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Xiao L, Zhou T, Zuo Z, Sun N, Zhao F. Spatiotemporal patterns of the pregnancy microbiome and links to reproductive disorders. Sci Bull (Beijing) 2024; 69:1275-1285. [PMID: 38388298 DOI: 10.1016/j.scib.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/04/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
The microbiome of females undergoes extensive remodeling during pregnancy, which is likely to have an impact on the health of both mothers and offspring. Nevertheless, large-scale integrated investigations characterizing microbiome dynamics across key body habitats are lacking. Here, we performed an extensive meta-analysis that compiles and analyzes microbiome profiles from >10,000 samples across the gut, vagina, and oral cavity of pregnant women from diverse geographical regions. We have unveiled unexpected variations in the taxonomic, functional, and ecological characteristics of microbial communities throughout the course of pregnancy. The gut microbiota showed distinct trajectories between Western and non-Western populations. The vagina microbiota exhibited fluctuating transitions at the genus level across gestation, while the oral microbiota remained relatively stable. We also identified distinctive microbial signatures associated with prevalent pregnancy-related disorders, including opposite variations in the oral and gut microbiota of patients with gestational diabetes and disrupted microbial networks in preterm birth. This study establishes a comprehensive atlas of the pregnancy microbiome by integrating multidimensional datasets and offers foundational insights into the intricate interplay between microbes and host factors that underlie reproductive health.
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Affiliation(s)
- Liwen Xiao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Tian Zhou
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Ningxia Sun
- Department of Reproductive Medicine, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Department of Reproductive Medicine, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Zou Y, Mao Q, Zhao Z, Zhou X, Pan Y, Zuo Z, Zhang W. Intratumoural and peritumoural CT-based radiomics for diagnosing lepidic-predominant adenocarcinoma in patients with pure ground-glass nodules: a machine learning approach. Clin Radiol 2024; 79:e211-e218. [PMID: 38044199 DOI: 10.1016/j.crad.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/10/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023]
Abstract
AIM To develop and validate a diagnostic model utilising machine-learning algorithms that differentiates lepidic predominant adenocarcinoma (LPA) from other pathological subtypes in patients with pure ground-glass nodules (pGGNs). MATERIALS AND METHODS This bicentric study was conducted across two medical centres and included 151 patients diagnosed with lung adenocarcinoma based on histopathological confirmation of pGGNs. The training cohort consisted of 99 patients from Institution 1, while the test cohort included 52 patients from Institution 2. Radiomics features were extracted from both tumours and the 2 mm peritumoural parenchyma. The tumoural and peritumoural radiomics were designated as Modeltumoural and Modelperitumoural, respectively. The diagnostic efficacy of various models was evaluated through the receiver operating characteristic (ROC) curve analysis. Subsequently, a machine-learning-based prediction model that combined Modeltumoural, Modelperitumoural, and Modelclinical-radiological was developed to differentiate LPA from other pathological subtypes in patients with pGGNs. RESULTS Modeltumoural achieved area under the curve (AUC) values of 0.762 and 0.783 in the training and validation sets, respectively. Modelperitumoural attained AUCs of 0.742 and 0.667, and Modelclinical-radiological generated an AUC of 0.727 and 0.739 in the training and validation sets, respectively. Among the machine-learning models evaluated, gradient boosting machines demonstrated the best diagnostic efficacy, with accuracy, AUC, F1 score, and log loss values of 0.885, 0.956, 0.943, and 0.260, respectively. CONCLUSION The combined model based on machine learning that incorporated tumour and peritumoural parenchyma, as well as clinical and imaging characteristics, may offer benefits in assessing the pathological subtype of pGGNs.
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Affiliation(s)
- Y Zou
- Department of Radiology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, 545006, China; Guangxi Key Clinical Specialties of Medical Imaging, Liuzhou, 545006, China; Liuzhou Key Laboratory of Molecular Imaging, Liuzhou, 545006, China
| | - Q Mao
- Department of Radiology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, 545006, China; Guangxi Key Clinical Specialties of Medical Imaging, Liuzhou, 545006, China; Liuzhou Key Laboratory of Molecular Imaging, Liuzhou, 545006, China
| | - Z Zhao
- Department of Radiology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, 545006, China; Guangxi Key Clinical Specialties of Medical Imaging, Liuzhou, 545006, China; Liuzhou Key Laboratory of Molecular Imaging, Liuzhou, 545006, China
| | - X Zhou
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, 411000, China
| | - Y Pan
- Department of Radiology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, 545006, China; Guangxi Key Clinical Specialties of Medical Imaging, Liuzhou, 545006, China; Liuzhou Key Laboratory of Molecular Imaging, Liuzhou, 545006, China
| | - Z Zuo
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, 411000, China
| | - W Zhang
- Department of Radiology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, 545006, China; Guangxi Key Clinical Specialties of Medical Imaging, Liuzhou, 545006, China; Liuzhou Key Laboratory of Molecular Imaging, Liuzhou, 545006, China.
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Zhou T, Xiao L, Zuo Z, Zhao F. MAMI: a comprehensive database of mother-infant microbiome and probiotic resources. Nucleic Acids Res 2024; 52:D738-D746. [PMID: 37819042 PMCID: PMC10767955 DOI: 10.1093/nar/gkad813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/04/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Extensive evidence has demonstrated that the human microbiome and probiotics confer great impacts on human health, particularly during critical developmental stages such as pregnancy and infancy when microbial communities undergo remarkable changes and maturation. However, a major challenge in understanding the microbial community structure and interactions between mothers and infants lies in the current lack of comprehensive microbiome databases specifically focused on maternal and infant health. To address this gap, we have developed an extensive database called MAMI (Microbiome Atlas of Mothers and Infants) that archives data on the maternal and neonatal microbiome, as well as abundant resources on edible probiotic strains. By leveraging this resource, we can gain profound insights into the dynamics of microbial communities, contributing to lifelong wellness for both mothers and infants through precise modulation of the developing microbiota. The functionalities incorporated into MAMI provide a unique perspective on the study of the mother-infant microbiome, which not only advance microbiome-based scientific research but also enhance clinical practice. MAMI is publicly available at https://bioinfo.biols.ac.cn/mami/.
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Affiliation(s)
- Tian Zhou
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Liwen Xiao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangqing Zhao
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F, Wei F. PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation. Microbiome 2023; 11:221. [PMID: 37805557 PMCID: PMC10559513 DOI: 10.1186/s40168-023-01657-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 08/23/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples. RESULTS The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes. CONCLUSIONS Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract.
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Affiliation(s)
- Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingyue Qu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenqiang Zuo
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Wang
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangqing Zhao
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zuo Z, Zeng W, Peng K, Mao Y, Wu Y, Zhou Y, Qi W. Development of a novel combined nomogram integrating deep-learning-assisted CT texture and clinical-radiological features to predict the invasiveness of clinical stage IA part-solid lung adenocarcinoma: a multicentre study. Clin Radiol 2023; 78:e698-e706. [PMID: 37487842 DOI: 10.1016/j.crad.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 11/30/2022] [Accepted: 07/01/2023] [Indexed: 07/26/2023]
Abstract
AIM To develop a novel combined nomogram based on deep-learning-assisted computed tomography (CT) texture (DL-TA) and clinical-radiological features for the preoperative prediction of invasiveness in patients with clinical stage IA lung adenocarcinoma manifesting as part-solid nodules (PSNs). MATERIALS AND METHODS This study was conducted from January 2015 to October 2021 at three centres: 355 patients with 355 PSN lung adenocarcinomas who underwent surgical resection were included and classified into the training (n=222) and validation (n=133) cohorts. PSN segmentation on CT images was performed automatically with a commercial deep-learning algorithm, and CT texture features were extracted. The least absolute shrinkage and selection operator was used for feature selection and transformed into a DL-TA score. The combined nomogram that incorporated the DL-TA score and identified clinical-radiological features was developed for the prediction of pathological invasiveness of the PSNs and validated in terms of discrimination and calibration. RESULTS The present study generated a combined nomogram for predicting the invasiveness of PSNs that included age, consolidation-to-tumour ratio, smoking status, and DL-TA score, with a C-index of 0.851 (95% confidence interval: 0.826-0.877) for the training cohort and 0.854 (95% confidence interval: 0.817-0.891) for the validation cohort, indicating good discrimination. Furthermore, the model had a Brier score of 0.153 for the training cohort and 0.135 for the validation cohort, indicating good calibration. CONCLUSION The developed combined nomogram consisting of the DL-TA score and clinical-radiological features and has the potential to predict the individual risk for the invasiveness of stage IA PSN lung adenocarcinomas.
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Affiliation(s)
- Z Zuo
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, Hunan 411000, China
| | - W Zeng
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, Hunan 411000, China
| | - K Peng
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Y Mao
- Department of Radiology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan 410004, China
| | - Y Wu
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, Hunan 411000, China
| | - Y Zhou
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, Hunan 411000, China
| | - W Qi
- Department of Radiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646100, China.
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Zuo Z, Zhao F. Gut microbiota-targeted interventions: from conventional approaches to genetic engineering. Sci Bull (Beijing) 2023:S2095-9273(23)00337-7. [PMID: 37258375 DOI: 10.1016/j.scib.2023.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310000, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Li Z, Zhang B, Wang N, Zuo Z, Wei H, Zhao F. A novel peptide protects against diet-induced obesity by suppressing appetite and modulating the gut microbiota. Gut 2023; 72:686-698. [PMID: 35803703 PMCID: PMC10086289 DOI: 10.1136/gutjnl-2022-328035] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/28/2022] [Indexed: 12/08/2022]
Abstract
OBJECTIVE The obesity epidemic and its metabolic complications continue to be a major global public health threat with limited effective treatments, especially drugs that can be taken orally. Peptides are a promising class of molecules that have gained increased interest for their applications in medicine and biotechnology. In this study, we focused on looking for peptides that can be administrated orally to treat obesity and exploring its mechanisms. DESIGN Here, a 9-amino-acid peptide named D3 was designed and administered orally to germ-free (GF) mice and wild-type (WT) mice, rats and macaques. The effects of D3 on body weight and other basal metabolic parameters were evaluated. The effects of D3 on gut microbiota were evaluated using 16S rRNA amplicon sequencing. To identify and confirm the mechanisms of D3, transcriptome analysis of ileum and molecular approaches on three animal models were performed. RESULTS A significant body weight reduction was observed both in WT (12%) and GF (9%) mice treated with D3. D3 ameliorated leptin resistance and upregulated the expression of uroguanylin (UGN), which suppresses appetite via the UGN-GUCY2C endocrine axis. Similar effects were also found in diet-induced obese rat and macaque models. Furthermore, the abundance of intestinal Akkermansia muciniphila increased about 100 times through the IFNγ-Irgm1 axis after D3 treatment, which may further inhibit fat absorption by downregulating Cd36. CONCLUSION Our results indicated that D3 is a novel drug candidate for counteracting diet-induced obesity as a non-toxic and bioactive peptide. Targeting the UGN-GUCY2C endocrine axis may represent a therapeutic strategy for the treatment of obesity.
