1
|
Deji Z, Tong Y, Huang H, Zhang Z, Fang M, Crabbe MJC, Zhang X, Wang Y. Correction: Influence of Environmental Factors and Genome Diversity on Cumulative COVID-19 Cases in the Highland Region of China: Comparative Correlational Study. Interact J Med Res 2024; 13:e59070. [PMID: 38598823 PMCID: PMC11043922 DOI: 10.2196/59070] [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] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
[This corrects the article DOI: .].
Collapse
Affiliation(s)
- Zhuoga Deji
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji UniversityShanghaiChina
- Information School, The University of SheffieldSheffieldUnited Kingdom
| | - Yuantao Tong
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji UniversityShanghaiChina
| | - Honglian Huang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji UniversityShanghaiChina
- Department of Clinical Laboratory Medicine CenterYueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Zeyu Zhang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji UniversityShanghaiChina
| | - Meng Fang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery HospitalShanghaiChina
| | - M James C Crabbe
- Wolfson College, Oxford UniversityOxfordUnited Kingdom
- Institute of Biomedical and Environmental Science & Technology, University of BedfordshireBedfordshireUnited Kingdom
- School of Life Sciences, Shanxi UniversityShanxiChina
| | - Xiaoyan Zhang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji UniversityShanghaiChina
| | - Ying Wang
- Department of Clinical Laboratory Medicine CenterYueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese MedicineShanghaiChina
| |
Collapse
|
2
|
Deji Z, Tong Y, Huang H, Zhang Z, Fang M, Crabbe MJC, Zhang X, Wang Y. Influence of Environmental Factors and Genome Diversity on Cumulative COVID-19 Cases in the Highland Region of China: Comparative Correlational Study. Interact J Med Res 2024; 13:e43585. [PMID: 38526532 DOI: 10.2196/43585] [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: 10/18/2022] [Revised: 07/20/2023] [Accepted: 03/06/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND The novel coronavirus SARS-CoV-2 caused the global COVID-19 pandemic. Emerging reports support lower mortality and reduced case numbers in highland areas; however, comparative studies on the cumulative impact of environmental factors and viral genetic diversity on COVID-19 infection rates have not been performed to date. OBJECTIVE The aims of this study were to determine the difference in COVID-19 infection rates between high and low altitudes, and to explore whether the difference in the pandemic trend in the high-altitude region of China compared to that of the lowlands is influenced by environmental factors, population density, and biological mechanisms. METHODS We examined the correlation between population density and COVID-19 cases through linear regression. A zero-shot model was applied to identify possible factors correlated to COVID-19 infection. We further analyzed the correlation of meteorological and air quality factors with infection cases using the Spearman correlation coefficient. Mixed-effects multiple linear regression was applied to evaluate the associations between selected factors and COVID-19 cases adjusting for covariates. Lastly, the relationship between environmental factors and mutation frequency was evaluated using the same correlation techniques mentioned above. RESULTS Among the 24,826 confirmed COVID-19 cases reported from 40 cities in China from January 23, 2020, to July 7, 2022, 98.4% (n=24,430) were found in the lowlands. Population density was positively correlated with COVID-19 cases in all regions (ρ=0.641, P=.003). In high-altitude areas, the number of COVID-19 cases was negatively associated with temperature, sunlight hours, and UV index (P=.003, P=.001, and P=.009, respectively) and was positively associated with wind speed (ρ=0.388, P<.001), whereas no correlation was found between meteorological factors and COVID-19 cases in the lowlands. After controlling for covariates, the mixed-effects model also showed positive associations of fine particulate matter (PM2.5) and carbon monoxide (CO) with COVID-19 cases (P=.002 and P<.001, respectively). Sequence variant analysis showed lower genetic diversity among nucleotides for each SARS-CoV-2 genome (P<.001) and three open reading frames (P<.001) in high altitudes compared to 300 sequences analyzed from low altitudes. Moreover, the frequencies of 44 nonsynonymous mutations and 32 synonymous mutations were significantly different between the high- and low-altitude groups (P<.001, mutation frequency>0.1). Key nonsynonymous mutations showed positive correlations with altitude, wind speed, and air pressure and showed negative correlations with temperature, UV index, and sunlight hours. CONCLUSIONS By comparison with the lowlands, the number of confirmed COVID-19 cases was substantially lower in high-altitude regions of China, and the population density, temperature, sunlight hours, UV index, wind speed, PM2.5, and CO influenced the cumulative pandemic trend in the highlands. The identified influence of environmental factors on SARS-CoV-2 sequence variants adds knowledge of the impact of altitude on COVID-19 infection, offering novel suggestions for preventive intervention.
