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GametesOmics:A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice

Genomics, Proteomics & Bioinformatics 2024年第1期22卷 121-130页

作者： Jianting An Jing Wang siming kong Shi Song Wei Chen Peng Yuan Qilong He Yidong Chen Ye Li Yi Yang Wei Wang Rong Li Liying Yan Zhiqiang Yan Jie Qiao State Key Laboratory of Female Fertility Promotion Center for Reproductive MedicineDepartment of Obstetrics and GynecologyPeking University Third HospitalBeijing 100191China National Clinical Research Center for Obstetrics and Gynecology Peking University Third HospitalBeijing 100191China Key Laboratory of Assisted Reproduction Ministry of EducationPeking UniversityBeijing 100191China Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology Beijing 100191China Peking-Tsinghua Center for Life Sciences Peking UniversityBeijing 100871China Beijing Advanced Innovation Center for Genomics Beijing 100191China

Gametogenesis plays an important role in the reproduction and evolution of *** transcriptomic and epigenetic alterations in this process can influence the reproductive capacity,fertilization,and embryonic *** rapidly increasing single-cell studies have provided valuable multi-omics ***,data from different layers and sequencing platforms have not been uniformed and integrated,which greatly limits their use for exploring the molecular mechanisms that underlie oogenesis and ***,we develop GametesOmics,a comprehensive database that integrates the data of gene expression,DNA methylation,and chromatin accessibility during oogenesis and spermatogenesis in humans and *** provides a user-friendly website and various tools,including Search and Advanced Search for querying the expression and epigenetic modification(s)of each gene;Tools with Differentially expressed gene(DEG)analysis for identifying DEGs,Correlation analysis for demonstrating the genetic and epigenetic changes,Visualization for displaying single-cell clusters and screening marker genes as well as master transcription factors(TFs),and MethylView for studying the genomic distribution of epigenetic *** also provides Genome Browser and Ortholog for tracking and comparing gene expression,DNA methylation,and chromatin accessibility between humans and *** offers a comprehensive resource for biologists and clinicians to decipher the cell fate transition in germ cell development,and can be accessed at http://***/.

关键词： Gametogenesis Oogenesis Spermatogenesis Transcriptomics Epigenomics

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Effects of SARS-CoV-2 infection on human reproduction

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Journal of Molecular Cell Biology 2021年第10期13卷 695-704页

作者： Ming Yang Jing Wang Yidong Chen siming kong Jie Qiao Center for Reproductive Medicine Department of Obstetrics and GynecologyPeking University Third HospitalBeijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive TechnologyBeijing 100191China National Clinical Research Center for Obstetrics and Gynecology Beijing 100191China Key Laboratory of Assisted Reproduction(Peking University) Ministry of EducationBeijing 100191China Beijing Advanced Innovation Center for Genomics Beijing 100871China Peking-Tsinghua Center for Life Sciences Peking UniversityBeijing 100871China Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest Peking UniversityBeijing 100871China Academy for Advanced Interdisciplinary Studies Peking UniversityBeijing 100871China

The worldwide infection of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)impacts human health and life on multiple *** infected with SARS-CoV-2 suffer from physical disorders and psychological *** present,no direct evidence indicates that SARS-CoV-2 negatively influences human reproduction,and the possibility that gametes and embryos are affected requires further *** evaluate the potential effects of SARS-CoV-2 infection on human reproduction and fetal health,this review summarizes the basic and clinical research of SARS-CoV-2 on reproduction up to date,hoping to offer guidance and advice to people at reproductive age and provide dues for the prevention and treatment of associated diseases.

关键词： COVID-19 SARS-CoV-2 reproduction vertical transmission

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Single-cell transcriptome analysis of the novel coronavirus (SARS-CoV-2) associated gene ACE2 expression in normal and non-obstructive azoospermia (NOA) human male testes

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Science China(Life Sciences) 2020年第7期63卷 1006-1015页

作者： Xixi Liu Yidong Chen Wenhao Tang Li Zhang Wei Chen Zhiqiang Yan Peng Yuan Ming Yang siming kong Liying Yan Jie Qiao Beijing Advanced Innovation Center for Genomics Department of Obstetrics and GynecologyThird HospitalCollege of Life SciencesPeking UniversityBeijing 100871China Center for Reproductive Medicine Department of Obstetrics and GynecologyPeking University Third HospitalBeijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive TechnologyBeijing 100191China National Clinical Research Center for Obstetrics and Gynecology Beijing 100191China Key Laboratory of Assisted Reproduction(Peking University) Ministryof EducationBeijing 100191China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China Department of Urology Peking University Third HospitalBeijing 100191China

