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Novel intertypic recombination of Echovirus 11 in the Enterovirus species B

Journal of Medical Virology 2024年第1期96卷 e29323页

作者： Gong, Yu-Nong Yang, Shu-Li Chen, Yi-Ching Liu, Yi-Chun Huang, Yhu-Chering Tsao, Kuo-Chien Research Center for Emerging Viral Infections College of Medicine Chang Gung University Taoyuan Taiwan International Master Degree Program for Molecular Medicine in Emerging Viral Infections College of Medicine Chang Gung University Taoyuan Taiwan Department of Laboratory Medicine Linkou Chang Gung Memorial Hospital Taoyuan Taiwan National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Zhunan Taiwan Department of Medical Biotechnology and Laboratory Science College of Medicine Chang Gung University Taoyuan Taiwan Department of Pediatrics Division of Pediatric Infectious Diseases Linkou Chang Gung Memorial Hospital Taoyuan Taiwan School of Medicine College of Medicine Chang Gung University Taoyuan Taiwan

Enteroviruses (EVs), single-stranded, positive-sense RNA viruses, can be classified into four species (A−D), which have previously been linked to a diverse range of disease manifestations and infections affecting the central nervous system. In the Enterovirus species B (EV-B), Echovirus type 11 (E11) has been observed to occasionally circulate in Taiwan, which was responsible for an epidemic of enterovirus infections in 2018. Here, 48 clinical specimens isolated in 2003, 2004, 2009, and 2018 were collected for the high-throughput sequencing. Notably, we identified 2018 Taiwanese strains having potential recombinations in the 3D gene, as well as one 2003 strain having a double recombination with E6 and Coxsackievirus B5 in the P2 and P3 regions, respectively. Additionally, one amino acid signature mutated from the Histidine (H) in throat swab specimens to the Tyrosine (Y) in cerebral spinal fluid specimens was detected at position 1496 (or 57) of the genomic coordinate (or 3A gene) to further demonstrate intra-host evolution in different organs. In conclusion, this study identifies potential intertypic recombination events and an intra-host signature mutation in E11 strains, isolated during a 2018 neurological disease outbreak in Taiwan, contributing to our understanding of its evolution and pathogenesis. © 2023 Wiley Periodicals LLC.

关键词： Echovirus Enterovirus high-throughput sequencing neurological disease recombination

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Proteomic profiling of tumor microenvironment and prognosis risk prediction in stage I lung adenocarcinoma

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Lung Cancer 2024年 191卷 107791-107791页

作者： Lu, Yueh-Feng Chang, Ya-Hsuan Chen, Yi-Ju Hsieh, Min-Shu Lin, Mong-Wei Hsu, Hsao-Hsun Han, Chia-Li Chen, Yu-Ju Yu, Sung-Liang Chen, Jin-Shing Chen, Hsuan-Yu Ph.D. Program in Translational Medicine National Taiwan University and Academia Sinica Taiwan Division of Radiation Oncology Department of Radiology Far Eastern Memorial Hospital New Taipei City Taiwan Institute of Molecular and Genomic Medicine National Health Research Institute Taiwan Institute of Chemistry Academia Sinica Taipei Taiwan Department of Pathology National Taiwan University Hospital and National Taiwan University College of Medicine Taipei Taiwan Department of Surgery National Taiwan University Hospital and National Taiwan University College of Medicine Taipei Taiwan Master Program in Clinical Genomics and Proteomics College of Pharmacy Taipei Medical University Taipei Taiwan Department of Clinical Laboratory Sciences and Medical Biotechnology National Taiwan University Taiwan Doctoral Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taiwan Center for Cancer Research Kaohsiung Medical University Taiwan Institute of Statistical Science Academia Sinica Taipei Taiwan

