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Author Correction: An organoid-based screen for epigenetic inhibitors that stimulate antigen presentation and potentiate T-cell-mediated cytotoxicity

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Nature biomedical engineering 2025年第2期9卷 281-282页

作者： Zhuolong Zhou Kevin Van der Jeught Yuanzhang Fang Tao Yu Yujing Li Zheng Ao Sheng Liu Lu Zhang Yang Yang Haniyeh Eyvani Mary L Cox Xiyu Wang Xiaoming He Guang Ji Bryan P Schneider Feng Guo Jun Wan Xinna Zhang Xiongbin Lu Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN USA. Department of Intelligent Systems Engineering Indiana University Bloomington IN USA. Center for Computational Biology and Bioinformatics Indiana University School of Medicine Indianapolis IN USA. Institute of Digestive Diseases Longhua Hospital Shanghai University of Traditional Chinese Medicine Shanghai China. Experiment Center for Science and Technology Shanghai University of Traditional Chinese Medicine Shanghai China. Melvin and Bren Simon Comprehensive Cancer Center Indiana University School of Medicine Indianapolis IN USA. Fischell Department of Bioengineering University of Maryland College Park MD USA. Division of Hematology/Oncology Department of Medicine Indiana University School of Medicine Indianapolis IN USA. Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN USA. xz48@iu.edu. Melvin and Bren Simon Comprehensive Cancer Center Indiana University School of Medicine Indianapolis IN USA. xz48@iu.edu. Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN USA. xiolu@iu.edu. Center for Computational Biology and Bioinformatics Indiana University School of Medicine Indianapolis IN USA. xiolu@iu.edu. Melvin and Bren Simon Comprehensive Cancer Center Indiana University School of Medicine Indianapolis IN USA. xiolu@iu.edu.

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Culture of mesenchymal stem cells in a collagen sponge to reduce the cell leak

Culture of mesenchymal stem cells in a collagen sponge to re...

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55th Society of Polymer Science Japan Symposium on Macromolecules

作者： Kawazoe, Naoki Akahane, Daisuke Chen, Guoping Shirasaki, Yoshio Yamamoto, Katsuyuki Tateishi, Tetsuya Biomaterials Center National Institute for Materials Science Namiki 1-1 Tyukuba Ibaraki 305-0044 Division of Bioengineering and Bioinformatics Graduate School of Information Science and Technology Institute for Human and Science Biomedical Engineering Advanced Indusrial Science and Technology

Collagen sponges have been used in tissue engineering to provide three dimensional scaffolds. However, it was difficult to distribute cells uniformly throughout the scaffolds because the seeded cells leak from the scaffolds. Here we prepared a collagen scaffold surrounded by a 10 micrometer mesh to prevent cell leakage from the scaffold and seeded human mesenchymal stem cells onto the scaffold. From the results of the high seed efficiency, the collagen/mesh scaffold in this study was useful for a culture of mesenchymal stem cells.

关键词： Cell culture

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From bulk, single-cell to spatial RNA sequencing

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International Journal of Oral Science 2021年第4期13卷 339-344页

作者： Xinmin Li Cun-Yu Wang UCLA Technology Center for Genomics&Bioinformatics Department of Pathology and Laboratory MedicineDavid Geffen School of MedicineUCLALos AngelesCAUSA Laboratory of Molecular Signaling Division of Oral Biology and MedicineSchool of Dentistry and Jonsson Comprehensive Cancer CenterUCLALos AngelesCAUSA Department of Bioengineering Henry Samueli School of Engineering and Applied ScienceUCLALos AngelesCAUSA

RNA sequencing(RNAseq)can reveal gene fusions,splicing variants,mutations/indels in addition to differential gene expression,thus providing a more complete genetic picture than DNA *** most widely used technology in genomics tool box has evolved from classic bulk RNA sequencing(RNAseq),popular single cell RNA sequencing(scRNAseq)to newly emerged spatial RNA sequencing(spRNAseq).Bulk RNAseq studies average global gene expression,scRNAseq investigates single cell RNA biology up to 20,000 individual cells simultaneously,while spRNAseq has ability to dissect RNA activities spatially,representing next generation of RNA *** article highlights these technologies,characteristic features and suitable applications in precision oncology.

