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SARS-CoV-2 ORF8 does not function in the nucleus as a histone mimic

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Protein & Cell 2024年第2期15卷 79-82页

作者： Ping Liu Junjie Hui Lei Wang national laboratory of biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China

Disruption of epigenetic regulation in host cells is a common evasion strategy used by viruses(Ozturkler and Kalkan 2021).Recently,Kee et al.(2022)reported that accessory protein ORF8 of SARS-CoV-2 can diffuse into the cell nucleus and mimic histone H3 through the ARKS motif,thereby interfering with H3 post-translational modifications(PTMs),disrupting gene transcription,and diminishing the antiviral response.

关键词： mimic thereby function

Deep learning-based optical aberration estimation enables offline digital adaptive optics and super-resolution imaging

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Photonics Research 2024年第3期12卷 474-484页

作者： CHANG QIAO HAOYU CHEN RUN WANG TAO JIANG YUWANG WANG DONG LI Department of Automation Tsinghua UniversityBeijing 100084China Institute for Brain and Cognitive Sciences Tsinghua UniversityBeijing 100084China national laboratory of biomacromolecules New Cornerstone Science LaboratoryCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China Beijing national Research Center for Information Science and Technology Tsinghua UniversityBeijing 100084China

Optical aberrations degrade the performance of fluorescence microscopy.Conventional adaptive optics(AO)leverages specific devices,such as the Shack–Hartmann wavefront sensor and deformable mirror,to measure and correct optical aberrations.However,conventional AO requires either additional hardware or a more complicated imaging procedure,resulting in higher cost or a lower acquisition speed.In this study,we proposed a novel space-frequency encoding network(SFE-Net)that can directly estimate the aberrated point spread functions(PSFs)from biological images,enabling fast optical aberration estimation with high accuracy without engaging extra optics and image acquisition.We showed that with the estimated PSFs,the optical aberration can be computationally removed by the deconvolution algorithm.Furthermore,to fully exploit the benefits of SFE-Net,we incorporated the estimated PSF with neural network architecture design to devise an aberration-aware deeplearning super-resolution model,dubbed SFT-DFCAN.We demonstrated that the combination of SFE-Net and SFT-DFCAN enables instant digital AO and optical aberration-aware super-resolution reconstruction for live-cell imaging.

关键词： optics resolution enable

Complicated target recognition by archaeal box C/D guide RNAs

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Science China(Life Sciences) 2024年第4期67卷 631-644页

作者： Jiayin Wang Songlin Wu Keqiong Ye Key laboratory of RNA Science and Engineering CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Box C/D RNAs guide the site-specific formation of 2′-O-methylated nucleotides(Nm)of RNAs in eukaryotes and archaea.Although C/D RNAs have been profiled in several archaea,their targets have not been experimentally determined.Here,we mapped Nm in r RNAs,t RNAs,and abundant small RNAs(s RNAs)and profiled C/D RNAs in the crenarchaeon Sulfolobus islandicus.The targets of C/D RNAs were assigned by analysis of base-pairing interactions,in vitro modification assays,and gene deletion experiments,revealing a complicated landscape of C/D RNA-target interactions.C/D RNAs widely use dual antisense elements to target adjacent sites in r RNAs,enhancing modification at weakly bound sites.Two consecutive sites can be guided with the same antisense element upstream of box D or D′,a phenomenon known as doublespecificity that is exclusive to internal box D′in eukaryotic C/D RNAs.Several C/D RNAs guide modification at a single non-canonical site.This study reveals the global landscape of RNA-guided 2′-O-methylation in an archaeon and unexpected targeting rules employed by C/D RNA.

关键词： C/D RNA 2′-O-methylation archaea guide RNA RNA modification

Plant RNA-binding proteins:Phase separation dynamics and functional mechanisms underlying plant development and stress responses

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Molecular Plant 2024年第4期17卷 531-551页

作者： Sheng Fan Yu Zhang Shaobo Zhu Lisha Shen Temasek Life Sciences laboratory 1 Research LinkNational University of Singapore1 Research LinkSingapore 117604Singapore Department of Biological Sciences National University of Singapore14 Science Drive 4Singapore 117543Singapore

