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Chen Y, Sun T, Liu C, Gu L, Yuan P. In silico approach uncovers the shared genetic landscape of type 2 diabetes mellitus and asthenozoospermia. Syst Biol Reprod Med 2024; 70:272-288. [PMID: 39292564 DOI: 10.1080/19396368.2024.2395545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 07/14/2024] [Accepted: 08/10/2024] [Indexed: 09/20/2024]
Abstract
Asthenozoospermia (AZS) is one of the most common types of male infertility. Current evidence revealed that type 2 diabetes mellitus (T2DM) is closely associated with declining semen quality, especially for poor sperm motility. This study aimed to uncover the genetic interrelationships and important biomarkers between AZS and T2DM. Transcriptome data regarding AZS and T2DM were downloaded from the Gene Expression Omnibus (GEO) database. We performed GO and pathway analysis, and protein-protein interaction (PPI) network construction for T2DM-related differentially expressed genes (DMRGs). Moreover, we calculated receiver operator characteristic (ROC) curve and conducted external independent validation. Expression of hub DMRGs was assessed for patients using the qPCR method. MiRNA interaction and immune infiltration were subsequently characterized. A total of 554 overlapping DMRGs were identified between the AZS/T2DM and healthy groups. These overlapping DMRG participated in the DNA damage-, energy metabolism-, and immune-related biological pathways. Module function analysis discovered that the top three PPI modules were tightly correlated with DNA damage-related processes. After external validation in other independent datasets, two hub DMRGs (TBC1D12 and SCG5) were obtained. ROC analysis revealed that TBC1D12 and SCG5 had good diagnostic performance (area under the curve > 0.75). Immune infiltration profile showed that the level of T cell co-stimulation and CD8+_T_cells were negatively related to the hub DMRGs expression. Mirna interaction analysis showed 15 significant hub DMRGs-miRNA interactions. The qPCR results showed that expression of TBC1D12 and SCG5 were significantly different between sperm samples from diabetic patients with AZS and controls. The present study revealed molecular signatures and critical pathways between the AZS and T2DM, and identified two hub DMRGs of TBC1D12 and SCG5. The data would provide novel understandings of shared pathogenic mechanisms in T2DM-associated AZS.
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Affiliation(s)
- Yinwei Chen
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Taotao Sun
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chang Liu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Longjie Gu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Penghui Yuan
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Yao R, Gao J, Heinrich M, Yu S, Xue T, Zhang B, Wei X, Qi Y, Gao W. Medicinal plants used by minority ethnic groups in China: Taxonomic diversity and conservation needs. JOURNAL OF ETHNOPHARMACOLOGY 2024; 334:118573. [PMID: 38996945 DOI: 10.1016/j.jep.2024.118573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/14/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Indigenous communities have long relied on medicinal plants (MPs) for primary healthcare. The ethnomedicinal knowledge are different among ethnic groups since the local flora and people's health beliefs generally vary among biocultural backgrounds. China with its diverse biocultural environment is rich in culturally important plant species including MPs. They are also essential in the context of conservation of plant resources and the related traditional medical knowledge, requiring an integrated perspective on these MPs. AIM OF THE STUDY Focusing on the MPs used by the minority ethnic groups, this study assesses the diversity of MPs in China used in local indigenous traditions, as well as their conservation needs. MATERIALS AND METHODS The MPs used by the 18 selected minority ethnic groups were extracted from an ethnic MP dictionary. After standardizing, the names then were compiled as an inventory. Next, following statistics were computed: the number of species in each order and family, species used by each ethnic group, species documented in the national herbal resource dataset, species adopted in drug standards, and species at different levels of conservation lists. The overall similarity of the MPs used by the ethnic groups included was achieved using a cluster and principal component analysis. RESULTS In total 5886 vascular plant species are reported as medicines in the 18 ethnic groups, which belong to 1657 genera and 243 families. It is found that 3195 species are used exclusively by one ethnic group, indicating their cultural salience and potential restrictedness in ecological terms. Moreover, 1159 species are included in national/regional drug standards, indicating their importance in the national medical flora. However, only 3541 species of them are documented in the national herbal resource dataset, and 761 species are at different levels of threatened status, highlighting the conservation needs of Chinese MPs and the related traditional medical knowledge. CONCLUSIONS Using a quantitative approach, for the first time the present study reveals the high level of taxonomic diversity of MPs used by minority ethnic groups of China. However, of these species, 40% are still not inventoried in the national herbal resource dataset, and more than half are used exclusively by one ethnic group, and around 13% are included in the conservation lists of different levels. These together urge the conservation of MP resources and related traditional medical knowledge. Additionally, we recommend fostering the cross-cultural communication the regional ethnomedicinal knowledge, for the purpose of maximizing the benefits of regional plants to human.
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Affiliation(s)
- Ruyu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China; Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jiejing Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; School of Life Science, Guizhou Normal University, Guiyang, 550025, China
| | - Michael Heinrich
- Research Group 'Pharmacognosy and Phytotherapy', UCL School of Pharmacy, University of London, London, WC1N1AX, United Kingdom
| | - Shengxiang Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; China National Botanical Garden, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tiantian Xue
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; China National Botanical Garden, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bengang Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Xueping Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Yaodong Qi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
| | - Weiwei Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
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Li Q, Yang J, Wang M, Jia R, Chen S, Liu M, Zhu D, Zhao X, Wu Y, Yang Q, Huang J, Ou X, Sun D, Tian B, He Y, Wu Z, Cheng A, Zhang S. Global distribution and genomic characteristics analysis of avian-derived mcr-1-positive Escherichia coli. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 285:117109. [PMID: 39353372 DOI: 10.1016/j.ecoenv.2024.117109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 09/23/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]
Abstract
The prevalence of avian-derived Escherichia coli (E. coli) carrying mcr-1 poses a significant threat to the development of the poultry industry and public health safety. Despite ongoing in-depth epidemiological research worldwide, a comprehensive macroscopic study based on genomics is still lacking. In response, this study collected 1104 genomic sequences of avian-derived mcr-1-positive E. coli (MCRPEC) from the NCBI public database, covering 31 countries. The majority of sequences originated from China (48.82 %), followed by the Netherlands (10.41 %). In terms of avian hosts, chicken accounted for the largest proportion (44.11 %), followed by gallus (24.09 %). Avian-derived MCRPEC also serves as a reservoir for other antibiotic resistance genes (ARGs), with 179 ARGs coexisting with mcr-1 identified. A total of 206 virulence-associated genes were also identified, revealing the pathogenic risks of MCRPEC. Pan-genome analysis revealed that avian-derived MCRPEC from different hosts, countries of origin, and serotypes exhibit minor SNP differences, indicating a high risk of cross-regional and cross-host transmission. The ST types of MCRPRC are diverse, with ST10 being the most prevalent (n=70). Spearman analysis showed a significant correlation between the number of ARGs and the insertion sequences (ISs) as well as plasmid replicon in ST10 strains. Furthermore, ST10 strains share a similar genetic basis with human-derived MCRPEC, suggesting the possibility of clonal dissemination. Pan-genome-wide association studies (pan-GWAS) indicated that the differential genes of MCRPEC from different countries and host sources are significantly different, mainly related to genes encoding type IV secretion systems and mobile genetic elements (MGEs). Plasmid mapping of showed that the prevalent plasmid types vary by country and host, with IncI2 and IncX4 being the main mcr-1-positive plasmids. Among the 12 identified mcr-1 genetic contexts with ISs, the Tn6330 transposon was the predominant carrier of mcr-1. In summary, the potential threat of avian-derived MCRPEC cannot be ignored, and long-term and comprehensive monitoring are essential.
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Affiliation(s)
- Qianlong Li
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jing Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Mafeng Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Xinxin Zhao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Ying Wu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Qiao Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Juan Huang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Xumin Ou
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Di Sun
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Bin Tian
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Yu He
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Zhen Wu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China.
| | - Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the P.R.China, PR China.
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Zhao T, Li H, Zhang M, Xu Y, Zhang M, Chen L. Systematic evaluation of multifactorial causal associations for Alzheimer's disease and an interactive platform MRAD developed based on Mendelian randomization analysis. eLife 2024; 13:RP96224. [PMID: 39392298 PMCID: PMC11469671 DOI: 10.7554/elife.96224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024] Open
Abstract
Alzheimer's disease (AD) is a complex degenerative disease of the central nervous system, and elucidating its pathogenesis remains challenging. In this study, we used the inverse-variance weighted (IVW) model as the major analysis method to perform hypothesis-free Mendelian randomization (MR) analysis on the data from MRC IEU OpenGWAS (18,097 exposure traits and 16 AD outcome traits), and conducted sensitivity analysis with six models, to assess the robustness of the IVW results, to identify various classes of risk or protective factors for AD, early-onset AD, and late-onset AD. We generated 400,274 data entries in total, among which the major analysis method of the IVW model consists of 73,129 records with 4840 exposure traits, which fall into 10 categories: Disease, Medical laboratory science, Imaging, Anthropometric, Treatment, Molecular trait, Gut microbiota, Past history, Family history, and Lifestyle trait. More importantly, a freely accessed online platform called MRAD (https://gwasmrad.com/mrad/) has been developed using the Shiny package with MR analysis results. Additionally, novel potential AD therapeutic targets (CD33, TBCA, VPS29, GNAI3, PSME1) are identified, among which CD33 was positively associated with the main outcome traits of AD, as well as with both EOAD and LOAD. TBCA and VPS29 were negatively associated with the main outcome traits of AD, as well as with both EOAD and LOAD. GNAI3 and PSME1 were negatively associated with the main outcome traits of AD, as well as with LOAD, but had no significant causal association with EOAD. The findings of our research advance our understanding of the etiology of AD.
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Affiliation(s)
- Tianyu Zhao
- Department of Pharmacology, College of Basic Medical Sciences, Jilin UniversityChangchunChina
| | - Hui Li
- Department of Neurology, Xuanwu Hospital, Capital Medical UniversityBeijingChina
- Neurology and Intracranial Hypertension & Cerebral Venous Disease Center National Health Commission of China, Xuanwu Hospital, Capital Medical UniversityBeijingChina
| | | | - Yang Xu
- Department of Pharmacology, College of Basic Medical Sciences, Jilin UniversityChangchunChina
| | - Ming Zhang
- Department of Pharmacology, College of Basic Medical Sciences, Jilin UniversityChangchunChina
| | - Li Chen
- Department of Pharmacology, College of Basic Medical Sciences, Jilin UniversityChangchunChina
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Jagtap U, Quan A, Ono Y, Lee J, Shen KA, Manakov S, Szabo G, Nasser I, Slack FJ. miR-21: A therapeutic target for delaying severe liver disease and hepatocellular carcinoma in high-fat-diet-fed mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.19.613915. [PMID: 39386656 PMCID: PMC11463666 DOI: 10.1101/2024.09.19.613915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Liver disease, including hepatocellular carcinoma (HCC), is a major global health concern, claiming approximately 2 million lives worldwide annually, yet curative treatments remain elusive. In this study, we aimed to investigate the role of microRNA-21-5p (miR-21) in metabolic dysfunction-associated steatotic liver disease (previously NAFLD), metabolic-associated steatohepatitis (previously NASH), and HCC within the context of a Western high-fat diet, without additional choline (HFD) and offering potential therapeutic insights. We found that reduced miR-21 levels correlated with liver disease progression in WT mice fed on HFD, while miR-21 knockout mice showed exacerbated metabolic dysfunction, including obesity, hepatomegaly, hyperglycemia, insulin resistance, steatosis, fibrosis, and HCC. Our study reveals that miR-21 plays a protective role in metabolic syndrome and in the progression of liver disease to cancer. MiR-21 directly targets Transforming growth factor beta-induced ( Tgfbi ), a gene also known to be significantly upregulated and a potential oncogene in HCC. Further, our study showed that intervention with the administration of a miR-21 mimic in WT livers effectively improves insulin sensitivity, steatosis, fibrosis, Tgfbi expression and tumor burden in HFD conditions. These findings indicate that miR-21 could serve as an effective strategy to delay or prevent liver disease in high-fat-diet environments. Significance Our study demonstrates in vivo that miR-21 has protective functions in the broad spectrum of high-fat diet-based, progressive liver disease and cancer, and we show potential therapeutic value of a microRNA-21 mimic. Graphical abstract
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Zheng X, Wang Y, Qiu X. Comprehensive analysis of MAPK genes in the prognosis, immune characteristics, and drug treatment of renal clear cell carcinoma using bioinformatic analysis and Mendelian randomization. Eur J Pharmacol 2024; 980:176840. [PMID: 39038636 DOI: 10.1016/j.ejphar.2024.176840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024]
Abstract
Mitogen-activated protein kinase (MAPK) signalling is vitally important in tumour development and progression. This study is the first to comprehensively analyse the role of MAPK-family genes in the progression, prognosis, immune-cell infiltration, methylation, and potential therapeutic value drug candidates in ccRCC. We identified a novel prognostic panel of six MAPK-signature genes (MAP3K12, MAP3K1, MAP3K5, MAPK1, MAPK8, MAPK9), and introduced a robust MAPK-signature risk model for predicting ccRCC prognosis. Model construction, evaluation, and external validation using datasets from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database demonstrated its stability, as well as high sensitivity and specificity. Enrichment analysis suggested the participation of immune-mediated mechanism in MAPK dysregulation in ccRCC. Immune-infiltration analysis confirmed the relationship and revealed that the MAPK-signature risk model might stratify immunotherapy response in ccRCC, which was verified in drug sensitivity analysis and validated in external ccRCC immunotherapy dataset (GSE67501). Potential therapeutic drug predictions for key MAPKs using DSigDB, Network Analyst, CTD, and DGIdb were subsequently verified by molecular docking with AutoDock Vina and PyMol. Mendelian randomization further demonstrated the possibilities of the MAPK-signature genes as targets for therapeutic drugs in ccRCC. Methylation analysis using UALCAN and MethSurv revealed the participation of epigenetic modifications in dysregulation and survival difference of MAPK pathway in ccRCC. Among the key MAPKs, MAP3K12 exhibited the highest significance, indicating its independent prognostic value as single gene in ccRCC. Knockout and overexpression validation experiments in vitro and in vivo found that MAP3K12 acted as a promoter of tumour progression in RCC, suggesting a pivotal role for MAP3K12 in the proliferation, migration, and invasion of RCC cells. Our findings proposed the potential of MAPK-signature genes as biomarkers for prognosis and therapy response, as well as targets for therapeutic drugs in ccRCC.
