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Sensitive determination of inosine RNA modification in single cell by chemical derivatization coupled with mass spectrometry analysis

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Chinese Chemical Letters 2023年第10期34卷 98-101页

作者： wan-bing tao Neng-Bin Xie Qing-Yun Cheng Yu-Qi Feng Bi-Feng Yuan College of Chemistry and Molecular Sciences Department of Radiation and Medical OncologyZhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan 430071China School of Public Health Wuhan UniversityWuhan 430071China Research Center of Public Health Renmin Hospital of Wuhan UniversityWuhan 430060China Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center Zhongnan Hospital of Wuhan UniversityWuhan Research Center for Infectious Diseases and CancerChinese Academy of Medical SciencesWuhan 430071China

Inosine is a vital RNA modification across three kingdoms of *** has been demonstrated that inosine plays important roles in modulation of the fate of *** the current study,we developed a highly sensitive method to determine inosine in a single cell by N-cyclohexyl-N’-β-(4-methylmorpholinium)ethylcarbodiimide p-toluenesulfonate(CMCT)derivatization in combination with mass spectrometry *** results showed that the detection sensitivity of inosine was increased by 556-fold after CMCT derivatization,with the limit of detection(LOD)being 4.5 *** the established method,we could detect inosine from 13.0 pg of total RNA of HEK293T ***,inosine in RNA from a single cell could also be clearly detected due to the improved detection ***,we found the level of inosine in RNA of sleep-deprived mice was significantly increased compared to the control mice,indicating that inosine is associated with sleep behavior and might be a potential indicator of sleep *** together,the chemical derivatization coupled with mass spectrometry analysis offers a valuable tool in determination of endogenous RNA modifications in a single cell,which should benefit the functional study of RNA modification in rare clinical samples.

关键词： Inosine RNA modification CMCT Derivatization Mass spectrometry Single cell

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Transformation of 5-Carboxylcytosine to Cytosine Through C-C Bond Cleavage in Human Cells Constitutes a Novel Pathway for DNA Demethylation

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CCS Chemistry 2021年第4期3卷 994-1008页

作者： Yang Feng Neng-Bin Xie wan-bing tao Jiang-Hui Ding Xue-Jiao You Cheng-Jie Ma Xiaoxue Zhang Chengqi Yi Xiang Zhou Bi-Feng Yuan Yu-Qi Feng Key Laboratory of Analytical Chemistry for Biology and Medicine(Ministry of Education) Sauvage Center for Molecular SciencesDepartment of ChemistryWuhan UniversityWuhan 430072 State Key Laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871 Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871 Department of Chemical Biology and Synthetic and Functional Biomolecules Center College of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871

Active demethylation of 5-methylcytosine(5mC)can be realized through ten-eleven translocation(TET)dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine(5hmC),5-formylcytosine(5fC),and 5-carboxylcytosine(5caC),followed by thymine DNA glycosylase(TDG)-initiated base excision repair(BER).The TDG-BER pathwaymay lead to the generation of DNA strand breaks,potentially compromising genome ***,direct decarboxylation of TET-produced 5caC is highly attractive because this mechanism allows for conversion of 5mC to cytosine without the formation of DNA strand ***,cleavage of the C–C bond in 5caC in human cells remains an open *** examined this reaction in cell extract and live cells using 5caC-carrying hairpin DNA *** incubation with whole-cell protein extract or transfection into human cells,we monitored the transformation of 5caC to cytosine through direct decarboxylation or BER using liquid chromatography–tandem mass spectrometry(LCMS/MS)analyses at both the mononucleotide and oligodeoxynucleotide *** results clearly showed the direct conversion of 5caC to cytosine in human cells,providing evidence to support a novel pathway for active DNA demethylation.