Collapse
Affiliation(s)
- Zhuoga Deji
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Information School, The University of Sheffield, Sheffield, United Kingdom
| | - Yuantao Tong
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Honglian Huang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Department of Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zeyu Zhang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Meng Fang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Bedfordshire, United Kingdom
- School of Life Sciences, Shanxi University, Shanxi, China
| | - Xiaoyan Zhang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ying Wang
- Department of Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| |
Collapse
|
3
|
Song Y, Liang Y, Ma W, Crabbe MJC, Ren Z. Complete Mitochondrial Genome and Phylogenetic Position of Nurudea zhengii Ren (Insecta, Hemiptera, Aphididae). Biochem Genet 2024:10.1007/s10528-024-10717-5. [PMID: 38456973 DOI: 10.1007/s10528-024-10717-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/24/2024] [Indexed: 03/09/2024]
Abstract
Nurudea zhengii Ren was identified by aphid morphological characteristics as well as the gall shape and host plant species, and placed in the tribe Fordini (Hemiptera, Aphididae, Eriosomatinae). Here, its whole genome was firstly sequenced by a genome-skimming method and its mitochondrial genome (mitogenome) was assembled to examine its genetic variation and phylogenetic position. The complete mitogenome of Nurudea zhengii is 15,392 bp in length, and consists of 13 protein-coding genes, 22 tRNAs, two rRNAs and one D-loop region. The gene order follows the mitogenomes of the other Rhus gall aphids, and similarly has an AT bias with the content of 83.9%. The majority strand is A-skewed and C-skewed, and shows opposite skewness for G-skewed in the minority strands. The ratios of nonsynonymous to synonymous substitution rates of protein-coding genes are lower than one except for ATP8, which indicated that ATP8 was undergoing positive selection. Phylogenetic analysis among the Rhus gall aphids based on 13 protein-coding genes and two rRNA genes showed that N. zhengii was sister to N. shiraii, and then clustered with N. yanoniella as a group with high support value. The two species, N. shiraii and N. yanoniella, share the same host plant Rhus chinensis, while the host of N. zhengii is R. hypoleuca. However, the phylogenetic relationship indicated that the taxa sharing the same host plant were not absolutely clustered as the closest taxa at least at species level.
Collapse
Affiliation(s)
- Yuzhen Song
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Yukang Liang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Wenli Ma
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - M James C Crabbe
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
- Wolfson College, Oxford University, Oxford, OX2 6UD, UK
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China.
| |
Collapse
|
4
|
Li X, Liu H, Wang Y, Crabbe MJC, Wang L, Ma W, Ren Z. Preparation of a novel metallothionein-AuNP composite material by genetic modification and AuS covalent combination. Int J Biol Macromol 2024; 262:129960. [PMID: 38325687 DOI: 10.1016/j.ijbiomac.2024.129960] [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: 10/12/2023] [Revised: 01/22/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
Metallothionein (MTs) can be used in the prevention and treatment of tumors and diabetes due to its antioxidant properties. However, it is necessary to solve its non-transmembrane properties and further improve its antioxidant activity, increase its fluorescence visualization and enhance its stability to meet practical applications in the biomedical field. Here, we report the preparation of a novel metallothionein-AuNP composite material with high transmembrane ability, fluorescence visualization, antioxidant activity, and stability by genetic modification (introducing transduction peptide TAT, fluorescence tag GFP and increasing sulfydryl groups) and immobilization technology (covalently bonding with AuNPs). The transmembrane activity of modified proteins was verified by immunofluorescence. Increasing the sulfhydryl content within a certain range can enhance the antioxidant activity of the protein. In addition, GFP were used to further simplify the imaging of the metallothionein-AuNP composite in cells. XPS results indicated that AuNPs can immobilize metallothionein through AuS covalent bonds. TGA characterization and degradation experiments showed that thermal and degradation stability of the immobilized material was significantly improved. This work provides new ideas to construct metallothionein composites with high transmembrane ability, antioxidant activity, fluorescence visualization and stability to meet novel applications in the biomedical field.
Collapse
Affiliation(s)
- Xuefen Li
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Hui Liu
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Yuxia Wang
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - M James C Crabbe
- School of Life Science, Shanxi University, Taiyuan 030006, PR China; Wolfson College, University of Oxford, Oxford OX2 6UD, UK; Institute of Biomedical and Environmental Science & Technology, School of Life Sciences, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, University Square, Luton LU1 3JU, UK
| | - Lan Wang
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Wenli Ma
- School of Life Science, Shanxi University, Taiyuan 030006, PR China.
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan 030006, PR China.
| |
Collapse
|
5
|
Ju T, Dong J, Wang B, Qu K, Cheng C, He X, Tian Y, Crabbe MJC, Wang Z, Chen Y. Cancer Development in Hepatocytes by Long-Term Induction of Hypoxic Hepatocellular Carcinoma Cell (HCC)-Derived Exosomes In Vivo and In Vitro. Mol Pharm 2023; 20:5579-5592. [PMID: 37844208 DOI: 10.1021/acs.molpharmaceut.3c00488] [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] [Indexed: 10/18/2023]
Abstract
Hypoxic tumor cell-derived exosomes play a key role in the occurrence, development, and metastasis of tumors. However, the mechanism of hypoxia-mediated metastasis remains unclear. In this study, hypoxic hepatocellular carcinoma cell (HCC-LM3)-derived exosomes (H-LM3-exos) were used to induce hepatocytes (HL-7702) over a long term (40 passages in 120 days). A nude mouse experiment further verified the effect of H-LM3-exos on tumor growth and metastasis. The process of cancer development in hepatocytes induced by H-LM3-exos was analyzed using both biological and physical techniques, and the results showed that the proliferation and soft agar growth abilities of the transformed cells were enhanced. The concentration of tumor markers secreted by transformed cells was increased, the cytoskeleton was disordered, and the migration ability was enhanced and was accompanied by epithelial-mesenchymal transition (EMT). Transcriptome results showed that differentially expressed genes between transformed cells and hepatocytes were enriched in cancer-related signaling pathways. The degree of cancer development in transformed cells was enhanced by an increase in H-LM3-exos-induced passages. Nude mice treated with different concentrations of H-LM3-exos showed different degrees of tumor growth and liver lesions. The physical properties of the cells were characterized by atomic force microscopy. Compared with the hepatocytes, the height and roughness of the transformed cells were increased, while the adhesion and elastic modulus were decreased. The changes in physical properties of primary tumor cells and hepatocytes in nude mice were consistent with this trend. Our study linking omics with the physical properties of cells provides a new direction for studying the mechanisms of cancer development and metastasis.
