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MedComm - Biomaterials and Applications 2023年第2期2卷

作者： Li, Ling Nie, Shihong Du, Ting Zhao, Jiaxuan Chen, Xiaoyuan West China School of Public Health West China Fourth Hospital and State Key Laboratory of Biotherapy Sichuan University Chengdu China Department of Radiation Oncology Cancer Center West China Hospital Sichuan University Chengdu China Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province Chengdu Medical College Chengdu China Departments of Diagnostic Radiology Surgery Chemical and Biomolecular Engineering and Biomedical Engineering Yong Loo Lin School of Medicine and Faculty of Engineering National University of Singapore Singapore Singapore Clinical Imaging Research Centre Centre for Translational Medicine Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore Nanomedicine Translational Research Program NUS Center for Nanomedicine Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Agency for Science Technology and Research (A*STAR) Singapore Singapore

DNA origami, a promising branch of structural DNA technology, refers to the technique of folding a single-stranded DNA scaffold into well-defined nanostructures. In recent years, DNA origami nanostructures have shown considerable promise in a variety of biomedical applications, owing to their biodegradability, unique programmability, and addressability. Despite their popularity, the biomedical application of DNA origami techniques, which exploits their unique programmability and addressability, is rare in previous studies. Most recently, mounting evidence has demonstrated the robustness of DNA origami nanostructures in the spatial organization of functional components at the nanoscale in the biomedical field. These examples provide typical paradigms to fully realize the potential of DNA origami techniques by taking advantage of their unique programmability and addressability. This minireview summarizes the recent advancements of DNA origami techniques in biosensing, biocatalysis, and drug delivery, and the representative examples using DNA origami nanostructures for the spatial organization of functional molecules with nanometric precision are highlighted. We further discuss the possible limitations and challenges for in vivo applications, including stability issues and potential immunogenicity, and finally, propose some strategies to overcome these obstacles to fully realize the potential of DNA origami techniques in biomedical applications. © 2023 The Authors. MedComm – Biomaterials and Applications published by John Wiley & Sons Australia, Ltd on behalf of Sichuan International Medical Exchange & Promotion Association (SCIMEA).

关键词： biocatalysis biosensing DNA nanotechnology DNA origami

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Corrigendum: FOXM1 mediates Dox resistance in breast cancer by enhancing DNA repair

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Carcinogenesis 2019年第7期40卷 936页

作者： Yun-Yong Park Sung Yun Jung Nicholas B Jennings Cristian Rodriguez-Aguayo Guang Peng Se-Ra Lee Sang Bae Kim Kyounghyun Kim Sun-Hee Leem Shiaw-Yih Lin Gabriel Lopez-Berestein Anil K Sood Ju-Seog Lee Department of Systems Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Department of Biochemistry and Molecular Biology Baylor College of Medicine Houston TX USA. Department of Gynecologic Oncology Houston TX USA. Department of Experimental Therapeutics The University of Texas MD Anderson Cancer Center Houston TX USA. Department of Biology and Biomedical Science Dong-A University Busan Korea. Institute of Biosciences and Technology Texas A&M University Health Science Center Houston TX USA. Deparment of Cancer Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Center for RNA Interference and Non-Coding RNA The University of Texas MD Anderson Cancer Center Houston TX USA.

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Proceedings of the EuBIC-MS 2020 Developers’ Meeting

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EuPA Open Proteomics 2020年 24卷 1-6页

作者： Christopher Ashwood Wout Bittremieux Eric W. Deutsch Nadezhda T. Doncheva Viktoria Dorfer Ralf Gabriels Vladimir Gorshkov Surya Gupta Andrew R. Jones Lukas Käll Dominik Kopczynski Lydie Lane Ludwig Lautenbacher Marc Legeay Marie Locard-Paulet Bart Mesuere Yasset Perez-Riverol Eugen Netz Sander Willems European Bioinformatics Community for Mass Spectrometry (info@***) Denmark Department of Cellular and Integrative Physiology University of Nebraska Medical Center Omaha USA Department of Computer Science University of Antwerp Antwerp Belgium Institute for Systems Biology Seattle WA 98109 USA Novo Nordisk Foundation Center for Protein Research University of Copenhagen Denmark Bioinformatics Research Group University of Applied Sciences Upper Austria Hagenberg Austria VIB-UGent Center for Medical Biotechnology VIB Ghent Belgium Department of Biochemistry and Molecular Biology University of Southern Denmark Denmark Institute of Systems Molecular and Integrative Biology University of Liverpool UK Science for Life Laboratory KTH - Royal Institute of Technology Solna Stockholm Sweden Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. Dortmund Germany SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine Faculty of Medicine Geneva University Geneva Switzerland Technical University of Munich Chair for Proteomics and Bioanalytics Freising Germany European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Applied Bioinformatics Dept. of Computer Science University of Tübingen Tübingen Germany Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA 92093 USA Center for non-coding RNA in Technology and Health Department of Veterinary and Animal Sciences University of Copenhagen Denmark Department of Biomolecular Medicine Ghent University Ghent Belgium Department of Applied Mathematics Computer Science and Statistics Ghent University Ghent Belgium Biomolecular Interactions Max Planck Institute for Developmental Biology Tübingen Germany

