In ultrafast optical imaging,it is critical to obtain the spatial structure,temporal evolution,and spectral composition of the object with snapshots in order to better observe and understand unrepeatable or irreversib...In ultrafast optical imaging,it is critical to obtain the spatial structure,temporal evolution,and spectral composition of the object with snapshots in order to better observe and understand unrepeatable or irreversible dynamic scenes.However,so far,there are no ultrafast optical imaging techniques that can simultaneously capture the spatial–temporal–spectral five-dimensional(5D)information of dynamic scenes.To break the limitation of the existing techniques in imaging dimensions,we develop a spectral-volumetric compressed ultrafast photography(SV-CUP)technique.In our SV-CUP,the spatial resolutions in the x,y and z directions are,respectively,0.39,0.35,and 3 mm with an 8.8 mm×6.3 mm field of view,the temporal frame interval is 2 ps,and the spectral frame interval is 1.72 nm.To demonstrate the excellent performance of our SV-CUP in spatial–temporal–spectral 5D imaging,we successfully measure the spectrally resolved photoluminescent dynamics of a 3D mannequin coated with CdSe quantum dots.Our SV-CUP brings unprecedented detection capabilities to dynamic scenes,which has important application prospects in fundamental research and applied science.展开更多
Coix lacryma-jobi,a plant species closely related to Zea and Sorghum,is an important food and medicinal crop in Asia.However,no reference genome of this species has been reported,and its exact phylogeny within the And...Coix lacryma-jobi,a plant species closely related to Zea and Sorghum,is an important food and medicinal crop in Asia.However,no reference genome of this species has been reported,and its exact phylogeny within the Andropogoneae remains unresolved.Here,we generated a high-quality genome assembly of coix comprising～1.73 Gb with 44485 predicted protein-coding genes.We found coix to be a typical diploid plant with an overall 1-to-1 syntenic relationship with the Sorghum genome,despite its drastic genome expansion(～2.3-fold)due mainly to the activity of transposable elements.Phylogenetic analysis revealed that coix diverged with sorghum～10.41 million years ago,which was～1.49 million years later than the divergence between sorghum and maize.Resequencing of 27 additional coix accessions revealed that they could be unambiguously separated into wild relatives and cultivars,and suggested that coix experienced a strong genetic bottleneck,resulting in the loss of about half of the genetic diversity during domestication,even though many traits have remained undomesticated.Our data not only provide novel comparative genomic and evolutionary insights into the Andropogoneae lineage,but also an important resource that will greatly benefit molecular breeding of this important crop.展开更多
Cereal is an essential source of calories and protein for the global population.Accurately predicting cereal quality before harvest is highly desirable in order to optimise management for farmers,grading harvest and c...Cereal is an essential source of calories and protein for the global population.Accurately predicting cereal quality before harvest is highly desirable in order to optimise management for farmers,grading harvest and categorised storage for enterprises,future trading prices,and policy planning.The use of remote sensing data with extensive spatial coverage demonstrates some potential in predicting crop quality traits.Many studies have also proposed models and methods for predicting such traits based on multiplatform remote sensing data.In this paper,the key quality traits that are of interest to producers and consumers are introduced.The literature related to grain quality prediction was analyzed in detail,and a review was conducted on remote sensing platforms,commonly used methods,potential gaps,and future trends in crop quality prediction.This review recommends new research directions that go beyond the traditional methods and discusses grain quality retrieval and the associated challenges from the perspective of remote sensing data.展开更多
Dasypyrum villosum is one of the most valuable gene resources in wheat improvement,especially for disease resistance.The mining of favorable genes from D.villosum is frustrated by the lack of a whole genome sequence.I...Dasypyrum villosum is one of the most valuable gene resources in wheat improvement,especially for disease resistance.The mining of favorable genes from D.villosum is frustrated by the lack of a whole genome sequence.In this study,we generated a doubled-haploid line,91C43^(DH),using microspore culture and obtained a 4.05-GB high-quality,chromosome-scale genome assembly for D.villosum.The assembly contains39727 high-confidence genes,and 85.31% of the sequences are repetitive.Two reciprocal translocation events were