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Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future Crop Breeding

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Molecular Plant 2021年第1期14卷 77-94页

作者： leiming wu Linqian Han Qing Li Guoying Wang Hongwei Zhang Lin Li National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China lnstitute of Crop Science Chinese Academy of Agricultural SciencesBeijing 100081China

The functional genes underlying phenotypic variation and their interactions represent“genetic mysteries”.Understanding and utilizing these genetic mysteries are key solutions for mitigating the current threats to agriculture posed by population growth and individual food preferences.Due to advances in highthroughput multi-omics technologies,we are stepping into an Interactome Big Data era that is certain to revolutionize genetic research.In this article,we provide a brief overview of current strategies to explore genetic mysteries.We then introduce the methods for constructing and analyzing the Interactome Big Data and summarize currently available interactome resources.Next,we discuss how Interactome Big Data can be used as a versatile tool to dissect genetic mysteries.We propose an integrated strategy that could revolutionize genetic research by combining Interactome Big Data with machine learning,which involves mining information hidden in Big Data to identify the genetic models or networks that control various traits,and also provide a detailed procedure for systematic dissection of genetic mysteries,Finally,we discuss three promising future breeding strategies utilizing the Interactome Big Data to improve crop yields and quality.

关键词： genetic mystery interactome big data machine learning crop breeding

All-optical logic devices based on black arsenic-phosphorus with strong nonlinear optical response and high stability

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Opto-Electronic Advances 2022年第1期5卷 13-23页

作者： leiming wu Taojian Fan Songrui Wei Yijun Xu Ye Zhang Dingtao Ma Yiqing Shu Yuanjiang Xiang Jun Liu Jianqing Li Krassimir Panajotov Yuwen Qin Han Zhang Institute of Microscale Optoelectronics Collaborative Innovation Centre for Optoelectronic Science&TechnologyKey Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceShenzhen Key Laboratory of Micro-Nano Photonic Information TechnologyGuangdong Laboratory of Artificial Intelligence and Digital Economy(SZ)Shenzhen UniversityShenzhen 518060China Faculty of Information Technology Macao University of Science and TechnologyMacao 519020China Department of Applied Physics and Photonics(IR-TONA) Vrije Universiteit BrusselsPleinlaan 2B-1050 BrusselsBelgium Institute of Advanced Photonics Technology School of Information EngineeringGuangdong University of TechnologyGuangzhou 510006China

The Kerr nonlinearity in two-dimensional(2D)nanomaterials is emerging as an appealing and intriguing research area due to their prominent light processing,modulation,and manipulation abilities.In this contribution,2D black arsenic-phosphorus(B-AsP)nanosheets(NSs)were applied in nonlinear photonic devices based on spatial self-phase modula-tion(SSPM)method.By applying the Kerr nonlinearity in 2D B-AsP,an all-optical phase-modulated system is proposed to realize the functions of“on”and“off”in all-optical switching.By using the same all-optical phase-modulated system,another optical logic gate is proposed,and the logical“or”function is obtained based on the 2D B-AsP NSs dispersions.Moreover,by using the SSPM method,a 2D B-AsP/SnS_(2) hybrid structure is fabricated,and the result illustrates that the hybrid structure possesses the ability of the unidirectional nonlinear excitation,which helps in obtaining the function of spatial asymmetric light propagation.This function is considered an important prerequisite for the realization of diode functionalization,which is believed to be a factor in important basis for the design of isolators as well.The initial investig-ations indicate that 2D B-AsP is applicable for designing optical logical devices,which can be considered as an import-ant development in all-optical information processing.

