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| 1 | Crop Phenomics and High-Throughput Phenotyping:Past Decades,Current Challenges,and Future Perspectives显示文摘Since whole-genome sequencing of many crops has been achieved,crop functional genomics studies have stepped into the big-data and high-throughput era.However,acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies.Nevertheless,recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years.In this article,we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades.We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies.Finally,we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap.It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding. | Wanneng Yang Hui Feng Xuehai Zhang Jian Zhang John H.Doonan William David Batchelor Lizhong Xiong Jianbing Yan | 2020 | Molecular Plant2020，13，2： | 38 |
| 2 | ZmCOL3, a CCT gene represses flowering in maize by interfering with the circadian clock and activating expression of ZmCCT显示文摘Flowering time is a trait vital to the adaptation of flowering plants to different environments.Here, we report that CCT domain genes play an important role in flowering in maize(Zea mays L.).Among the 53 CCT family genes we identified in maize, 28 were located in flowering time quantitative trait locus regions and 15 were significantly associated with flowering time, based on candidate-gene association mapping analysis.Furthermore, a CCT gene named ZmCOL3 was shown to be a repressor of flowering.Overexpressing ZmCOL3 delayed flowering time by approximately 4 d, in either long-day or short-day conditions.The absence of one cytosine in the ZmCOL3 3'UTR and the presence of a 551 bp fragment in the promoter region are likely the causal polymorphisms contributing to the maize adaptation from tropical to temperate regions.We propose a modified model of the maize photoperiod pathway, wherein ZmCOL3 acts as an inhibitor of flowering either by transactivating transcription of ZmCCT, one of the key genes regulating maize flowering, or by interfering with the circadian clock. | Minliang Jin Xiangguo Liu Wei Jia Haijun Liu Wenqiang Li Yong Peng Yanfang Du Yuebin Wang Yuejia Yin Xuehai Zhang Qing Liu Min Deng Nan Li Xiyan Cui Dongyun Hao Jianbing Yan | 2018 | Journal of Integrative Plant Biology2018，60，6： | 14 |
| 3 | Validation and modification of the AJCC 8th TNM staging system for pancreatic ductal adenocarcinoma in a Chinese cohort:A nationwide pancreas data center analysis显示文摘Objective:To validate the 8 th edition of the American Joint Committee on Cancer(AJCC)staging system for pancreatic ductal adenocarcinoma(PDAC)in a Chinese cohort of radically resected patients and to develop a refined staging system for PDAC.Methods:Data were collected from the China Pancreas Data Center(CPDC)for patients with resected PDAC in 2016 and 2017,and cancer-specific survival(CSS)was evaluated using the Kaplan-Meier method and log-rank test.Univariate and multivariate analyses based on Cox regression were performed to identify prognostic factors.The recursive partitioning analysis(RPA),Kaplan-Meier method,and log-rank test were performed on the training dataset to generate a proposed modification for the 8 th TNM staging system utilizing the preoperative carbohydrate antigen(CA)19-9 level.Validation was performed for both staging systems in the validation cohort.Results:A total of 1,676 PDAC patients were retrieved,and the median CSS was significantly different between the 8 th TNM groupings,with no significant difference in survival between stage IB and IIA.The analysis of T and N stages demonstrated a better prognostic value in the N category.Multivariate analysis showed that the preoperative serum CA19-9 level was the strongest prognostic indicator among all the independent risk factors.All patients with CA19-9>500 U/mL had similar survival,and we proposed a new staging system by combining IB and IIA and stratifying all patients with high CA19-9 into stage III.The modified staging system had a better performance for predicting CSS than the 8 th AJCC staging scheme.Conclusions:The 8 th AJCC staging system for PDAC is suitable for a Chinese cohort of resected patients,and the N category has a better prognostic value than the T category.Our modified staging system has superior accuracy in predicting survival than the 8 th AJCC TNM staging system. | Hao Hu Chang Qu Bingjun Tang Weikang Liu Yongsu Ma Yiran Chen Xuehai Xie Yan Zhuang Hongqiao Gao Xiaodong Tian Yinmo Yang | 2021 | Chinese Journal of Cancer Research2021，33，4： | 3 |