detected,and 7VS-4VL is a unique translocation in D.villosum.The prolamin seed storage protein-coding genes were found to be duplicated;in particular,the genes encoding low-molecular-weight glutenin at the Glu-V3 locus were significantly expanded.RNA sequencing(RNA-seq)analysis indicated that,after Blumeria graminearum f.sp tritici(Bgt)inoculation,there were more upregulated genes involved in the pattern-triggered immunity and effector-triggered immunity defense pathways in D.villosum than in Triticum urartu.MNase hypersensitive sequencing(MH-seq)identified two Bgt-inducible MH sites(MHSs),one in the promoter and one in the 3'terminal region of the powdery mildew resistance(Pm)gene NLR1-V.Each site had two subpeaks and they were termed MHS1(MHS1.1/1.2)and MHS2(MHS2.1/2.2).Bgt-inducible MHS2.2 was uniquely present in D.villosum,and MHS1.1 was more inducible in D.villosum than in wheat,suggesting that MHSs may be critical for regulation of NLR1-V expression and plant defense.In summary,this study provides a valuable genome resource for functional genomics studies and wheat-D.villosum introgression breeding.The identified regulatory mechanisms may also be exploited to develop new strategies for enhancing Pm resistance by optimizing gene expression in wheat.展开更多
Structured illumination microscopy (SIM) has been widely applied to investigate intricate biological dynamics due to its outstanding super-resolution imaging speed. Incorporating compressive sensing into SIM brings th...Structured illumination microscopy (SIM) has been widely applied to investigate intricate biological dynamics due to its outstanding super-resolution imaging speed. Incorporating compressive sensing into SIM brings the possibility to further improve the super-resolution imaging speed. Nevertheless, the recovery of the superresolution information from the compressed measurement remains challenging in experiments. Here, we report structured illumination microscopy with complementary encoding-based compressive imaging (CECI-SIM) to realize faster super-resolution imaging. Compared to the nine measurements to obtain a super-resolution image in a conventional SIM, CECI-SIM can achieve a super-resolution image by three measurements;therefore, a threefold improvement in the imaging speed can be achieved. This faster imaging ability in CECI-SIM is experimentally verified by observing tubulin and actin in mouse embryonic fibroblast cells. This work provides a feasible solution for high-speed super-resolution imaging, which would bring significant applications in biomedical research.展开更多
Euglena gracilis 277, a unicellular green alga, demonstrated remarkable ability to transport Nd3+ to the cell compartments. For a given amount of Nd3+ and cells, the results of ICP-AES indicated that the cellular upta...Euglena gracilis 277, a unicellular green alga, demonstrated remarkable ability to transport Nd3+ to the cell compartments. For a given amount of Nd3+ and cells, the results of ICP-AES indicated that the cellular uptake of Nd3+ was independent of Nd3+ concentration in thebulk solution. The average uptake of Nd3+ per celi (mMd) is proportional to a parameter ξ-theratio of neodymium content to the celi counts of the system. A novel approach for probing cellular neodymium by tetraiodotetra chlorofluorescein (I4TCF) has been devised. Data derived from the cryosections of !4TCF-Nd3+ stained cells and EDAX of the fast freezing ultrathin cryosections indicate that Nd3+ is distributed over the celi compartments. Chloroplasts are the major compartments as the residence of Nd3+ in the alga. The transport should be against a concentration gradient of Nd3+ on the order of five, even higher. it is proposed that a calcium ion channel would play an important role in the Nd3+ transportation.展开更多
New acquired and reprocessed three-dimensional(3D)seismic data were used to delineate the distribution and characterization of bottom simulating reflections(BSRs)in the Chaoshan Sag,in the eastern part of Dongsha Isla...New acquired and reprocessed three-dimensional(3D)seismic data were used to delineate the distribution and characterization of bottom simulating reflections(BSRs)in the Chaoshan Sag,in the eastern part of Dongsha Island,South China Sea.Three submarine canyons with different scales were interpreted from the 3D seismic data,displaying three stages of canyon development and are related with the variation of BSR.Abundant faults were identified from the coherence and ant-tracing attributions extracted from 3D seismic data,which provide the evidence for fluid migration from deeper sediments to the gas hydrate stability zone(GHSZ).The uplift of Dongsha Island created a large number of faults and leads to the increased seafloor erosion.The erosion caused the cooling of the seafloor sediments and deepening of the base of the gas hydrate stability zone,which is attributed to the presence of paleo-BSR and BSR downward shift in the study area.Hence,methane gas may be released during the BSR resetting and gas hydrate dissociation related with seafloor erosion.展开更多