关键词： epigenetics DNA demethylation 5-carboxylcytosine decarboxylation mass spectrometry stable isotope labeling

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Cholesterol metabolism: physiological versus pathological aspects in intracerebral hemorrhage

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Neural Regeneration Research 2025年第4期20卷 1015-1030页

作者： Ruoyu Huang Qiuyu Pang Lexin Zheng Jiaxi Lin Hanxi Li Lingbo wan tao wang Department of Forensic Science School of Basic Medicine and Biological SciencesSuzhou Medicine College of Soochow UniversitySuzhouJiangsu ProvinceChina

Cholesterol is an important component of plasma membranes and participates in many basic life functions,such as the maintenance of cell membrane stability,the synthesis of steroid hormones,and *** plays a key role in the establishment and maintenance of the central nervous *** brain contains 20%of the whole body’s cholesterol,80%of which is located within myelin.A huge number of processes(e.g.,the sterol regulatory element-binding protein pathway and liver X receptor pathway)participate in the regulation of cholesterol metabolism in the brain via mechanisms that include cholesterol biosynthesis,intracellular transport,and *** brain injuries or diseases involving crosstalk among the processes above can affect normal cholesterol metabolism to induce detrimental ***,we hypothesized that cholesterol-related molecules and pathways can serve as therapeutic targets for central nervous system *** hemorrhage is the most severe hemorrhagic stroke subtype,with high mortality and *** cholesterol levels are associated with the risk of intracerebral ***,secondary pathological changes after intracerebral hemorrhage are associated with cholesterol metabolism dysregulation,such as neuroinflammation,demyelination,and multiple types of programmed cell *** cholesterol accumulation in the brain has been found after intracerebral *** this paper,we review normal cholesterol metabolism in the central nervous system,the mechanisms known to participate in the disturbance of cholesterol metabolism after intracerebral hemorrhage,and the links between cholesterol metabolism and cell *** also review several possible and constructive therapeutic targets identified based on cholesterol metabolism to provide cholesterol-based perspectives and a reference for those interested in the treatment of intracerebral hemorrhage.

关键词： cell death cholesterol metabolism intracerebral hemorrhage myelination therapeutic target

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2016年全国研究生数学建模竞赛E题赛题点评

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数学的实践与认识 2017年第15期47卷 143-148页

作者：汪晓银万兵涛天津工业大学理学院天津300387

首先阐明了2016年全国研究生数学建模竞赛E题"粮食最低收购价政策问题研究"的研究背景和问题研究的实际意义.接着,针对每一个问题,从研究思路、研究方法、研究结论等方面均作了详细的叙述.最后,对学生论文中出现的问题、难点以及创新性... 详细信息

首先阐明了2016年全国研究生数学建模竞赛E题"粮食最低收购价政策问题研究"的研究背景和问题研究的实际意义.接着,针对每一个问题,从研究思路、研究方法、研究结论等方面均作了详细的叙述.最后,对学生论文中出现的问题、难点以及创新性等方面做了点评.

关键词：数学建模赛题点评粮食最低收购价

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Risk factors for postoperative pancreatic fistula: Analysis of 539 successive cases of pancreaticoduodenectomy

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World Journal of Gastroenterology 2016年第34期22卷 7797-7805页

作者： bing-Yang Hu tao wan Wen-Zhi Zhang Jia-Hong Dong Institute and Hospital of Hepatobiliary Surgery Chinese PLA General HospitalBeijing 100853China Hepato-Pancreato-Biliary Center Beijing Tsinghua Changgung HospitalBeijing 102218 China

