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Metabolic pathway databases and moot repositories

Frontiers of Electrical and Electronic Engineering in China 2018年第1期6卷 30-39页

作者： Abraham A. Labena Yi-Zhou Gao Chuan Dong Hong-li Hua feng-biao guo School of Life Science and Technology University of Electronic Science and Technology of China Chengdu 610054 China College of Computational and Naturay Sciences Dilla University Dilla P.O.box. 419 Et'hiopia School of Life Science and Technology Center for Informational Biology University of Electronic Science and Technology of China Chengdu 610054 China

Background： The number of biological Knowledge bases/databases storing metabolic pathway information and models has been growing rapidly. These resources are diverse in the type of information/data, the analytical tools, and objectives. Here we present a review of the most popular metabolic pathway databases and model repositories, focusing on their scope, content including reactions, enzymes, compounds, and genes, and applicability. The review aims to help researchers choose a suitable database or model repository according to the information and data required, by providing an insight look of each pathway resource. Results： Four pathways databases and three model repositories were selected on the basis of popularity and diversity. Our review showed that the pathway resources vary in many aspects, such as their scope, content, access to data and the tools. In addition, inconsistencies have been observed in nomenclature and representation of database entities. The three model repositories reviewed do not offer a brief description of the models＇ characteristics such as simulation conditions. Conclusions： The inconsistencies among the databases in representing their contents may hamper the maximal use of the knowledge accumulated in these databases in particular and the area of systems biology＇ at large. Therefore, it is strongly recommended that the database creators and the metabolic network models developers should follow international standards for the nomenclature of reactions and metabolites. Besides, computationally generated models that could be obtained from model repositories should be utilized with manual curations as they lack some important components that are necessary for full functionality of the models.

关键词： metabolic pathway database model repository

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The 7th National Conference on Bioinformatics and Systems Biology of China

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Frontiers of Electrical and Electronic Engineering in China 2017年第2期5卷 199-201页

作者： Zhirong Sun Kui Hua Xuegong Zhang feng-biao guo Jian Huang MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic & Systems Biology TNLIST Department of Automation Tsinghua University Beijing 100084 China Bioinformatics Center in School of Life Science and Technology University of Electronic Science and Technology of China Chengdu 610054 China Center of Bioinformatics (COBI) Key Laboratory for Neuro Information of Ministry of Education University of Electronic Science and Technology of China Chengdu 610054 China

The 7th National Conference on Bioinformatics and System Biology and the International Workshop on Advanced Bioinformatics and Precision Medicine was successfully held in Chengdu, Sichuan Province, China, on October 7-9, 2016. The conference is organized by Chinese Society for Cell Biology （CSCB）, National Natural Science Foundation of China （NSFC）, and MOE Key Laboratory of Bioinformatics, Tsinghua University, and hosted by University of Electronic Science and Technology of China （UESTC）. Prof. Runsheng Chen of Institute of Biophysics, CAS, is the organizing chair of the conference, and Prof. Zhirong Sun of Tsinghua University is the general secretary. Professors feng-biao guo and Jian Huang of UESTC led the local organization team. A total of about 1,047 professionals and graduate students from all over the country and several US universities attended the conference.

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Why strong strand-specific composition biases occur in some special bacterial genomes?

Why strong strand-specific composition biases occur in some ...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息...

作者： feng-biao guo School of Life Science and Technology University of Electronic Science and echnology of China

