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Design of antiviral AGO2-dependent short hairpin RNAs

Virologica Sinica 2024年第4期39卷 645-654页

作者： Yuanyuan Bie Jieling Zhang Jiyao Chen Yumin Zhang Muhan Huang Leike Zhang Xi Zhou Yang Qiu Key Laboratory of Virology and Biosafety Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China State Key Laboratory of Virology Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China University of Chinese Academy of sciences Beijing 100049China School of life sciences Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230027China

The increasing emergence and re-emergence of RNA virus outbreaks underlines the urgent need to develop effective *** interference(RNAi)is a sequence-specific gene silencing mechanism that is triggered by small interfering RNAs(siRNAs)or short hairpin RNAs(shRNAs),which exhibits significant promise for antiviral ***2-dependent shRNA(agshRNA)generates a single-stranded guide RNA and presents significant advantages over traditional siRNA and *** this study,we applied a logistic regression algorithm to a previously published chemically siRNA efficacy dataset and built a machine learning-based model with high predictive *** this model,we designed siRNA sequences targeting diverse RNA viruses,including human enterovirus A71(EV71),Zika virus(ZIKV),dengue virus 2(DENV2),mouse hepatitis virus(MHV)and severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),and transformed them into *** validated the performance of our agshRNA design by evaluating antiviral efficacies of agshRNAs in cells infected with different *** the agshRNA targeting EV71 as an example,we showed that the anti-EV71 effect of agshRNA was more potent compared with the corresponding siRNA and ***,the antiviral effect of agshRNA is dependent on AGO2-processed guide RNA,which can load into the RNA-induced silencing complex(RISC).We also confirmed the antiviral effect of agshRNA in ***,this work develops a novel antiviral strategy that combines machine learning-based algorithm with agshRNA design to custom design antiviral agshRNAs with high efficiency.

关键词： AgshRNA Antiviral strategy Machine learning model

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MYB2 and MYB108 regulate lateral root development by interacting with LBD29 in Arabidopsis thaliana

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Journal of Integrative Plant Biology 2024年第8期66卷 1675-1687页

作者： Feng Zhang Junxia Wang Tingting Ding Xuefeng Lin Haiying Hu Zhaojun Ding Huiyu Tian The Key Laboratory of Plant Development and environmental Adaptation Biology Ministry of EducationSchool of Life SciencesShandong UniversityQingdao 266237China Advanced Medical Research institute Cheeloo College of MedicineShandong UniversityJinan 250012China

AUXIN RESPONSE FACTOR 7(ARF7)-mediated auxin signaling plays a key role in lateral root(LR)development by regulating downstream LATERAL ORGAN BOUNDARIES DOMAIN(LBD)transcription factor genes,including LBD16,LBD18,and *** proteins are believed to regulate the transcription of downstream genes as homodimers or ***,whether LBD29 forms dimers with other proteins to regulate LR development remains ***,we determined that the Arabidopsis thaliana(L.)*** transcription factors MYB2 and MYB108 interact with LBD29 and regulate auxin-induced LR *** MYB2 and MYB108 were induced by auxin in an ARF7-dependent *** of MYB2 by fusion with an SRDX domain severely affected auxin-induced LR formation and the ability of LBD29 to induce LR *** contrast,overexpression of MYB2 or MYB108 resulted in greater LR numbers,except in the lbd29 mutant *** findings underscore the interdependence and importance of MYB2,MYB108,and LBD29 in regulating LR *** addition,MYB2–LBD29 and MYB108–LBD29 complexes promoted the expression of CUTICLE DESTRUCTING FACTOR 1(CDEF1),a member of the GDSL(Gly-Asp-Ser-Leu)lipase/esterase family involved in LR *** summary,this study identified MYB2–LBD29 and MYB108–LBD29 regulatory modules that act downstream of ARF7 and intricately control auxin-mediated LR development.

关键词： ARF7 auxin lateral roots LBD29 MYB108 MYB2

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A probe into the acid deposition mitigation path in China over the last four decades and beyond

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National Science Review 2024年第4期11卷 84-92页

作者： Qian Yu Xiaodong Ge Haotian Zheng Jia Xing Lei Duan Dongwei Lv Dian Ding Zhaoxin Dong Yisheng Sun Posch Maximilian Danni Xie Yu Zhao Bin Zhao Shuxiao Wang Jan Mulder Thorj?rn Larssen Jiming Hao State Key Laboratory of environmental Simulation and Pollution Control School of EnvironmentTsinghua University State Key Laboratory of Pollution Control &Resource Reuse and School of the Environment Nanjing University State environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex School of EnvironmentTsinghua University International institute for Applied System Analysis(IIASA) School of Land Engineering Chang'an University Faculty of environmental sciences and Natural Resource Management Norwegian University of Life Sciences Norwegian institute for Water Research

