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Front Cover: Design, Synthesis, and Characterization of Novel Styryl Dyes as Fluorescent Probes for Tau Aggregate Detectionin Vitroand in Cells (Chem. Asian J. 6/2024)

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Chemistry – An Asian Journal 2024年第6期19卷

作者： Withsakorn Sangsuwan Kriangsak Faikhruea Kotchakorn Supabowornsathit Don Sangsopon Praewphan Ingrungruanglert Hathaichanok Chuntakaruk Napatsaporn Nuntavanotayan Kittiporn Nakprasit Nipan Israsena Thanyada Rungrotmongkol Pitak Chuawong Tirayut Vilaivan Chanat Aonbangkhen Center of Excellence in Natural Products Chemistry (CENP) Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand Department of Chemistry and Center of Excellence for Innovation in Chemistry Faculty of Science Special Research Unit for Advanced Magnetic Resonance (AMR) Kasetsart University Bangkok 10900 Thailand These authors are contributed equally. Organic Synthesis Research Unit Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand Stem Cell and Cell Therapy Research Unit and Department of Pharmacology Faculty of Medicine Chulalongkorn University Bangkok 10330 Thailand Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok 10330 Thailand Center of Excellence in Structural and Computational Biology Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand

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Democratising Knowledge Representation with BioCypher

arXiv

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arXiv 2022年

作者： Lobentanzer, Sebastian Aloy, Patrick Baumbach, Jan Bohar, Balazs Charoentong, Pornpimol Danhauser, Katharina Doğan, Tunca Dreo, Johann Dunham, Ian Fernandez-Torras, Adrià Gyori, Benjamin M. Hartung, Michael Hoyt, Charles Tapley Klein, Christoph Korcsmaros, Tamas Maier, Andreas Mann, Matthias Ochoa, David Pareja-Lorente, Elena Popp, Ferdinand Preusse, Martin Probul, Niklas Schwikowski, Benno Sen, Bünyamin Strauss, Maximilian T. Turei, Denes Ulusoy, Erva Heidrun Wodke, Judith Andrea Saez-Rodriguez, Julio Heidelberg University Faculty of Medicine Heidelberg University Hospital Institute for Computational Biomedicine Bioquant Heidelberg Germany The Barcelona Institute of Science and Technology Catalonia Barcelona Spain Catalonia Barcelona Spain Institute for Computational Systems Biology University of Hamburg Germany Earlham Institute Norwich United Kingdom Biological Research Centre Szeged Hungary Heidelberg University Im Neuenheimer Feld 267 Heidelberg69120 Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Department of Pediatrics Dr. von Hauner Children’s Hospital University Hospital LMU Munich Germany Biological Data Science Lab Department of Computer Engineering Hacettepe University Ankara Turkey Department of Bioinformatics Graduate School of Health Sciences Hacettepe University Ankara Turkey Computational Systems Biomedicine Lab Department of Computational Biology Institut Pasteur Université Paris Cité Paris France Bioinformatics and Biostatistics Hub Institut Pasteur Université Paris Cité Paris France Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Open Targets Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Laboratory of Systems Pharmacology Harvard Medical School Boston United States Imperial College London London United Kingdom Quadram Institute Bioscience Norwich United Kingdom Proteomics Program Novo Nordisk Foundation Centre for Protein Research University of Copenhagen Copenhagen Denmark Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Neuherberg Germany Medical Informatics Laboratory University Medicine Greifswald Germany

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to nonspecialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://***) frees up valuable developer time;we encourage further development and usage by the community. © 2022, CC BY-NC-ND.

关键词： Ontology

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A linked data graph approach to integration of immunological data

A linked data graph approach to integration of immunological...

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IEEE International Conference on bioinformatics and Biomedicine

作者： Syed Ahmad Chan Bukhari Jeff Mandell Steven H. Kleinstein Kei-Hoi Cheung Division of Computer Science Mathematics and Science Lesley H. & William L. Collins College of Professional Studies St. John's University Interdepartmental Program in Computational Biology and Bioinformatics Yale University Department of Pathology Interdepartmental Program in Computational Biology and Bioinformatics Yale University Department of Emergency Medicine and Yale Center for Medical Informatics Computationa Biology and Bioinformaticcs Yale University