The 2020 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers’ meeting was held from January 13 th to January 17 th 2020 in Nyborg, Denmark. Among the participants were scientists as well as developers working in the field of computational mass spectrometry (MS) and proteomics. The 4-day program was split between introductory keynote lectures and parallel hackathon sessions. During the latter, the participants developed bioinformatics tools and resources addressing outstanding needs in the community. The hackathons allowed less experienced participants to learn from more advanced computational MS experts, and to actively contribute to highly relevant research projects. We successfully produced several new tools that will be useful to the proteomics community by improving data analysis as well as facilitating future research. All keynote recordings are available on https://***/10.5281/zenodo.3890181 .

关键词： Computational mass spectrometry Mass spectrometry Proteomics Bioinformatics Spectrum clustering Phosphoproteomics XIC extraction Proteomics graph networks Predicted spectra Metaproteomics Functional annotations Benchmark development

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Erratum to “Circulating Levels of Microrna from Children with Newly Diagnosed Type 1 Diabetes and Healthy Controls: Evidence That miR-25 Associates to Residual Beta-Cell Function and Glycaemic Control during Disease Progression”

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Journal of Diabetes Research 2012年第1期2012卷 672865-672865页

作者： Lotte B. Nielsen Cheng Wang Kaspar Sørensen Claus H. Bang-Berthelsen Lars Hansen Marie-Louise M. Andersen Philip Hougaard Anders Juul Chen-Yu Zhang Flemming Pociot Henrik B. Mortensen Department of Pediatrics Herlev Hospital 2730 Herlev Denmarkherlevhospital.dk Faculty of Health Sciences University of Copenhagen 2200 Copenhagen Denmarkku.dk Jiangsu Engineering Research Center for microRNA Biology and Biotechnology State Key Laboratory of Pharmaceutical Biotechnology School of Life Sciences Nanjing University Nanjing 210093 *** Department of Growth and Reproduction Rigshospitalet and Faculty of Health Sciences University of Copenhagen 2100 Copenhagen Denmarkku.dk Glostrup Research Institute Glostrup Hospital and Center for Non-Coding RNA in Technology and Health University of Copenhagen 2600 Glostrup Denmarkku.dk Department of Statistics University of Southern Denmark 5000 Odense Denmarksdu.dk

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Biomechanical research using advanced micro-nano devices: In-Vitro cell Characterization focus

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Journal of Advanced Research 2024年

作者： Yan, Shiqiang Lu, Yan An, Changming Hu, Wanglai Chen, Yaofeng Li, Ziwen Wei, Wenbo Chen, Zongzheng Zeng, Xianhai Xu, Wei Lv, Zhenghua Pan, Fan Gao, Wei Wu, Yongyan Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology Longgang Otolaryngology Hospital Guangdong Shenzhen 518172 China Center of Cancer Immunology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Guangdong Shenzhen 518055 China Department of Otolaryngology Head & Neck Surgery The First Hospital Jinzhou Medical University Liaoning Jinzhou 121001 China Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer Department of Otolaryngology Head & Neck Surgery First Hospital of Shanxi Medical University Shanxi Taiyuan 030001 China Department of Head and Neck Surgery National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing 100021 China Translational Research Institute People's Hospital of Zhengzhou University Academy of Medical Science Henan International Joint Laboratory of Non-coding RNA and Metabolism in Cancer Zhengzhou University Henan Zhengzhou 450003 China Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy Shenzhen University Guangdong Shenzhen 518055 China College of Chemistry & Pharmacy Northwest A&F University Shaanxi Yangling 712100 China The First Affiliated Hospital of Shenzhen University Shenzhen Second People's Hospital Guangdong Shenzhen 518035 China Department of Otolaryngology-Head and Neck Surgery Shandong Provincial ENT Hospital Shandong University Shandong Jinan 250022 China