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Affiliation(s)
- Xinyi Zheng
- Department of Pharmacy, Huashan Hospital, Fudan University, 12 Middle Urumqi Road, Shanghai, 200040, China
| | - Yiqiu Wang
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China; State Key Laboratory of Oncogenes and Related Genes, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Xiaoyan Qiu
- Department of Pharmacy, Huashan Hospital, Fudan University, 12 Middle Urumqi Road, Shanghai, 200040, China.
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Zhang C, Zhang Y, Liu B, Chen Y, Xie Y, Huang H, Liu Z, He Z. Proteome and Metabolome Profiling of Anticoagulant Disorders Induced by Familial Protein S Deficiency. J Proteome Res 2024; 23:4538-4552. [PMID: 39265992 PMCID: PMC11460325 DOI: 10.1021/acs.jproteome.4c00399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/30/2024] [Accepted: 09/05/2024] [Indexed: 09/14/2024]
Abstract
Protein S deficiency (PSD) is an autosomal dominant disorder characterized by congenital thrombophilia. Studies on PSD are limited yet, resulting in a lack of clarity about molecular changes during abnormal coagulation. Proteomics and metabolomics analyses were conducted on the plasma of PSD patients based on liquid and gas chromatography-mass spectrometry (LC- and GC-MS). Differential proteins and metabolites of PSD were then filtered by univariate statistical analysis and subjected to network analysis using the ingenuity pathway analysis (IPA) platform. The proteome and metabolome of PSD were obviously disturbed, and the biological pathway of coagulation and complement cascades was the most affected. During PSD, overall levels of anticoagulant protein decreased and negative regulation of thrombin production was reduced, causing the formation of fibrin clots and platelet aggregation. Furthermore, 9 differential proteins correlated significantly with protein S, comprising A2M, AGT, APOE, FGG, GPLD1, IGHV1-69, CFHR5, CPN2, and CA1. The biological networks suggested that the pathways of acute phase response, FXR/RXR activation, serotonin receptor signaling, and p70S6K signaling were associated with PSD, indicating an interaction disorder of inflammatory immune and lipid metabolism. The findings may contribute to knowledge of available functional molecules and biological pathways of familial PSD and help with treatment improvement. Data are available via ProteomeXchange with identifier PXD055111 and MetaboLights with reference number MTBLS2653.
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Affiliation(s)
- Caiping Zhang
- Guangdong
Provincial Key Laboratory of Translational Cancer Research of Chinese
Medicines, Joint International Research Laboratory of Translational
Cancer Research of Chinese Medicines, International Institute for
Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Yimin Zhang
- Guangdong
Provincial Key Laboratory of Translational Cancer Research of Chinese
Medicines, Joint International Research Laboratory of Translational
Cancer Research of Chinese Medicines, International Institute for
Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Binjie Liu
- Guangdong
Provincial Key Laboratory of Translational Cancer Research of Chinese
Medicines, Joint International Research Laboratory of Translational
Cancer Research of Chinese Medicines, International Institute for
Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Yongxv Chen
- Guangdong
Provincial Key Laboratory of Translational Cancer Research of Chinese
Medicines, Joint International Research Laboratory of Translational
Cancer Research of Chinese Medicines, International Institute for
Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Yue Xie
- Department
of Pharmacy, Shenzhen Bao’an Traditional
Chinese Medicine Hospital, Shenzhen 518133, China
| | - Huiting Huang
- Department
of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangzhou University of Chinese
Medicine, Guangzhou, Guangdong 510403, China
| | - Zhongqiu Liu
- Guangdong
Provincial Key Laboratory of Translational Cancer Research of Chinese
Medicines, Joint International Research Laboratory of Translational
Cancer Research of Chinese Medicines, International Institute for
Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Zhuoru He
- Guangdong
Provincial Key Laboratory of Translational Cancer Research of Chinese
Medicines, Joint International Research Laboratory of Translational
Cancer Research of Chinese Medicines, International Institute for
Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
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Lu Y, Qin M, Qi X, Yang M, Zhai F, Zhang J, Yan Z, Yan L, Qiao J, Yuan P. Sex differences in human pre-gastrulation embryos. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2721-y. [PMID: 39327393 DOI: 10.1007/s11427-024-2721-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 09/02/2024] [Indexed: 09/28/2024]
Abstract
Human fetuses exhibit notable sex differences in growth rate and response to the intrauterine environment, yet their origins and underlying mechanisms remain uncertain. Here, we conduct a detailed investigation of sex differences in human pre-gastrulation embryos. The lower methylation and incomplete inactivation of the X chromosome in females, as well as the sex-specific cell-cell communication patterns, contribute to sex-differential transcription. Male trophectoderm is more inclined toward syncytiotrophoblast differentiation and exhibits a stronger hormone secretion capacity, while female trophectoderm tends to retain cytotrophoblast program with stronger mitochondrial function as well as higher vasculogenesis and immunotolerance signals. Male primitive endoderm initiates the anterior visceral endoderm transcriptional program earlier than females. The cell cycle activities of the epiblast and primitive endoderm are higher in males compared to females, while the situation is opposite in the trophectoderm. In conclusion, our study provides in-depth insights into the sex differences in human pre-gastrulation embryos and contributes to unraveling the origins of the sex differences in human fetal development.
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Affiliation(s)
- Yongjie Lu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Meng Qin
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xintong Qi
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Ming Yang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Fan Zhai
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jiaqi Zhang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Zhiqiang Yan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
| | - Liying Yan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
| | - Peng Yuan
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
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9
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Fazal A, Yang M, Han H, Lu G, Hao C, Lai X, Song Y, Ma H, Yin T, Qi J, Sun S, Niu K, Wen Z, Yang Y. Impact of dual Bt-transgenic maize (2A7) on soil microbial communities and enzyme activities: A comparative study with control variety Z58. ENVIRONMENTAL RESEARCH 2024; 263:120006. [PMID: 39299448 DOI: 10.1016/j.envres.2024.120006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 09/10/2024] [Accepted: 09/13/2024] [Indexed: 09/22/2024]
Abstract
The impacts of transgenic crops on soil microbiology and fertility are critical in determining their biosafety. While transgenic crops can alter soil microbes, their effects are often context-dependent; therefore, the ecological importance of these changes remains a topic of ongoing research. Using high-throughput sequencing, we investigated the effects of Bacillus thuringiensis (Bt) maize expressing the mcry1Ab and mcry2Ab genes (2A7) on soil nutrient dynamics, as well as the diversity and function of soil microbial communities, including bacteria and fungi, within different soil compartments. Our findings revealed a plant-shaped rhizosphere (RS) microbial community as a result of the selective recruitment of microorganisms from the surrounding environment. The transgene insertion had a significant impact on the RS niche, and several species eventually became associated with Z58 and 2A7 plants. For example, Neocosmospora rubicola fungal and Pantoea dispersa bacterial microorganisms were significantly decreased in the dual Bt-transgenic 2A7 rhizosphere but enriched in the Z58 rhizospheres. The activity of soil enzymes such as urease, invertase, and alkaline phosphatase was boosted by Bt-transgenic 2A7. LefSe analysis identified significant bacterial and fungal biomarker species that were responsible for the differential effects of Bt-transgenic 2A7 and control Z58 within rhizosphere soils. Mantel analysis further demonstrated that the root exudates of 2A7 altered nutrient-acquisition enzymes by influencing biomarker taxa. PICRUSt2 functional characterization revealed a significantly higher abundance of the phosphate-starvation-inducible protein in control Z58 than in Bt-transgenic 2A7. Furthermore, taxonomy, alpha (Shannon diversity), and beta diversity analyses all revealed niche-driven microbial profile differentiation. Niche partitioning also had a significant impact on N- and P-related COGs as well. Our findings suggests that Bt-transgenic 2A7 modulates rhizosphere microbial communities by affecting biomarker taxa and soil enzyme activity. These findings will promote sustainable agriculture practices by advancing our knowledge of the ecological effects of Bt crops on soil microbial communities.
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Affiliation(s)
- Aliya Fazal
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Minkai Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Hongwei Han
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Guihua Lu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; School of Life Sciences, Huaiyin Normal University, Huaian, 223300, China
| | - Chenyu Hao
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Lai
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yuhang Song
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Hanke Ma
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinliang Qi
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Shucun Sun
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Kechang Niu
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zhongling Wen
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| | - Yonghua Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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10
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Linazi G, Maimaiti A, Abulaiti Z, Shi H, Zhou Z, Aisa MY, Kang Y, Abulimiti A, Dilimulati X, Zhang T, Wusiman P, Wang Z, Abulaiti A. Prognostic value of anoikis-related genes revealed using multi-omics analysis and machine learning based on lower-grade glioma features and tumor immune microenvironment. Heliyon 2024; 10:e36989. [PMID: 39286119 PMCID: PMC11402926 DOI: 10.1016/j.heliyon.2024.e36989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/19/2024] Open
Abstract
Background The investigation explores the involvement of anoikis-related genes (ARGs) in lower-grade glioma (LGG), seeking to provide fresh insights into the disease's underlying mechanisms and to identify potential targets for therapy. Methods We applied unsupervised clustering techniques to categorize LGG patients into distinct molecular subtypes based on ARGs with prognostic significance. Additionally, various machine learning algorithms were employed to pinpoint genes most strongly correlated with patient outcomes, which were then used to develop and assess risk profiles. Results Our analysis identified two distinct molecular subtypes of LGG, each with significantly different prognoses. Patients in Cluster 2 had a median survival of 2.036 years, markedly shorter than the 7.994 years observed in Cluster 1 (P < 0.001). We also constructed a six-gene ARG signature that efficiently classified patients into two risk categories, showing median survival durations of 4.084 years for the high-risk group and 10.304 years for the low-risk group (P < 0.001). Significantly, the immune profiles, tumor mutation characteristics, and drug sensitivity varied greatly among these risk groups. The high-risk group was characterized by a "cold" tumor microenvironment (TME), a lower IDH1 mutation rate (61.7 % vs. 91.4 %), a higher TP53 mutation rate (53.7 % vs. 38.9 %), and greater sensitivity to targeted therapies such as QS11 and PF-562271. Furthermore, our nomogram, integrating risk scores with clinicopathological features, demonstrated strong predictive accuracy for clinical outcomes in LGG patients, with an AUC of 0.903 for the first year. The robustness of this prognostic model was further validated through internal cross-validation and across three external cohorts. Conclusions The evidence from our research suggests that ARGs could potentially serve as reliable indicators for evaluating immunotherapy effectiveness and forecasting clinical results in patients with LGG.
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Affiliation(s)
- Gu Linazi
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Aierpati Maimaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Zulihuma Abulaiti
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Hui Shi
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Zexin Zhou
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Mizhati Yimiti Aisa
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Yali Kang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Ayguzaili Abulimiti
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Xierzhati Dilimulati
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Tiecheng Zhang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Patiman Wusiman
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Zengliang Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
| | - Aimitaji Abulaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, China
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11
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Tan B, Tao T, Lin D, Yu Q, Sun F, Li Z. Exploration of the potential mechanism of Yiyi Tongfeng Formula in the treatment of acute gouty arthritis based on network pharmacology and molecular docking: A review. Medicine (Baltimore) 2024; 103:e39609. [PMID: 39287271 PMCID: PMC11404889 DOI: 10.1097/md.0000000000039609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/23/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024] Open
Abstract
The global prevalence of gout is on the rise. Yiyi Tongfeng Formula (YTF), a traditional herbal compound, has gained recognition for its efficacy in managing acute gouty arthritis (AGA). Despite its widespread use, the underlying mechanisms of YTF in AGA treatment remain largely undefined. This study employed network pharmacology and molecular docking to elucidate these mechanisms. We utilized the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, SymMap database, and various literature sources to identify active components and corresponding targets of YTF. Relevant AGA-associated targets were identified through the Genecards, Drugbank, Therapeutic Target Database, and Online Mendelian Inheritance in Man databases. A protein-protein interaction network was constructed to delineate interactions between YTF targets and AGA. Key ingredients and central targets were further analyzed using Cytoscape. Functional enrichment analyses, including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, were conducted via Metascape. Additionally, molecular docking studies were performed using PyMOL and AutoDock4. It was found that quercetin, kaempferol, and luteolin may be the main active components of YTF for AGA treatment. Gene Ontology enrichment analysis shows that the main biological processes involved are cellular responses to lipids, and inflammatory responses. Kyoto Encyclopedia of Genes and Genomes enrichment analysis suggests the involvement of the IL-17 signaling pathway, AGE-RAGE signaling pathway in diabetic complications, TNF signaling pathway, and so on. The findings suggest a multi-faceted therapeutic approach of YTF in treating AGA, involving multiple components, targets, biological processes, and signaling pathways. This comprehensive mechanism offers a foundation for further experimental validation.
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Affiliation(s)
- Boyang Tan
- College of Integrative Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Tao Tao
- College of Integrative Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Dongyang Lin
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Qingyuan Yu
- College of Integrative Medicine, Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Fengling Sun
- Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Zhenhua Li
- Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, Jilin, China
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12
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Bian X, Li X, Qu C, Zhang M, Li D, Wang Y, Jiang J, Liu G. Transcriptome sequencing-based analysis of primary vein development in Betula pendula 'Dalecarlica'. Gene 2024; 933:148948. [PMID: 39277147 DOI: 10.1016/j.gene.2024.148948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 09/09/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
Keymessage The study revealed the major biological processes occurred at three developmental stages and identified candidate genes involved in primary vein development of birch plants. Vascular tissues usually mirror the surrounding leaf shape and its development plays a fundamental role in plant performance. However, the information of vascular development in birch trees, especially primary vein development, remains unclear. Therefore, we conducted the anatomical observation on primary veins from leaves at different development stages in Betula pendula 'Dalecarlica'. With the development of primary vein, dynamic changes in mechanical tissue thickness and primary vein diameter were consistent with each other, and the sum of phloem, xylem and cambium thickness was significantly varied. Transcriptome analysis indicated that primary vein development could be divided into three stages, namely Stage I, II and III, which were in aggreement with anatomical observation. Expression of marker genes associated with vascular tissues revealed that pro-vasculature development occurred at Stage I and II, and phloem development occurred at Stage III. GO enrichment analysis of differentially expressed genes (DEGs) showed that shared DEGs at Stage II were mainly engaged in cell division and cell cycle, and shared DEGs at Stage III were mainly engaged in phosphorylation. Decreased cell division and cell cycle as well as activation of lignin biosynthesis might contribute to primary vein development. Combining phenotypic traits, we performed weighted gene co-expression network analysis and identified a cytochrome P450 84A (CYP84A) family gene (BpF5H1). Based on analyses of gene families, expression patterns and yeast-two hybrid assay results, we proposed a potential electron transfer pathway involving BpF5H1 and three cytochrome b5 proteins during primary vein development in B. pendula 'Dalecarlica'. These results could shed some light on which biological processes occurred during primary vein formation and provide some valuable clues for vascular morphogenesis in woody plants.