Various super-resolution microscopy techniques have been presented to explore fine structures of biological specimens.However,the super-resolution capability is often achieved at the expense of reducing imaging speed ...Various super-resolution microscopy techniques have been presented to explore fine structures of biological specimens.However,the super-resolution capability is often achieved at the expense of reducing imaging speed by either point scanning or multiframe computation.The contradiction between spatial resolution and imaging speed seriously hampers the observation of high-speed dynamics of fine structures.To overcome this contradiction,here we propose and demonstrate a temporal compressive super-resolution microscopy(TCSRM)technique.This technique is to merge an enhanced temporal compressive microscopy and a deep-learning-based super-resolution image reconstruction,where the enhanced temporal compressive microscopy is utilized to improve the imaging speed,and the deep-learning-based super-resolution image reconstruction is used to realize the resolution enhancement.The high-speed super-resolution imaging ability of TCSRM with a frame rate of 1200 frames per second(fps)and spatial resolution of 100 nm is experimentally demonstrated by capturing the flowing fluorescent beads in microfluidic chip.Given the outstanding imaging performance with high-speed super-resolution,TCSRM provides a desired tool for the studies of high-speed dynamical behaviors in fine structures,especially in the biomedical field.展开更多
To explain the effect of joint roughness on joint peak shear strength(JPSS)and investigate the effect of different contact states of joint surface on JPSS,we try to clarify the physical mechanism of the effect of join...To explain the effect of joint roughness on joint peak shear strength(JPSS)and investigate the effect of different contact states of joint surface on JPSS,we try to clarify the physical mechanism of the effect of joint cavity percentage(JCP)on JPSS from the perspective of the three-dimensional(3D)distribution characteristics of the actual contact joint surface,and propose a JPSS model considering the JCP.Shear tests for red sandstone joints with three different surface morphologies and three different JCPs were performed under constant normal load condition.Based on test fitting results,the reduction effect of the JCP on JPSS is investigated,and a JPSS model for cavity-containing joints is obtained.However,the above model only considers the influence of JCP by fitting test data,and does not reveal the physical mechanism of JCP affecting the JPSS.Based on the peak dilation angle model for consideration of the actual contact joint morphology,and the influence of JCP on the roughness of the actual contact joint surface,a theoretical model of the JPSS considering the JCP is proposed.The derivation process does not depend on the test fitting,but is entirely based on the joint mechanical law,and its physical significance is clear.It is proposed that the essence of the influence of the JCP on JPSS is that the JCP first affects the normal stress of the actual contact joints,further affects the roughness of actual contact joints,and then affects the shear strength.展开更多
基金partially partially supported by the National Natural Science Foundation of China(Grant Nos.91850202,11774094,12074121,11804097,11727810,and 12034008)the Science and Technology Commission of Shanghai Municipality(Grant Nos.19560710300 and 20ZR1417100)Ministère des Relations internationales et de la Francophonie du Québec。
文摘In ultrafast optical imaging,it is critical to obtain the spatial structure,temporal evolution,and spectral composition of the object with snapshots in order to better observe and understand unrepeatable or irreversible dynamic scenes.However,so far,there are no ultrafast optical imaging techniques that can simultaneously capture the spatial–temporal–spectral five-dimensional(5D)information of dynamic scenes.To break the limitation of the existing techniques in imaging dimensions,we develop a spectral-volumetric compressed ultrafast photography(SV-CUP)technique.In our SV-CUP,the spatial resolutions in the x,y and z directions are,respectively,0.39,0.35,and 3 mm with an 8.8 mm×6.3 mm field of view,the temporal frame interval is 2 ps,and the spectral frame interval is 1.72 nm.To demonstrate the excellent performance of our SV-CUP in spatial–temporal–spectral 5D imaging,we successfully measure the spectrally resolved photoluminescent dynamics of a 3D mannequin coated with CdSe quantum dots.Our SV-CUP brings unprecedented detection capabilities to dynamic scenes,which has important application prospects in fundamental research and applied science.