Collapse
Affiliation(s)
- Tuoyu Ju
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, China
| | - Jianjun Dong
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, China
| | - Bowei Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, China
| | - Kaige Qu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, China
| | - Can Cheng
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, China
| | - Xiuxia He
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, China
| | - Yanling Tian
- School of Engineering, University of Warwick, Coventry CF4 7AL, U.K
| | - M James C Crabbe
- Wolfson College, University of Oxford, Oxford OX2 6UD, U.K
- Institute of Biomedical and Environmental Science & Technology, and Institute for Research in Applicable Computing, University of Bedfordshire, Luton LU1 3JU, U.K
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, China
- Institute of Biomedical and Environmental Science & Technology, and Institute for Research in Applicable Computing, University of Bedfordshire, Luton LU1 3JU, U.K
| | - Yujuan Chen
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun 130022, China
| |
Collapse
|
6
|
Lu M, He W, Xu Z, Lu Y, Crabbe MJC, De J. The effect of high altitude on ephedrine content and metabolic variations in two species of Ephedra. Front Plant Sci 2023; 14:1236145. [PMID: 37908827 PMCID: PMC10613977 DOI: 10.3389/fpls.2023.1236145] [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] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/19/2023] [Indexed: 11/02/2023]
Abstract
Ephedra is an important plant in Chinese medicine; however, there are few reports on two species of Ephedra which are distributed at high altitudes from 3000 to 5200 meters. We collected a total of 84 individuals representing five Ephedra gerardiana and nine Ephedra saxatilis populations respectively located from 3158 to 5200 meters altitude, and determined the relative content of 213 metabolites using UHPLC-MS/MS (Ultra-High-Performance Liquid Chromatography-tandem mass spectrometry). 37 Chemical compositions were annotated using the KEGG (Kyoto Encyclopaedia of Genes and Genomes) database. From the top five significant enrichments in metabolic KEGG pathway analysis, we found a total of 166 compounds belonging to phenylpropanoids, 123 flavonoids, 67 metabolites carried by ABC transporters, and 61 in purine metabolism. We identified the top 8 altitude-related compounds in two species. Ephedrine and pseudoephedrine were found to be associated with altitude in both E. saxatilis and E. gerardiana. To verify which environmental factors influenced the metabolic content, the soil moisture and temperature of each population site were collected, and quantitative analysis of ephedrine and pseudoephedrine was performed using UHPLC-MS (Ultra-High-Performance liquid chromatography-tandem mass spectrometry). After detection, soil moisture ranged from 0.074 to 0.177 mm3/mm3, and temperature ranged from 9.7°C to 23.9°C. The content of ephedrine ranged from (0.84 ± 0.49)% to (2.01 ± 0.41)% in E. saxatilis, which was positively correlated with soil moisture; the content of pseudoephedrine ranged from (0.72 ± 0.45)% to (1.11 ± 0.57)% and was negatively correlated with soil moisture. In contrast to these results, in E. gerardiana, the content of ephedrine and pseudoephedrine was negatively correlated with soil moisture. Furthermore, the trends of alkaloid contents in two kinds of Ephedra were similar when the temperature was lower than 17°C even if the sum was various. With the increase in soil moisture and temperature, the total alkaloid content of E. saxatilis was higher than that of E. gerardiana. When the soil moisture was lower, the alkaloid content of the two Ephedra species was higher. These results provide useful data for the future separation of new compounds, and for seed homogeneous growth to determine artificial breeding of Ephedra located at high altitudes.
Collapse
Affiliation(s)
- Mengnan Lu
- School of Ecology and environment, Tibet University, Lhasa, Tibet, China
| | - Wenjia He
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Ziyan Xu
- School of Pharmacy, Fudan University, Shanghai, China
| | - Yan Lu
- School of Pharmacy, Fudan University, Shanghai, China
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science & Technology, School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Ji De
- School of Ecology and environment, Tibet University, Lhasa, Tibet, China
| |
Collapse
|
7
|
Zhang Z, Fang M, Wu R, Zong H, Huang H, Tong Y, Xie Y, Cheng S, Wei Z, Crabbe MJC, Zhang X, Wang Y. Large-Scale Biomedical Relation Extraction Across Diverse Relation Types: Model Development and Usability Study on COVID-19. J Med Internet Res 2023; 25:e48115. [PMID: 37632414 PMCID: PMC10551783 DOI: 10.2196/48115] [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: 04/11/2023] [Revised: 07/03/2023] [Accepted: 08/25/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND Biomedical relation extraction (RE) is of great importance for researchers to conduct systematic biomedical studies. It not only helps knowledge mining, such as knowledge graphs and novel knowledge discovery, but also promotes translational applications, such as clinical diagnosis, decision-making, and precision medicine. However, the relations between biomedical entities are complex and diverse, and comprehensive biomedical RE is not yet well established. OBJECTIVE We aimed to investigate and improve large-scale RE with diverse relation types and conduct usability studies with application scenarios to optimize biomedical text mining. METHODS Data sets containing 125 relation types with different entity semantic levels were constructed to evaluate the impact of entity semantic information on RE, and performance analysis was conducted on different model architectures and domain models. This study also proposed a continued pretraining strategy and integrated models with scripts into a tool. Furthermore, this study applied RE to the COVID-19 corpus with article topics and application scenarios of clinical interest to assess and demonstrate its biological interpretability and usability. RESULTS The performance analysis revealed that RE achieves the best performance when the detailed semantic type is provided. For a single model, PubMedBERT with continued pretraining performed the best, with an F1-score of 0.8998. Usability studies on COVID-19 demonstrated the interpretability and usability of RE, and a relation graph database was constructed, which was used to reveal existing and novel drug paths with edge explanations. The models (including pretrained and fine-tuned models), integrated tool (Docker), and generated data (including the COVID-19 relation graph database and drug paths) have been made publicly available to the biomedical text mining community and clinical researchers. CONCLUSIONS This study provided a comprehensive analysis of RE with diverse relation types. Optimized RE models and tools for diverse relation types were developed, which can be widely used in biomedical text mining. Our usability studies provided a proof-of-concept demonstration of how large-scale RE can be leveraged to facilitate novel research.