关键词： B-AsP nanomaterial all-optical phase-modulated system spatial asymmetric light propagation

Hic74,a novel alanine and glycine rich matrix protein related to nacreous layer formation in the mollusc Hyriopsis cumingii

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Aquaculture and Fisheries 2017年第3期2卷 119-123页

作者： Xiaojun Liu Can Jin leiming wu Shaojian Dong Shimei Zeng Jiale Li Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries Shanghai Ocean UniversityMinistry of AgricultureShanghai 201306China E-Institute of Shanghai Universities Shanghai Ocean UniversityShanghai 201306China

Organic matrix proteins play an important role in the biomineralization of mollusc shells.We have identified and characterized a novel matrix protein,namely hic74,isolated from the mantle of the freshwater mussel Hyriopsis cumingii.The hic74 gene encodes a 850 amino acid protein that is rich in alanine(ala,30.8%),glycine(gly,25.8%)and serine(ser,10.6%),with ala mainly existing in poly-ala forms within the ala/gly-rich regions.Quantitative PCR expression analysis demonstrated that hic74 was specifically amplified from the mantle and in situ hybridization showed a strong signal in the epithelial cells in the pallial region of the mantle.Lower levels of expression were detected during the early stages of pearl sac formation but increased and remained constant during nacreous layer formation suggesting that hic74 might be involved in this process.

关键词： Hyriopsis cumingii Freshwater mussel Matrix protein Pearl Biomineralization

Ultrasensitive biosensors based on long-range surface plasmon polariton and dielectric waveguide modes

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Photonics Research 2016年第6期4卷 262-266页

作者： leiming wu Jun Guo Hailin Xu Xiaoyu Dai Yuanjiang Xiang SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province College of Optoelectronic EngineeringShenzhen University College of Physics and Energy Shenzhen University

An ultrasensitive biosensor based on hybrid structure and composed of long-range surface plasmon polariton(LRSPP) and dielectric planar waveguide(PWG) modes is proposed. Both PWG and LRSPP modes have strong resonances to form strong coupling between the two modes, and the two modes can couple to enhance sensitivity of sensors. In the hybrid structure, PWG is composed of cytop–Si–cytop multilayers and the LRSPP configuration is composed of cytop–metal–sensing medium multilayer slabs. The highest imaging sensitivities of 2264 and3619 RIU-1were realized in the proposed sensors based on Au and Al-monolayer graphene, respectively, which are nearly 1.2 and 1.9 times larger than the 1910 RIU-1sensitivity of the conventional LRSPR sensor(LRSPP sensor). Moreover, it is demonstrated that the PWG-coupled LRSPP biosensor is applicable to the sensing medium,with refractive index in the vicinity of 1.34.

关键词： RIU Ultrasensitive biosensors based on long-range surface plasmon polariton and dielectric waveguide modes

Broadband nonlinear optical resonance and all-optical switching of liquid phase exfoliated tungsten diselenide

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Photonics Research 2018年第11期6卷 1040-1047页

作者： YUE JIA YOUXIAN SHAN leiming wu XIAOYU DAI DIANYUAN FAN YUANJIANG XIANG SZU-NUS Collaborative Center and International Collaborative Laboratory of 2D Materials for Optoelectronic Science & Technology of Ministry of Education College of Optoelectronic Engineering Shenzhen University Engineering Technology Research Center for 2D Material Information Function Devices and Systems of Guangdong Province College of Optoelectronic Engineering Shenzhen University

As a kind of two-dimensional transition metal dichalcogenide material, tungsten diselenide(WSe_2) has attracted increasing attention, owing to its gapped electronic structure, relatively high carrier mobility, and valley pseudospin, all of which show its valuable nonlinear optical properties. There are few studies on the nonlinear optical properties of WSe_2 and correlation with its electronic structure. In this paper, the effects of spatial self-phase modulation(SSPM) and distortion influence of WSe_2 ethanol suspensions are systematically studied, namely,the nonlinear refractive index and third-order nonlinear optical effect. We obtained the WSe_2 dispersions SSPM distortion formation mechanism, and through it, we calculated the nonlinear refractive index n_2,nonlinear susceptibility χ^(3), and their wavelength dependence under the excitation of 457 nm, 532 nm, and671 nm lasers. Moreover, by use of its strong and broadband nonlinear optical response, all-optical switching of two different laser beams due to spatial cross-phase modulation has been realized experimentally. Our results are useful for future optical devices, such as all-optical switching and all-optical information conversion.