Being infected by SARS-CoV-2 may cause damage to multiple organs in patients, such as the lung, liver and heart. Angiotensin-converting enzyme 2(ACE2), reported as a SARS-CoV-2 receptor, is also expressed in human male testes. This suggests a potential risk in human male reproductive system. However, the characteristics of ACE2-positive cells and the expression of other SARS-CoV-2 process-related genes are still worthy of further investigation. Here, we performed singlecell RNA seq(scRNA-seq) analysis on 853 male embryo primordial germ cells(PGCs) and 2,854 normal testis cells to assess the effects of the SARS-CoV-2 virus on the male reproductive system from embryonic stage to adulthood. We also collected and constructed the scRNA-seq library on 228 Sertoli cells from three non-obstructive azoospermia(NOA) patients to assess the effects at disease state. We found that ACE2 expressing cells existed in almost all testis cell types and Sertoli cells had highest expression level and positive cells ratio. Moreover, ACE2 was also expressed in human male PGCs. In adulthood, the level of ACE2 expression decreased with the increase of age. We also found that ACE2 positive cells had high expressions of stress response and immune activation-related genes. Interestingly, some potential SARS-CoV-2 process-related genes such as TMPRSS2, BSG, CTSL and CTSB had different expression patterns in the same cell type. Furthermore, ACE2 expression level in NOA donors’ Sertoli cells was significantly decreased. Our work would help to assess the risk of SARS-CoV-2 infection in the male reproductive system.

关键词： SARS-CoV-2 COVID-19 testis cells ACE2 TMPRSS2 fetal adult normal NOA

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A biocompatible Horner-Wadsworth-Emmons(HWE)reaction triggered by a bioorthogonal proximity-induced platform

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Chinese Chemical Letters 2024年第8期35卷 217-220页

作者： Yayue Wang Haojie Yang Jie Li Qiao kong siming Zhou Hongbao Sun Lili Pan Qiyong Gong Ping Feng Haoxing Wu Department of Radiology and Huaxi MR Research Center(HMRRC) Functional and Molecular Imaging Key Laboratory of Sichuan ProvinceFrontiers Science Center for Disease Related Molecular NetworkWest China HospitalSichuan UniversityChengdu 610041China Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province Sichuan UniversityChengdu 610041China Department of Nuclear Medicine Laboratory of Clinical Nuclear MedicineWest China HospitalSichuan UniversityChengdu 610041China Reseacrch Unit of Psychoradiology Chinese Academy of Medical SciencesChengdu 610041China Department of Pharmacy West China HospitalSichuan UniversityChengdu 610041China Clinical Trial Center and National Medical Products Administration Key Laboratory for Clinical Research and Evaluation of Innovative Drugs West China HospitalSichuan UniversityChengdu 610041China

Here,we present a novel bioorthogonal platform that enables precise positioning of attached moieties in close proximity,thereby facilitating the discovery and optimization of biocompatible *** this platform,we achieve a Horner-Wadsworth-Emmons(HWE)reaction under physiological conditions,generating a fluorophore in situ with a yield of up to 93%.This proximity platform should facilitate the discovery of various types of biocompatible reactions,making it a versatile tool for biomedical applica-tions.

关键词： Biocompatible reactions Horner-Wadsworth-Emmons reaction Bioorthogonal reactions Tetrazines Proximity effects

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Conformation and Counterion Distribution of Polyelectrolyte in Solution as Viewed from Dielectric Approach

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Chinese Journal of Polymer Science 2024年第9期42卷 1278-1301,I0005页

作者： kong-Shuang Zhao College of Chemistry Beijing Normal UniversityBeijing 100875China

Polyelectrolyte solutions are more variable than uncharged macromolecule due to electrical interaction between charged molecules and surrounding ***,the subject of polyelectrolyte solutions has attracted a wide range of interests in both basic and applied research,and has also been extensively ***,the understanding of the molecular dynamics and conformation of polyelectrolytes in solution remains to be deepened,and universal consensus on some key issues have not been *** methods have contributed to solving the above problems in different ways,including dielectric relaxation spectroscopy(DRS).In this perspective,we briefly reviewed the history of dielectric spectroscopic research on polyelectrolyte solution,with emphasis on summarizing our *** particular,we expound the characteristics of DRS and its ability to obtain the internal information of the system of ***,we evaluate the advantages and limitations of the dielectric method and discussed future prospects of this field.