Objectives: With the increasing popularity of CT screening, more cases of early-stage lung cancer are being diagnosed. However, 24.5% of stage I non-small-cell lung cancer (NSCLC) patients still experience treatment failure post-surgery. Biomarkers to predict lung cancer patients at high risk of recurrence are needed. Materials and methods: We collected protein mass spectrometry data from the Taiwan Lung Cancer Moonshot Project and performed bioinformatics analysis on proteins with differential expressions between tumor and adjacent normal tissues in 74 stage I lung adenocarcinoma (LUAD) cases, aiming to explore the tumor microenvironment related prognostic biomarkers. Findings were further validated in 6 external cohorts. Results: The analysis of differentially expressed proteins revealed that the most enriched categories of diseases and biological functions were cellular movement, immune cell trafficking, and cancer. Utilizing proteomic profiling of the tumor microenvironment, we identified five prognostic biomarkers (ADAM10, MIF, TEK, THBS2, MAOA). We then developed a risk score model, which independently predicted recurrence-free survival and overall survival in stage I LUAD. Patients with high risk scores experienced worse recurrence-free survival (adjusted hazard ratio = 8.28, p < 0.001) and overall survival (adjusted hazard ratio = 6.88, p = 0.013). Findings had been also validated in the external cohorts. Conclusion: The risk score model derived from proteomic profiling of tumor microenvironment can be used to predict recurrence risk and prognosis of stage I LUAD. © 2024 Elsevier B.V.

关键词： Lung adenocarcinoma Mass spectrometry Prognostic biomarker Proteomic Tumor microenvironment

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Revealing potential Rab proteins participate in regulation of secretory autophagy machinery

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The Kaohsiung journal of medical sciences 2024年第7期40卷 642-649页

作者： Pei-Wen Lin Man-Ling Chu Yu-Wen Liu Yu-Cing Chen Yao-Hsiang Shih Sheng-Hui Lan Shang-Ying Wu I-Ying Kuo Hong-Yi Chang Hsiao-Sheng Liu Ying-Ray Lee Master of Science Program in Tropical Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan. Department of Microbiology and Immunology College of Medicine National Cheng Kung University Tainan Taiwan. Department of Anatomy School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan. Department of Life Sciences and Institute of Genome Sciences National Yang Ming Chiao Tung University Taipei Taiwan. Department of Microbiology and Immunology School of Medicine College of Medicine Taipei Medical University Taipei Taiwan. Department of Biotechnology College of Life Science Kaohsiung Medical University Kaohsiung Taiwan. Center for Cancer Research Kaohsiung Medical University Kaohsiung Taiwan. Teaching and Research Center Kaohsiung Municipal Hsiao-Kang Hospital Kaohsiung Taiwan. Department of Microbiology and Immunology College of Medicine Kaohsiung Medical University Kaohsiung Taiwan. Faculty of Post-Baccalaureate Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan. Center for Tropical Medicine and Infectious Disease Kaohsiung Medical University Kaohsiung Taiwan.

Autophagy can be classified as degradative and secretory based on distinct functions. The small GTPase proteins Rab8a and Rab37 are responsible for secretory autophagy-mediated exocytosis of IL-1β, insulin, and TIMP1 (tissue inhibitor of 54 metalloproteinase 1). Other Rab family members participating in secretory autophagy are poorly understood. Herein, we identified 26 overlapped Rab proteins in purified autophagosomes of mouse pancreatic β-cell "Min-6" and human lung cancer cell "CL1-5-Q89L" with high secretory autophagy tendency by LC-MS/MS proteomics analysis. Six Rab proteins (Rab8a, Rab11b, Rab27a, Rab35, Rab37, and Rab7a) were detected in autophagosomes of four cell lines, associating them with autophagy-related vesicle trafficking. We used CL1-5-Q89L cell line model to evaluate the levels of Rab proteins colocalization with autophagy LC3 proteins and presence in purified autophagosomes. We found five Rab proteins (Rab8a, Rab11b, Rab27a, Rab35, and Rab37) are highly expressed in the autophagosome compared to the normal control by immunoblotting under active secretion conditions. However, only Rab8a, Rab35, and Rab37 showing high colocalization with LC3 protein by cofocal microscopy. Despite the discrepancy between the image and immunoblotting analysis, our data sustains the speculation that Rab8a, Rab11b, Rab27a, Rab35, and Rab37 are possibly associated with the secretory autophagy machinery. In contrast, Rab7a shows low colocalization with LC3 puncta and low level in the autophagosome, suggesting it regulates different vesicle trafficking machineries. Our findings open a new direction toward exploring the role of Rab proteins in secretory autophagy-related cargo exocytosis and identifying the cargoes and effectors regulated by specific Rab proteins.

