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PTMD: A Database of Human Disease-associated Post-translational Modifications

Genomics, Proteomics & Bioinformatics 2018年第4期16卷 244-251页

作者： Haodong Xu Yongbo Wang Shaofeng Lin Wankun Deng Di Peng Qinghua Cui Yu Xue Department of Bioinformatics & Systems Biology MOE Key Laboratory of Molecular Biophysics College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering Huazhong University of Science and Technology Department of Biomedical informatics School of Basic Medical Sciences MOE Key Laboratory of Molecular Cardiovascular Sciences Center for Non-coding RNA Medicine Peking University

Various posttranslational modifications （PTMs） participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM–disease associations （PDAs）would be a great help for both academic research and clinical use. In this work, we reported PTMD,a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of diseaseassociated PTM events. By reconstructing a disease–gene network, we observed that breast cancers have the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http：//***.

关键词： Posttranslational modification Phosphorylation PTM-disease association Disease-gene network AKT1

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植物乳杆菌KCCM 11613P发酵的旋覆花花瓣提取物的抗黑素生成的作用(英文)

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Journal of Zhejiang University-science B(Biomedicine & Biotechnology) 2017年第9期18卷 816-824页

作者： Eun-hye PARK Won-young BAE Jae-yeon KIM Kee-tae KIM Hyun-dong PAIK Department of Food science and Biotechnology of Animal Resources Konkuk University Bio/molecular informatics center Konkuk University

目的:研究植物乳杆菌发酵对旋覆花花瓣提取物对酪氨酸酶的抑制效果,为开发旋覆花提取物作为潜在的皮肤增白成分提供依据。创新点:发现旋覆花植物乳杆菌发酵的提取物可以作为有效的美白材料。方法:比较研究了植物乳杆菌发酵的旋覆花花瓣... 详细信息

目的:研究植物乳杆菌发酵对旋覆花花瓣提取物对酪氨酸酶的抑制效果,为开发旋覆花提取物作为潜在的皮肤增白成分提供依据。创新点:发现旋覆花植物乳杆菌发酵的提取物可以作为有效的美白材料。方法:比较研究了植物乳杆菌发酵的旋覆花花瓣提取物对酪氨酸酶活性的抑制作用,并测定了提取物中总黄酮和多酚类化合物的含量。通过体外酪氨酸酶和左旋多巴(L-DOPA)染色来测定其对皮肤的美白活性。结论:旋覆花花瓣经过72小时的发酵后,其提取物中总黄酮含量提高13.4%。采用500μg/ml发酵和未发酵的提取物处理B16F10细胞,细胞活性分别为100.26%和92.15%。此外,发酵72小时后,该提取物对酪氨酸酶活性的抑制率由29.33%上升到41.74%。未处理的对照组B16F10细胞酪氨酸酶活性增加到145.69%。结果表明,旋覆花发酵提取物对酪氨酸酶活性呈剂量依赖性抑制是促黑激素(α-MSH)的刺激引起。旋覆花植物乳杆菌发酵的提取物可以作为有效的美白材料。

关键词：旋覆花类黄酮植物乳杆菌抗氧化剂酪氨酸酶抑制剂

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通过Lactobacillus plantarum KCCM 11613P乳杆菌发酵改善洋甘菊的抗氧化和细胞毒性（英文）

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Journal of Zhejiang University-science B(Biomedicine & Biotechnology) 2017年第2期18卷 152-160页

作者： Eun-Hye PARK Won-Young BAE Su-Jin EOM Kee-Tae KIM Hyun-Dong PAIK Department of Food Sctence and Btotechnology of Animal Resources Konkuk University Seoul 05029 Korea Bio/molecular informatics center Konkuk University Seoul 05029 Korea

目的:研究洋甘菊(Matricaria chamomilla)经Lactobacillus plantarum乳杆菌发酵,可以改善其抗氧化和细胞毒性。方法:通过Folin-Denis方法测量酚类物质的总含量(TP);通过二苯代苦味酰肼(DPPH)法和β-胡萝卜素漂白法评价抗氧化活性;通过MT... 详细信息

