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NORMA:The Network Makeup Artist—A Web Tool for Network Annotation Visualization

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Genomics, Proteomics & Bioinformatics 2022年第3期20卷 578-586页

作者： Mikaela Koutrouli Evangelos Karatzas Katerina Papanikolopoulou Georgios A.Pavlopoulos Institute for Fundamental biomedical research BSRC“Alexander Fleming”Vari 16672Greece Department of Informatics and Telecommunications University of AthensAthens 15703Greece

The Network Makeup Artist(NORMA) is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Precalculated annotations(e.g., Gene Ontology, Pathway enrichment, community detection,or clustering results) can be uploaded and visualized in a network, either as colored pie-chart nodes or as color-filled areas in a 2D/3D Venn-diagram-like style. In the case where no annotation exists,algorithms for automated community detection are offered. Users can adjust the network views using standard layout algorithms or allow NORMA to slightly modify them for visually better group separation. Once a network view is set, users can interactively select and highlight any group of interest in order to generate publication-ready figures. Briefy, with NORMA, users can encode three types of information simultaneously. These are 1) the network, 2) the communities or annotations of interest, and 3) node categories or expression values. Finally, NORMA offers basic topological analysis and direct topological comparison across any of the selected networks. NORMA service is available at http://***, whereas the code is available at https://***/Pavlopoulos Lab/NORMA.

关键词： Network annotation Visualization Topological analysis Community detection Functional enrichment visualization

Expression of Mammalian BM88/CEND1 in Drosophila Affects Nervous System Development by Interfering with Precursor Cell Formation

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Neuroscience Bulletin 2019年第6期35卷 979-995页

作者： Athanasios Tzortzopoulos Dimitra Thomaidou Maria Gaitanou Rebecca Matsas Efthimios Skoulakis Department of Clinical Biochemistry Aghia Sophia Children's Hospital11527 AthensGreece Laboratory of Cellular and Molecular Neurobiology Hellenic Pasteur Institute11521 AthensGreece "alexander fleming"biomedical sciences research Centre 16672 AthensGreece

We used Drosophila melanogaster as an experimental model to express mouse and pig BM88/CEND1(cell cycle exit and neuronal differentiation 1) in order to investigate its potential functional effects on Drosophila neurogenesis. BM88/CEND1 is a neuron-specific protein whose function is implicated in triggering cells to exit from the cell cycle and differentiate towards a neuronal phenotype. Transgenic flies expressing either mouse or pig BM88/CEND1 in the nervous system had severe neuronal phenotypes with variable expressivity at various stages of embryonic development. In early embryonic stage 10,BM88/CEND1 expression led to an increase in the neuralspecific antigenicity of neuroectoderm at the expense of precursor cells [neuroblasts(Nbs) and ganglion mother cells(GMCs)] including the defective formation and differentiation of the MP2 precursors, whereas at later stages(12–15), protein accumulation induced gross morphological defects primarily in the CNS accompanied by a reduction of Nb and GMC markers. Furthermore, the neuronal precursor cells of embryos expressing BM88/CEND1 failed to carry out proper cell-cycle progression as revealed by the disorganized expression patterns of specific cell-cycle markers. BM88/CEND1 accumulation in the Drosophila eye affected normal eye disc development by disrupting the ommatidia. Finally, we demonstrated that expression of BM88/CEND1 modified/reduced the levels of activated MAP kinase indicating a functional effect of BM88/CEND1 on the MAPK signaling pathway. Our findings suggest that the expression of mammalian BM88/CEND1 in Drosophila exerts specific functional effects associated with neuronal precursor cell formation during embryonic neurogenesis and proper eye disc *** study also validates the use of Drosophila as a powerful model system in which to investigate gene function and the underlying molecular mechanisms.

