Article
Multidisciplinary Sciences
Kazi Alamgir Hossain, Humaira Anjume, K. M. Mazharul Alam, Ashabul Yeamin, Salma Akter, M. Anwar Hossain, Munawar Sultana
Summary: This study reveals the first emergence of the SA-2018 lineage of ME-SA topotype of FMDV serotype O in Bangladesh, as well as the predominance of the Ind-2001e sublineage in 2019-2021. A novel sublineage, designated as MYMBD21, was identified under the SA-2018 lineage. Amino acid sequence analysis of the VP1 protein showed significant differences from existing vaccine strains, indicating potential vaccine escape mutations. This calls for further genome-wide analysis and monitoring to implement strategic vaccination and effective FMD control in Bangladesh.
SCIENTIFIC REPORTS
(2023)
Article
Biotechnology & Applied Microbiology
Ernesto Garay, Diego Fontana, Lautaro Leschiutta, Ricardo Kratje, Claudio Prieto
Summary: Chimeric virus-like particles were generated by identifying suitable regions in rabies glycoprotein to expose a major antigenic site of foot-and-mouth disease virus (FMDV), demonstrating a novel heterologous display platform concept. The study successfully identified appropriate insertion sites for heterologous sequences without affecting proper folding of the protein, leading to exposed foreign antigens recognized by antibodies. This work provides a foundation for the development of a heterologous antigen display platform based on rabies VLPs.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Zhixun Zhao, Caiyun Huang, Xueliang Zhu, Zheng Qi, Yimei Cao, Pinghua Li, Huifang Bao, Pu Sun, Xingwen Bai, Yuanfang Fu, Kun Li, Jing Zhang, Xueqing Ma, Jian Wang, Hong Yuan, Dong Li, Zaixin Liu, Qiang Zhang, Zengjun Lu
Summary: In this study, a dual live vector vaccine against Foot-and-mouth disease (FMD) and Peste des petits ruminant disease (PPR) was constructed using the MVA-GFP recombinant virus skeleton. The recombinant virus successfully expressed the target proteins and the empty capsid of FMDV. This study laid the foundation for the successful construction of a live vector vaccine against FMD and PPR.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Virology
Jonathan Arzt, Ian H. Fish, Miranda R. Bertram, George R. Smoliga, Ethan J. Hartwig, Steven J. Pauszek, Lauren Holinka-Patterson, Fayna C. Diaz-San Segundo, Tatjana Sitt, Elizabeth Rieder, Carolina Stenfeldt
Summary: Research showed that cattle can be simultaneously infected with two different serotypes of foot-and-mouth disease virus (FMDV), with different outcomes depending on the timing of exposure to the viruses. Dominant interserotypic recombinant FMDVs were discovered in upper respiratory tract samples of superinfected animals, indicating the potential role of persistently infected FMDV carriers in generating novel viral strains.
JOURNAL OF VIROLOGY
(2021)
Article
Infectious Diseases
Jitendra K. Biswal, Beeragere Parameshwaraiah Sreenivasa, Jajati K. Mohapatra, Saravanan Subramaniam, Veena Jumanal, Suresh H. Basagoudanavar, Valia Valappil Dhanesh, Madhusudan Hosamani, Ramasamy Periyasamy Tamil Selvan, Narayanan Krishnaswamy, Rajeev Ranjan, Bramhadev Pattnaik, Raj Kumar Singh, Bishnu Prasad Mishra, Aniket Sanyal
Summary: Foot-and-mouth disease is a significant threat to animal health worldwide. The current vaccine has limitations in terms of heat susceptibility, requiring cold chain storage. This study successfully generated a more thermostable mutant vaccine strain, which has the potential to replace the existing strain.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Virology
Hu Dong, Yuanlu Lu, Yun Zhang, Suyu Mu, Nan Wang, Ping Du, Xiaoying Zhi, Xiaobo Wen, Xiangxi Wang, Shiqi Sun, Yanming Zhang, Huichen Guo
Summary: This study identified thermostable FMDV mutants by high-temperature screening, with an important alanine-to-threonine mutation at position 13 in the VP1 protein for capsid stability. These mutants showed improved stability and immunogenicity compared to the wild-type virus, potentially aiding in the development of a stable vaccine against FMDV serotype O.
JOURNAL OF VIROLOGY
(2021)
Article
Infectious Diseases
Carolina Stenfeldt, Miranda R. Bertram, Haillie C. Meek, Ethan J. Hartwig, George R. Smoliga, Megan C. Niederwerder, Diego G. Diel, Scott A. Dee, Jonathan Arzt
Summary: The study investigated the infectivity of foot-and-mouth disease virus (FMDV) in commercial pig feed and feed ingredients, determining the minimum infectious dose required for pigs to develop the disease. The results indicated that FMDV can remain infectious in pig feed ingredients for durations compatible with transoceanic transport, with variations in feeding conditions and virus strains affecting the probability of infection. This information can be used to model the risk of FMDV incursions and regulate feed importation to minimize the risk of unintentional importation.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Tingting Ren, Haotai Chen, Xinsheng Liu, Yanxue Wang, Aixia Fan, Linlin Qi, Li Pan, Wenlong Bai, Yongguang Zhang, Yuefeng Sun
Summary: The ID1 protein promotes the degradation of FOXO1, suppresses interferon production, and inhibits HDAC4, ultimately suppressing the replication of FDMV and potentially other viruses.
