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Suo A, Wu C, Fan G, Li T, Wu F, Cong K. Optimization of fermentation conditions and quality evaluation of Chaenomeles sinensis glutinous rice wine. J Food Sci Technol 2024; 61:1138-1147. [PMID: 38562590 PMCID: PMC10981636 DOI: 10.1007/s13197-024-05934-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 10/19/2022] [Accepted: 01/09/2024] [Indexed: 04/04/2024]
Abstract
The present study was conducted to optimize fermentation conditions for preparation of Chaenomeles sinensis Glutinous Rice Wine (CRW). The dynamic changes of main substances in the liquor during fermentation process, aroma components, biologically active substances and antioxidant capacity in the CRW after 6 months of aging were tested. The results showed that under optimized conditions, the yield and alcohol content of wine was 44.97 and 20.00%, respectively. After aging, 64 aroma components were detected in the wine, mainly alcohols and esters. The alcohol content of the CRW was 14.8%. Polyphenols and flavonoids reached 0.23 g/L and 0.037 g/L respectively. Furthermore, the CRW had an excellent free radical scavenging ability. Supplementary Information The online version contains supplementary material available at 10.1007/s13197-024-05934-0.
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Affiliation(s)
- Andi Suo
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Caie Wu
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Gongjian Fan
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Tingting Li
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
- Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Fangfang Wu
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Kaiping Cong
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
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Li J, Zhang J, Li K, Cao J, Li H. A multimodal framework based on deep belief network for human locomotion intent prediction. Biomed Eng Lett 2024; 14:559-569. [PMID: 38645596 PMCID: PMC11026357 DOI: 10.1007/s13534-024-00351-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/06/2023] [Accepted: 12/30/2023] [Indexed: 04/23/2024] Open
Abstract
Accurate prediction of human locomotion intent benefits the seamless switching of lower limb exoskeleton controllers in different terrains to assist humans in walking safely. In this paper, a deep belief network (DBN) was developed to construct a multimodal framework for recognizing various locomotion modes and predicting transition tasks. Three fusion strategies (data level, feature level, and decision level) were explored, and optimal network performance was obtained. This method could be tested on public datasets. For the continuous performance of steady state, the best prediction accuracy achieved was 97.64% in user-dependent testing and 96.80% in user-independent testing. During the transition state, the system accurately predicted all transitions (user-dependent: 96.37%, user-independent: 95.01%). The multimodal framework based on DBN can accurately predict the human locomotion intent. The experimental results demonstrate the potential of the proposed model in the volition control of the lower limb exoskeleton.
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Affiliation(s)
- Jiayi Li
- School of Mechanical Engineering, Hebei University of Technology, Tianjin, 300401 China
| | - Jianhua Zhang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Kexiang Li
- School of Mechanical and Materials Engineering, North China University of Technology, Beijing, 100144 China
| | - Jian Cao
- School of Mechanical Engineering, Hebei University of Technology, Tianjin, 300401 China
| | - Hui Li
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083 China
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Li Y, Chen Z, Liu Y, Liu Z, Wu T, Zhang Y, Peng L, Huang X, Huang S, Lin X, Xie X, Jiang L. Ultra-low frequency magnetic energy focusing for highly effective wireless powering of deep-tissue implantable electronic devices. Natl Sci Rev 2024; 11:nwae062. [PMID: 38628571 PMCID: PMC11020258 DOI: 10.1093/nsr/nwae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/03/2024] [Accepted: 02/19/2024] [Indexed: 04/19/2024] Open
Abstract
The limited lifespan of batteries is a challenge in the application of implantable electronic devices. Existing wireless power technologies such as ultrasound, near-infrared light and magnetic fields cannot charge devices implanted in deep tissues, resulting in energy attenuation through tissues and thermal generation. Herein, an ultra-low frequency magnetic energy focusing (ULFMEF) methodology was developed for the highly effective wireless powering of deep-tissue implantable devices. A portable transmitter was used to output the low-frequency magnetic field (<50 Hz), which remotely drives the synchronous rotation of a magnetic core integrated within the pellet-like implantable device, generating an internal rotating magnetic field to induce wireless electricity on the coupled coils of the device. The ULFMEF can achieve energy transfer across thick tissues (up to 20 cm) with excellent transferred power (4-15 mW) and non-heat effects in tissues, which is remarkably superior to existing wireless powering technologies. The ULFMEF is demonstrated to wirelessly power implantable micro-LED devices for optogenetic neuromodulation, and wirelessly charged an implantable battery for programmable electrical stimulation on the sciatic nerve. It also bypassed thick and tough protective shells to power the implanted devices. The ULFMEF thus offers a highly advanced methodology for the generation of wireless powered biodevices.
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Affiliation(s)
- Yuanyuan Li
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Zhipeng Chen
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
- School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Yuxin Liu
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Zijian Liu
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Tong Wu
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Yuanxi Zhang
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Lelun Peng
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Xinshuo Huang
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Shuang Huang
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xudong Lin
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Xi Xie
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Lelun Jiang
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
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Wang B, Su Y, Ma C, Xu L, Mao Q, Cheng W, Lu Q, Zhang Y, Wang R, Lu Y, He J, Chen S, Chen L, Li T, Gao L. Impact of perioperative low-molecular-weight heparin therapy on clinical events of elderly patients with prior coronary stents implanted > 12 months undergoing non-cardiac surgery: a randomized, placebo-controlled trial. BMC Med 2024; 22:171. [PMID: 38649992 PMCID: PMC11036782 DOI: 10.1186/s12916-024-03391-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Little is known about the safety and efficacy of discontinuing antiplatelet therapy via LMWH bridging therapy in elderly patients with coronary stents implanted for > 12 months undergoing non-cardiac surgery. This randomized trial was designed to compare the clinical benefits and risks of antiplatelet drug discontinuation via LMWH bridging therapy. METHODS Patients were randomized 1:1 to receive subcutaneous injections of either dalteparin sodium or placebo. The primary efficacy endpoint was cardiac or cerebrovascular events. The primary safety endpoint was major bleeding. RESULTS Among 2476 randomized patients, the variables (sex, age, body mass index, comorbidities, medications, and procedural characteristics) and percutaneous coronary intervention information were not significantly different between the bridging and non-bridging groups. During the follow-up period, the rate of the combined endpoint in the bridging group was significantly lower than in the non-bridging group (5.79% vs. 8.42%, p = 0.012). The incidence of myocardial injury in the bridging group was significantly lower than in the non-bridging group (3.14% vs. 5.19%, p = 0.011). Deep vein thrombosis occurred more frequently in the non-bridging group (1.21% vs. 0.4%, p = 0.024), and there was a trend toward a higher rate of pulmonary embolism (0.32% vs. 0.08%, p = 0.177). There was no significant difference between the groups in the rates of acute myocardial infarction (0.81% vs. 1.38%), cardiac death (0.24% vs. 0.41%), stroke (0.16% vs. 0.24%), or major bleeding (1.22% vs. 1.45%). Multivariable analysis showed that LMWH bridging, creatinine clearance < 30 mL/min, preoperative hemoglobin < 10 g/dL, and diabetes mellitus were independent predictors of ischemic events. LMWH bridging and a preoperative platelet count of < 70 × 109/L were independent predictors of minor bleeding events. CONCLUSIONS This study showed the safety and efficacy of perioperative LMWH bridging therapy in elderly patients with coronary stents implanted > 12 months undergoing non-cardiac surgery. An alternative approach might be the use of bridging therapy with half-dose LMWH. TRIAL REGISTRATION ISRCTN65203415.
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Affiliation(s)
- Bin Wang
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yanhui Su
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China
| | - Cong Ma
- Health Management Institute, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Lining Xu
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qunxia Mao
- National Research Institute for Family Planning, Beijing, China
| | - Wenjia Cheng
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qingming Lu
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China
| | - Ying Zhang
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China
| | - Rong Wang
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yan Lu
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jing He
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China
| | - Shihao Chen
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lei Chen
- Department of Thoracic Surgery of The First Medical Center, General Hospital of Chinese People's Liberation Army, Beijing, 100853, China.
| | - Tianzhi Li
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Linggen Gao
- Department of Comprehensive Surgery, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China.
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Liu L, Wang Z, Fang Y, Yang R, Pu Y, Meng X, Liu W. Small GTPase Rab7 is involved in stress adaptation to carbon starvation to ensure the induced cellulase biosynthesis in Trichoderma reesei. Biotechnol Biofuels Bioprod 2024; 17:55. [PMID: 38643207 PMCID: PMC11032611 DOI: 10.1186/s13068-024-02504-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND The saprophytic filamentous fungus Trichoderma reesei represents one of the most prolific cellulase producers. The bulk production of lignocellulolytic enzymes by T. reesei not only relies on the efficient transcription of cellulase genes but also their efficient secretion after being translated. However, little attention has been paid to the functional roles of the involved secretory pathway in the high-level production of cellulases in T. reesei. Rab GTPases are key regulators in coordinating various vesicle trafficking associated with the eukaryotic secretory pathway. Specifically, Rab7 is a representative GTPase regulating the transition of the early endosome to the late endosome followed by its fusion to the vacuole as well as homotypic vacuole fusion. Although crosstalk between the endosomal/vacuolar pathway and the secretion pathway has been reported, the functional role of Rab7 in cellulase production in T. reesei remains unknown. RESULTS A TrRab7 was identified and characterized in T. reesei. TrRab7 was shown to play important roles in T. reesei vegetative growth and vacuole morphology. Whereas knock-down of Trrab7 significantly compromised the induced production of T. reesei cellulases, overexpression of the key transcriptional activator, Xyr1, restored the production of cellulases in the Trrab7 knock-down strain (Ptcu-rab7KD) on glucose, indicating that the observed defective cellulase biosynthesis results from the compromised cellulase gene transcription. Down-regulation of Trrab7 was also found to make T. reesei more sensitive to various stresses including carbon starvation. Interestingly, overexpression of Snf1, a serine/threonine protein kinase known as an energetic sensor, partially restored the cellulase production of Ptcu-rab7KD on Avicel, implicating that TrRab7 is involved in an energetic adaptation to carbon starvation which contributes to the successful cellulase gene expression when T. reesei is transferred from glucose to cellulose. CONCLUSIONS TrRab7 was shown to play important roles in T. reesei development and a stress response to carbon starvation resulting from nutrient shift. This adaptation may allow T. reesei to successfully initiate the inducing process leading to efficient cellulase production. The present study provides useful insights into the functional involvement of the endosomal/vacuolar pathway in T. reesei development and hydrolytic enzyme production.
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Affiliation(s)
- Lin Liu
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Zhixing Wang
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Yu Fang
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Renfei Yang
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Yi Pu
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China.
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbiology Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao, 266237, People's Republic of China.
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Yang PT, Tang L, Yang SQ, Shi QL, Wang YQ, Qin YX, Wang JG, Li Y. Remnant cholesterol trajectory and subclinical arteriosclerosis: a 10-year longitudinal study of Chinese adults. Sci Rep 2024; 14:9037. [PMID: 38641617 PMCID: PMC11031569 DOI: 10.1038/s41598-024-59173-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/08/2024] [Indexed: 04/21/2024] Open
Abstract
We aimed to identify different trajectories of remnant cholesterol (RC) and investigate the association of RC trajectories with vascular endothelial function and atherosclerosis progression in a longitudinal cohort of the Chinese population. A total of 521 participants were included in the flow-mediated vasodilation (FMD) subcohort study, and 7775 participants were included in the brachial-ankle pulse wave velocity (baPWV) subcohort study. All participants had ≥ 3 medical examinations during the 10-year follow-up period. In the FMD subcohort study, three distinct RC trajectories were identified according to the RC range and changing pattern over time: "low" (57.58%), "moderate" (30.90%) and "high" (11.52%). The proportion of the three groups with vascular endothelial dysfunction (FMD < 7.0%) was 20.00%, 39.75% and 60.00% respectively. Taking the low group as a reference, participants in the moderate and high groups had over 1.88 and 2.94 times the odds of vascular endothelial dysfunction (P = 0.048). In the baPWV subcohort study, three distinct RC trajectories were also identified: "low" (54.29%), "moderate" (38.97%) and "high" (6.74%). The proportion of the three groups with atherosclerosis (baPWV > 1400 cm/s) was 38.79%, 51.26% and 59.01% respectively. Taking the low group as a reference, participants in the moderate and high groups had over 1.46 and 2.16 times the odds of atherosclerosis (P < 0.001). The findings indicated that distinct RC trajectories are significantly associated with vascular endothelial function and atherosclerosis. Regular monitoring to identify persistent increases in RC may be more helpful in identifying individuals with a high risk of cardiovascular disease.
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Affiliation(s)
- Ping-Ting Yang
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
| | - Li Tang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
| | - Sai-Qi Yang
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
| | - Qiu-Ling Shi
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
| | - Ya-Qin Wang
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yue-Xiang Qin
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jian-Gang Wang
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Ying Li
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Hu C, Xia Y, Zeng D, Ye M, Mei T. Effect of resistance circuit training on comprehensive health indicators in older adults: a systematic review and meta-analysis. Sci Rep 2024; 14:8823. [PMID: 38627495 PMCID: PMC11021536 DOI: 10.1038/s41598-024-59386-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
The aging process leads to the degeneration of body structure and function. The objective of this study is to conduct a systematic review and meta-analysis of the effects of resistance circuit training (RCT) on comprehensive health indicators of older adults. PubMed, Embase, and Web of Science were searched until August 2023. Primary outcomes were body composition, muscle strength, cardiorespiratory endurance, blood pressure, and functional autonomy. Muscle function and exercise intensity subgroups were analyzed. RCT reduces body fat (MD = - 5.39 kg, 95% CI - 10.48 to - 0.29), BMI (MD = - 1.22, 95% CI - 2.17 to - 0.26), and body weight (MD = - 1.28 kg, 95% CI - 1.78 to - 0.78), and increases lean body mass (MD = 1.42 kg, 95% CI 0.83-2.01) in older adults. It improves upper limb strength (SMD = 2.09, 95% CI 1.7-2.48), lower limb strength (SMD = 2.03, 95% CI 1.56-2.51), cardiorespiratory endurance (MD = 94 m, 95% CI 25.69-162.67), and functional autonomy (MD = - 1.35, 95% CI - 1.73 to - 0.96). High-intensity RCT benefits BMI and body weight, while low-intensity exercise reduces blood pressure. RCT improves muscle function in push, pull, hip, and knee movements in older adults. RCT improves body composition, muscle strength, cardiorespiratory endurance, blood pressure, and functional autonomy in older adults. High-intensity training is superior for body composition, while moderate to low intensity training is more effective for lowering blood pressure.