Background: Cells in the body reside in a dynamic microenvironment subjected to various physical stimuli, where mechanical stimulation plays a crucial role in regulating cellular physiological behaviors and functions. Aim of Review: Investigating the mechanisms and interactions of mechanical transmission is essential for understanding the physiological and functional interplay between cells and physical stimuli. Therefore, establishing an in vitro biomechanical stimulation cell culture system holds significant importance for research related to cellular biomechanics. Key Scientific Concepts of Review: In this review, we primarily focused on various biomechanically relevant cell culture systems and highlighted the advancements and prospects in their preparation processes. Firstly, we discussed the types and characteristics of biomechanics present in the microenvironment within the human body. Subsequently, we introduced the research progress, working principles, preparation processes, potential advantages, applications, and challenges of various biomechanically relevant in vitro cell culture systems. Additionally, we summarized and categorized currently commercialized biomechanically relevant cell culture systems, offering a comprehensive reference for researchers in related fields. © 2024

关键词： Biomechanical stimulation Cell culture systems Cellular biomechanics In vitro models Microenvironment

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A biomarker framework for liver aging: the Aging Biomarker Consortium consensus statement

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Life Medicine 2024年第1期3卷 5页

作者： Aging Biomarker Consortium, Mengmeng Jiang Zhuozhao Zheng Xuan Wang Yanhao Chen Jing Qu Qiurong Ding Weiqi Zhang You-Shuo Liu Jichun Yang Weiqing Tang Yunlong Hou Jinhan He Lin Wang Pengyu Huang Lin-Chen Li Zhiying He Qiang Gao Qian Lu Lai Wei Yan-Jiang Wang Zhenyu Ju Jian-Gao Fan Xiong Zhong Ruan Youfei Guan Guang-Hui Liu Gang Pei Jian Li Yunfang Wang State Key Laboratory of Membrane Biology Institute of Zoology Chinese Academy of Sciences Beijing 100101 China Institute for Stem Cell and Regeneration Chinese Academy of Sciences Beijing 100101 China Department of Radiology Beijing Tsinghua Changgung Hospital School of Clinical Medicine Tsinghua University Beijing 102218 China Hepatopancreatobiliary Center Beijing Tsinghua Changgung Hospital School of Clinical Medicine Tsinghua University Beijing 102218 China CAS Key Laboratory of Nutrition Metabolism and Food Safety Shanghai Institute of Nutrition and Health University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai 200031 China State Key Laboratory of Stem Cell and Reproductive Biology Institute of Zoology Chinese Academy of Sciences Beijing 100101 China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics Chinese Academy of Sciences and China National Center for Bioinformation Beijing 100101 China Department of Geriatrics the Second Xiangya Hospital and the Institute of Aging and Geriatrics Central South University Changsha 410011 China Department of Physiology and Pathophysiology School of Basic Medical Sciences State Key Laboratory of Vascular Homeostasis and Remodeling Center for Non-coding RNA Medicine Peking University Health Science Center Beijing 100191 China The Key Laboratory of Geriatrics Beijing Institute of Geriatrics Institute of Geriatric Medicine Chinese Academy of Medical Sciences Beijing Hospital/National Center of Gerontology of National Health Commission Beijing 100730 China Yiling Pharmaceutical Academician Workstation Shijiazhuang 050035 China Department of Pharmacy West China Hospital of Sichuan University Chengdu 610041 China Department of Hepatobiliary Surgery Xijing Hospital Fourth Military Medical University Xi?an 710032 China State Key Laboratory of Advanced Medical Materials and Devices Engineering Research Center of Pulmonary and Critical Care Medicine Technology and Device

In human aging, liver aging per se not only increases susceptibility to liver diseases but also increases vulnerability of other organs given its central role in regulating metabolism. Total liver function tends to be well maintained in the healthy elderly, so liver aging is generally difficult to identify early. In response to this critical challenge, the Aging Biomarker Consortium of China has formulated an expert consensus on biomarkers of liver aging by synthesizing the latest scientific literature, comprising insights from both scientists and clinicians. This consensus provides a comprehensive assessment of biomarkers associated with liver aging and presents a systematic framework to characterize these into three dimensions: functional, imaging, and humoral. For the functional domain, we highlight biomarkers associated with cholesterol metabolism and liver-related coagulation function. For the imaging domain, we note that hepatic steatosis and liver blood flow can serve as measurable biomarkers for liver aging. Finally, in the humoral domain, we pinpoint hepatokines and enzymatic alterations worthy of attention. The aim of this expert consensus is to establish a foundation for assessing the extent of liver aging and identify early signs of liver aging-related diseases, thereby improving liver health and the healthy life expectancy of the elderly population.

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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-rna recognition: A computational analysis of protein-rna complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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