关键词： Drosophila Neurogenesis BM88/CEND1 Nervous system Protein function

Exploring unconventional attributes of red blood cells and their potential applications in biomedicine

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Protein & Cell 2024年第5期15卷 315-330页

作者： Alkmini T.Anastasiadi Vasiliki-Zoi Arvaniti Krystalyn E.Hudson Anastasios G.Kriebardis Constantinos Stathopoulos Angelo D’Alessandro Steven L.Spitalnik Vassilis L.Tzounakas Department of Biochemistry School of MedicineUniversity of Patras26504 PatrasGreece Department of Pathology and Cell Biology Columbia University Irving Medical CenterNew York CityNY 10032USA Laboratory of Reliability and Quality Control in Laboratory Hematology(HemQcR) Department of Biomedical SciencesSchool of Health&Caring SciencesUniversity of West Attica(UniWA)12243 EgaleoGreece Department of Biochemistry and Molecular Genetics University of Colorado Anschutz Medical Campus13001 AuroraCOUSA Present address:Institute for Fundamental biomedical research(IFBR) Biomedical Sciences Research Center“Alexander Fleming”Vari11527 AthensGreece

We need to talk about red blood *** cells are defined as cells containing distinct nuclei and other membranous ***,red blood cells(RBCs)lack a nucleus and organelles—perhaps to limit the generation of reactive oxygen species(Zhang et al.,2011)—and are filled with hemoglobin(Hb).This oxygen carrier is limited to the cytosol by the cell membrane and cytoskeleton,which maintain cellular integrity and deformability as RBCs pass through narrow capillaries(Gratzer,1994)to perform their primary function of gas exchange.

关键词： membranous maintain

Decoding altitude-activated regulatory mechanisms occurring during apple peel ripening

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Horticulture research 2020年第1期7卷 1149-1160页

作者： Evangelos Karagiannis Michail Michailidis Georgia Tanou Federico Scossa Eirini Sarrou George Stamatakis Martina Samiotaki Stefan Martens Alisdair R.Fernie Athanassios Molassiotis Laboratory of Pomology Department of AgricultureAristotle University of Thessaloniki54124 ThessalonikiGreece Institute of Soil and Water Resources ELGO-DEMETERThermiThessaloniki 57001Greece Max-Planck-Institute of Molecular Plant Physiology Am Müehlenberg 1.Potsdam-Golm 14476Germany Council for Agricultural research and Economics Research Center for Genomics and BioinformaticsVia Ardeatina 54600178 RomeItaly Institute of Plant Breeding and Genetic Resources ELGO-DEMETERThermiThessaloniki 57001Greece biomedical sciences research center“alexander fleming” Vari 16672Greece Fondazione Edmund Mach Centro Ricerca e InnovazioneDepartment of Food Quality and NutritionVia E.Mach138010 San Michele all’AdigeTNItaly

Apple(Malus domestica Borkh)is an important fruit crop cultivated in a broad range of environmental *** fruit ripening is a physiological process,whose molecular regulatory network response to different environments is still not sufficiently investigated and this is particularly true of the peel *** this study,the influence of environmental conditions associated with low(20 m)and high(750 m)altitude on peel tissue ripening was assessed by physiological measurements combined with metabolomic and proteomic analyses during apple fruit development and *** apple fruit ripening was itself not affected by the different environmental conditions,several key color parameters,such as redness and color index,were notably induced by high *** with this observation,increased levels of anthocyanin and other phenolic compounds,including cyanidin-3-O-galactoside,quercetin-3-O-rhamnoside,quercetin-3-O-rutinoside,and chlorogenic acid were identified in the peel of apple grown at high ***,the high-altitude environment was characterized by elevated abundance of various carbohydrates(e.g.,arabinose,xylose,and sucrose)but decreased levels of glutamic acid and several related proteins,such as glycine hydroxymethyltransferase and glutamate–glyoxylate *** processes affected by high altitude were the TCA cycle,the synthesis of oxidative/defense enzymes,and the accumulation of photosynthetic *** the obtained data we were able to construct a metabolite-protein network depicting the impact of altitude on peel *** combined analyses presented here provide new insights into physiological processes linking apple peel ripening with the prevailing environmental conditions.