Collapse
Affiliation(s)
- Zeyu Zhang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Department of Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Meng Fang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Rebecca Wu
- University of California, Berkeley, Berkeley, CA, United States
| | - Hui Zong
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Honglian Huang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yuantao Tong
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yujia Xie
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shiyang Cheng
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ziyi Wei
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Xiaoyan Zhang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ying Wang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Department of Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| |
Collapse
|
8
|
Wang B, Dong J, Yang F, Ju T, Li J, Wang J, Wang Y, Crabbe MJC, Tian Y, Wang Z. Use of Atomic Force Microscopy in UVB-Induced Chromosome Damage Provides Important Bioinformation for Cell Damage Assessment. Langmuir 2023; 39:13212-13221. [PMID: 37681704 DOI: 10.1021/acs.langmuir.3c01644] [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] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The chromosomal structure derived from UVB-stimulated HaCaT cells was detected by atomic force microscopy (AFM) to evaluate the effect of UVB irradiation. The results showed that the higher the UVB irradiation dose, the more the cells that had chromosome aberration. At the same time, different representative types of chromosome structural aberrations were investigated. We also revealed damage to both DNA and cells under the corresponding irradiation doses. It was found that the degree of DNA damage was directly proportional to the irradiation dose. The mechanical properties of cells were also changed after UVB irradiation, suggesting that cells experienced a series of chain reactions from inside to outside after irradiation. The high-resolution imaging of chromosome structures by AFM after UVB irradiation enables us to relate the damage between chromosomes, DNA, and cells caused by UVB irradiation and provides specific information on genetic effects.
Collapse
Affiliation(s)
- Bowei Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Jianjun Dong
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Fan Yang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Tuoyu Ju
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Jiani Li
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Junxi Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Ying Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - M James C Crabbe
- Wolfson College, University of Oxford, Oxford OX2 6UD, U.K
- Institute of Biomedical and Environmental Science & Technology, and Institute for Research in Applicable Computing, University of Bedfordshire, Luton LU1 3JU, U.K
| | - Yanling Tian
- School of Engineering, University of Warwick, Coventry CV4 7AL, U.K
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- Institute of Biomedical and Environmental Science & Technology, and Institute for Research in Applicable Computing, University of Bedfordshire, Luton LU1 3JU, U.K
| |
Collapse
|
9
|
Wu X, Luo D, Zhang Y, Jin L, Crabbe MJC, Qiao Q, Li G, Zhang T. Integrative analysis of the metabolome and transcriptome reveals the potential mechanism of fruit flavor formation in wild hawthorn ( Crataegus chungtienensis). Plant Divers 2023; 45:590-600. [PMID: 37936817 PMCID: PMC10625895 DOI: 10.1016/j.pld.2023.02.001] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/16/2023] [Accepted: 02/05/2023] [Indexed: 11/09/2023]
Abstract
Hawthorns are important medicinal and edible plants with a long history of health protection in China. Besides cultivated hawthorn, other wild hawthorns may also have excellent medicinal and edible value, such as Crataeguschungtienensis, an endemic species distributed in the Southwest of China. In this study, by integrating the flavor-related metabolome and transcriptome data of the ripening fruit of C. chungtienensis, we have developed an understanding of the formation of hawthorn fruit quality. The results show that a total of 849 metabolites were detected in the young and mature fruit of C. chungtienensis, of which flavonoids were the most detected metabolites. Among the differentially accumulated metabolites, stachyose, maltotetraose and cis-aconitic acid were significantly increased during fruit ripening, and these may be important metabolites affecting fruit flavor change. Moreover, several flavonoids and terpenoids were reduced after fruit ripening compared with young fruit. Therefore, using the unripe fruit of C. chungtienensis may allow us to obtain more medicinal active ingredients such as flavonoids and terpenoids. Furthermore, we screened out some differentially expressed genes (DEGs) related to fruit quality formation, which had important relationships with differentially accumulated sugars, acids, flavonoids and terpenoids. Our study provides new insights into flavor formation in wild hawthorn during fruit development and ripening, and at the same time this study lays the foundation for the improvement of hawthorn fruit flavor.