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Affiliation(s)
- Zhanzhan Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bing Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Hong Wei
- Laboratory Animal Department, College of Basic Medicine Army Medical University, Chongqing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China .,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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Liu Y, Fan H, Shao Y, Zhang J, Zuo Z, Wang J, Zhao F, Jiang L. Gut microbiota dysbiosis associated with different types of demyelinating optic neuritis in patients. Mult Scler Relat Disord 2023; 72:104619. [PMID: 36931077 DOI: 10.1016/j.msard.2023.104619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/06/2023] [Accepted: 03/11/2023] [Indexed: 03/14/2023]
Abstract
BACKGROUND Demyelinating optic neuritis (DON) causes rapid vision loss in young and middle-aged people. The limited efficacy of treatment and the toxic side effects of drugs significantly affect the quality of life of patients with DON. Therefore, DON pathogenesis has always been a research hotspot in terms of prevention and treatment. Studies have suggested that gut microbiota imbalances may be involved in autoimmune disease development via the modulation of multiple inflammatory cytokines and anti-inflammatory metabolites. Therefore, this study aims to explore gut microbiota differences between healthy controls (HCs) and patients with DON. METHODS A total of 54 patients with DON and 41 HCs were recruited. Fecal and blood samples were collected before and after intravenous methylprednisolone pulse (IVMP) treatment. The Shannon index, gut microbiota structure, and differential bacteria were evaluated and compared. RESULTS The Shannon diversity index was decreased in patients with DON (p < 0.001) but was higher after IVMP treatment (p < 0.05). In patients with DON, Blautia, Escherichia-Shigella, and Ruminococcus showed higher abundances, whereas Bacteroides, Faecalibacterium, Roseburia, Parabacteroides, Romboutsia, and Alistipes showed lower abundances compared to that in the HCs. After IVMP treatment, the Shannon index of the myelin oligodendrocyte glycoprotein-immunoglobulin G (+) (MOG-IgG (+)) and both aquaporin-4 (AQP4)-IgG (-) and MOG-IgG (-) groups increased (p < 0.05). Bacteroides was negatively correlated with interleukin (IL)-21, IL-17E, and tumor necrosis factor-α levels (p < 0.05, r = -0.54; p < 0.05, r= -0.50; p < 0.05, r =-0.55, respectively). Escherichia was positively correlated with macrophage inflammatory protein-3α (p < 0.05, r = 0.51). Alistipes was negatively correlated with soluble CD40 ligand (p < 0.05, r = -0.52). CONCLUSION The gut microbiota differed significantly between patients with DON and HCs; however, IVMP treatment may restore gut microbiota diversity and structure in patients with DON. Moreover, gut microbiota changes may play a role in DON pathogenesis.
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Affiliation(s)
- Yi Liu
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China; China Emergency General Hospital, Beijing 100028, China
| | - Huimin Fan
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yonghui Shao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Jing Zhang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China; Department of Ophthalmology, Beijing Puren Hospital, Beijing 100062, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfeng Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
| | - Libin Jiang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China.
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Zhou J, Dai Y, Zuo Z, Liu T, Li S. Famine Exposure during Early Life and Risk of Cancer in Adulthood: A Systematic Review and Meta-Analysis. J Nutr Health Aging 2023; 27:550-558. [PMID: 37498102 DOI: 10.1007/s12603-023-1947-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/20/2023] [Indexed: 07/28/2023]
Abstract
OBJECTIVES Emerging evidences have explored the association between famine exposure during early life and cancer risk in adulthood, but the results remain controversial and inconsistent. This study aimed to provide a comprehensive evidence on the relation of famine exposure to later cancer risk. DESIGN Systematic review and meta-analysis. METHODS Relevant reports published up to March, 2022 were identified by searching PubMed, Embase, Web of sciences and Medline databases. Pooled relative ratios (RRs) with 95% confidence intervals (CIs) were used to evaluate the effect famine exposure on cancer risk. RESULTS Totally, 18 published articles with 6,061,147 subjects were included in this study. Compared with unexposed group, early life famine exposure dramatically increased the risk of cancer in adulthood (RR=1.13, 95% CI: 1.04-1.22). The pooled RRs were different in terms of sex, exposure severity, exposure period, famine type, study design type and cancer location. A remarkably elevated risk for cancer was discerned in women exposed to famine (RR=1.09, 95% CI: 1.00-1.18), severe exposure (RR=1.12, 95% CI: 1.02-1.22) and adolescence exposure (RR=1.76, 95% CI: 1.02-2.50), Chinese famine exposure (RR=1.55, 95% CI: 1.29-1.82) and cohort studies (RR=1.28, 95% CI: 1.13-1.42). Moreover, a significant association of early-life famine exposure with increased risk of breast (RR=1.16, 95% CI: 1.05-1.27) and stomach cancers (RR=1.89, 95% CI: 1.24-2.54) was observed. CONCLUSION This meta-analysis suggests that exposure to famine during early life may increase the risk of cancer in adulthood. The above-mentioned association is pronounced in women exposed to famine, severe exposure, adolescence exposure, Chinese famine, cohort studies, breast and stomach cancers. It is essential for decision-makers to take targeted measures for improving population awareness regarding the long-term effect of early life nutritional status.
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Affiliation(s)
- J Zhou
- Suyi Li, Department of Oncology, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of the University of Science and Technology of China, No. 107 Huanhu East Road, Hefei, Anhui, China. ; Ting Liu, Department of Pharmaceutics, School of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, China.
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Yang M, Xue Q, Zuo Z, Zhou J, Zhang S, Li M, Zhou H, Zhang M, Kumar S, Li W, Chen G, Zhao D, Xiang H. Aliidiomarina halalkaliphila sp. nov., a haloalkaliphilic bacterium isolated from a soda lake in Inner Mongolia Autonomous Region, China. Int J Syst Evol Microbiol 2022; 72. [PMID: 35244531 PMCID: PMC9558577 DOI: 10.1099/ijsem.0.005263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A haloalkaliphilic strain (IM 1326T) was isolated from brine sampled at a soda lake in the Inner Mongolia Autonomous Region, China. Cells of the strain were rod-shaped and motile. Strain IM 1326T was able to grow at 4–42 °C (optimum, 37 °C) with 0–13.0 % (w/v) NaCl concentrations (optimum at 4.0–6.0 %) and at pH 7.5–11.0 (optimum at 9.0–10.0). The 16S rRNA gene phylogenetic analysis revealed that the isolate belongs to the genus Aliidiomarina and is closely related to the type strains of Aliidiomarina sanyensis (95.8 % sequence similarity), Aliidiomarina shirensis (95.7 %), Aliidiomarina iranensis (95.4 %) and Aliidiomarina haloalkalitolerans (95.3 %). The whole genome of strain IM 1326T was sequenced, and the genomic DNA G+C content was 49.7 mol%. Average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the isolate and the related Aliidiomarina species were 68.1–84.9 %, 76–78 % and 18.4–20.4 %, respectively. The respiratory quinone was ubiquinone-8. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminophospholipid. The predominant cellular fatty acids were summed feature 9 (10-methyl-C16 : 0/iso-C17 : 1 ω9c, 22.2 %), iso-C15 : 0 (16.1 %) and iso-C17 : 0 (13.1 %). Based on the results of phylogenetic analysis, genome relatedness, and the physiological and chemotaxonomic properties of the isolate, strain IM 1326T is considered to represent a novel species of the genus Aliidiomarina, for which the name Aliidiomarina halalkaliphila sp. nov. is proposed (type strain IM 1326T=CGMCC 1.17056T=JCM 34227T).
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Affiliation(s)
- Ming Yang
- Sichuan Normal University, Sichuan 610101, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Qiong Xue
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Zhenqiang Zuo
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Shengjie Zhang
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Heng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Manqi Zhang
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Sumit Kumar
- Enzyme and Microbial Biochemistry Lab, Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Wei Li
- Sichuan Normal University, Sichuan 610101, PR China
| | - Guiying Chen
- Sichuan Normal University, Sichuan 610101, PR China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
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11
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Huang L, Bai J, Zong R, Zhou J, Zuo Z, Chai X, Wang Z, An J, Zhuo Y, Boada F, Yu X, Ling Z, Qu B, Pan L, Zhang Z. Sodium MRI at 7T for Early Response Evaluation of Intracranial Tumors following Stereotactic Radiotherapy Using the CyberKnife. AJNR Am J Neuroradiol 2022; 43:181-187. [PMID: 35121584 PMCID: PMC8985677 DOI: 10.3174/ajnr.a7404] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 11/05/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND AND PURPOSE Conventionally, early treatment response to stereotactic radiotherapy in intracranial tumors is often determined by structural MR imaging. Tissue sodium concentration is altered by cellular integrity and energy status in cells. In this study, we aimed to investigate the feasibility of sodium MR imaging at 7T for the preliminary evaluation of radiotherapeutic efficacy for intracranial tumors. MATERIALS AND METHODS Data were collected from 16 patients (12 men and 4 women, 24-75 years of age) with 22 intracranial tumors who were treated with stereotactic radiation therapy using CyberKnife at our institution between December 1, 2016, and August 15, 2019. Sodium MR imaging was performed at 7T before and 48 hours, 1 week, and 1 month after CyberKnife radiation therapy. Tissue sodium concentration (TSC) was calculated and analyzed based on manually labeled regions of tumors. RESULTS Ultra-high-field sodium MR imaging clearly showed the intratumoral signal, which is significantly higher than that of normal tissue (t = 5.250, P <.001)., but the edema zone has some influence. The average TSC ratios of tumor to CSF in the 22 tumors, contralateral normal tissues, edema zones, frontal cortex, and frontal white matter were 0.66 (range, 0.23-1.5), 0.30 (range, 0.15-0.43), 0.58 (range, 0.25-1.21), 0.25 (range, 0.17-0.42), and 0.30 (range, 0.19-0.49), respectively. A total of 12 tumors in 8 patients were scanned at 48 hours, 1 week, and 1 month after treatment. The average TSC at 48 hours after treatment was 0.06 higher than that before treatment and began to decrease at 1 week. The TSC ratios of 10 continued to decline and 2 tumors increased at 1 month, respectively. Tumor volume decreased by 2.4%-99% after 3 months. CONCLUSIONS Changes in the TSC can be quantified by sodium MR imaging at 7T and used to detect radiobiologic alterations in intracranial tumors at early time points after CyberKnife radiation therapy.