基金supported by the National Key Research and Development Program(2016YFD0101003)of China and the National Natural Science Foundation of China(91735305,91435206,91635303-3,31701430 and 31421005).
文摘Coix lacryma-jobi,a plant species closely related to Zea and Sorghum,is an important food and medicinal crop in Asia.However,no reference genome of this species has been reported,and its exact phylogeny within the Andropogoneae remains unresolved.Here,we generated a high-quality genome assembly of coix comprising～1.73 Gb with 44485 predicted protein-coding genes.We found coix to be a typical diploid plant with an overall 1-to-1 syntenic relationship with the Sorghum genome,despite its drastic genome expansion(～2.3-fold)due mainly to the activity of transposable elements.Phylogenetic analysis revealed that coix diverged with sorghum～10.41 million years ago,which was～1.49 million years later than the divergence between sorghum and maize.Resequencing of 27 additional coix accessions revealed that they could be unambiguously separated into wild relatives and cultivars,and suggested that coix experienced a strong genetic bottleneck,resulting in the loss of about half of the genetic diversity during domestication,even though many traits have remained undomesticated.Our data not only provide novel comparative genomic and evolutionary insights into the Andropogoneae lineage,but also an important resource that will greatly benefit molecular breeding of this important crop.
基金This study was supported by the National Natural Science Foundation of China(42271396)the Natural Science Foundation of Shandong Province(ZR2022MD017)+1 种基金the Key R&D Project of Hebei Province(22326406D)The European Space Agency(ESA)and Ministry of Science and Technology of China(MOST)Dragon(57457).
文摘Cereal is an essential source of calories and protein for the global population.Accurately predicting cereal quality before harvest is highly desirable in order to optimise management for farmers,grading harvest and categorised storage for enterprises,future trading prices,and policy planning.The use of remote sensing data with extensive spatial coverage demonstrates some potential in predicting crop quality traits.Many studies have also proposed models and methods for predicting such traits based on multiplatform remote sensing data.In this paper,the key quality traits that are of interest to producers and consumers are introduced.The literature related to grain quality prediction was analyzed in detail,and a review was conducted on remote sensing platforms,commonly used methods,potential gaps,and future trends in crop quality prediction.This review recommends new research directions that go beyond the traditional methods and discusses grain quality retrieval and the associated challenges from the perspective of remote sensing data.
基金financially supported by the National Key Agriculture Projects(NK2022060101)National Key Research and Development Program(2022YFF1002900,2020YFE0202900)+3 种基金the Fundamental Research Funds for the Central University(XUEKEN2022012)Jiangsu Provincial Key Research and Development Program(BE2021375,BE2022346)Seed Industry Revitalization Project of Jiangsu Province(JBGS2021006,2021013,2021047)Joint Research of Improved Wheat Variety of Anhui,and Jiangsu Agricultural Technology System(JATS)(JATS[2021]463,JATS[2022]464).
文摘Dasypyrum villosum is one of the most valuable gene resources in wheat improvement,especially for disease resistance.The mining of favorable genes from D.villosum is frustrated by the lack of a whole genome sequence.In this study,we generated a doubled-haploid line,91C43^(DH),using microspore culture and obtained a 4.05-GB high-quality,chromosome-scale genome assembly for D.villosum.The assembly contains39727 high-confidence genes,and 85.31% of the sequences are repetitive.Two reciprocal translocation events were detected,and 7VS-4VL is a unique translocation in D.villosum.The prolamin seed storage protein-coding genes were found to be duplicated;in particular,the genes encoding low-molecular-weight glutenin at the Glu-V3 locus were significantly expanded.RNA sequencing(RNA-seq)analysis indicated that,after Blumeria graminearum f.sp tritici(Bgt)inoculation,there were more upregulated genes involved in the pattern-triggered immunity and effector-triggered immunity defense pathways in D.villosum than in Triticum urartu.MNase hypersensitive sequencing(MH-seq)identified two Bgt-inducible MH sites(MHSs),one in the promoter and one in the 3'terminal region of the powdery mildew resistance(Pm)gene NLR1-V.Each site had two subpeaks and they were termed MHS1(MHS1.1/1.2)and MHS2(MHS2.1/2.2).Bgt-inducible MHS2.2 was uniquely present in D.villosum,and MHS1.1 was more inducible in D.villosum than in wheat,suggesting that MHSs may be critical for regulation of NLR1-V expression and plant defense.In summary,this study provides a valuable genome resource for functional genomics studies and wheat-D.villosum introgression breeding.The identified regulatory mechanisms may also be exploited to develop new strategies for enhancing Pm resistance by optimizing gene expression in wheat.
