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Serum proteomic approach to identifying differentially expressed proteins in effusive feline infectious peritonitis

Scientific Reports 2025年第1期15卷 1-12页

作者： Wassamon Moyadee Jatuporn Rattanasrisomporn Sittiruk Roytrakul Janthima Jaresitthikunchai Narumon Phaonakrop Kiattawee Choowongkomon Sekkarin Ploypetch Natthasit Tansakul Amonpun Rattanasrisomporn Graduate Program in Animal Health and Biomedical Sciences Faculty of Veterinary Medicine Kasetsart University Bangkok Thailand Department of Companion Animal Clinical Sciences Faculty of Veterinary Medicine Kasetsart University Bangkok Thailand National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency Pathum Thani Thailand Department of Biochemistry Faculty of Science Kasetsart University Bangkok Thailand Department of Clinical Sciences and Public Health Faculty of Veterinary Science Mahidol University Nakhon Pathom Thailand Department of Pharmacology Faculty of Veterinary Medicine Kasetsart University Bangkok Thailand Interdisciplinary of Genetic Engineering and Bioinformatics Graduate School Kasetsart University Bangkok Thailand

Feline infectious peritonitis (FIP) is a lethal, viral-induced immune-mediated disease that remains a challenge for diagnosis and treatment in cats. Proteomic profiling, which analyzes the protein content of biological samples, offers the potential to identify novel biomarkers that could improve the diagnosis and management of FIP. This study aims to assess the serum proteome and identify proteins that differentiate healthy cats from cats diagnosed with effusive FIP using liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS). A total of 30 cats diagnosed with effusive FIP and 27 clinically normal cats were enrolled. Twenty-three proteins were significantly (p< 0.01, ≥ fivefold change in abundance) differentially expressed between cats with effusive FIP and controls. Among these, the P2X purinoceptor, DNA topoisomerase, Notch receptor 2, and cadherin-17 were identified as key proteins of interest in cats with effusive FIP. Our findings suggest that these differentially expressed proteins could serve as potential diagnostic biomarkers and therapeutic targets for FIP. However, further studies are needed to validate these findings and explore their potential applications.

关键词： Biomarkers Cats Coronavirus Feline infectious peritonitis Proteomics Serum

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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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Avatar-Like Body Imaging of Dermal Exposure to Melamine in Factory Workers Analyzed by Ambient Mass Spectrometry

SSRN

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SSRN 2022年

作者： Wu, Ming-Tsang Hsu, Yu-Ming Wu, Chia-Fang Huang, Min-Zong Shiea, Jentaie Pan, Chih-Hung Liu, Chia-Chu Chen, Chu-Chih Wang, Yin-Han Cheng, Ching-Mei Research Center for Environmental Medicine Kaohsiung Medical University Kaohsiung Taiwan Graduate Institute of Clinical Medicine Department of Chemistry National Sun Yat-Sen University Kaohsiung Taiwan Institute of Labor Occupational Safety and Health Ministry of Labor Executive Yuan Taipei Taiwan Department of Urology Kaohsiung Medical University Hospital Kaohsiung Medical University Taiwan Division of Biostatistics and Bioinformatics Institute of Population Health Sciences National Health Research Institutes Taiwan Department of Laboratory Medicine Kaohsiung Municipal Hsiao-Kang Hospital Kaohsiung Taiwan PhD Program of Environmental and Occupational Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Graduate Institute of Clinical Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Public Health Kaohsiung Medical University Kaohsiung Taiwan Department of Family Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan

Ambient mass spectrometry thermal desorption-electrospray ionization/mass spectrometry (TD-ESI/MS) can rapidly identify chemicals without pretreatment of biological samples. This study used a high-throughput and semi-quantitative TD-ESI/MS screening technique for probe skin sampling of melamine workers occupationally exposed to different ambient melamine concentrations to create avatar-like body images, which were then used to study temporal and dynamic changes in nephrotoxic melamine exposure. We enrolled four voluntary melamine workers, each from one of four factory worksites. Melamine exposure was highest in manufacturing and molding, followed by grinding and polishing, packing, and administration, the lowest. Skin samples were collected Friday (end-of-shift) and Monday (pre-shift). Early morning one-spot urine samples were also collected right after skin sampling. In total, 2198 probe skin samples were collected and subjected to semi-quantitative TD-ESI/MS analyses of melamine chemical within 40 hours. Converted standardized body image scores revealed exposure to be highest in the manufacturing worker on Friday and lowest in the administrative worker on Monday. The absolute differences (Friday − Monday) of standardized body image scores were all significantly positive in each individual worker and across all four workers (permutation test, all p-values © 2022, The Authors. All rights reserved.