关键词： representing RNAseq spatially

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Front Cover: Computational Assessment of Clinical Drugs against SARS-CoV-2: Foreseeing Molecular Mechanisms and Potent Mpro Inhibitors (ChemPhysChem 2/2025)

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ChemPhysChem 2025年第2期26卷

作者： Saroj Kumar Panda Pratyush Pani Parth Sarthi Sen Gupta Nimai Mahanandia Malay Kumar Rana Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Berhampur Ganjam Odisha 760010 India Authors contributed equally. Department of Biological Sciences Indian Institute of Science Education and Research (IISER) Berhampur Ganjam Odisha 760010 India School of Biosciences and Bioengineering D Y Patil International University (DYPIU) Akurdi Pune Maharashtra 411044 India Division of Agricultural Bioinformatics ICAR-Indian Agricultural Statistics Research Institute Pusa New Delhi 110012 India

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Massively parallel jumping assay decodes Alu retrotransposition activity

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Nature Communications 2025年第1期16卷 1-13页

作者： Matharu, Navneet Zhao, Jingjing Sohota, Ajuni Deng, Linbei Hung, Yan Li, Zizheng An, Kelly Sims, Jasmine Rattanasopha, Sawitree Meyer, Thomas J. Carbone, Lucia Kircher, Martin Ahituv, Nadav Department of Bioengineering and Therapeutic Sciences University of California San Francisco San Francisco CA United States Institute for Human Genetics University of California San Francisco San Francisco CA United States Division of Genetics Oregon National Primate Research Center Beaverton OR United States CCR Collaborative Bioinformatics Resource (CCBR) Frederick National Laboratory for Cancer Research Leidos Biomedical Research Inc. Frederick MD United States Department of Medicine Knight Cardiovascular Institute Oregon Health and Science University Portland OR United States Department of Molecular and Medical Genetics Oregon Health and Science University Portland OR United States Department of Medical Informatics and Clinical Epidemiology Oregon Health and Science University Portland OR United States Berlin Institute of Health of Health at Charité—Universitätsmedizin Berlin Berlin Germany Institute of Human Genetics University Medical Center Schleswig-Holstein University of Lübeck Lübeck Germany

The human genome contains millions of copies of retrotransposons that are silenced but many of these copies have potential to become active if mutated, having phenotypic consequences, including disease. However, it is not thoroughly understood how nucleotide changes in retrotransposons affect their jumping activity. Here, we develop a massively parallel jumping assay (MPJA) that tests the jumping potential of thousands of transposons en masse. We generate a nucleotide variant library of four Alu retrotransposons containing 165,087 different haplotypes and test them for their jumping ability using MPJA. We found 66,821 unique jumping haplotypes, allowing us to pinpoint domains and variants vital for transposition. Mapping these variants to the Alu-RNA secondary structure revealed stem-loop features that contribute to jumping potential. Combined, our work provides a high-throughput assay that assesses the ability of retrotransposons to jump and identifies nucleotide changes that have the potential to reactivate them in the human genome. © The Author(s) 2025.

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Biophysical approaches for studying the integrity and function of tight junctions

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MCB Molecular and Cellular Biomechanics 2005年第3期2卷 105-123页

作者： Vedula, S.R.K. Lim, T.S. Kausalya, P.J. Hunziker, W. Rajagopal, G. Lim, C.T. Division of Bioengineering Department of Mechanical Engineering National University of Singapore Singapore Singapore Bioinformatics Institute Singapore Singapore Institute of Molecular and Cell Biology Singapore 138673 Singapore