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Affiliation(s)
- Chenxi Hu
- Institute of Artificial Intelligence in Sports, Capital University of Physical Education and Sports, Beijing, 100191, China
- Department of Chinese Academy of Sport and Health, Beijing Sport University, Beijing, 100084, China
| | - Yunpeng Xia
- Department of Chinese Academy of Sport and Health, Beijing Sport University, Beijing, 100084, China
| | - Dongye Zeng
- School of Sports Medicine and Rehabilitation, Beijing Sport University, Beijing, 100084, China
| | - Mingyi Ye
- Department of Chinese Academy of Sport and Health, Beijing Sport University, Beijing, 100084, China
| | - Tao Mei
- Department of Chinese Academy of Sport and Health, Beijing Sport University, Beijing, 100084, China.
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Rui J, Li K, Wei H, Guo X, Zhao Z, Wang Y, Song W, Abudunaibi B, Chen T. MODELS: a six-step framework for developing an infectious disease model. Infect Dis Poverty 2024; 13:30. [PMID: 38632643 PMCID: PMC11022334 DOI: 10.1186/s40249-024-01195-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024] Open
Abstract
Since the COVID-19 pandemic began, a plethora of modeling studies related to COVID-19 have been released. While some models stand out due to their innovative approaches, others are flawed in their methodology. To assist novices, frontline healthcare workers, and public health policymakers in navigating the complex landscape of these models, we introduced a structured framework named MODELS. This framework is designed to detail the essential steps and considerations for creating a dependable epidemic model, offering direction to researchers engaged in epidemic modeling endeavors.
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Affiliation(s)
- Jia Rui
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen city, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen City, China
| | - Kangguo Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen city, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen City, China
| | - Hongjie Wei
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen city, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen City, China
| | - Xiaohao Guo
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen city, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen City, China
| | - Zeyu Zhao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen city, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen City, China
| | - Yao Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen city, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen City, China
| | - Wentao Song
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen city, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen City, China
| | - Buasiyamu Abudunaibi
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen city, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen City, China
| | - Tianmu Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen city, China.
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen City, China.
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Luo S, Xu R, Xie P, Liu X, Ling C, Liu Y, Zhang X, Xia Z, Chen Z, Tang J. EGFR of platelet regulates macrophage activation and bacterial phagocytosis function. J Inflamm (Lond) 2024; 21:10. [PMID: 38632608 PMCID: PMC11022435 DOI: 10.1186/s12950-024-00382-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Beyond their crucial role in hemostasis, platelets possess the ability to regulate inflammation and combat infections through various mechanisms. Stringent control of macrophage activation is essential during innate immune responses in sepsis. Macrophages are considered crucial phagocytic cells that aid in the elimination of pathogens. Platelet interactions with monocytes-macrophages are known to be significant in the response against bacterial infections, but the primary mediator driving these interactions remains unclear. EGFR plays critical role in the regulation of inflammation and infection through various mechanisms. RESULTS The overexpression of platelets by thrombopoietin (TPO) leads to the sequestration of both pro-inflammatory (IL-6/IL-1) and anti-inflammatory (IL-10) cytokines in the organ tissue of septic mice. Epidermal growth factor receptor (EGFR) is critical for platelet activation in sepsis. EGFR-licensed platelets enhance macrophage immune function, including the production of reactive oxygen species (ROS) and the clearance of bacteria. Platelet EGFR also induces M1 macrophage polarization by increasing the expression of inducible nitric oxide synthase (iNOS) and CD64. CONCLUSION EGFR can activate platelet immune function. Moreover, activated platelets efficiently regulate bacterial phagocytosis and pro-inflammatory function of macrophages through an EGFR-dependent pathway.
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Affiliation(s)
- Shuhua Luo
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, 524000, Zhanjiang, Guangdong, China
- Guang Dong Medical University, 524000, Zhanjiang, Guangdong, China
| | - Riping Xu
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, 524000, Zhanjiang, Guangdong, China
| | - Pengyun Xie
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, 524000, Zhanjiang, Guangdong, China
| | - Xiaolei Liu
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, 524000, Zhanjiang, Guangdong, China
- Guang Dong Medical University, 524000, Zhanjiang, Guangdong, China
| | - Chunxiu Ling
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, 524000, Zhanjiang, Guangdong, China
- Guang Dong Medical University, 524000, Zhanjiang, Guangdong, China
| | - Yusha Liu
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, 524000, Zhanjiang, Guangdong, China
- Guang Dong Medical University, 524000, Zhanjiang, Guangdong, China
| | - Xuedi Zhang
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, 524000, Zhanjiang, Guangdong, China
- Guang Dong Medical University, 524000, Zhanjiang, Guangdong, China
| | - Zhengyuan Xia
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, 524000, Zhanjiang, Guangdong, China
| | - Zhanghui Chen
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, 524000, Zhanjiang, Guangdong, China.
| | - Jing Tang
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, 524000, Zhanjiang, Guangdong, China.
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10
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Song N, Mei S, Wang X, Hu G, Lu M. Focusing on mitochondria in the brain: from biology to therapeutics. Transl Neurodegener 2024; 13:23. [PMID: 38632601 PMCID: PMC11022390 DOI: 10.1186/s40035-024-00409-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Mitochondria have multiple functions such as supplying energy, regulating the redox status, and producing proteins encoded by an independent genome. They are closely related to the physiology and pathology of many organs and tissues, among which the brain is particularly prominent. The brain demands 20% of the resting metabolic rate and holds highly active mitochondrial activities. Considerable research shows that mitochondria are closely related to brain function, while mitochondrial defects induce or exacerbate pathology in the brain. In this review, we provide comprehensive research advances of mitochondrial biology involved in brain functions, as well as the mitochondria-dependent cellular events in brain physiology and pathology. Furthermore, various perspectives are explored to better identify the mitochondrial roles in neurological diseases and the neurophenotypes of mitochondrial diseases. Finally, mitochondrial therapies are discussed. Mitochondrial-targeting therapeutics are showing great potentials in the treatment of brain diseases.
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Affiliation(s)
- Nanshan Song
- Department of Pharmacology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shuyuan Mei
- The First Clinical Medical College, Nanjing Medical University, Nanjing, 211166, China
| | - Xiangxu Wang
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Neuroprotective Drug Discovery Key Laboratory, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Gang Hu
- Department of Pharmacology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Neuroprotective Drug Discovery Key Laboratory, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China.
| | - Ming Lu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Neuroprotective Drug Discovery Key Laboratory, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China.
- Changzhou Second People's Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, 213000, China.
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11
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Mao JY, Li DK, Zhang D, Yang QW, Long Y, Cui N. Utility of paired plasma and drainage fluid mNGS in diagnosing acute intra-abdominal infections with sepsis. BMC Infect Dis 2024; 24:409. [PMID: 38632536 PMCID: PMC11022345 DOI: 10.1186/s12879-024-09320-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) has been increasingly applied in sepsis. We aimed to evaluate the diagnostic and therapeutic utility of mNGS of paired plasma and peritoneal drainage (PD) fluid samples in comparison to culture-based microbiological tests (CMTs) among critically ill patients with suspected acute intra-abdominal infections (IAIs). METHODS We conducted a prospective study from October 2021 to December 2022 enrolling septic patients with suspected IAIs (n = 111). Pairwise CMTs and mNGS of plasma and PD fluid were sent for pathogen detection. The mNGS group underwent therapeutic regimen adjustment based on mNGS results for better treatment. The microbial community structure, clinical features, antibiotic use and prognoses of the patients were analyzed. RESULTS Higher positivity rates were observed with mNGS versus CMTs for both PD fluid (90.0% vs. 48.3%, p < 0.005) and plasma (76.7% vs. 1.6%, p < 0.005). 90% of enrolled patients had clues of suspected pathogens combining mNGS and CMT methods. Gram-negative pathogens consist of most intra-abdominal pathogens, including a great variety of anaerobes represented by Bacteroides and Clostridium. Patients with matched plasma- and PD-mNGS results had higher mortality and sepsis severity. Reduced usage of carbapenem (30.0% vs. 49.4%, p < 0.05) and duration of anti-MRSA treatment (5.1 ± 3.3 vs. 7.0 ± 8.4 days, p < 0.05) was shown in the mNGS group in our study. CONCLUSIONS Pairwise plasma and PD fluid mNGS improves microbiological diagnosis compared to CMTs for acute IAI. Combining plasma and PD mNGS could predict poor prognosis. mNGS may enable optimize empirical antibiotic use.
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Affiliation(s)
- Jia-Yu Mao
- Department of Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 100730, Beijing, China
| | - Dong-Kai Li
- Department of Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 100730, Beijing, China
| | - Dong Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Qi-Wen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yun Long
- Department of Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 100730, Beijing, China.
| | - Na Cui
- Department of Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 100730, Beijing, China.
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12
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Xu Q, Lei S, Zhu Y, Liu Z, Zhang Z, Wang D, Ma K, Liu X. Investigating the influence of excavating a tunnel undercrossing an existing tunnel at zero distance. PLoS One 2024; 19:e0301428. [PMID: 38625862 PMCID: PMC11020911 DOI: 10.1371/journal.pone.0301428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/15/2024] [Indexed: 04/18/2024] Open
Abstract
In urban areas with limited underground space, the new tunnel construction introduces additional loads and displacements to existing tunnels, raising serious safety concerns. These concerns become particularly pronounced in the case of closely undercrossing excavation at zero-distance. The conventional elastic foundation beam model, which assumes constant reaction coefficients for the subgrade, fails to account for foundation loss. In this study, the existing tunnel is modeled as an Euler-Bernoulli beam supported by the Pasternak elastic foundation, and the foundation loss caused by zero-distance undercrossing excavations is considered. Furthermore, an analytical solution is proposed to evaluate the mechanical response in segments, by establishing governing differential equations and boundary conditions for the excavation and neutral zones, and underpinning loads are also considered. The analytical solution is validated in two case studies. Finally, a parametric analysis is performed to explore the influence of various parameters on the mechanical response of the existing tunnel.
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Affiliation(s)
- Qiang Xu
- School of Civil Engineering, Shijiazhuang Tiedao University, Shijiazhuang, China
- State Key Laboratory of Mechanical Behavior and System Safety of Traffic Engineering Structures, Shijiazhuang Tiedao University, Shijiazhuang, China
| | - Shengxiang Lei
- School of Civil Engineering, Shijiazhuang Tiedao University, Shijiazhuang, China
- China Railway Construction Corporation Limited, Beijing, China
| | - Yongquan Zhu
- China Railway Construction Corporation Limited, Beijing, China
| | - Zhichun Liu
- School of Civil Engineering, Shijiazhuang Tiedao University, Shijiazhuang, China
| | - Zhenbo Zhang
- School of Civil Engineering, Shijiazhuang Tiedao University, Shijiazhuang, China
| | - Dapeng Wang
- School of Civil Engineering, Shijiazhuang Tiedao University, Shijiazhuang, China
| | - Kaimeng Ma
- School of Civil Engineering, Shijiazhuang Tiedao University, Shijiazhuang, China
| | - Xiaodong Liu
- Shandong Hi-Speed Construction Management Group Co., Ltd., Jinan, China
- Shandong Hi-Speed Group Co., Ltd., Jinan, China
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13
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Li P, Cai M, Miao S, Li Y, Sun L, Wang J, Gorjian M. Comparison and evaluation of overcoring and hydraulic fracturing stress measurements. Sci Rep 2024; 14:8771. [PMID: 38627533 PMCID: PMC11021550 DOI: 10.1038/s41598-024-59550-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
The stress measurements determined by both the overcoring (OC) and hydraulic fracturing (HF) methods in the Shuichang iron mine and Sanshandao gold mine were compared and evaluated, respectively. The results indicate that the independent OC and HF data in the two mines reveal the same dominant faulting stress regime. The σH orientations derived from the OC and HF methods in the Shuichang iron mine are dominantly oriented in the N81.1°W-N89.4°W and N77.0°E-N88.0°E, respectively, and the σH orientations yielded from the OC and HF techniques in the Sanshandao gold mine are predominantly in the N30°W-N90°W and N55.5°W-N60.4°W, respectively; hence, the σH orientations obtained by the two different methods in the two mines are comparatively similar. In addition, the shapes of the probability density diagrams using an improved Bayesian regression approach of the three principal stresses measured by the OC and HF methods in the same mine are quite similar, and all the obtained Kolmogorov-Smirnov test p-values are larger than the selected significance level of 0.01, indicating that the stress data interpreted by the two methods approximately follow the same distribution law. Thus, the performance of the two techniques and the reliability of the measured data are satisfactory.
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Affiliation(s)
- Peng Li
- Key Laboratory of Ministry of Education for Efficient Mining and Safety of Metal Mines, University of Science and Technology Beijing, No.30 Xueyuan Road, Haidian District, Beijing, 100083, China.
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Xuzhou, 221116, China.
| | - Meifeng Cai
- Key Laboratory of Ministry of Education for Efficient Mining and Safety of Metal Mines, University of Science and Technology Beijing, No.30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Shengjun Miao
- Key Laboratory of Ministry of Education for Efficient Mining and Safety of Metal Mines, University of Science and Technology Beijing, No.30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Yuan Li
- Key Laboratory of Ministry of Education for Efficient Mining and Safety of Metal Mines, University of Science and Technology Beijing, No.30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Liang Sun
- Key Laboratory of Intelligent Bionic Unmanned Systems of Ministry of Education, University of Science and Technology Beijing, No.30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Jiangtao Wang
- Key Laboratory of Intelligent Bionic Unmanned Systems of Ministry of Education, University of Science and Technology Beijing, No.30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Mostafa Gorjian
- .Geological Engineering, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
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14
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Liu H, Wang S, Chen M, Ji H, Zhang D. Effects of Lactobacillus-fermented low-protein diets on the growth performance, nitrogen excretion, fecal microbiota and metabolomic profiles of finishing pigs. Sci Rep 2024; 14:8612. [PMID: 38616198 PMCID: PMC11016537 DOI: 10.1038/s41598-024-58832-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/03/2024] [Indexed: 04/16/2024] Open
Abstract
This study investigated the effects of Lactobacillus-fermented low-protein diet on the growth performance, nitrogen balance, fecal microbiota, and metabolomic profiles of finishing pigs. A total of 90 finishing pigs were assigned to one of three dietary treatments including a normal protein diet (CON) as well as two experimental diets in which a low-protein diet supplemented with 0 (LP) or 1% Lactobacillus-fermented low-protein feed (FLP). In comparison with CON, the LP and FLP significantly increased average daily gain (P = 0.044), significantly decreased feed to gain ratio (P = 0.021), fecal nitrogen (P < 0.01), urine nitrogen (P < 0.01), and total nitrogen (P < 0.01), respectively. The LP group exhibited increased abundances of unclassified_f_Selenomonadaceae, Coprococcus, Faecalibacterium, and Butyricicoccus, while the abundances of Verrucomicrobiae, Verrucomicrobiales, Akkermansiaceae, and Akkermansia were enriched in the FLP group. Low-protein diet-induced metabolic changes were enriched in sesquiterpenoid and triterpenoid biosynthesis and Lactobacillus-fermented low-protein feed-induced metabolic changes were enriched in phenylpropanoid biosynthesis and arginine biosynthesis. Overall, low-protein diet and Lactobacillus-fermented low-protein diet improved the growth performance and reduce nitrogen excretion, possibly via altering the fecal microbiota and metabolites in the finishing pigs. The present study provides novel ideas regarding the application of the low-protein diet and Lactobacillus-fermented low-protein diet in swine production.