关键词： altitude network prevailing

基于NMR的代谢组学方法最新进展及应用(英文)

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波谱学杂志 2006年第1期23卷 101-127页

作者： LINDON J C HOLMES E NICHOLSON J K Biological Chemistry Biomedical Sciences Division Imperial College London Sir Alexander Fleming Building South Kensington London SW7 2AZ UK

代谢组学的定义“对病理/生理刺激以及基因改变时生物体系动态的代谢响应进行多参数的定量测量”已被广泛接受.本文对代谢组学研究的最新进展及其在系统生物学中所发挥的作用进行了综述.在代谢组学方法研究方面,着重讨论了现代NMR技术... 详细信息

代谢组学的定义“对病理/生理刺激以及基因改变时生物体系动态的代谢响应进行多参数的定量测量”已被广泛接受.本文对代谢组学研究的最新进展及其在系统生物学中所发挥的作用进行了综述.在代谢组学方法研究方面,着重讨论了现代NMR技术的进展及其对代谢组学所产生的影响,同时也包括用于分离的HPLC及其与质谱的连用技术.对代谢组学广泛应用的概述,主要包括:对正常生理变化的新认识;药物和其他外源性化学物质的副作用;外源性物质对环境污染的影响以及逐渐增多的代谢组学方法在疾病检测中应用.

关键词：核磁共振液相色谱-质谱联用代谢物生物标记疾病检测毒性环境

A pilot study of the dynamics of tissue oxygenation in vivo using time-resolved phosphorescence imaging

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Journal of Innovative Optical Health sciences 2021年第5期4卷 15-24页

作者： Natalia Kazachkina Julia Lymar Vladislav Shcheslavskiy alexander Savitsky A.N.Bach Institute of Biochemistry research center of Biotechnology of the Russian Academy of sciences Moscow 119071Russian Federation Institute of Experimental Oncology and biomedical Technologies Privolzhsky research Medical University Sq Minin and Pozharsky10/1603005 Nizhny Novgorod Russian Federation Becker and Hickl GmbH Nunsdorfer Ring 7-912277 BerlinGermany

Oxygenation of tissues plays an important role in the development and progression of tumor to treatment *** of metalloporphyrines phosphorescence quenching by oxygen is one of the ways to measure dynamics of the oxygen concentration in the tissues by phosphorescence lifetime imaging of meso-tetra(sulfophenyl)tetrabenzoporphyrin Pd(Ⅱ)(TBP)using the time-correlated single photon counting(TCSPC)*** has been shown that phosphorescence lifetime of the sensor in S37 tumor in vivo varied in the range of 130 to 290μs after both topical and intravenous administration of *** indicates that oxygen level in tumors was lower compared to normal tissues where TBP phosphorescence has not been *** lifetimes of TBP increased in the solid tumor and in the muscle after photodynamic therapy of solid tumor that demonstrates oxygen consumption during treatment and possibly stopping the blood flow and hence the oxygen supply to the tissues.

关键词： Phosphorescence oxygen sensor metalloporphyrines TCSPC

Machine learning-enabled optimization of melt electro-writing three-dimensional printing

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Aggregate 2024年第3期5卷 258-267页

作者： Ahmed Choukri Abdullah Olgac Ozarslan Sara Soltanabadi Farshi Sajjad Rahmani Dabbagh Savas Tasoglu Department of Mechanical Engineering KoçUniversitySariyerTurkey Department of biomedical sciences and Engineering KoçUniversitySariyerTurkey KoçUniversity Arçelik research center for Creative Industries(KUAR) KoçUniversitySariyerTurkey Koc University Is Bank Artiﬁcial Intelligence Lab(KUIS AILab) KoçUniversitySariyerTurkey KoçUniversity Translational Medicine research center(KUTTAM) KoçUniversitySariyerTurkey Bogaziçi Institute of biomedical Engineering Bogaziçi UniversityCengelkoyTurkey