关键词： tungsten diselenide nonlinear all-optical switching

稻-虾共作模式下水体和土壤细菌群落特征研究

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扬州大学学报（农业与生命科学版） 2024年第2期45卷 29-41页

作者：覃宝利韩光明吴雷明张家宏王守红朱凌宇毕建花寇祥明葛恒来陈选青唐金玉江苏里下河地区农业科学研究所江苏扬州225007 江苏省生态农业工程技术研究中心江苏扬州225008 扬州银谷农业生态发展有限公司江苏扬州225119 浙江省农业科学院水生生物研究所杭州310021

为探究稻-虾共作模式对稻田水体、土壤细菌群落结构和多样性的影响,采用16S rDNA基因高通量测序技术对夏季稻-虾共作和水稻单作模式下稻田水体、土壤细菌群落组成及多样性进行比较。结果表明:与水稻单作相比,稻-虾共作模式水体细菌群落... 详细信息

为探究稻-虾共作模式对稻田水体、土壤细菌群落结构和多样性的影响,采用16S rDNA基因高通量测序技术对夏季稻-虾共作和水稻单作模式下稻田水体、土壤细菌群落组成及多样性进行比较。结果表明:与水稻单作相比,稻-虾共作模式水体细菌群落丰富度和多样性均呈上升趋势,土壤细菌群落丰富度变化不明显,但多样性有所下降,尤其9月显著下降。在细菌群落组成方面,稻-虾共作模式增加水体放线菌门(Actinobacteria)和蓝细菌门(Cyanobacteria)相对丰度,降低变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)、酸杆菌门(Acidobacteria)和芽孢杆菌目(Bacillus)相对丰度,增加致病菌不动杆菌属(Acinetobacter)的相对丰度;降低土壤放线菌门(Actinorny cetes)、酸杆菌门(Acidobacteria)和根瘤菌目(Rhizobiales)相对丰度,增加变形菌门、硝化螺旋菌门(Nitrospirae)和Steroidobacterales目的相对丰度。功能预测分析发现,稻-虾共作模式下细菌碳水化合物代谢通路相对丰度在水体中呈上升趋势,在土壤中呈下降趋势。综上,稻-虾共作模式可改变水体、土壤细菌群落与功能,提高水体细菌群落的丰富度和多样性,降低土壤细菌群落的多样性。

关键词：稻-虾共作细菌群落多样性功能预测

Distinct clinical profiles and mutation landscapes of gliomas originating from the neocortex,mesocortex,and cerebellum

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Genes & Diseases 2024年第1期11卷 53-56页

作者： Ye Cheng Lei Zhang Xiaolong wu Hiroaki Wakimoto Haoming Geng Yukui Wei Geng Xu Xinru Xiao Jie Bai Yaming Wang Zeliang Hu leiming Wang Qingtang Lian Department of Neurosurgery Xuanwu HospitalCapital Medical UniversityBeijing 100053China Brain Tumor Research Center Massachusetts General HospitalDepartment of NeurosurgeryHarvard Medical SchoolBostonMA02134USA Department of Pathology Xuanwu HospitalCapital Medical UniversityBeijing 100053China

Gliomas originating from anatomically and developmentally distinct brain regions have different clinical outcomes.However,the molecular landscape underlying this difference remains largelyunknown.We analyzed key molecular mutations via sequencing and correlated them with clinical characteristics in 180 adult patients with gliomas originating from the neocortex,mesocortex,and cerebellum.Cases of cerebellar origin had significantly longer survival than those of supratentorial origin,consistent with higher rates of mutation in key genes associated with supratentorial gliomas.

关键词： clinical cortex glioma