Article
Immunology
Kay Childs, Yongjie Harvey, Ryan Waters, Timothy Woma, Ginette Wilsden, Hualu Sun, Peng Sun, Julian Seago
Summary: Foot-and-mouth disease is a highly contagious viral disease of livestock that has a severe economic impact on the agriculture industry in many regions. Current vaccines are not effective against the contemporary strains of the disease, particularly in East Africa. Researchers have identified stable strains of the virus and developed a quadrivalent vaccine that generates high neutralizing antibody titers and provides good cross-protection against regional strains.
Article
Microbiology
Shuo Li, Ruichong Zhao, Hetao Song, Songjia Pan, Yun Zhang, Hu Dong, Manyuan Bai, Shiqi Sun, Huichen Guo, Shuanghui Yin
Summary: This study demonstrates that intranasal immunization with FMD calcium phosphate mineralized virus-like particles (CaP-VLPs) can effectively induce local mucosal immune and systemic immune responses, which are specifically enhanced by S adjuvant.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Virology
David J. King, Graham Freimanis, Chris Neil, Andrew Shaw, Tobias J. Tuthill, Emma Laing, Donald P. King, Lidia Lasecka-Dykes
Summary: This study investigates the impact of serum-neutralising antibodies on the evolution of foot-and-mouth disease virus (FMDV) using an in vitro system. The presence of sub-neutralising dilutions of specific antisera delayed the onset of virus-induced cytopathic effect (CPE) and resulted in genetic mutations in the virus. These findings highlight the various ways in which FMDV populations can escape neutralising antibodies and support the use of in vitro approaches to study the evolution of viruses and the immune system's response.
Article
Immunology
Ntungufhadzeni M. Rathogwa, Katherine A. Scott, Pamela Opperman, Jacques Theron, Francois F. Maree
Summary: This study compared the efficacy of two adjuvant formulations combined with a structurally stabilized SAT2 vaccine antigen and found that the Montanide ISA 206B-adjuvanted vaccine elicited a higher SAT2 neutralizing antibody response and three times higher systemic IFN-gamma responses compared to the Quil-A Saponin-adjuvanted vaccine group at 14- and 28-days post-vaccination. Serum antibodies from the immunized animals reacted similarly to both the parental vaccine virus and mutated viruses simulating antigenic drift in nature.
Article
Immunology
Young-Hoon Ahn, W. A. Gayan Chathuranga, Young-Jung Shim, D. K. Haluwana, Eun-Hee Kim, In-Joong Yoon, Yong-Taik Lim, Sung Ho Shin, Hyundong Jo, Seong Yun Hwang, Hyun Mi Kim, Min Ja Lee, Jong-Hyeon Park, Sung-Sik Yoo, Jong-Soo Lee
Summary: Foot-and-mouth disease (FMD) is a contagious disease affecting cloven-hoofed mammals, with high potency vaccines being crucial for disease prevention in endemic regions. The study revealed that the novel water-in-oil emulsion CAvant(R)SOE as a vaccine adjuvant significantly enhanced immune responses in mice and pigs when used with inactivated FMD vaccines, providing effective protection against heterologous FMDV challenge. These results suggest that CAvant(R)SOE-adjuvanted vaccines have great potential for controlling FMD in pigs.
Article
Virology
Chen Li, Jiabao Shi, Haiwei Wang, Efrain E. Rivera-Serrano, Decheng Yang, Guohui Zhou, Chao Sun, Craig E. Cameron, Li Yu
Summary: This study demonstrates the importance of FMDV genetic diversity in viral virulence and transmissibility in susceptible animals. The generation of a high-fidelity FMDV variant with a single amino acid substitution in polymerase highlights the impact of viral population diversity on interhost viral spread. Furthermore, the high genetic diversity of type O FMDV may contribute to its dominance in the global epidemic by increasing both virulence and transmissibility.
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yun-Jung Hwang, Kyung-Kwan Lee, Jong-Won Kim, Kwang-Hyo Chung, Sang-Jick Kim, Wan-Soo Yun, Chang-Soo Lee
Summary: The study introduces an optical and electrochemical dual-modal approach for the specific detection of foot-and-mouth disease virus serotypes O and A, offering high sensitivity and accuracy.