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Affiliation(s)
- L. Huang
- From the Departments of Neurosurgery (L.H., R.Z., J.Z., X.Y., Z.L., L.P.),Department of Neurosurgery (L.H.), The Hospital of 81st Group Army PLA, Zhangjiakou, China
| | - J. Bai
- Radiation Oncology (J.B., B.Q.), The First Medical Center of PLA General Hospital, Beijing, China
| | - R. Zong
- From the Departments of Neurosurgery (L.H., R.Z., J.Z., X.Y., Z.L., L.P.)
| | - J. Zhou
- From the Departments of Neurosurgery (L.H., R.Z., J.Z., X.Y., Z.L., L.P.)
| | - Z. Zuo
- State Key Laboratory of Brain and Cognitive Science (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Beijing, China,CAS Center for Excellence in Brain Science and Intelligence Technology (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Chinese Academy of Sciences, Beijing, China
| | - X. Chai
- State Key Laboratory of Brain and Cognitive Science (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Beijing, China,CAS Center for Excellence in Brain Science and Intelligence Technology (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Chinese Academy of Sciences, Beijing, China
| | - Z. Wang
- State Key Laboratory of Brain and Cognitive Science (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Beijing, China,CAS Center for Excellence in Brain Science and Intelligence Technology (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Chinese Academy of Sciences, Beijing, China
| | - J. An
- Siemens Shenzhen Magnetic Resonance Ltd (J.A.), Shenzhen, China
| | - Y. Zhuo
- State Key Laboratory of Brain and Cognitive Science (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Beijing, China,CAS Center for Excellence in Brain Science and Intelligence Technology (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Chinese Academy of Sciences, Beijing, China
| | - F. Boada
- Department of Radiology (F.B.), Center for Advanced Imaging Innovation and Research, New York University Grossman School of Medicine, New York, New York
| | - X. Yu
- From the Departments of Neurosurgery (L.H., R.Z., J.Z., X.Y., Z.L., L.P.)
| | - Z. Ling
- From the Departments of Neurosurgery (L.H., R.Z., J.Z., X.Y., Z.L., L.P.)
| | - B. Qu
- Radiation Oncology (J.B., B.Q.), The First Medical Center of PLA General Hospital, Beijing, China
| | - L. Pan
- From the Departments of Neurosurgery (L.H., R.Z., J.Z., X.Y., Z.L., L.P.)
| | - Z. Zhang
- State Key Laboratory of Brain and Cognitive Science (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Beijing, China,CAS Center for Excellence in Brain Science and Intelligence Technology (Z. Zou., X.C., Z.W., Y. Z., Z. Zhang.), Chinese Academy of Sciences, Beijing, China
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12
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Xue Q, Zhao D, Zuo Z, Zhou J, Xiang H. Correction to: Natronorubrum halalkaliphilum sp. nov., a haloalkaliphilic archaeon isolated from soda lake in Inner Mongolia Autonomous Region, China. Arch Microbiol 2021; 204:18. [DOI: 10.1007/s00203-021-02633-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Zuo Z, Li Y, Peng K, Li X, Tan Q, Mo Y, Lan Y, Zeng W, Qi W. CT texture analysis-based nomogram for the preoperative prediction of visceral pleural invasion in cT1N0M0 lung adenocarcinoma: an external validation cohort study. Clin Radiol 2021; 77:e215-e221. [PMID: 34916048 DOI: 10.1016/j.crad.2021.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/12/2021] [Indexed: 12/29/2022]
Abstract
AIM To develop a nomogram based on computed tomography (CT) texture analysis for the preoperative prediction of visceral pleural invasion in patients with cT1N0M0 lung adenocarcinoma. MATERIALS AND METHODS A dataset of chest CT containing lung nodules was collected from two institutions, and all surgically resected nodules were classified pathologically based on the presence of visceral pleural invasion. Each nodule on the CT image was segmented automatically by artificial-intelligence software and its CT texture features were extracted. The dataset was divided into training and external validation cohorts according to the institution, and a nomogram for predicting visceral pleural invasion was developed and validated. RESULTS Of a total of 313 patients enrolled from two independent institutions, 63 were diagnosed with visceral pleural invasion. Three-dimensional (3D) CT long diameter, skewness, and sphericity, and chronic obstructive pulmonary disease were identified as independent predictors for visceral pleural invasion by multivariable logistic regression. The nomogram based on multivariable logistic regression showed great discriminative ability, as indicated by a C-index of 0.890 (95% confidence interval [CI]: 0.867-0.914) and 0.864 (95% CI: 0.817-0.911) for the training and external validation cohorts, respectively. Additionally, calibration of the nomogram revealed good predictive ability, as indicated by the Brier score (0.108 and 0.100 for the training and external validation cohorts, respectively). CONCLUSIONS A nomogram was developed that could compute the probability of visceral pleural invasion in patients with cT1N0M0 lung adenocarcinoma with good calibration and discrimination. The nomogram has potential as a reliable tool for clinical evaluation and decision-making.
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Affiliation(s)
- Z Zuo
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, Hunan, China
| | - Y Li
- Department of Radiology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - K Peng
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - X Li
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, Hunan, China
| | - Q Tan
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, Hunan, China
| | - Y Mo
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, Hunan, China
| | - Y Lan
- Department of Radiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - W Zeng
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, Hunan, China
| | - W Qi
- Department of Radiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
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14
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Xue Q, Zhao D, Zhang S, Zhou H, Zuo Z, Zhou J, Li M, Xiang H. Highly integrated adaptive mechanisms in Spiribacter halalkaliphilus, a bacterium abundant in Chinese soda-saline lakes. Environ Microbiol 2021; 23:6463-6482. [PMID: 34587356 PMCID: PMC9292931 DOI: 10.1111/1462-2920.15794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 11/29/2022]
Abstract
Soda-saline lakes are polyextreme environments inhabited by many haloalkaliphiles, including one of the most abundant Spiribacter species. However, its mechanisms of adaptation are not ecophysiologically characterized. Based on a large-scale cultivation strategy, we obtained a representative isolate of this Spiribacter species whose relative abundance was the highest (up to 15.63%) in a wide range of salinities in the soda-saline lakes in Inner Mongolia, China. This species is a chemoorganoheterotrophic haloalkaliphile. It has a small and streamlined genome and utilizes a wide variety of compatible solutes to resist osmotic pressure and multiple monovalent cation/proton antiporters for pH homeostasis. In addition to growth enhancement by light under microaerobic conditions, cell growth, organic substrate consumption and polyhydroxybutyrate biosynthesis were also improved by inorganic sulfide. Both quantitative RT-PCR and enzymatic assays verified that sulfide:quinone oxidoreductase was upregulated during this process. Metatranscriptomic analysis indicated that all genes related to environmental adaptation were transcribed in natural environments. Overall, this study has identified a novel abundant haloalkaliphile with multiple and highly integrated adaptive strategies and found that inorganic sulfide was able to improve the adaptation of a heterotroph to polyextreme environments.
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Affiliation(s)
- Qiong Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenqiang Zuo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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15
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Wang L, Huang G, Hou R, Qi D, Wu Q, Nie Y, Zuo Z, Ma R, Zhou W, Ma Y, Hu Y, Yang Z, Yan L, Wei F. Multi-omics reveals the positive leverage of plant secondary metabolites on the gut microbiota in a non-model mammal. Microbiome 2021; 9:192. [PMID: 34548111 PMCID: PMC8456708 DOI: 10.1186/s40168-021-01142-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 08/10/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Flavonoids are important plant secondary metabolites (PSMs) that have been widely used for their health-promoting effects. However, little is known about overall flavonoid metabolism and the interactive effects between flavonoids and the gut microbiota. The flavonoid-rich bamboo and the giant panda provide an ideal system to bridge this gap. RESULTS Here, integrating metabolomic and metagenomic approaches, and in vitro culture experiment, we identified 97 flavonoids in bamboo and most of them have not been identified previously; the utilization of more than 70% flavonoid monomers was attributed to gut microbiota; the variation of flavonoid in bamboo leaves and shoots shaped the seasonal microbial fluctuation. The greater the flavonoid content in the diet was, the lower microbial diversity and virulence factor, but the more cellulose-degrading species. CONCLUSIONS Our study shows an unprecedented landscape of beneficial PSMs in a non-model mammal and reveals that PSMs remodel the gut microbiota conferring host adaptation to diet transition in an ecological context, providing a novel insight into host-microbe interaction. Video abstract.
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Affiliation(s)
- Le Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangping Huang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
| | - Qi Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yonggang Nie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenqiang Zuo
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458, Guangzhou, China
| | - Rui Ma
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
| | - Wenliang Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yingjie Ma
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhisong Yang
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Li Yan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458, Guangzhou, China.
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16
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Shen L, Qian B, Xiao J, Zhu Y, Hussain S, Deng J, Peng G, Zuo Z, Zou L, Yu S, Ma X, Zhong Z, Ren Z, Wang Y, Liu H, Zhou Z, Cai D, Hu Y, Zong X, Cao S. Characterization of serum adiponectin and leptin in healthy perinatal dairy cows or cows with ketosis, and their effectson ketosis involved indices. Pol J Vet Sci 2021; 23:373-381. [PMID: 33006850 DOI: 10.24425/pjvs.2020.134681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We investigated changes in concentrations of ADP (adiponectin), LEP (leptin), BHBA (beta-hydroxybutyric acid), NEFA (non-esterified fatty acid), Glucose (Glu) and INS (insulin) in serum of healthy perinatal dairy cows and cows with ketosis. Twenty-one healthy cows and seventeen cows with ketosis from a herd of a total 60 Holstein cows (near dry period i.e. 56 days antepartum) were selected. Blood was collected through the tail vein every 7 days, from 56 day antepartum to 56 day postpartum. Serum ADP, LEP, BHBA, NEFA, Glu, and INS concentrations were determined, and ketosis was diagnosed through serum BHBA (≥1.2 mmol/L). We showed the concentration of serum adipokines and energy balancing indices were stable during antepar- tum period. However, ADP concentration increased while LEP decreased, and there were a significant increase in cows with ketosis compared to that of in healthy cows. Serum BHBA and NEFA concentrations increased significantly at first, and then gradually decreased in both healthy cows and cows with ketosis. However, cows with ketosis showed higher concentrations of BHBA and NEFA which restored later. The serum concentration of Glu in both healthy dairy cows and cows with ketosis showed a decreasing trend. INS concentration in healthy cows was decreased while it was increased in cows with ketosis. The results reflect the extent of hypo- glycemia and lipid mobilization postpartum, suggest IR exists in cows with ketosis while serum ADP and LEP might play roles in the development of ketosis.