关键词： Chemical analysis

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Lymphatic endothelial mTORC1 instructs metabolic and developmental signaling during lymphangiogenesis

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Developmental Cell 2025年

作者： Han, Fei Simeroth, Summer Zhu, Jie Gryniuk, Irma Pranay, Atul Chen, Weiqing Wang, Yuan Cai, Yuanyuan Shen, Zhiyuan Wang, Guangyu Griffin, Courtney T. Xia, Lijun Yu, Pengchun Cardiovascular Biology Research Program Oklahoma Medical Research Foundation Oklahoma City 73104 OK United States Department of Cell Biology University of Oklahoma Health Sciences Center Oklahoma City 73104 OK United States Aging and Metabolism Research Program Oklahoma Medical Research Foundation Oklahoma City 73104 OK United States Center for Bioinformatics and Computational Biology Houston Methodist Research Institute Houston TX United States Department of Physiology Biophysics & Systems Biology Weill Cornell Graduate School of Medical Science Weill Cornell Medicine Cornell University New York NY United States Department of Radiation Oncology Rutgers Cancer Institute and Robert Wood Johnson Medical School Rutgers University New Brunswick NJ United States Center for Cardiovascular Regeneration Houston Methodist Research Institute Houston TX United States Center for RNA Therapeutics Houston Methodist Research Institute Houston TX United States Department of Cardiothoracic Surgery Weill Cornell Medicine Cornell University New York NY United States Department of Biochemistry and Physiology University of Oklahoma Health Sciences Center Oklahoma City OK United States

The lymphatic vasculature comprises lymphatic capillaries and collecting vessels. To support lymphatic development, lymphatic endothelial cells (LECs) utilize nutrients to fuel lymphangiogenic processes. Meanwhile, LECs maintain constant prospero homeobox 1 (PROX1) expression critical for lymphatic specification. However, molecular mechanisms orchestrating nutrient metabolism while sustaining PROX1 levels in LECs remain unclear. Here, we show that loss of RAPTOR, an indispensable mechanistic target of rapamycin complex 1 (mTORC1) component, downregulates PROX1 and impairs lymphatic capillary growth and differentiation of collecting lymphatics in mice. Mechanistically, mTORC1 inhibition in mouse and human LECs causes Myc reduction, which decreases hexokinase 2 (HK2) and glutaminase (GLS), inhibiting glycolysis and glutaminolysis. Myc or HK2/GLS ablation impedes lymphatic capillary and collecting vessel formation. Interestingly, mTORC1 regulation of PROX1 is independent of Myc-HK2/GLS signaling. Moreover, genetic interaction analysis indicates that Myc and PROX1 play crucial roles in mTORC1-regulated lymphatic development. Collectively, our findings identify mTORC1 as a key regulator of metabolic programs and PROX1 expression during lymphangiogenesis. © 2025 Elsevier Inc.

关键词： glutaminase glutaminolysis glycolysis hexokinase 2 lymphangiogenesis lymphatic endothelial cell lymphatic vessel mTORC1 Myc PROX1

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A zinc finger-dependent, PRDM13-driven mechanism regulates retinal progenitor cell fate from mouse embryonic stem cells via WNT signaling

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Stem cell reports 2025年 102508页