| 4 | Evaluation of the relative risk of stroke in patients with hypertension using cerebrovascular hemodynamic accumulative score显示文摘The relative risk(RR)of stroke in patients with hypertension was evaluated by using synthetic index of cerebrovascular hemodynamics.A total of 7,371 patients with hypertension with ages i40 years were selected from a population-based cohort study of the risk factors for stroke.The data on the baseline investigation of risk factors,the determination of cerebrovascular hemodynamic parameters(CVHP),and stroke follow-up were analyzed.The RR of stroke in patients with hypertension was evaluated by CVHP scores.Univariate analysis indicated that hypertension,complicated by other risk factors,had significant statistical association with the onset of stroke.RRs for stroke when hypertension complicated with decrease of hemodynamic scores,heart disease,cigarette smoking and alcohol consumption were 4.93(95%CI,3.26–7.45),1.90(95%CI,1.36–2.66),1.99(95%CI,1.42–2.79)and 1.73(95%CI,1.19–2.53)respectively.In multivariate analysis,hemodynamic score,age,sex,cigarette smoking,family history of stroke and systolic blood pressure were selected by the Cox regression for inclusion in the final analysis.Among them,the RR of hemodynamic score was highest.The analysis of doseresponse relationships indicated that when the hemodynamic scores in patients with hypertension were lower than 75 points,the RR of stroke at 75,60,45,30 and 15 points were 2.85,4.43,4.54,5.40 and 9.88,respectively.The risk of stroke in patients with hypertension is closely asso ciated with hemodynamic impairment and the hemodynamic score may be used for quantitative evaluation of relative risks of stroke. | HUANG Jiuyi WANG Guiqing GUO Jiping CAO Yifeng WANG Yan YANG Yongju YU Xuehai | 2007 | Frontiers of Medicine2007，1，3： | 2 |
| 5 | Controlled fabrication of polyaniline spherical and cubic shells with hierarchical nanostructures 显示文摘 | Fei Jinbo Cui Yue Yan Xuehai | 2009 | ACS Nano2009，3，11： | 1 |
| 6 | Controlled Preparation of MnO2 Hierarchical Hollow Nanostructures and Their Application in Water Treatment显示文摘 | Fei Jinbo Cui Yue Yan Xuehai | 2008 | Advanced Materials2008，20，： | 1 |
| 7 | A novel synthetic strategy to aromatic-diisocyanate-based waterborne polyurethanes显示文摘 | Wei Xin Ying Yan Yu Xuehai | 1998 | J Appl Polym Sci1998，70，8： | 1 |
| 8 | Bio-inspired photosystem for green energy显示文摘Science,2016,351,74-77;Angew.Chem.Int.Ed.,2016,55,12503-12507Over billions years of evolution,biosystems have developed elaborate architectures to realize efficient substance metabolism and energy conversion.Using and/or mimicking biological process has provided us an elegant strategy for design and fabrication of biologically functional systems,such as photosystem.To realize efficient energy production,it | Xuehai Yan | 2017 | Green Energy & Environment2017，2，2： | 0 |
| 9 | The lysine methyltransferase SMYD2 facilitates neointimal hyperplasia by regulating the HDAC3-SRF axis显示文摘Coronary restenosis is an important cause of poor long-term prognosis in patients with coronary heart disease.Here,we show that lysine methyltransferase SMYD2 expression in the nucleus is significantly elevated in serum-and PDGF-BB-induced vascular smooth muscle cells(VSMCs),and in tissues of carotid artery injury-induced neointimal hyperplasia.Smyd2 overexpression in VSMCs(Smyd2-vTg)facilitates,but treatment with its specific inhibitor LLY-507 or SMYD2 knockdown significantly inhibits VSMC phenotypic switching and carotid artery injury-induced neointima formation in mice.Transcriptome sequencing revealed that SMYD2 knockdown represses the expression of serum response factor(SRF)target genes and that SRF overexpression largely reverses the inhibitory effect of SMYD2 knockdown on VSMC proliferation.HDAC3 directly interacts with and deacetylates SRF,which enhances SRF transcriptional activity in VSMCs.Moreover,SMYD2 promotes HDAC3 expression via tri-methylation of H3K36 at its promoter.RGFP966,a specific inhibitor of HDAC3,not only counteracts the pro-proliferation effect of SMYD2 overexpression on VSMCs,but also inhibits carotid artery injury-induced neointima formation in mice.HDAC3 partially abolishes the inhibitory effect of SMYD2 knockdown on VSMC proliferation in a deacetylase activity-dependent manner.Our results reveal that the SMYD2-HDAC3-SRF axis constitutes a novel and critical epigenetic mechanism that regulates VSMC phenotypic switching and neointimal hyperplasia. | Xiaoxuan Zhong Xiang Wei Yan Xu Xuehai Zhu Bo Huo Xian Guo Gaoke Feng Zihao Zhang Xin Feng Zemin Fang Yuxuan Luo Xin Yi Ding-Sheng Jiang | 2024 | Acta Pharmaceutica Sinica B2024，14，2： | 0 |