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Affiliation(s)
- Xiuyan Bian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University and Chinese Academy of Forestry, Harbin 150040, China
| | - Xiaoyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University and Chinese Academy of Forestry, Harbin 150040, China
| | - Chang Qu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Manman Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Danyang Li
- Core facility of Wuhan University, Wuhan 430072, China
| | - Yunjiao Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University and Chinese Academy of Forestry, Harbin 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University and Chinese Academy of Forestry, Harbin 150040, China.
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13
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Zeng Z, Hu Y, Xiang J, Su J, Tan H, Lai T, Chen X, Fang G, Li L, Luo L. Cucurbitacin B targets STAT3 to induce ferroptosis in non-small cell lung cancer. Eur J Pharmacol 2024; 978:176805. [PMID: 38950838 DOI: 10.1016/j.ejphar.2024.176805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/03/2024]
Abstract
Cucurbitacin B (CuB) is a compound found in plants like Cucurbitaceae that has shown promise in fighting cancer, particularly in lung cancer. However, the specific impact of CuB on ferroptosis and how it works in lung cancer cells has not been fully understood. Our research has discovered that CuB can effectively slow down the growth of non-small cell lung cancer (NSCLC) cells. Even in small amounts, it was able to inhibit the growth of various NSCLC cell lines. This inhibitory effect was reversed when ferroptosis inhibitors DFO, Lip-1 and Fer-1 were introduced. CuB was found to increase the levels of reactive oxygen species (ROS), lipid ROS, MDA, and ferrous ions within H358 lung cancer cells, leading to a decrease in GSH, mitochondrial membrane potential (MMP) and changes in ferroptosis-related proteins in a dose-dependent manner. These findings were also confirmed in A549 lung cancer cells. In A549 cells, different concentrations of CuB induced the accumulation of intracellular lipid ROS, ferrous ions and changes in ferroptosis-related indicators in a concentration-dependent manner. Meanwhile, the cytotoxic effect induced by CuB in A549 cells was counteracted by ferroptosis inhibitors DFO and Fer-1. Through network pharmacology, we identified potential targets related to ferroptosis in NSCLC cells treated with CuB, with STAT3 targets showing high scores. Further experiments using molecular docking and cell thermal shift assay (CETSA) revealed that CuB interacts with the STAT3 protein. Western blot and immunofluorescence staining demonstrated that CuB inhibits the phosphorylation of STAT3 (P-STAT3) in H358 cells. Silencing STAT3 enhanced CuB-induced accumulation of lipid ROS and iron ions, as well as the expression of ferroptosis-related proteins. On the other hand, overexpression of STAT3 reversed the effects of CuB-induced ferroptosis. The results indicate that CuB has the capability to suppress STAT3 activation, resulting in ferroptosis, and could be a promising treatment choice for NSCLC.
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Affiliation(s)
- Zeyao Zeng
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Yingying Hu
- Department of Pathophysiology, Guangdong Medical University, Zhanjiang, 524002, Guangdong, China
| | - Jing Xiang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Jiating Su
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Huiting Tan
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Tianli Lai
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Xinming Chen
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Guixuan Fang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Li Li
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China.
| | - Lianxiang Luo
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China.
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14
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Wang K, Wang A, Deng J, Yang J, Chen G, Chen Q, Ye M, Lin D. Tert-butylhydroquinone promotes skin flap survival by inhibiting oxidative stress mediated by the Nrf2/HO-1 signalling pathway. Br J Pharmacol 2024. [PMID: 39233316 DOI: 10.1111/bph.17321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND AND PURPOSE Skin flaps are among the most important means of wound repair in clinical settings. However, partial or even total distal necrosis may occur after a flap operation, with severe consequences for both patients and doctors. This study investigated whether tert-butylhydroquinone (TBHQ), a known agonist of the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2), and an antioxidant, could promote skin flap survival. EXPERIMENTAL APPROACH McFarlane skin flap models were established in male Sprague-Dawley rats and then randomly divided into control, low-dose TBHQ, and high-dose TBHQ treatment groups. On postoperative day 7, the survival and blood flow of the skin flaps were assessed. Using flap tissue samples, angiogenesis, inflammation, apoptosis, autophagy, and Nrf2/haem oxygenase 1 (HO-1) signalling pathway activity were measured with immunohistochemical techniques and western blotting. KEY RESULTS TBHQ dose-dependently stimulated the Nrf2/HO-1 signalling pathway, inducing autophagy through the up-regulation of LC3B and beclin 1 and concurrently suppressing p62 expression. Additionally, TBHQ hindered apoptosis by enhancing Bcl-2 expression while inhibiting the expression of Bax. It suppressed inflammation by inhibiting the expression of interleukin 1β, interleukin 6, and tumour necrosis factor-α and enhanced angiogenesis by promoting the expression of vascular endothelial growth factor. CONCLUSION AND IMPLICATIONS In summary, TBHQ promoted flap survival in rats by up-regulating the Nrf2/HO-1 signalling pathway. As TBHQ is already widely used as a food additive, it could offer an acceptable means of improving clinical outcomes following skin flap surgery in patients.
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Affiliation(s)
- Kaitao Wang
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - An Wang
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jiapeng Deng
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jialong Yang
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Guodong Chen
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Qingyu Chen
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Minle Ye
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Dingsheng Lin
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
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15
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Agüera-Lorente A, Alonso-Pardavila A, Larrinaga M, Boyano MD, González E, Falcón-Pérez JM, Asumendi A, Apraiz A. Small extracellular vesicle-based human melanocyte and melanoma signature. Pigment Cell Melanoma Res 2024; 37:569-582. [PMID: 38158521 DOI: 10.1111/pcmr.13158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/10/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Intercellular communication is a cell-type and stimulus-dependent event driven not only by soluble factors but also by extracellular vesicles (EVs). EVs include vesicles of different size and origin that contain a myriad of molecules. Among them, small EVs (sEV; <200 nm) have been shown to modulate not just regional cell responses but also distant organ behavior. In cancer, distant organ modulation by sEVs has been associated to disease dissemination, which is one of the main concerns in melanoma. Description of broadly conserved alterations in sEV-contained molecules represents a strategy to identify key modifications in cellular communication as well as new disease biomarkers. Here, we characterize proteomes of cutaneous melanocyte and melanoma-derived sEVs to deepen on the landscape of normal and disease-related cell communication. Results reveal the presence of unique protein signatures for melanocytes and melanoma cells that reflect cellular transformation-related profound modifications. Melanocyte-derived sEVs are enriched in oxidative metabolism (e.g., aconitase 2, ACO2) or pigmentation (e.g., tyrosinase, TYR) related proteins while melanoma-derived sEVs reflect a generalized decrease in mature melanocytic markers (e.g., melanoma antigen recognized by T-cells 1, MART-1, also known as MLANA) and an increase in epithelial to mesenchymal transition (EMT)-related adhesion molecules such as tenascin C (TNC).
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Affiliation(s)
- Andrea Agüera-Lorente
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, Leioa, Spain
| | | | - María Larrinaga
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, Leioa, Spain
| | - María Dolores Boyano
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Esperanza González
- Exosomes Laboratory, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Derio, Spain
| | - Juan Manuel Falcón-Pérez
- Exosomes Laboratory, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
- Metabolomics Platform, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Aintzane Asumendi
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Aintzane Apraiz
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
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16
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Wang X, Li C, Huang S, Gao H, Li Y, Chen X, Huang L, Luo J, Zhang L, Zhou X. Pathogenic and Comparative Genomic Analysis of Ralstonia pseudosolanacearum Isolated from Casuarina. PLANT DISEASE 2024; 108:2809-2819. [PMID: 38687570 DOI: 10.1094/pdis-01-24-0118-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Casuarina equisetifolia is crucial in protecting coastal regions of China against typhoon attacks but has faced a substantial challenge due to wilt disease caused by pathogens of the Ralstonia solanacearum species complex (RSSC). Although the initial outbreak of Casuarina wilt in the 1970s was effectively controlled by disease-resistant C. equisetifolia varieties, the disease has recently re-emerged in coastal regions of Guangdong. In this study, we report the isolation, characterization, and comparative genomic analysis of 11 RSSC strains from diseased C. equisetifolia at various locations along the coast of Guangdong. Phylogenomic analysis showed that the strains were closely related and clustered with phylotype I strains previously isolated from peanuts. Single-gene-based analysis further suggested these strains could be derived from strains present in Guangdong since the 1980s, indicating a historical context to their current pathogenicity. Casuarina-isolated strains exhibited notably higher virulence against C. equisetifolia and peanuts than the representative RSSC strains GMI1000 and EP1, suggesting host-specific adaptations that possibly contributed to the recent outbreak. Comparative genomic analysis among RSSC strains revealed a largely conserved genome structure and high levels of conservation in gene clusters encoding extracellular polysaccharide biosynthesis, secretion systems, and quorum sensing regulatory systems. However, we also found a number of unique genes in the Casuarina-isolated strains that were absent in GMI1000 and EP1, and vice versa, pointing to potential genetic factors underpinning their differential virulence. These unique genes offer promising targets for future functional studies. Overall, our findings provide crucial insights into the RSSC pathogens causing Casuarina wilt in Guangdong, guiding future efforts in disease control and prevention.
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Affiliation(s)
- Xiaoqing Wang
- Guangdong Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Chuhao Li
- Guangdong Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Shaohua Huang
- Guangdong Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Huagui Gao
- Guangdong Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yonglin Li
- Guangdong Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xuemei Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Liangzhou Huang
- Forestry Research Institute of Zhanjiang City, Zhanjiang 524037, Guangdong, China
| | - Jianhua Luo
- Forestry Research Institute of Zhanjiang City, Zhanjiang 524037, Guangdong, China
| | - LianHui Zhang
- Guangdong Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiaofan Zhou
- Guangdong Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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17
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Sun X, Su L, Zhen J, Wang Z, Panhwar KA, Ni SQ. The contribution of swine wastewater on environmental pathogens and antibiotic resistance genes: Antibiotic residues and beyond. CHEMOSPHERE 2024; 364:143263. [PMID: 39236924 DOI: 10.1016/j.chemosphere.2024.143263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/07/2024] [Accepted: 09/02/2024] [Indexed: 09/07/2024]
Abstract
Swine wastewater application can introduce antibiotics, antibiotic resistance genes (ARGs) into environments. Herein, the full-scale transmission of antibiotics, ARGs and their potential carriers from an intensive swine feedlot to its surroundings were explored. Results showed that lincomycin and doxycycline hydrochloride were dominant antibiotics in this ecosystem. Lincomycin concentration were strongly associated with soil bacterial communities. According to the risk quotient (RQ), lincomycin was identified as posing higher ecological risk in aquatic environments. ARGs and mobile genetic elements (MGEs) abundance in wastewater were reduced after anaerobic treatment. Notably, ARGs composition of environmental samples were clustered into two groups based on if they were directly affected by the wastewater. However, there were no remarkable difference of ARGs abundance among environmental samples. The total abundance of ARGs was positively related to that of MGEs. Pathogens Escherichia coli and Enterococcus revealed strong connection with qnrS, tet and sul. Overall, this study highlights the importance of responsible antibiotics use in livestock production and appropriate treatment technology before agricultural application and discharge.
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Affiliation(s)
- Xiaojie Sun
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Lei Su
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Jianyuan Zhen
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhibin Wang
- School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Kashif Ali Panhwar
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China
| | - Shou-Qing Ni
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong, 266237, China.
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18
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Ali F, Tang Z, Mo G, Zhang B, Ling X, Qiu Z. Taxonomic and functional changes in wheat rhizosphere microbiome caused by imidazoline-based herbicide and genetic modification. ENVIRONMENTAL RESEARCH 2024; 262:119726. [PMID: 39102937 DOI: 10.1016/j.envres.2024.119726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/07/2024]
Abstract
Genetically modified (GM) crop cultivation has received a lot of attention in recent years due to the substantial public debate. Consequently, an in-depth investigation of excessively used GM herbicide-tolerant crops is a vital step for the biosafety of genetically modified plants. Several studies have been conducted to study the impact of transgenic GM crops on soil microbial composition; however, research into the effects of non-transgenic GM crops is inadequate. In the current work, high-throughput sequencing was used to evaluate the impact of the acetolactate synthase (ALS)-mutant (WK170B), its control (YN19B), and the imazamox (IM) herbicide on the wheat rhizobiome. Under normal growth conditions, our work revealed a minimal impact of ALS-mutant WK170B on the rhizosphere microbiome compared to the control YN10B, except for some cyanobacterial microorganisms that showed a significant increase in abundance. This suggests that the gene mutation could potentially have a beneficial impact on the bacterial communities present in the rhizosphere. Following IM exposure, taxonomic analysis revealed a significant reduction in the relative abundance of Ralstonia pickettii and an unidentified member of the genus Ancylothrix 8 PC. Analyses of both alpha and beta diversity revealed a statistically significant increase in both microbial richness and species diversity. IM-induced relative abundance modulation was also evident through Linear discriminant analysis Effect Size (LEfSe), MetaStat, and heatmap analyses. The SIMPER analysis revealed that the microbial taxa Massilia, Limnobacter, Hydrogenophaga, Ralstonia, Nitrospira, and Ramlibacter exhibited the highest vulnerability to IM exposure. The functional attributes analysis revealed that the relative abundance of genes associated with the extracellular matrix-receptor interaction, which is responsible for structural support and stress response, increased significantly following IM exposure. Collectively, our study identifies key microbial taxa in the wheat rhizobiome that are sensitive to IM herbicides and provides a foundation for assessing the environmental risks associated with IM herbicide use.
