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Chen X, Hu C, Shu Z, Wang X, Zhao Y, Song W, Chen X, Jin M, Xiu Y, Guo X, Kong X, Jiang Y, Guan J, Gongga L, Wang L, Wang B. Isovanillic acid protects mice against Staphylococcus aureus by targeting vWbp and Coa. Future Microbiol 2023; 18:735-749. [PMID: 37526178 DOI: 10.2217/fmb-2022-0219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023] Open
Abstract
Aim: Our primary objective was to investigate the protective effects and mechanisms of isovanillic acid in mice infected with Staphylococcus aureus Newman. Methods: In vitro coagulation assays were used to validate vWbp and Coa as inhibitory targets of isovanillic acid. The binding mechanism of isovanillic acid to vWbp and Coa was investigated using molecular docking and point mutagenesis. Importantly, a lethal pneumonia mouse model was used to assess the effect of isovanillic acid on survival and pathological injury in mice. Results & Conclusion: Isovanillic acid reduced the virulence of S. aureus by directly binding to inhibit the clotting activity of vWbp and Coa, thereby reducing lung histopathological damage and improving the survival rate in mice with pneumonia.
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Affiliation(s)
- Xiangqian Chen
- Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Chunjie Hu
- Changchun University of Chinese Medicine, Changchun, 130117, China
- Proctology Department, Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Zunhua Shu
- Changchun University of Chinese Medicine, Changchun, 130117, China
- The Third Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, 130118, China
| | - Xingye Wang
- Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Yicheng Zhao
- Changchun University of Chinese Medicine, Changchun, 130117, China
- Center for Pathogen Biology & Infectious Diseases, Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun,130021, China
| | - Wu Song
- Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Xiaoyu Chen
- Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Mengli Jin
- Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Yang Xiu
- Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Xuerui Guo
- School of Pharmacy, Jilin University, Changchun, 130021, China
| | - Xiangri Kong
- Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Yijing Jiang
- Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Jiyu Guan
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Lanzi Gongga
- Tibet University Medical College, Tibet, 850000, China
| | - Li Wang
- Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Bingmei Wang
- Changchun University of Chinese Medicine, Changchun, 130117, China
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Kalpana S, Lin WY, Wang YC, Fu Y, Lakshmi A, Wang HY. Antibiotic Resistance Diagnosis in ESKAPE Pathogens-A Review on Proteomic Perspective. Diagnostics (Basel) 2023; 13:1014. [PMID: 36980322 PMCID: PMC10047325 DOI: 10.3390/diagnostics13061014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Antibiotic resistance has emerged as an imminent pandemic. Rapid diagnostic assays distinguish bacterial infections from other diseases and aid antimicrobial stewardship, therapy optimization, and epidemiological surveillance. Traditional methods typically have longer turn-around times for definitive results. On the other hand, proteomic studies have progressed constantly and improved both in qualitative and quantitative analysis. With a wide range of data sets made available in the public domain, the ability to interpret the data has considerably reduced the error rates. This review gives an insight on state-of-the-art proteomic techniques in diagnosing antibiotic resistance in ESKAPE pathogens with a future outlook for evading the "imminent pandemic".
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
| | | | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA
| | - Amrutha Lakshmi
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, India
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
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Xia J, Liu J, Xu F, Zhou H. Proteomic profiling of lysine acetylation and succinylation in Staphylococcus aureus. Clin Transl Med 2022; 12:e1058. [PMID: 36177763 PMCID: PMC9523452 DOI: 10.1002/ctm2.1058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 01/28/2023] Open
Affiliation(s)
- Jingyan Xia
- Department of Oncology RadiationSecond Affiliated Hospital, Zhejiang University School of MedicineHangzhouChina
| | - Jinliang Liu
- Department of Infectious DiseasesSecond Affiliated Hospital, Zhejiang University School of MedicineHangzhouChina
| | - Feng Xu
- Department of Infectious DiseasesSecond Affiliated Hospital, Zhejiang University School of MedicineHangzhouChina,Research Center for Life Science and Human HealthBinjiang Institute of Zhejiang UniversityHangzhouChina
| | - Hui Zhou
- Department of Infectious DiseasesSecond Affiliated Hospital, Zhejiang University School of MedicineHangzhouChina
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Wang B, Wang Y, Chen Y, Gao M, Ren J, Guo Y, Situ C, Qi Y, Zhu H, Li Y, Guo X. DeepSCP: utilizing deep learning to boost single-cell proteome coverage. Brief Bioinform 2022; 23:6598882. [DOI: 10.1093/bib/bbac214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/20/2022] [Accepted: 05/06/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Multiplexed single-cell proteomes (SCPs) quantification by mass spectrometry greatly improves the SCP coverage. However, it still suffers from a low number of protein identifications and there is much room to boost proteins identification by computational methods. In this study, we present a novel framework DeepSCP, utilizing deep learning to boost SCP coverage. DeepSCP constructs a series of features of peptide-spectrum matches (PSMs) by predicting the retention time based on the multiple SCP sample sets and fragment ion intensities based on deep learning, and predicts PSM labels with an optimized-ensemble learning model. Evaluation of DeepSCP on public and in-house SCP datasets showed superior performances compared with other state-of-the-art methods. DeepSCP identified more confident peptides and proteins by controlling q-value at 0.01 using target–decoy competition method. As a convenient and low-cost computing framework, DeepSCP will help boost single-cell proteome identification and facilitate the future development and application of single-cell proteomics.
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Affiliation(s)
- Bing Wang
- School of Medicine , Southeast University, Nanjing 210009 , China
- Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166 , China
| | - Yue Wang
- Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166 , China
| | - Yu Chen
- Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166 , China
| | - Mengmeng Gao
- Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166 , China
| | - Jie Ren
- Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166 , China
| | - Yueshuai Guo
- Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166 , China
| | - Chenghao Situ
- Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166 , China
| | - Yaling Qi
- Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166 , China
| | - Hui Zhu
- Department of Clinical Laboratory , Sir Run Run Hospital, Nanjing Medical University, Nanjing 211166 , China
| | - Yan Li
- School of Medicine , Southeast University, Nanjing 210009 , China
- Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166 , China
| | - Xuejiang Guo
- Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166 , China
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