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Affiliation(s)
- Hui Liu
- Institute of Animal Science and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Sixin Wang
- Institute of Animal Science and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Meixia Chen
- Institute of Animal Science and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Haifeng Ji
- Institute of Animal Science and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Dongyan Zhang
- Institute of Animal Science and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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15
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Qiu S, Liu J, Chen J, Li Y, Bu T, Li Z, Zhang L, Sun W, Zhou T, Hu W, Yang G, Yuan L, Duan Y, Xing C. Targeted delivery of MerTK protein via cell membrane engineered nanoparticle enhances efferocytosis and attenuates atherosclerosis in diabetic ApoE -/- Mice. J Nanobiotechnology 2024; 22:178. [PMID: 38614985 PMCID: PMC11015613 DOI: 10.1186/s12951-024-02463-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/04/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND Clearance of apoptotic cells by efferocytosis is crucial for prevention of atherosclerosis progress, and impaired efferocytosis contributes to the aggravated atherosclerosis. RESULTS In this study, we found that diabetic ApoE-/- mice showed aggravated atherosclerosis as hyperglycemia damaged the efferocytosis capacity at least partially due to decreased expression of Mer tyrosine kinase (MerTK) on macrophages. To locally restore MerTK in the macrophages in the plaque, hybrid membrane nanovesicles (HMNVs) were thus developed. Briefly, cell membrane from MerTK overexpressing RAW264.7 cell and transferrin receptor (TfR) overexpressing HEK293T cell were mixed with DOPE polymers to produce nanovesicles designated as HMNVs. HMNVs could fuse with the recipient cell membrane and thus increased MerTK in diabetic macrophages, which in turn restored the efferocytosis capacity. Upon intravenous administration into diabetic ApoE-/- mice, superparamagnetic iron oxide nanoparticles (SMN) decorated HMNVs accumulated at the aorta site significantly under magnetic navigation, where the recipient macrophages cleared the apoptotic cells efficiently and thus decreased the inflammation. CONCLUSIONS Our study indicates that MerTK decrease in macrophages contributes to the aggravated atherosclerosis in diabetic ApoE-/- mice and regional restoration of MerTK in macrophages of the plaque via HMNVs could be a promising therapeutic approach.
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Affiliation(s)
- Shuo Qiu
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China
| | - Jiahan Liu
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China
| | - Jianmei Chen
- Department of Health Medicine, The Fourth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yangni Li
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China
| | - Te Bu
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China
| | - Zhelong Li
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China
| | - Liang Zhang
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China
| | - Wenqi Sun
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China
| | - Tian Zhou
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China
| | - Wei Hu
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China
| | - Guodong Yang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Air Force Medical University, Xi'an, China
| | - Lijun Yuan
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China.
| | - Yunyou Duan
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China.
| | - Changyang Xing
- Department of Ultrasound Medicine, Tangdu Hospital, Air Force Medical University, No.569, Xinsi Road, Xi'an, 710038, China.
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Cao M, Cui B. Clinically relevant plasma proteome for adiposity depots: evidence from systematic mendelian randomization and colocalization analyses. Cardiovasc Diabetol 2024; 23:126. [PMID: 38614964 PMCID: PMC11016216 DOI: 10.1186/s12933-024-02222-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/31/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND The accumulation of visceral and ectopic fat comprise a major cause of cardiometabolic diseases. However, novel drug targets for reducing unnecessary visceral and ectopic fat are still limited. Our study aims to provide a comprehensive investigation of the causal effects of the plasma proteome on visceral and ectopic fat using Mendelian randomization (MR) approach. METHODS We performed two-sample MR analyses based on five large genome-wide association study (GWAS) summary statistics of 2656 plasma proteins, to screen for causal associations of these proteins with traits of visceral and ectopic fat in over 30,000 participants of European ancestry, as well as to assess mediation effects by risk factors of outcomes. The colocalization analysis was conducted to examine whether the identified proteins and outcomes shared casual variants. RESULTS Genetically predicted levels of 14 circulating proteins were associated with visceral and ectopic fat (P < 4.99 × 10- 5, at a Bonferroni-corrected threshold). Colocalization analysis prioritized ten protein targets that showed effect on outcomes, including FST, SIRT2, DNAJB9, IL6R, CTSA, RGMB, PNLIPRP1, FLT4, PPY and IL6ST. MR analyses revealed seven risk factors for visceral and ectopic fat (P < 0.0024). Furthermore, the associations of CTSA, DNAJB9 and IGFBP1 with primary outcomes were mediated by HDL-C and SHBG. Sensitivity analyses showed little evidence of pleiotropy. CONCLUSIONS Our study identified candidate proteins showing putative causal effects as potential therapeutic targets for visceral and ectopic fat accumulation and outlined causal pathways for further prevention of downstream cardiometabolic diseases.
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Affiliation(s)
- Min Cao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Bin Cui
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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17
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Hu H, Li A, Shi C, Chen L, Zhao Z, Yin X, Zhang Q, Huang Y, Pan H. Mulberry branch fiber improved lipid metabolism and egg yolk fatty acid composition of laying hens via the enterohepatic axis. Microbiome 2024; 12:73. [PMID: 38605412 PMCID: PMC11010431 DOI: 10.1186/s40168-024-01788-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/04/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND The utilization of mulberry branch fiber (MF), the largest by-product of the sericulture industry, is an important issue. Supplementation with MF as a dietary fiber for poultry may serve as a useful application. However, little is known about the effects of MF on liver lipid metabolism and egg yolk fatty acid composition of laying hens and their underlying mechanisms. In this study, we performed a multi-omics investigation to explore the variations in liver lipid metabolism, egg yolk fatty acid composition, gut microbiota, and the associations among them induced by dietary MF in laying hens. RESULTS Dietary MF had no harmful effects on the laying performance or egg quality in laying hens. The enzyme activities associated with lipid metabolism in the liver were altered by the addition of 5% MF, resulting in reduced liver fat accumulation. Furthermore, dietary 5% MF induced the variation in the fatty acid profiles of egg yolk, and increased the polyunsaturated fatty acid (PUFA) content. We observed a significant reduction in the diversity of both gut bacteria and changes in their compositions after the addition of MF. Dietary MF significantly increased the abundance of genes involved in fatty acid biodegradation, and short-chain fatty acids biosynthesis in the gut microbiota of laying hens. The significant correlations were observed between the liver lipid metabolism enzyme activities of hepatic lipase, lipoprotein lipase, and total esterase with gut microbiota, including negative correlations with gut microbiota diversity, and multiple correlations with gut bacteria and viruses. Moreover, various correlations between the contents of PUFAs and monounsaturated fatty acids in egg yolk with the gut microbiota were obtained. Based on partial-least-squares path modeling integrated with the multi-omics datasets, we deduced the direct effects of liver enzyme activities and gut bacterial compositions on liver fat content and the roles of liver enzyme activities and gut bacterial diversity on egg yolk fatty acid composition. CONCLUSIONS The results indicate that dietary MF is beneficial to laying hens as it reduces the liver fat and improves egg yolk fatty acid composition through the enterohepatic axis. Video Abstract.
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Affiliation(s)
- Hong Hu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Anjian Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Changyou Shi
- University of Maryl and School of Medicine, Baltimore, MD, 21228, USA
| | - Liang Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing, 100193, China
| | - Zelong Zhao
- Shanghai BIOZERON Biotechnology Co., Ltd, Shanghai, 201800, China
| | - Xiaojian Yin
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Qiang Zhang
- WOD Poultry Research Institute, Beijing, 100193, China
| | - Ying Huang
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Hongbin Pan
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
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18
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Wang L, Ma C, Wang L, Ding Q, Yang H, Wang B, Wu Q. Successful ECMO treatment in patients with cerebral hemorrhage and PROC gene mutation associated with VTE: a case report. Thromb J 2024; 22:36. [PMID: 38609929 PMCID: PMC11010424 DOI: 10.1186/s12959-024-00601-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
In this report, we report a case of a middle-aged male, admitted to the ICU with cerebral hemorrhage resulting from a severe high-altitude fall. The patient encountered significant challenges in oxygenation index correction, attributed to extensive embolism in both the primary and branch pulmonary arteries. Consequently, the patient underwent an immediate initiation of veno-arterial extracorporeal membrane oxygenation (VA-ECMO) therapy, persisting for 20 days. During this treatment period, a mutation in the protein C (PROC) gene was identified. The medical team meticulously navigated the delicate balance between anticoagulation and bleeding risks. Eventually, the patient was successfully weaned off VA-ECMO and subsequently discharged. This report aims to delve into the etiology and therapeutic approaches of this uncommon case, with the intention of offering insightful reference for managing similar clinical scenarios in the future.
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Affiliation(s)
- Lijie Wang
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Sichuan Province, No. 37, Guo Xue Xiang, Chengdu, China
| | - Chengyong Ma
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Sichuan Province, No. 37, Guo Xue Xiang, Chengdu, China
| | - Luping Wang
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Sichuan Province, No. 37, Guo Xue Xiang, Chengdu, China
| | - Qianrong Ding
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Sichuan Province, No. 37, Guo Xue Xiang, Chengdu, China
| | - Hao Yang
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Sichuan Province, No. 37, Guo Xue Xiang, Chengdu, China
| | - Bo Wang
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Sichuan Province, No. 37, Guo Xue Xiang, Chengdu, China.
| | - Qin Wu
- Department of Critical Care Medicine, West China Hospital of Sichuan University, Sichuan Province, No. 37, Guo Xue Xiang, Chengdu, China.
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19
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Du M, Wang T, Peng W, Feng R, Goh M, Chen Z. Bacteria-driven nanosonosensitizer delivery system for enhanced breast cancer treatment through sonodynamic therapy-induced immunogenic cell death. J Nanobiotechnology 2024; 22:167. [PMID: 38610042 PMCID: PMC11010413 DOI: 10.1186/s12951-024-02437-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Sonodynamic therapy (SDT) has shown promise as a non-invasive cancer treatment due to its local effects and excellent tissue penetration. However, the limited accumulation of sonosensitizers at the tumor site hinders its therapeutic efficacy. Although nanosonosensitizers have improved local tumor accumulation through passive targeting via the enhanced permeability and retention effect (EPR), achieving sufficient accumulation and penetration into tumors remains challenging due to tumor heterogeneity and inaccurate targeting. Bacteria have become a promising biological carrier due to their unique characteristic of active targeting and deeper penetration into the tumor. METHODS In this study, we developed nanosonosensitizers consisting of sonosensitizer, hematoporphyrin monomethyl ether (HMME), and perfluoro-n-pentane (PFP) loaded poly (lactic-co-glycolic) acid (PLGA) nanodroplets (HPNDs). These HPNDs were covalently conjugated onto the surface of Escherichia coli Nissle 1917 (EcN) using carbodiimine chemistry. EcN acted as an active targeting micromotor for efficient transportation of the nanosonosensitizers to the tumor site in triple-negative breast cancer (TNBC) treatment. Under ultrasound cavitation, the HPNDs were disrupted, releasing HMME and facilitating its uptakes by cancer cells. This process induced reactive oxygen species (ROS)-mediated cell apoptosis and immunogenic cell death (ICD) in vitro and in vivo. RESULTS Our bacteria-driven nanosonosensitizer delivery system (HPNDs@EcN) achieved superior tumor localization of HMME in vivo compared to the group treated with only nanosonosensitizers. This enhanced local accumulation further improved the therapeutic effect of SDT induced-ICD therapeutic effect and inhibited tumor metastasis under ultrasound stimulation. CONCLUSIONS Our research demonstrates the potential of this ultrasound-responsive bacteria-driven nanosonosensitizer delivery system for SDT in TNBC. The combination of targeted delivery using bacteria and nanosonosensitizer-based therapy holds promise for achieving improved treatment outcomes by enhancing local tumor accumulation and stimulating ICD.
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Affiliation(s)
- Meng Du
- Key Laboratory of Medical Imaging Precision Theranostics and Radiation Protection, College of Hunan Province, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, 410004, China
- Institute of Medical Imaging, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Medical Imaging Centre, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Ting Wang
- Key Laboratory of Medical Imaging Precision Theranostics and Radiation Protection, College of Hunan Province, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, 410004, China
- Institute of Medical Imaging, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Medical Imaging Centre, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Wangrui Peng
- Key Laboratory of Medical Imaging Precision Theranostics and Radiation Protection, College of Hunan Province, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, 410004, China
- Institute of Medical Imaging, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The Seventh Affiliated Hospital, Hengyang Medical School, University of South China (Hunan Provincial Veterans Administration Hospital), Changsha, Hunan, 410118, China
| | - Renjie Feng
- Key Laboratory of Medical Imaging Precision Theranostics and Radiation Protection, College of Hunan Province, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, 410004, China
- Institute of Medical Imaging, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- The Seventh Affiliated Hospital, Hengyang Medical School, University of South China (Hunan Provincial Veterans Administration Hospital), Changsha, Hunan, 410118, China
| | - MeeiChyn Goh
- Key Laboratory of Medical Imaging Precision Theranostics and Radiation Protection, College of Hunan Province, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, 410004, China
- Institute of Medical Imaging, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Zhiyi Chen
- Key Laboratory of Medical Imaging Precision Theranostics and Radiation Protection, College of Hunan Province, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, 410004, China.
- Institute of Medical Imaging, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
- The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, 410004, China.