| 10 | Assembly Induced Super-Large Red-Shifted Absorption:The Burgeoning Field of Organic Near-Infrared Materials显示文摘Supramolecular assembly of organic dye compounds with J-aggregation leads to a red-shifted absorption spectrum that greatly facilitates the construction of near-infrared(NIR)materials.A considerable improvement of the material functions requires that the absorption red-shift be larger than 100 nm,but such a super-large red-shift is challenging,and the rules leading to the super-large red-shifted absorption is still not explicit.In this review,we focused on those J-aggregated organic dye materials with super-large red-shifted absorption.The nature of the super-large red-shift is originated fromthe intermolecular charge transfer between neighboring chromophores.The super-large red-shift can be obtained by tuning either the molecular structure or kinetic assembly process in a delicate manner.Materials with super-large red-shifted absorption have been successfully applied to biological imaging,phototherapy,electronic devices,and solar cells,and show great potential in many other fields.The elaboration of assembly induced super-large red-shifted absorption is promising for design of supramolecular NIR materials with tuned structures,enhanced functionalities,and a wide array of applications. | Luyang Zhao Xiaokang Ren Xuehai Yan | 2021 | CCS Chemistry2021，3，5： | 0 |
| 11 | iCREPCP:A deep learning-based web server for identifying base-resolution cis-regulatory elements within plant core promoters显示文摘Dear Editor,A central question of plant biology is how to specify the temporal and spatial patterns as well as the quantitative levels of gene expression,which are significantly associated with important agronomic traits.There has been a growing consensus in the past decade that the two key factors determining gene expression level are cis-regulatory modules(CRMs)and trans-acting factors(TAFs)(Schmitz et al.,2022).Common CRMs include gene-proximal promoters and distal enhancers,which are both considered to be complex assemblies of cis-regulatory elements(CREs).It is the binding or interaction between CREs and TAFs(often transcription factors[TFs])in a ubiquitous or cell-specific manner that determines in which cell,at what time,and at what level a gene is expressed.Therefore,the identification of plant CRMs or critical CREs will not only help us understand transcriptional regulatory mechanisms in plants but also serve as an essential prerequisite for plant breeding 4.0—breeding by genome editing(Gao,2021). | Kaixuan Deng Qizhe Zhang Yuxin Hong Jianbing Yan Xuehai Hu | 2023 | Plant Communications2023，4，1： | 0 |
| 12 | Kinetically Controlled Self-Assembly of Phthalocyanine–Peptide Conjugate Nanofibrils Enabling Superlarge Redshifted Absorption显示文摘Supramolecular assembly could in principle lead to redshifted absorption through J-aggregation of chromophores,which would be a highly promising method for achieving near-infrared materials with improved functionality and flexibility.To effectively enhance the material functionalities,one of the great challenges remaining is to achieve an aggregation statewith a redshift larger than 100 nm. | Luyang Zhao Shukun Li Yamei Liu Ruirui Xing Xuehai Yan | 2019 | CCS Chemistry2019，1，2： | 0 |
| 13 | Self-assembly of biomimetic light-harvesting complexes capable of hydrogen evolution显示文摘Biomimetics provides us a new perspective to understand complex biological process and strategy to fabricate functional materials. However,a great challenge still remains to design and fabricate biomimetic materials using a facile but effective method. Here, we develop a biomimetic light harvesting architecture based on one-step co-assembly of amphiphilic amino acid and porphyrin. Amphiphilic amino acid can self-assemble into nanofibers via π-stacking and hydrogen binding interactions. Negatively charged porphyrin adsorbs on the surface of the assembled nanofibers through electrostatic force, and the nanofibers further organize into porous urchin-like microspheres induced presumably by hydrophobic interaction. The assembled amphiphilic amino acid nanofibers work as a template to tune the organization of porphyrin with an architecture principle analogous to natural light harvesting complex. The co-assembled microspheres exhibit enhanced light capture due to the light reflection in the porous structure. Reaction center(platinum nanoparticles) can be effectively coupled with the light harvesting microspheres via photoreduction. After visible light illumination, hydrogen evolution occurs on the hybrid microspheres. | Kai Liu Manzar Abass Qianli Zou Xuehai Yan | 2017 | Green Energy & Environment2017，2，1： | 0 |