关键词： Rab protein secretory autophagy unconventional protein secretion

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*** as digital platform for vegetation analysis and estimation of carbon stock in KEHATI aqua park

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AIP Conference Proceedings 2024年第1期3026卷

作者： Nanda Satya Nugraha Dian Pratama Putra Mohammad Prasanto Bimantio Amallia Ferhat Rama Zakaria Rudi Nirwantono Teddy Suparyanto Bens Pardamean Faculty of Forestry Institute of Agriculture STIPER Yogyakarta Indonesia 55282 Faculty of Agriculture Institute of Agriculture STIPER Yogyakarta Indonesia 55282 Faculty of Agricultural Technology Institute of Agriculture STIPER Yogyakarta Indonesia 55282 PT. Tirta Investama Pabrik Klaten Klaten Central Java Indonesia 57474 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 1148 Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

KEHATI AQUA Park is one of the green areas managed by PT. Tirta Investama Klaten (Klaten Factory). This area is located in Wangen and Ponggok Villages, Polanharjo District, Klaten Regency, Central Java, and is an integral part of the company’s seriousness in carbon reduction movement. When maintenance of the area is important for the sustainability of the park, there is however no data on the trees inventory in the area. Therefore, this study aims to invent the trees at KEHATI AQUA Park and evaluate the potential of the area to become a carbon sink using *** application. This study was conducted at the KEHATI AQUA Park. The census method was performed to collect tree data, and the result was recorded in *** application. The carbon stock calculation was estimated using the application according to the tree data submitted in the application. The study included a total of 1048 plantation spots in 51 tree species. From those numbers, about 738 trees existed, and the remaining spots were blank spaces. Based on the condition of the trees, those were 660 good trees, 17 dry trees, and 61 under pest infection. The carbon stock estimation at KEHATI AQUA Park Klaten in the next five years (2026) is around 40 tons of carbon. Therefore, it can be concluded that the park is valuable as an area to preserve biodiversity and as a carbon sink.

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Quality and production enhancement of fish mint, Houttuynia cordata Thunb., cultivated in a hydroponic planting system with designed plant growth-promoting additives

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Heliyon 2024年第7期10卷 e28755页

作者： Loo, Yen Chi Tsai, Yi-Hong Chen, Hsieh Hsieh, Hui-Ping Chen, Yen-Chang Chen, Hsueh-Er Lin, Zhi-Hu Huang, Hung-Tse Liu, I.-M. Liaw, Chia-Ching Chang, Fang-Rong Graduate Institute of Natural Products College of Pharmacy Kaohsiung Medical University Kaohsiung 807378 Taiwan Department of Pharmacy and Master Program College of Pharmacy and Health Care Tajen University Pingtung County 907101 Taiwan Graduate Institute of Science Education and Environment Education College of Science National Kaohsiung Normal University Kaohsiung 807 Taiwan Department of Research and Development We-Win Bio-Medical Co. Ltd. Kaohsiung 807 Taiwan Division of Materia Medica Development National Research Institute of Chinese Medicine Taipei 112026 Taiwan Institute of Traditional Medicine National Yang Ming Chiao Tung University Taipei 112026 Taiwan Department of Biochemical Science and Technology National Chiayi University Chiayi 600355 Taiwan Department of Medical Research Kaohsiung Medical University Hospital Kaohsiung 807377 Taiwan Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung 807378 Taiwan Department of Marine Biotechnology and Resources National Sun Yat-sen University Kaohsiung 804201 Taiwan