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Affiliation(s)
- Farman Ali
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Zhaocheng Tang
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Gangao Mo
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Baolong Zhang
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xitie Ling
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Zeyu Qiu
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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19
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Wang X, Ji H, Zhong L, Zeng W, Ouyang Z, Li R. A Transcriptome Analysis of Poncirus trifoliata, an Aurantioideae Species Tolerant to Asian Citrus Psyllid, Has Identified Potential Genes and Events Associated with Psyllid Resistance. INSECTS 2024; 15:589. [PMID: 39194794 DOI: 10.3390/insects15080589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 08/29/2024]
Abstract
Citrus huanglongbing (HLB) is a devastating disease for citrus production, largely caused by the Asian citrus psyllid (ACP). Poncirus trifoliata exhibits high resistance to ACP; however, this resistance is weakened when C. sinensis is co-cultivated. This study aimed to identify the differentially expressed genes (DEGs) during ACP feeding and to uncover potential ACP resistance genes in P. trifoliata. In comparison to independent cultivation, 1247 and 205 DEGs were identified in P. trifoliata when co-cultivated with C. sinensis after 7 and 14 days, respectively. Analysis of enriched Gene Ontology categories revealed that DEGs were significantly associated with the cell wall, glucometabolic activities, and secondary metabolites. Additionally, these genes were found to be involved in phytohormone signaling, cell wall metabolism, redox state homeostasis, and secondary metabolites, as well as a number of transcription factor genes (TFs). Furthermore, we examined the impact of the ACP feeding factor on the gene expression patterns in P. trifoliata. Results showed an increase in the JA signaling pathway and various TFs. The RNA-seq results were verified using reverse transcription quantitative PCR. Our findings shed light on the molecular basis of ACP resistance in P. trifoliata and identified potential genes associated with this resistance.
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Affiliation(s)
- Xinyou Wang
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Haoran Ji
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Leijian Zhong
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Wei Zeng
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
| | - Zhigang Ouyang
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
- National Navel Orange Engineering Research Center, Ganzhou 341000, China
- Jiangxi Provincial Key Laboratory of Pest and Disease Control of Featured Horticultural Plants, Ganzhou 341000, China
| | - Ruimin Li
- College of Life Sciences, Gannan Normal University, Ganzhou 341000, China
- National Navel Orange Engineering Research Center, Ganzhou 341000, China
- Jiangxi Provincial Key Laboratory of Pest and Disease Control of Featured Horticultural Plants, Ganzhou 341000, China
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20
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Zou X, Ptáček LJ, Fu YH. The Genetics of Human Sleep and Sleep Disorders. Annu Rev Genomics Hum Genet 2024; 25:259-285. [PMID: 38669479 DOI: 10.1146/annurev-genom-121222-120306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Healthy sleep is vital for humans to achieve optimal health and longevity. Poor sleep and sleep disorders are strongly associated with increased morbidity and mortality. However, the importance of good sleep continues to be underrecognized. Mechanisms regulating sleep and its functions in humans remain mostly unclear even after decades of dedicated research. Advancements in gene sequencing techniques and computational methodologies have paved the way for various genetic analysis approaches, which have provided some insights into human sleep genetics. This review summarizes our current knowledge of the genetic basis underlying human sleep traits and sleep disorders. We also highlight the use of animal models to validate genetic findings from human sleep studies and discuss potential molecular mechanisms and signaling pathways involved in the regulation of human sleep.
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Affiliation(s)
- Xianlin Zou
- Department of Neurology, University of California, San Francisco, California, USA; , ,
| | - Louis J Ptáček
- Department of Neurology, University of California, San Francisco, California, USA; , ,
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, California, USA
- Weill Institute for Neurosciences, University of California, San Francisco, California, USA
- Institute of Human Genetics, University of California, San Francisco, California, USA
| | - Ying-Hui Fu
- Institute of Human Genetics, University of California, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, California, USA; , ,
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, California, USA
- Weill Institute for Neurosciences, University of California, San Francisco, California, USA
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21
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Zhou Z, Zhu R, Song Y, Zhang W, Sun B, Zhang Z, Yao H. Penguin-Driven Dissemination and High Enrichment of Antibiotic Resistance Genes in Lake Sediments across Antarctica. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39083437 DOI: 10.1021/acs.est.4c02732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Numerous penguins can propagate pathogens with antibiotic resistance genes (ARGs) into Antarctica. However, the effects of penguin dissemination on the lake ARGs still have received little attention via guano deposition. Here, we have profiled ARGs in ornithogenic sediments subject to penguin guano (OLS) and nonornithogenic sediments (NOLS) from 16 lakes across Antarctica. A total of 191 ARGs were detected in all sediment samples, with a much higher abundance and diversity in OLS than in NOLS. Surprisingly, highly diverse and abundant ARGs were found in the OLS with a detection frequency of >40% and an absolute abundance of (2.34 × 109)-(4.98 × 109) copies g-1, comparable to those in coastal estuarine sediments and pig farms. The strong correlations of identified resistance genes with penguin guano input amount, environmental factors, mobile genetic elements, and bacterial community, in conjunction with network and redundancy analyses, all indicated that penguins were responsible for the dissemination and high enrichment of ARGs in lake sediments via the guano deposition, which might greatly outweigh local human-activity effects. Our results revealed that ARGs could be carried into lakes across the Antarctica through penguin migration, food chains, and guano deposition, which were closely connected with the widespread pollution of ARGs at the global scale.
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Affiliation(s)
- Zeming Zhou
- Institute of Polar Environment & Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Renbin Zhu
- Institute of Polar Environment & Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yixin Song
- Institute of Polar Environment & Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Wanying Zhang
- Institute of Polar Environment & Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Bowen Sun
- Institute of Polar Environment & Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Zulin Zhang
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, U.K
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
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22
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Occean JR, Yang N, Sun Y, Dawkins MS, Munk R, Belair C, Dar S, Anerillas C, Wang L, Shi C, Dunn C, Bernier M, Price NL, Kim JS, Cui CY, Fan J, Bhattacharyya M, De S, Maragkakis M, de Cabo R, Sidoli S, Sen P. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. Nat Commun 2024; 15:6357. [PMID: 39069555 PMCID: PMC11284234 DOI: 10.1038/s41467-024-50725-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/15/2024] [Indexed: 07/30/2024] Open
Abstract
DNA hydroxymethylation (5hmC), the most abundant oxidative derivative of DNA methylation, is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been implicated in age-related diseases, its functional role in aging remains unknown. Here, using mouse liver and cerebellum as model organs, we show that 5hmC accumulates in gene bodies associated with tissue-specific function and restricts the magnitude of gene expression changes with age. Mechanistically, 5hmC decreases the binding of splicing associated factors and correlates with age-related alternative splicing events. We found that various age-related contexts, such as prolonged quiescence and senescence, drive the accumulation of 5hmC with age. We provide evidence that this age-related transcriptionally restrictive function is conserved in mouse and human tissues. Our findings reveal that 5hmC regulates tissue-specific function and may play a role in longevity.
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Affiliation(s)
- James R Occean
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Yan Sun
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Marshall S Dawkins
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Showkat Dar
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Lin Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Changyou Shi
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Christopher Dunn
- Flow Cytometry Unit, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Michel Bernier
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Nathan L Price
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Julie S Kim
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Chang-Yi Cui
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jinshui Fan
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | | | - Supriyo De
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA.
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23
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Akki AJ, Patil SA, Hungund S, Sahana R, Patil MM, Kulkarni RV, Raghava Reddy K, Zameer F, Raghu AV. Advances in Parkinson's disease research - A computational network pharmacological approach. Int Immunopharmacol 2024; 139:112758. [PMID: 39067399 DOI: 10.1016/j.intimp.2024.112758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
Parkinson's disease (PD), the second most prevalent neurodegenerative disorder, is projected to see a significant rise in incidence over the next three decades. The precise treatment of PD remains a formidable challenge, prompting ongoing research into early diagnostic methodologies. Network pharmacology, a burgeoning field grounded in systems biology, examines the intricate networks of biological systems to identify critical signal nodes, facilitating the development of multi-target therapeutic molecules. This approach systematically maps the components of Parkinson's disease, thereby reducing its complexity. In this review, we explore the application of network pharmacology workflows in PD, discuss the techniques employed in this field, and evaluate the current advancements and status of network pharmacology in the context of Parkinson's disease. The comprehensive insights will pave newer paths to explore early disease biomarkers and to develop diagnosis with a holistic in silico, in vitro, in vivo and clinical studies.
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Affiliation(s)
- Ali Jawad Akki
- Faculty of Science and Technology, BLDE (Deemed-to-be University), Vijayapura 586 103, India
| | - Shruti A Patil
- Faculty of Science and Technology, BLDE (Deemed-to-be University), Vijayapura 586 103, India
| | - Sphoorty Hungund
- Faculty of Science and Technology, BLDE (Deemed-to-be University), Vijayapura 586 103, India
| | - R Sahana
- Department of Computer Science and Engineering, RV Institute of Technology and Management, 560 076 Bengaluru, India
| | - Malini M Patil
- Department of Computer Science and Engineering, RV Institute of Technology and Management, 560 076 Bengaluru, India.
| | - Raghavendra V Kulkarni
- Faculty of Science and Technology, BLDE (Deemed-to-be University), Vijayapura 586 103, India
| | - K Raghava Reddy
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 12 2006, Australia
| | - Farhan Zameer
- Department of Dravyaguna (Ayurveda Pharmacology), Alva's Ayurveda Medical College, and PathoGutOmics Laboratory, ATMA Research Centre, Dakshina Kannada 574 227, India.
| | - Anjanapura V Raghu
- Department of Basic Sciences, Faculty of Engineering and Technology, CMR University, 562149 Bangalore, India.
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24
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Deng J, Wang K, Yang J, Wang A, Chen G, Ye M, Chen Q, Lin D. β-Caryophyllene promotes the survival of random skin flaps by upregulating the PI3K/AKT signaling pathway. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 130:155726. [PMID: 38815406 DOI: 10.1016/j.phymed.2024.155726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/28/2024] [Accepted: 05/07/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Flap transplantation is a widely used plastic repair technique in surgical procedures, aimed at addressing skin defects resulting from diverse wounds and diseases. However, due to the insufficient blood supply after flap surgery, the occurrence of ischemia-reperfusion injury, and an excessive sterile inflammatory response, flaps frequently develop complications (e.g., partial or complete ischemic necrosis). These complications have adverse effects on wound healing and repair. β-Caryophyllene (BCP) is a bicyclic sesquiterpene that is widely present in plants. It mitigates oxidative stress and inflammatory responses, demonstrates neuroprotective and analgesic properties, and serves a protective function in organs or tissues subjected to ischemia-reperfusion injury. However, no study has confirmed whether BCP can be used in the field of flap transplantation to improve the flap survival rate. METHODS To assess the impact of BCP on random flap survival, we constructed a modified McFarlane random flap model on the rat. After 7 consecutive days of gavage with different doses of BCP, we measured the survival area ratio, angiogenesis, blood perfusion, tissue inflammation level, apoptosis-related protein levels, and the PI3K/AKT signaling pathway expression of the random flap. RESULTS BCP treatment increased the survival area of the flap in a dose-dependent manner after random flap transplantation in rats. BCP mainly promoted the formation of tissue blood vessels, improved flap blood perfusion, limited the local inflammatory response, and reduced apoptosis. In addition, we demonstrated that BCP works primarily by promoting the PI3K/AKT signaling expression while enhancing the phosphorylation of AKT. Administration of wortmannin, a selective inhibitor of PI3K, eliminated the effects of BCP. CONCLUSION BCP can promote the survival of random flaps by upregulating the PI3K/AKT signaling pathway, increasing tissue blood perfusion, and limiting the inflammatory response and apoptosis.
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Affiliation(s)
- Jiapeng Deng
- Department of Orthopedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine. Wenzhou Medical University, Wenzhou 325000 PR China
| | - Kaitao Wang
- Department of Orthopedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine. Wenzhou Medical University, Wenzhou 325000 PR China
| | - Jialong Yang
- Department of Orthopedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine. Wenzhou Medical University, Wenzhou 325000 PR China
| | - An Wang
- Department of Orthopedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine. Wenzhou Medical University, Wenzhou 325000 PR China
| | - Guodong Chen
- Department of Orthopedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine. Wenzhou Medical University, Wenzhou 325000 PR China
| | - Minle Ye
- Department of Orthopedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine. Wenzhou Medical University, Wenzhou 325000 PR China
| | - Qingyu Chen
- Department of Orthopedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine. Wenzhou Medical University, Wenzhou 325000 PR China
| | - Dingsheng Lin
- Department of Orthopedics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine. Wenzhou Medical University, Wenzhou 325000 PR China.
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25
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Hou W, Hou W, Zhao X. Exploring transcriptomic databases: unraveling circadian gene disruptions in lower grade glioma. Sci Rep 2024; 14:16960. [PMID: 39043735 PMCID: PMC11266536 DOI: 10.1038/s41598-024-67559-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
The study explored the role of circadian rhythm genes (CRGs) in lower grade glioma (LGG) development and found that certain genes, such as CRY1, NPAS2, and RORB, were associated with increased or decreased risk of LGG. The study also investigated the correlation between CRGs and immune cell infiltration, revealing a negative association with macrophage infiltration and a positive correlation with B cell and CD8 + T cell infiltration. Additionally, the study identified major mutated CRGs, including PER2, BMAL1, CLOCK, and BMAL2, and their potential interaction with other CNS-associated genes. The study suggests that CRGs play a crucial role in immune response and tumorigenesis in LGG patients and warrants further investigation.
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Affiliation(s)
- Weiyu Hou
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, 030012, China
| | - Weiming Hou
- Department of Medical Engineering, Air Force Medical Center, PLA, Beijing, 100142, China
| | - Xueming Zhao
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, 030012, China.