ISBN: (纸本)9781728118680

Systems biology involves the integration of multiple data types (across different data sources) to offer a more complete picture of the biological system being studied. While many existing biological databases are implemented using the traditional SQL (Structured Query Language) database technology, NoSQL database technologies have been explored as a more relationship-based, flexible and scalable method of data integration. In this paper, we describe how to use the Neo4J graph database to integrate a variety of types of data sets in the context of systems vaccinology. Specifically, we have converted into a common graph model diverse types of vaccine response measurement data from the NIH/NIAID ImmPort data repository, pathway data from Reactome, influenza virus strains from WHO, and taxonomic data from NCBI Taxon. While Neo4J provides a graph-based query language (Cypher) for data retrieval, we develop a web-based dashboard for users to easily browse and visualize data without the need to learn Cypher. In addition, we have prototyped a natural language query interface for users to interact with our system. In conclusion, we demonstrate the feasibility of using a graph-based database for storing and querying immunological data with complex biological relationships. Querying a graph database through such relationships has the potential to reveal novel relationships among heterogeneous biological data.

关键词： ontology knowledgebase graph database immunology influenza vaccine graphic library Knowledge Bases Influenza Vaccines Ontology Immunology data integration Passwords DNA Integration integration data types Data sources SQL

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Spectral neighbor joining for reconstruction of latent tree models

arXiv

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arXiv 2020年

作者： Jaffe, Ariel Amsel, Noah Nadler, Boaz Chang, Joseph T. Kluger, Yuval Program in Applied Mathematics Yale University New HavenCT06511 United States Department of Computer Science Weizmann Institute of Science Rehovot76100 Israel Department of Statistics Yale University New HavenCT06520 United States Interdepartmental Program in Computational Biology and Bioinformatics New HavenCT06511 Singapore Department of Pathology New HavenCT06511 United States

A key assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example is phylogenetics, where the tree models the evolutionary lineages of various organisms. Given a set of independent realizations of the random variables at the leaves of the tree, a common task is to infer the underlying tree topology. In this work we develop Spectral Neighbor Joining (SNJ), a novel method to recover latent tree graphical models. In contrast to distance based methods, SNJ is based on a spectral measure of similarity between all pairs of observed variables. We prove that SNJ is consistent, and derive a sufficient condition for correct tree recovery from an estimated similarity matrix. Combining this condition with a concentration of measure result on the similarity matrix, we bound the number of samples required to recover the tree with high probability. We illustrate via extensive simulations that SNJ requires fewer samples to accurately recover trees in regimes where the tree contains a large number of leaves or long edges. We provide theoretical support for this observation by analyzing the model of a perfect binary tree. Copyright © 2020, The Authors. All rights reserved.

关键词： Recovery

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Industrialized Gut Microbiota Promote Intestinal Inflammation in Mice

SSRN

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SSRN 2021年

作者： Vangay, Pajau Ward, Tonya Lucas, Sarah Beura, Lalit K. Sabas, Dominique Abramson, Max Till, Lisa Hoops, Suzie L. Kashyap, Purna Hunter, Ryan Masopust, Dave Knights, Dan Bioinformatics and Computational Biology Program University of Minnesota MinneapolisMN55455 United States BioTechnology Institute University of Minnesota MinneapolisMN55455 United States Department of Microbiology and Immunology University of Minnesota MinneapolisMN55455 United States Department of Food Science and Nutrition University of Minnesota MinneapolisMN55455 United States Department of Neuroscience Macalester College St. PaulMN55105 United States Division of Gastroenterology and Hepatology Department of Internal Medicine Mayo Clinic RochesterMN55905 United States

Immigration to a highly industrialized nation has been associated with metabolic disease and simultaneous shifts in microbiota composition, but the underlying mechanisms are challenging to test in human studies. Here, we assessed the differential effects of human gut microbiota collected from the United States (US) and rural Thailand on the murine gut mucosa and immune system. Colonization of germ-free mice with microbiota from US individuals resulted in an increased accumulation of innate-like CD8 T cells in the small intestine lamina propria and intra-epithelial compartments when compared to colonization with microbiota from Thai individuals. Both TCRgd and CD8aa T cells showed marked increase in mice receiving the Western microbiota and, interestingly this phenotype was also associated with an increase in intestinal mucus thickness. Serendipitously, an accidentally infected group of mice corroborated this association between elevated inflammatory response and increased mucus thickness. These results suggest that Western-associated human gut microbes contribute to a pro-inflammatory immune response. © 2021, The Authors. All rights reserved.