Background:DNA replication,particularly that of microbes,includes a set of asymmetric mechanisms,among which is a division into lagging and leading strands.Due to the asymmetric replication mechanism,nucleotide compositions between the two replicating strands of bacteria are usually biased.Since 1998,foreign researchers have found that a total of 10 bacterial genomes have so extremely strong strand-specific composition bias that genes on the two strands have separate codon usages.However,it is still unclear why the strong bias exist only in some special genomes and not in others and which genomes should have so strong bias. Methods:Sequence and annotation files of nearly 1000 bacterial genomes were obtained from NCBI ftp site on June 2006.All of published work from other groups adopted one single method,namely CA of RSCU and this leads to the peripheral analysis.Comparatively,we combined multiple methods to analyze hundreds of bacterial genomes.Among them,the Z curve method is used in this issue for the first time.To analyze gene content associated with the strong bias,we resort to comparative genomics method.That is to say,we will compare the contents of replication associated genes between the two bacterial groups with and without strong biases.Also,statistic analyses such as t test is employed. Results:Based on the series of works,we found that most of bacterial genomes with strong composition bias are obligate intracellular parasites or symbionts.From the point of gene content,genomes with strong bias tend to lose genes responsible for mutation repair. From the evolutionary point of view,these genomes have much fewer recombinants event and lower translation selections.Furthermore,we found some other common genomic characters of these genomes,for example,they tend to have small genome sizes. Conclusions:Through a five-year sequential studies,we have found the common genomic characters of obligate intracellular bacteria with strong strand composition bias. Also,this work has provided analyzing methods and scien

关键词： Strand composition bias bacterial genomes gene content mutation versus selection

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The E3 ubiquitin ligase TRAF6 controls CTLA-4 turnover and promotes T-cell-mediated antitumor immunity

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Cellular & Molecular Immunology 2024年第1期21卷 97-99页

作者： Xiao-Liang Jie Hua guo Guang-biao Zhou State Key Laboratory of Molecular Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical College100021 BejingChina

Yu et al.[1]reported that the tumor necrosis factor(TNF)receptor OX40(CD134)-TNF receptor-associated factor 6(TRAF6)axis mediates Lys63-linked ubiquitination and subsequent lysosomal degradation of cytotoxic T-lymphocyte antigen 4(CTLA-4),leading to the enhancement of CD8^(+)T-cell-mediated antitumor immunity.Their findings unveil a previously unknown mechanism in controlling the stability of the immune checkpoint CTLA-4 and provide a potential therapeutic target for the improvement of Tcell-based immunotherapy.

关键词： immunity OX40 ubiquitin

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Impacts of pancreatic exocrine insufficiency on gut microbiota

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2024年第4期25卷 271-279页

作者： Yulin guo feng CAO Fei LI Department of General Surgery Xuanwu Hospital of Capital Medical UniversityBeijing 100053China Acute Pancreatitis Clinical Center of Capital Medical University Beijing 100053China

Pancreatic exocrine insufficiency(PEI)can be induced by various kinds of diseases,including chronic pancreatitis,acute pancreatitis,and post-pancreatectomy.The main pathogenetic mechanism of PEI involves the decline of trypsin synthesis,disorder of pancreatic fluid flow,and imbalance of secretion feedback.Animal studies have shown that PEI could induce gut bacterial overgrowth and dysbiosis,with the abundance of Lactobacillus and Bifidobacterium increasing the most,which could be partially reversed by pancreatic enzyme replacement therapy.Clinical studies have also confirmed the association between PEI and the dysbiosis of gut microbiota.Pancreatic exocrine secretions and changes in duodenal p H as well as bile salt malabsorption brought about by PEI may affect and shape the abundance and composition of gut microbiota.In turn,the gut microbiota may impact the pancreatic exocrine acinus through potential bidirectional crosstalk.Going forward,more and higher-quality studies are needed that focus on the mechanism underlying the impact of PEI on the gut microbiota.

关键词： Pancreatic exocrine insufficiency Gut microbiota Gut microbiome Pancreatic enzyme replacement therapy

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Acetaminophen overdose-induced acute liver injury can be alleviated by static magnetic field

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Zoological Research 2024年第3期45卷 478-490页

作者： Han-Xiao Chen Xin-Yu Wang biao Yu Chuan-Lin feng guo-feng Cheng Lei Zhang Jun-Jun Wang Ying Wang Ruo-Wen guo Xin-Miao Ji Wen-Jing Xie Wei-Li Chen Chao Song Xin Zhang CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology High Magnetic Field LaboratoryHefei Institutes of Physical ScienceChinese Academy of SciencesHefeiAnhui 230031China Science Island Branch of Graduate School University of Science and Technology of ChinaHefeiAnhui 230026China Institutes of Physical Science and Information Technology Anhui UniversityHefeiAnhui 230601China

