)and N_(2)O emissions winter wheat yields

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