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Genetic analysis of transcription factors in dopaminergic neuronal development in Parkinson’s disease

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Chinese Medical Journal 2024年第4期137卷 450-456页

作者： Yuwen Zhao lixia Qin Hongxu Pan Tingwei Song Yige Wang Xiaoxia Zhou Yaqin Xiang jinchen li Zhenhua liu Qiying Sun Jifeng Guo Xinxiang Yan Beisha Tang Qian Xu Department of Neurology Xiangya HospitalCentral South UniversityChangshaHunan 410008China Department of Neurology The Second Xiangya HospitalCentral South UniversityChangshaHunan 410011China Bioinformatics Center National Clinical Research Center for Geriatric Disorders Xiangya HospitalCentral South UniversityChangshaHunan 410008China Department of Geriatrics Xiangya HospitalCentral South UniversityChangshaHunan 410008China Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics School of Life SciencesCentral South UniversityChangshaHunan 410008China Key Laboratory of Hunan Province in Neurodegenerative Disorders Central South UniversityChangshaHunan 410008China

Background:Genetic variants of dopaminergic transcription factor-encoding genes are suggested to be Parkinson’s disease(PD)risk factors;however,no comprehensive analyses of these genes in patients with PD have been ***,we aimed to genetically analyze 16 dopaminergic transcription factor genes in Chinese patients with ***:Whole-exome sequencing(WES)was performed using a Chinese cohort comprising 1917 unrelated patients with familial or sporadic early-onset PD and 1652 ***,whole-genome sequencing(WGS)was performed using another Chinese cohort comprising 1962 unrelated patients with sporadic late-onset PD and 1279 ***:We detected 308 rare and 208 rare protein-altering variants in the WES and WGS cohorts,***-based association analyses of rare variants suggested that MSX1 is enriched in sporadic late-onset ***,the significance did not pass the Bonferroni ***,72 and 1730 common variants were found in the WES and WGS cohorts,***,single-variant logistic association analyses did not identify significant associations between common variants and ***:Variants of 16 typical dopaminergic transcription factors might not be major genetic risk factors for PD in Chinese ***,we highlight the complexity of PD and the need for extensive research elucidating its etiology.

关键词： Parkinson’s disease Transcription factors Dopaminergic neurons Genetic Variants

基于铑催化亲核环化/炔烃芳基化的3-烯基吲哚合成

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大连理工大学学报 2024年第4期64卷 331-337页

作者：李锦晨叶智识大连理工大学化学学院辽宁大连116024

3-烯基吲哚是一类重要的生物碱骨架,广泛存在于天然产物、药物及生理活性化合物.为发展高效且简洁的3-烯基吲哚合成方法,采用了铑催化亲核环化/炔烃芳基化串联反应.首先利用N-(2-(环丙基乙炔基)苯基)-4-甲基苯磺酰胺为模型底物,探索邻... 详细信息

3-烯基吲哚是一类重要的生物碱骨架,广泛存在于天然产物、药物及生理活性化合物.为发展高效且简洁的3-烯基吲哚合成方法,采用了铑催化亲核环化/炔烃芳基化串联反应.首先利用N-(2-(环丙基乙炔基)苯基)-4-甲基苯磺酰胺为模型底物,探索邻氨基苯乙炔类化合物胺铑化形成的3-吲哚铑中间体与模型底物另一分子中炔基的插入反应.通过金属前体、配体和溶剂等反应条件的系统优化,发现在以Rh(COD)_(2)BF_(4)为金属前体,4,5-二(二-叔丁基膦)-9,9-二甲基氧杂蒽(^(t)BuXantphos)为配体,四氢呋喃(THF)为溶剂,80℃下反应获得了94%的产率和24∶1的区域选择性.反应表明其具有优秀的底物普适性和良好的官能团兼容性,从中等到优秀的产率和从良好到优秀的区域选择性.机理研究表明磺酰基在反应中具有定位导向作用,不但促进3-吲哚铑中间体与炔烃插入反应,而且控制反应的区域选择性.

关键词：环化芳基化 3-烯基吲哚铑

HCRVD: A Vulnerability Detection System Based on CST-PDG Hierarchical Code Representation Learning

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Computers, Materials & Continua 2024年第6期79卷 4573-4601页

作者： Zhihui Song jinchen Xu Kewei li Zheng Shan School of Cyberspace Security Information Engineering UniversityZhengzhou450001China

Prior studies have demonstrated that deep learning-based approaches can enhance the performance of source code vulnerability detection by training neural networks to learn vulnerability patterns in code ***,due to limitations in code representation and neural network design,the validity and practicality of the model still need to be ***,due to differences in programming languages,most methods lack cross-language detection *** address these issues,in this paper,we analyze the shortcomings of previous code representations and neural *** propose a novel hierarchical code representation that combines Concrete Syntax Trees(CST)with Program Dependence Graphs(PDG).Furthermore,we introduce a Tree-Graph-Gated-Attention(TGGA)network based on gated recurrent units and attention mechanisms to build a Hierarchical Code Representation learning-based Vulnerability Detection(HCRVD)*** system enables cross-language vulnerability detection at the *** experiments show that HCRVD surpasses many competitors in vulnerability detection *** benefits from the hierarchical code representation learning method,and outperforms baseline in cross-language vulnerability detection by 9.772%and 11.819%in the C/C++and Java datasets,***,HCRVD has certain ability to detect vulnerabilities in unknown programming languages and is useful in real open-source *** shows good validity,generality and practicality.