Melt electrowriting(MEW)is a solvent-free(i.e.,no volatile chemicals),a high-resolution three-dimensional(3D)printing method that enables the fabrication of semi-ﬂexible structures with rigid *** its advantages,the MEW pro-cess is sensitive to changes in printing parameters(e.g.,voltage,printing pressure,and temperature),which can causeﬂuid column breakage,jet lag,and/orﬁber pulsing,ultimately deteriorating the resolution and printing *** spite of the commonly used error-and-trial method to determine the most suitable parameters,here,we present a machine learning(ML)-enabled image analysis-based method for determining the optimum MEW printing parameters through an easy-to-use graph-ical user interface(GUI).We trainedﬁve different ML algorithms using 168 MEW 3D print samples,among which the Gaussian process regression ML model yielded 93%accuracy of the variability in the dependent variable,0.12329 on root mean square error for the validation set and 0.015201 mean square error in predicting line *** of ML with a control feedback loop and MEW can reduce the error-and-trial steps prior to the 3D printing process,decreasing the printing time(i.e.,increasing the overall throughput of MEW)and material waste(i.e.,improving the cost-effectiveness of MEW).Moreover,embedding a trained ML model with the feedback control system in a GUI facilitates a more straightforward use of ML-based optimization techniques in the industrial section(i.e.,for users with no ML skills).

关键词： 3D printing additive manufacturing feedback control image analysis machine learning melt electrowriting optimization polymer

In vivo assessment of the toxic potential of Dissotis rotundifolia whole plant extract in Sprague–Dawley rats

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Asian Pacific Journal of Tropical Biomedicine 2016年第7期6卷 574-579页

作者： Charles Ansah Michael Buenor Adinortey Jerry Asiedu-Larbi Benjamin Aboagye Du-Bois Asante alexander Kwadwo Nyarko Department of Pharmacology Faculty of Pharmacy and Pharmaceutical SciencesCollege of Health SciencesKwame Nkrumah University of Science and Technology Department of Biochemistry School of Biological Sciences College of Agriculture and Natural Sciences University of Cape Coast Pharmacology Unit Centre for Plant Medicine Research Department of biomedical and Forensic sciences School of Biological Sciences College of Agriculture and Natural SciencesUniversity of Cape Coast Department of Clinical Pathology Noguchi Memorial Institute for Medical ResearchUniversity of Ghana

Objective: To assess the toxic potential of Dissotis rotundifolia(***) whole plant extract in Spraque–Dawley rats within a 2-week period of ***: Methanolic extract of D. rotundifolia was administered orally once daily at dose levels of 0,100, 300 and 1 000 mg/kg body weight for 14 days. Toxicity was assessed using mortality, clinical signs, body and organ weights, hematological indices,serum chemistry parameters and histopathological ***: There were no treatment-related mortalities or differences in clinical signs,hematology and serum biochemistry. This was confirmed by micrographs obtained from histopathological ***: The results obtained from the sub-acute toxicological assessment of D. rotundifolia extract suggest that the extract is non-toxic at doses up to 1 000 mg/kg/day administered for a period of 14 days.

关键词： Dissotis rotundifolia Ghana Melastomataceae Toxic potential

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代谢组学:一个迅速发展的新兴学科(英文)

生物化学与生物物理进展 2006年第5期33卷 401-417页

作者：唐惠儒王玉兰中国科学院武汉物理与数学研究所波谱与原子分子物理国家重点实验室武汉430071 Biological Chemistry Biomedical Sciences DivisionSchool of Life SciencesImperial College LondonSir Alexander Fleming BuildingSouth KensingtonLondon SW7 2AZ UK

对代谢组学的含义,中心任务,研究方法,样品要求,应用及其发展方向进行了简要综述. 系统生物学概念的诞生标志着研究哲学由“还原论”向“整体论”的变化. 系统生物学的中心任务就是要针对生物系统整体 (无论它是生物细胞,多细胞组织,器... 详细信息