作者： Brian W Basinski Yuanhao Huang Qiang Li Charukesi D Sivakumar Tyler J Carman Hana M Pan Jing Xu D Ford Hannum Jie Liu Rajesh C Rao Department of Ophthalmology and Visual Science W.K. Kellogg Eye Center University of Michigan Ann Arbor MI 48105 USA Molecular and Cellular Pathology Graduate Program Department of Pathology University of Michigan Ann Arbor MI 48105 USA. Department of Computational Medicine and Bioinformatics Ann Arbor MI 48105 USA. Department of Ophthalmology and Visual Science W.K. Kellogg Eye Center University of Michigan Ann Arbor MI 48105 USA. Molecular and Cellular Pathology Graduate Program Department of Pathology University of Michigan Ann Arbor MI 48105 USA Department of Computational Medicine and Bioinformatics Ann Arbor MI 48105 USA Department of Human Genetics University of Michigan Ann Arbor MI 48105 USA Rogel Cancer Center University of Michigan Ann Arbor MI 48105 USA Center of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI 48105 USA Center for RNA Biomedicine University of Michigan Ann Arbor MI 48105 USA A. Alfred Taubman Medical Research Institute University of Michigan Ann Arbor MI 48105 USA Section of Ophthalmology Surgical Service Veterans Administration Ann Arbor Healthcare System Ann Arbor MI 48105 USA. Electronic address: rajeshr@umich.edu.

The transcriptional regulation underlying eye field (retinal primordium) development requires precise control, yet the mechanisms guiding lineage-specific differentiation within the central nervous system (CNS) remain incompletely understood. Using neuroectoderm (NE) organoids derived from mouse embryonic stem cells, we investigate the role of PRDM13 in eye field specification. We demonstrate that Prdm13 expression inhibits RX eye field fate but permits non-eye field NE differentiation, an effect that depends on its first and second zinc-finger domains. Prdm13 activates the WNT/β-catenin signaling pathway during differentiation, leading to downregulation of key transcription factors crucial for establishing the eye field. Pharmacological inhibition of WNT signaling abolishes PRDM13-mediated suppression, restoring RX eye field differentiation. Our work reveals a previously undescribed PRDM13-WNT signaling axis that regulates lineage-specific neural differentiation of embryonic stem cells.

关键词： PRDM13 WNT organoids retinal development stem cells

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Detecting Hemileia vastatrix using Vision AI as Supporting to Food Security for Smallholder Coffee Commodities

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IOP Conference Series: Earth and Environmental Science 2022年第1期998卷

作者： Teddy Suparyanto Erick Firmansyah Tjeng Wawan Cenggoro Digdo Sudigyo Bens Pardamean Faculty of Agricultural Technology Institute of Agriculture STIPER Yogyakarta Indonesia 55282 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

The loss of food crops during the COVID-19 pandemic threatens food security in Indonesia as one of the world's top coffee producers. This affects the insecurity of coffee commodities which is influenced by several factors other than the pandemic such as pests, plant diseases, and extreme weather. Plant diseases, such as leaf rust, are a significant factor in the insecurity problem in coffee commodities. The fungus Hemileia vastatrix B et Br causes leaf rust disease, which is a pest that frequently damages coffee plants. This disease not only interferes with plant growth but also causes a decrease in coffee quality and quantity. This initial research aims to carry out early prevention of these diseases as supporting to food security in smallholder coffee commodities. An AI-based visual detection application is the result of this research. We collected 100 images of coffee leaves from various coffee plants. The image is reshaped to 256 x 256 pixels and randomly trimmed to 224 x 224 pixels to fulfill the size requirements of a standard Deep Learning technique. Each image was classified into two classes by a plant pest and disease specialist. The dataset was divided into training, validation, and testing series with a ratio of 60:20:20 for training procedures. The Convolutional Neural Network (CNN) research method used a variation of the ResNet CNN model with 18 layers. The best model validation was 59%.