Collapse
Affiliation(s)
- Xien Wu
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Dengli Luo
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Yingmin Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Ling Jin
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, UK
- Institute of Biomedical and Environmental Science & Technology, School of Life Sciences, University of Bedfordshire, Park Square, Luton, UK
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Qin Qiao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China
| | - Guodong Li
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| |
Collapse
|
10
|
He H, Crabbe MJC, Ren Z. Genome-wide identification and characterization of the chemosensory relative protein genes in Rhus gall aphid Schlechtendalia chinensis. BMC Genomics 2023; 24:222. [PMID: 37118660 PMCID: PMC10142413 DOI: 10.1186/s12864-023-09322-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/19/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND The Rhus gall aphid Schlechtendalia chinensis specially uses the only species Rhus chinensis and certain moss species (Mniaceae) as its primary host plant and secondary host plants, respectively. Rhus galls are formed on the primary host by the sucking of aphids, and used in traditional medicine as well as other various areas due to their high tannin contents. Chemoreception is critical for insect behaviors such as host searching, location and identification of mates and reproductive behavior. The process of chemoreception is mediated by a series of protein gene families, including odorant-binding proteins (OBPs), chemosensory proteins (CSPs), olfactory receptors (ORs), gustatory receptors (GRs), ionotropic receptors (IRs), and sensory neuron membrane proteins (SNMPs). However, there have been no reports on the analysis of molecular components related to the chemoreception system of S. chinensis at the genome level. RESULTS We examined the genes of eight OBPs, nine CSPs, 24 ORs, 16 GRs, 22 IRs, and five SNMPs in the S. chinensis genome using homological searches, and these chemosensory genes appeared mostly on chromosome 1. Phylogenetic and gene number analysis revealed that the gene families, e.g., ORs, GRs, CSPs and SNMPs in S. chinensis, have experienced major contractions by comparing to Myzus persicae, while the two gene families OBPs and IRs had slight expansion. The current results might be related to the broader host range of M. persicae versus the specialization of S. chinensis on only a host plant. There were 28 gene pairs between genomes of S. chinensis and Acyrthosiphon pisum in the chemoreceptor gene families by collinear comparison. Ka/Ks ratios (< 1) indicated that the genes of S. chinensis were mainly affected by purification selection during evolution. We also found the lower number and expression level of chemoreception genes in S. chinensis than in other 11 aphid species, such as ORs, GRs and IRs, which play an important role in host search. CONCLUSION Our study firstly identified the genes of the different chemosensory protein gene families in the S. chinensis genome, and analyzed their general features and expression profile, demonstrating the importance of chemoreception in the aphid and providing new information for further functional research.
Collapse
Affiliation(s)
- Hongli He
- School of Life Science, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - M James C Crabbe
- School of Life Science, Shanxi University, Taiyuan, 030006, Shanxi, China
- Wolfson College, Oxford University, Oxford, OX2 6UD, UK
- Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton, LU1 3JU, UK
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan, 030006, Shanxi, China.
| |
Collapse
|
11
|
Zhuang J, Jiang Z, Chen D, Li J, Crabbe MJC, Qiu M, Zheng Y, Qu W. Thyroid-Disrupting Effects of Exposure to Fipronil and Its Metabolites from Drinking Water Based on Human Thyroid Follicular Epithelial Nthy-ori 3-1 Cell Lines. Environ Sci Technol 2023; 57:6072-6084. [PMID: 37022920 DOI: 10.1021/acs.est.2c08627] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Fipronil is a broad-spectrum insecticide used for plants and poultry. Owing to its widespread use, fipronil and its metabolites (fipronil sulfone, fipronil desulfinyl, and fipronil sulfide), termed FPM, can be frequently detected in drinking water and food. Fipronil can affect the thyroid function of animals, but the effects of FPM on the human thyroid remain unclear. We employed human thyroid follicular epithelial Nthy-ori 3-1 cells to examine combined cytotoxic responses, thyroid-related functional proteins including the sodium-iodide symporter (NIS), thyroid peroxidase (TPO), deiodinases I-III (DIO I-III), and the nuclear factor erythroid-derived factor 2-related factor 2 (NRF2) pathway induced by FPM of 1-1000-fold concentrations detected in school drinking water collected from a heavily contaminated area of the Huai River Basin. Thyroid-disrupting effects of FPM were evaluated by examining biomarkers of oxidative stress and thyroid function and tetraiodothyronine (T4) levels secreted by Nthy-ori 3-1 cells after FPM treatment. FPM activated the expression of NRF2, HO-1 (heme oxygenase 1), TPO, DIO I, and DIO II but inhibited NIS expression and increased the T4 level of thyrocytes, indicating that FPM can disrupt the function of human thyrocytes through oxidative pathways. Given the adverse impact of low FPM concentrations on human thyrocytes, supportive evidence from rodent studies, and the critical importance of thyroid hormones on development, the effects of FPM on the neurodevelopment and growth of children warrant priority attention.
Collapse
Affiliation(s)
- Jianhui Zhuang
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Zhiqiang Jiang
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Dawei Chen
- China National Center for Food Safety Risk Assessment, Beijing 100022, China
| | - Jingguang Li
- China National Center for Food Safety Risk Assessment, Beijing 100022, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford OX2 6UD, U.K
- Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton LU1 3JU, U.K
| | - Meiyue Qiu
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Yuxin Zheng
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, No. 308 Ningxia Road, Qingdao 266071, China
| | - Weidong Qu
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| |
Collapse
|
12
|
Cao Q, Huang L, Li J, Qu P, Tao P, Crabbe MJC, Zhang T, Qiao Q. Integrated transcriptome and methylome analyses reveal the molecular regulation of drought stress in wild strawberry (Fragaria nilgerrensis). BMC Plant Biol 2022; 22:613. [PMID: 36575384 PMCID: PMC9795625 DOI: 10.1186/s12870-022-04006-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Fragaria nilgerrensis, which is a diploid wild strawberry with excellent drought-resistance, would provide useful candidate genes for improving drought resistance of cultivated strawberry. So far, its molecular regulatory networks involved in drought stress are unclear. We therefore investigated the drought response regulatory networks of F. nilgerrensis based on the integrated analysis of DNA methylation, transcriptome and physiological traits during four time points under drought stress. RESULTS: The most differentially expressed genes and the physiological changes were found at 8 days (T8) compared with 0 day (T0, control). Methylome analysis revealed slight dynamic changes in genome-wide mC levels under drought conditions, while the most hypomethylated and hypermethylated regions were identified at T4 and T8. Association analysis of the methylome and transcriptome revealed that unexpressed genes exhibited expected hypermethylation levels in mCHG and mCHH contexts, and highly expressed genes exhibited corresponding hypomethylation levels in the gene body, but mCG contexts showed the opposite trend. Then, 835 differentially methylated and expressed genes were identified and grouped into four clustering patterns to characterize their functions. The genes with either negative or positive correlation between methylation and gene expression were mainly associated with kinases, Reactive Oxygen Species (ROS) synthesis, scavenging, and the abscisic acid (ABA) signal pathway. Consistently, weighted gene co-expression network analysis (WGCNA) revealed Hub genes including NCED, CYP707A2, PP2Cs and others that play important roles in the ABA signaling pathway. CONCLUSION F. nilgerrensis drought is dominated by ABA-dependent pathways, possibly accompanied by ABA-independent crosstalk. DNA methylation may affect gene expression, but their correlation was more subtle and multiple types of association exist. Maintaining the balance between ROS regeneration and scavenging is an important factor in drought resistance in F. nilgerrensis. These results deepen our understanding of drought resistance and its application in breeding in strawberry plants.