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Affiliation(s)
- L Shen
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - B Qian
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - J Xiao
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Y Zhu
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - S Hussain
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - J Deng
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - G Peng
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Z Zuo
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - L Zou
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - S Yu
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - X Ma
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Z Zhong
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Z Ren
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Y Wang
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - H Liu
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Z Zhou
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - D Cai
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Y Hu
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - X Zong
- Sichuan Agricultural University - Chengdu Campus, Academic Affairs Office, Chengdu, Sichuan, 611130, China
| | - S Cao
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
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Zhang J, Hou L, Zuo Z, Ji P, Zhang X, Xue Y, Zhao F. Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nat Biotechnol 2021; 39:836-845. [PMID: 33707777 DOI: 10.1038/s41587-021-00842-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/08/2023]
Abstract
Reconstructing the sequence of circular RNAs (circRNAs) from short RNA sequencing reads has proved challenging given the similarity of circRNAs and their corresponding linear messenger RNAs. Previous sequencing methods were unable to achieve high-throughput detection of full-length circRNAs. Here we describe a protocol for enrichment and full-length sequencing of circRNA isoforms using nanopore technology. Circular reverse transcription and size selection achieves a 20-fold higher enrichment of circRNAs from total RNA compared to previous methods. We developed an algorithm, called circRNA identifier using long-read sequencing data (CIRI-long), to reconstruct the sequence of circRNAs. The workflow was validated with simulated data and by comparison to Illumina sequencing as well as quantitative real-time RT-PCR. We used CIRI-long to analyze adult mouse brain samples and systematically profile circRNAs, including mitochondria-derived and transcriptional read-through circRNAs. We identified a new type of intronic self-ligated circRNA that exhibits special splicing and expression patterns. Our method takes advantage of nanopore long reads and enables unbiased reconstruction of full-length circRNA sequences.
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Affiliation(s)
- Jinyang Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lingling Hou
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Peifeng Ji
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiaorong Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. .,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
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Zhang J, Hou L, Zuo Z, Ji P, Zhang X, Xue Y, Zhao F. Author Correction: Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nat Biotechnol 2021; 39:893. [PMID: 33941933 DOI: 10.1038/s41587-021-00934-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jinyang Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lingling Hou
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Zhenqiang Zuo
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Peifeng Ji
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiaorong Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. .,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
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Zhang M, Yao Y, Zuo Z, Cheng Z. Discordant lymphoma consisting of NK/T-cell lymphoma and Hodgkin's lymphoma seen on FDG PET. Rev Esp Med Nucl Imagen Mol 2021; 40:184-185. [PMID: 33509690 DOI: 10.1016/j.remn.2020.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/04/2020] [Accepted: 03/20/2020] [Indexed: 11/28/2022]
Affiliation(s)
- M Zhang
- Department of Breast Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Y Yao
- PET/CT Center, Department of Nuclear Medicine, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Z Zuo
- Department of Pathology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Z Cheng
- PET/CT Center, Department of Nuclear Medicine, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
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Zuo Z, Zhao D, Zhou J, Han J, Xiang H. Halalkalirubrum salinum gen. nov., sp. nov., a halophilic archaeon isolated from a saline lake. Antonie Van Leeuwenhoek 2021; 114:83-94. [PMID: 33389352 DOI: 10.1007/s10482-020-01502-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/22/2020] [Indexed: 10/22/2022]
Abstract
A novel extremely halophilic archaeon, strain N1521T, was isolated from a saline lake in Tibet, China. Cells of the strain were pleomorphic and Gram-stain-negative. It produced red pigments. Growth was observed at 4-42 °C (optimum, 37 °C), pH 7.0-10.5 (optimum, 8.0-9.5), NaCl 11%-25% (optimum, 15%) and in the presence of 0-0.1 M MgCl2 (optimum, 0.05 M) in aerobic conditions. The minimum NaCl concentration that prevented cell lysis was 2% (w/v). The major polar lipids of strain N1521T were phosphatidylglycerol sulfate, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol and an unidentified glycolipid. The DNA G + C content was 58.37 mol%. According to 16S rRNA gene sequence comparisons, strain N1521T revealed the highest sequence similarity to Haloprofundus halophilus NK23T (91.38%) and Halogranum amylolyticum TNN58T (91.00%), and low sequence similarities (< 91%) with other genera in the order Haloferacales. Phylogenetic analysis based on the 16S rRNA gene and rpoB' gene sequence showed that strain N1521T was distinct from the members of the order Haloferacales. The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values calculated from whole genome-sequence comparison between strain N1521T and the members of the order Haloferacales were in the ranges of 15.1-18.2%, 68.8-73.0%, and 58.4-63.9%, respectively. Phylogenetic tree reconstructions based on the whole-genome sequences revealed that strain N1521T was closer to the members of the family Halorubraceae. Based on the data obtained, strain N1521T is thus considered to represent a novel species of a new genus within the family Halorubraceae, for which the name Halalkalirubrum salinum gen. nov., sp. nov. is proposed. The type strain is N1521T (= CGMCC 1.16693 = JCM 33785).
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Affiliation(s)
- Zhenqiang Zuo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Xue Q, Zuo Z, Zhou H, Zhou J, Zhang S, Han J, Zhao D, Xiang H. Salinadaptatus halalkaliphilus gen. nov., sp. nov., a haloalkaliphilic archaeon isolated from salt pond in Inner Mongolia Autonomous Region, China. Int J Syst Evol Microbiol 2020; 71. [PMID: 33275091 DOI: 10.1099/ijsem.0.004584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A haloalkaliphilic strain XQ-INN 246T was isolated from the sediment of a salt pond in Inner Mongolia Autonomous Region, China. Cells of the strain were rods, motile and strictly aerobic. The strain was able to grow in the presence of 2.6-5.3 M NaCl (optimum concentration is 4.4 M) at 30-50 °C (optimum temperature is 42 °C) and pH 7.0-10.0 (optimum pH is 8.0-8.5). The whole genome sequencing of strain XQ-INN 246T revealed a genome size of 4.52 Mbp and a DNA G+C content of 62.06 mol%. Phylogenetic tree based on 16S rRNA gene sequences and concatenated amino acid sequences of 122 single-copy conserved proteins revealed a robust lineage of the strain XQ-INN 246T with members of related genera of the family Natrialbaceae. The strain possessed the polar lipids of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. No glycolipids were detected. Based on phylogenetic analysis, phenotypic characteristics, chemotaxonomic properties and genome relatedness, the isolate was proposed as the type strain of a novel species of a new genus within the family Natrialbaceae, for which the name Salinadaptatus halalkaliphilus gen. nov., sp. nov. is proposed. The type strain is XQ-INN 246T (=CGMCC 1.16692T=JCM 33751T).
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Affiliation(s)
- Qiong Xue
- University of Chinese Academy of Sciences, 100049, Beijing, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Zhenqiang Zuo
- University of Chinese Academy of Sciences, 100049, Beijing, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Heng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Shengjie Zhang
- University of Chinese Academy of Sciences, 100049, Beijing, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Hua Xiang
- University of Chinese Academy of Sciences, 100049, Beijing, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
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Huang D, Zhang Z, Lin K, Zuo Z, Chen Q, Qian D, Zhu W, Li J. Extensible artificial intelligence model predicts post-ablation AF recurrence using coronary sinus electrogram. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.0560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Atrial fibrillation (AF) is a major public health problem with significant adverse outcomes and catheter ablation is a widely adopted treatment. The CABANA trial showed that catheter ablation reduced AF recurrence to a greater extent than medications. However, some of patients who underwent this procedure still experience relapse. Here, we present an innovative way to identify this subgroup using an artificial intelligence (AI) -assisted coronary sinus electrogram.
Hypothesis
Our hypothesis is that credible features in the electrogram can be extracted by AI for prediction, therefore rigorous drug administration, close follow-up or potential second procedure can be applied to these patients.
Methods
67 patients from two independent hospitals (SPH & ZSH) with non-valvular persistent AF undergoing circumferential pulmonary vein isolation were enrolled in this study, 23 of which experienced recurrence 6 months after the procedure. We collected standard 2.5-second fragments of coronary sinus electrogram from ENSITE NAVX (SPH) and Carto (ZSH)system before the ablation started. A total of 1429 fragments were obtained and a transfer learning-based ResNet model was employed in our study. Fragments from ZSH were used for training and SPH for validation of deep convolutional neural networks (DCNN). The AI model performance was evaluated by accuracy, recall, precision, F-Measure and AUC.
Results
The prediction accuracy of the DCNN in single center reached 96%, while that in different ablation systems reached 74.3%. Also, the algorithm yielded values for the AUC, recall, precision and F-Measure of 0.76, 86.1%, 95.9% and 0.78, respectively, which shows satisfactory classification results and extensibility in different cardiology centers and brands of electroanatomic mapping instruments.
Conclusions
Our work has revealed the potential intrinsic correlation between coronary sinus electrical activity and AF recurrence using DCNN-based model. Moreover, the DCNN model we developed shows great prospects in the relapse prediction for personalized post-procedural management.