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20
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Liu X, Shen L, Wan M, Xie H, Wang Z. Peripheral extracellular vesicles in neurodegeneration: pathogenic influencers and therapeutic vehicles. J Nanobiotechnology 2024; 22:170. [PMID: 38610012 PMCID: PMC11015679 DOI: 10.1186/s12951-024-02428-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Neurodegenerative diseases (NDDs) such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis epitomize a class of insidious and relentless neurological conditions that are difficult to cure. Conventional therapeutic regimens often fail due to the late onset of symptoms, which occurs well after irreversible neurodegeneration has begun. The integrity of the blood-brain barrier (BBB) further impedes efficacious drug delivery to the central nervous system, presenting a formidable challenge in the pharmacological treatment of NDDs. Recent scientific inquiries have shifted focus toward the peripheral biological systems, investigating their influence on central neuropathology through the lens of extracellular vesicles (EVs). These vesicles, distinguished by their ability to breach the BBB, are emerging as dual operatives in the context of NDDs, both as conveyors of pathogenic entities and as prospective vectors for therapeutic agents. This review critically summarizes the burgeoning evidence on the role of extracerebral EVs, particularly those originating from bone, adipose tissue, and gut microbiota, in modulating brain pathophysiology. It underscores the duplicity potential of peripheral EVs as modulators of disease progression and suggests their potential as novel vehicles for targeted therapeutic delivery, positing a transformative impact on the future landscape of NDD treatment strategies. Search strategy A comprehensive literature search was conducted using PubMed, Web of Science, and Scopus from January 2000 to December 2023. The search combined the following terms using Boolean operators: "neurodegenerative disease" OR "Alzheimer's disease" OR "Parkinson's disease" OR "Amyotrophic lateral sclerosis" AND "extracellular vesicles" OR "exosomes" OR "outer membrane vesicles" AND "drug delivery systems" AND "blood-brain barrier". MeSH terms were employed when searching PubMed to refine the results. Studies were included if they were published in English, involved human subjects, and focused on the peripheral origins of EVs, specifically from bone, adipose tissue, and gut microbiota, and their association with related diseases such as osteoporosis, metabolic syndrome, and gut dysbiosis. Articles were excluded if they did not address the role of EVs in the context of NDDs or did not discuss therapeutic applications. The titles and abstracts of retrieved articles were screened using a dual-review process to ensure relevance and accuracy. The reference lists of selected articles were also examined to identify additional relevant studies.
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Affiliation(s)
- Xixi Liu
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- National Clinical Research Center for Geriatric Disorders (Xiangya Hospital), Changsha, Hunan, 410008, China
- Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Changsha, Hunan, 410008, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, Hunan, 410008, China
| | - Meidan Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Hui Xie
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders (Xiangya Hospital), Changsha, Hunan, 410008, China.
| | - Zhenxing Wang
- Department of Orthopedics, Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- Hunan Key Laboratory of Angmedicine, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders (Xiangya Hospital), Changsha, Hunan, 410008, China.
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21
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Wang Y, Lyu D, Cheng C, Zhou T, Tu W, Xiao Y, Zuo C, Fan L, Liu S. Preoperative nomogram for predicting spread through air spaces in clinical-stage IA non-small cell lung cancer using 18F-fluorodeoxyglucose positron emission tomography/computed tomography. J Cancer Res Clin Oncol 2024; 150:185. [PMID: 38598007 PMCID: PMC11006761 DOI: 10.1007/s00432-024-05674-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 02/29/2024] [Indexed: 04/11/2024]
Abstract
PURPOSE This study aims to assess the predictive value of 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) radiological features and the maximum standardized uptake value (SUVmax) in determining the presence of spread through air spaces (STAS) in clinical-stage IA non-small cell lung cancer (NSCLC). METHODS A retrospective analysis was conducted on 180 cases of NSCLC with postoperative pathological assessment of STAS status, spanning from September 2019 to September 2023. Of these, 116 cases from hospital one comprised the training set, while 64 cases from hospital two formed the testing set. The clinical information, tumor SUVmax, and 13 related CT features were analyzed. Subgroup analysis was carried out based on tumor density type. In the training set, univariable and multivariable logistic regression analyses were employed to identify the most significant variables. A multivariable logistic regression model was constructed and the corresponding nomogram was developed to predict STAS in NSCLC, and its diagnostic efficacy was evaluated in the testing set. RESULTS SUVmax, consolidation-to-tumor ratio (CTR), and lobulation sign emerged as the best combination of variables for predicting STAS in NSCLC. Among these, SUVmax and CTR were identified as independent predictors for STAS prediction. The constructed prediction model demonstrated area under the curve (AUC) values of 0.796 and 0.821 in the training and testing sets, respectively. Subgroup analysis revealed a 2.69 times higher STAS-positive rate in solid nodules compared to part-solid nodules. SUVmax was an independent predictor for predicting STAS in solid nodular NSCLC, while CTR and an emphysema background were independent predictors for STAS in part-solid nodular NSCLC. CONCLUSION Our nomogram based on preoperative 18F-FDG PET/CT radiological features and SUVmax effectively predicts STAS status in clinical-stage IA NSCLC. Furthermore, our study highlights that metabolic parameters and CT variables associated with STAS differ between solid and part-solid nodular NSCLC.
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Affiliation(s)
- Yun Wang
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Deng Lyu
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Chao Cheng
- Department of Nuclear Medicine, Changhai Hospital, Navy Medical University, Shanghai, 200433, China
| | - Taohu Zhou
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Wenting Tu
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Yi Xiao
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, 415 Fengyang Road, Huangpu District, Shanghai, 200003, China
| | - Changjing Zuo
- Department of Nuclear Medicine, Changhai Hospital, Navy Medical University, Shanghai, 200433, China.
| | - Li Fan
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, 415 Fengyang Road, Huangpu District, Shanghai, 200003, China.
| | - Shiyuan Liu
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, 415 Fengyang Road, Huangpu District, Shanghai, 200003, China.
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22
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Li F, Wang Z, Cao Y, Pei B, Luo X, Liu J, Ge P, Luo Y, Ma S, Chen H. Intestinal Mucosal Immune Barrier: A Powerful Firewall Against Severe Acute Pancreatitis-Associated Acute Lung Injury via the Gut-Lung Axis. J Inflamm Res 2024; 17:2173-2193. [PMID: 38617383 PMCID: PMC11016262 DOI: 10.2147/jir.s448819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/20/2024] [Indexed: 04/16/2024] Open
Abstract
The pathogenesis of severe acute pancreatitis-associated acute lung injury (SAP-ALI), which is the leading cause of mortality among hospitalized patients in the intensive care unit, remains incompletely elucidated. The intestinal mucosal immune barrier is a crucial component of the intestinal epithelial barrier, and its aberrant activation contributes to the induction of sustained pro-inflammatory immune responses, paradoxical intercellular communication, and bacterial translocation. In this review, we firstly provide a comprehensive overview of the composition of the intestinal mucosal immune barrier and its pivotal roles in the pathogenesis of SAP-ALI. Secondly, the mechanisms of its crosstalk with gut microbiota, which is called gut-lung axis, and its effect on SAP-ALI were summarized. Finally, a number of drugs that could enhance the intestinal mucosal immune barrier and exhibit potential anti-SAP-ALI activities were presented, including probiotics, glutamine, enteral nutrition, and traditional Chinese medicine (TCM). The aim is to offer a theoretical framework based on the perspective of the intestinal mucosal immune barrier to protect against SAP-ALI.
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Affiliation(s)
- Fan Li
- Department of General Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
| | - Zhengjian Wang
- Department of Hepatobiliary Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, People’s Republic of China
| | - Yinan Cao
- Department of General Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
| | - Boliang Pei
- Department of General Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
| | - Xinyu Luo
- Department of General Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
| | - Jin Liu
- Department of General Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
| | - Peng Ge
- Department of General Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
| | - Yalan Luo
- Department of General Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
| | - Shurong Ma
- Department of General Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
| | - Hailong Chen
- Department of General Surgery, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
- Laboratory of Integrative Medicine, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, People’s Republic of China
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23
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Wang T, Song D, Li X, Luo Y, Yang D, Liu X, Kong X, Xing Y, Bi S, Zhang Y, Hu T, Zhang Y, Dai S, Shao Z, Chen D, Hou J, Ballestar E, Cai J, Zheng F, Yang JY. MiR-574-5p activates human TLR8 to promote autoimmune signaling and lupus. Cell Commun Signal 2024; 22:220. [PMID: 38589923 PMCID: PMC11000404 DOI: 10.1186/s12964-024-01601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/28/2024] [Indexed: 04/10/2024] Open
Abstract
Endosomal single-stranded RNA-sensing Toll-like receptor-7/8 (TLR7/8) plays a pivotal role in inflammation and immune responses and autoimmune diseases. However, the mechanisms underlying the initiation of the TLR7/8-mediated autoimmune signaling remain to be fully elucidated. Here, we demonstrate that miR-574-5p is aberrantly upregulated in tissues of lupus prone mice and in the plasma of lupus patients, with its expression levels correlating with the disease activity. miR-574-5p binds to and activates human hTLR8 or its murine ortholog mTlr7 to elicit a series of MyD88-dependent immune and inflammatory responses. These responses include the overproduction of cytokines and interferons, the activation of STAT1 signaling and B lymphocytes, and the production of autoantigens. In a transgenic mouse model, the induction of miR-574-5p overexpression is associated with increased secretion of antinuclear and anti-dsDNA antibodies, increased IgG and C3 deposit in the kidney, elevated expression of inflammatory genes in the spleen. In lupus-prone mice, lentivirus-mediated silencing of miR-574-5p significantly ameliorates major symptoms associated with lupus and lupus nephritis. Collectively, these results suggest that the miR-574-5p-hTLR8/mTlr7 signaling is an important axis of immune and inflammatory responses, contributing significantly to the development of lupus and lupus nephritis.
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Affiliation(s)
- Tao Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, 361102, China
- The Key Laboratory of Urinary Tract Tumors and Calculi, Department of Urology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, 361003, China
| | - Dan Song
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, 361102, China
| | - Xuejuan Li
- Wuhu Hospital of East China Normal University, Wuhu, Anhui, 241000, China
- Kidney Health Institute, Health Science Center, East China Normal University, Minhang, Shanghai, 200241, China
- Department of Nephrology, The Second Hospital, Dalian Medical University, Dalian, 116144, China
| | - Yu Luo
- School of Nursing, The Third Military Medical University, Chongqing, 400038, China
| | - Dianqiang Yang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, 361102, China
| | - Xiaoyan Liu
- Department of Nephrology, The Second Hospital, Dalian Medical University, Dalian, 116144, China
| | - Xiaodan Kong
- Department of Rheumatology, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Yida Xing
- Department of Rheumatology, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Shulin Bi
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, 361102, China
| | - Yan Zhang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, 361102, China
| | - Tao Hu
- College of Medicine, Xiamen University, Xiang'an, Xiamen, 361102, China
| | - Yunyun Zhang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, 361102, China
| | - Shuang Dai
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, 361102, China
| | - Zhiqiang Shao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, 361102, China
| | - Dahan Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, 361102, China
| | - Jinpao Hou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, 361102, China
| | - Esteban Ballestar
- Wuhu Hospital of East China Normal University, Wuhu, Anhui, 241000, China
- Kidney Health Institute, Health Science Center, East China Normal University, Minhang, Shanghai, 200241, China
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, 08916, Spain
| | - Jianchun Cai
- Department of Gastrointestinal Surgery, Institute of Gastrointestinal Oncology, Zhongshan Hospital of Xiamen University, Medical College of Xiamen University, Xiamen, Fujian, 361005, China.
| | - Feng Zheng
- Wuhu Hospital of East China Normal University, Wuhu, Anhui, 241000, China.
- Kidney Health Institute, Health Science Center, East China Normal University, Minhang, Shanghai, 200241, China.
- Department of Nephrology, The Second Hospital, Dalian Medical University, Dalian, 116144, China.
- The Advanced Institute for Molecular Medicine, Dalian Medical University, Dalian, 116144, China.
| | - James Y Yang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiang'an, Xiamen, 361102, China.
- Wuhu Hospital of East China Normal University, Wuhu, Anhui, 241000, China.
- Kidney Health Institute, Health Science Center, East China Normal University, Minhang, Shanghai, 200241, China.
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24
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Zhang X, Xiong Z, He Y, Zheng N, Zhao S, Wang J. Epiberberine: a potential rumen microbial urease inhibitor to reduce ammonia release screened by targeting UreG. Appl Microbiol Biotechnol 2024; 108:289. [PMID: 38587649 PMCID: PMC11001712 DOI: 10.1007/s00253-024-13131-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
Rumen microbial urease inhibitors have been proposed for regulating nitrogen emission and improving nitrogen utilization efficiency in ruminant livestock industry. However, studies on plant-derived natural inhibitors of rumen microbial urease are limited. Urease accessory protein UreG, plays a crucial role in facilitating urease maturation, is a new target for design of urease inhibitor. The objective of this study was to select the potential effective inhibitor of rumen microbial urease from major protoberberine alkaloids in Rhizoma Coptidis by targeting UreG. Our results showed that berberine chloride and epiberberine exerted superior inhibition potential than other alkaloids based on GTPase activity study of UreG. Berberine chloride inhibition of UreG was mixed type, while inhibition kinetics type of epiberberine was uncompetitive. Furthermore, epiberberine was found to be more effective than berberine chloride in inhibiting the combination of nickel towards UreG and inducing changes in the second structure of UreG. Molecular modeling provided the rational structural basis for the higher inhibition potential of epiberberine, amino acid residues in G1 motif and G3 motif of UreG formed interactions with D ring of berberine chloride, while interacted with A ring and D ring of epiberberine. We further demonstrated the efficacy of epiberberine in the ruminal microbial fermentation with low ammonia release and urea degradation. In conclusion, our study clearly indicates that epiberberine is a promising candidate as a safe and effective inhibitor of rumen microbial urease and provides an optimal strategy and suitable feed additive for regulating nitrogen excretion in ruminants in the future. KEY POINTS: • Epiberberine is the most effective inhibitor of rumen urease from Rhizoma Coptidis. • Urease accessory protein UreG is an effective target for design of urease inhibitor. • Epiberberine may be used as natural feed additive to reducing NH3 release in ruminants.
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Affiliation(s)
- Xiaoyin Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhanbo Xiong
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yue He
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Yang F, Zhang L, Zhang X, Guan J, Wang B, Wu X, Song M, Wei A, Liu Z, Huo D. Genome-wide investigation of UDP-Glycosyltransferase family in Tartary buckwheat (Fagopyrum tataricum). BMC Plant Biol 2024; 24:249. [PMID: 38580941 PMCID: PMC10998406 DOI: 10.1186/s12870-024-04926-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/18/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum) belongs to Polygonaceae family and has attracted increasing attention owing to its high nutritional value. UDP-glycosyltransferases (UGTs) glycosylate a variety of plant secondary metabolites to control many metabolic processes during plant growth and development. However, there have been no systematic reports of UGT superfamily in F. tataricum. RESULTS We identified 173 FtUGTs in F. tataricum based on their conserved UDPGT domain. Phylogenetic analysis of FtUGTs with 73 Arabidopsis UGTs clustered them into 21 families. FtUGTs from the same family usually had similar gene structure and motif compositions. Most of FtUGTs did not contain introns or had only one intron. Tandem repeats contributed more to FtUGTs amplification than segmental duplications. Expression analysis indicates that FtUGTs are widely expressed in various tissues and likely play important roles in plant growth and development. The gene expression analysis response to different abiotic stresses showed that some FtUGTs were involved in response to drought and cadmium stress. Our study provides useful information on the UGTs in F. tataricum, and will facilitate their further study to better understand their function. CONCLUSIONS Our results provide a theoretical basis for further exploration of the functional characteristics of FtUGTs and for understanding the growth, development, and metabolic model in F. tataricum.