对代谢组学的含义,中心任务,研究方法,样品要求,应用及其发展方向进行了简要综述. 系统生物学概念的诞生标志着研究哲学由“还原论”向“整体论”的变化. 系统生物学的中心任务就是要针对生物系统整体 (无论它是生物细胞,多细胞组织,器官还是生物整体),建立定量,普适,整体和可预测 (QUIP) 的认知. 具体而言,系统生物学研究就是要将给定生物系统的基因,转录,蛋白质和代谢水平所发生的事件,相关性及其对所涉及生物过程的意义进行整体性认识. 从而出现了许多的“组”和“组学”的新概念. 但是现已提出的一百多个“组”和“组学”,可以大体归纳为“基因组”/“基因组学”,“转录组”/“转录组学”,“蛋白质组”/“蛋白质组学”和“代谢组”/“代谢组学”四个方面. 显而易见,DNA,mRNA 以及蛋白质的存在为生物过程的发生提供了物质基础 (但这个过程有可能不发生!),而代谢物质所反映的是已经发生了的生物学事件. 因此代谢组学是对一个生物系统进行全面认识的不可缺少的一部分,是全局系统生物学 (global systems biology) 的重要基础,也是系统生物学的一个重要组成部分. 在现有的英文表述中,代谢组学同时存在两个不同的词汇和概念,即metabonomics 和 metabolomics. 尽管前者多用在动物系统而后者多用于植物和微生物系统,但这些概念的本质从他们的定义中能够得到较细致的了解. Metabonomics 的最初定义是就生物系统对生理和病理刺激以及基因改变的代谢应答的定量测定(“the quantitative measurement of the multi-parametric metabolic response of living systems to pathophysiological stimuli or geneticmodifications”). 我们认为这个定义现在可以更广泛地表述为:代谢组学是关于定量描述生物内源性代谢物质的整体及其对内因和外因变化应答规律的科学 (“Metabonomics is the branch of science concerned with the quantitative understandings of themetabolite complement of integrated living systems and its dynamic responses to the changes of both endogenous factors (such asphysiology and development) and exogenous factors (such as environmental factors and xenobiotics).”). 其中心任务包括 (1) 对内源性代谢物质的整体及其动态变化规律进行检测,量化和编录,(2) 确定此变化规律和生物过程的有机联系. Metabolomics 存在多个定义,但其精髓是:对一个生物系统的细胞在给定时间和给定条件下所有小分子代谢物质的定量分析(the quantitativemeasurement of all low molecular weight metabolites in an organism's cells at a specified time under specific environmentalconditions). 因此,metabolomics 可以译作“代谢物组学”. 不难看出,前者是对生物系统进行的整体和动态的认识 (不仅关心代谢物质的整体也关注其动态变化规律),而后者强调分析而且是个静态的认识概念. 因此可以认为,metabolomics 是metabonomics 的一个组成部分 (参看定义). 近年又有人提出了“dynamic metabolomics”的概念,这个概念所表达的含义十分接近“metabonomics”本身的含义. 所以,可以预见,随着这门新兴学科的发展和更深入讨论,这两个概念必将趋向一致. 因此我们建议,在中文表述中将“代谢组学”一词和英文中的 metabonomics 相对应,以避免不必要的混淆和争议. 就细胞系统而言,不仅存在细胞自身的代谢物质组成问题,存在细胞之间代谢物质交换的问题,也存在代谢过程所发生的位点问题. 因此,简单地分析代谢物质的总组成 (即代谢组) 缺乏“整体论”所要求的全面性,其意义有一定局限. 代谢组学属于全局系统生物学 (Global systems biology) 研究方法,便于对复杂体系的整体进行认识. 譬如,一个正常工作的人体包括“人体”本身和与之共同进化而来且共生的消化道微生物群体 (或称菌群),孤立地研究“

关键词：代谢组学核磁共振代谢物系统生物学