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26
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Su Y, Yu H, Gao C, Sun S, Liang Y, Liu G, Zhang X, Dong Y, Liu X, Chen G, Shao H, McMinn A, Wang M. Effects of vegetation cover and aquaculture pollution on viral assemblages in mangroves sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135147. [PMID: 39029189 DOI: 10.1016/j.jhazmat.2024.135147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/07/2024] [Accepted: 07/06/2024] [Indexed: 07/21/2024]
Abstract
Mangrove forests, a critical coastal ecosystem, face numerous anthropogenic threats, particularly from aquaculture activities. Despite the acknowledged significance of viruses in local and global biogeochemical cycles, there is limited knowledge regarding the community structure, genomic diversity, and ecological roles of viruses in mangrove forests ecosystems, especially regarding their responses to aquaculture. In this study, we identified 17,755 viral operational taxonomic units (vOTUs) from nine sediments viromes across three distinct ecological regions of the mangrove forests ecosystem: mangrove, bare flat, and aquaculture regions. Viral assemblages varied among three regions, and the pathogenic viruses associated with marine animals, such as the white spot syndrome virus (WSSV) from Nimaviridae, were identified in this study. The relative abundance of Nimaviridae in the bare flat region was higher than in other regions. Furthermore, viruses in distinct mangrove forests sediments regions have adapted to their environments by adopting distinct survival strategies and encoding various auxiliary metabolic genes involved in carbon metabolism and antibiotic resistance. These adaptations may have profound impacts on biogeochemical cycles. This study provides the first insights into the effects of vegetation cover and aquaculture on the community structure and ecological roles of viruses in mangrove forests sediments. These findings are crucial for understanding the risks posed by anthropogenic threats to mangrove forests ecosystems and informing effective management strategies.
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Affiliation(s)
- Yue Su
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hao Yu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Chen Gao
- Haide College, Ocean University of China, Qingdao, China
| | - Shujuan Sun
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China.
| | - Gang Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Xinran Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yue Dong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Xiaoshou Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Guangcheng Chen
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China; Observation and Research Station of Coastal Wetland Ecosystem in Beibu Gulf, Ministry of Natural Resources, Beihai, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MoE Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Haide College, Ocean University of China, Qingdao, China; UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China; The Affiliated Hospital of Qingdao University, Qingdao 266000, China.
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27
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Occean JR, Yang N, Sun Y, Dawkins MS, Munk R, Belair C, Dar S, Anerillas C, Wang L, Shi C, Dunn C, Bernier M, Price NL, Kim JS, Cui CY, Fan J, Bhattacharyya M, De S, Maragkakis M, deCabo R, Sidoli S, Sen P. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.15.528714. [PMID: 36824863 PMCID: PMC9949049 DOI: 10.1101/2023.02.15.528714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
DNA hydroxymethylation (5hmC), the most abundant oxidative derivative of DNA methylation, is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been implicated in age-related diseases, its functional role in aging remains unknown. Here, using mouse liver and cerebellum as model organs, we show that 5hmC accumulates in gene bodies associated with tissue-specific function and restricts the magnitude of gene expression changes with age. Mechanistically, 5hmC decreases the binding of splicing associated factors and correlates with age-related alternative splicing events. We found that various age-related contexts, such as prolonged quiescence and senescence, drive the accumulation of 5hmC with age. We provide evidence that this age-related transcriptionally restrictive function is conserved in mouse and human tissues. Our findings reveal that 5hmC regulates tissue-specific function and may play a role in longevity.
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28
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Embarcadero-Jiménez S, Araujo-Palomares CL, Moreno-Perlín T, Ramírez-Álvarez N, Quezada-Hernández C, Batista-García RA, Sanchez-Flores A, Calcáneo-Hernández G, Silva-Jiménez H. Physiology and comparative genomics of the haloalkalitolerant and hydrocarbonoclastic marine strain Rhodococcus ruber MSA14. Arch Microbiol 2024; 206:328. [PMID: 38935150 DOI: 10.1007/s00203-024-04050-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Marine hydrocarbonoclastic bacteria can use polycyclic aromatic hydrocarbons as carbon and energy sources, that makes these bacteria highly attractive for bioremediation in oil-polluted waters. However, genomic and metabolic differences between species are still the subject of study to understand the evolution and strategies to degrade PAHs. This study presents Rhodococcus ruber MSA14, an isolated bacterium from marine sediments in Baja California, Mexico, which exhibits adaptability to saline environments, a high level of intrinsic pyrene tolerance (> 5 g L- 1), and efficient degradation of pyrene (0.2 g L- 1) by 30% in 27 days. Additionally, this strain demonstrates versatility by using naphthalene and phenanthrene as individual carbon sources. The genome sequencing of R. ruber MSA14 revealed a genome spanning 5.45 Mbp, a plasmid of 72 kbp, and three putative megaplasmids, lengths between 110 and 470 Kbp. The bioinformatics analysis of the R. ruber MSA14 genome revealed 56 genes that encode enzymes involved in the peripheral and central pathways of aromatic hydrocarbon catabolism, alkane, alkene, and polymer degradation. Within its genome, R. ruber MSA14 possesses genes responsible for salt tolerance and siderophore production. In addition, the genomic analysis of R. ruber MSA14 against 13 reference genomes revealed that all compared strains have at least one gene involved in the alkanes and catechol degradation pathway. Overall, physiological assays and genomic analysis suggest that R. ruber MSA14 is a new haloalkalitolerant and hydrocarbonoclastic strain toward a wide range of hydrocarbons, making it a promising candidate for in-depth characterization studies and bioremediation processes as part of a synthetic microbial consortium, as well as having a better understanding of the catabolic potential and functional diversity among the Rhodococci group.
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Affiliation(s)
- Salvador Embarcadero-Jiménez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Cynthia Lizzeth Araujo-Palomares
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Tonatiuh Moreno-Perlín
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, C.P. 62209, México
| | - Nancy Ramírez-Álvarez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Cristina Quezada-Hernández
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, C.P. 62209, México
- Departamento de Biología Animal, Biología Vegetal y Ecología, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas s/n, Jaén, 23071, España
| | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Unidad Universitaria de Secuenciación Masiva y Bioinformática, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, C.P. 62210, México
| | - Gabriela Calcáneo-Hernández
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, C.P. 04510, México
| | - Hortencia Silva-Jiménez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México.
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29
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Cao X, Jiang Z, Bu X, Li Q, Tian Y, Xu Z, Zhang B, Yuan X. MicroRNA-204-5p Attenuates Oxidative Stress, Apoptosis and Inflammation by Targeting TXNIP in Diabetic Cataract. Biochem Genet 2024:10.1007/s10528-024-10863-w. [PMID: 38896379 DOI: 10.1007/s10528-024-10863-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024]
Abstract
Diabetic cataract (DC) is a major cause of blindness in diabetic patients and it is characterized by early onset and rapid progression. MiR-204-5p was previously identified as one of the top five down-regulated miRNAs in human DC lens tissues. We aimed to determine the expression of miR-204-5p in human lens epithelial cells (HLECs) and explore its effects and mechanisms in regulating the progression of DC. The expression of miR-204-5p in the anterior capsules of DC patients and HLECs was examined by RT-qPCR. Bioinformatics tools were then used to identify the potential target of miR-204-5p. The relationship between miR-204-5p and the target gene was confirmed through a dual luciferase reporter assay. Additionally, the regulatory mechanism of oxidative stress, apoptosis, and inflammation in DC was investigated by overexpressing miR-204-5p using miR-204-5p agomir. The expression of miR-204-5p was downregulated in the anterior capsules of DC patients and HLECs. Overexpression of miR-204-5p reduced ROS levels, pro-apoptosis genes (Bid, Bax, caspase-3), and IL-1β production in HG-treated HLECs. TXNIP was the direct target of miR-204-5p by dual luciferase reporter assay. Therefore, this study demonstrated that miR-204-5p effectively reduced oxidative damage, apoptosis, and inflammation in HLECs under HG conditions by targeting TXNIP. Targeting miR-204-5p could be a promising therapeutic strategy for the potential treatment of DC.
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Affiliation(s)
- Xiang Cao
- Tianjin Eye Hospital, Nankai University Affiliated Eye Hospital, Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Institute, Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin, 300020, China
- Department of Ophthalmology, Affiliated People's Hospital, Jiangsu University, Zhenjiang, Jiangsu, 212002, China
| | - Zhixin Jiang
- Tianjin Eye Hospital, Nankai University Affiliated Eye Hospital, Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Institute, Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin, 300020, China
| | - Xiaofei Bu
- Tianjin Eye Hospital, Nankai University Affiliated Eye Hospital, Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Institute, Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin, 300020, China
| | - Qingyu Li
- Tianjin Eye Hospital, Nankai University Affiliated Eye Hospital, Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Institute, Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin, 300020, China
| | - Ye Tian
- Tianjin Eye Hospital, Nankai University Affiliated Eye Hospital, Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Institute, Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin, 300020, China
| | - Zijiao Xu
- Tianjin Eye Hospital, Nankai University Affiliated Eye Hospital, Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Institute, Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin, 300020, China
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Boyang Zhang
- Tianjin Eye Hospital, Nankai University Affiliated Eye Hospital, Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Institute, Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin, 300020, China
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Xiaoyong Yuan
- Tianjin Eye Hospital, Nankai University Affiliated Eye Hospital, Clinical College of Ophthalmology, Tianjin Medical University, Tianjin Eye Institute, Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin, 300020, China.
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30
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Xie Y, Gong S, Wang L, Yang Z, Yang C, Li G, Zha H, Lv S, Xiao B, Chen X, Di Z, He Q, Wang J, Weng Q. Unraveling the treatment effects of huanglian jiedu decoction on drug-induced liver injury based on network pharmacology, molecular docking and experimental validation. BMC Complement Med Ther 2024; 24:219. [PMID: 38849824 PMCID: PMC11157734 DOI: 10.1186/s12906-024-04517-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024] Open
Abstract
Huanglian Jiedu Decoction (HJD) is a well-known Traditional Chinese Medicine formula that has been used for liver protection in thousands of years. However, the therapeutic effects and mechanisms of HJD in treating drug-induced liver injury (DILI) remain unknown. In this study, a total of 26 genes related to both HJD and DILI were identified, which are corresponding to a total of 41 potential active compounds in HJD. KEGG analysis revealed that Tryptophan metabolism pathway is particularly important. The overlapped genes from KEGG and GO analysis indicated the significance of CYP1A1, CYP1A2, and CYP1B1. Experimental results confirmed that HJD has a protective effect on DILI through Tryptophan metabolism pathway. In addition, the active ingredients Corymbosin, and Moslosooflavone were found to have relative strong intensity in UPLC-Q-TOF-MS/MS analysis, showing interactions with CYP1A1, CYP1A2, and CYP1B1 through molecule docking. These findings could provide insights into the treatment effects of HJD on DILI.
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Affiliation(s)
- Yaochen Xie
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Shuchen Gong
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
- Taizhou Institute of Zhejiang University, Taizhou, 318000, China
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lingkun Wang
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Zhaoxu Yang
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Chen Yang
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Guilin Li
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Huiyan Zha
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Shuying Lv
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Boneng Xiao
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoyu Chen
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
| | - Zhenning Di
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qiaojun He
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China
- ZJU-Xinchang Joint Innovation Center (TianMu Laboratory), Gaochuang Hi-Tech Park, Xinchang, 312500, Zhejiang, China
- Department of Cardiology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jincheng Wang
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China.
- Taizhou Institute of Zhejiang University, Taizhou, 318000, China.
- Beijing Life Science Academy, Beijing, 102200, China.
| | - Qinjie Weng
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti- Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China.
- Taizhou Institute of Zhejiang University, Taizhou, 318000, China.
- ZJU-Xinchang Joint Innovation Center (TianMu Laboratory), Gaochuang Hi-Tech Park, Xinchang, 312500, Zhejiang, China.
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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31
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Yang M, Chen T, Liu Y, Huang L. Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams. IMETA 2024; 3:e184. [PMID: 38898979 PMCID: PMC11183158 DOI: 10.1002/imt2.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/24/2024] [Accepted: 03/01/2024] [Indexed: 06/21/2024]
Abstract
Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such as metabolomics, genomics, transcriptomics, and proteomics, their utility is undeniable. However, the operational complexity has been compounded by the absence of standardized data formats and the need to switch between various platforms for generating different Venn diagrams. To address these challenges, we introduce the EVenn platform, a versatile tool offering a unified interface for efficient data exploration and visualization of diverse Venn diagrams. EVenn (http://www.ehbio.com/test/venn) streamlines the data upload process with a standardized format, enhancing the capabilities for multimodule analysis. This comprehensive protocol outlines various applications of EVenn, featuring representative results of multiple Venn diagrams, data uploads in the centralized data center, and step-by-step case demonstrations. Through these functionalities, EVenn emerges as a valuable and user-friendly tool for the in-depth exploration of multiomics data.
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Affiliation(s)
- Mei Yang
- Institute of Traditional Chinese MedicineTianjin University of Traditional Chinese MedicineTianjinChina
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Tong Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Yong‐Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Luqi Huang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
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32
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Wen C, An Q, Zhou T, Yang F, Yan C. Integrating subjective feelings into the evaluation of ecological restoration outcomes of urban green space: Indicator framework from bibliometrics analysis and evidence synthesis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 360:121121. [PMID: 38744204 DOI: 10.1016/j.jenvman.2024.121121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
Despite much progress has been made in the evaluation of ecological restoration outcomes, there is still a lack of a suitable framework for evaluating the ecological restoration outcomes of urban green space. In view of this, this study systematically analyzed the characteristics and differences between the evaluation index systems of ecological restoration outcome and urban green space quality evaluation, and then discussed the relationship between objective elements of landscape and people's subjective feelings. On this basis, an ecological restoration outcome evaluation framework was developed for urban green space considering people's subjective feelings. It was found that the existing studies of ecological restoration outcome evaluation mainly focused on the change of ecological components and structure, while urban green space environmental quality evaluation on the cultural services. Common ecological components and structure and people's subjective feelings were not all synergy or trade-off relations, in fact, there were still cases of trade-off and synergy relations co-existing. Therefore, a framework was constructed for evaluating the ecological restoration outcome of urban green space, including ecological components and structure, ecological services, social services, and people's subjective feelings.