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Affiliation(s)
- Fan Yang
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Lei Zhang
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Xiao Zhang
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Jingru Guan
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Bo Wang
- MARA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoying Wu
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Minli Song
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Aili Wei
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Zhang Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Dongao Huo
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, 030619, China.
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Jiang J, Luo Y, Fei P, Zhu Z, Peng J, Lu J, Zhu D, Wu H. Effect of adaptive laboratory evolution of engineered Escherichia coli in acetate on the biosynthesis of succinic acid from glucose in two-stage cultivation. BIORESOUR BIOPROCESS 2024; 11:34. [PMID: 38647614 PMCID: PMC10997558 DOI: 10.1186/s40643-024-00749-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/14/2024] [Indexed: 04/25/2024] Open
Abstract
Escherichia coli MLB (MG1655 ΔpflB ΔldhA), which can hardly grow on glucose with little succinate accumulation under anaerobic conditions. Two-stage fermentation is a fermentation in which the first stage is used for cell growth and the second stage is used for product production. The ability of glucose consumption and succinate production of MLB under anaerobic conditions can be improved significantly by using acetate as the solo carbon source under aerobic condition during the two-stage fermentation. Then, the adaptive laboratory evolution (ALE) of growing on acetate was applied here. We assumed that the activities of succinate production related enzymes might be further improved in this study. E. coli MLB46-05 evolved from MLB and it had an improved growth phenotype on acetate. Interestingly, in MLB46-05, the yield and tolerance of succinic acid in the anaerobic condition of two-stage fermentation were improved significantly. According to transcriptome analysis, upregulation of the glyoxylate cycle and the activity of stress regulatory factors are the possible reasons for the elevated yield. And the increased tolerance to acetate made it more tolerant to high concentrations of glucose and succinate. Finally, strain MLB46-05 produced 111 g/L of succinic acid with a product yield of 0.74 g/g glucose. SYNOPSIS.
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Affiliation(s)
- Jiaping Jiang
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yuanchan Luo
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Peng Fei
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Zhengtong Zhu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jing Peng
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Juefeng Lu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Du Zhu
- Key Lab of Bioprocess Engineering of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China.
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Sun W, Jon K, Zhu W. Multiple phenotype association tests based on sliced inverse regression. BMC Bioinformatics 2024; 25:144. [PMID: 38575890 PMCID: PMC10996256 DOI: 10.1186/s12859-024-05731-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 03/05/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Joint analysis of multiple phenotypes in studies of biological systems such as Genome-Wide Association Studies is critical to revealing the functional interactions between various traits and genetic variants, but growth of data in dimensionality has become a very challenging problem in the widespread use of joint analysis. To handle the excessiveness of variables, we consider the sliced inverse regression (SIR) method. Specifically, we propose a novel SIR-based association test that is robust and powerful in testing the association between multiple predictors and multiple outcomes. RESULTS We conduct simulation studies in both low- and high-dimensional settings with various numbers of Single-Nucleotide Polymorphisms and consider the correlation structure of traits. Simulation results show that the proposed method outperforms the existing methods. We also successfully apply our method to the genetic association study of ADNI dataset. Both the simulation studies and real data analysis show that the SIR-based association test is valid and achieves a higher efficiency compared with its competitors. CONCLUSION Several scenarios with low- and high-dimensional responses and genotypes are considered in this paper. Our SIR-based method controls the estimated type I error at the pre-specified level α .
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Affiliation(s)
- Wenyuan Sun
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun, 130024, Jilin, China
- Department of Mathematics, College of Science, Yanbian University, Yanji, 133002, Jilin, China
| | - Kyongson Jon
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun, 130024, Jilin, China
- Faculty of Mathematics, Kim Il Sung University, Pyongyan , 999093, Democratic People's Republic of Korea
| | - Wensheng Zhu
- Key Laboratory for Applied Statistics of MOE, School of Mathematics and Statistics, Northeast Normal University, Changchun, 130024, Jilin, China.
- School of Mathematical Sciences, Harbin Normal University, Harbin, 150025, Heilongjiang, China.
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28
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Chu H, Tian Z, Hu L, Zhang H, Chang H, Bai J, Liu D, Lu L, Cheng J, Jiang H. High-Temperature Tolerance Protein Engineering through Deep Evolution. Biodes Res 2024; 6:0031. [PMID: 38572349 PMCID: PMC10988389 DOI: 10.34133/bdr.0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Protein engineering aimed at increasing temperature tolerance through iterative mutagenesis and high-throughput screening is often labor-intensive. Here, we developed a deep evolution (DeepEvo) strategy to engineer protein high-temperature tolerance by generating and selecting functional sequences using deep learning models. Drawing inspiration from the concept of evolution, we constructed a high-temperature tolerance selector based on a protein language model, acting as selective pressure in the high-dimensional latent spaces of protein sequences to enrich those with high-temperature tolerance. Simultaneously, we developed a variant generator using a generative adversarial network to produce protein sequence variants containing the desired function. Afterward, the iterative process involving the generator and selector was executed to accumulate high-temperature tolerance traits. We experimentally tested this approach on the model protein glyceraldehyde 3-phosphate dehydrogenase, obtaining 8 variants with high-temperature tolerance from just 30 generated sequences, achieving a success rate of over 26%, demonstrating the high efficiency of DeepEvo in engineering protein high-temperature tolerance.
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Affiliation(s)
- Huanyu Chu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Zhenyang Tian
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
- Tianjin Zhonghe Gene Technology Co., LTD, Tianjin 300308, P. R. China
| | - Lingling Hu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
- College of Biotechnology,
Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Hejian Zhang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
- College of Biotechnology,
Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Hong Chang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
- College of Biotechnology,
Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Jie Bai
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
- College of Biotechnology,
Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Dingyu Liu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Lina Lu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Jian Cheng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
| | - Huifeng Jiang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, P. R. China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
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29
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Zhang M, Song Y, Wang C, Sun G, Zhuang L, Guo M, Ren L, Wangdue S, Dong G, Dai Q, Cao P, Yang R, Liu F, Feng X, Bennett EA, Zhang X, Chen X, Wang F, Luan F, Dong W, Lu G, Hao D, Hou H, Wang H, Qiao H, Wang Z, Hu X, He W, Xi L, Wang W, Shao J, Sun Z, Yue L, Ding Y, Tashi N, Tsho Y, Tong Y, Yang Y, Zhu S, Miao B, Wang W, Zhang L, Hu S, Ni X, Fu Q. Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs. Mol Biol Evol 2024; 41:msae062. [PMID: 38507661 PMCID: PMC11003542 DOI: 10.1093/molbev/msae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024] Open
Abstract
Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.
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Affiliation(s)
- Ming Zhang
- China-Central Asia “the Belt and Road” Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, School of Culture Heritage, Northwest University, Xi’an, China
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Yanbo Song
- School of Archaeology, Shandong University, Jinan, China
| | - Caihui Wang
- China-Central Asia “the Belt and Road” Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, School of Culture Heritage, Northwest University, Xi’an, China
| | - Guoping Sun
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Hangzhou, China
| | | | | | - Lele Ren
- School of History and Culture, Lanzhou University, Lanzhou, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xiaoling Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xi Chen
- Department of Cultural Heritage and Museology, Nanjing Normal University, Nanjing, China
| | - Fen Wang
- School of Archaeology, Shandong University, Jinan, China
| | - Fengshi Luan
- School of Archaeology, Shandong University, Jinan, China
| | - Wenbin Dong
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan, China
| | - Guoquan Lu
- School of Archaeology, Shandong University, Jinan, China
| | - Daohua Hao
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan, China
| | - Hongwei Hou
- Gansu Provincial Institute of Cultural Relics and Archaeology, Lanzhou, China
| | - Hui Wang
- Gansu Provincial Institute of Cultural Relics and Archaeology, Lanzhou, China
- Fudan Archaeological Science Institute, Fudan University, Shanghai, China
| | - Hong Qiao
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Zhongxin Wang
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Xiaojun Hu
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Lin Xi
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Weilin Wang
- School of Archaeology and Museology, Shanxi University, Taiyuan, China
| | - Jing Shao
- Shaanxi Academy of Archaeology, Xi’an, China
| | | | | | - Yan Ding
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yang Tsho
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, China
| | - Yangheshan Yang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Shilun Zhu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Bo Miao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- Science and Technology Archaeology, National Centre for Archaeology, Beijing, China
| | - Lizhao Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Songmei Hu
- Joint International Research Laboratory of Environmental and Social Archaeology, Shandong University, Qingdao, China
- Shaanxi Academy of Archaeology, Xi’an, China
| | - Xijun Ni
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
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30
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Ma X, Wang M, Ying T, Wu Y. Reforming solid tumor treatment: the emerging potential of smaller format antibody-drug conjugate. Antib Ther 2024; 7:114-122. [PMID: 38566971 PMCID: PMC10983081 DOI: 10.1093/abt/tbae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/23/2024] [Accepted: 02/07/2024] [Indexed: 04/04/2024] Open
Abstract
In recent years, substantial therapeutic efficacy of antibody-drug conjugates (ADCs) has been validated through approvals of 16 ADCs for the treatment of malignant tumors. However, realization of the maximum clinical use of ADCs requires surmounting extant challenges, mainly the limitations in tumor penetration capabilities when targeting solid tumors. To resolve the hurdle of suboptimal tumor penetration, miniaturized antibody fragments with engineered formats have been harnessed for ADC assembly. By virtue of their reduced molecular sizes, antibody fragment-drug conjugates hold considerable promise for efficacious delivery of cytotoxic agents, thus conferring superior therapeutic outcomes. This review will focus on current advancements in novel ADC development utilizing smaller antibody formats from ~6 to 80 kDa, with particular emphasis on single-domain antibodies, which have been widely applied in novel ADC design. Additionally, strategies to optimize clinical translation are discussed, including half-life extension, acceleration of internalization, and reduction of immunogenic potential.
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Affiliation(s)
- Xiaojie Ma
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Mingkai Wang
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Tianlei Ying
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Engineering Research Center for Synthetic Immunology, Fudan University, Shanghai 200032, China
| | - Yanling Wu
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Engineering Research Center for Synthetic Immunology, Fudan University, Shanghai 200032, China
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31
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Huang J, Xu X, Zhou Y, Xin Z, Cao Q, He R, Hou T, Ding Y, Lu J, Wang T, Zhao Z, Xu Y, Wang W, Ning G, Xu M, Wang L, Bi Y, Li M. Age-specific difference in the temporal relationships between updated cardiovascular health construct and arterial stiffness in middle-aged and older adults. GeroScience 2024; 46:2051-2062. [PMID: 37814197 PMCID: PMC10828153 DOI: 10.1007/s11357-023-00965-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/25/2023] [Indexed: 10/11/2023] Open
Abstract
Previous studies have found that the association between modifiable risk factors and arterial stiffness varied with age. We aimed to explore the age-specific difference in the relationship between new cardiovascular health (CVH) score and arterial stiffness and further detected the age-specific temporal relationships in a prospective cohort study. During a median 4.3 years follow-up, 3757 participants were recruited in this study. A modified AHA "Life's Essential 8" construct (mLE8 with lacking information on diet habits) was used to evaluate CVH. Branchial-ankle pulse wave velocity (baPWV) was measured to assess arterial stiffness. Data were analyzed with logistic regression models, restricted cubic splines (RCS), and cross-lagged path analysis (age < 60 vs. age ≥ 60). In age-stratified analysis, moderate (OR = 2.21, 95% CI 1.11-4.43) and low (OR = 3.37, 95% CI 1.63-7.00) CVH were related with a higher incidence of elevated baPWV compared to high CVH in middle-aged adults, while this association was not detected in older adults. RCS curve showed a steeper linear association between CVH score and elevated baPWV in middle-aged adults than older individuals. In the cross-lagged path analysis, the decline in CVH score preceded the increment in arterial stiffness in middle-aged adults, but they appeared to alter simultaneously in older adults. Our study detected an age-specific difference in the relationship between mLE8 CVH score and elevated baPWV and showed that low CVH preceded alterations of baPWV in middle-aged adults, suggesting the importance of improvement in CVH during the early stage of the lifespan.
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Affiliation(s)
- Jiaojiao Huang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoli Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingxia Zhou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhuojun Xin
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiuyu Cao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruixin He
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianzhichao Hou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Ding
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jieli Lu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tiange Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyun Zhao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Long Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Mian Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Li GL, Han YQ, Su BQ, Yu HS, Zhang S, Yang GY, Wang J, Liu F, Ming SL, Chu BB. Porcine reproductive and respiratory syndrome virus 2 hijacks CMA-mediated lipolysis through upregulation of small GTPase RAB18. PLoS Pathog 2024; 20:e1012123. [PMID: 38607975 PMCID: PMC11014436 DOI: 10.1371/journal.ppat.1012123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 03/14/2024] [Indexed: 04/14/2024] Open
Abstract
RAB GTPases (RABs) control intracellular membrane trafficking with high precision. In the present study, we carried out a short hairpin RNA (shRNA) screen focused on a library of 62 RABs during infection with porcine reproductive and respiratory syndrome virus 2 (PRRSV-2), a member of the family Arteriviridae. We found that 13 RABs negatively affect the yield of PRRSV-2 progeny virus, whereas 29 RABs have a positive impact on the yield of PRRSV-2 progeny virus. Further analysis revealed that PRRSV-2 infection transcriptionally regulated RAB18 through RIG-I/MAVS-mediated canonical NF-κB activation. Disrupting RAB18 expression led to the accumulation of lipid droplets (LDs), impaired LDs catabolism, and flawed viral replication and assembly. We also discovered that PRRSV-2 co-opts chaperone-mediated autophagy (CMA) for lipolysis via RAB18, as indicated by the enhanced associations between RAB18 and perlipin 2 (PLIN2), CMA-specific lysosomal associated membrane protein 2A (LAMP2A), and heat shock protein family A (Hsp70) member 8 (HSPA8/HSC70) during PRRSV-2 infection. Knockdown of HSPA8 and LAMP2A impacted on the yield of PRRSV-2 progeny virus, implying that the virus utilizes RAB18 to promote CMA-mediated lipolysis. Importantly, we determined that the C-terminal domain (CTD) of HSPA8 could bind to the switch II domain of RAB18, and the CTD of PLIN2 was capable of associating with HSPA8, suggesting that HSPA8 facilitates the interaction between RAB18 and PLIN2 in the CMA process. In summary, our findings elucidate how PRRSV-2 hijacks CMA-mediated lipid metabolism through innate immune activation to enhance the yield of progeny virus, offering novel insights for the development of anti-PRRSV-2 treatments.