Funding Acknowledgement
Type of funding source: Foundation. Main funding source(s): The National Natural Science Foundation of China
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Affiliation(s)
- D Huang
- Shanghai Sixth People's Hospital of Shanghai Jiaotong University, Shanghai, China
| | - Z Zhang
- Shanghai Sixth People's Hospital of Shanghai Jiaotong University, Shanghai, China
| | - K Lin
- Shanghai Sixth People's Hospital of Shanghai Jiaotong University, Shanghai, China
| | - Z Zuo
- Shanghai Sixth People's Hospital of Shanghai Jiaotong University, Shanghai, China
| | - Q Chen
- Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, cardiology, Shanghai, China
| | - D Qian
- School of Biomedical Engineering,Shanghai JIaotong university, Shanghai, China
| | - W Zhu
- Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, cardiology, Shanghai, China
| | - J Li
- Shanghai Sixth People's Hospital of Shanghai Jiaotong University, Shanghai, China
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Cheng A, Yip E, Tsang J, Chan P, Choi A, Yiu B, Kam J, Young G, So K, Zuo Z, Cheung Y, Zhou K, Lam T. PCN10 ORAL H2RA for Taxane Hypersensitivity Prevention: A Pharmacokinetic-Guided Decision. Value Health Reg Issues 2020. [DOI: 10.1016/j.vhri.2020.07.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Collias D, Leenay RT, Slotkowski RA, Zuo Z, Collins SP, McGirr BA, Liu J, Beisel CL. A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9. Sci Adv 2020; 6:eabb4054. [PMID: 32832642 PMCID: PMC7439565 DOI: 10.1126/sciadv.abb4054] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/28/2020] [Indexed: 05/16/2023]
Abstract
CRISPR technologies have overwhelmingly relied on the Streptococcus pyogenes Cas9 (SpyCas9), with its consensus NGG and less preferred NAG and NGA protospacer-adjacent motifs (PAMs). Here, we report that SpyCas9 also recognizes sequences within an N(A/C/T)GG motif. These sequences were identified on the basis of preferential enrichment in a growth-based screen in Escherichia coli. DNA binding, cleavage, and editing assays in bacteria and human cells validated recognition, with activities paralleling those for NAG(A/C/T) PAMs and dependent on the first two PAM positions. Molecular-dynamics simulations and plasmid-clearance assays with mismatch-intolerant variants supported induced-fit recognition of an extended PAM by SpyCas9 rather than recognition of NGG with a bulged R-loop. Last, the editing location for SpyCas9-derived base editors could be shifted by one nucleotide by selecting between (C/T)GG and adjacent N(C/T)GG PAMs. SpyCas9 and its enhanced variants thus recognize a larger repertoire of PAMs, with implications for precise editing, off-target predictions, and CRISPR-based immunity.
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Affiliation(s)
- D. Collias
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - R. T. Leenay
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - R. A. Slotkowski
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Z. Zuo
- College of Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76129, USA
| | - S. P. Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - B. A. McGirr
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - J. Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76129, USA
| | - C. L. Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
- Helmholtz Institute of RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97078 Würzburg, Germany
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Wan G, Cao F, Cai X, Yu X, Zuo Z, Song Y, Xu T, Li Y, Yu Y, Wang X, Wang X. 7P Prognostic value of the immune infiltration score in early breast cancer patients receiving dual HER2 blockade with trastuzumab and pertuzumab: An exploratory analysis of a randomized clinical trial. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.03.143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Shen L, Zhu Y, Xiao J, Deng J, Peng G, Zuo Z, Yu S, Ma X, Zhong Z, Ren Z, Zhou Z, Liu H, Zong X, Cao S. Relationship of adiponectin, leptin, visfatin and IGF-1 in cow's venous blood and venous cord blood with calf birth weight. Pol J Vet Sci 2020; 22:541-548. [PMID: 31560471 DOI: 10.24425/pjvs.2019.129962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Intrauterine fetal development process is complicated and affected by many regulating factors such as maternal nutritional status, transcription factors and adipokines. Adipokines are kinds of active substances secreted by adipose tissue, including more than 50 kinds of molecules. To explore the correlation between calf birth weights and adipokines including adiponectin, leptin, visfatin, and IGF-1 in cows venous and venous cord blood. Fifty-four healthy multiparous Chinese Holstein cows were used; in which, cows with a calf weight less than 40 kg were included in group A (n=9); those with a calf weight between 40 kg~45 kg were included in group B (n=25) and ≥45 kg were included in group C (n=20), venous blood and cord venous blood was collected. An ELISA kit was used to evaluate the concentration of adiponectin, leptin, visfatin, and IGF-1, correlations between index-index and index-calf birth weight were analysed. In both cows venous and cord venous blood, adiponectin, leptin, visfatin, and IGF-1 levels were significantly correlated with each other (p⟨0.01), and levels of these adipokines in venous blood were significantly higher than cord venous blood (p⟨0.01). Adiponectin, leptin, visfatin, and IGF-1 in venous cord blood were positively correlated with calf birth weights, and significantly correlated with calf birth weights respectively (p⟨0.01). Our study showed that adiponectin, leptin, and IGF-1 were found in venous blood and cord venous blood, and adiponectin, leptin, and IGF-1 in venous and cord venous blood potentially inter-regulated each other; adiponectin, leptin, and IGF-1 in venous blood were not significantly correlated with calf birth weights, while adiponectin, leptin, visfatin, and IGF-1 in venous cord blood were significantly correlated with calf birth weights, respectively.
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Affiliation(s)
- L Shen
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Y Zhu
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - J Xiao
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - J Deng
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - G Peng
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Z Zuo
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - S Yu
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - X Ma
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Z Zhong
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Z Ren
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - Z Zhou
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - H Liu
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
| | - X Zong
- Sichuan Agricultural University - Chengdu Campus, Academic Affairs Office, Chengdu, Sichuan, 611130, China
| | - S Cao
- Sichuan Agricultural University - Chengdu Campus, The Key Laboratory of Animal Disease and Human Health of Sichuan Province, The Medical Research Center for Cow Disease Chengdu, Sichuan, 611130, China
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Liu X, Hao Q, Hou L, Xia X, Zhao W, Zhang Y, Ge M, Liu Y, Zuo Z, Yue J, Dong B. Ethnic Groups Differences in the Prevalence of Sarcopenia Using the AWGS Criteria. J Nutr Health Aging 2020; 24:665-671. [PMID: 32510121 DOI: 10.1007/s12603-020-1381-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
OBJECTIVES To estimate the prevalence of sarcopenia in different ethnic groups and the association with cultural life styles in west China. DESIGN A cross-sectional study. SETTINGS The communities in Yunnan, Guizhou, Sichuan, and Xinjiang provinces. PARTICIPANTS 4500 participants aged 50 years or older in west China were enrolled in this study. Sarcopenia was defined according to the diagnostic algorithm of the Asia Working Group for Sarcopenia (AWGS). MEASUREMENTS We measured gait speed, handgrip strength and muscle mass by using bioelectrical impedance analysis (BIA) for all eligible participants. Life-style information were collected by reviewers. Relationships between sarcopenia and ethnic groups were analyzed using univariate and multivariate analyses. RESULTS We found 869 (19.31%) adults aged 50 years old or older were sarcopenia. The mean age is 62.4±8.3 years. The main ethnic groups enrolled in this study is Han, Tibetan, Qiang, Yi and Hui. The crude prevalence of sarcopenia is 22.3% in Han, 18.2% in Tibetan, 11.8% in Qiang, 34.7% in Yi and 26.7% in Hui. Compared to Han, after adjusting sex and age, Qiang has a lower prevalence of sarcopenia (odds ratio [OR]: 0.44, 95% CI 0.35-0.55), Yi has a higher prevalence of sarcopenia (OR: 1.78, 95% CI 1.29-2.43). While adding adjusting other potential cofounders, sarcopenia is still less prevalent in Qiang (OR: 0.44, 95% CI 0.34-0.57). CONCLUSIONS The crude prevalence of sarcopenia is 22.3% in Han, 18.2% in Tibetan, 11.8% in Qiang, 34.7% in Yi and 26.7% in Hui. Sarcopenia was less prevalent in Qiang compared with Han. Further studies to determine related factors of sarcopenia among different ethnic groups are recommended.
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Affiliation(s)
- X Liu
- Birong Dong, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guo Xue Xiang Renmin Nan Lu Chengdu, Sichuan,China, Fax: 86-28-85422321, 610041, Email address: . Jirong Yue, Professor, Department of Geriatrics, West China Hospital, Sichuan University, No. 37, Guo Xue Xiang, Chengdu, Sichuan, China, Fax: 86-28-85422321, 610041, Email address:
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Zhang Y, Ge M, Zhao W, Hou L, Xia X, Liu X, Zuo Z, Zhao Y, Yue J, Dong B. Association Between Number of Teeth, Denture Use and Frailty: Findings from the West China Health and Aging Trend Study. J Nutr Health Aging 2020; 24:423-428. [PMID: 32242210 DOI: 10.1007/s12603-020-1346-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Frailty and poor oral health are both common age-related conditions. However, the association between oral health and frailty has not been explored thoroughly among older Chinese adults. We aimed to investigate the associations between number of teeth, denture use, and frailty among older adults in western China. DESIGN Cross-sectional study. SETTING Community-based. PARTICIPANTS Participants were 4037 community-dwelling individuals aged 60 and older from the West China Health and Aging Trend (WCHAT) study. MEASUREMENTS Frailty was assessed using the physical frailty phenotype (PFP) and categorized as non-frail, prefrail and frail. In addition, number of teeth and denture use were examined by calibrated dentists. Multinomial logistic regression models were performed to examine the association between number of teeth, denture use, and frailty. RESULTS The overall prevalence of frailty was 6.7% among 4037 participants aged 60 and older in western China. Participants with no more than 20 teeth were associated with higher odds of being prefrail or frail whether wearing dentures or not. Denture using could not help lower the odds of being prefrail or frail for older adults with fewer teeth. CONCLUSIONS This study suggested that frailty was associated with having fewer teeth (≤20 teeth) among older Chinese adults. Future research involving targeted interventions addressing number of teeth may help provide information to establish effective strategies for frailty prevention in older adults.
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Affiliation(s)
- Y Zhang
- Professor Birong Dong, Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, GuoXueXiang, Chengdu, Sichuan, China, 610041. E-mail address: , Fax: +86-028-85421550, Tel: +86-028-85421550
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Wang B, Zuo Z, Chen H, Qiu B, Du M, Gao Y. The comparison of thoracoscopic-laparoscopic esophagectomy and open esophagectomy: A meta-analysis. Indian J Cancer 2018; 54:115-119. [PMID: 29199673 DOI: 10.4103/ijc.ijc_192_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The objective of this study was to perform a meta-analysis to evaluate the effects of thoracoscopic-laparoscopic esophagectomy (TLE) and open esophagectomy (OE) in the treatment of esophageal cancer. METHODS A literature search was performed using PubMed, Embase, and Google Scholar databases for relevant keywords and the medical subject headings. After we had screened further, 13 clinical trials were included in the final meta-analysis. Specific odds ratios (ORs), standardized mean differences (SMDs), mean differences (MDs), and confidence intervals (CIs) were calculated. RESULTS The outcomes of treatment effects included anastomotic leakage, blood loss, number of lymph nodes harvested, and operating time. Comparing OE for esophageal cancer patients, the pooled OR of anastomotic leakage was 0.89 (95% CI = [0.47, 1.68]), the pooled SMD of blood loss was - 0.56 (95% CI = [-0.77, -0.35]), the pooled MD of lymph nodes harvested was - 0.93 (95% CI = [-2.35, 0.50]), and the pooled SMD of operating time was 0.31 (95% CI = [0.02, 0.59]). CONCLUSION TLE was found to significantly decrease patients' blood loss. There is no difference of anastomotic leakage and the number of lymph nodes harvested between TLE and OE.