Fish mint, Houttuynia cordata Thunb. (HCT) is an edible vegetable that has also been used in traditional folk medicines. As both a medicinal herb and a dietary source, HCT has been clinically proven to be a pivotal ingredient in formulas administered to alleviate COVID-19 symptoms. With the increasing market demand for imported materials, ensuring the quality consistency of HCT becomes a significant concern. In this study, the growing time for hydroponically-cultivated HCT with seaweed extract and amino acids added (HCTW) reduced by half compared to conventional soil-cultivated HCT (HCTS). Key quantified components in HCTW, flavonoid glycosides and caffeoylquinic acid derivatives, exhibited a 143% increase over HCTS. These crucial constituents were responsible for possessing antioxidant activity (IC₅₀ < 25 μg/mL) and anti-nitrite oxide production (IC₅₀ < 20 μg/mL). An economically-designed hydroponic system with appropriate additives is proposed to replace HCTS with improvements of growth time, overall production yields, and bioactive qualities. © 2024 The Authors

关键词： anti-inflammation Antioxidant Flavonoid glycosides Houttuynia cordata Thunb. Hydroponics Plant growth-promoting additive

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Agar-altered foaming bacterial cellulose with carvacrol for active food packaging applications

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Food Packaging and Shelf Life 2024年 42卷

作者： Kusuma, Anita Chandra Chou, Yu-Chieh Hsieh, Chen-Che Santoso, Shella Permatasari Go, Alchris Woo Lin, Hong-Ting Victor Hsiao, I.-Lun Lin, Shin-Ping Master Program in Food Safety Taipei Medical University 250 Wu-Hsing Street Taipei 11031 Taiwan Ph.D. Program in Drug Discovery and Development Industry Taipei Medical University 250 Wu-Hsing Street Taipei 11031 Taiwan Institute of Biotechnology National Taiwan University 1 Roosevelt Rd. Section 4 Taipei 10617 Taiwan Department of Chemical Engineering Widya Mandala Surabaya Catholic University Kalijudan 37 Surabaya 60114 Indonesia Department of Chemical Engineering National Taiwan University of Science and Technology 43 Keelung Road Section 4 Taipei 10607 Taiwan Department of Food Science National Taiwan Ocean University No. 2 Pei-Ning Road Keelung 20224 Taiwan School of Food Safety Taipei Medical University 250 Wu-Hsing Street Taipei 11031 Taiwan TMU Research Center for Digestive Medicine Taipei Medical University 250 Wu-Hsing Street Taipei 11031 Taiwan Research Center of Biomedical Device Taipei Medical University 250 Wu-Hsing Street Taipei 11031 Taiwan

Bacterial cellulose (BC) is a biodegradable nanoscale film produced by microorganisms, which possesses great mechanical properties and biocompatibility. In this study, we produced foaming BC (FBC) utilizing foam medium with different concentrations of agar. In addition, carvacrol was loaded into the agar/FBC to establish active packaging material. Evaluation by characterization tests indicated that agar/FBC provided lower crystallinity (59.8%∼71.4%) and a high swelling ability (94.7%∼97.9%) compared to BC (92.2% and 96.1%). The 1.5% agar/FBC with carvacrol group exhibited the significantly highest antimicrobial properties against Escherichia coli and Staphylococcus aureus. Moreover, release measurements showed that greater agar addition contributed to higher protein and carvacrol release extents out of the film. Finally, a sea bass packaging test indicated that carvacrol with 1.5% agar/FBC presented a higher antimicrobial ability against Shewanella putrefaciens, great inhibition of lipid oxidation (67.5%), and a slower spoilage degree (49.8%) which suggested that agar/FBC with carvacrol has potential for active food packaging. © 2024 Elsevier Ltd

关键词： Agar Bacterial cellulose Carvacrol Foaming bacterial cellulose Food packaging Sea bass

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Improved prediction of drug-drug interactions using ensemble deep neural networks

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Medicine in Drug Discovery 2023年 17卷