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Affiliation(s)
- Guo-Li Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Ying-Qian Han
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Bing-Qian Su
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Hai-Shen Yu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Shuang Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Guo-Yu Yang
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Jiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, Henan Province, China
| | - Fang Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
| | - Sheng-Li Ming
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Bei-Bei Chu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, Henan Province, China
- International Joint Research Center of National Animal Immunology, Henan Agricultural University, Zhengzhou, Henan Province, China
- Longhu Advanced Immunization Laboratory, Zhengzhou, Henan Province, China
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Zhai Y, Chao J, Wang Y, Zhang P, Tang F, Zou Q. TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments. PLoS Comput Biol 2024; 20:e1011988. [PMID: 38557416 PMCID: PMC11008887 DOI: 10.1371/journal.pcbi.1011988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/11/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Accurate multiple sequence alignment (MSA) is imperative for the comprehensive analysis of biological sequences. However, a notable challenge arises as no single MSA tool consistently outperforms its counterparts across diverse datasets. Users often have to try multiple MSA tools to achieve optimal alignment results, which can be time-consuming and memory-intensive. While the overall accuracy of certain MSA results may be lower, there could be local regions with the highest alignment scores, prompting researchers to seek a tool capable of merging these locally optimal results from multiple initial alignments into a globally optimal alignment. In this study, we introduce Two Pointers Meta-Alignment (TPMA), a novel tool designed for the integration of nucleic acid sequence alignments. TPMA employs two pointers to partition the initial alignments into blocks containing identical sequence fragments. It selects blocks with the high sum of pairs (SP) scores to concatenate them into an alignment with an overall SP score superior to that of the initial alignments. Through tests on simulated and real datasets, the experimental results consistently demonstrate that TPMA outperforms M-Coffee in terms of aSP, Q, and total column (TC) scores across most datasets. Even in cases where TPMA's scores are comparable to M-Coffee, TPMA exhibits significantly lower running time and memory consumption. Furthermore, we comprehensively assessed all the MSA tools used in the experiments, considering accuracy, time, and memory consumption. We propose accurate and fast combination strategies for small and large datasets, which streamline the user tool selection process and facilitate large-scale dataset integration. The dataset and source code of TPMA are available on GitHub (https://github.com/malabz/TPMA).
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Affiliation(s)
- Yixiao Zhai
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Quzhou People’s Hospital, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Jiannan Chao
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Yizheng Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Pinglu Zhang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Furong Tang
- Quzhou People’s Hospital, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
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Liu L, Hu H, Wu J, Koleske AJ, Chen H, Wang N, Yu K, Wu Y, Xiao X, Zhang Q. Integrin α3 is required for high-frequency repetitive transcranial magnetic stimulation-induced glutamatergic synaptic transmission in mice with ischemia. CNS Neurosci Ther 2024; 30:e14498. [PMID: 37867481 PMCID: PMC11017422 DOI: 10.1111/cns.14498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/16/2023] [Accepted: 10/01/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Repetitive transcranial magnetic stimulation (rTMS) is an effective therapy in post-stroke motor recovery. However, the underlying mechanisms of rTMS regulates long-lasting changes with synaptic transmission and glutamate receptors function (including AMPARs or NMDARs) remains unclear. METHODS Mice were received 10-Hz rTMS treatment once daily on the third day after photothrombotic (PT) stroke for 18 days. Motor behaviors and the Western blot were used to evaluate the therapeutic efficacy of 10-Hz rTMS in the mice with PT model. Moreover, we used wild-type (WT) and NEX-α3-/- mice to further explore the 10-Hz rTMS effect. RESULTS We found that 10-Hz rTMS improved the post-stroke motor performance in the PT mice. Moreover, the levels of AMPAR, vGlut1, and integrin α3 in the peri-infarct were significantly increased in the rTMS group. In contrast, 10-Hz rTMS did not induce these aforementioned effects in NEX-α3-/- mice. The amplitude of AMPAR-mediated miniature excitatory postsynaptic currents (EPSCs) and evoked EPSCs was increased in the WT + rTMS group, but did not change in NEX-α3-/- mice with rTMS. CONCLUSIONS In this study, 10-Hz rTMS improved the glutamatergic synaptic transmission in the peri-infract cortex through effects on integrin α3 and AMPARs, which resulted in motor function recovery after stroke.
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Affiliation(s)
- Li Liu
- Department of Rehabilitation Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Han Hu
- Behavioral and Cognitive Neuroscience CenterInstitute of Science and Technology for Brain‐Inspired Intelligence, Fudan UniversityShanghaiChina
| | - Junfa Wu
- Department of Rehabilitation Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Anthony J. Koleske
- Departments of Molecular Biophysics and Biochemistry and NeuroscienceYale UniversityNew HavenConnecticutUSA
| | - Hongting Chen
- Behavioral and Cognitive Neuroscience CenterInstitute of Science and Technology for Brain‐Inspired Intelligence, Fudan UniversityShanghaiChina
| | - Nianhong Wang
- Department of Rehabilitation Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Kewei Yu
- Department of Rehabilitation Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Yi Wu
- Department of Rehabilitation Medicine, Huashan HospitalFudan UniversityShanghaiChina
| | - Xiao Xiao
- Behavioral and Cognitive Neuroscience CenterInstitute of Science and Technology for Brain‐Inspired Intelligence, Fudan UniversityShanghaiChina
| | - Qun Zhang
- Department of Rehabilitation Medicine, Huashan HospitalFudan UniversityShanghaiChina
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Nazmina G, Khan A, Jiang J, Miao Z, Khan SN, Khan MI, Shah AH, Shah AH, Khisroon M, Haack TB. Exome sequencing identifies homozygous variants in MBOAT7 associated with neurodevelopmental disorder. Clin Genet 2024; 105:423-429. [PMID: 38088234 DOI: 10.1111/cge.14469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 02/24/2024]
Abstract
Intellectual disability (ID) is a large group of neurodevelopmental disorders characterized by a congenital limitation in intellectual functioning (reasoning, learning, and problem solving), adaptive behavior (conceptual, social, and practical skills), originated at birth and manifested before the age of 18. By whole exome sequencing of five consanguineous Pakistani families presenting hallmark features of ID, global developmental delay, aggressive and self-injurious behaviors, microcephaly, febrile seizures and facial dysmorphic features, we identified three novel homozygous missense variants (NM_024298.5: c.588G > T; p.Trp196Cys, c.736 T > C; p.Tyr246His and c.524A > C; p. Asp175Ala) and one rare homozygous in-frame deletion variant (c.758_778del;p.Glu253_Ala259del) in membrane-bound O-acyltransferase family member 7 (MBOAT7) gene previously associated with autosomal recessive neurodevelopmental disorder. The segregation of the variants was validated by Sanger sequencing in all family members. In silico homology modeling of wild-type and mutated proteins revealed substantial changes in the structure of both proteins, indicating a possible effect on function. The identification and validation of new pathogenic MBOAT7 variants in five cases of autosomal recessive ID further highlight the importance of this genes in proper brain function and development.
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Affiliation(s)
- Gul Nazmina
- Department of Zoology, University of Peshawar, Peshawar, Pakistan
| | - Amjad Khan
- Faculty of Biological Sciences, Department of Zoology, University of Lakki Marwat, Khyber Pakhtunkhwa, Pakistan
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Alexander von Humboldt Fellowship Foundation, Berlin, Germany
| | - Jiuhong Jiang
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Zhichao Miao
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shahid Niaz Khan
- Department of Zoology, Kohat University of Science and Technology, Kohat, Pakistan
| | | | - Abdul Haleem Shah
- Institute of Biological sciences, Gomal University, Dera Ismail Khan, Pakistan
| | - Ayesha Haleem Shah
- Institute of Biological sciences, Gomal University, Dera Ismail Khan, Pakistan
| | | | - Tobias B Haack
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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Tian XC, Chen ZY, Nie S, Shi TL, Yan XM, Bao YT, Li ZC, Ma HY, Jia KH, Zhao W, Mao JF. Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification. Hortic Res 2024; 11:uhae041. [PMID: 38638682 PMCID: PMC11024640 DOI: 10.1093/hr/uhae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/02/2024] [Indexed: 04/20/2024]
Abstract
Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.
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Affiliation(s)
- Xue-Chan Tian
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhao-Yang Chen
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Tian-Le Shi
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xue-Mei Yan
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yu-Tao Bao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhi-Chao Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hai-Yao Ma
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Kai-Hua Jia
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Wei Zhao
- Department of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, Umeå 90187, Sweden
| | - Jian-Feng Mao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Department of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, Umeå 90187, Sweden
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Zhou J, Zha F, Liu F, Wan L, Zhou M, Long J, Chen M, Xue K, Wang Y. Reliability and validity of a graphical computerized adaptive test Longshi scale for rapid assessment of activities of daily living in stroke survivors. Sci Rep 2024; 14:7625. [PMID: 38561344 PMCID: PMC10985115 DOI: 10.1038/s41598-024-57671-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Stroke survivors frequently experience difficulties in daily activities, such as bathing, feeding, and mobility. This study aimed to evaluate the reliability and validity of a computer-adaptive test-Longshi scale (CAT-LS) for assessing activities of daily living (ADL) in stroke survivors. This cross-sectional study collected data using an electronic application. The ADL function of stroke survivors in rehabilitation departments of hospitals was assessed using both the CAT-LS and BI. Correlations between the CAT-LS and Barthel index (BI) and concurrent validity were evaluated using Pearson's correlation test and multiple linear regression. Interrater reliability was evaluated using the intraclass correlation coefficient based on a two-way random effect. The internal consistency of the CAT-LS was assessed using Cronbach's coefficient (α) and corrected item-total correlations. Overall, 103 medical institutions in China were used in this study. In total, 7151 patients with stroke were included in this study. The CAT-LS classified patients into three ADL groups (bedridden, domestic, and community) with significantly different BI scores (P < 0.05). The CAT-LS results obtained using the decision-tree scoring model were consistent with the scores for each BI item. A strong correlation was observed between CAT-LS and BI (Pearson's r: 0.6-0.894, P < 0.001). The CAT-LS demonstrated good internal consistency (Cronbach's α, 0.803-0.894) and interrater reliability (ICC, 0.928-0.979). CAT-LS is time-efficient and requires < 1 min to administer. The CAT-LS is a reliable and valid tool for assessing ADL function in stroke survivors and can provide rapid and accurate assessments that reduce the burden on healthcare professionals. Further validation of this tool in other populations and settings is necessary.Study registration number: No.: ChiCTR2000034067; http://www.chictr.org.cn/showproj.aspx?proj=54770 .
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Affiliation(s)
- Jing Zhou
- Department of Rehabilitation, First Affiliated Hospital of Shenzhen University/Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518035, Guangdong, China
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Biological Science, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Fubing Zha
- Department of Rehabilitation, First Affiliated Hospital of Shenzhen University/Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518035, Guangdong, China
| | - Fang Liu
- Department of Rehabilitation, First Affiliated Hospital of Shenzhen University/Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518035, Guangdong, China
| | - Li Wan
- Department of Rehabilitation, First Affiliated Hospital of Shenzhen University/Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518035, Guangdong, China
| | - Mingchao Zhou
- Department of Rehabilitation, First Affiliated Hospital of Shenzhen University/Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518035, Guangdong, China
| | - Jianjun Long
- Department of Rehabilitation, First Affiliated Hospital of Shenzhen University/Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518035, Guangdong, China
| | - Miaoling Chen
- Department of Rehabilitation, First Affiliated Hospital of Shenzhen University/Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518035, Guangdong, China
| | - Kaiwen Xue
- Department of Rehabilitation, First Affiliated Hospital of Shenzhen University/Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518035, Guangdong, China
| | - Yulong Wang
- Department of Rehabilitation, First Affiliated Hospital of Shenzhen University/Shenzhen Second People's Hospital, 3002 Sungang West Road, Futian District, Shenzhen, 518035, Guangdong, China.
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Wang Y, Lyu D, Hu L, Wu J, Duan S, Zhou T, Tu W, Xiao Y, Fan L, Liu S. CT-Based Intratumoral and Peritumoral Radiomics Nomograms for the Preoperative Prediction of Spread Through Air Spaces in Clinical Stage IA Non-small Cell Lung Cancer. J Imaging Inform Med 2024; 37:520-535. [PMID: 38343212 PMCID: PMC11031508 DOI: 10.1007/s10278-023-00939-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 04/20/2024]
Abstract
The study aims to investigate the value of intratumoral and peritumoral radiomics and clinical-radiological features for predicting spread through air spaces (STAS) in patients with clinical stage IA non-small cell lung cancer (NSCLC). A total of 336 NSCLC patients from our hospital were randomly divided into the training cohort (n = 236) and the internal validation cohort (n = 100) at a ratio of 7:3, and 69 patients from the other two external hospitals were collected as the external validation cohort. Univariate and multivariate analyses were used to select clinical-radiological features and construct a clinical model. The GTV, PTV5, PTV10, PTV15, PTV20, GPTV5, GPTV10, GPTV15, and GPTV20 models were constructed based on intratumoral and peritumoral (5 mm, 10 mm, 15 mm, 20 mm) radiomics features. Additionally, the radscore of the optimal radiomics model and clinical-radiological predictors were used to construct a combined model and plot a nomogram. Lastly, the ROC curve and AUC value were used to evaluate the diagnostic performance of the model. Tumor density type (OR = 6.738) and distal ribbon sign (OR = 5.141) were independent risk factors for the occurrence of STAS. The GPTV10 model outperformed the other radiomics models, and its AUC values were 0.887, 0.876, and 0.868 in the three cohorts. The AUC values of the combined model constructed based on GPTV10 radscore and clinical-radiological predictors were 0.901, 0.875, and 0.878. DeLong test results revealed that the combined model was superior to the clinical model in the three cohorts. The nomogram based on GPTV10 radscore and clinical-radiological features exhibited high predictive efficiency for STAS status in NSCLC.
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Affiliation(s)
- Yun Wang
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China
| | - Deng Lyu
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China
| | - Lei Hu
- Department of Radiology Medicine, The People's Hospital of Chizhou, Chizhou, Anhui, 247100, China
| | - Junhong Wu
- Department of Radiology Medicine, The People's Hospital of Guigang, Guigang, Guangxi Zhuang Autonomous Region, 537100, China
| | - Shaofeng Duan
- GE Healthcare, Precision Health Institution, Shanghai, China
| | - Taohu Zhou
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China
| | - Wenting Tu
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China
| | - Yi Xiao
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China
| | - Li Fan
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China.
| | - Shiyuan Liu
- Department of Radiology, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China.