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Affiliation(s)
- Ce Wen
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiuying An
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Zhou
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Yang
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Changzhou Yan
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
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Alshehri FF, Alshehri ZS. Network pharmacology-based screening of active constituents of Avicennia marina and their clinical biochemistry related mechanism against breast cancer. J Biomol Struct Dyn 2024; 42:4506-4521. [PMID: 37306420 DOI: 10.1080/07391102.2023.2220801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/29/2023] [Indexed: 06/13/2023]
Abstract
Breast cancer is the second major cause of cancer death in women globally. Avicennia marina is a medicinal plant that belongs to the family Acanthaceae and is known as grey or white mangrove. It has antioxidant, antiviral, anticancer, anti-inflammatory, and antibacterial activity in the treatment of various diseases including cancer. The goal of the study is to use a network pharmacology method to identify the potential phenomena of bioactive compounds of A. marina in the treatment of breast cancer and explore clinical biochemistry related aspects. A total of 74 active compounds of A. marina were retrieved from various databases as well as a literature review and collectively 429 targets of these compounds were identified by STITCH and Swiss Target Prediction databases. Breast cancer related 15606 potential targets were retrieved from the GeneCards database. A Venn diagram was drawn to find common key targets. To check the biological functions, the GO enrichment and KEGG pathways analysis of 171 key targets were performed through the DAVID database. To understand the interactions among key targets, Protein-protein interaction (PPI) studies were completed using the STRING database, and the Protein-Protein Interaction (PPI) network, as well as the compound-target-pathway network, was constructed using Cytoscape 3.9.0. Finally, molecular docking analysis of 5 hub genes named tumor protein 53 (TP53), catenin beta 1 (CTNNB1), interleukin 6 (IL6), tumor necrosis factor (TNF), and RAC-alpha serine/threonine protein kinases 1 (AKT1) with the active constituent of A. marina against breast cancer were performed. Additionally, a molecular docking study demonstrates that active drugs have a higher affinity for the target that may be used to decrease breast cancer. The molecular dynamic simulation analysis predicted the very stable behavior of docked complexes with no global structure deviations seen. The MMGBSA further supported strong intermolecular interactions with net energy values as; AKT1_Betulinic_acid (-20.97 kcal/mol), AKT1_Stigmasterol (-44.56 kcal/mol), TNF_Betulinic_acid (-28.68 kcal/mol) and TNF_Stigmastero (-29.47 kcal/mol).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faez Falah Alshehri
- College of Applied Medical Sciences, Shaqra University, Aldawadmi, Saudi Arabia
| | - Zafer Saad Alshehri
- College of Applied Medical Sciences, Shaqra University, Aldawadmi, Saudi Arabia
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Jiang YZ, Hu LY, Chen MS, Wang XJ, Tan CN, Xue PP, Yu T, He XY, Xiang LX, Xiao YN, Li XL, Ran Q, Li ZJ, Chen L. GATA binding protein 2 mediated ankyrin repeat domain containing 26 high expression in myeloid-derived cell lines. World J Stem Cells 2024; 16:538-550. [PMID: 38817334 PMCID: PMC11135246 DOI: 10.4252/wjsc.v16.i5.538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/12/2024] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Thrombocytopenia 2, an autosomal dominant inherited disease characterized by moderate thrombocytopenia, predisposition to myeloid malignancies and normal platelet size and function, can be caused by 5'-untranslated region (UTR) point mutations in ankyrin repeat domain containing 26 (ANKRD26). Runt related transcription factor 1 (RUNX1) and friend leukemia integration 1 (FLI1) have been identified as negative regulators of ANKRD26. However, the positive regulators of ANKRD26 are still unknown. AIM To prove the positive regulatory effect of GATA binding protein 2 (GATA2) on ANKRD26 transcription. METHODS Human induced pluripotent stem cells derived from bone marrow (hiPSC-BM) and urothelium (hiPSC-U) were used to examine the ANKRD26 expression pattern in the early stage of differentiation. Then, transcriptome sequencing of these iPSCs and three public transcription factor (TF) databases (Cistrome DB, animal TFDB and ENCODE) were used to identify potential TF candidates for ANKRD26. Furthermore, overexpression and dual-luciferase reporter experiments were used to verify the regulatory effect of the candidate TFs on ANKRD26. Moreover, using the GENT2 platform, we analyzed the relationship between ANKRD26 expression and overall survival in cancer patients. RESULTS In hiPSC-BMs and hiPSC-Us, we found that the transcription levels of ANKRD26 varied in the absence of RUNX1 and FLI1. We sequenced hiPSC-BM and hiPSC-U and identified 68 candidate TFs for ANKRD26. Together with three public TF databases, we found that GATA2 was the only candidate gene that could positively regulate ANKRD26. Using dual-luciferase reporter experiments, we showed that GATA2 directly binds to the 5'-UTR of ANKRD26 and promotes its transcription. There are two identified binding sites of GATA2 that are located 2 kb upstream of the TSS of ANKRD26. In addition, we discovered that high ANKRD26 expression is always related to a more favorable prognosis in breast and lung cancer patients. CONCLUSION We first discovered that the transcription factor GATA2 plays a positive role in ANKRD26 transcription and identified its precise binding sites at the promoter region, and we revealed the importance of ANKRD26 in many tissue-derived cancers.
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Affiliation(s)
- Yang-Zhou Jiang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Lan-Yue Hu
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Mao-Shan Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Xiao-Jie Wang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Cheng-Ning Tan
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Pei-Pei Xue
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Teng Yu
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Xiao-Yan He
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Li-Xin Xiang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Yan-Ni Xiao
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Xiao-Liang Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Qian Ran
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Zhong-Jun Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China
| | - Li Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Third Military Medical University, Chongqing 400037, China
- Hematopoietic Acute Radiation Syndrome Medical and Pharmaceutical Basic Research Innovation Center, Ministry of Education of the People's Republic of China, Chongqing 400037, China.
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Chen H, Liu F, Chen J, Ji K, Cui Y, Ge W, Wang Z. Identification, molecular evolution, codon bias, and expansion analysis of NLP transcription factor family in foxtail millet ( Setaria italica L.) and closely related crops. Front Genet 2024; 15:1395224. [PMID: 38836039 PMCID: PMC11148446 DOI: 10.3389/fgene.2024.1395224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/02/2024] [Indexed: 06/06/2024] Open
Abstract
The NODULE-INCEPTION-like protein (NLP) family is a plant-specific transcription factor (TF) family involved in nitrate transport and assimilation in plants, which are essential for improving plant nitrogen use efficiency. Currently, the molecular nature and evolutionary trajectory of NLP genes in the C4 model crop foxtail millet are unknown. Therefore, we performed a comprehensive analysis of NLP and molecular evolution in foxtail millet by scanning the genomes of foxtail millet and representative species of the plant kingdom. We identified seven NLP genes in the foxtail millet genome, all of which are individually and separately distributed on different chromosomes. They were not structurally identical to each other and were mainly expressed on root tissues. We unearthed two key genes (Si5G004100.1 and Si6G248300.1) with a variety of excellent characteristics. Regarding its molecular evolution, we found that NLP genes in Gramineae mainly underwent dispersed duplication, but maize NLP genes were mainly generated via WGD events. Other factors such as base mutations and natural selection have combined to promote the evolution of NLP genes. Intriguingly, the family in plants showed a gradual expansion during evolution with more duplications than losses, contrary to most gene families. In conclusion, this study advances the use of NLP genetic resources and the understanding of molecular evolution in cereals.
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Affiliation(s)
- Huilong Chen
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Fang Liu
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jing Chen
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Kexin Ji
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Yutong Cui
- College of Management, North China University of Science and Technology, Tangshan, Hebei, China
| | - Weina Ge
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Zhenyi Wang
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
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Wang WX, Yang C, Xiong W, Chen CY, Li N. Transcriptome-wide identification of ARF gene family in medicinal plant Polygonatum kingianum and expression analysis of PkARF members in different tissues. Mol Biol Rep 2024; 51:648. [PMID: 38727802 DOI: 10.1007/s11033-024-09608-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Polygonatum kingianum holds significant importance in Traditional Chinese Medicine due to its medicinal properties, characterized by its diverse chemical constituents including polysaccharides, terpenoids, flavonoids, phenols, and phenylpropanoids. The Auxin Response Factor (ARF) is a pivotal transcription factor known for its regulatory role in both primary and secondary metabolite synthesis. However, our understanding of the ARF gene family in P. kingianum remains limited. METHODS AND RESULTS We employed RNA-Seq to sequence three distinct tissues (leaf, root, and stem) of P. kingianum. The analysis revealed a total of 31,558 differentially expressed genes (DEGs), with 43 species of transcription factors annotated among them. Analyses via gene ontology and the Kyoto Encyclopedia of Genes and Genomes demonstrated that these DEGs were predominantly enriched in metabolic pathways and secondary metabolite biosynthesis. The proposed temporal expression analysis categorized the DEGs into nine clusters, suggesting the same expression trends that may be coordinated in multiple biological processes across the three tissues. Additionally, we conducted screening and expression pattern analysis of the ARF gene family, identifying 12 significantly expressed PkARF genes in P. kingianum roots. This discovery lays the groundwork for investigations into the role of PkARF genes in root growth, development, and secondary metabolism regulation. CONCLUSION The obtained data and insights serve as a focal point for further research studies, centred on genetic manipulation of growth and secondary metabolism in P. kingianum. Furthermore, these findings contribute to the understanding of functional genomics in P. kingianum, offering valuable genetic resources.
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Affiliation(s)
- Wen-Xiang Wang
- School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, 404120, China
| | - Ce Yang
- School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, 404120, China
| | - Wei Xiong
- Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Chongqing, 404120, China
| | - Chun-Yu Chen
- School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, 404120, China.
| | - Ning Li
- School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, 404120, China.
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Nie R, Zhang W, Tian H, Li J, Ling Y, Zhang B, Zhang H, Wu C. Proteo-transcriptomic profiles reveal key regulatory pathways and functions of LDHA in the ovulation of domestic chickens (Gallus gallus). J Anim Sci Biotechnol 2024; 15:68. [PMID: 38725063 PMCID: PMC11083957 DOI: 10.1186/s40104-024-01019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/03/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND In poultry, the smooth transition of follicles from the preovulatory-to-postovulatory phase impacts egg production in hens and can benefit the poultry industry. However, the regulatory mechanism underlying follicular ovulation in avians is a complex biological process that remains unclear. RESULTS Critical biochemical events involved in ovulation in domestic chickens (Gallus gallus) were evaluated by transcriptomics, proteomics, and in vitro assays. Comparative transcriptome analyses of the largest preovulatory follicle (F1) and postovulatory follicle (POF1) in continuous laying (CL) and intermittent laying (IL) chickens indicated the greatest difference between CL_F1 and IL_F1, with 950 differentially expressed genes (DEGs), and the smallest difference between CL_POF1 and IL_POF1, with 14 DEGs. Additionally, data-independent acquisition proteomics revealed 252 differentially abundant proteins between CL_F1 and IL_F1. Perivitelline membrane synthesis, steroid biosynthesis, lysosomes, and oxidative phosphorylation were identified as pivotal pathways contributing to ovulation regulation. In particular, the regulation of zona pellucida sperm-binding protein 3, plasminogen activator, cathepsin A, and lactate dehydrogenase A (LDHA) was shown to be essential for ovulation. Furthermore, the inhibition of LDHA decreased cell viability and promoted apoptosis of ovarian follicles in vitro. CONCLUSIONS This study reveals several important biochemical events involved in the process of ovulation, as well as crucial role of LDHA. These findings improve our understanding of ovulation and its regulatory mechanisms in avian species.
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Affiliation(s)
- Ruixue Nie
- State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wenhui Zhang
- State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Haoyu Tian
- State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Junying Li
- State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yao Ling
- State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Bo Zhang
- State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hao Zhang
- State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Changxin Wu
- State Key Laboratory of Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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Sun Z, Chen Z, Yin M, Wu X, Guo B, Cheng X, Quan R, Sun Y, Zhang Q, Fan Y, Jin C, Yin Y, Hou X, Liu W, Shu M, Xue X, Shi Y, Chen B, Xiao Z, Dai J, Zhao Y. Harnessing developmental dynamics of spinal cord extracellular matrix improves regenerative potential of spinal cord organoids. Cell Stem Cell 2024; 31:772-787.e11. [PMID: 38565140 DOI: 10.1016/j.stem.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/07/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024]
Abstract
Neonatal spinal cord tissues exhibit remarkable regenerative capabilities as compared to adult spinal cord tissues after injury, but the role of extracellular matrix (ECM) in this process has remained elusive. Here, we found that early developmental spinal cord had higher levels of ECM proteins associated with neural development and axon growth, but fewer inhibitory proteoglycans, compared to those of adult spinal cord. Decellularized spinal cord ECM from neonatal (DNSCM) and adult (DASCM) rabbits preserved these differences. DNSCM promoted proliferation, migration, and neuronal differentiation of neural progenitor cells (NPCs) and facilitated axonal outgrowth and regeneration of spinal cord organoids more effectively than DASCM. Pleiotrophin (PTN) and Tenascin (TNC) in DNSCM were identified as contributors to these abilities. Furthermore, DNSCM demonstrated superior performance as a delivery vehicle for NPCs and organoids in spinal cord injury (SCI) models. This suggests that ECM cues from early development stages might significantly contribute to the prominent regeneration ability in spinal cord.
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Affiliation(s)
- Zheng Sun
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenni Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Man Yin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianming Wu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Guo
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaokang Cheng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui Quan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuting Sun
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongheng Fan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Jin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyun Yin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianglin Hou
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiyuan Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muya Shu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoyu Xue
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ya Shi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhifeng Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianwu Dai
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Tianjin Key Laboratory of Biomedical Materials, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, China.
| | - Yannan Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Han D, Yang Y, Guo Z, Chen K, Dai S, Zhu Y, Wang Y, Yu Z, Wang K, Liu P, Rong C, Yu Y. Metagenomics profiling of the microbial community and functional differences in solid-state fermentation vinegar starter (seed Pei) from different Chinese regions. Front Microbiol 2024; 15:1389737. [PMID: 38756727 PMCID: PMC11096547 DOI: 10.3389/fmicb.2024.1389737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/01/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction The starter used in solid-state fermentation (SSF) vinegar, known as seed Pei is a microbial inoculant from the previous batch that is utilized during the acetic acid fermentation stage. The seed Pei, which has a notable impact on vinegar fermentation and flavor, is under-researched with comparative studies on microorganisms. Methods Herein metagenomics was employed to reveal the microbes and their potential metabolic functions of four seed Pei from three regions in China. Results The predominant microbial taxa in all four starters were bacteria, followed by viruses, eukaryotes, and archaea, with Lactobacillus sp. or Acetobacter sp. as main functional taxa. The seed Pei used in Shanxi aged vinegar (SAV) and Sichuan bran vinegar (SBV) exhibited a higher similarity in microbial composition and distribution of functional genes, while those used in two Zhenjiang aromatic vinegar (ZAV) differed significantly. Redundancy analysis (RDA) of physicochemical factors and microbial communities indicated that moisture content, pH, and reducing sugar content are significant factors influencing microbial distribution. Moreover, seven metagenome-assembled genomes (MAGs) that could potentially represent novel species were identified. Conclusions There are distinctions in the microbiome and functional genes among different seed Pei. The vinegar starters were rich in genes related to carbohydrate metabolism. This research provides a new perspective on formulating vinegar fermentation starters and developing commercial fermentation agents for vinegar production.