Collapse
Affiliation(s)
- Qiang Cao
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Lin Huang
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Jiamin Li
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Peng Qu
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Pang Tao
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, 650205, Kunming, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, OX26UD, UK
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Park Square, LU1 3JU, Luton, UK
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, 650500, Kunming, China.
| | - Qin Qiao
- College of Horticulture and Landscape, Yunnan Agricultural University, 650201, Kunming, China.
| |
Collapse
|
13
|
Zhu X, Li RYM, Crabbe MJC, Sukpascharoen K. Can a chatbot enhance hazard awareness in the construction industry? Front Public Health 2022; 10:993700. [PMID: 36530655 PMCID: PMC9749401 DOI: 10.3389/fpubh.2022.993700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/24/2022] [Indexed: 12/05/2022] Open
Abstract
Safety training enhances hazard awareness in the construction industry. Its effectiveness is a component of occupational safety and health. While face-to-face safety training has dominated in the past, the frequent lockdowns during COVID-19 have led us to rethink new solutions. A chatbot is messaging software that allows people to interact, obtain answers, and handle sales and inquiries through a computer algorithm. While chatbots have been used for language education, no study has investigated their usefulness for hazard awareness enhancement after chatbot training. In this regard, we developed four Telegram chatbots for construction safety training and designed the experiment as the treatment factor. Previous researchers utilized eye-tracking in the laboratory for construction safety research; most have adopted it for qualitative analyses such as heat maps or gaze plots to study visual paths or search strategies via eye-trackers, which only studied the impact of one factor. Our research has utilized an artificial intelligence-based eye-tracking tool. As hazard awareness can be affected by several factors, we filled this research void using 2-way interaction terms using the design of experiment (DOE) model. We designed an eye-tracking experiment to study the impact of site experience, Telegram chatbot safety training, and task complexity on hazard awareness, which is the first of its kind. The results showed that Telegram chatbot training enhanced the hazard awareness of participants with less onsite experience and in less complex scenarios. Low-cost chatbot safety training could improve site workers' danger awareness, but the design needs to be adjusted according to participants' experience. Our results offer insights to construction safety managers in safety knowledge sharing and safety training.
Collapse
Affiliation(s)
- Xiaoe Zhu
- Chakrabongse Bhuvanarth International Institute for Interdisciplinary Studies, Rajamangala University of Technology Tawan-Ok, Bangkok, Thailand
| | - Rita Yi Man Li
- Sustainable Real Estate Research Center, Hong Kong Shue Yan University, Hong Kong, Hong Kong SAR, China,*Correspondence: Rita Yi Man Li
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom,Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Luton, United Kingdom,School of Life Sciences, Shanxi University, Taiyuan, China
| | - Khunanan Sukpascharoen
- Chakrabongse Bhuvanarth International Institute for Interdisciplinary Studies, Rajamangala University of Technology Tawan-Ok, Bangkok, Thailand,Khunanan Sukpascharoen
| |
Collapse
|
14
|
Tong Y, Tan F, Huang H, Zhang Z, Zong H, Xie Y, Huang D, Cheng S, Wei Z, Fang M, Crabbe MJC, Wang Y, Zhang X. ViMRT: a text-mining tool and search engine for automated virus mutation recognition. Bioinformatics 2022; 39:6808671. [PMID: 36342236 PMCID: PMC9805560 DOI: 10.1093/bioinformatics/btac721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/24/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
MOTIVATION Virus mutation is one of the most important research issues which plays a critical role in disease progression and has prompted substantial scientific publications. Mutation extraction from published literature has become an increasingly important task, benefiting many downstream applications such as vaccine design and drug usage. However, most existing approaches have low performances in extracting virus mutation due to both lack of precise virus mutation information and their development based on human gene mutations. RESULTS We developed ViMRT, a text-mining tool and search engine for automated virus mutation recognition using natural language processing. ViMRT mainly developed 8 optimized rules and 12 regular expressions based on a development dataset comprising 830 papers of 5 human severe disease-related viruses. It achieved higher performance than other tools in a test dataset (1662 papers, 99.17% in F1-score) and has been applied well to two other viruses, influenza virus and severe acute respiratory syndrome coronavirus-2 (212 papers, 96.99% in F1-score). These results indicate that ViMRT is a high-performance method for the extraction of virus mutation from the biomedical literature. Besides, we present a search engine for researchers to quickly find and accurately search virus mutation-related information including virus genes and related diseases. AVAILABILITY AND IMPLEMENTATION ViMRT software is freely available at http://bmtongji.cn:1225/mutation/index.
