Article
Immunology
Lihua Deng, Cedric Ly, Sina Abdollahi, Yu Zhao, Immo Prinz, Stefan Bonn
Summary: This study provides a general method for collecting and preprocessing TCR-pMHC binding data and generates comprehensive datasets for comparing prediction models. The performance evaluation of five deep learning models reveals that they have limitations in generalization and robustness. These findings suggest that TCR-pMHC binding prediction remains challenging and requires further improvement in data quality and algorithmic approaches.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
D. V. Shevyrev, V. P. Tereshchenko, S. V. Sennikov
Summary: The interaction between TCR and pMHC is crucial for adaptive immunity, and besides affinity, the kinetic and mechanical characteristics also play a significant role in antigen recognition and T-cell activation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Lukas Susac, Mai T. Vuong, Christoph Thomas, Soren von Bulow, Caitlin O'Brien-Ball, Ana Mafalda Santos, Ricardo A. Fernandes, Gerhard Hummer, Robert Tampe, Simon J. Davis
Summary: This study reveals the structure of a tumor-reactive TCR complex bound to a melanoma-specific human class I pMHC, providing insights into the initiation of TCR signaling when the receptor binds to pMHC molecules.
Article
Immunology
Even Walseng, Bo Wang, Chunning Yang, Pooja Patel, Chihao Zhao, Hanzhi Zhang, Peng Zhao, Yariv Mazor
Summary: T cell engagers, a type of immunotherapy, face challenges in targeting low density tumor-specific antigens. This study demonstrates the importance of design parameters for developing T cell engagers that can efficiently target these antigens.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Reka Mizsei, Xiaolong Li, Wan-Na Chen, Monika Szabo, Jia-Huai Wang, Gerhard Wagner, Ellis L. Reinherz, Robert J. Mallis
Summary: T lymphocytes distinguish between healthy and diseased cells by recognizing peptides presented by MHC molecules through the T-cell receptor. Pre-T-cell receptors interact with peptides presented by MHC during alpha-beta T lymphocyte development, forming a weak affinity complex with a distinct interface. Methods such as small-scale linkage screening protocols using bismaleimide linkers and NMR verification have been used to study these interactions.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Cell Biology
Lihui Wang, Xun Lan
Summary: In this study, a system called YAMTAD was designed for rapid screening of TCR-pMHC interactions. The system showed high sensitivity and specificity in identifying antigens for a given TCR and recognizing TCRs for a given pMHC. Additionally, the system demonstrated the enrichment of high-affinity TCR-pMHC interactions through library-on-library screening.
Article
Cell Biology
Yingjie Guo, Chenxi Wu, Zhian Yuan, Yansu Wang, Zhen Liang, Yang Wang, Yi Zhang, Lei Xu
Summary: This article introduces a gene-based method to detect gene-gene interactions by adding additive constraints to the model, and experimental results show that this method outperforms previous experiments in detecting gene-gene interactions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Immunology
Caleb Y. Kim, Heather L. Parrish, Michael S. Kuhns
Summary: The Cα domain of αβTCR plays a crucial role in fine-tuning TCR signaling and regulating the response to self-pMHC II interactions. Mutation in the Cα domain results in increased CD4(+) T cell numbers and enhanced response to pMHC II antigens.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Minghao Yang, Zhi-An Huang, Wei Zhou, Junkai Ji, Jun Zhang, Shan He, Zexuan Zhu
Summary: This paper introduces a computational framework called MIX-TPI to predict T-cell receptor (TCR) and peptide-major histocompatibility complex (pMHC) interactions. MIX-TPI utilizes amino acid sequences and physicochemical properties, extracts relevant features using convolutional neural networks, and incorporates a self-attention fusion layer for classification. Experimental results demonstrate the superior performance of MIX-TPI compared to other state-of-the-art methods in predicting TCR-pMHC interactions.
Correction
Psychiatry
Josefin Werme, Sophie van der Sluis, Danielle Posthuma, Christiaan A. de Leeuw
Summary: A correction to this paper has been published at https://doi.org/10.1038/s41398-021-01334-6.
TRANSLATIONAL PSYCHIATRY
(2021)
Article
Construction & Building Technology
Enrico Zacchei, Nuno Simoes, Antonio Vieira, Miguel Esteves, Helder Silva
Summary: This study proposes a mechanical model for insulating glasses (IGs) under different loadings and boundary conditions, and validates it using finite element analysis and experimental measurements. The results show that the numerical approach provides more accurate predictions of the IGs' performance compared to analytical code models, particularly for two side supported IGs under linear loadings. The interactions between gas and glass plates are more significant for larger IGs.