作者： Thanh Hoa Vo Ngan Thi Kim Nguyen Nguyen Quoc Khanh Le Master Program in Clinical Genomics and Proteomics College of Pharmacy Taipei Medical University Taipei 110 Taiwan Department of Science School of Science and Computing South East Technological University Waterford X91 K0EK Ireland Pharmaceutical and Molecular Biotechnology Research Center (PMBRC) South East Technological University Waterford X91 K0EK Ireland Undergraduate Program of Nutrition Science National Taiwan Normal University Taipei Taiwan Professional Master Program in Artificial Intelligence in Medicine College of Medicine Taipei Medical University Taipei 106 Taiwan Research Center for Artificial Intelligence in Medicine Taipei Medical University Taipei 106 Taiwan Translational Imaging Research Center Taipei Medical University Hospital Taipei 110 Taiwan

Nowadays, combining multiple drugs is the optimal therapy to decelerate the pathologic process, which contains various underlying adverse effects due to drug-drug interactions (DDIs). Artificial intelligence (AI) has the potential to evaluate the interaction, pharmacodynamics, and possible side effects between drugs. Over the past years, many AI-based DDI prediction techniques, including both machine learning and deep learning, that harness available big data have been presented. Although significant progressives have been gained through previous methods, improvements are still crucial. In this work, we introduce an ensemble deep neural network that can help to improve the predictive performance of DDIs. As a result, our prediction model could predict 86 types of DDIs on a benchmark dataset with an average accuracy of 93.80%. Our ensemble classifier produces better performance when compared with the existing proposed methods on the same dataset. Our model's high performance places it among the top list of those well-built pharmacovigilance-assisted tools that facilitate the detection of DDIs to support medical decisions and drug development. We released our source codes and models at https://***/khanhlee/edn-ddi.

关键词： Drug-drug interactions Simplified molecular-input line-entry system Ensemble deep learning Drug adverse effects Prediction model Clinical decision support system

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Converting hydroponic effluent into high PUFA-rich biomass by mixotrophically cultivated microalga Chlorella sp. through light regulation for sustainable production of bioingredient and bioenergy

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Journal of Environmental Chemical Engineering 2025年第3期13卷

作者： Nanthakrit Sriket Antira Wichaphian Apiwit Kamngoen Jeeraporn Pekkoh Wasu Pathom-aree Yupa Chromkaew Benjamas Cheirsilp Wageeporn Maneechote Yoong Kit Leong Sirasit Srinuanpan Master of Science Program in Applied Microbiology (International Program) Department of Biology Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand Department of Biology Faculty of Science Chiang Mai University Chiang Mai 50200 Thailand Microbial Biorefinery and Biochemical Process Engineering Research Group Chiang Mai University Chiang Mai 50200 Thailand Center of Excellence in Microbial Diversity and Sustainable Utilization Chiang Mai University Chiang Mai 50200 Thailand Department of Plant and Soil Sciences Faculty of Agriculture Chiang Mai University Chiang Mai 50200 Thailand Program of Biotechnology Faculty of Agro-Industry Prince of Songkla University Hat Yai Songkhla 90110 Thailand Office of Research Administration Office of the University Chiang Mai University Chiang Mai 50200 Thailand Department of Chemical and Materials Engineering Tunghai University Taichung 407 Taiwan

Currently, addressing global environmental challenges—particularly the management of nutrients and resource recovery from hydroponic effluent (HE)—is crucial for promoting sustainable agriculture and fostering circularity in the pursuit of a net-zero future. This study aimed to evaluate the potential of Chlorella sp. to convert HE into high-value biomass rich in polyunsaturated fatty acids (PUFAs) under mixotrophic conditions with optimized light illumination. The results demonstrated that supplementing HE with half the concentration of commercial JM medium, and optimizing with blue light, a 16-hour light/8-hour dark photoperiod, and a light intensity of 50 µmol/m 2 /s resulted in a biomass production of 4.04 g/L, containing 16.81 % lipids and 34.04 % PUFAs. These conditions also achieved significant pollutant removal from HE, including 93.33 % nitrate reduction, 100 % ammonia removal, 99.08 % phosphate removal, and 92.68 % reduction in chemical oxygen demand. The nutritional profile of the fatty acids suggests potential applications in the functional ingredient sector, while their characteristics indicate strong potential as biodiesel feedstock, meeting international biodiesel fuel standards. Overall, this study presents an eco-friendly model for nutrient recovery from hydroponic effluent using Chlorella sp., promoting sustainable agriculture, reducing environmental impact, and contributing to bioresource innovation.