Collapse
Affiliation(s)
- Yuantao Tong
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Fanglin Tan
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Honglian Huang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zeyu Zhang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hui Zong
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yujia Xie
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Danqi Huang
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shiyang Cheng
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ziyi Wei
- Research Center for Translational Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Meng Fang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford OX2 6UD, UK
- Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton LU1 3JU, UK
- School of Life Sciences, Shanxi University, Taiyuan 030006, China
| | - Ying Wang
- To whom correspondence should be addressed. or
| | | |
Collapse
|
15
|
Xue P, Wang H, Yang L, Jiang Z, Li H, Liu Q, Zhang Q, Andersen ME, Crabbe MJC, Hao L, Qu W. NRF2-ARE signaling is responsive to haloacetonitrile-induced oxidative stress in human keratinocytes. Toxicol Appl Pharmacol 2022; 450:116163. [PMID: 35842135 DOI: 10.1016/j.taap.2022.116163] [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: 05/31/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 11/30/2022]
Abstract
Humans are exposed to disinfection by-products through oral, inhalation, and dermal routes, during bathing and swimming, potentially causing skin lesions, asthma, and bladder cancer. Nuclear factor E2-related factor 2 (NRF2) is a master regulator of the adaptive antioxidant response via the antioxidant reaction elements (ARE) orchestrating the transcription of a large group of antioxidant and detoxification genes. Here we used an immortalized human keratinocyte model HaCaT cells to investigate NRF2-ARE as a responder and protector in the acute cytotoxicity of seven haloacetonitriles (HANs), including chloroacetonitrile (CAN), bromoacetonitrile (BAN), iodoacetonitrile (IAN), bromochloroacetonitrile (BCAN), dichloroacetonitrile (DCAN), dibromoacetonitrile (DBAN), and trichloroacetonitrile (TCAN) found in drinking water and swimming pools. The rank order of cytotoxicity among the HANs tested was IAN ≈ BAN ˃ DBAN ˃ BCAN ˃ CAN ˃ TCAN ˃ DCAN based on their LC50. The HANs induced intracellular reactive oxygen species accumulation and activated cellular antioxidant responses in concentration- and time-dependent fashions, showing elevated NRF2 protein levels and ARE activity, induction of antioxidant genes, and increased glutathione levels. Additionally, knockdown of NRF2 by lentiviral shRNAs sensitized the HaCaT cells to HANs-induced cytotoxicity, emphasizing a protective role of NRF2 against the cytotoxicity of HANs. These results indicate that HANs cause oxidative stress and activate NRF2-ARE-mediated antioxidant response, which in turn protects the cells from HANs-induced cytotoxicity, highlighting that NRF2-ARE activity could be a sensitive indicator to identify and characterize the oxidative stress induced by HANs and other environmental pollutants.
Collapse
Affiliation(s)
- Peng Xue
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Huihui Wang
- Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Lili Yang
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Zhiqiang Jiang
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Hongliang Li
- Pudong New Area Center for Diseases Control & Prevention, Pudong New Area, Shanghai 200120, China
| | - Qinxin Liu
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, GA 30322, USA
| | | | - M James C Crabbe
- Wolfson College, Oxford University, Oxford OX2 6UD, UK; Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton LU1 3JU, UK
| | - Lipeng Hao
- Pudong New Area Center for Diseases Control & Prevention, Pudong New Area, Shanghai 200120, China
| | - Weidong Qu
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China.
| |
Collapse
|
16
|
Zheng W, Zhao H, Liu Q, Crabbe MJC, Qu W. Spatial-temporal distribution, cancer risk, and disease burden attributed to the dietary dioxins exposure of Chinese residents. Sci Total Environ 2022; 832:154851. [PMID: 35351502 DOI: 10.1016/j.scitotenv.2022.154851] [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] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
This study analyzed the characteristics of dioxins represented by polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) as well as dioxin-like polychlorinated biphenyls (dl-PCBs) in food from China. The spatial-temporal distribution characteristics of dioxins dietary intake, cancer risk, and disease burden were evaluated among the Chinese population. In the temporal dimension, descending trends in animal-origin-food were found both in dietary intake PCDD/Fs and dl-PCBs, with the reverse for plant-origin-food. The probability assessments of dietary intakes showed that after 2007, the exposure level of PCDD/Fs through diets of urban and rural residents in China was significantly lower than that before 2007 (p < 0.05). The spatial distribution results showed that the southern coastal regions were high exposure regions of dietary intakes of PCDD/Fs and dl-PCBs. Cancer risk and disease burden of dietary dioxins showed downward trends after 2007 both under an average exposure scenario and an extreme exposure scenario. After 2007, the disease burden resulting from exposure to dl-PCBs became higher and approached the median of values reported by the WHO, while the disease burden resulting from exposure to PCDD/Fs approached the lower level of 95% CI reported by the WHO. The results indicate that accompanying the National Implementation Plan and a series of subsequent scientific guidance documents launched for reducing dioxins pollution in 2007, the health benefits and the health risks caused by dl-PCBs should be given further attention and evaluation in future studies.
Collapse
Affiliation(s)
- Weiwei Zheng
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, PR China; Key Laboratory of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, PR China
| | - Huijuan Zhao
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, PR China; Key Laboratory of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, PR China
| | - Qinxin Liu
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, PR China; Key Laboratory of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, PR China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford OX2 6UD, United Kingdom; Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton LU1 3JU, United Kingdom
| | - Weidong Qu
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, PR China; Key Laboratory of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, PR China.
| |
Collapse
|
17
|
Zhang T, Qiao Q, Du X, Zhang X, Hou Y, Wei X, Sun C, Zhang R, Yun Q, Crabbe MJC, Van de Peer Y, Dong W. Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe). J Integr Plant Biol 2022; 64:1487-1501. [PMID: 35748532 DOI: 10.1111/jipb.13318] [Citation(s) in RCA: 10] [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] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosome-level genome sequence of the hawthorn cultivar "Qiu Jinxing." We assembled an 823.41 Mb genome encoding 40 571 genes and further anchored the 779.24 Mb sequence into 17 pseudo-chromosomes, which account for 94.64% of the assembled genome. Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae (apple tribe) at approximately 35.4 Mya. Notably, genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome. In addition, our results indicated that the Maleae share a unique ancient tetraploidization event; however, no recent independent whole-genome duplication event was specifically detected in hawthorn. The amplification of non-specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome. Furthermore, we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms. We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleo-polyploid origin patterns (autopolyploidization or allopolyploidization) of Maleae. Overall, our study provides an improved context for understanding the evolution of Maleae species, and this new high-quality reference genome provides a useful resource for the horticultural improvement of hawthorn.