Acetaminophen(APAP),the most frequently used mild analgesic and antipyretic drug worldwide,is implicated in causing 46%of all acute liver failures in the USA and between 40%and 70%in Europe.The predominant pharmacological intervention approved for mitigating such overdose is the antioxidant N-acetylcysteine(NAC);however,its efficacy is limited in cases of advanced liver injury or when administered at a late stage.In the current study,we discovered that treatment with a moderate intensity static magnetic field(SMF)notably reduced the mortality rate in mice subjected to high-dose APAP from 40%to 0%,proving effective at both the initial liver injury stage and the subsequent recovery stage.During the early phase of liver injury,SMF markedly reduced APAPinduced oxidative stress,free radicals,and liver damage,resulting in a reduction in multiple oxidative stress markers and an increase in the antioxidant glutathione(GSH).During the later stage of liver recovery,application of vertically downward SMF increased DNA synthesis and hepatocyte proliferation.Moreover,the combination of NAC and SMF significantly mitigated liver damage induced by high-dose APAP and increased liver recovery,even 24 h post overdose,when the effectiveness of NAC alone substantially declines.Overall,this study provides a noninvasive non-pharmaceutical tool that offers dual benefits in the injury and repair stages following APAP overdose.Of note,this tool can work as an alternative to or in combination with NAC to prevent or minimize liver damage induced by APAP,and potentially other toxic overdoses.

关键词： Acetaminophen Acute liver injury Static magnetic fields Oxidative stress DNA synthesis

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Impact of Alcian blue and periodic acid Schiff expression on the prognosis of gastric signet ring cell carcinoma

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World Journal of Gastrointestinal Oncology 2024年第3期16卷 687-698页

作者： Juan Lin Zhu-feng Chen guo-Dong guo Xin Chen Shengli Clinical Medical College Fujian Medical UniversityFuzhou 350001Fujian ProvinceChina Department of Pathology Fujian Provincial HospitalFuzhou 350001Fujian ProvinceChina Department of Internal Medicine Fujian Provincial HospitalFuzhou 350001Fujian ProvinceChina

BACKGROUND The Alcian blue(AB)and periodic acid Schiff(PAS)stains are representative mucus markers in gastric signet ring cell carcinoma(SRCC).They are low-cost special staining methods used to detect acidic mucus and neutral mucus,respectively.However,the clinical importance of the special combined AB and PAS stain is unclear.AIM To investigate AB expression,PAS expression and the AB-to-PAS(A/P)ratio in gastric SRCC patients and to assess patient prognosis.METHODS Paraffin-embedded sections from 83 patients with gastric SRCC were stained with AB and PAS,and signet ring cell positivity was assessed quantitatively.Immuno-histochemical staining for Ki67,protein 53(P53)and human epidermal growth factor receptor 2(HER2)was performed simultaneously.The cancer-specific survival(CSS)rate was estimated via Kaplan-Meier analysis.Cox proportional hazards models were used for univariate and multivariate survival analyses.RESULTS Kaplan-Meier survival analysis revealed that the 3-year CSS rate was significantly greater in the high-PAS-expression subgroup than in the low-PAS-expression subgroup(P0.5 group(P=0.042).Univariate Cox regression analysis revealed that the factors affecting prognosis included tumor diameter,lymph node metastasis,vessel carcinoma embolus,tumor stage,the A/P ratio and the expression of Ki67,P53 and the PAS.Cox multivariate regression analysis confirmed that low PAS expression[hazard ratio(HR)=3.809,95%confidence interval(CI):1.563-9.283,P=0.003]and large tumor diameter(HR=2.761,95%CI:1.086-7.020,P=0.033)were independent risk factors for poor prognosis.CONCLUSION A/P>0.5 is potentially a risk factor for prognosis,and low PAS expression is an independent risk factor in the prognosis of gastric SRCC.PAS expression and the A/P ratio could help in predicting the clinical prognosis of patients with SRCC.