RNA-binding proteins(RBPs)accompany RNA from synthesis to decay,mediating every aspect of RNA metabolism and impacting diverse cellular and developmental processes in eukaryotes.Many RBPs undergo phase separation along with their bound RNA to form and function in dynamic membraneless biomolecular condensates for spatiotemporal coordination or regulation of RNA metabolism.Increasing evidence suggests that phase-separating RBPs with RNA-binding domains and intrinsically disordered regions play important roles in plant development and stress adaptation.Here,we summarize the current knowledge about how dynamic partitioning of RBPs into condensates controls plant development and enables sensing of experimental changes to confer growth plasticity under stress conditions,with a focus on the dynamics and functional mechanisms of RBP-rich nuclear condensates and cytoplasmic granules in mediating RNA metabolism.We also discuss roles of multiple factors,such as environmental signals,protein modifications,and N6-methyladenosine RNA methylation,in modulating the phase separation behaviors of RBPs,and highlight the prospects and challenges for future research on phase-separating RBPs in crops.

关键词： RNA-binding proteins phase separation biomolecular condensates RNA metabolism development stress resilience

Functional genomics of Brassica napus:Progresses,challenges,and perspectives

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Journal of Integrative Plant Biology 2024年第3期66卷 484-509页

作者： Zengdong Tan Xu Han Cheng Dai Shaoping Lu Hanzi He Xuan Yao Peng Chen Chao Yang Lun Zhao Qing-Yong Yang Jun Zou Jing Wen Dengfeng Hong Chao Liu Xianhong Ge Chuchuan Fan Bing Yi Chunyu Zhang Chaozhi Ma Kede Liu Jinxiong Shen Jinxing Tu Guangsheng Yang Tingdong Fu Liang Guo Hu Zhao national Key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Yazhouwan national laboratory Sanya 572025China

Brassica napus,commonly known as rapeseed or canola,is a major oil crop contributing over 13%to the stable supply of edible vegetable oil worldwide.Identification and understanding the gene functions in the B.napus genome is crucial for genomic breeding.A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B.napus.In this review,we present an overview of the progress made in the functional genomics of B.napus,including the availability of germplasm resources,omics databases and cloned functional genes.Based on the current progress,we also highlight the main challenges and perspectives in this field.The advances in the functional genomics of B.napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B.napus and will expedite the breeding of high quality,high resistance and high yield in B.napus varieties.

关键词： accelerate breeding Brassica napus functional genomics high resistance high yield

Adaptive learning-based optimal tracking control system design and analysis of a disturbed nonlinear hypersonic vehicle model

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Science China Technological Sciences 2024年第6期67卷 1893-1906页

作者： AN Kai WANG ZhenGuo HUANG Wei national University of Defense Technology Hypersonic Technology laboratory

We propose an adaptive learning-based optimal control scheme for height-velocity control models considering model uncertainties and external disturbances of hypersonic winged-cone vehicles. The longitudinal nonlinear model is first established and transformed into the control-oriented error equations, and the control scheme is organized by a steady-compensation combination. To overcome and eliminate the impact of model uncertainties and external disturbances, an adaptive radial basis function neural network(RBFNN) is designed by a q-gradient approach. Taking the height-velocity error system with estimated uncertainties into account, the adaptive learning-based optimal tracking control(ALOTC) scheme is proposed by combining the critic-only adaptive dynamic programming(ADP) framework and parameter optimization of system settling time. Furthermore,a novel weight update law is proposed to satisfy the online iteration requirements, and the algorithm convergence and closedloop stability are discussed by the Lyapunov theory. Finally, four simulation cases are provided to prove the effectiveness,accuracy, and robustness of the proposed scheme for the hypersonic longitudinal control system.

关键词： optimal tracking control adaptive dynamic programming RBFNN hypersonic vehicle

Machine Learning Analysis of Impact of Western US Fires on Central US Hailstorms

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Advances in Atmospheric Sciences 2024年第7期41卷 1450-1462页

作者： Xinming LIN Jiwen FAN Yuwei ZHANG ZJason HOU Pacific Northwest national laboratory RichlandWA 99354USA Argonne national laboratory LemontIL 60439USA