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Du Y, Nie J, Zhang J, Fang Y, Wei W, Wang J, Zhang S, Wang J, Li X. Disrupted topological organization of the default mode network in mild cognitive impairment with subsyndromal depression: A graph theoretical analysis. CNS Neurosci Ther 2024; 30:e14547. [PMID: 38105496 PMCID: PMC11017411 DOI: 10.1111/cns.14547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 10/26/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023] Open
Abstract
AIMS Subsyndromal depression (SSD) is common in mild cognitive impairment (MCI). However, the neural mechanisms underlying MCI with SSD (MCID) are unclear. The default mode network (DMN) is associated with cognitive processes and depressive symptoms. Therefore, we aimed to explore the topological organization of the DMN in patients with MCID. METHODS Forty-two MCID patients, 34 MCI patients without SSD (MCIND), and 36 matched healthy controls (HCs) were enrolled. The resting-state functional connectivity of the DMN of the participants was analyzed using a graph theoretical approach. Correlation analyses of network topological metrics, depressive symptoms, and cognitive function were conducted. Moreover, support vector machine (SVM) models were constructed based on topological metrics to distinguish MCID from MCIND. Finally, we used 10 repeats of 5-fold cross-validation for performance verification. RESULTS We found that the global efficiency and nodal efficiency of the left anterior medial prefrontal cortex (aMPFC) of the MCID group were significantly lower than the MCIND group. Moreover, small-worldness and global efficiency were negatively correlated with depressive symptoms in MCID, and the nodal efficiency of the left lateral temporal cortex and left aMPFC was positively correlated with cognitive function in MCID. In cross-validation, the SVM model had an accuracy of 0.83 [95% CI 0.79-0.87], a sensitivity of 0.88 [95% CI 0.86-0.90], a specificity of 0.75 [95% CI 0.72-0.78] and an area under the curve of 0.88 [95% CI 0.85-0.91]. CONCLUSIONS The coexistence of MCI and SSD was associated with the greatest disrupted topological organization of the DMN. The network topological metrics could identify MCID and serve as biomarkers of different clinical phenotypic presentations of MCI.
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Affiliation(s)
- Yang Du
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Jing Nie
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Jian‐Ye Zhang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuan Fang
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Wen‐Jing Wei
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Jing‐Hua Wang
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Shao‐Wei Zhang
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
| | - Jin‐Hong Wang
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xia Li
- Department of Geriatric Psychiatry, Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina
- Alzheimer's Disease and Related Disorders CenterShanghai Jiao Tong UniversityShanghaiChina
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Liang P, Wu Y, Zheng S, Zhang J, Yang S, Wang J, Ma S, Zhang M, Gu Z, Liu Q, Jiang W, Xing Q, Wang B. Paxillin phase separation promotes focal adhesion assembly and integrin signaling. J Cell Biol 2024; 223:e202209027. [PMID: 38466167 PMCID: PMC10926639 DOI: 10.1083/jcb.202209027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/04/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2024] Open
Abstract
Focal adhesions (FAs) are transmembrane protein assemblies mediating cell-matrix connection. Although protein liquid-liquid phase separation (LLPS) has been tied to the organization and dynamics of FAs, the underlying mechanisms remain unclear. Here, we experimentally tune the LLPS of PXN/Paxillin, an essential scaffold protein of FAs, by utilizing a light-inducible Cry2 system in different cell types. In addition to nucleating FA components, light-triggered PXN LLPS potently activates integrin signaling and subsequently accelerates cell spreading. In contrast to the homotypic interaction-driven LLPS of PXN in vitro, PXN condensates in cells are associated with the plasma membrane and modulated by actomyosin contraction and client proteins of FAs. Interestingly, non-specific weak intermolecular interactions synergize with specific molecular interactions to mediate the multicomponent condensation of PXN and are efficient in promoting FA assembly and integrin signaling. Thus, our data establish an active role of the PXN phase transition into a condensed membrane-associated compartment in promoting the assembly/maturation of FAs.
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Affiliation(s)
- Peigang Liang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuchen Wu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shanyuan Zheng
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiaqi Zhang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shuo Yang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jinfang Wang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Suibin Ma
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mengjun Zhang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhuang Gu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingfeng Liu
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenxue Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Qiong Xing
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Bo Wang
- State Key Laboratory of Cellular Stress Biology, Faculty of Medicine and Life Sciences, School of Life Sciences, Xiamen University, Xiamen, China
- Shenzhen Research Institute of Xiamen University, Shenzhen, China
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Lu W, Wu G, Miao X, Ma J, Wang Y, Xu H, Shentu D, Xue S, Xia Q, Wang Y, Wang L. The radiomics nomogram predicts the prognosis of pancreatic cancer patients with hepatic metastasis after chemoimmunotherapy. Cancer Immunol Immunother 2024; 73:87. [PMID: 38554161 PMCID: PMC10981596 DOI: 10.1007/s00262-024-03644-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/29/2024] [Indexed: 04/01/2024]
Abstract
OBJECTIVE To construct a prognostic model based on MR features and clinical data to evaluate the progression free survival (PFS), overall survival (OS) and objective response rate (ORR) of pancreatic cancer patients with hepatic metastases who received chemoimmunotherapy. METHODS 105 pancreatic cancer patients with hepatic metastases who received chemoimmunotherapy were assigned to the training set (n = 52), validation set (n = 22), and testing set (n = 31). Multi-lesion volume of interest were delineated, multi-sequence radiomics features were extracted, and the radiomics models for predicting PFS, OS and ORR were constructed, respectively. Clinical variables were extracted, and the clinical models for predicting PFS, OS and ORR were constructed, respectively. The nomogram was jointly constructed by radiomics model and clinical model. RESULT The ORR exhibits no significant correlation with either PFS or OS. The area under the curve (AUC) of nomogram for predicting 6-month PFS reached 0.847 (0.737-0.957), 0.786 (0.566-1.000) and 0.864 (0.735-0.994) in the training set, validation set and testing set, respectively. The AUC of nomogram for predicting 1-year OS reached 0.770 (0.635-0.906), 0.743 (0.479-1.000) and 0.818 (0.630-1.000), respectively. The AUC of nomogram for predicting ORR reached 0.914 (0.828-1.00), 0.938 (0.840-1.00) and 0.846 (0.689-1.00), respectively. CONCLUSION The prognostic models based on MR imaging features and clinical data are effective in predicting the PFS, OS and ORR of chemoimmunotherapy in pancreatic cancer patients with hepatic metastasis, and can be used to evaluate the prognosis of patients.
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Affiliation(s)
- Wenxin Lu
- Department of Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Guangyu Wu
- Department of Radiology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Xianyuan Miao
- Department of Oncology, Ning Bo Hangzhou Bay Hospital, Ningbo, 315336, China
| | - Jingyu Ma
- Department of Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yanling Wang
- Department of Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Haiyan Xu
- Department of Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Daiyuan Shentu
- Department of Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Shengbai Xue
- Department of Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Qing Xia
- Department of Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yu Wang
- Department of Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
| | - Liwei Wang
- Department of Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
- State Key Laboratory of Systems Medicine for Cancer of Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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Yang S, Lin X, Gao Y, Liang N, Han Y, Sun H, Qu S, Chen H. The association between gout flares and monosodium urate burden assessed using musculoskeletal ultrasound in patients with gout. Ther Adv Musculoskelet Dis 2024; 16:1759720X241240837. [PMID: 38559313 PMCID: PMC10981851 DOI: 10.1177/1759720x241240837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Background Ultrasound (US) has a high sensitivity in detecting monosodium urate (MSU) deposition in gout patients. However, the value of US in predicting gout flares has been reported only in a few monocentric studies. Objective To investigate the association between gout flares in the previous year and US-detected MSU burden using two different US scores. Design A retrospective study. Methods Patients with gout were consecutively recruited to undergo musculoskeletal US examinations of their knees, ankles, and feet. The score derived from Outcome Measure in Rheumatology (hereinafter referred to as MSU score) and musculoskeletal US features-based (hereinafter referred to as MSKF score) were used to quantify the MSU burden of gout. Odds ratios for frequent gout flares were calculated. Results We enrolled 1894 patients with gout (mean age: 45 years; gout duration: 5 years; males: 96.1%), experiencing a median of three flares over the past year. Of these, 428 (22.6%) patients reported frequent (⩾7) gout flares. The MSU and MSKF median scores were 6 and 9, respectively. For each five-point increase in MSU and MSKF score, the odds ratio of frequent gout flares increased 1.13-fold and 1.24-fold, respectively. The area under the curve (AUC) for the MSU and MSKF score was 0.635 [95% confidence interval (CI): 0.604-0.665] and 0.688 (95% CI: 0.659-0.718), respectively, (AUC difference 0.054, p value for AUC difference < 0.001). Conclusion The MSU and MSKF scores were significantly associated with the number of gout flares in the previous year. The MSKF score outperformed the MSU score in terms of frequent gout flare discrimination.
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Affiliation(s)
- Shaoling Yang
- Department of Endocrinology and Metabolism, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaojing Lin
- Department of Endocrinology and Metabolism, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yining Gao
- Department of Endocrinology and Metabolism, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Nan Liang
- Department of Endocrinology and Metabolism, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yali Han
- Department of Endocrinology and Metabolism, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hang Sun
- Department of Endocrinology and Metabolism, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shen Qu
- Department of Endocrinology and Metabolism, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, No. 301 Yanchang Middle Road, Shanghai 200072, China
| | - Haibing Chen
- Department of Endocrinology and Metabolism, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, No. 301 Yanchang Middle Road, Shanghai 200072, China
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Zhang J, Xu C, Tang X, Sun S, Liu S, Yang L, Chen Y, Yang Q, Wei TYW, Wu X, Wang J, Wang C, Yan X, Yang L, Niu Y, Gou D, Shyy JYJ, Liu B. Endothelium-specific SIRT7 targeting ameliorates pulmonary hypertension through Krüpple-like factor 4 deacetylation. Cardiovasc Res 2024; 120:403-416. [PMID: 38198357 PMCID: PMC10981524 DOI: 10.1093/cvr/cvae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/11/2023] [Accepted: 11/29/2023] [Indexed: 01/12/2024] Open
Abstract
AIMS Pulmonary hypertension (PH) is a pulmonary vascular disease characterized by a high mortality rate. Pulmonary arterial endothelium cells (PAECs) serve as a primary sensor of various environmental cues, such as shear stress and hypoxia, but PAEC dysfunction may trigger vascular remodelling during the onset of PH. This study aimed to illustrate the role of Sirtuin 7 (SIRT7) in endothelial dysfunction during PH and explore the potential therapeutic strategy for PH. METHODS AND RESULTS SIRT7 levels were measured in human and murine experimental PH samples. Bioinformatic analysis, immunoprecipitation, and deacetylation assay were used to identify the association between SIRT7 and Krüpple-like factor 4 (KLF4), a key transcription factor essential for endothelial cell (EC) homeostasis. Sugen5416 + hypoxia (SuHx)-induced PH mouse models and cell cultures were used for the study of the therapeutic effect of SIRT7 for PH. SIRT7 level was significantly reduced in lung tissues and PAECs from PH patients and the SuHx-induced PH mouse model as compared with healthy controls. Pulmonary endothelium-specific depletion of Sirt7 increased right ventricular systolic pressure and exacerbated right ventricular hypertrophy in the SuHx-induced PH model. At the molecular level, we identified KLF4 as a downstream target of SIRT7, which deacetylated KLF4 at K228 and inhibited the ubiquitination-proteasome degradation. Thus, the SIRT7/KLF4 axis maintained PAEC homeostasis by regulating proliferation, migration, and tube formation. PAEC dysfunction was reversed by adeno-associated virus type 1 vector-mediated endothelial overexpression of Sirt7 or supplementation with nicotinamide adenine dinucleotide (NAD)+ intermediate nicotinamide riboside which activated Sirt7; both approaches successfully reversed PH phenotypes. CONCLUSION The SIRT7/KLF4 axis ensures PAEC homeostasis, and pulmonary endothelium-specific SIRT7 targeting might constitute a PH therapeutic strategy.
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Affiliation(s)
- Jin Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Marshall Laboratory of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SKL-SAI), International Cancer Center, School of Basic Medical Sciences, Shenzhen University Medical School, 1066 Xueyuan Blvd, Nanshan District, Shenzhen 518055, China
| | - Chenzhong Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Marshall Laboratory of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SKL-SAI), International Cancer Center, School of Basic Medical Sciences, Shenzhen University Medical School, 1066 Xueyuan Blvd, Nanshan District, Shenzhen 518055, China
| | - Xiaolong Tang
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SKL-SAI), International Cancer Center, School of Basic Medical Sciences, Shenzhen University Medical School, 1066 Xueyuan Blvd, Nanshan District, Shenzhen 518055, China
| | - Shimin Sun
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SKL-SAI), International Cancer Center, School of Basic Medical Sciences, Shenzhen University Medical School, 1066 Xueyuan Blvd, Nanshan District, Shenzhen 518055, China
| | - Siqi Liu
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SKL-SAI), International Cancer Center, School of Basic Medical Sciences, Shenzhen University Medical School, 1066 Xueyuan Blvd, Nanshan District, Shenzhen 518055, China
| | - Langmei Yang
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SKL-SAI), International Cancer Center, School of Basic Medical Sciences, Shenzhen University Medical School, 1066 Xueyuan Blvd, Nanshan District, Shenzhen 518055, China
| | - Yuqin Chen
- State Key Laboratory of Respiratory Diseases, National Center for Respiratory Medicine, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Qifeng Yang
- State Key Laboratory of Respiratory Diseases, National Center for Respiratory Medicine, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Tong-You Wade Wei
- Division of Cardiology, Department of Medicine, University of California, San Diego 9500 Gilman Dr, La Jolla, CA 92023, USA
| | - Xiaojing Wu
- Cardiovascular Department of Shenzhen University General Hospital, Shenzhen 518055, China
| | - Jian Wang
- State Key Laboratory of Respiratory Diseases, National Center for Respiratory Medicine, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong 510120, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong 510005, China
| | - Chen Wang
- Department of Cardiology, First Affiliated Hospital of Xi’an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Xiaosong Yan
- Department of Pathology, The Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi 710003, China
| | - Lei Yang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Vascular Disease Research Center, College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Blvd, Nanshan District, Shenzhen, 518060, China
| | - Yanqin Niu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Vascular Disease Research Center, College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Blvd, Nanshan District, Shenzhen, 518060, China
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Vascular Disease Research Center, College of Life Sciences and Oceanography, Shenzhen University, 1066 Xueyuan Blvd, Nanshan District, Shenzhen, 518060, China
| | - John Y J Shyy
- Division of Cardiology, Department of Medicine, University of California, San Diego 9500 Gilman Dr, La Jolla, CA 92023, USA
| | - Baohua Liu
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SKL-SAI), International Cancer Center, School of Basic Medical Sciences, Shenzhen University Medical School, 1066 Xueyuan Blvd, Nanshan District, Shenzhen 518055, China
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Zhang L, Zhu Q, Tan Y, Deng M, Zhang L, Cao Y, Guo X. Mitogen-activated protein kinases MPK3 and MPK6 phosphorylate receptor-like cytoplasmic kinase CDL1 to regulate soybean basal immunity. Plant Cell 2024; 36:963-986. [PMID: 38301274 PMCID: PMC10980351 DOI: 10.1093/plcell/koae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Abstract
Soybean cyst nematode (SCN; Heterodera glycines Ichinohe), one of the most devastating soybean (Glycine max) pathogens, causes significant yield loss in soybean production. Nematode infection triggers plant defense responses; however, the components involved in the upstream signaling cascade remain largely unknown. In this study, we established that a mitogen-activated protein kinase (MAPK) signaling module, activated by nematode infection or wounding, is crucial for soybeans to establish SCN resistance. GmMPK3 and GmMPK6 directly interact with CDG1-LIKE1 (GmCDL1), a member of the receptor-like cytoplasmic kinase (RLCK) subfamily VII. These kinases phosphorylate GmCDL1 at Thr-372 to prevent its proteasome-mediated degradation. Functional analysis demonstrated that GmCDL1 positively regulates immune responses and promotes SCN resistance in soybeans. GmMPK3-mediated and GmMPK6-mediated phosphorylation of GmCDL1 enhances GmMPK3 and GmMPK6 activation and soybean disease resistance, representing a positive feedback mechanism. Additionally, 2 L-type lectin receptor kinases, GmLecRK02g and GmLecRK08g, associate with GmCDL1 to initiate downstream immune signaling. Notably, our study also unveils the potential involvement of GmLecRKs and GmCDL1 in countering other soybean pathogens beyond nematodes. Taken together, our findings reveal the pivotal role of the GmLecRKs-GmCDL1-MAPK regulatory module in triggering soybean basal immune responses.