China currently has the highest acid deposition globally, yet research on its status, impacts, causes and controls is lacking. Here, we compiled data and calculated critical loads regarding acid deposition. The results showed that the abatement measures in China have achieved a sharp decline in the emissions of acidifying pollutants and a continuous recovery of precipitation p H, despite the drastic growth in the economy and energy consumption. However, the risk of ecological acidification and eutrophication showed no significant decrease. With similar emission reductions, the decline in areas at risk of acidification in China(7.0%) lags behind those in Europe(20%) or the USA(15%). This was because, unlike Europe and the USA, China's abatement strategies primarily target air quality improvement rather than mitigating ecological impacts. Given that the area with the risk of eutrophication induced by nitrogen deposition remained at 13%of the country even under the scenario of achieving the dual targets of air quality and carbon dioxide mitigation in 2035, we explored an enhanced ammonia abatement pathway. With a further 27% reduction in ammonia by 2035, China could largely eliminate the impacts of acid deposition. This research serves as a valuable reference for China's future acid deposition control and for other nations facing similar challenges.

关键词： acid deposition critical loads acidification eutrophication ammonia abatement

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Heteroatom doping regulates the catalytic performance of singleatom catalyst supported on graphene for ORR

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Nano Research 2024年第3期17卷 1086-1093页

作者： Ji-Kai Sun Yu-Wei Pan Meng-Qian Xu Lei Sun Shaolong Zhang Wei-Qiao Deng Dong Zhai institute of Molecular sciences and Engineering Institute of Frontier and Interdisciplinary ScienceShandong UniversityQingdao 266237China College of Chemistry and environmental Engineering Shenzhen UniversityShenzhen 518060China

Replacing fossil fuels with fuel cells is a feasible way to reduce global energy shortages and environmental ***,the oxygen reduction reaction(ORR)at the cathode has sluggish kinetics,which limits the development of fuel *** is significant to develop catalysts with high catalytic activity of *** single-atom catalysts(SACs)of Pt supported on heteroatom-doped graphene are potential candidates for *** we studied the SACs of Pt with different heteroatoms doping and screened out Pt-C_(4) and Pt-C_(3)O_(1) structures with only 0.13 V overpotential for ***,it is found that B atoms doping could weaken the adsorption capacity of Pt,while N or O atoms doping could enhance *** regularity was verified on Fe *** the electronic interaction analysis between Pt and adsorbate,we explained the mechanism of this regularity and further proposed a new descriptor named corrected d-band center(ε_(d-corr))to describe *** descriptor is an appropriate reflection of the number of free electrons of the SACs,which could evaluate its adsorption *** work provides a purposeful regulatory strategy for the design of ORR catalysts.

关键词： single-atom catalyst(SAC) oxygen reduction reaction(ORR) heteroatom doping corrected d-band center descriptor

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Multiple isotopes reveal the driving mechanism of high NO_(3)^(-) level and key processes of nitrogen cycling in the lower reaches of Yellow River

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Journal of environmental sciences 2024年第4期138卷 597-606页

作者： Qianqian Zhang Huiwei Wang Lu Liu Tianlun Zhai Xueqing Zhang Hebei and China Geological Survey Key Laboratory of Groundwater Remediation Institute of Hydrogeology and Environmental GeologyChinese Academy of Geological SciencesHebei 050061China Geo-environmental Monitoring institute of Hebei Province Hebei 050011China Hebei Provincial Laboratory of Water environmental Science Hebei 050037China Hebei Provincial Academy of Ecological environmental Science Hebei 050037China

The continuous increase of nitrate(NO_(3)^(-))level in rivers is a hot issue in the ***,the driving mechanism of high NO_(3)^(-)level in large rivers is still lacking,which has limited the use of river water and increased the cost of water *** this study,multiple isotopes and source resolution models are applied to identify the driving mechanism of high NO_(3)^(-)level and key processes of nitrogen cycling in the lower reaches of the Yellow River(LRYR).The major sources of NO_(3)^(-)were sewage and manure(SAM)in the low-flow season and soil nitrogen(SN)and chemical fertilizer(CF)in the high-flow *** was the most key process of nitrogen cycling in the ***,in the biological removal processes,denitrification may not occur *** temporal variation of contributions of NO_(3)^(-)sources were estimated by a source resolution model in the *** proportional contributions of SAM and CF to NO_(3)^(-)in the low-flow and high-flow season were 32.5%-52.3%,44.2%-46.2%and 36.0%-40.8%,54.9%-56.9%,*** driving mechanisms of high NO_(3)^(-)level were unreasonable sewage discharge,intensity rainfall runoff,nitrification and lack of nitrate removal *** control the NO_(3)^(-)concentration,targeted measures should be implemented to improve the capacity of sewage and wastewater treatment,increase the utilization efficiency of nitrogen fertilizer and construct ecological *** study deepens the understanding of the driving mechanism of high nitrate level and provides a vital reference for nitrogen pollution control in rivers to other area of the world.