Article
Chemistry, Multidisciplinary
Xiaoli An, Qifeng Bai, Fang Bai, Danfeng Shi, Huanxiang Liu, Xiaojun Yao
FRONTIERS IN CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Xiaoli An, Qifeng Bai, Zhitong Bing, Hongli Liu, Qianqian Zhang, Huanxiang Liu, Xiaojun Yao
ACS CHEMICAL NEUROSCIENCE
(2020)
Article
Biotechnology & Applied Microbiology
Hong Yuan, Pinghua Li, Huifang Bao, Pu Sun, Xingwen Bai, Qifeng Bai, Na Li, Xueqing Ma, Yimei Cao, Yuanfang Fu, Kun Li, Jing Zhang, Dong Li, Yingli Chen, Jie Zhang, Zengjun Lu, Zaixin Liu
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Qifeng Bai, Shuoyan Tan, Horacio Perez-Sanchez, Haixia Feng, Liya Feng, HuanXiang Liu, Xiaojun Yao
FRONTIERS IN CHEMISTRY
(2019)
Article
Biochemical Research Methods
Qifeng Bai, Shuoyan Tan, Tingyang Xu, Huanxiang Liu, Junzhou Huang, Xiaojun Yao
Summary: Deep learning has been successfully applied in medicine and two-dimensional ligand design. MolAICal software combines the merits of deep learning model and classical algorithm to generate 3D drugs in the 3D pocket of protein targets, showing great potential in drug design.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Chemistry, Multidisciplinary
Qifeng Bai, Shuo Liu, Yanan Tian, Tingyang Xu, Antonio Jesus Banegas-Luna, Horacio Perez-Sanchez, Junzhou Huang, Huanxiang Liu, Xiaojun Yao
Summary: De novo drug design involves building novel ligands by assembling atoms or fragments, while molecular dynamics simulation studies the interaction mechanism between ligands and receptors based on molecular force field. Deep learning methods and interpretable machine learning can improve the efficiency and accuracy of drug design and simulations. Further application of deep learning and IML can promote technical development in drug discovery.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Review
Mathematics
Suya Jin, Guiyan Liu, Qifeng Bai
Summary: Deep learning is a field of artificial intelligence that uses neural networks to extract patterns from large datasets. It has seen rapid development in recent years and has been successfully applied in various disciplines. This article provides an overview of deep-learning techniques, their applications in COVID-19 research, and specific examples of their use in diagnosis, prognosis, and treatment management. Deep learning can analyze medical imaging, lab test results, and other data to diagnose diseases, predict disease progression, recommend treatment plans, and assist in drug development and prevention strategies. However, challenges include the lack of diverse data and the need for more interpretable models.
Proceedings Paper
Computer Science, Artificial Intelligence
Aimin Yang, Qifeng Bai, Jigang Wang, Nankai Lin, Xiaotian Lin, Guanqiu Qin, Junheng He
Summary: This paper presents the solution of team BERT 4EVER for the NLPCC 2022 Shared Task 7, which aims to measure social bias in dialogue scenarios. The team constructs a framework based on prompt learning and contrastive learning to achieve fine-grained dialogue social bias measurement. They achieved second place in the final test with an F-macro of 59.02%.
NATURAL LANGUAGE PROCESSING AND CHINESE COMPUTING, NLPCC 2022, PT II
(2022)
Article
Chemistry, Physical
Liya Feng, Horacio Perez-Sanchez, Qifeng Bai
Summary: This study investigates the interaction between Smoothened (SMO) and cholesterol using molecular dynamics simulations and Markov state model analysis. The results suggest that covalently bound cholesterol has better stability and configuration transformation pathways compared to noncovalently bound cholesterol at the residue Asp95 position of SMO.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Review
Biochemistry & Molecular Biology
Sha Zhu, Qifeng Bai, Lanqing Li, Tingyang Xu
Summary: Drug repositioning plays a significant role in drug development and machine learning methods can accelerate this process. This article focuses on the repurposing potential of type 2 diabetes mellitus drugs for various diseases.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Computer Science, Artificial Intelligence
Yuquan Li, Chang-Yu Hsieh, Ruiqiang Lu, Xiaoqing Gong, Xiaorui Wang, Pengyong li, Shuo Liu, Yanan Tian, Dejun Jiang, Jiaxian Yan, Qifeng Bai, Huanxiang Liu, Shengyu Zhang, Xiaojun Yao
Summary: Improving drug discovery efficiency is a long-standing challenge, and graph learning methods have been developed to search potential drug candidates with speed and cost advantages. However, existing methods lack adaptability to new data. In this paper, a flexible method is proposed, which achieves better prediction performance on all tested datasets and provides robustness and interpretability. This method can serve as a reliable tool for predicting molecular interactions and properties in drug discovery.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Biochemistry & Molecular Biology
Xiaoli An, Qifeng Bai, Zhitong Bing, Huanxiang Liu, Xiaojun Yao
Summary: This study elucidates the mechanism of conformational coupling between different sites of the protein, highlighting the crucial role of flexibility in certain regions for agonist binding and action. The results provide important structural information for the design of novel GPR40 agonists.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Qifeng Bai, Jian Ma, Shuo Liu, Tingyang Xu, Antonio Jesus Banegas-Luna, Horacio Perez-Sanchez, Yanan Tian, Junzhou Huang, Huanxiang Liu, Xiaojun Yao
Summary: WADDAICA is a webserver that integrates deep learning models and classical algorithms for drug design, with good scoring power based on the PDBbind database. It provides a user-friendly web interface for drug design jobs submission.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Physical
Jintu Zhang, Qifeng Bai, Horacio Perez-Sanchez, Shuxia Shang, Xiaoli An, Xiaojun Yao
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2019)