Cell-cell adhesion is an extremely important phenomenon as it influences several biologically important processes such as inflammation, cell migration, proliferation, differentiation and even cancer metastasis. Furthermore, proteins involved in cell-cell adhesion are also important from the perspective of facilitating better drug delivery across epithelia. The adhesion forces imparted by proteins involved in cell-cell adhesion have been the focus of research for sometime. However, with the advent of nanotechnological techniques such as the atomic force microscopy (AFM), we can now quantitatively probe these adhesion forces not only at the cellular but also molecular level. Here, we review the structure and function of tight junction proteins, highlighting some mechanistic studies performed to quantify the adhesion occurring between these proteins and where possible their association with human diseases. In particular, we will highlight two important experimental techniques, namely the micropipette step pressure technique and the AFM that allow us to quantify these adhesion forces at both the cellular and molecular levels, respectively. Copyright © 2005 Tech Science Press.

关键词： Biomedical engineering

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End-to-end computational approach to the design of RNA biosensors for detecting miRNA biomarkers of cervical cancer

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Synthetic and Systems Biotechnology 2022年第2期7卷 802-814页

作者： Priyannth Ramasami S.Baabu Shivaramakrishna Srinivasan Swetha Nagarajan Sangeetha Muthamilselvan Thamarai Selvi Raghavv R.Suresh Ashok Palaniappan Department of Bioinformatics School of Chemical and BiotechnologySASTRA Deemed UniversityThanjavurTamil Nadu 613401India Department of Bioengineering School of Chemical and BiotechnologySASTRA Deemed UniversityThanjavurTamil Nadu613401India School of Advanced Materials Science and Engineering Sungkyunkwan University(SKKU)Suwon16419Republic of Korea Life Sciences Division TCS ResearchTata Consultancy ServicesChennaiTamil Nadu600042India

Cervical cancer is a global public health subject as it affects women in the reproductive ages,and accounts for the second largest burden among cancer patients worldwide with an unforgiving 50%mortality *** scant awareness and limited access to effective diagnosis have led to this enormous disease burden,calling for point-of-care,minimally invasive diagnosis ***,an end-to-end quantitative unified pipeline for diagnosis has been developed,beginning with identification of optimal biomarkers,concurrent design of toehold switch sensors,and finally simulation of the designed diagnostic circuits to assess *** miRNA expression data in the public domain,we identified miR-21-5p and miR-20a-5p as blood-based miRNA biomarkers specific to early-stage cervical cancer employing a multi-tier algorithmic *** riboregulators called toehold switches specific to the biomarker panel were then *** predict the dynamic range of toehold switches for use in genetic circuits as biosensors,we used a generic grammar of these switches,and built a neural network model of dynamic range using thermodynamic features derived from mRNA secondary structure and ***-generation toehold switches were used to overcome the design challenges associated with miRNA *** resultant model yielded an adj.R^(2)~0.71,outperforming earlier models of toehold-switch dynamic *** kinetics modelling was performed to predict the sensitivity of the second-generation toehold switches to the miRNA *** showed a linear response between 10 nM and 100 nM before *** study demonstrates an end-to-end computational workflow for the efficient design of genetic circuits geared towards the effective detection of unique genomic/nucleic-acid *** approach has the potential to replace iterative experimental trial and error,and focus time,money,and *** software including the toehold grammar parser,neu

关键词： Cervical cancer biosensor miRNA biomarker Synthetic toehold switches Genetic circuit design Reaction network modelling Toehold efficacy modelling Toehold switch grammar Machine learning

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A workflow-based application for exploration of biomedical data sets

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in bioinformatics) 2011年 6990 LNCS卷 148-157页

作者： Dander, Andreas Handler, Michael Netzer, Michael Pfeifer, Bernhard Seger, Michael Baumgartner, Christian Institute for Bioinformatics and Translational Research UMIT Hall in Tirol Austria Oncotyrol Center for Personalized Cancer Medicine Innsbruck Austria Biocenter Division for Bioinformatics Innsbruck Medical University Innsbruck Austria Institute of Electrical Electronic and Bioengineering UMIT Hall in Tirol Austria