关键词： Pathology

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Heterogeneous photocatalytic degradation of diuron on zinc oxide: Influence of surface-dependent adsorption on kinetics,degradation pathway,and toxicity of intermediates

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Journal of Environmental Sciences 2019年第10期31卷 97-111页

作者： Sutaporn Meephon Thanyada Rungrotmongkol Somchintana Puttamat Supareak Praserthdam Varong Pavarajarn Center of Excellence in Particle Technology Department of Chemical Engineering Faculty of Engineering Chulalongkorn University Bangkok 10330 Thailand Biocatalyst and Environmental Biotechnology Research Unit Department of Biochemistry Faculty of Science Chulalongkorn UniversityBangkok 10330 Thailand Bioinformatics and Computational Biology Program Graduated School Chulalongkorn University Bangkok 10330 Thailand Department of Chemistry Faculty of Science Thammasat University Pathumthani 12120 Thailand Center of Excellence on Catalysis and Catalytic Reaction Engineering Department of Chemical Engineering Faculty of EngineeringChulalongkorn University Bangkok 10330 Thailand Research Program in Hazardous Substance Management in Agricultural Industry Center of Excellence on Hazardous Substance Management(HSM) Bangkok 10330 Thailand

Heterogeneous photocatalytic reaction has been generally applied for degradation of toxic *** of a compound using the same kind of catalyst that was synthesized differently are commonly found in ***,the reported degradation intermediates are normally *** issue is especially important for the degradation of toxic compounds because intermediates may be more toxic than their parent compounds and understanding the reason is necessary if appropriate catalysts are to be *** work systematically compares the photocatalytic degradation of diuron,a toxic recalcitrant herbicide,on two forms of zinc oxide(ZnO),i.e.,conventional particles with zinc-and oxygen-terminated polar surfaces as the dominating planes,and nanorods with mixed-terminated nonpolar *** and theoretical results indicate that both the rate of reaction and the degradation pathway depend on the adsorption configuration of diuron onto the *** molecules adsorb in different alignments on the two surfaces,contributing to the formation of different degradation *** the aliphatic and aromatic sides of diuron adsorb on the polar surfaces simultaneously,leading to an attack by hydroxyl radicals from both *** the other hand,on the mixed-terminated surface,only the aliphatic part adsorbs and is *** exposed surface is therefore the key factor controlling the degradation *** diuron degradation on ZnO,a catalyst confined tomixed-terminated surfaces,i.e.,ZnO nanorods,is more desirable,as it avoids the formation of intermediates with potent phytotoxicity and cytogenotoxicity.

关键词： Diuron Photocatalysis Adsorption Degradation pathway Mechanism Toxicity

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Rewriting regulatory DNA to dissect and reprogram gene expression

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Cell 2025年第12期188卷 3349-3366.e23页

作者： Martyn, Gabriella E. Montgomery, Michael T. Jones, Hank Guo, Katherine Doughty, Benjamin R. Linder, Johannes Bisht, Deepa Xia, Fan Cai, Xiangmeng S. Chen, Ziwei Cochran, Kelly Lawrence, Kathryn A. Munson, Glen Pampari, Anusri Fulco, Charles P. Sahni, Nidhi Kelley, David R. Lander, Eric S. Kundaje, Anshul Engreitz, Jesse M. Department of Genetics Stanford University School of Medicine Stanford 94305 CA United States Basic Science and Engineering Initiative Stanford Children's Health Betty Irene Moore Children's Heart Center Stanford 94305 CA United States Calico Life Sciences LLC South San Francisco 94080 CA United States Department of Genitourinary Medical Oncology Division of Cancer Medicine The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Department of Genomic Medicine The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Houston 77230 TX United States Department of Bioengineering Stanford University Stanford 94305 CA United States Department of Computer Science Stanford University Stanford 94305 CA United States Novo Nordisk Foundation Center for Genomic Mechanisms of Disease Broad Institute of MIT and Harvard Cambridge 02142 MA United States Gene Regulation Observatory Broad Institute of MIT and Harvard Cambridge 02142 MA United States Broad Institute of MIT and Harvard Cambridge 02142 MA United States Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston 77230 TX United States Quantitative and Computational Biosciences Program Baylor College of Medicine Houston 77030 TX United States Department of Biology MIT Cambridge 02139 MA United States Department of Systems Biology Harvard Medical School Boston 02115 MA United States Stanford Cardiovascular Institute Stanford University Stanford 94305 CA United States