AIM To analyze the risk factors for pancreatic fistula after *** We conducted a retrospective analysis of 539 successive cases of pancreaticoduodenectomy performed at our hospital from March 2012 to October 2015. Pancreatic fistula was diagnosed in strict accordance with the definition of pancreatic fistula from the International Study Group on Pancreatic Fistula. The risk factors for pancreatic fistula were analyzed by univariate analysis and multivariate logistic regression *** A total of 269(49.9%) cases of pancreatic fistula occurred after pancreaticoduodenectomy,including 71(13.17%) cases of grade A pancreatic fistula,178(33.02%) cases of grade B,and 20(3.71%) cases of grade C. Univariate analysis showed no significant correlation between postoperative pancreatic fistula(POPF) and the following factors: age,hypertension,alcohol consumption,smoking,history of upper abdominal surgery,preoperative jaundice management,preoperative bilirubin,preoperative albumin,pancreatic duct drainage,intraoperative blood loss,operative time,intraoperative blood transfusion,Braun anastomosis,and pancreaticoduodenectomy(with or without pylorus preservation). Conversely,a significant correlation was observed between POPF and the following factors: gender(male vs female: 54.23% vs 42.35%,P = 0.008),diabetes(non-diabetic vs diabetic: 51.61% vs 39.19%,P = 0.047),body mass index(BMI)(≤ 25 vs > 25: 46.94% vs 57.82%,P = 0.024),blood glucose level(≤ 6.0 mmol/L vs > 6.0 mmol/L: 54.75% vs 41.14%,P = 0.002),pancreaticojejunal anastomosis technique(pancreatic duct-jejunum double-layer mucosa-to-mucosa pancreaticojejunal anastomosis vs pancreatic-jejunum single-layer mucosa-tomucosa anastomosis: 57.54% vs 35.46%,P = 0.000),diameter of the pancreatic duct(≤ 3 mm vs > 3 mm: 57.81% vs 38.36%,P = 0.000),and pancreatic texture(soft vs hard: 56.72% vs 29.93%,P = 0.000). Multivariate logistic regression analysis showed that gender(male),BMI > 25,pancreatic duct

关键词： Pancreaticoduodenectomy Pancreatic fistula Pancreaticojejunal anastomosis Pancreatic duct Complications

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Hybrid Bayesian estimation tree learning with discrete and fuzzy labels

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Frontiers of Computer Science 2013年第6期7卷 852-863页

作者： Zengchang QIN tao wan Intelligent Computing and Machine Learning Lab School of Automation Science and Electrical Engineering Beihang University Beijing 100191 China School of Biological Science and Medical Engineering Beihang University Beijing 100191 China Department of Biomedical Engineering Case Western Reserve University Cleveland OH 44106 USA

Classical decision tree model is one of the classical machine learning models for its simplicity and effectiveness in applications. However, compared to the DT model, probability estimation trees （PETs） give a better estimation on class probability. In order to get a good probability estimation, we usually need large trees which are not desirable with respect to model transparency. Linguistic decision tree （LDT） is a PET model based on label semantics. Fuzzy labels are used for building the tree and each branch is associated with a probability distribution over classes. If there is no overlap between neighboring fuzzy labels, these fuzzy labels then become discrete labels and a LDT with discrete labels becomes a special case of the PET model. In this paper, two hybrid models by combining the naive Bayes classifier and PETs are proposed in order to build a model with good performance without losing too much transparency. The first model uses naive Bayes estimation given a PET, and the second model uses a set of small-sized PETs as estimators by assuming the independence between these trees. Empirical studies on discrete and fuzzy labels show that the first model outperforms the PET model at shallow depth, and the second model is equivalent to the naive Bayes and PET.

关键词： fuzzy labels label semantics random set probability estimation tree mass assignment linguistic decision tree naive Bayes

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Metadata Feedback and Utilization for Data Deduplication Across wan

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Journal of Computer Science & Technology 2016年第3期31卷 604-623页

作者： bing Zhou Jiang-tao Wen State Key Laboratory on Intelligent Technology and Systems Tsinghua University Beijing 100084 China Tsinghua National Laboratory for Information Science and Technology Tsinghua University Beijing 100084 China Department of Computer Science and Technology Tsinghua University Beijing 100084 China

Data deduplication for file communication across wide area network （wan） in the applications such as file synchronization and mirroring of cloud environments usually achieves significant bandwidth saving at the cost of significant time overheads of data deduplication. The time overheads include the time required for data deduplication at two geographi- cally distributed nodes （e.g., disk access bottleneck） and the duplication query/answer operations between the sender and the receiver, since each query or answer introduces at least one round-trip time （RTT） of latency. In this paper, we present a data deduplication system across wan with metadata feedback and metadata utilization （MFMU）, in order to harness the data deduplication related time overheads. In the proposed MFMU system, selective metadata feedbacks from the receiver to the sender are introduced to reduce the number of duplication query/answer operations. In addition, to harness the metadata related disk I/O operations at the receiver, as well as the bandwidth overhead introduced by the metadata feedbacks, a hysteresis hash re-chunking mechanism based metadata utilization component is introduced. Our experimental results demonstrated that MFMU achieved an average of 20%~40% deduplication acceleration with the bandwidth saving ratio not reduced by the metadata feedbacks, as compared with the ＂baseline＂ content defined chunking （CDC） used in LBFS （Low-bandwith Network File system） and exiting state-of-the-art Bimodal chunking algorithms based data deduplication solutions.