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Affiliation(s)
- B Wang
- Department of Thoracic Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Z Zuo
- Thoracic Cancer Treatment Center, Armed Police Beijing Corps Hospital, Beijing, China
| | - H Chen
- Department of Thoracic Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - B Qiu
- Department of Thoracic Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - M Du
- Department of Thoracic Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Y Gao
- Department of Thoracic Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Wang Y, Han R, Zuo Z. Dexmedetomidine post-treatment induces neuroprotection via activation of extracellular signal-regulated kinase in rats with subarachnoid haemorrhage. Br J Anaesth 2016; 116:384-92. [PMID: 26865131 DOI: 10.1093/bja/aev549] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Dexmedetomidine, a sedative agent, provides neuroprotection when administered during or before brain ischaemia. This study was designed to determine whether dexmedetomidine post-treatment induces neuroprotection against subarachnoid haemorrhage (SAH) and the mechanisms for this effect. METHODS Subarachnoid haemorrhage was induced by endovascular perforation to the junction of the right middle and anterior cerebral arteries in adult rats. Dexmedetomidine was applied immediately or 2 h after onset of SAH. Neurological outcome was evaluated 2 days after SAH. Right frontal cortex area 1 was harvested 24 h after SAH for western blotting. RESULTS Subarachnoid haemorrhage reduced neurological scores and increased brain oedema and blood-brain barrier permeability. These effects were attenuated by dexmedetomidine post-treatment. Neuroprotection by dexmedetomidine was abolished by PD98095, an inhibitor of extracellular signal-regulated kinase (ERK) activation. Phospho-ERK, the activated form of ERK, was increased by dexmedetomidine; this activation was inhibited by PD98095. CONCLUSIONS Dexmedetomidine post-treatment provides neuroprotection against SAH. This effect appears to be mediated by ERK.
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Affiliation(s)
- Y Wang
- Department of Anesthesiology, University of Virginia, Charlottesville, VA 22901, USA Department of Anaesthesiology, Beijing Tian Tan Hospital, Capital Medical University, Beijing 100050, China
| | - R Han
- Department of Anaesthesiology, Beijing Tian Tan Hospital, Capital Medical University, Beijing 100050, China
| | - Z Zuo
- Department of Anesthesiology, University of Virginia, Charlottesville, VA 22901, USA
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Gong T, Liu R, Zuo Z, Che Y, Yu H, Song C, Yang C. Metabolic Engineering of Pseudomonas putida KT2440 for Complete Mineralization of Methyl Parathion and γ-Hexachlorocyclohexane. ACS Synth Biol 2016; 5:434-42. [PMID: 26854500 DOI: 10.1021/acssynbio.6b00025] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Agricultural soils are often cocontaminated with multiple pesticides. Unfortunately, microorganisms isolated from natural environments do not possess the ability to simultaneously degrade different classes of pesticides. Currently, we can use the approaches of synthetic biology to create a strain endowed with various catabolic pathways that do not exist in a natural microorganism. Here, we describe the metabolic engineering of a biosafety Pseudomonas putida strain KT2440 for complete mineralization of methyl parathion (MP) and γ-hexachlorocyclohexane (γ-HCH) by functional assembly of the MP and γ-HCH mineralization pathways. The engineered strain was genetically stable, and no growth inhibition was observed. Such a strain not only would reduce the toxicity of MP and γ-HCH but also would prevent the accumulation of potentially toxic intermediates in the environment. Furthermore, expression of Vitreoscilla hemoglobin improved the ability of the engineered strain to sequester O2. The inoculation of the engineered strain to soils treated with MP and γ-HCH resulted in a higher degradation rate than in noninoculated soils. Moreover, introduced GFP may be used to monitor the activity of the engineered strain during bioremediation. The engineered strain may be a promising candidate for in situ bioremediation of soil cocontaminated with MP and γ-HCH.
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Affiliation(s)
- Ting Gong
- Key
Laboratory of Molecular Microbiology and Technology for Ministry of
Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Ruihua Liu
- Key
Laboratory of Molecular Microbiology and Technology for Ministry of
Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Zhenqiang Zuo
- Key
Laboratory of Molecular Microbiology and Technology for Ministry of
Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - You Che
- Key
Laboratory of Molecular Microbiology and Technology for Ministry of
Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Huilei Yu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Cunjiang Song
- Key
Laboratory of Molecular Microbiology and Technology for Ministry of
Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Chao Yang
- Key
Laboratory of Molecular Microbiology and Technology for Ministry of
Education and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
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Hu M, Fok B, Wo S, Lee V, Zuo Z, Tomlinson B. Influence of farnesoid X receptor and bile acid transporter polymorphisms on the pharmacokinetics of ursodeoxycholic acid. Atherosclerosis 2015. [DOI: 10.1016/j.atherosclerosis.2015.04.411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Chung CH, Guthrie VB, Masica DL, Tokheim C, Kang H, Richmon J, Agrawal N, Fakhry C, Quon H, Subramaniam RM, Zuo Z, Seiwert T, Chalmers ZR, Frampton GM, Ali SM, Yelensky R, Stephens PJ, Miller VA, Karchin R, Bishop JA. Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing. Ann Oncol 2015; 26:1216-1223. [PMID: 25712460 PMCID: PMC4516044 DOI: 10.1093/annonc/mdv109] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/23/2015] [Accepted: 02/18/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND To determine genomic alterations in head and neck squamous cell carcinoma (HNSCC) using formalin-fixed, paraffin-embedded (FFPE) tumors obtained through routine clinical practice, selected cancer-related genes were evaluated and compared with alterations seen in frozen tumors obtained through research studies. PATIENTS AND METHODS DNA samples obtained from 252 FFPE HNSCC were analyzed using next-generation sequencing-based (NGS) clinical assay to determine sequence and copy number variations in 236 cancer-related genes plus 47 introns from 19 genes frequently rearranged in cancer. Human papillomavirus (HPV) status was determined by presence of the HPV DNA sequence in all samples and corroborated with high-risk HPV in situ hybridization (ISH) and p16 immunohistochemical (IHC) staining in a subset of tumors. Sequencing data from 399 frozen tumors in The Cancer Genome Atlas and University of Chicago public datasets were analyzed for comparison. RESULTS Among 252 FFPE HNSCC, 84 (33%) were HPV positive and 168 (67%) were HPV negative by sequencing. A subset of 40 tumors with HPV ISH and p16 IHC results showed complete concordance with NGS-derived HPV status. The most common genes with genomic alterations were PIK3CA and PTEN in HPV-positive tumors and TP53 and CDKN2A/B in HPV-negative tumors. In the pathway analysis, the PI3K pathway in HPV-positive tumors and DNA repair-p53 and cell cycle pathways in HPV-negative tumors were frequently altered. The HPV-positive oropharynx and HPV-positive nasal cavity/paranasal sinus carcinoma shared similar mutational profiles. CONCLUSION The genomic profile of FFPE HNSCC tumors obtained through routine clinical practice is comparable with frozen tumors studied in research setting, demonstrating the feasibility of comprehensive genomic profiling in a clinical setting. However, the clinical significance of these genomic alterations requires further investigation through application of these genomic profiles as integral biomarkers in clinical trials.
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Affiliation(s)
- C H Chung
- Department of Oncology; Department of Otolaryngology-Head and Neck Surgery.
| | - V B Guthrie
- Department of Biomedical Engineering, Institute for Computational Medicine
| | - D L Masica
- Department of Biomedical Engineering, Institute for Computational Medicine
| | - C Tokheim
- Department of Biomedical Engineering, Institute for Computational Medicine
| | | | - J Richmon
- Department of Otolaryngology-Head and Neck Surgery
| | - N Agrawal
- Department of Otolaryngology-Head and Neck Surgery
| | - C Fakhry
- Department of Oncology; Department of Otolaryngology-Head and Neck Surgery; Department of Milton J. Dance Head and Neck Center, Baltimore
| | - H Quon
- Department of Radiation Oncology
| | - R M Subramaniam
- Department of Oncology; Department of Otolaryngology-Head and Neck Surgery; Department of Radiology and Radiological Sciences
| | - Z Zuo
- Department of Medicine, University of Chicago, Chicago
| | - T Seiwert
- Department of Medicine, University of Chicago, Chicago
| | | | | | - S M Ali
- Foundation Medicine, Inc., Cambridge, USA
| | - R Yelensky
- Foundation Medicine, Inc., Cambridge, USA
| | | | - V A Miller
- Foundation Medicine, Inc., Cambridge, USA
| | - R Karchin
- Department of Oncology; Department of Biomedical Engineering, Institute for Computational Medicine
| | - J A Bishop
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore
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Wang Y, Zhang C, Gong T, Zuo Z, Zhao F, Fan X, Yang C, Song C. An upp-based markerless gene replacement method for genome reduction and metabolic pathway engineering in Pseudomonas mendocina NK-01 and Pseudomonas putida KT2440. J Microbiol Methods 2015; 113:27-33. [DOI: 10.1016/j.mimet.2015.03.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/26/2015] [Accepted: 03/27/2015] [Indexed: 11/25/2022]
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Zhao P, Ji G, Xue H, Yu W, Zhao X, Ding M, Yang Y, Zuo Z. Isoflurane postconditioning improved long-term neurological outcome possibly via inhibiting the mitochondrial permeability transition pore in neonatal rats after brain hypoxia–ischemia. Neuroscience 2014; 280:193-203. [DOI: 10.1016/j.neuroscience.2014.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 09/05/2014] [Accepted: 09/05/2014] [Indexed: 12/19/2022]
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Wang L, Zuo Z, Zhang P, He S. Unconscious Processing of Direct Gaze: fMRI Evidence. J Vis 2014. [DOI: 10.1167/14.10.1271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Cao J, Wang Z, Mi W, Zuo Z. Isoflurane unveils a critical role of glutamate transporter type 3 in regulating hippocampal GluR1 trafficking and context-related learning and memory in mice. Neuroscience 2014; 272:58-64. [PMID: 24797327 PMCID: PMC4077290 DOI: 10.1016/j.neuroscience.2014.04.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 04/04/2014] [Accepted: 04/21/2014] [Indexed: 12/31/2022]
Abstract
Glutamate transporter type 3 (EAAT3) may play a role in cognition. Isoflurane enhances EAAT3 trafficking to the plasma membrane. Thus, we used isoflurane to determine how EAAT3 might regulate learning and memory and the trafficking of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors, such as GluR1, to the plasma membrane, a fundamental biochemical process for learning and memory. Here, isoflurane increased EAAT3 but did not change GluR1 levels in the plasma membrane of wild-type mouse hippocampus. Isoflurane increased protein phosphatase activity in the wild-type and EAAT3(-/-) mouse hippocampus. Also, isoflurane reduced GluR1 in the plasma membrane and decreased phospho-GluR1 in EAAT3(-/-) mice. The phosphatase inhibitor okadaic acid attenuated these effects. Finally, isoflurane inhibited context-related fear conditioning in EAAT3(-/-) mice but not in wild-type mice. Thus, isoflurane may increase GluR1 trafficking to the plasma membrane via EAAT3 and inhibit GluR1 trafficking via protein phosphatase. Lack of EAAT3 effects leads to decreased GluR1 trafficking and impaired cognition after isoflurane exposure in EAAT3(-/-) mice.