Regulatory DNA provides a platform for transcription factor binding to encode cell-type-specific patterns of gene expression. However, the effects and programmability of regulatory DNA sequences remain difficult to map or predict. Here, we develop variant effects from flow-sorting experiments with CRISPR targeting screens (Variant-EFFECTS) to introduce hundreds of designed edits to endogenous regulatory DNA and quantify their effects on gene expression. We systematically dissect and reprogram 3 regulatory elements for 2 genes in 2 cell types. These data reveal endogenous binding sites with effects specific to genomic context, transcription factor motifs with cell-type-specific activities, and limitations of computational models for predicting the effect sizes of variants. We identify small edits that can tune gene expression over a large dynamic range, suggesting new possibilities for prime-editing-based therapeutics targeting regulatory DNA. Variant-EFFECTS provides a generalizable tool to dissect regulatory DNA and to identify genome editing reagents that tune gene expression in an endogenous context. © 2025 Elsevier Inc.

关键词： CRISPR enhancers gene regulation high-throughput screening non-coding variants predictive models prime editing RNA FlowFISH sequence design transcription factors

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Rapid identification and monitoring of cooking oil fume-based toxic volatile organic aldehydes in lung tissue for predicting exposure level and cancer risks

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Chemosphere 2023年第1期339卷 139704页

作者： Prakasham, Karthikeyan Gurrani, Swapnil Wu, Chia-Fang Wu, Ming-Tsang Hsieh, Tusty-Jiuan Peng, Chiung-Yu Huang, Po-Chin Krishnan, Anbarasu Tsai, Pei-Chien Lin, Yu-Chia Tsai, Bongee Lin, Yuan-Chung Ponnusamy, Vinoth Kumar Kaohsiung City807 Taiwan Kaohsiung City807 Taiwan International Master Program of Translational Medicine College of Engineering and Science National United University Miaoli Taiwan Kaohsiung City807 Taiwan Department of Public Health College of Health Sciences Kaohsiung Medical University Kaohsiung City807 Taiwan Miaoli County 35053 Taiwan Department of Computational Biology Institute of Bioinformatics Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Tamil Nadu Chennai602105 India Kaohsiung City807 Taiwan Corporation No.392 Yucheng Rd. Zuoying District. Kaohsiung City813 Taiwan Center for Emerging Contaminants Research National Sun Yat-Sen University Kaohsiung City804 Taiwan Institute of Environmental Engineering National Sun Yat-Sen University Kaohsiung City804 Taiwan Kaohsiung Medical University Kaohsiung City807 Taiwan Department of Medical Research China Medical University Hospital China Medical University Taichung Taiwan Department of Family Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan

Cooking oil fumes (COFs) comprised of a mixture of cancer-causing volatile organic aldehydes (VOAs), particularly trans, trans-2,4-decadienal (t,t-DDE), 4-hydroxy-hexenal (4-HHE), and 4-hydroxy-nonenal (4-HNE). Monitoring toxic VOAs levels in people exposed to different cooking conditions is vital to predicting the cancer risk. For this purpose, we developed a fast tissue extraction (FaTEx) technique combined with UHPLC-MS/MS to monitor three toxic VOAs in mice lung tissue samples. FaTEx pre-treatment protocol was developed by combining two syringes for extraction and clean-up process. The various procedural steps affecting the FaTEx sample pre-treatment process were optimized to enhance the target VOAs’ extraction efficiency from the sample matrix. Under the optimal experimental conditions, results exhibit good correlation coefficient values > 0.99, detection limits were between 0.5–3 ng/g, quantification limits were between 1–10 ng/g, and the matrix effect was © 2023 Elsevier Ltd

关键词： Diseases

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Development of a quantitative structure-response relationships to estimate concentrations of plasticizer metabolites in urine without reference standards using non-targeted analysis with liquid chromatography high-resolution mass spectrometry

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Analytica Chimica Acta 2025年 1364卷 344215页

作者： Yong-Lai Feng Jerrie Feng Anca Baesu Vanessa Martinez Yan Li Exposure and Biomonitoring Division Environmental Health Science and Research Bureau Health Canada 251 Sir Frederick Banting Driveway Ottawa Ontario K1A 0K9 Canada Bioinformatics and Computational Biology Program Faculty of Arts & Science University of Toronto 25 Harbord Street Toronto Ontario M5S 3G5 Canada Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie-Curie Ottawa Ontario K1N 6N5 Canada