基金National Natural Science Foundation of China(12034008, 12074121, 12274129, 12274139, 12304338,12325408, 12734274, 62105101, 62175066, 92150301)Science and Technology Commission of Shanghai Municipality (20ZR1417100, 21JM0010700, 21XD1400900)。
文摘Structured illumination microscopy (SIM) has been widely applied to investigate intricate biological dynamics due to its outstanding super-resolution imaging speed. Incorporating compressive sensing into SIM brings the possibility to further improve the super-resolution imaging speed. Nevertheless, the recovery of the superresolution information from the compressed measurement remains challenging in experiments. Here, we report structured illumination microscopy with complementary encoding-based compressive imaging (CECI-SIM) to realize faster super-resolution imaging. Compared to the nine measurements to obtain a super-resolution image in a conventional SIM, CECI-SIM can achieve a super-resolution image by three measurements;therefore, a threefold improvement in the imaging speed can be achieved. This faster imaging ability in CECI-SIM is experimentally verified by observing tubulin and actin in mouse embryonic fibroblast cells. This work provides a feasible solution for high-speed super-resolution imaging, which would bring significant applications in biomedical research.
文摘压缩超快成像(compressed ultrafast photography,CUP)是目前最快的被动式单次超快光学成像技术,它通过数据获取和图像重构两个步骤实现超快事件的捕捉,已发展为记录不可逆或难以重复超快事件的一种有力工具,且能够探测荧光动力学等自发光瞬态场景.然而,传统的迭代优化型算法在图像重构上的保真度较低,而端到端型深度学习算法则严重依赖训练数据,训练复杂度高、通用性不足,这限制了CUP对超快现象进行高空间分辨率的观测.为此,我们开发了一种新型的免训练自监督式神经网络算法,其通过即插即用框架(plug-and-play,PnP)与深度图像先验(deep image prior,DIP)的结合可实现CUP的低复杂度高保真图像重建,简称为PnP-DIP算法.PnP-DIP基于交替方向乘子法(alternating direction method of multipliers,ADMM),利用DIP和PnP去噪器解决图像恢复子问题,可以在防止数据过拟合和噪声累积的同时,显著提高图像重建的精度与收敛速度.通过数值模拟,我们理论上证明了PnP-DIP算法在重构原始动态信息方面相比传统ADMM算法具有更高的保真度.同时,我们分别利用PnPDIP对自主研制CUP系统观测的皮秒激光脉冲和X射线闪烁体的时空强度演化数据进行重构,实验上验证了其优越的图像重构性能.这一研究有望推动CUP在高时空分辨观测需求中的应用,并为超快动力学的实时探测作出重大贡献.
文摘Euglena gracilis 277, a unicellular green alga, demonstrated remarkable ability to transport Nd3+ to the cell compartments. For a given amount of Nd3+ and cells, the results of ICP-AES indicated that the cellular uptake of Nd3+ was independent of Nd3+ concentration in thebulk solution. The average uptake of Nd3+ per celi (mMd) is proportional to a parameter ξ-theratio of neodymium content to the celi counts of the system. A novel approach for probing cellular neodymium by tetraiodotetra chlorofluorescein (I4TCF) has been devised. Data derived from the cryosections of !4TCF-Nd3+ stained cells and EDAX of the fast freezing ultrathin cryosections indicate that Nd3+ is distributed over the celi compartments. Chloroplasts are the major compartments as the residence of Nd3+ in the alga. The transport should be against a concentration gradient of Nd3+ on the order of five, even higher. it is proposed that a calcium ion channel would play an important role in the Nd3+ transportation.