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Affiliation(s)
- Lei Zhang
- National Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qun Zhu
- National Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuanhua Tan
- National Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Miaomiao Deng
- National Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Lei Zhang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Yangrong Cao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiaoli Guo
- National Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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45
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Chen R, An Y, Xu M. Prognostic difference between surgery and external radiation in patients with stage I liver cancer based on competitive risk model and conditional survival rate. PLoS One 2024; 19:e0298014. [PMID: 38547200 PMCID: PMC10977706 DOI: 10.1371/journal.pone.0298014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 01/17/2024] [Indexed: 04/02/2024] Open
Abstract
PURPOSE This study aimed to assess the difference in prognosis of patients with early-stage liver cancer after surgery or external radiation. METHODS Between 2010 and 2015, 2155 patients with AJCC 7th stage I liver cancer were enrolled in the SEER database. Among these, 1972 patients had undergone surgery and 183 had undergone external beam radiation. The main research endpoints were overall survival (OS) and disease-specific survival (DSS). The competitive risk model was used to calculate the risk ratio of liver cancer-specific deaths when there was a competitive risk. Propensity Score Matching (PSM) method using a 1:1 ratio was used to match confounders such as sex, age, and treatment method. Conditional survival was dynamically assessed for patient survival after surgery or external radiation. RESULTS Multivariate analysis of the competitive risk model showed that age, disease diagnosis time, grade, and treatment [surgery and external beam radiation therapy (EBRT)] were independent prognostic factors for patients with hepatocellular carcinoma. Surgery had a higher survival improvement rate than that of EBRT. As the survival of patients with liver cancer increased, the survival curve of surgery declined more slowly than that of radiotherapy patients and stabilized around 3 years after surgery. The survival curve of radiotherapy patients significantly dropped within 4 years and then stabilized. CONCLUSION Surgery was better than EBRT for patients with stage I liver cancer. Close follow-up was required for 3 years after surgery or 4 years after external radiation. This study can help clinicians make better informed clinical decisions.
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Affiliation(s)
- Rong Chen
- Department of Oncology, Zhongda Hospital, Southeast University, Nanjing, Jiangsu Province, China
| | - Yanli An
- Medical School of Southeast University, Nanjing, Jiangsu Province, China
| | - Muhao Xu
- Medical School of Southeast University, Nanjing, Jiangsu Province, China
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Ma Y, Zheng B, Li J, Meng W, Xu K, Ye Y. Characterization of the complete mitochondrial genome of Desmaulus extinctorium (Littorinimorpha, Calyptraeoidea, Calyptraeidae) and molecular phylogeny of Littorinimorpha. PLoS One 2024; 19:e0301389. [PMID: 38547307 PMCID: PMC10977763 DOI: 10.1371/journal.pone.0301389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
For the purpose of determining the placement of Calyptraeidae within the Littorinimorpha, we hereby furnish a thorough analysis of the mitochondrial genome (mitogenome) sequence of Desmaulus extinctorium. This mitogenome spans 16,605 base pairs and encompasses the entire set of 37 genes, including 13 PCGs, 22 tRNAs and two rRNAs, with an evident AT bias. Notably, tRNASer1 and tRNASer2 lack dihydrouracil (DHU) arms, resulting in an inability to form a secondary structure. Similarly, tRNAAla lacks a TΨC arm, rendering it incapable of forming a secondary structure. In contrast, the remaining tRNAs demonstrate a characteristic secondary structure reminiscent of a cloverleaf. A comparison with ancestral gastropods reveals distinct differences in three gene clusters (or genes), encompassing 15 tRNAs and eight PCGs. Notably, inversions and translocations represent the major types of rearrangements observed in D. extinctorium. Phylogenetic analysis demonstrates robust support for a monophyletic grouping of all Littorinimorpha species, with D. extinctorium representing a distinct Calyptraeoidea clade. In summary, this investigation provides the first complete mitochondrial dataset for a species of the Calyptraeidae, thus providing novel insights into the phylogenetic relationships within the Littorinimorpha.
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Affiliation(s)
- Yanwen Ma
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Biqi Zheng
- Department of Natural Resources, Ningde Marine Center, Ningde, 352000, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Wei Meng
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
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47
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Ji B, Zou H, Xu L, Xie X, Peng S. MUSCLE: multi-view and multi-scale attentional feature fusion for microRNA-disease associations prediction. Brief Bioinform 2024; 25:bbae167. [PMID: 38605642 PMCID: PMC11009512 DOI: 10.1093/bib/bbae167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/02/2024] [Accepted: 03/31/2024] [Indexed: 04/13/2024] Open
Abstract
MicroRNAs (miRNAs) synergize with various biomolecules in human cells resulting in diverse functions in regulating a wide range of biological processes. Predicting potential disease-associated miRNAs as valuable biomarkers contributes to the treatment of human diseases. However, few previous methods take a holistic perspective and only concentrate on isolated miRNA and disease objects, thereby ignoring that human cells are responsible for multiple relationships. In this work, we first constructed a multi-view graph based on the relationships between miRNAs and various biomolecules, and then utilized graph attention neural network to learn the graph topology features of miRNAs and diseases for each view. Next, we added an attention mechanism again, and developed a multi-scale feature fusion module, aiming to determine the optimal fusion results for the multi-view topology features of miRNAs and diseases. In addition, the prior attribute knowledge of miRNAs and diseases was simultaneously added to achieve better prediction results and solve the cold start problem. Finally, the learned miRNA and disease representations were then concatenated and fed into a multi-layer perceptron for end-to-end training and predicting potential miRNA-disease associations. To assess the efficacy of our model (called MUSCLE), we performed 5- and 10-fold cross-validation (CV), which got average the Area under ROC curves of 0.966${\pm }$0.0102 and 0.973${\pm }$0.0135, respectively, outperforming most current state-of-the-art models. We then examined the impact of crucial parameters on prediction performance and performed ablation experiments on the feature combination and model architecture. Furthermore, the case studies about colon cancer, lung cancer and breast cancer also fully demonstrate the good inductive capability of MUSCLE. Our data and code are free available at a public GitHub repository: https://github.com/zht-code/MUSCLE.git.
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Affiliation(s)
- Boya Ji
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, China
| | - Haitao Zou
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, China
- College of Information Science and Engineering, Guilin University of Technology, Guilin 541006, China
| | - Liwen Xu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, China
| | - Xiaolan Xie
- College of Information Science and Engineering, Guilin University of Technology, Guilin 541006, China
| | - Shaoliang Peng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, China
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Tian Z, Han C, Xu L, Teng Z, Song W. MGCNSS: miRNA-disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy. Brief Bioinform 2024; 25:bbae168. [PMID: 38622356 PMCID: PMC11018511 DOI: 10.1093/bib/bbae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/14/2024] [Accepted: 03/31/2024] [Indexed: 04/17/2024] Open
Abstract
Identifying disease-associated microRNAs (miRNAs) could help understand the deep mechanism of diseases, which promotes the development of new medicine. Recently, network-based approaches have been widely proposed for inferring the potential associations between miRNAs and diseases. However, these approaches ignore the importance of different relations in meta-paths when learning the embeddings of miRNAs and diseases. Besides, they pay little attention to screening out reliable negative samples which is crucial for improving the prediction accuracy. In this study, we propose a novel approach named MGCNSS with the multi-layer graph convolution and high-quality negative sample selection strategy. Specifically, MGCNSS first constructs a comprehensive heterogeneous network by integrating miRNA and disease similarity networks coupled with their known association relationships. Then, we employ the multi-layer graph convolution to automatically capture the meta-path relations with different lengths in the heterogeneous network and learn the discriminative representations of miRNAs and diseases. After that, MGCNSS establishes a highly reliable negative sample set from the unlabeled sample set with the negative distance-based sample selection strategy. Finally, we train MGCNSS under an unsupervised learning manner and predict the potential associations between miRNAs and diseases. The experimental results fully demonstrate that MGCNSS outperforms all baseline methods on both balanced and imbalanced datasets. More importantly, we conduct case studies on colon neoplasms and esophageal neoplasms, further confirming the ability of MGCNSS to detect potential candidate miRNAs. The source code is publicly available on GitHub https://github.com/15136943622/MGCNSS/tree/master.
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Affiliation(s)
- Zhen Tian
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China
| | - Chenguang Han
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
| | - Lewen Xu
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
| | - Zhixia Teng
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Wei Song
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
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Wang M, Gao XH, Zhang L. A Review of Dupilumab in the Treatment of Atopic Dermatitis in Infants and Children. Drug Des Devel Ther 2024; 18:941-951. [PMID: 38560522 PMCID: PMC10981892 DOI: 10.2147/dddt.s457761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Atopic dermatitis (AD), a common pruritic and chronic inflammatory skin disease, has a major impact on a patient's quality of life. It is characterized by dry, itchy, and eczema-like rashes. AD is more prevalent in young children and has been linked to a variety of other allergy disorders. Traditional drug therapy has certain limitations for treating young children with AD. However, biologics have good clinical application prospects in the medical treatment of young patients. Dupilumab, a fully human monoclonal antibody, specifically binds to the IL-4 Rα subunit, inhibiting IL-4 and IL-13 signaling and blocking the occurrence of type 2 inflammatory response. It has a good effect on treating infants and children with moderate-to-severe AD. This review explores the safety and efficacy of dupilumab in the treatment of AD in infants and children and the impact of early intervention on AD progression, with the aim of informing clinical practice in the use of dupilumab for the treatment of young patients with AD.
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Affiliation(s)
- Mingyue Wang
- Department of Dermatology, the First Hospital of China Medical University, Shenyang, 110001, People’s Republic of China
- NHC Key Laboratory of Immunodermatology, China Medical University, Shenyang, People’s Republic of China
- Key Laboratory of Immunodermatology, China Medical University, Ministry of Education, Shenyang, People’s Republic of China
- National and Local Joint Engineering Research Center of Immunodermatological Theranostics, Shenyang, People’s Republic of China
| | - Xing-Hua Gao
- Department of Dermatology, the First Hospital of China Medical University, Shenyang, 110001, People’s Republic of China
- NHC Key Laboratory of Immunodermatology, China Medical University, Shenyang, People’s Republic of China
- Key Laboratory of Immunodermatology, China Medical University, Ministry of Education, Shenyang, People’s Republic of China
- National and Local Joint Engineering Research Center of Immunodermatological Theranostics, Shenyang, People’s Republic of China
| | - Li Zhang
- Department of Dermatology, the First Hospital of China Medical University, Shenyang, 110001, People’s Republic of China
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Wang Z, Wang S, Li Y, Guo J, Wei Y, Mu Y, Zheng L, Li W. A new paradigm for applying deep learning to protein-ligand interaction prediction. Brief Bioinform 2024; 25:bbae145. [PMID: 38581420 PMCID: PMC10998640 DOI: 10.1093/bib/bbae145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/21/2024] [Accepted: 03/18/2024] [Indexed: 04/08/2024] Open
Abstract
Protein-ligand interaction prediction presents a significant challenge in drug design. Numerous machine learning and deep learning (DL) models have been developed to accurately identify docking poses of ligands and active compounds against specific targets. However, current models often suffer from inadequate accuracy or lack practical physical significance in their scoring systems. In this research paper, we introduce IGModel, a novel approach that utilizes the geometric information of protein-ligand complexes as input for predicting the root mean square deviation of docking poses and the binding strength (pKd, the negative value of the logarithm of binding affinity) within the same prediction framework. This ensures that the output scores carry intuitive meaning. We extensively evaluate the performance of IGModel on various docking power test sets, including the CASF-2016 benchmark, PDBbind-CrossDocked-Core and DISCO set, consistently achieving state-of-the-art accuracies. Furthermore, we assess IGModel's generalizability and robustness by evaluating it on unbiased test sets and sets containing target structures generated by AlphaFold2. The exceptional performance of IGModel on these sets demonstrates its efficacy. Additionally, we visualize the latent space of protein-ligand interactions encoded by IGModel and conduct interpretability analysis, providing valuable insights. This study presents a novel framework for DL-based prediction of protein-ligand interactions, contributing to the advancement of this field. The IGModel is available at GitHub repository https://github.com/zchwang/IGModel.
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Affiliation(s)
- Zechen Wang
- School of Physics, Shandong University, South Shanda Road, 250100 Shandong, China
| | - Sheng Wang
- Shanghai Zelixir Biotech, Xiangke Road, 200030, Shanghai, China
| | - Yangyang Li
- School of Physics, Shandong University, South Shanda Road, 250100 Shandong, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Rua de Luís Gonzaga Gomes, Macao, China
| | - Yanjie Wei
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Xueyuan Road 1068, Shenzhen, 518055 Guang Dong, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Liangzhen Zheng
- Shanghai Zelixir Biotech, Xiangke Road, 200030, Shanghai, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Xueyuan Road 1068, Shenzhen, 518055 Guang Dong, China
| | - Weifeng Li
- School of Physics, Shandong University, South Shanda Road, 250100 Shandong, China
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