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Anomaly Detection in Climate Data Using Stacked and Densely Connected Long Short-Term Memory Model

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Journal of Computers (Taiwan) 2020年第4期31卷 42-53页

作者： Saleh Abbas, Bahtiar Wahyono, Teguh Heryadi, Yaya Soeparno, Haryono Doctor of Computer Science Binus Graduate Program Bina Nusantara University Jakarta Indonesia Faculty of Information Technology Satya Wacana Christian University Salatiga Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Department of Industrial Engineering Bina Nusantara University Jakarta Indonesia

Climate anomalies are considered as an important factor closely related to many disasters causing many human losses, such as airline crash, wildfires, drought and flooding in many areas. Many researchers have projected that the rising global temperature will increase the draught, especially in the mid-latitude areas. Taking those problems into account, studies on anomaly detection in climate are crucial. While climate prediction aims to analyze and model regular pattern of climate, climate anomaly studies aim to model climate deviation from its previous general patterns. Long Short Term Memory (LSTM) is a method employed in this research because it has been proven to work effectively in several anomaly detection studies, especially for data with similar characteristics. This paper presents empirical results of using Basic LSTM, Densely Connected (DC) LSTM, and Stacked-DC LSTM models to detect temperature anomaly as a manifestation of climate change in Semarang City. The results show that Stacked DC LSTM produced higher accuracy in detecting anomaly than the other two methods. © 2020 Computer Society of the Republic of China. All rights reserved.

关键词： Long short-term memory

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Structural basis and synergism of ATP and Na⁺ activation in bacterial K⁺ uptake system KtrAB

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Nature Communications 2024年第1期15卷 3850页

作者： Chiang, Wesley Tien Chang, Yao-Kai Hui, Wei-Han Chang, Shu-Wei Liao, Chen-Yi Chang, Yi-Chuan Chen, Chun-Jung Wang, Wei-Chen Lai, Chien-Chen Wang, Chun-Hsiung Luo, Siou-Ying Huang, Ya-Ping Chou, Shan-Ho Horng, Tzyy-Leng Hou, Ming-Hon Muench, Stephen P. Chen, Ren-Shiang Tsai, Ming-Daw Hu, Nien-Jen Graduate Institute of Biochemistry National Chung Hsing University Taichung 402202 Taiwan Institute of Biological Chemistry Academia Sinica Taipei 115201 Taiwan Department of Civil Engineering National Taiwan University Taipei 106319 Taiwan Department of Biomedical Engineering National Taiwan University Taipei 10663 Taiwan Life Science Group Scientific Research Division National Synchrotron Radiation Research Center Hsinchu 30092 Taiwan Institute of Molecular Biology National Chung Hsing University Taichung 402202 Taiwan Graduate Institute of Chinese Medical Science China Medical University Taichung 406040 Taiwan Department of Applied Mathematics Feng Chia University Taichung 407102 Taiwan Institute of Genomics and Bioinformatics National Chung Hsing University Taichung 402202 Taiwan School of Biomedical Sciences Faculty of Biological Sciences and the Astbury Centre for Structural Molecular Biology University of Leeds Leeds LS2 9JT United Kingdom Department of Life Science Tunghai University Taichung 407224 Taiwan Institute of Biochemical Sciences National Taiwan University Taipei 106319 Taiwan Ph.D Program in Translational Medicine National Chung Hsing University Taichung 402202 Taiwan

The K+ uptake system KtrAB is essential for bacterial survival in low K+ environments. The activity of KtrAB is regulated by nucleotides and Na+. Previous studies proposed a putative gating mechanism of KtrB regulated...

The K⁺ uptake system KtrAB is essential for bacterial survival in low K⁺ environments. The activity of KtrAB is regulated by nucleotides and Na⁺. Previous studies proposed a putative gating mechanism of KtrB regulated by KtrA upon binding to ATP or ADP. However, how Na⁺ activates KtrAB and the Na⁺ binding site remain unknown. Here we present the cryo-EM structures of ATP- and ADP-bound KtrAB from Bacillus subtilis (BsKtrAB) both solved at 2.8 Å. A cryo-EM density at the intra-dimer interface of ATP-KtrA was identified as Na⁺, as supported by X-ray crystallography and ICP-MS. Thermostability assays and functional studies demonstrated that Na⁺ binding stabilizes the ATP-bound BsKtrAB complex and enhances its K⁺ flux activity. Comparing ATP- and ADP-BsKtrAB structures suggests that BsKtrB Arg417 and Phe91 serve as a channel gate. The synergism of ATP and Na⁺ in activating BsKtrAB is likely applicable to Na⁺-activated K⁺ channels in central nervous system. © The Author(s) 2024.