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Meta-analysis study of the therapeutic impact of Mesenchymal stem cells derived exosomes for chronic kidney diseases

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Biochemistry and Biophysics Reports 2025年 43卷

作者： Himanshu Gunjan Ramendera Pati Pandey Riya Mukherjee Chung-Ming Chang Graduate Institute of Biomedical Sciences Chang Gung University No. 259 Wenhua 1st Road Guishan District Taoyuan City 33302 Taiwan ROC School of Health Sciences and Technology (SoHST) UPES Bidholi Dehradun 248007 Uttarakhand India Department of Biotechnology and Microbiology SRM University Delhi-NCR Sonepat Haryana India Master & Ph.D. Program in Biotechnology Industry Chang Gung University No. 259 Wenhua 1st Road Guishan District Taoyuan City 33302 Taiwan ROC Department of Medical Biotechnology and Laboratory Science Chang Gung University No. 259 Wenhua 1st Road Guishan District Taoyuan City 33302 Taiwan ROC

Mesenchymal stem cell-derived exosomes (EXOs) represent a promising avenue for treating chronic kidney diseases (CKD), though their precise impact remains somewhat elusive. To address this gap, we conducted a systematic analysis, scouring databases and clinical trial repositories for relevant studies from 2019 to 2023. Seventeen papers were meticulously selected for their focus on mesenchymal stem cell-derived exosomes (MSC-EXOs) and their potential in CKD treatment. Our comprehensive meta-analysis, incorporating 15 preclinical and 6 clinical studies, underscores the efficacy of MSC-EXOs in improving renal function while attenuating tubular injury, inflammation, apoptosis, collagen deposition, and renal fibrosis. Notably, post-treatment with MSC-EXOs exhibited significant associations with various CKD markers, with pooled proportions indicating a considerable impact on blood urea nitrogen (BUN) and serum creatinine (SCR) levels. Subgroup analyses based on animal models further elucidated heterogeneity within the studies. In conclusion, MSC-EXOs demonstrate promise in enhancing renal function and reducing CKD risk, as evidenced by both preclinical and clinical data. Their efficacy in lowering SCR and BUN levels while enhancing filtration rate suggests MSC-EXOs as a viable and secure alternative to cell-based therapies, thereby providing valuable insights for personalized CKD treatments despite inherent limitations.

关键词： Mesenchymal stem cells Exosome Chronic kidney diseases Renal fibrosis Meta-analysis

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#2685 SLC34A2 EXACERBATES TUBULAR INTERSTITIAL FIBROSIS VIA INDUCTION OF APOPTOSIS AND CELL CYCLE ARREST IN S PHASE

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Nephrology Dialysis Transplantation 2023年第SUPPLEMENT_1期38卷

作者： Hu, Liang-Shuan Chang, Sheng-Cheng Tsai, Chia-Hui Wu, Chun-Ching Nguyen, Phuong Thao Hoang Chang, Wei-Che Chang, Wei-Ya Yang, Ya-Chien Jao, Tzu-Ming National Taiwan University College of Medicine International Joint Degree Master's Program in Agro-Biomedical Science in Food and Health Taipei Taiwan Rep. of China Kaohsiung Veterans General Hospital Department of Medical Education and Research Kaohsiung Taiwan Rep. of China National Taiwan University College of Medicine Department of Clinical Laboratory Sciences and Medical Biotechnology Taipei Taiwan Rep. of China

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