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Affiliation(s)
- J Cao
- Department of Anesthesiology, University of Virginia, Charlottesville, VA 22908, United States; Department of Anesthesiology and Operation Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Z Wang
- Department of Anesthesiology, University of Virginia, Charlottesville, VA 22908, United States; Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - W Mi
- Department of Anesthesiology and Operation Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Z Zuo
- Department of Anesthesiology, University of Virginia, Charlottesville, VA 22908, United States.
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Liu R, Zuo Z, Xu Y, Song C, Jiang H, Qiao C, Xu P, Zhou Q, Yang C. Twin-arginine signal peptide of Bacillus subtilis YwbN can direct Tat-dependent secretion of methyl parathion hydrolase. J Agric Food Chem 2014; 62:2913-2918. [PMID: 24620988 DOI: 10.1021/jf405694n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The twin-arginine translocation (Tat) pathway exports folded proteins across the cytoplasmic membranes of bacteria and archaea. Two parallel Tat pathways (TatAdCd and TatAyCy systems) with distinct substrate specificities have previously been discovered in Bacillus subtilis. In this study, to secrete methyl parathion hydrolase (MPH) into the growth medium, the twin-arginine signal peptide of B. subtilis YwbN was used to target MPH to the Tat pathway of B. subtilis. Western blot analysis and MPH assays demonstrated that active MPH was secreted into the culture supernatant of wild-type cells. No MPH secretion occurred in a total-tat2 mutant, indicating that the observed export in wild-type cells was mediated exclusively by the Tat pathway. Export was fully blocked in a tatAyCy mutant. In contrast, the tatAdCd mutant was still capable of secreting MPH. These results indicated that the MPH secretion directed by the YwbN signal peptide was specifically mediated by the TatAyCy system. The N-terminal sequence of secreted MPH was determined as AAPQVR, demonstrating that the YwbN signal peptide had been processed correctly. This is the first report of functional secretion of a heterologous protein via the B. subtilis TatAyCy system. This study highlights the potential of the TatAyCy system to be used for secretion of other heterologous proteins in B. subtilis.
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Affiliation(s)
- Ruihua Liu
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, §Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, and ¶Key Laboratory of Pollution Processes and Environmental Criteria for Ministry of Education, College of Environmental Science and Engineering, Nankai University , Tianjin 300071, People's Republic of China
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Deng Y, Ng ESK, Kwan YW, Lau CBS, Cheung DWS, Koon JCM, Zhang Z, Zuo Z, Leung PC, Fung KP, Lam FFY. Cerebral vasodilator properties of Danshen and Gegen: a study of their combined efficacy and mechanisms of actions. Phytomedicine 2014; 21:391-399. [PMID: 24192211 DOI: 10.1016/j.phymed.2013.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/07/2013] [Accepted: 09/29/2013] [Indexed: 06/02/2023]
Abstract
Danshen and Gegen are two commonly used Chinese herbal medicines for treatment of cardiovascular diseases. The aim of the present study was to elucidate the combination effects of these two herbs on cerebral vascular tone and their underlying mechanisms of actions. Basilar artery rings were obtained from rats and precontracted with U46619. Cumulative administrations of aqueous extracts of Danshen, Gegen, or the two herbs combined (DG; ratio 7:3) produced concentration-dependent relaxation of the artery rings. Statistical analysis on these findings produced a combination index (CI) of 1.041 at ED50, which indicates the two herbs produced additive vasodilator effects when used as a combined decoction. Removal of the endothelium had no effect on the vasodilator properties of Danshen, Gegen, and DG. However, their maximum effects (Imax) were significantly blunted by a KATP channel inhibitor glibenclamide, a non-selective K(+) channel inhibitor tetraethylammonium (TEA), and by a combination of K(+) channel inhibitors (glibenclamide+TEA+iberiotoxin+4-aminopyridine+barium chloride). In addition, Danshen, Gegen, and DG produced augmentation of KATP currents and inhibited Ca(2+) influx in vascular smooth muscle cells isolated from rat basilar arteries. Furthermore, these agents inhibited CaCl2-induced contraction in the artery rings. In conclusion, the present study showed that Danshen and Gegen produced additive vasodilator effects on rat cerebral basilar arteries. These effects were independent of endothelium-derived relaxant factors (EDRF), but required the opening of KATP channels and inhibition of Ca(2+) influx in the vascular smooth muscle cells. It is suspected that the cerebral vasodilator effects of Danshen and Gegen produced either on their own or in combination, can help patients with obstructive cerebrovascular diseases.
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Affiliation(s)
- Y Deng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - E S K Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - Y W Kwan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - C B S Lau
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; State Key Laboratory of Phytochemistry and Plant Resources in West China, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - D W S Cheung
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; State Key Laboratory of Phytochemistry and Plant Resources in West China, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - J C M Koon
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; State Key Laboratory of Phytochemistry and Plant Resources in West China, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - Z Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - Z Zuo
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - P C Leung
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; State Key Laboratory of Phytochemistry and Plant Resources in West China, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - K P Fung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; State Key Laboratory of Phytochemistry and Plant Resources in West China, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - F F Y Lam
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region.
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Ok CY, Hasserjian RP, Fox PS, Stingo F, Zuo Z, Young KH, Patel K, Medeiros LJ, Garcia-Manero G, Wang SA. Application of the international prognostic scoring system-revised in therapy-related myelodysplastic syndromes and oligoblastic acute myeloid leukemia. Leukemia 2014; 28:185-9. [PMID: 23787392 DOI: 10.1038/leu.2013.191] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- C Y Ok
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - R P Hasserjian
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - P S Fox
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - F Stingo
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Z Zuo
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - K H Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - K Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L J Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - G Garcia-Manero
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - S A Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Zhang J, Jiang W, Zuo Z. Pyrrolidine dithiocarbamate attenuates surgery-induced neuroinflammation and cognitive dysfunction possibly via inhibition of nuclear factor κB. Neuroscience 2013; 261:1-10. [PMID: 24365462 DOI: 10.1016/j.neuroscience.2013.12.034] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 12/12/2013] [Accepted: 12/15/2013] [Indexed: 01/14/2023]
Abstract
Surgery induces learning and memory impairment. Neuroinflammation may contribute to this impairment. Nuclear factor κB (NF-κB) is an important transcription factor to regulate the expression of inflammatory cytokines. We hypothesize that inhibition of NF-κB by pyrrolidine dithiocarbamate (PDTC) reduces neuroinflammation and the impairment of learning and memory. To test this hypothesis, four-month-old male Fischer 344 rats were subjected to right carotid exploration under propofol and buprenorphine anesthesia. Some rats received two doses of 50mg/kg PDTC given intraperitoneally 30min before and 6h after the surgery. Rats were tested in the Barnes maze and fear conditioning paradigm begun 6days after the surgery. Expression of various proteins related to inflammation was examined in the hippocampus at 24h or 21days after the surgery. Here, surgery, but not anesthesia alone, had a significant effect on prolonging the time needed to identify the target hole during the training sessions of the Barnes maze. Surgery also increased the time for identifying the target hole in the long-term memory test and decreased context-related learning and memory in fear conditioning test. Also, surgery increased nuclear expression of p65, a NF-κB component, decreased cytoplasmic amount of inhibitor of NF-κB, and increased the expression of interleukin-1β, interleukin-6, ionized calcium binding adaptor molecule 1 and active matrix metalloproteinase 9 (MMP-9). Finally, surgery enhanced IgG extravasation in the hippocampus. These surgical effects were attenuated by PDTC. These results suggest that surgery, but not propofol-based anesthesia, induces neuroinflammation and impairment of learning and memory. PDTC attenuates these effects possibly by inhibiting NF-κB activation and the downstream MMP-9 activity.
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Affiliation(s)
- J Zhang
- Department of Anesthesiology, University of Virginia, Charlottesville, VA, USA; Department of Anesthesiology, Shanghai 6th People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - W Jiang
- Department of Anesthesiology, Shanghai 6th People's Hospital, Shanghai Jiaotong University, Shanghai, China.
| | - Z Zuo
- Department of Anesthesiology, University of Virginia, Charlottesville, VA, USA.