目的:研究洋甘菊(Matricaria chamomilla)经Lactobacillus plantarum乳杆菌发酵,可以改善其抗氧化和细胞毒性。方法:通过Folin-Denis方法测量酚类物质的总含量(TP);通过二苯代苦味酰肼(DPPH)法和β-胡萝卜素漂白法评价抗氧化活性;通过MTT法测定AGS、He La、Lo Vo、MCF-7和MRC-5(正常)细胞的细胞毒性作用。结论:发酵后洋甘菊的TP含量从21.75 mg GAE/g降至18.76 mg GAE/g(GAE:子酸当量),但是DPPH自由基清除率在发酵72 h后比未发酵的高11.1%。由于发酵期间p H的降低,在β-胡萝卜素漂白之后,其抗氧化效果降低。此外,发酵72 h后的洋甘菊对癌细胞有约95%的细胞毒性作用,但是MRC-5细胞的作用不敏感。这些结果表明,洋甘菊的发酵可用于开发天然抗氧化和抗癌产品。

关键词：乳杆菌（Lactobacillus plantarum）洋甘菊（Matricaria chamomilla）类黄酮细胞毒性

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Use of a rat model to characterize 35 arterial pulse wave parameters in a comparative study of isoflurane and Zoletil/ xylazine anesthesia and the effect of Acanthopanax senticosus extract

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动物模型与实验医学(英文) 2023年第5期6卷 474-488页

作者： Anton Misak Marian Grman Lenka Tomasova Ondrej Makara Zuzana Rostakova Iveta Waczulikova Karol Ondrias Institute of Clinical and Translational Research Department of Molecular PhysiologyBiomedical Research CenterSlovak Academy of SciencesBratislavaSlovak Republic Forest Arboretum Liptovsky Hradok Liptovsky HradokSlovak Republic Institute of Measurement science Department of Theoretical MethodsSlovak Academy of SciencesBratislavaSlovak Republic Faculty of Mathematics Physics and InformaticsComenius UniversityBratislavaSlovak Republic

Background : Information obtained from arterial pulse waveforms (APW) can be usefulfor characterizing the cardiovascular system. To achieve this, it is necessary to know thedetailed characteristics of APWs in different states of an organism, which would allowAPW parameters (APW- Ps) to be assigned to particular (patho)physiological conditions.Therefore, our work aimed to characterize 35 APW- Ps in rats under the influence ofisoflurane (ISO) and Zoletil/xylazine (ZO/XY) anesthesia and to study the effect of rootextract from Acanthopanax senticosus (ASRE) in these anesthetic conditions.Methods : The right jugular vein of anesthetized rats was cannulated for the administrationof ASRE and the left carotid artery for the detection of APWs from which 35APW- Ps were evaluated.Results : We obtained data on 35 APW- Ps, which significantly depended on the anesthesia,and thus, they characterized the cardiovascular system under these two conditions.ASRE transiently modulated all 35 APW- Ps, including a transient decrease insystolic and diastolic blood pressure (BP) and heart rate or increases in pulse BP, d P /d t max , and systolic and diastolic areas. Whereas the transient effects of ASRE weresimilar, the extract had prolonged disturbing effects on the cardiovascular system inrats under ZO/XY but not under ISO anesthesia. This negative effect can result fromthe disturbance caused by ZO/XY anesthesia on the cardiovascular system.Conclusions : We characterized 35 APW- Ps of rats under ISO and ZO/XY anesthesiaand found that ASRE contains compounds that can modulate the properties of thecardiovascular system, which significantly depended on the status of the cardiovascularsystem. This should be considered when using ASRE as a nutritional supplementby individuals with cardiovascular problems.