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Retraction Note: REHAB FUN: an assistive technology in neurological motor disorders rehabilitation of children with cerebral palsy

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Neural Computing and Applications 2024年第28期36卷 17757-17757页

作者： de Oliveira, Juliana M. Munoz, Roberto Ribeiro, Sidarta Wu, Wanqing de Albuquerque, Victor Hugo C. Graduate Program in Applied Informatics Laboratory of Bioinformatics University of Fortaleza Fortaleza Brazil Escuela de Ingeniería Civil Informática Centro de Investigación y Desarrollo en Ingeniería en Salud Universidad de Valparaíso Valparaíso Chile Brain Institute Federal University of Rio Grande do Norte (UFRN) Natal Brazil CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems Shenzhen Institute of Advanced Technology-Chinese Academy of Sciences (SIAT-CAS) Shenzhen China

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Environmental melamine exposure and adverse kidney outcomes in patients with type 2 diabetes mellitus

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Environmental Pollution 2023年第Part1期331卷 121883页

作者： Tsai, Yi-Chun Wu, Chia-Fang Hung, Wei-Wen Yu, Ping-Shaou Liu, Chia-Chu Hsieh, Tusty-Jiuan Chen, Chu-Chih Li, Sih-Syuan Chen, Jia-Jen Chiu, Yi-Wen Hwang, Shang-Jyh Wu, Ming-Tsang Division of Nephrology Department of Internal Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Division of General Medicine Department of Internal Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Center for Liquid Biopsy and Cohort Research Kaohsiung Medical University Kaohsiung Taiwan School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan International Master Program of Translational Medicine National United University Miaoli Taiwan Division of Endocrinology and Metabolism Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Kaohsiung Municipal CiJin Hospital Kaohsiung Taiwan Research Center for Precision Environmental Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Urology Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Graduate Institute of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Division of Biostatistics and Bioinformatics Institute of Population Health Sciences National Health Research Institutes Taiwan Department of Public Health College of Health Sciences Kaohsiung Medical University Kaohsiung Taiwan Department of Family Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung City Taiwan Program in Environmental and Occupational Medicine College of Medicine Kaohsiung Medical University Kaohsiung City Taiwan

The impact of melamine exposure on kidney outcomes in type 2 diabetes mellitus (T2D) patients remains unclear. In this prospective cohort study, 561 T2D patients during October 2016 and June 2020 were enrolled and followed until December 2021. Baseline one-spot urinary corrected melamine levels were measured by LC-MS/MS. Average daily intake (ADI) of melamine represented environmental melamine exposure in daily life, and was estimated using urinary corrected melamine level by creatinine excretion (CE)-based model. Primary kidney outcomes were defined as doubling of serum creatinine levels or end stage kidney disease (ESKD), and secondary kidney outcomes included rapid decline in kidney function as estimated glomerular filtration rate (eGFR) decline >5 ml/min/1.73 m2/year. Baseline median urinary corrected melamine levels and estimated DI of melamine were 0.8 μg/mmol and 0.3 μg/kg/day in 561 T2D patients. During 3.7 years of follow-up, urinary corrected melamine level was positively correlated with reaching composite outcomes of either doubling of serum creation levels or ESKD and rapid decline in kidney function. Those with the highest quartile of urinary corrected melamine had 2.96-fold risk of composite outcomes of either doubling of serum creation levels or ESKD and 2.47-fold risk of eGFR decline >5 ml/min/1.73 m2/year. Estimated ADI of melamine also had significant correlation with adverse kidney outcomes. Furthermore, the positive relationship between melamine exposure and rapid decline in kidney function was only found in T2D patients with male, baseline eGFR ≥60 ml/min/1.73 m2 or glycated hemoglobin ≤7%. In conclusion, melamine exposure is significantly associated with adverse kidney outcomes in T2D patients, especially in those with male, well sugar control or good baseline kidney function. © 2023 Elsevier Ltd

关键词： Melamine Kidney outcomes Type 2 diabetes mellitus

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