ISBN: (纸本)9783642237393

Based on the biotechnological revolution in the past years, molecular biology has become increasingly data-driven. Knowledge Discovery in Databases, a well-known process in the field of bioinformatics, is supporting the biological research process from data integration, knowledge mining to data interpretation. This work proposes a new software suite, termed Knowledge Discovery in Databases Designer (KD3), covering the complete Knowledge Discovery in Databases process using a workflow-oriented architecture. Three different application-oriented modules are implemented in KD3: First, the Designer for designing specific workflows. These workflows can be used by the Interpreter, which allows to load and parameterize existing workflows. The Launcher encapsulates one dedicated workflow into an independent application to answer one specific biomedical question. KD3 offers a variety of implemented methods, which can be easily extended with new customized components using functional objects. All components can be connected to workflows, which may contain elements of other applications. © 2011 Springer-Verlag Berlin Heidelberg.

关键词： Data mining

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High-Speed Observations of Acoustic Droplet Ejection of a Shear-Thinning Polymer Solution in an External High-Voltage Electric Field

High-Speed Observations of Acoustic Droplet Ejection of a Sh...

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IEEE International Symposium on Applications of Ferroelectrics (ISAF)

作者： Joni Mäkinen Nobuki Kudo Jere Hyvönen Mamoru Hashimoto Edward Hæggström Ari Salmi Department of Physics Faculty of Science University of Helsinki Helsinki Finland Division of Bioengineering and Bioinformatics Faculty of Information Science and Technology Hokkaido University Sapporo Japan

ISBN: (数字)9798350371901

ISBN: (纸本)9798350371918

High-speed observations of ultrasonic ejection of a viscoelastic, shear-thinning, polymer solution, 1 wt% PEO dissolved in water, for the purpose of electrospinning initiation are presented. A focused ultrasound source at 2.68 MHz is used for the ejection. A high-voltage electric field is applied between the solution and a conducting plate above. With a suitable ultrasonic ejection of the solution, electrospinning is initiatied as the electric field pulls a thinning jet from the solution, eventually producing a *** ultrasonic pulse regimes are investigated for the ejection: short (≤ 100 cycles) but high-amplitude (≈ 4.4 MPa), and long (≥ 5000 cycles) but low-amplitude (≈ 0.8 MPa) pulsing. Three different types of ejections leading to the electric field being able to pull a jet from the solution are observed. Most notably, we observed an unstable drop-chain formation which lead to the jetting of liquid from the drop-chain, which was further pulled by the electric field into a thinning jet.

关键词： Ultrasonic imaging Liquids High-voltage techniques Acoustics Polymers Electric fields Frequency control

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Single-cell RNA-sequencing and subcellular spatial transcriptomics facilitate the translation of liver microphysiological systems for regulatory application

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Journal of Pharmaceutical Analysis 2023年第7期13卷 691-693页

作者： Dan Li Zhou Fang Qiang Shi Nicholas Zhang Binsheng Gong Weida Tong Ahmet F.Coskun Joshua Xu Division of Bioinformatics and Biostatistics National Center for Toxicological ResearchU.S.Food and Drug AdministrationJeffersonAR72079USA Wallace H.Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory UniversityAtlantaGA30332USA Machine Learning Graduate Program Georgia Institute of TechnologyAtlantaGA30332USA Division of Systems Biology National Center for Toxicological ResearchU.S.Food and Drug AdministrationJeffersonAR72079USA Interdisciplinary Bioengineering Graduate Program Georgia Institute of TechnologyAtlantaGA30332USA Parker H.Petit Institute for Bioengineering and Bioscience Georgia Institute of TechnologyAtlantaGA30332USA

Reducing the use of animal models in drug development and safety assessment has long been supported by the *** and Drug Administration(FDA).The report by Royal Society for the Prevention of Cruelty to Animals indicates that in 2020,experiments involved the use of over 100 million animals,with the United States leading the list by utilizing 20 million *** ethical considerations associated with animal testing and the costs in terms of time and money,animal models are not always effective in predicting human reactions to drug *** animal testing has been the traditional method for assessing the safety and efficacy of drugs.

关键词： money utilizing testing

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