基金the National Key R&D Program of China(No.2017YFC0307301-1)the National Natural Science Foundation of China(No.41676041)+1 种基金the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)(No.GML2019ZD0104)the National High Technology Research and Development Program of China(863 Program)(No.2013AA092601)。
文摘New acquired and reprocessed three-dimensional(3D)seismic data were used to delineate the distribution and characterization of bottom simulating reflections(BSRs)in the Chaoshan Sag,in the eastern part of Dongsha Island,South China Sea.Three submarine canyons with different scales were interpreted from the 3D seismic data,displaying three stages of canyon development and are related with the variation of BSR.Abundant faults were identified from the coherence and ant-tracing attributions extracted from 3D seismic data,which provide the evidence for fluid migration from deeper sediments to the gas hydrate stability zone(GHSZ).The uplift of Dongsha Island created a large number of faults and leads to the increased seafloor erosion.The erosion caused the cooling of the seafloor sediments and deepening of the base of the gas hydrate stability zone,which is attributed to the presence of paleo-BSR and BSR downward shift in the study area.Hence,methane gas may be released during the BSR resetting and gas hydrate dissociation related with seafloor erosion.
基金the National Natural Science Foundation of China(91850202,92150301,12074121,62105101,62175066,11727810,12034008,12274129,12274139)Science and Technology Commission of Shanghai Municipality(21XD1400900,20ZR1417100,21JM0010700).
文摘Various super-resolution microscopy techniques have been presented to explore fine structures of biological specimens.However,the super-resolution capability is often achieved at the expense of reducing imaging speed by either point scanning or multiframe computation.The contradiction between spatial resolution and imaging speed seriously hampers the observation of high-speed dynamics of fine structures.To overcome this contradiction,here we propose and demonstrate a temporal compressive super-resolution microscopy(TCSRM)technique.This technique is to merge an enhanced temporal compressive microscopy and a deep-learning-based super-resolution image reconstruction,where the enhanced temporal compressive microscopy is utilized to improve the imaging speed,and the deep-learning-based super-resolution image reconstruction is used to realize the resolution enhancement.The high-speed super-resolution imaging ability of TCSRM with a frame rate of 1200 frames per second(fps)and spatial resolution of 100 nm is experimentally demonstrated by capturing the flowing fluorescent beads in microfluidic chip.Given the outstanding imaging performance with high-speed super-resolution,TCSRM provides a desired tool for the studies of high-speed dynamical behaviors in fine structures,especially in the biomedical field.
基金supported by the National Natural Science Foundation of China (Nos.52208328 and 52104090)Open Research Fund Program of State Key Laboratory of Hydroscience and Engineering (No.sklhse-2021-C-06).
文摘To explain the effect of joint roughness on joint peak shear strength(JPSS)and investigate the effect of different contact states of joint surface on JPSS,we try to clarify the physical mechanism of the effect of joint cavity percentage(JCP)on JPSS from the perspective of the three-dimensional(3D)distribution characteristics of the actual contact joint surface,and propose a JPSS model considering the JCP.Shear tests for red sandstone joints with three different surface morphologies and three different JCPs were performed under constant normal load condition.Based on test fitting results,the reduction effect of the JCP on JPSS is investigated,and a JPSS model for cavity-containing joints is obtained.However,the above model only considers the influence of JCP by fitting test data,and does not reveal the physical mechanism of JCP affecting the JPSS.Based on the peak dilation angle model for consideration of the actual contact joint morphology,and the influence of JCP on the roughness of the actual contact joint surface,a theoretical model of the JPSS considering the JCP is proposed.The derivation process does not depend on the test fitting,but is entirely based on the joint mechanical law,and its physical significance is clear.It is proposed that the essence of the influence of the JCP on JPSS is that the JCP first affects the normal stress of the actual contact joints,further affects the roughness of actual contact joints,and then affects the shear strength.
基金partially supported by the National Natural Science Foundation of China(92150301,12074121,62105101,62175066,12274129,and 12274139)the Science and Technology Commission of Shanghai Municipality(21XD1400900,21JM0010700,and 20ZR1417100).