关键词： Vulnerability detection deep learning CST-PDG code representation tree-graph-gated-attention network cross-language

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锦绣之丘全龄友好公园,北京,中国

世界建筑 2024年第6期 90-95页

作者：无李金晨(摄影) 湛雨桐(摄影) 杨展展侯芳孙媛媛张楠岳晓涵钱锋程楠李潇郑艺王琦李金鑫北京清华同衡规划设计研究院有限公司不详

2021年,北京市园林局提出“全龄友好型公园”的新概念,并在全市范围内完成了10余处全龄友好型公园改造。2022年继续开展30处“全龄友好型公园”提升改造,增强城市的生态惠民能力和市民的绿色获得感。石景山锦绣之丘全龄友好公园就是202... 详细信息

2021年,北京市园林局提出“全龄友好型公园”的新概念,并在全市范围内完成了10余处全龄友好型公园改造。2022年继续开展30处“全龄友好型公园”提升改造,增强城市的生态惠民能力和市民的绿色获得感。石景山锦绣之丘全龄友好公园就是2022年提升改造的重点项目之一。项目建设地点位于石景山区西长安街街旁,背靠首钢老山小区,与区政府和商业中心隔街相对。周边的人群复合,主要包括社区居民和商务区办公人员等。公园总面积1.66hm~2,现状整体地势呈斜坡状,南低北高,最大高差约10m,是老山山脉的延续,极具石景山特色。尽管位置优越,但该场地闲置多年,杂木丛生,难以进入和使用,周围居民对其的改造需求迫切。

关键词：商业中心公园改造公园总面积办公人员重点项目项目建设地点商务区西长安街

Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-coding Variants

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Genomics, Proteomics & Bioinformatics 2023年第3期21卷 649-661页

作者： Zheng Wang Guihu Zhao Bin li Zhenghuan Fang Qian Chen Xiaomeng Wang Tengfei Luo Yijing Wang Qiao Zhou Kuokuo li Lu Xia Yi Zhang Xun Zhou Hongxu Pan Yuwen Zhao Yige Wang lin Wang Jifeng Guo Beisha Tang Kun Xia jinchen li National Clinical Research Centre for Geriatric Disorders Department of GeriatricsXiangya HospitalCentral South UniversityChangsha 410008China Department of Neurology Xiangya HospitalCentral South UniversityChangsha 410008China Centre for Medical Genetics&Hunan Key Laboratory of Medical Genetics School of Life SciencesCentral South UniversityChangsha 410008China Reproductive Medicine Center Xiangya HospitalCentral South UniversityChangsha 410008China

Non-coding variants in the human genome significantly influence human traits and complex diseases via their regulation and modification ***,an increasing number of computational methods are developed to predict the effects of variants in human non-coding ***,it is difficult for inexperienced users to select appropriate computational methods from dozens of available *** solve this issue,we assessed 12 performance metrics of 24 methods on four independent non-coding variant benchmark datasets:(1)rare germline variants from clinical relevant sequence variants(ClinVar),(2)rare somatic variants from Catalogue Of Somatic Mutations In Cancer(COSMIC),(3)common regulatory variants from curated expression quantitative trait locus(eQTL)data,and(4)disease-associated common variants from curated genomewide association studies(GWAS).All 24 tested methods performed differently under various conditions,indicating varying strengths and weaknesses under different ***,the performance of existing methods was acceptable for rare germline variants from ClinVar with the area under the receiver operating characteristic curve(AUROC)of 0.4481–0.8033 and poor for rare somatic variants from COSMIC(AUROC=0.4984–0.7131),common regulatory variants from curated eQTL data(AUROC=0.4837–0.6472),and disease-associated common variants from curated GWAS(AUROC=0.4766–0.5188).We also compared the prediction performance of 24 methods for non-coding de novo mutations in autism spectrum disorder,and found that the combined annotation-dependent depletion(CADD)and context-dependent tolerance score(CDTS)methods showed better ***,we assessed the performance of 24 computational methods under diverse scenarios,providing preliminary advice for proper tool selection and guiding the development of new techniques in interpreting non-coding variants.