关键词： Nitrate Driving mechanism Nitrogen cycle Source apportionment Transformation Yellow River

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Perfluorooctane sulfonate promotes the migration of colorectal cancer cells by inducing epithelial-mesenchymal transition

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Journal of environmental sciences 2024年第11期145卷 1-12页

作者： Fangfang Li Lu Chen Bi-Xia Peng Yuyang Lei Minjie Li Liang-Hong Guo institute of environmental and Health sciences China Jiliang UniversityHangzhou 310018China Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province Hangzhou 310015China College of Quality and Safety Engineering China Jiliang UniversityHangzhou 310018China College of life sciences China Jiliang UniversityHangzhou 310018China

The potential association between colorectal cancer(CRC)and environmental pollutants is *** studies have found that some perfluoroalkyl acids,including perfluorooctane sulfonate(PFOS),induced colorectal tumors in experimental animals and promoted the migration of and invasion by CRC cells in vitro,but the underlying mechanism is ***,we investigated the effects of PFOS on the proliferation and migration of CRC cells and the potentialmechanisms involving activating the PI3K/Akt-NF-κB signal pathway and epithelial-mesenchymal transition(EMT).It was found that PFOS promoted the growth andmigration of HCT116 cells at non-cytotoxic concentrations and increased the mRNA expression of the migration-related angiogenic cytokines vascular endothelial growth factor(VEGF)and interleukin-8(IL-8).In a mechanistic investigation,the up-stream signal pathway PI3K/Akt-NF-κB was activated by PFOS,and the process was suppressed by LY294002(PI3K/Akt inhibitor)and BAY11-7082(NF-κB inhibitor)respectively,leading to less proliferation of HCT116 ***,matrix metalloproteinases(MMP)and EMT-related markers were up-regulated after PFOS exposure,and were also suppressed respectively by LY294002 and ***,the up-regulation of EMT markers was suppressed by a MMP inhibitor *** together,our results indicated that PFOS promotes colorectal cancer cell migration and proliferation by activating the PI3K/Akt-NF-κB signal pathway and epithelial-mesenchymal *** could be a potential toxicological mechanism of PFOS-induced malignant development of colorectal cancer.

关键词： Perfluorooctane sulfonate Colorectal cancer Cell migration PI3K/Akt-NF-κB Epithelial-mesenchymal transition

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Population genomic data reveal low genetic diversity,divergence and local adaptation among threatened Reeves's Pheasant(Syrmaticus reevesii)

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Avian Research 2024年第1期15卷 1-11页

作者： Qi Lu Pengcheng Wang Jiang Chang De Chen Shenghan Gao Jacob Hoglund Zhengwang Zhang Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering College of Life SciencesBeijing Normal UniversityBeijing100875China Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjing210023China State Key Laboratory of environmental Criteria and Risk Assessment Chinese Research Academy of Environmental SciencesBeijing100012China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing100101China Department of Ecology and Genetics Animal EcologyUppsala UniversityUppsalaSweden

Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened ***’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat *** is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened ***,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic ***,we identified candidate genes linked with adaptation across the current distribution of Reeves’s *** present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 *** also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those *** comparing with other threatened species,we found that Reeves’s Pheasants have low genetic *** of homozygosity suggest that the Shennongjia population has experienced serious *** demographic history results indicated that three populations experienced several declines during the glacial *** adaptative analysis among the populations identified 241 candidate genes under directional *** are involved in a large variety of processes,including the immune response and *** results suggest that the three populations should be considered as three different conservation *** current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.

关键词： Conservation genetics Local adaptation Pheasant Whole-genome sequencing

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Brominated flame retardants in surface sediment from Western Guangdong,South China:Occurrence,distribution and toxicity in Caenorhabditis elegans

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Journal of environmental sciences 2024年第11期145卷 97-106页

作者： Xiaoxia Chen Ping Ding Haibo Chen Tingzhen Li Min Zhang Yunjiang Yu Guocheng Hu State environmental Protection Key Laboratory of environmental Pollution Health Risk Assessment South China Institute of Environmental SciencesMinistry of Ecology and EnvironmentGuangzhou 510655China institute for environmental pollution and health School of Environmental and Chemical EngineeringShanghai UniversityShanghai 200444China Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir Chongqing Three Gorges UniversityChongqing 404000China