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Lee N, Hui DSC, Zuo Z, Ngai KLK, Lui GCY, Wo SK, Tam WWS, Chan MCW, Wong BCK, Wong RYK, Choi KW, Sin WWY, Lee ELY, Tomlinson B, Hayden FG, Chan PKS. A Prospective Intervention Study on Higher-Dose Oseltamivir Treatment in Adults Hospitalized With Influenza A and B Infections. Clin Infect Dis 2013; 57:1511-9. [DOI: 10.1093/cid/cit597] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Wang L, Zuo Z, Zhang P, He S. Object sensitivity in subcortical nuclei and their functional connections with cortical areas. J Vis 2013. [DOI: 10.1167/13.9.498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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45
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He L, Zuo Z, Chen L. Supramodal number-selective representation in human left parietal lobe at 7T. J Vis 2013. [DOI: 10.1167/13.9.883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Xie Y, Wang S, Zuo Z, Zhang G, Cao L, Li T. Identification of a novel HLA-B*27 allele, B*27:79 and the B*27 subtype polymorphism in the Hunan ethnic Han population of China. Int J Immunogenet 2013; 40:524-7. [PMID: 23590408 DOI: 10.1111/iji.12045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 01/14/2013] [Accepted: 01/14/2013] [Indexed: 11/26/2022]
Abstract
This article describes a novel HLA-B*27 allele, HLA-B*27:79, which was identified in a Hunan Han ethnic individual of China by a PCR sequence-based typing method. The new sequence has one nucleotide mutation at position 437(A→T) compared with the allele B*27:04:01. This nucleotide change causes an amino acid substitution from Aspartate (Asp) to Valine (Val) at codon 122. This is the first report of mutation at this position in the HLA-B locus. Then, we investigated the HLA-B*27 subtype polymorphism of the Hunan Han population, and the results showed that B*27:04, B*27:05 and B*27:06 are the predominant subtypes with the allele frequencies 0.97%, 0.26% and 0.10% respectively.
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Affiliation(s)
- Y Xie
- Changsha Blood Center, Changsha, Hunan Province, China
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Chang J, Lei H, Liu Q, Qin S, Ma K, Luo S, Zhang X, Huang W, Zuo Z, Fu H, Xia Y. Optimization of culture of mesenchymal stem cells: a comparison of conventional plate and microcarrier cultures. Cell Prolif 2012; 45:430-7. [PMID: 22925502 DOI: 10.1111/j.1365-2184.2012.00836.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES There has been increasing interest in mesenchymal stem cells (MSCs) because of their potential use for regenerative therapy; however, there is no well-defined protocol for MSCs culture. This study compares techniques of conventional plate and microcarrier culturing of MSCs. METHODS AND RESULTS Here, different conditions for isolation and expansion of rat MSCs have been examined and it was found that plating density and plating time in primary culture played important roles for culture of these rat MSCs. When plated at 10(8) /cm(2) density for 72 h, in primary culture, recycling stem cells (RS cells) predominated, and characteristics of rat MSCs (including morphology, growth rate, phenotype and differentiation potentials) remained stable during expansion until passage 14. For subculture of the cells, it was found that their growth rate when incubated at 33 °C was higher than those incubated at 37 °C, and maximal increase was 10- and 6-fold respectively. When cultured using microcarriers, at a density of 1 × 10(5) /mg beads, growth kinetics, phenotype and differentiation potentials also remained constant for cells between passage 2nd and 14th; their maximal number increased 16-fold. CONCLUSIONS Compared to conventional plate culture, culture using gelatine porous microcarrier Cultispher-S was superior for large-scale production of rat MSCs.
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Affiliation(s)
- J Chang
- Cardiology Department, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Zuo Z, Ouyang W, Li J, Costa M, Huang C. Cyclooxygenase-2 (COX-2) mediates arsenite inhibition of UVB-induced cellular apoptosis in mouse epidermal Cl41 cells. Curr Cancer Drug Targets 2012; 12:607-16. [PMID: 22463588 DOI: 10.2174/156800912801784802] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 02/24/2012] [Accepted: 02/24/2012] [Indexed: 12/29/2022]
Abstract
Inorganic arsenic is an environmental human carcinogen, and has been shown to act as a co-carcinogen with solar ultraviolet (UV) radiation in mouse skin tumor induction even at low concentrations. However, the precise mechanism of its co-carcinogenic action is largely unknown. Apoptosis plays an essential role as a protective mechanism against neoplastic development in the organism by eliminating genetically damaged cells. Thus, suppression of apoptosis is thought to contribute to carcinogenesis. It is known that cyclooxygenase-2 (COX-2) can promote carcinogenesis by inhibiting cell apoptosis under stress conditions; and our current studies investigated the potential contribution of COX-2 to the inhibitory effect of arsenite in UV-induced cell apoptosis in mouse epidermal Cl41 cells. We found that treatment of cells with low concentration (5 μM) arsenite attenuated cellular apoptosis upon UVB radiation accompanied with a coinductive effect on COX-2 expression and nuclear factor-κB (NFκB) transactivation. Our results also showed that the COX-2 induction by arsenite and UVB depended on an NFκB pathway because COX-2 co-induction could be attenuated in either p65-deficient or p50-deficient cells. Moreover, UVB-induced cell apoptosis could be dramatically reduced by the introduction of exogenous COX-2 expression, whereas the inhibitory effect of arsenite on UVB-induced cell apoptosis could be impaired in COX-2 knockdown C141 cells. Our results indicated that COX-2 mediated the anti-apoptotic effect of arsenite in UVB radiation through an NFκB-dependent pathway. Given the importance of apoptosis evasion during carcinogenesis, we anticipated that COX-2 induction might be at least partially responsible for the co-carcinogenic effect of arsenite on UVB-induced skin carcinogenesis.
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Affiliation(s)
- Z Zuo
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, 10987, USA
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Deng Y, Ng ESK, Yeung JHK, Kwan YW, Lau CBS, Koon JCM, Zhou L, Zuo Z, Leung PC, Fung KP, Lam FFY. Mechanisms of the cerebral vasodilator actions of isoflavonoids of Gegen on rat isolated basilar artery. J Ethnopharmacol 2012; 139:294-304. [PMID: 22120017 DOI: 10.1016/j.jep.2011.11.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/12/2011] [Accepted: 11/12/2011] [Indexed: 05/31/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Gegen (root of Pueraria lobata) is used in traditional Chinese medicine for treatment of cardiovascular diseases. In this study, the relaxant actions of three of its isoflavonoids; puerarin, daidzein, and daidzin, were investigated on rat-isolated cerebral basilar artery. MATERIALS AND METHODS Rat basilar artery rings were precontracted with 100 nM U46619. Involvement of endothelium-dependent mechanisms was investigated by mechanical removal of the endothelium and inhibitors of nitric oxide synthase (NOS) and cyclooxygenase (COX) enzymes. Adenylyl cyclase- and guanylyl cyclase-dependent pathways were investigated using their respective inhibitors 9-(tetrahydro-2-furanyl)-9H-purine-6-amine (SQ22536) and 1H-[1,2,4]oxadiazolo [4,3-[alpha]]-quinoxalin-1-one (ODQ). K(+) channels were investigated by pretreatment of the artery rings with various K(+) channel inhibitors, and Ca(2+) channels were investigated in artery rings incubated with Ca(2+)-free buffer and primed with 100 nM U46619 for 5 min prior to adding CaCl(2) to elicit contraction. RESULTS Puerarin, daidzein, and daidzin produced concentration-dependent relaxation of the artery rings with concentration that produced 50% inhibition (IC(50)) of 304 ± 49 μM, 20 ± 7 μM, and 140 ± 21 μM, respectively. Removal of the endothelium produced no change on their vasorelaxant responses except the maximum response (I(max)) to puerarin was inhibited by 28%. The NOS inhibitor N(G)-nitro-l-arginine methyl ester (L-NAME; 100 μM) also produced 45% inhibition on the puerarin-induced vasorelaxant response, but not the COX inhibitor flurbiprofen (10 μM). SQ22536 (100 μM) and ODQ (100μM) did not affect the vasodilator responses to puerarin, daidzein and daidzin, but glibenclamide (1μM), tetraethylammonium (TEA, 100mM) or a combination of K(+) channel inhibitors (100nM iberiotoxin+1mM 4-aminopyridine+100 μM barium chloride+1 μM glibenclamide+100mM TEA) reduced their I(max). The contractile response to CaCl(2) was attenuated by 61% and 34% in the presence of daidzein and daidzin, respectively, whereas, puerarin did not significantly affect the contraction. CONCLUSIONS The vasorelaxant action of daidzein and daidzin involved opening of K(+) channels and inhibition of Ca(2+) influx in the vascular smooth muscle cells. There is no evidence supporting involvement of endothelium-derived relaxing factors (EDRFs) in their actions. In contrast, puerarin produced vasodilatation via an endothelium-dependent mechanism involving nitric oxide production and an endothelium-independent pathway mediated by the opening of K(+) channels. The cerebral vasodilator activities of all these three isoflavonoids may be beneficial to patients with obstructive cerebrovascular diseases.
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Affiliation(s)
- Y Deng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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Li L, Zuo Z. Isoflurane postconditioning induces neuroprotection via Akt activation and attenuation of increased mitochondrial membrane permeability. Neuroscience 2011; 199:44-50. [PMID: 22040798 DOI: 10.1016/j.neuroscience.2011.10.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 10/11/2011] [Accepted: 10/13/2011] [Indexed: 01/08/2023]
Abstract
We have shown that isoflurane application at the onset of reperfusion (postconditioning) reduces brain ischemic injury in rats. This study was designed to determine whether this protection involved activation of prosurvival protein kinases and maintenance of normal mitochondrial membrane permeability. Two-month-old male rats were subjected to a 90-min middle cerebral arterial occlusion. They then were exposed or were not exposed to 2% isoflurane for 1 h. Ischemic penumbral cerebral cortex was harvested immediately and separated into the mitochondrial and cytosolic fractions. We showed that the mitochondrial nicotinamide adenine dinucleotide content in the ischemic penumbral cortex was significantly reduced, suggesting an increased mitochondrial membrane permeability. This increase was partly attenuated by isoflurane postconditioning. The mitochondrial adenosine diphosphate content in the penumbral cortex was reduced no matter whether the animals were postconditioned with isoflurane. The mitochondrial adenosine triphosphate concentration was not different among various experimental conditions. The phospho-Akt in the cytosolic and mitochondrial fractions of the ischemic penumbral cortex was higher than that in the control cortex. This increase trended to be higher in animals with isoflurane postconditioning. A similar change pattern was observed in the mitochondrial phospho-glycogen synthase kinase 3β, an Akt substrate that can regulate the mitochondrial membrane permeability. Isoflurane postconditioning reduced oxygen-glucose deprivation-induced injury of rat cortical neuronal cultures and increased phospho-Akt in these cells. The isoflurane postconditioning-induced protection in the neuronal cultures was decreased by the Akt inhibitor LY294002. These results suggest that isoflurane postconditioning effects may be mediated by Akt and involve reduced mitochondrial membrane permeability.
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Affiliation(s)
- L Li
- Department of Anesthesiology, University of Virginia, Charlottesville, VA 22908, USA
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