Background Plasticizers are characterized as endocrine disruptors, and human exposure to these chemicals can adversely affect the reproductive system. Non-targeted analysis (NTA) using liquid chromatography – high resolution mass spectrometry (LC-HRMS) is a discovery-based approach for screening and identifying hundreds of compounds and metabolites in human samples without a priori knowledge of the chemical species that would be present in the sample. However, while NTA methods need to be standardized in order to provide reliable and reproducible qualitative results, there is also an urgent need to develop NTA methods that can provide quantitative information for identified compounds . Results We describe a quantitative structure-response relationship (QSRR) in NTA using LC-electrospray ionization (ESI)-HRMS that was established by combining retention behavior and structural descriptors. This relationship can be used to estimate the signal response factors of chemicals and we can utilize the estimated response factors to approximate the concentrations of plasticizer metabolites without reference standards. The model consists of 12 variables, being retention time and 11 molecular descriptors, that can estimate response factors of eleven testing chemicals with an error less than 30 %. The study demonstrated that the model can be updated with routine (e.g. daily) calibration curves and estimate concentrations of unknown metabolites in urine with an error less than 50 % for most compounds. The model can be applied to two different ionization systems without having a significant impact on its prediction accuracy. Significance While NTA provides the important information on identification of unknown and new chemicals/metabolites, it is crucial to provide quantitative concentrations for these compounds identified in NTA to support exposure assessment. Our approach enables a fast and simple estimation of the concentration of unknown metabolites of phthalates and their alter

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Titania Nanosheets Generates Peroxynitrite for S-Nitrosylation and Enhanced p53 Function in Lung Cancer Cells

Research Square

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Research Square 2021年

作者： Soonnarong, Rapeepun Tungsukruthai, Sucharat Nutho, Bodee Rungrotmongkol, Thanyada Vinayanuwattikun, Chanida Maluangnont, Tosapol Chanvorachote, Pithi Interdisciplinary Program of Pharmacology Graduate School Chulalongkorn University Bangkok Thailand Cell-based Drug and Health Products Development Research Unit Chulalongkorn University Bangkok Thailand Departments of Pharmacology and Physiology Faculty of Pharmaceutical Sciences Bangkok Thailand Department of Pharmacology Faculty of Science Mahidol University Bangkok Thailand Biocatalyst and Environmental Biotechnology Reseach Unit Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok Thailand Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok Thailand Division of Medical Oncology Department of Medicine Chulalongkorn University Bangkok Thailand College of Materials Innovation and Technology King Mongkut’s Institute of Technology Ladkrabang Bangkok Thailand

Background: Metal oxide nanomaterials are increasingly being exploited in cancer therapy thanks to their unique properties, which can enhance the efficacy of current cancer therapies. However, the nanotoxicity and mechanism of Ti0.8O2 nanosheets for specific site-targeting strategies in NSCLC have not yet been investigated. Methods: The effects of Ti0.8O2 nanosheets on cytotoxicity in NSCLC cells and normal cells were examined. The apoptosis characteristics, including condensed and fragmented nuclei, as assessed by positive staining with annexin V. The cellular uptake of the nanosheets and the induction of stress fiber were assessed via transmission electron microscopy (TEM) and scanning electron microscopy (SEM) analyses, respectively. We also evaluated the expression of protein in death mechanism to identify the molecular mechanisms behind the toxicity of these cells. We investigated the relationship between S-nitrosylation and the increase in p53 stability by molecular dynamics. Results: Ti0.8O2 nanosheets caused cytotoxicity in several lung cancer cells, but not in normal cells. The nanosheets could enter lung cancer cells and exert an apoptosis induction. Results for protein analysis further indicated the activation of p53, increased Bax, decreased Bcl-2 and Mcl-1, and activation of caspase-3. The nanosheets also exhibited a substantial apoptosis effect in drug-resistant metastatic primary lung cancer cells, and it was found that the potency of the nanosheets was dramatically higher than that of cisplatin and etoposide. In terms of their mechanism of action, we found that the mode of apoptosis induction was through the generation of cellular ONOO− mediated the S-nitrosylation of p53 at C182. Molecular dynamics analysis further showed that the S-nitrosylation of one C182 stabilized the p53 dimer. Consequently, this nitrosylation of the protein led to an upregulation of p53 through its stabilization. Conclusions: Taking all the evidence together, we provided info

关键词： Molecular dynamics

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