关键词： Alcian blue Periodic acid-Schiff Prognosis Gastric Signet ring cell carcinoma

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Seismic safety assessment with non-Gaussian random processes for train-bridge coupled systems

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Earthquake Engineering and Engineering Vibration 2024年第1期23卷 241-260页

作者： Zhao Han Gao Lei Wei biao Tan Jincheng guo Peidong Jiang Lizhong Xiang Ping Key Laboratory of Geomechanics and Embankment Engineering of Ministry of Education Hohai UniversityNanjing 210024China School of Civil Engineering Central South UniversityChangsha 410075China

Extensive high-speed railway(HSR)network resembled the intricate vascular system of the human body,crisscrossing mainlands.Seismic events,known for their unpredictability,pose a significant threat to both trains and bridges,given the HSR’s extended operational duration.Therefore,ensuring the running safety of train-bridge coupled(TBC)system,primarily composed of simply supported beam bridges,is paramount.Traditional methods like the Monte Carlo method fall short in analyzing this intricate system efficiently.Instead,efficient algorithm like the new point estimate method combined with moment expansion approximation(NPEM-MEA)is applied to study random responses of numerical simulation TBC systems.Validation of the NPEM-MEA’s feasibility is conducted using the Monte Carlo method.Comparative analysis confirms the accuracy and efficiency of the method,with a recommended truncation order of four to six for the NPEM-MEA.Additionally,the influences of seismic magnitude and epicentral distance are discussed based on the random dynamic responses in the TBC system.This methodology not only facilitates seismic safety assessments for TBC systems but also contributes to standard-setting for these systems under earthquake conditions.

关键词： train-bridge coupled(TBC)system random vibration new point estimate method(NPEM) seismic safety assessment moment expansion approximation(MEA) non-Gaussian distributions

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Exploiting sound for emerging applications of extracellular vesicles

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Nano Research 2024年第2期17卷 462-475页

作者： Zhuhao Wu Hongwei Cai Chunhui Tian Zheng Ao Lei Jiang feng guo Department of Intelligent Systems Engineering Indiana UniversityBloomingtonIN 47405USA

Extracellular vesicles are nano-to micro-scale,membrane-bound particles released by cells into extracellular space,and act as carriers of biomarkers and therapeutics,holding promising potential in translational medicine.However,the challenges remain in handling and detecting extracellular vesicles for disease diagnosis as well as exploring their therapeutic capability for disease treatment.Here,we review the recent engineering and technology advances by leveraging the power of sound waves to address the challenges in diagnostic and therapeutic applications of extracellular vesicles and biomimetic nanovesicles.We first introduce the fundamental principles of sound waves for understanding different acoustic-assisted extracellular vesicle technologies.We discuss the acoustic-assisted diagnostic methods including the purification,manipulation,biosensing,and bioimaging of extracellular vesicles.Then,we summarize the recent advances in acoustically enhanced therapeutics using extracellular vesicles and biomimetic nanovesicles.Finally,we provide perspectives into current challenges and future clinical applications of the promising extracellular vesicles and biomimetic nanovesicles powered by sound.

关键词： extracellular vesicles exosomes biomimetic nanovesicles acoustics disease diagnostics therapeutics

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A class of natural pinus koraiensis population system with time delay and diffusion term

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International Journal of Biomathematics 2024年第2期17卷 233-262页

作者： guo-feng feng Jiaqi Chen Bin Ge School of Mathematical Sciences Harbin Engineering University Harbin 150001 P.R.China

In this paper,we consider the long-term sustainability of the northeast Korean pine.We propose a class of natural Korean pine population system with time delay and diffusion term.First,by analyzing the roots distribution of the characteristic equation,we study the stability of the model system with diffusion terms and prove the occurrence of Hopf bifurcation.Second,we introduce lactation time delay into a population model with a diffusion term,based on stability theory of ordinary differential equation,norm form methods and center manifold theorem,the stability of bifurcating periodic solutions and the relevant formula for the direction of Hopf bifurcation are given.Finally,some numerical simulations are given.

关键词： Pinus koraiensis populations delay diffusion term Hopf bifurcation periodic solution

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