| 14 | Bio-inspired short peptide self-assembly:From particles to functional materials显示文摘Natural systems are typically featured with tremendous molecular complexity and construct exquisite architectures and functional materials through precise spatial and temporal control.Supramolecular self-assembly from peptides and proteins is believed to be the key player.Thus,knowledge of the fundamental mechanisms driving peptides into vast functional hierarchical structures will certainly help the rational control of self-assembly process,leading to more precise structural organization and functional optimization.In this review,we briefly summarize the recent progress of this burgeoning field mainly from two directions:peptide-based self-assembly and co-assembly with other functional molecules,each part is further divided into two subparts and representative examples are given for each subpart according to their development timeline.At the end of each part,brief summaries of the closely related applications are outlined.For the closing remarks,we conclude with our own understanding of the area and perspectives are given based on recent developments.Overall,this review could be suitable for both new readers to gain a comprehensive overview of the area and experienced readers to get a summary of the development in short peptide self-assembly from particles to functional materials. | Li Wang Guizhi Shen Xuehai Yan | 2022 | Particuology2022，20，5： | 0 |
| 15 | Self-assembling bile pigments for cancer diagnosis and therapy显示文摘Nanomaterials that integrate multiple functions provide promising opportunities for noninvasive and targeted cancer diagnosis and therapy.However,the unclear metabolic pathway to nanomaterials brought difficulties to clinical application.Selfassembling bile pigments are endogenous functional materials with excellent biocompatibility and low toxicity.Functional materials based on endogenous bile pigments provide a decent solution to this dilemma.In this review,the features and functions of self-assembling bile pigments are discussed in detail for cancer diagnosis and treatment applications.Emphases are put on the intrinsic physicochemical characteristics of bile pigments and their applications,including drug delivery,photoacoustic imaging,photothermal therapy,and anti-inflammation therapy.This review will promote the exploration of these areas and tremendously realize the innovative applications of self-assembling biliverdin/bilirubin nanomaterials toward cancer diagnosis and therapy. | Kaiwei Chen Ruirui Xing Xuehai Yan | 2021 | Aggregate2021，2，1： | 0 |
| 16 | VAMP726 from maize and Arabidopsis confers pollen resistance to heat and UV radiation by influencing lignin content of sporopollenin显示文摘Sporopollenin in the pollen cell wall protects male gametophytes from stresses.Phenylpropanoid derivatives,including guaiacyl(G)lignin units,are known to be structural components of sporopollenin,but the exact composition of sporopollenin remains to be fully resolved.We analyzed the phenylpropanoid derivatives in sporopollenin from maize and Arabidopsis by thioacidolysis coupled with nuclear magnetic resonance(NMR)and gas chromatography–mass spectrometry(GC–MS).The NMR and GC–MS results confirmed the presence of p-hydroxyphenyl(H),G,and syringyl(S)lignin units in sporopollenin from maize and Arabidopsis.Strikingly,H units account for the majority of lignin monomers in sporopollenin from these species.We next performed a genome-wide association study to explore the genetic basis of maize sporopollenin composition and identified a vesicle-associated membrane protein(ZmVAMP726)that is strongly associated with lignin monomer composition of maize sporopollenin.Genetic manipulation of VAMP726 affected not only lignin monomer composition in sporopollenin but also pollen resistance to heat and UV radiation in maize and Arabidopsis,indicating that VAMP726 is functionally conserved in monocot and dicot plants.Our work provides new insight into the lignin monomers that serve as structural components of sporopollenin and characterizes VAMP726,which affects sporopollenin composition and stress resistance in pollen. | Wenqi Yang Dongdong Yao Haiyang Duan Junli Zhang Yaling Cai Chen Lan Bing Zhao Yong Mei Yan Zheng Erbing Yang Xiaoduo Lu Xuehai Zhang Jihua Tang Ke Yu Xuebin Zhang | 2023 | Plant Communications2023，4，6： | 0 |
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