关键词： Acanthopanax senticosus arterial pulse waveform blood pressure hemodynamic parameters isoflurane Zoletil/xylazine

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Achieving ultrahigh electrochemical performance by surface design and nanoconfined water manipulation

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National science Review 2022年第6期9卷 143-152页

作者： Haisheng Li Kui Xu Pohua Chen Youyou Yuan Yi Qiu Ligang Wang Liu Zhu Xiaoge Wang Guohong Cai Liming Zheng Chun Dai Deng Zhou Nian Zhang Jixin Zhu Jinglin Xie Fuhui Liao Hailin Peng Yong Peng Jing Ju Zifeng Lin Junliang Sun College of Chemistry and molecular Engineering Beijing National Laboratory for Molecular Sciences Peking University Key Laboratory of Flexible Electronics and Institute of Advanced Materials Jiangsu National Synergetic Innovation Center for Advanced MaterialsNanjing Tech University Core Labs King Abdullah University of Science and Technology Electron Microscopy Centre of Lanzhou University Lanzhou University School of Chemical and Environmental Engineering China University of Mining and Technology State Key Laboratory of Functional Materials for informatics Shanghai Institute of Microsystem and Information TechnologyChinese Academy of Sciences Analytical Instrumentation center Peking University School of Physical science and Technology Electron Microscopy Centre of Lanzhou University and Key Laboratory of Magnetism and Magnetic Materials of the Ministry of Education Lanzhou University College of Materials science and Engineering Sichuan University

The effects of nanoconfined water and the charge storage mechanism are crucial to achieving the ultrahigh electrochemical performance of two-dimensional transition metal carbides(MXenes). We propose a facile method to manipulate nanoconfined water through surface chemistry modification. By introducing oxygen and nitrogen surface groups, more active sites were created for Ti3C2MXene, and the interlayer spacing was significantly increased by accommodating three-layer nanoconfined water. Exceptionally high capacitance of 550 F g-1(2000 F cm-3) was obtained with outstanding high-rate performance. The atomic scale elucidation of the layer-dependent properties of nanoconfined water and pseudocapacitive charge storage was deeply probed through a combination of ‘computational and experimental microscopy’. We believe that an understanding of, and a manipulation strategy for, nanoconfined water will shed light on ways to improve the electrochemical performance of MXene and other two-dimensional materials.

关键词： two-dimensional material, MXene nanoconfined water energy storage mechanism supercapacitors

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Single-cell RNA sequencing-based immunological feature analysis of a COVID-19 patient with recurrent positive SARS-CoV-2 RNA

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Chinese Medical Journal 2022年第8期135卷 1000-1002页

作者： Bin Su Ruya Sun Lili Zhang Jiaying Zhang Xia Feng Zhenhuan Cao Wei Hou Xianghua Guo Qing Ge Qinghua Cui Yuan Zhou Yingmin Ma Ronghua Jin Yingmei Feng Beijing Youan Hospital Capital Medical UniversityBeijing 100069China Department of Biomedical informatics School of Basic Medical SciencesKey Laboratory of Molecular Cardiovascular Sciences of the Ministry of EducationCenter for Non-coding RNA MedicinePeking University Health Science CenterBeijing 100191China Department of Immunology Key Laboratory of Medical ImmunologyMinistry of HealthSchool of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China Beijing Ditan Hospital Capital Medical UniversityBeijing 100102China

To the Editor:Since the outbreak in December 2019,severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has infected>2.4 billion people worldwide,resulting in>4.9 million deaths.To understand the pathogenesis of SARS-CoV-2 infection,single-cell RNA-sequencing(scRNA-seq)profiles of peripheral blood mononuclear cells(PBMCs)have been constructed in coronavirus disease-2019(COVID-19)patients at different disease stages.

关键词： acute respiratory pathogenesis

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Asymmetric α-Pentadienylation of β-Ketocarbonyls and Aldehydes by Synergistic Pd/Chiral Primary Amine Catalysis

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Chinese Journal of Chemistry 2023年第24期41卷 3533-3538页

作者： Chang You Sanzhong Luo center of Basic molecular science Department of ChemistryTsinghua UniversityBeijing100084 China

Direct alkylation with skipped enynes or cyclopropropylacetylenes represents an ideal process for the installation of pentadienyl group in terms of atom- and step-economy.The development of catalytic asymmetric versions has been frequently pursued and most of the successes have been achieved with enolizable aldehydes.We herein describe a synergistic chiral primary amine/Pd catalysis for asymmetric α-pentadienylation of β-ketocarbonyls and aldehydes with skipped enynes or cyclopropropylacetylenes.The reaction features the construction of acyclic all-carbon quaternary centers with high enantioselectivity,and good functional group tolerance and scalability.