关键词： Polyelectrolyte Dielectric relaxation spectroscopy Chain conformation Thermosensitive microgel PNIPAM microgel Spherical polyelectrolyte brushes

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Quantifying the age peaks,age ranges and weights of detrital ages based on the EM algorithm

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Geoscience Frontiers 2024年第4期15卷 217-229页

作者： Jintao kong Linfin branch of PetroChina Coalbed Methane Company Limited Linfen 041000Shanxi ProvinceChina PetroChina Coalbed Methane Company Limited Beijing 100028China College of Earth Sciences Jilin UniversityChangchun 130061Jilin ProvinceChina

Detrital geochronology fundamentally involves the quantification of major age ranges and their weights winthin an age *** study presents a streamlined approach,modeling the age distribution of detrital zircons using a normal mixture model,and employs the Expectation-Maximization(EM)algorithm for precise estimations.A method is introduced to automatically select appropriate initial mean values for EM algorithm,enhancing its efficacy in detrital *** process entails multiple trials with varying numbers of age components leading to diverse k-component *** model with the lowest Bayesian Information Criterion(BIC)is identified as the most *** accurate component number and weight determination,a substantial sample size(n>200)is advisable. Our findings based on both synthetic and empirical datasets confirm that the normal mixture model,refined by the EM algorithm,reliably identifies key age parameters with minimal *** a kind of probability density estimator,the normal mixture model offers a novel visualization tool for detrital data and an alternative foundation for KDE in calculating existing similarity *** focus of this study is the critical examination of quantitative metrics for comparing detrital zircon age *** a case study,this study demonstrates that metrics based on empirical cumulative probability distribution(such as K-S and Kuiper statistics)may lead to erroneous *** employment of the Kullback-Leibler(KL)divergence,a metric grounded in probability density estimation,is *** critical values,simulated via the Monte Carlo method,provide more objective benchmarks for these quantitative metrics. All methodologies discussed are encapsulated in a series of MATLAB scripts,available as open-source code and a standalone application,facilitating wider adoption and application in the field.

关键词： Detrital zircongeochronology Expectation-Maximization algorithm Kullback-Leibler divergence Quantifying comparison Age peaks,ageranges,andweights

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Flat jet electrochemical milling of TC4 alloy with tailoring backward parallel flow

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Chinese Journal of Aeronautics 2024年第4期37卷 574-592页

作者： Huanghai kong Ningsong QU College of Mechanical and Electrical Engineering Nanjing University of Aeronautics and AstronauticsNanjing 210016China

In flat jet electrochemical milling, the electrolyte forms a backward parallel flow after impacting the workpiece, resulting in a weak current density distribution on the workpiece. Poor surface quality usually occurs on the machined titanium alloy surface because it inevitably suffers from the weak current density. In this study, a method of flat jet electrochemical milling with tailoring the backward parallel flow was proposed to eliminate the negative effects caused by the weak current density. Multiphysics simulations are carried out to comprehend the mechanism of flat jetEC milling with tailoring backward parallel flow and better construct the novel tool *** on flat jet electrochemical milling of TC4 alloy with and without tailoring backward parallel flow are conducted. The results reveal that, compared with flat jet electrochemical milling without tailoring backward parallel flow, the recommended tool reduces the surface roughness by86% to 93%, and improves the material removal rate by 93% to 163% with different feed ***, the recommended tool is more conducive to maintaining the inherent hardness of the material. Finally, a surface with low Sa of 0.37 μm is obtained.

关键词： Flat jet electrochemical milling TC4 alloy Surface roughness Micro-hardness Material removal rate

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Soil inorganic amendments produce safe rice by reducing the transfer of Cd and increasing key amino acids in brown rice

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Journal of Environmental Sciences 2024年第2期136卷 121-132页

作者： Fanyi kong Shenggao Lu Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment Key Laboratory of Environmental Remediation and Ecosystem HealthMinistry of EducationCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou 310058China

The digestibility of cadmium(Cd)in brown rice is directly related to amino acid metabolism in rice and human *** our field study,three kinds of alkaline calcium-rich soil inorganic amendments(SIAs)at three dosages were applied to produce safe rice and improve the quality of rice in Cd-contaminated *** the increased application of SIA,Cd content in iron plaque on rice root significantly increased,the transfer of Cd from rice root to grain significantly decreased,and then Cd content in brown rice decreased *** vitro digestibility of Cd in brown rice was estimated by a physiologically based extraction *** showed that more than 70%of Cd in brown rice could be digested by simulated gastrointestinal *** on the total and digestible Cd contents in brown rice to evaluate the health risk,the application of 2.25 ton SIA/ha could produce safe rice in acidic slightly Cd-contaminated paddy *** amino acids(AAs)in brown rice were determined by high-performance liquid *** contents of 5 key AAs(KAAs)that actively respond to environmental changes increased significantly with the increased application of *** structural equation model indicated that KAAs could be affected by the Cd translocation capacity from rice root to grain,and consequently altered the ratio of indigestible Cd in brown *** formation of indigestible KAAs-Cd complexes by combining KAAs(phenylalanine,leucine,histidine,glutamine,and asparagine)with Cd in brown rice could be considered a potential mechanism for reducing the digestibility of Cd.