关键词： Non-coding variant Pathogenicity estimation Functional prediction Performance assessment Prediction model

Comparative study on cultivation of microalgae for nutrient removal and lipid production in different artificial wastewaters

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International Journal of Agricultural and Biological Engineering 2017年第1期10卷 107-114页

作者： Hao Rui Yu Zhen li jinchen Gao Min Ma Weiling Zhu Yi College of Food Science and Nutritional Engineering China Agricultural UniversityBeijing 10083China

Wastewater contains high concentration of nutrients,like nitrogen and phosphorus,which have been identified as the main reasons for water eutrophication and serious ecological ***,cultivating a tolerant and adaptive microalgae strain in wastewater is considered as a promising approach for sustainable biomass/lipid *** potential usages of Desmodesmus *** biomass and lipid production within different artificial wastewater(AW)were investigated and the removal efficiencies of nutrient were *** maximum removal rate of chemical oxygen demand,ammonia nitrogen,nitrate nitrogen and phosphate were 272 mg/(L·d),14.021 mg/(L·d),7.774 mg/(L·d)and 3.347 mg/(L·d),respectively in AW2,AW3,AW5 and *** biomass(1.159 g/L)and lipid(280 mg/L)productions were observed in AW5,while the highest lipid content achieved was 37.42%in *** acid analysis showed that lipids extracted from AW-cultivated Desmodesmus *** 59.57%-77.79%polyunsaturated fatty acids(30.6%-44.47%was linoleic acid).

关键词： microalgae Desmodesmus sp. artificial wastewater nutrient removal biomass production lipid production

Mapping of de novo mutations in primary biliary cholangitis to a disease-specific co-expression network underlying homeostasis and metabolism

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Journal of Genetics and Genomics 2022年第2期49卷 145-154页

作者： Lu Wang jinchen li Chan Wang Ruqi Tang Jialong liang Yuhua Gong Yaping Dai Ningling Ding Jian Wu Na Dai Lei liu Yi Zhao Youlin Shao Weifeng Zhao Peng Jiang Xingjuan Shi Weichang Chen Ye Tian Xiangdong liu Xiong Ma Zhongsheng Sun Key Laboratory of Developmental Genes and Human Diseases Institute of Life SciencesSoutheast University2 Sipailou RoadNanjingJiangsu 210096China Beijing Institutes of life Science Chinese Academy of SciencesNo.1 West Beichen RoadChaoyang DistrictBeijing 100101China Department of Gastroenterology and Hepatology Shanghai Institute of Digestive DiseasesShanghai Jiao Tong University School of Medicine Afﬁliated Renji Hospital145 Shandong Middle RoadShanghai 200001China Department of Laboratory Medicine The Third People’s Hospital of Zhenjiang300 DaijiamenZhenjiangJiangsu 212021China Department of Laboratory Medicine The Fifth People’s Hospital of Wuxi1215 Guangrui RoadWuxiJiangsu 214000China Department of Hepatology The Fifth People’s Hospital of SuzhouSoochow University10 Guangqian RoadSuzhouJiangsu 215131China Department of Rheumatology First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Gastroenterology Jiangsu University Afﬁliated Kunshan Hospital91 Qianjin West RoadKunshanJiangsu 215300China Department of Gastroenterology Yixing People’s Hospital75 Tongzhenguan RoadYixinJiangsu 214200China Department of Gastrointestinal Endoscopy Eastern Hepatobiliary Surgery Hospital700 Moyu North RoadShanghai 201800China Department of Hepatology The Third People’s Hospital of Changzhou300 Lanling North RoadChangzhouJiangsu 213001China Department of Infectious Diseases First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Gastroenterology First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Radiology Second Afﬁliated Hospital of Soochow University1055 Sanxiang RoadSuzhouJiangsu 215004China Institute of Genomic Medicine Wenzhou Medical UniversityUniversity TownChashanWenzhouZhejiang 325035China

Primary biliary cholangitis(PBC) is an autoimmune disease involving dysregulation of a broad array of homeostatic and metabolic processes. Although considerable single-nucleotide polymorphisms have been unveiled, a large fraction of risk factors remains enigmatic. Candidate genes with rare mutations that tend to confer more deleterious effects need to be identified. To help pinpoint cellular and developmental mechanisms beyond common noncoding variants, we integrate whole exome sequencing with integrative network analysis to investigate genes harboring de novo mutations. Prominent convergence has been revealed on a network of disease-specific co-expression comprised of 55 genes associated with homeostasis and metabolism. The transcription factor gene MEF2 D and the DNA repair gene PARP2 are highlighted as hub genes and identified to be up-and down-regulated, respectively, in peripheral blood data set. Enrichment analysis demonstrates that altered expression of MEF2 D and PARP2 may trigger a series of molecular and cellular processes with pivotal roles in PBC pathophysiology. Our study identifies genes with de novo mutations in PBC and suggests that a subset of genes in homeostasis and metabolism tend to act in synergy through converging on co-expression network, providing novel insights into the etiology of PBC and expanding the pool of molecular candidates for discovering clinically actionable biomarkers.