关键词： data deduplication wide area network (wan) metadata feedback metadata utilization

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Preparation of a cationic azobenzene dye-montmorillonite intercalation compound and its photochemical behavior

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Journal of University of Science and Technology Beijing 2006年第3期13卷 281-286页

作者： tao wan Yi Yuan Wenqiong He College of Materials and Chemistry ＆ Chemical Engineering Chengdu University of Technology Chengdu 610059 China

Montmorillonite/cationic azobenzene dye （GTL） intercalation compounds were prepared by the conventional ion exchange method. As compared with that of pure GTL, the thermal stability of the intercalated GTL was greatly enhanced, and the absorption band corresponding to azobenzene group in intercalated GTL shifted towards a longer wavelength by 55 nm, which could be ascribed to the strong conjugation of GTL supramolecular order structure （J cluster） confined in a nanoscale space of montmorillonite interlayer gallery. The microstructures of the resulting intercalation compounds could be successfully controlled by varying the amount of dye loaded as evidenced by the basal spacing of the intercalation compounds. The intercalated azo dye in the montmorillonite interlayer space exhibited reversible trans-to-cis photoisomerization and thermal cis-to-trans reaction. FTIR proved the successful intercalation of GTL into the silicate layer.

关键词： Na-montmorillonite azobenzene intercalation photoisomerization

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A Mutual Evaluation Based Trust Management Method for Wireless Sensor Networks

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Chinese Journal of Electronics 2017年第2期26卷 407-415页

作者： GUO Jingjing MA Jianfeng wan tao School of Cyber Engineering Xidian University The State Key Laboratory of Integrated Services Networks Xidian University School of Information Engineering East China Jiaotong University

We propose a lightweight trust system for the clustered wireless sensor networks based on the mutual evaluation between the cluster heads and sensor *** evaluate the trust level of a cluster head in two aspects,namely,trust level as a service provider and a *** consider multidimensional trust attributes to compute the global trust value of a *** means of the Petri net(PN),we illustrate the performance of an entity in our trust *** analyses as well as simulations are done and the results showed that our model with linear computational complexity had less memory and communication overhead when compared with the current state-ofart trust management *** addition,our model can detect malicious and selfish entities(especially the malicious cluster head) and resist various attacks efficiently.

关键词： Trust management Petri nets(PNs) Clustered wireless sensor networks

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Effects of postthermal treatment and UV irradiation on the structure of titania-polyacrylate nanocomposites

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Journal of University of Science and Technology Beijing 2006年第4期13卷 372-379页

作者： tao wan Fei Feng Yuechuan wang State Key Laboratory of Polymer Materials Engineering College of Polymer Science and Engineering Sichuan University Chengdu 610065 China College of Materials and Chemistry ＆ Chemical Engineering Chengdu University of Technology Chengdu 610059 China

The effects of postthermal treatment and irradiation time on the structure and thermal stability of TiO2/polyacrylate nanocomposites by a sol-gel process in reverse micelles and subsequent rapid photopolymerization were investigated, and the hybrid films were characterized by thermal gravimetry analysis （TGA）, X-ray photoelectron spectrum （XPS）, and atomic force microscopy （AFM）. XPS data suggested that the prolongation of irradiation time and the postthermal treatment promoted titania formation, with the former affecting more remarkably. TGA data showed that TiO2-hybrid films could upgrade the decomposition onset temperature （Tonset） as well as the temperature at which there is a maximum mass loss rate （Tmax）. AFM data demonstrated that the inorganic titania particles with a mean diameter of 25.26-28.84 nm were homogeneously distributed in the organic matrix.

关键词： titanium dioxide reverse micelles sol-gel method photopolymerization nanocomposites

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