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Affiliation(s)
- Dong Han
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yunsong Yang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhantong Guo
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ken Chen
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Shuwen Dai
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yuanyuan Zhu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yuqin Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhen Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ke Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Chunchi Rong
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yongjian Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, China
- Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Jiangsu University of Science and Technology, Zhenjiang, China
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Shi R, Gao S, Huang H, Jiang K, Wang D. Integrating network pharmacology with microRNA microarray analysis to identify the role of miRNAs in thrombosis treated by the Dahuang Zhechong pill. Comput Biol Med 2024; 173:108338. [PMID: 38531252 DOI: 10.1016/j.compbiomed.2024.108338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/15/2024] [Accepted: 03/17/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND Thrombotic diseases are the leading causes of death worldwide, urging for improvements in treatment strategies. Dahuang Zhechong pill (DHZCP) is a traditional Chinese medicine widely used for treating thrombotic diseases; however, the underlying mechanisms remain unclear. This study aimed to explore the potential mechanisms of DHZCP in treating thrombosis with a focus on bioinformatics and miRNAs. METHODS We used network pharmacology to explore the targets of thrombosis treated with DHZCP and performed microarray analysis to acquire miRNA profiles and predict the target genes in thrombin-stimulated MEG-01 cells treated with DHZCP. Based on the overlapping of targets, we carried out a component-target-miRNA network and enrichment analysis and validated the selected miRNAs and mRNAs using quantitative reverse transcription-polymerase chain reaction. RESULTS Our data showed 850 targets of 230 active ingredients of DHZCP and 1214 thrombosis-related genes; 235 targets were common. We identified 32 miRNAs that were regulated by thrombin stimulation but regulated reversely by DHZCP treatment in MEG-01 cells, and predicted 1846 targets with function annotation. We analyzed conjointly 23 integrating targets from network pharmacology and microarray. HIF1A, PIK3CA, MAPK1 and BCL2L1 emerged as key nodes in the network diagrams. We confirmed the differential expression of seven miRNAs, one mRNA (BCL2L1) and platelet surface protein. CONCLUSIONS This study showed that miRNAs and their targets, such as BCL2L1, played crucial roles in platelet activation during DHZCP intervention in thrombosis, highlighting their potential to alleviate platelet activation and increase cell apoptosis. The study's findings could help develop new strategies for improving thrombosis treatment.
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Affiliation(s)
- Rui Shi
- Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China; Hunan Key Laboratory of Traditional Chinese Medicine for Gan of State Administration, Central South University, Changsha, 410008, China.
| | - Shan Gao
- Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China; Hunan Key Laboratory of Traditional Chinese Medicine for Gan of State Administration, Central South University, Changsha, 410008, China
| | - Huichao Huang
- Department of Infectious Disease, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Ke Jiang
- Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China; Hunan Key Laboratory of Traditional Chinese Medicine for Gan of State Administration, Central South University, Changsha, 410008, China
| | - Dongsheng Wang
- Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China; Hunan Key Laboratory of Traditional Chinese Medicine for Gan of State Administration, Central South University, Changsha, 410008, China.
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Duan R, Liu Y, Zhang Y, Shi J, Xue R, Liu R, Miao Y, Zhou X, Lv Y, Shen H, Xie X, Ai X. The impact of exercise on the gut microbiota in middle-aged amateur serious runners: a comparative study. Front Physiol 2024; 15:1343219. [PMID: 38737829 PMCID: PMC11082653 DOI: 10.3389/fphys.2024.1343219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/11/2024] [Indexed: 05/14/2024] Open
Abstract
Introduction Exercise, health, and the gut microbiota (GM) are strongly correlated. Research indicates that professional athletes, especially ultra-marathon runners, have unique GM characteristics. However, more research has focused on elite athletes, with little attention given to amateur sports enthusiasts, especially those in the middle-aged population. Therefore, this study focuses on the impact of long-term running on the composition and potential functions of the GM in middle-aged individuals. Methods We compared the GM of 25 middle-aged serious runnerswith 22 sedentary healthy controls who had minimal exercise habitsusing 16S rRNA gene sequencing. Additionally, we assessed dietary habits using a food frequency questionnaire. Results and Discussion Statistical analysis indicates that there is no significant difference in dietary patterns between the control group and serious runners. Diversity analysis results indicate that there is no significant difference in α diversity between the two groups of GM, but there is a significant difference in β diversity. Analysis of the composition of GM reveals that Ruminococcus and Coprococcus are significantly enriched in serious runners, whereas Bacteroides, Lachnoclostridium, and Lachnospira are enriched in the control group. Differential analysis of functional pathway prediction results reveals significant differences in the functional metabolism levels of GM between serious runners and the control group. Further correlation analysis results indicate that this difference may be closely related to variations in GM. In conclusion, our results suggest that long-term exercise can lead to changes in the composition of the GM. These changes have the potential to impact the overall health of the individual by influencing metabolic regulation.
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Affiliation(s)
- Rui Duan
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Yu Liu
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Yonglian Zhang
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Jinrong Shi
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Rong Xue
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Ruijie Liu
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Yuanxin Miao
- Research Institute of Agricultural Biotechnology, Jingchu University of Technology, Jingmen, Hubei, China
| | - Xianfeng Zhou
- School of Life Sciences and Health Engineering, Hubei University of Technology, Wuhan, China
- Maintainbiotech Ltd., Wuhan, Hubei, China
| | | | - Hexiao Shen
- Maintainbiotech Ltd., Wuhan, Hubei, China
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiongwei Xie
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
| | - Xu Ai
- Jingmen Central Hospital, Hubei Clinical Medical Research Center for Functional Colorectal Diseases, Jingmen, Hubei, China
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Yang J, Deng J, Wang K, Wang A, Chen G, Chen Q, Ye M, Wu X, Wang X, Lin D. Tetrahydropalmatine promotes random skin flap survival in rats via the PI3K/AKT signaling pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 324:117808. [PMID: 38280663 DOI: 10.1016/j.jep.2024.117808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/13/2024] [Accepted: 01/19/2024] [Indexed: 01/29/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Flap necrosis is the most common complication after flap transplantation, but its prevention remains challenging. Tetrahydropalmatine (THP) is the main bioactive component of the traditional Chinese medicine Corydalis yanhusuo, with effects that include the activation of blood circulation, the promotion of qi, and pain relief. Although THP is widely used to treat various pain conditions, its impact on flap survival is unknown. AIM OF THE STUDY To explore the effect and mechanism of THP on skin flap survival. MATERIALS AND METHODS In this study, we established a modified McFarlane flap model, and the flap survival rate was calculated after 7 days of THP treatment. Angiogenesis and blood perfusion were evaluated using lead oxide/gelatin angiography and laser Doppler, respectively. Flap tissue obtained from zone II was evaluated histopathologically, by hematoxylin and eosin staining, and in assays for malondialdehyde content and superoxide dismutase activity. Immunofluorescence was performed to detect interleukin (IL)-6, tumor necrosis factor (TNF)-α, hypoxia-inducible factor (HIF)-1α, Bcl-2, Bax, caspase-3, caspase-9, SQSTM1/P62, Beclin-1, and LC3 expression, and Western blot to assess PI3K/AKT signaling pathway activation and Vascular endothelial growth factor (VEGF) expression. The role played by the autophagy pathway in flap necrosis was examined using rapamycin, a specific inhibitor of mTOR. RESULTS Experimentally, THP improved the survival rate of skin flaps, promoted angiogenesis, and improved blood perfusion. THP administration reduced the inflammatory response, oxidative stress, and apoptosis in addition to inhibiting autophagy via the PI3K/AKT/mTOR pathway. Rapamycin partially reversed these effects. CONCLUSION THP promotes skin flap survival via the PI3K/AKT signaling pathway.
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Affiliation(s)
- Jialong Yang
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Jiapeng Deng
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Kaitao Wang
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - An Wang
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Guodong Chen
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Qingyu Chen
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Minle Ye
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Xinyu Wu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, The First School of Clinical Medical, Wenzhou Medical, China
| | - Xinye Wang
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Dingsheng Lin
- Department of Hand and Plastic Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, The Second School of Medicine, Wenzhou Medical University, Wenzhou, 325000, China.
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Li X, Guo Z, Zhou Y, Zhang B, Ruan H, Chen W. Three new discovery effector proteins from Candidatus Liberibacter asiaticus psy62 inhibit plant defense through interaction with AtCAT3 and AtGAPA. PLANT CELL REPORTS 2024; 43:130. [PMID: 38652336 DOI: 10.1007/s00299-024-03220-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
KEY MESSAGE We identify three SDEs that inhibiting host defence from Candidatus Liberibacter asiaticus psy62, which is an important supplement to the pathogenesis of HLB. Candidatus Liberibacter asiaticus (CLas) is the main pathogen of citrus Huanglongbing (HLB). 38 new possible sec-dependent effectors (SDEs) of CLas psy62 were predicted by updated predictor SignalP 5.0, which 12 new SDEs were found using alkaline phosphate assay. Among them, SDE4310, SDE4435 and SDE4955 inhibited hypersensitivity reactions (HR) in Arabidopsis thaliana (Arabidopsis, At) and Nicotiana benthamiana leaves induced by pathogens, which lead to a decrease in cell death and reactive oxygen species (ROS) accumulation. And the expression levels of SDE4310, SDE4435, and SDE4955 genes elevated significantly in mild symptom citrus leaves. When SDE4310, SDE4435 and SDE4955 were overexpressed in Arabidopsis, HR pathway key genes pathogenesis-related 2 (PR2), PR5, nonexpressor of pathogenesis-related 1 (NPR1) and isochorismate synthase 1 (ICS1) expression significantly decreased and the growth of pathogen was greatly increased relative to control with Pst DC3000/AvrRps4 treatment. Our findings also indicated that SDE4310, SDE4435 and SDE4955 interacted with AtCAT3 (catalase 3) and AtGAPA (glyceraldehyde-3-phosphate dehydrogenase A). In conclusion, our results suggest that SDE4310, SDE4435 and SDE4955 are CLas psy62 effector proteins that may have redundant functions. They inhibit ROS burst and cell death by interacting with AtCAT3 and AtGAPA to negatively regulate host defense.
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Affiliation(s)
- Xue Li
- MOE Key Laboratory of Laser Life Science, Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Zetian Guo
- MOE Key Laboratory of Laser Life Science, Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yue Zhou
- MOE Key Laboratory of Laser Life Science, Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Baihong Zhang
- MOE Key Laboratory of Laser Life Science, Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Huaqin Ruan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wenli Chen
- MOE Key Laboratory of Laser Life Science, Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, China.
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Xu X, He M, Xue Q, Li X, Liu A. Genome-based taxonomic classification of the genus Sulfitobacter along with the proposal of a new genus Parasulfitobacter gen. nov. and exploring the gene clusters associated with sulfur oxidation. BMC Genomics 2024; 25:389. [PMID: 38649849 PMCID: PMC11034169 DOI: 10.1186/s12864-024-10269-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The genus Sulfitobacter, a member of the family Roseobacteraceae, is widely distributed in the ocean and is believed to play crucial roles in the global sulfur cycle. However, gene clusters associated with sulfur oxidation in genomes of the type strains of this genus have been poorly studied. Furthermore, taxonomic errors have been identified in this genus, potentially leading to significant confusion in ecological and evolutionary interpretations in subsequent studies of the genus Sulfitobacter. This study aims to investigate the taxonomic status of this genus and explore the metabolism associated with sulfur oxidation. RESULTS This study suggests that Sulfitobacter algicola does not belong to Sulfitobacter and should be reclassified into a novel genus, for which we propose the name Parasulfitobacter gen. nov., with Parasulfitobacter algicola comb. nov. as the type species. Additionally, enzymes involved in the sulfur oxidation process, such as the sulfur oxidization (Sox) system, the disulfide reductase protein family, and the sulfite dehydrogenase (SoeABC), were identified in almost all Sulfitobacter species. This finding implies that the majority of Sulfitobacter species can oxidize reduced sulfur compounds. Differences in the modular organization of sox gene clusters among Sulfitobacter species were identified, along with the presence of five genes with unknown function located in some of the sox gene clusters. Lastly, this study revealed the presence of the demethylation pathway and the cleavage pathway used by many Sulfitobacter species to degrade dimethylsulfoniopropionate (DMSP). These pathways enable these bacteria to utilize DMSP as important source of sulfur and carbon or as a defence strategy. CONCLUSIONS Our findings contribute to interpreting the mechanism by which Sulfitobacter species participate in the global sulfur cycle. The taxonomic rearrangement of S. algicola into the novel genus Parasulfitobacter will prevent confusion in ecological and evolutionary interpretations in future studies of the genus Sulfitobacter.
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Affiliation(s)
- Xiaokun Xu
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Mengdan He
- School of Basic Medical Sciences, Shandong Second Medical University, 261042, Weifang, Shandong, P. R. China
| | - Qingjie Xue
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Xiuzhen Li
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China
| | - Ang Liu
- Department of Pathogenic Biology, College of Basic Medicine, Jining Medical University, 272067, Jining, Shandong, P. R. China.
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Su Z, Sun JY, Gao M, Sun W, Kong X. Molecular mechanisms and potential therapeutic targets in the pathogenesis of hypertension in visceral adipose tissue induced by a high-fat diet. Front Cardiovasc Med 2024; 11:1380906. [PMID: 38689862 PMCID: PMC11058983 DOI: 10.3389/fcvm.2024.1380906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
Background Hypertension (HTN) presents a significant global public health challenge with diverse causative factors. The accumulation of visceral adipose tissue (VAT) due to a high-fat diet (HFD) is an independent risk factor for HTN. While various studies have explored pathogenic mechanisms, a comprehensive understanding of impact of VAT on blood pressure necessitates bioinformatics analysis. Methods Datasets GSE214618 and GSE188336 were acquired from the Gene Expression Omnibus and analyzed to identify shared differentially expressed genes between HFD-VAT and HTN-VAT. Gene Ontology enrichment and protein-protein interaction analyses were conducted, leading to the identification of hub genes. We performed molecular validation of hub genes using RT-qPCR, Western-blotting and immunofluorescence staining. Furthermore, immune infiltration analysis using CIBERSORTx was performed. Results This study indicated that the predominant characteristic of VAT in HTN was related to energy metabolism. The red functional module was enriched in pathways associated with mitochondrial oxidative respiration and ATP metabolism processes. Spp1, Postn, and Gpnmb in VAT were identified as hub genes on the pathogenic mechanism of HTN. Proteins encoded by these hub genes were closely associated with the target organs-specifically, the resistance artery, aorta, and heart tissue. After treatment with empagliflozin, there was a tendency for Spp1, Postn, and Gpnmb to decrease in VAT. Immune infiltration analysis confirmed that inflammation and immune response may not be the main mechanisms by which visceral adiposity contributes to HTN. Conclusions Our study pinpointed the crucial causative factor of HTN in VAT following HFD. Spp1, Postn, and Gpnmb in VAT acted as hub genes that promote elevated blood pressure and can be targets for HTN treatment. These findings contributed to therapeutic strategies and prognostic markers for HTN.