CASE STUDIES IN CONSTRUCTION MATERIALS
(2023)
Article
Plant Sciences
Xu Han, Qingqing Tang, Liping Xu, Zhilin Guan, Jinxing Tu, Bin Yi, Kede Liu, Xuan Yao, Shaoping Lu, Liang Guo
Summary: This study investigated the genotype-by-environment interaction for flowering time in Brassica napus. A large number of single nucleotide polymorphisms were used to associate with flowering time and related climatic indexes. Stable main-effect quantitative trait nucleotides and QTN-by-environment interactions for flowering time were identified. Climatic factors highly correlated with flowering time were also found. Differentially expressed genes analysis identified candidate genes for stable QTNs and QEIs for flowering time, as well as main-effect QTNs for flowering-time-related climatic index. The candidate genes identified in this study could be used for breeding B. napus varieties with optimized flowering time for specific environments.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Ting Peng, Yingping Hou, Haowei Meng, Yong Cao, Xiaotian Wang, Lumeng Jia, Qing Chen, Yang Zheng, Yujie Sun, Hebing Chen, Tingting Li, Cheng Li
Summary: A nucleolus Hi-C (nHi-C) experimental technique was developed to enrich nucleolus-associated chromatin interactions and revealed specific heterochromatin interaction patterns within and around nucleoli in human cells. The research provides a global view of these interactions and demonstrates the important role of nucleoli in the organization of 3D genome architecture.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Joseph S. Murray
Summary: The interaction between the human T-cell antigen receptor and the peptide plus major histocompatibility complex protein involves specific molecular mechanisms, and the mobility of each variable domain differs with respect to the two classes of MHC proteins, which is crucial for understanding the link between TCR function and mechanical forces.
MOLECULAR IMMUNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Fabien Jammes, Julien Schmidt, George Coukos, Sebastian J. Maerkl
Summary: We have developed an integrated microfluidic cellular processing unit that can autonomously isolate and analyze the cell-surface dissociation rates, and recover selected cells. By performing high-throughput single-cell experiments, we have characterized the pMHC-TCR interactions on live CD8+ T cells.
Article
Biochemical Research Methods
Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Jiangning Song, Tatsuya Akutsu
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
(2019)
Article
Oncology
Chien-Chin Lee, Wen-Hsin Chang, Ya-Sian Chang, Jinn-Moon Yang, Chih-Shiang Chang, Kai-Cheng Hsu, Yun-Ti Chen, Ting-Yuan Liu, Yu-Chia Chen, Shyr-Yi Lin, Yang-Chang Wu, Jan-Gowth Chang
MOLECULAR ONCOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Kowit Hengphasatporn, Kitiporn Plaimas, Apichat Suratanee, Peemapat Wongsriphisant, Jinn-Moon Yang, Yasuteru Shigeta, Warinthorn Chavasiri, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol
Article
Oncology
Yi-Hsuan Chuang, Chia-Hwa Lee, Chun-Yu Lin, Chia-Lin Liu, Sing-Han Huang, Jung-Yu Lee, Yi-Yuan Chiu, Jih-Chin Lee, Jinn-Moon Yang
Article
Chemistry, Multidisciplinary
Nikhil Pathak, Yun-Ti Chen, Yen-Chao Hsu, Nung-Yu Hsu, Chih-Jung Kuo, Hui Ping Tsai, Jaw-Jou Kang, Chih-Heng Huang, Sui-Yuan Chang, Yu-Hsiu Chang, Po-Huang Liang, Jinn-Moon Yang
Summary: This study focused on the key drug target, the viral 3C-like (3CL) protease, to identify six protease pharmacophore clusters (PPCs) with diverse active site conformations. Through virtual screening, seven drug candidates were identified, including Boceprevir, Telaprevir, and Nelfinavir, with varying levels of protease inhibition and antiviral activity. Analysis of binding mechanisms of protease inhibitors revealed the role of PPC core anchors in enabling drug repurposing.