关键词： Primary biliary cholangitis de novo mutations Whole exome sequencing Transcriptional networks Co-expression

Gut microbiota regulation of inflammatory cytokines and MicroRNAs in diabetes-associated cognitive dysfunction

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Gut microbiota regulation of inflammatory cytokines and Micr...

Targeted sequencing and integrative analysis of 3,195 Chinese patients with neurodevelopmental disorders prioritized 26 novel candidate genes

第五届益生菌益生元科学大会

作者： Hongying Huang Tong Zhao jinchen li Jingyi Shen Rong Xiao Weiwei Ma School of Public Health Beijing Key Laboratory of Environmental ToxicologyCapital Medical University

Aims:Type 2 diabetes mellitus（T2DM） has a major comorbidity known as diabetes-associated cognitive dysfunction（DACD）.In order to provide new rationale for the treatment of cognitive dysfunction in diabetes,this study was conducted in the middle-aged and elderly population to examine the differences in gut microbiota between DACD and T2DM patients as well as to further explore the role of erythrocyte membrane fatty acids,inflammatory factors and microRNAs（miRs） in gut microbiota-mediated cognitive ***:We gathered patients with type 2 diabetes and divided them into groups with and without cognitive impairment based on Montreal cognitive assessment（MoCA） scores and educational *** then used 16S rRNA sequencing technology to examine the differences in gut microbiota between the two groups,and correlation analysis to examine the relationships between the different microbiota and clinical ***:The abundance of norank_fubacteriumoprostanoligenesroup,Acidaminococcus,Enterorhabdus and norank_flostridiumethylpentosumroup was higher in DACD patients compared to T2DM patients at the genus level（Pligenesroup（B=0.352,Pligenesroup（B=0.342,P<0.01）.Conclusion:We therefore hypothesize that cognitive impairment in T2DM patients is associated with altered gut microbial composition,and that the effect of microbiota on cognition may be mediated through IL-12 and miR-142.

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Journal of Genetics and Genomics 2021年第4期48卷 312-323页

作者： Tao Wang Yi Zhang liqui liu Yan Wang Huiqian Chen Tianda Fan jinchen li Kun Xia Zhongsheng Sun Center for Medical Genetics&Hunan Key Laboratory of Medical Genetics School of Life SciencesCentral South UniversityChangshaHunan 410083China Beijing Institutes of life Science Chinese Academy of SciencesBeijing 100101China DIAGenes Precision Medicine Beijing 102600China National Clinical Research Centre for Geriatric Disorders Department of GeriatricsXiangya HospitalCentral South UniversityChangshaHunan 410083China Shanghai Adeptus Biotechnology Shanghai 200126China Institute of Genomic Medicine Wenzhou Medical UniversityWenzhouZhejiang 325035China Department of Neurology Xiangya HospitalCentral South UniversityChangsha Hunan410083China CAS Center for Excellence in Brain Science and Intelligences Technology(CEBSIT) Shanghai 200031China School of Basic Medical Science Central South UniversityChangshaHunan410083China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory of Integrated Management of Pest Insects and Rodents Chinese Academy of SciencesBeijing 100101China

Neurodevelopmental disorders(NDDs)are a set of complex disorders characterized by diverse and cooccurring clinical *** genetic contribution in patients with NDDs remains largely ***,we sequence 519 NDD-related genes in 3,195 Chinese probands with neurodevelopmental phenotypes and identify 2,522 putative functional mutations consisting of 137 de novo mutations(DNMs)in 86 genes and 2,385 rare inherited mutations(RIMs)with 22 X-linked hemizygotes in 13 genes,2 homozygous mutations in 2 genes and 23 compound heterozygous mutations in 10 ***,the DNMs of16,807 probands with NDDs are retrieved from public datasets and combine in an integrated analysis with the mutation data of our Chinese NDD probands by taking 3,582 in-house controls of Chinese origin as *** prioritize 26 novel candidate ***,six of these genes d ITSN1,UBR3,CADM1,RYR3,FLNA,and PLXNA3 d preferably contribute to autism spectrum disorders(ASDs),as demonstrated by high co-expression and/or interaction with ASD genes confirmed via rescue experiments in a mouse ***,these genes are differentially expressed in the ASD cortex in a significant manner and involved in ASD-associated ***,our study expands the genetic spectrum of Chinese NDDs,further facilitating both basic and translational research.

关键词： De novo mutations X-linked variants Rare inherited variants Homozygous mutations Neurodevelopmental disorders Autism spectrum disorders Candidate genes