Fires,including wildfires,harm air quality and essential public services like transportation,communication,and utilities.These fires can also influence atmospheric conditions,including temperature and aerosols,potentially affecting severe convective storms.Here,we investigate the remote impacts of fires in the western United States(WUS)on the occurrence of large hail(size:≥2.54 cm)in the central US(CUS)over the 20-year period of 2001–20 using the machine learning(ML),Random Forest(RF),and Extreme Gradient Boosting(XGB)methods.The developed RF and XGB models demonstrate high accuracy(>90%)and F1 scores of up to 0.78 in predicting large hail occurrences when WUS fires and CUS hailstorms coincide,particularly in four states(Wyoming,South Dakota,Nebraska,and Kansas).The key contributing variables identified from both ML models include the meteorological variables in the fire region(temperature and moisture),the westerly wind over the plume transport path,and the fire features(i.e.,the maximum fire power and burned area).The results confirm a linkage between WUS fires and severe weather in the CUS,corroborating the findings of our previous modeling study conducted on case simulations with a detailed physics model.

关键词： wildfire severe convective storm hailstorm machine learning

Epigenetic control on transcription of vernalization genes and whole-genome gene expression profile induced by vernalization in common wheat

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Plant Diversity 2024年第3期46卷 386-394页

作者： Yunzhen Li Liujie Jin Xinyu Liu Chao He Siteng Bi Sulaiman Saeed Wenhao Yan national Key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China

Vernalization is necessary for winter wheat to flower.However,it is unclear whether vernalization is also required for spring wheat,which is frequently sown in fall,and what molecular mechanisms underlie the vernalization response in wheat varieties.In this study,we examined the molecular mechanisms that regulate vernalization response in winter and spring wheat varieties.For this purpose,we determined how major vernalization genes(VRN1,VRN2,and VRN3)respond to vernalization in these varieties and whether modifications to histones play a role in changes in gene expression.We also identified genes that are differentially regulated in response to vernalization in winter and spring wheat varieties.We found that in winter wheat,but not in spring wheat,VRN1 expression decreases when returned to warm temperature following vernalization.This finding may be associated with differences between spring and winter wheat in the levels of tri-methylation of lysine 27 on histone H3(H3K27me3)and tri-methylation of lysine 4 on histone H3(H3K4me3)at the VRN1 gene.Analysis of winter wheat transcriptomes before and after vernalization revealed that vernalization influences the expression of several genes,including those involved in leucine catabolism,cysteine biosynthesis,and flavonoid biosynthesis.These findings provide new candidates for further study on the mechanism of vernalization regulation in wheat.

关键词： Wheat Vernalization VRN1 Histone modification Regulate network

Broadband high-efficiency plasmonic metalens with negative dispersion characteristic

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Photonics Research 2024年第4期12卷 813-820页

作者： YONG-QIANG LIU YONG ZHU HONGCHENG YIN JINHAI SUN YAN WANG YONGXING CHE national Key laboratory of Scattering and Radiation Beijing 100854China

Controlling the dispersion characteristic of metasurfaces(or metalenses) along a broad bandwidth is of great importance to develop high-performance broadband metadevices. Different from traditional lenses that rely on the material refractive index along the light trajectory, metasurfaces or metalenses provide a new regime of dispersion control via a sub-wavelength metastructure, which is known as negative chromatic dispersion.However, broadband metalenses design with high-performance focusing especially with a reduced device dimension is a significant challenge in society. Here, we design, fabricate, and demonstrate a broadband highperformance diffractive-type plasmonic metalens based on a circular split-ring resonator metasurface with a relative working bandwidth of 28.6%. The metalens thickness is only 0.09λ0(λ0is at the central wavelength),which is much thinner than previous broadband all-dielectric metalenses. The full-wave simulation results show that both high transmissive efficiency above 80%(the maximum is even above 90%) and high average focusing efficiency above 45%(the maximum is 56%) are achieved within the entire working bandwidth of 9–12 GHz.Moreover, an average high numerical aperture of 0.7(NA = 0.7) of high-efficiency microwave metalens is obtained in the simulations. The broadband high-performance metalens is also fabricated and experimental measurements verify its much higher average focusing efficiency of 55%(the maximum is above 65% within the broad bandwidth) and a moderate high NA of 0.6. The proposed plasmonic metalens can facilitate the development of wavelength-dependent broadband diffractive devices and is also meaningful to further studies on arbitrary dispersion control in diffractive optics based on plasmonic metasurfaces.

关键词： resonator dispersion high