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Affiliation(s)
- Zhenyang Su
- School of Medicine, Southeast University, Nanjing, China
| | - Jin-Yu Sun
- Department of Cardiology, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Min Gao
- Department of Cardiology, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Xiangqing Kong
- School of Medicine, Southeast University, Nanjing, China
- Department of Cardiology, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
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Feng S, Li N, Chen H, Liu Z, Li C, Zhou R, Zhang Y, Cao R, Ma X, Song X. Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants. MOLECULAR HORTICULTURE 2024; 4:13. [PMID: 38589963 PMCID: PMC11003162 DOI: 10.1186/s43897-024-00090-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/03/2024] [Indexed: 04/10/2024]
Abstract
The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA family members and performed a large-scale analysis by scanning 406 plant genomes. The results showed that the ARF and Aux/IAA gene families originated from charophytes. The ARF family sequences were more conserved than the Aux/IAA family sequences. Dispersed duplications were the common expansion mode of ARF and Aux/IAA families in bryophytes, ferns, and gymnosperms; however, whole-genome duplication was the common expansion mode of the ARF and Aux/IAA families in basal angiosperms, magnoliids, monocots, and dicots. Expression and regulatory network analyses revealed that the Arabidopsis thaliana ARF and Aux/IAA families responded to multiple hormone, biotic, and abiotic stresses. The APETALA2 and serum response factor-transcription factor gene families were commonly enriched in the upstream and downstream genes of the ARF and Aux/IAA gene families. Our study provides a comprehensive overview of the evolutionary trajectories, structural functions, expansion mechanisms, expression patterns, and regulatory networks of these two gene families.
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Affiliation(s)
- Shuyan Feng
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Nan Li
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Huilong Chen
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhuo Liu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Chunjin Li
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Rong Zhou
- Department of Food Science, Aarhus University, Aarhus, 8200, Denmark
| | - Yingchao Zhang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
| | - Xiao Ma
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
- College of Horticultural Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066600, China.
| | - Xiaoming Song
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
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Ding H, Wang M, Wang M, Wu S, Guo Y, Gao Y, Li L, Bao Z, Wang B, Hu J. Synchronously sexual maturity in hermaphrodite fish as revealed by transcriptome analysis in Plectropomus leopardus. Gene 2024; 901:148166. [PMID: 38242379 DOI: 10.1016/j.gene.2024.148166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/16/2023] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Leopard coral grouper (Plectropomus leopardus) is a type of hermaphrodite fish, but the mechanisms of gonadal development and gametogenesis remain unclear. In the present study, we performed histological observation and transcriptomic analysis during the process of sexual differentiation in P. leopardus. According to the histological results, sexual differentiation was completed at 15 months old, developed synchronously in male and female individuals at 2 years old, and matured synchronously at 3 years old. Comparative transcriptomic analyses showed that the gonadal had differentiated by 15 months old, with enrichment of pathways associated with cell proliferation, transcriptional metabolism, and germline stem cell differentiation. Furthermore, cilium movement and fatty acid anabolism, which are associated with spermatogenesis and oocyte growth, were significantly enriched at 3 years old. In addition, key genes associated with male and female sex differentiation, such as amh, dmrt1, dmrt2a, zp4, sox3, gdf9, and gsdf, were identified by weighted gene co-expression network analysis (WGCNA). Finally, the localization and expression of the key genes amh and sox3 were observed in different cell types within the testes and ovaries, reflecting the development of the testes and ovaries, respectively. All the evidence indicates that P. leopardus is a hermaphrodite and synchronously sexually mature fish. Our study complements the gonadal development patterns of hermaphroditic fish by providing new insights into the molecular mechanisms underlying sexual differentiation and sex change in hermaphroditic groupers.
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Affiliation(s)
- Hui Ding
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya, China
| | - Mengya Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya, China
| | - Mingyi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya, China
| | - Shaoxuan Wu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya, China
| | - Yilan Guo
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya, China
| | - Yurui Gao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya, China
| | - Lin Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya, China; Hainan Seed Industry Laboratory, Sanya 572025, China; Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou 511458, China
| | - Bo Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya, China; Hainan Seed Industry Laboratory, Sanya 572025, China.
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao/Sanya, China; Hainan Seed Industry Laboratory, Sanya 572025, China; Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou 511458, China.
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Han B, Wang Y, Ge W, Wang J, Yu S, Yan J, Hua L, Zhang X, Yan Z, Wang L, Zhao J, Huang C, Yang B, Wang Y, Ma Q, Zhao Y, Jiang H, Zhang Y, Liang S, Zhao J, Sun Z, Shen W, Gui Y. Changes in seminal plasma microecological dynamics and the mechanistic impact of core metabolite hexadecanamide in asthenozoospermia patients. IMETA 2024; 3:e166. [PMID: 38882497 PMCID: PMC11170967 DOI: 10.1002/imt2.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/12/2023] [Accepted: 11/30/2023] [Indexed: 06/18/2024]
Abstract
Asthenozoospermia (AZS) is a prevalent contributor to male infertility, characterized by a substantial decline in sperm motility. In recent years, large-scale studies have explored the interplay between the male reproductive system's microecology and its implications for reproductive health. Nevertheless, the direct association between seminal microecology and male infertility pathogenesis remains inconclusive. This study used 16S rDNA sequencing and multi-omics analysis to conduct a comprehensive investigation of the seminal microbial community and metabolites in AZS patients. Patients were categorized into four distinct groups: Normal, mild AZS (AZS-I), moderate AZS (AZS-II), and severe AZS (AZS-III). Microbiome differential abundance analysis revealed significant differences in microbial composition and metabolite profiles within the seminal plasma of these groups. Subsequently, patients were classified into a control group (Normal and AZS-I) and an AZS group (AZS-II and AZS-III). Correlation and cross-reference analyses identified distinct microbial genera and metabolites. Notably, the AZS group exhibited a reduced abundance of bacterial genera such as Pseudomonas, Serratia, and Methylobacterium-Methylorubrum in seminal plasma, positively correlating with core differential metabolite (hexadecanamide). Conversely, the AZS group displayed an increased abundance of bacterial genera such as Uruburuella, Vibrio, and Pseudoalteromonas, with a negative correlation with core differential metabolite (hexadecanamide). In vitro and in vivo experiments validated that hexadecanamide significantly enhanced sperm motility. Using predictive metabolite-targeting gene analysis and single-cell transcriptome sequencing, we profiled the gene expression of candidate target genes PAOX and CA2. Protein immunoblotting techniques validated the upregulation protein levels of PAOX and CA2 in sperm samples after hexadecanamide treatment, enhancing sperm motility. In conclusion, this study uncovered a significant correlation between six microbial genera in seminal plasma and the content of the metabolite hexadecanamide, which is related to AZS. Hexadecanamide notably enhances sperm motility, suggesting its potential integration into clinical strategies for managing AZS, providing a foundational framework for diagnostic and therapeutic advancements.
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Affiliation(s)
- Baoquan Han
- Department of Urology Shenzhen University General Hospital Shenzhen China
- Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital Shenzhen-Peking University-The Hong Kong University of Science and Technology Medical Center Shenzhen China
| | - Yongyong Wang
- Department of Reproductive Medicine, Qingdao Hospital University of Healthy and Rehabilitation Sciences (Qingdao Municipal Hospital) Qingdao China
| | - Wei Ge
- College of Life Sciences Qingdao Agricultural University Qingdao China
| | - Junjie Wang
- College of Life Sciences Qingdao Agricultural University Qingdao China
| | - Shuai Yu
- Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital Shenzhen-Peking University-The Hong Kong University of Science and Technology Medical Center Shenzhen China
| | - Jiamao Yan
- College of Life Sciences Qingdao Agricultural University Qingdao China
| | - Lei Hua
- Department of Urology Shenzhen University General Hospital Shenzhen China
| | - Xiaoyuan Zhang
- College of Life Sciences Qingdao Agricultural University Qingdao China
| | - Zihui Yan
- College of Life Sciences Qingdao Agricultural University Qingdao China
| | - Lu Wang
- College of Life Sciences Qingdao Agricultural University Qingdao China
| | - Jinxin Zhao
- College of Life Sciences Qingdao Agricultural University Qingdao China
| | - Cong Huang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center Shenzhen China
| | - Bo Yang
- Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital Shenzhen-Peking University-The Hong Kong University of Science and Technology Medical Center Shenzhen China
| | - Yan Wang
- Department of Urology Peking University Shenzhen Hospital Shenzhen China
| | - Qian Ma
- Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital Shenzhen-Peking University-The Hong Kong University of Science and Technology Medical Center Shenzhen China
| | - Yong Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences Chinese Academy of Agricultural Sciences Beijing China
| | - Hui Jiang
- Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital Shenzhen-Peking University-The Hong Kong University of Science and Technology Medical Center Shenzhen China
| | - Yunqi Zhang
- STI-Zhilian Research Institute for Innovation and Digital Health Beijing China
| | - Shaolin Liang
- STI-Zhilian Research Institute for Innovation and Digital Health Beijing China
- Institute for Six-sector Economy Fudan University Shanghai China
| | - Jianjuan Zhao
- STI-Zhilian Research Institute for Innovation and Digital Health Beijing China
| | - Zhongyi Sun
- Department of Urology Shenzhen University General Hospital Shenzhen China
| | - Wei Shen
- College of Life Sciences Qingdao Agricultural University Qingdao China
| | - Yaoting Gui
- Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital Shenzhen-Peking University-The Hong Kong University of Science and Technology Medical Center Shenzhen China
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Molina JJ, Kohler KN, Gager C, Andersen MJ, Wongso E, Lucas ER, Paik A, Xu W, Donahue DL, Bergeron K, Klim A, Caparon MG, Hultgren SJ, Desai A, Ploplis VA, Flick MJ, Castellino FJ, Flores-Mireles AL. Fibrinolytic-deficiencies predispose hosts to septicemia from a catheter-associated UTI. Nat Commun 2024; 15:2704. [PMID: 38538626 PMCID: PMC10973455 DOI: 10.1038/s41467-024-46974-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Catheter-associated urinary tract infections (CAUTIs) are amongst the most common nosocomial infections worldwide and are difficult to treat partly due to development of multidrug-resistance from CAUTI-related pathogens. Importantly, CAUTI often leads to secondary bloodstream infections and death. A major challenge is to predict when patients will develop CAUTIs and which populations are at-risk for bloodstream infections. Catheter-induced inflammation promotes fibrinogen (Fg) and fibrin accumulation in the bladder which are exploited as a biofilm formation platform by CAUTI pathogens. Using our established mouse model of CAUTI, here we identified that host populations exhibiting either genetic or acquired fibrinolytic-deficiencies, inducing fibrin deposition in the catheterized bladder, are predisposed to severe CAUTI and septicemia by diverse uropathogens in mono- and poly-microbial infections. Furthermore, here we found that Enterococcus faecalis, a prevalent CAUTI pathogen, uses the secreted protease, SprE, to induce fibrin accumulation and create a niche ideal for growth, biofilm formation, and persistence during CAUTI.
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Affiliation(s)
- Jonathan J Molina
- Integrated Biomedical Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Kurt N Kohler
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Christopher Gager
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Marissa J Andersen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Ellsa Wongso
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Elizabeth R Lucas
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Andrew Paik
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Wei Xu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Deborah L Donahue
- W. M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN, 46556, USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Karla Bergeron
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Aleksandra Klim
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michael G Caparon
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Alana Desai
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Urology, University of Washington Medical Center, Seattle, WA, 98133-9733, USA
| | - Victoria A Ploplis
- W. M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN, 46556, USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Matthew J Flick
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- UNC Blood Research Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Francis J Castellino
- W. M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN, 46556, USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Ana L Flores-Mireles
- Integrated Biomedical Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
- W. M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN, 46556, USA.
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Zhang L, Yan C, Wen C. Vertical distribution characteristics and transport paths of antibiotic resistance genes in constructed wetland system. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133555. [PMID: 38262322 DOI: 10.1016/j.jhazmat.2024.133555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Although the migration and diffusion of antibiotic resistance genes (ARGs) in soil-plant systems have attracted much attention, the migration and diffusion characteristics between constructed wetlands and soil-plant systems differ greatly. Therefore, it is necessary to conduct research on vertical transmission and diffusion of ARGs in constructed wetlands. The vertical distribution and transmission of ARGs in constructed wetlands were explored via metagenomic analysis. The results showed that the proportion of multidrug ARGs was the largest, ranging from 24.2% to 47.5%. The shared characteristics of ARGs were similar to those of bacteria, and there were fewer unique ARGs and microbial species in mesophyll tissue. Sourcetracker analysis revealed that ARGs transfer between plants and atmosphere was bidirectional, but the diffusion of ARGs to atmosphere through plants was relatively weak. ARGs were mainly transmitted to atmosphere/surrounding environment through substrate and influent, and the contributions of substrate to ARGs in atmosphere/surrounding environment were 59.2% and 78.6%, respectively. ARGs involved in foliar attachment mainly originated from peripheral inputs. ARGs showed nonspecific selection for the host at phylum, class and order levels. These findings suggest that more attention should be given to the potential risks of ARGs in constructed wetlands, to formulate effective control and management strategies.
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Affiliation(s)
- Ling Zhang
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Materials Sciences and Engineering, Xinxiang Engineering Research Center for Wastewater Treatment Energy Saving and Emission Reduction, Henan Institute of Technology, Xinxiang 453003, China
| | - Changzhou Yan
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Ce Wen
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
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