Article
Biochemistry & Molecular Biology
Wei-Chung Chiou, Jui-Chieh Chen, Yun-Ti Chen, Jinn-Moon Yang, Lih-Hwa Hwang, Yi-Shuan Lyu, Hsin-Yi Yang, Cheng Huang
Summary: The COVID-19 pandemic has caused a global health crisis, and developing effective treatments is crucial. This study investigates the role of SARS-CoV-2 3CLpro in viral replication and identifies natural compounds PGG and EGCG as potential inhibitors. The findings highlight the therapeutic potentials of PGG and EGCG for treating SARS-CoV-2 infection.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Wei-Chung Chiou, Meng-Shiuan Hsu, Yun-Ti Chen, Jinn-Moon Yang, Yeou-Guang Tsay, Hsiu-Chen Huang, Cheng Huang
Summary: Researchers have identified several FDA-approved drugs that can effectively inhibit the proteolytic activity of SARS-CoV-2 virus, demonstrating their therapeutic potential for treating COVID-19 and other Betacoronavirus infections.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2021)
Article
Cell Biology
Tai-Ting Lee, Po-Lin Chen, Matthew P. Su, Jian-Chiuan Li, Yi-Wen Chang, Rei-Wen Liu, Hsueh-Fen Juan, Jinn-Moon Yang, Shih-Peng Chan, Yu-Chen Tsai, Sophia von Stockum, Elena Ziviani, Azusa Kamikouchi, Horng-Dar Wang, Chun-Hong Chen
Summary: By using the Drosophila melanogaster model, researchers discovered that the mitochondrial outer membrane protein Fis1 plays a crucial role in muscle dysfunction and several age-related conditions, with mutations leading to damaged mitochondria, increased oxidative stress, and decreased muscle function. Mutations in Fis1 also affect mitochondrial proteostasis in fly muscle, reducing flight capabilities and lifespan, indicating the significance of Fis1 in fly mitochondrial dynamics.
Article
Biology
Nung-Yu Hsu, Nikhil Pathak, Yun-Ti Chen, Yen-Chao Hsu, Jinn-Moon Yang
Summary: The study developed pharmacophore anchor models of ATAT1 for drug design and investigating binding mechanisms. The models predicted potential ATAT1 inhibitors through virtual screening, providing new insights for future inhibitor discovery and lead optimization.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2021)
Article
Medicine, Research & Experimental
Yong-Chun Luo, Sing-Han Huang, Nikhil Pathak, Yi-Hsuan Chuang, Jinn-Moon Yang
Summary: The study demonstrates that MENS therapy can improve biochemical indexes and affect pathways related to fatty acid metabolism, PPAR signaling, and cell cycle in STZ-induced diabetes. Comparison with anti-diabetic compounds shows that MENS and these compounds have similar effect pathways highly correlated to diabetes processes such as PPAR signaling, bile secretion, and insulin signaling pathways.
Article
Pharmacology & Pharmacy
Wei-Chung Chiou, Hsu-Feng Lu, Nung-Yu Hsu, Tein-Yao Chang, Yuan-Fan Chin, Ping-Cheng Liu, Jir-Mehng Lo, Yeh B. Wu, Jinn-Moon Yang, Cheng Huang
Summary: The study found that the flavonoid ugonin J (UJ) has therapeutic activity against SARS-CoV-2 infection by inhibiting the virus protease and displaying anti-inflammatory properties. UJ shows strong interactions with the active site of the virus protease and has a low cytotoxic effect, making it a promising direct-acting antiviral agent for treating SARS-CoV-2.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Environmental Sciences
Lok-Yee Joyce Li, Shin-Yi Wang, Jinn-Moon Yang, Chih-Jou Chen, Cheng-Yu Tsai, Lucas Yee-Yan Wu, Cheng-Jung Wu
Summary: This research compared in-class face- and smartphone-touching behaviors of medical students before and after health education during the COVID-19 pandemic. The study found that comprehensive health education and reminders effectively reduced the rate of these behaviors.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2021)
Article
Nanoscience & Nanotechnology
Yi-Ju Chen, Yung-An Huang, Chris T. Ho, Jinn-Moon Yang, Jui- Chao, Ming-Chia Li, Eric Hwang
Summary: The study found that using nanodiamond surface topography can accelerate the development of primary neurons from both the central and peripheral nervous systems. It was discovered that miR6236 is the predominant molecule responsible for converting the surface topography into biological responses, and depleting it enhances neuroregeneration, thus raising therapeutic potential for promoting nervous system regeneration.
ACS APPLIED BIO MATERIALS
(2021)
Proceedings Paper
Engineering, Biomedical
Yun-Ti Chen, Cheng-Hsuan Wu, Yi-Cyun Chen, Yen-Chao Hsu, Yu-Wei Huang, Jinn-Moon Yang
2020 IEEE 20TH INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOENGINEERING (BIBE 2020)
(2020)
Proceedings Paper
Engineering, Biomedical
Chu-Yun Lin, Jung-Yu Lee, Sing-Han Huang, Yen-Chao Hsu, Nung-Yu Hsu, Jinn-Moon Yang
2020 IEEE 20TH INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOENGINEERING (BIBE 2020)
(2020)