关键词： α-Pentadienylation Synergistic catalysis Chiral primary amine Pd catalysis Hydrocarbons

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CHDbase:A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 216-227页

作者： Wei-Zhen Zhou Wenke Li Huayan Shen Ruby W.Wang Wen Chen Yujing Zhang Qingyi Zeng Hao Wang Meng Yuan Ziyi Zeng Jinhui Cui Chuan-Yun Li Fred Y.Ye Zhou Zhou State Key Laboratory of Cardiovascular Disease Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular DiseasesCenter of Laboratory MedicineFuwai HospitalNational Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100037China International Joint informatics Laboratory&Jiangsu Key Laboratory of Data Engineering and Knowledge Service School of Information ManagementNanjing UniversityNanjing 210023China Institute of molecular Medicine Peking UniversityBeijing 100871China

Congenital heart disease(CHD)is one of the most common causes of major birth defects,with a prevalence of 1%.Although an increasing number of studies have reported the etiology of CHD,the findings scattered throughout the literature are difficult to retrieve and utilize in research and clinical practice.We therefore developed CHDbase,an evidence-based knowledgebase of CHD-related genes and clinical manifestations manually curated from 1114 publications,linking 1124 susceptibility genes and 3591 variations to more than 300 CHD types and related syndromes.Metadata such as the information of each publication and the selected population and samples,the strategy of studies,and the major findings of studies were integrated with each item of the research record.We also integrated functional annotations through parsing50 databases/tools to facilitate the interpretation of these genes and variations in disease pathogenicity.We further prioritized the significance of these CHD-related genes with a gene interaction network approach and extracted a core CHD sub-network with 163 genes.The clear genetic landscape of CHD enables the phenotype classification based on the shared genetic origin.Overall,CHDbase provides a comprehensive and freely available resource to study CHD susceptibilities,supporting a wide range of users in the scientific and medical communities.CHDbase is accessible at http://***.

关键词： Congenital heart disease Congenital heart defect Database Genetics Classification

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A tRF oligomerizes Nucleolin to stabilize metastasis-favoring transcripts

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science China(Life sciences) 2023年第3期66卷 646-648页

作者： Jiawei Guo Yong Peng Laboratory of molecular Oncology Frontiers Science Center for Disease-related Molecular Network State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University

Apart from bringing amino acids to ribosomes for protein biogenesis,transfer RNA(t RNA)can be cleaved into small non-coding RNAs,named as t RFs or ts RNAs.These small RNA fragments were firstly thought as random degradation products of t RNAs until the induction of certain t RFs were observed in specific stress conditions(Li et al.,2008).

关键词： metastasis bringing

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OStme: Online consensus survival analysis web server for tumor microenvironment components of pan-cancers

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Genes & Diseases 2023年第6期10卷 2256-2259页

作者： Longxiang Xie Qiang Wang Xiaoyu Ma Guo Zhao Zhongyi Yan Huimin Li Wan Zhu Zhanjie Zuo Xiangqian Guo Department of Preventive Medicine Institute of Biomedical InformaticsBioinformatics CenterHenan Provincial Engineering Center for Tumor Molecular MedicineAcademy for Advanced Interdisciplinary StudiesSchool of SoftwareSchool of Basic Medical SciencesHenan UniversityKaifengHenan 475004China Department of Anesthesia Stanford UniversityStanfordCA 94305United States Thoracic Cancer Treatment center Armed Police Beijing Corps HospitalBeijing 100027China

Tumor microenvironment(TME)is the environment around the tumor cells,consisting of extracellular matrix,nonmalignant stromal cells,and various types of immune cells(like macrophages,B and T lymphocytes).1 TME has been recurrently reported to play important roles in the progression of cancers.1 The mechanism study of TME may offer opportunities for targeted/immune therapies.However,how TME components impact the prognosis of cancer patients remains to be determined.

关键词： cancers microenvironment prognosis

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