Sediment is the ultimate sink of environmental pollutants.A total of 128 surface sediment sampleswere collected from8 rivers and 3 reservoirs in Maoming City,Guangdong *** study assessed the content and distribution of brominated flame retardants in *** acute toxicity effects of tetrabromobisphenol A(TBBPA)and hexabromocyclododecane(HBCDs)in sediments were evaluated using Caenorhabditis elegans as model *** concentration of TBBPA in sediments ranged from not detected(ND)to 12.59μg/kg andwas mainly distributed in the central area,whichwas affected by the emission of TBBPA from residential and *** concentration of HBCDs ranged from ND to 6.31μg/kg,and the diastereoisomer distribution was consistent,showing a trend close to the South China *** composition pattern of HBCDs in the surface sediments from rivers were 41.73%-62.33%,7.89%-25.54%,and 18.76%-40.65%forα-,β-,andγ-HBCD,respectively,and in the sediments from reservoirs were 26.15%-45.52%,7.44%-19.23%,and 47.04%-61.89%forα-,β-,andγ-HBCD,*** the sum of concentrations of TBBPA and HBCD in sediments were above high levels,reactive oxygen species in nematodes significantly increased,resulting in an oxidative stress *** permeabilitywas also enhanced,causing intestinal *** addition,in terms of this study,TBBPA had a greater impact on biotoxicity compared to HBCDs,and more attention should be paid to the toxic effects of the river ecosystem organisms in Maoming City,Guangdong *** study can complement the pollution database in the study area and provide basic data for pollution control.

关键词： Tetrabromobisphenol A(TBBPA) Hexabromocyclododecane(HBCDs) Sediment Caenorhabditis elegans Biotoxicity

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Investigation into the roles of interfacial H_(2)O structure in catalytic oxidation of HCHO and CO over CuMnO_(2) catalysts

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Journal of environmental sciences 2024年第3期137卷 310-320页

作者： Chunyan Ma Jushuang Pan Cheng Chen Yuanyuan Dong Feng Yao Fengbang Wang Maoyong Song Key Laboratory of environmental Nanotechnology and Health Effects Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China University of Chinese Academy of sciences Beijing 100049China No.52 institute of China North Industries Group Yantai Branch Co.Ltd. Yantai 264000China

The rapid deactivation of cost-effective MnO_(2)-based catalysts in humid air limits their application in practice,and the identification of the role of water in an oxidation process is significant for developing water-resistant MnO_(2)-based ***,CuMnO_(2)showed a20.3%HCHO conversion in 10 hr at room temperature in humid air with relative humidity of 40%,but deactivated in 3 hr in dry *** excellent activity and stability of HCHO oxidation in humid air were attributed to the positive effect of H_(2)O on HCHO oxidation to the H_(2)O-HOCH_(2)OH supermolecule assemblies via hydrogen bonds formed on CuMnO_(2).H_(2)O-HOCH_(2)OH supermolecule assemblies tend to be oxidized to carbonate,which is further oxidized to CO_(2).Furthermore,CuMnO_(2)exhibited a much poorer activity of CO oxidation in humid air,but the CO conversion was still 100%in 10 hr in dry air.H_(2)O showed a competitive adsorption effect to CO on CuMnO_(2).CuMnO_(2)could be applied in HCHO elimination in humid air and CO elimination in dry air.

关键词： H_(2)O-HOCH_(2)OH supermolecule HCHO oxidation Humid air CuMnO_(2) CO oxidation

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A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants

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Science China(life sciences) 2024年第6期67卷 1280-1291页

作者： Yong Zhang Xiaotuo Zhang Qi Tang Lei Li Ting Jiang Yixiao Fang Hong Zhang Jixian Zhai Guodong Ren Binglian Zheng State Key Laboratory of Genetic Engineering Institute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China

Lariat RNA is concomitantly produced by excised intron during RNA splicing,which is usually debranched by DBR1,an RNA debranching ***,increasing evidence showed that some lariat RNA could escape *** is known about how and why these lariat RNAs could be *** comparing the atlas of lariat RNAs between the non-dividing cell(mature pollen)and three actively dividing tissues(young shoot apex,young seeds,and young roots),we identified hundreds to thousands of lariat RNA naturally retained in each tissue,and the incidence of lariat RNA retention is much less in shoot apex while much more in *** lariat RNAs derived from the same intron or different lariat RNAs from the same pre-m RNA could be retained in one tissue while degraded in the other *** deciphering lariat RNA sequences,we identified an AG-rich(RAAAAVAAAR)motif and a UC-rich(UCUCUYUCUC)motif for pollen-specific and the other three tissues-retained lariat RNAs,*** of the pollen-specific AG-rich motif indeed enhanced lariat RNA retention in ***,hundreds of lariat RNAs harbored mi RNA binding sites,and dual-luciferase reporter assay showed that these natural lariat RNAs had the potential to protect expression of mi RNA target ***,our results uncover that selective retention of lariat RNA is an actively regulatory process,and provide new insights into understanding how lariat RNA metabolism may impact mi RNA activity.

关键词： intron turnover lariat RNA miRNA RNA splicing DBR1

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