关键词： Cadmium digestibility Soil inorganic amendments Safe rice Amino acid Priming effect Health risk

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Competition of Composition Fluctuation Modes in Weakly Segregated Salt-doped Symmetric Diblock Copolymers

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Chinese Journal of Polymer Science 2024年第9期42卷 1375-1385,I0008页

作者： Yuan-Xin Zhou Xian kong South China Advanced Institute for Soft Matter Science and Technology School of Emergent Soft MatterSouth China University of TechnologyGuangzhou510640China Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices South China University of TechnologyGuangzhou510640China

Salt-doped block copolymers have widespread applications in batteries,fuel cells,semiconductors,and various industries,where their properties crucially depend on phase separation ***,investigations into salt-doped diblock copolymers have predominantly focused on microphase separation,overlooking the segregation between ionic and polymeric *** study employs weak segregation theory to explore the interplay between phase separation dominated by the polymer-modulated mode and the salt-out-modulated mode,corresponding to microscopic and macroscopic phase separations,*** comparing diblock copolymers doped with salts to those doped with neutral solvents,we elucidate the significant role of charged species in modulating phase *** phase separation mode exhibits a transition between the polymer-modulated and salt-out-modulated modes at different *** systems doped with neutral solvents,this transition is stepwise,while in salt-ion-doped systems,it is *** a sufficiently large Flory-Huggins parameter between ions and polymers,the salt-out-modulated mode becomes dominant,promoting macrophase *** to the solvation effect of salt ions,salt-doped systems are more inclined to undergo microphase ***,we explore factors influencing the critical wavenumber of phase separation,including doping level and the Flory-Huggins parameters between two blocks and between ions and polymeric *** findings reveal that in a neutral solvent environment,these factors alter only the boundary between micro-and macro-phase separations,leaving the critical wavenumber unchanged in microphase separation ***,in a salt-doped environment,the critical wavenumber of microphase separation varies with these *** provides valuable insights into the pivotal role of electrostatics in the phase separation of salt-doped block copolymers.

关键词： Block copolymer Phase separation Field theory Salt-doped

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SARS-CoV-2 Entry Factors: ACE2 and TMPRSS2 Are Expressed in Peri-Implantation Embryos and the Maternal–Fetal Interface

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Engineering 2020年第10期6卷 1311-1320页

作者： Wei Chen Peng Yuan Ming Yang Zhiqiang Yan siming kong Jie Yan Xixi Liu Yidong Chen Jie Qiao Liying Yan Center for Reproductive Medicine Department of Obstetrics and GynecologyPeking University Third HospitalBeijing 100191China Key Laboratory of Assisted Reproduction(Peking University) Ministry of EducationBeijing 100191China Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology Peking University Third HospitalBeijing 100191China Academy for Advanced Interdisciplinary Studies Peking UniversityBeijing 100871China Peking-Tsinghua Center for Life Sciences Peking UniversityBeijing 100871China National Clinical Research Center for Obstetrics and Gynecology Beijing 100191China Beijing Advanced Innovation Center for Genomics Beijing 100871China Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest Beijing 100191China

在全球肆虐的严重急性呼吸综合征冠状病毒2(severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)导致了大量人群感染,血管紧张素转化酶2(angiotensin-converting enzyme 2, ACE2)是SARS-CoV和SARS-CoV-2的受体蛋白。然而是否存在SARS-CoV-2的垂直传播仍颇有争议。为了探讨SARS-CoV-2垂直传播的潜在风险,我们利用已发表的单细胞转录组数据观察了围着床期胚胎和母胎界面上ACE2和TMPRSS2(编码跨膜丝氨酸蛋白酶2)的转录表达情况。结果显示,ACE2和TMPRSS2在第6天(D6)围着床期胚胎的滋养外胚层(trophectoderm, TE)细胞、妊娠第8周的合胞滋养层(syncytiotrophoblast at 8 weeks of gestation, STB8W)细胞以及妊娠第24周的绒毛外滋养层(extravillous trophoblasts at 24 weeks of gestation, EVT24W)细胞中均存在明显的共表达现象,表明这些细胞类群可能易被SARS-CoV-2感染。在这三个细胞类群中,ACE2阳性表达细胞相对于阴性细胞在自噬和免疫相关过程中存在差异。尽管ACE2的表达水平在围着床期胚胎中没有表现出性别偏差,但是其在D6 TE、第6天围着床期胚胎的原始内胚层(D6 primitive endoderm, D6 PE)细胞以及ACE2阳性表达的STB细胞中存在明显的性别差异。这表明围着床期发育第6天以及妊娠期胚胎对SARS-CoV-2的易感性可能存在性别差异。我们的结果揭示了胚胎移植过程中,围着床期以及妊娠期胚胎面临着SARS-CoV-2的潜在感染风险。

关键词： SARS-CoV-2 ACE2 垂直传播胎盘围着床期

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