Collapse
Affiliation(s)
- Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Qin Qiao
- School of Agriculture, Yunnan University, Kunming, 650091, China
| | - Xiao Du
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization of Ministry of Education, Nanning Normal University, Guangxi, Nanning, 530001, China
| | - Xiao Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yali Hou
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xin Wei
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Chao Sun
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Rengang Zhang
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Quanzheng Yun
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, UK
- Institute of Biomedical and Environmental Science & Technology, School of Life Sciences, University of Bedfordshire, Park Square, Luton, UK
- School of Life Sciences, Shanxi University, Taiyuan, 030006, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Center for Plant Systems Biology, Ghent University, VIB, 9052, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| |
Collapse
|
18
|
Li X, Wang Y, Crabbe MJC, Wang L, Ma W, Ren Z. Genetically modified metallothionein/cellulose composite material as an efficient and environmentally friendly biosorbent for Cd 2+ removal. Int J Biol Macromol 2022; 218:543-555. [PMID: 35902013 DOI: 10.1016/j.ijbiomac.2022.07.144] [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: 04/20/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022]
Abstract
Metallothioneins (MTs) are a class of cysteine-rich metal-binding proteins. Cadmium (Cd) is one of the toxic heavy metal pollutants. In our previous research, the full-length cDNA of MT (Cd specificity) from freshwater crab (Sinopotamon henanense) (ShMT) was cloned and genetically modified to ShMT3 by site-directed mutagenesis to enhance the tolerance for Cd2+, however, it was limited in actual Cd2+ adsorption due to instability. Here, ShMT3-CBM, a novel recombinant fusion protein, was prepared. CBM is a carbohydrate binding module that can specifically bind cellulose while ShMT3 can effectively chelate Cd2+. The biosorbent Cellulose1-ShMT3-CBM was obtained by screening suitable cellulose materials. The selective adsorption experiments showed that Cellulose1-ShMT3-CBM had a preference for Cd2+. In low-concentration Cd2+ solutions, the removal efficiency was >99 %, and the adsorption equilibrium was reached within 15 min. The saturated adsorption capacity of Cellulose1-ShMT3-CBM for Cd2+ is 180.35 ± 4.67 mg/g (Dry Weight). Regeneration experiments showed that adsorption efficiency was maintained after six cycles. The MTT experiment showed that Cellulose1-ShMT3-CBM had low cytotoxicity. Meanwhile, Cellulose1-ShMT3-CBM can preferentially remove Cd2+ in actual water samples and boiler sewage. In this study, an environmentally friendly biosorbent which can adsorb Cd2+ efficiently and quickly was prepared for actual water treatment.
Collapse
Affiliation(s)
- Xuefen Li
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Yuxia Wang
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - M James C Crabbe
- School of Life Science, Shanxi University, Taiyuan 030006, PR China; Wolfson College, University of Oxford, Oxford OX2 6UD, UK; Institute of Biomedical and Environmental Science & Technology, School of Life Sciences, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, University Square, Luton LU1 3JU, UK
| | - Lan Wang
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Wenli Ma
- School of Life Science, Shanxi University, Taiyuan 030006, PR China.
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan 030006, PR China.
| |
Collapse
|
19
|
Wu X, Luo D, Zhang Y, Yang C, Crabbe MJC, Zhang T, Li G. Comparative Genomic and Phylogenetic Analysis of Chloroplast Genomes of Hawthorn (Crataegus spp.) in Southwest China. Front Genet 2022; 13:900357. [PMID: 35860470 PMCID: PMC9289535 DOI: 10.3389/fgene.2022.900357] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022] Open
Abstract
The hawthorns (Crataegus spp.) are widely distributed and famous for their edible and medicinal values. There are ∼18 species and seven varieties of hawthorn in China distributed throughout the country. We now report the chloroplast genome sequences from C. scabrifolia, C. chungtienensis and C. oresbia, from the southwest of China and compare them with the previously released six species in Crataegus and four species in Rosaceae. The chloroplast genome structure of Crataegus is typical and can be divided into four parts. The genome sizes are between 159,654 and 159,898bp. The three newly sequenced chloroplast genomes encode 132 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analysis of the chloroplast genomes revealed six divergent hotspot regions, including ndhA, rps16-trnQ-UUG, ndhF-rpl32, rps16-psbK, trnR-UCU-atpA and rpl32-trnL-UAG. According to the correlation and co-occurrence analysis of repeats with indels and SNPs, the relationship between them cannot be ignored. The phylogenetic tree constructed based on the complete chloroplast genome and intergenic region sequences indicated that C. scabrifolia has a different origin from C. chungtienensis and C. oresbia. We support the placement of C. hupehensis, C. cuneata, C. scabrifolia in C. subg. Crataegus and C. kansuensis, C. oresbia, C. kansuensis in C. subg. Sanguineae. In addition, based on the morphology, geographic distribution and phylogenetic relationships of C. chungtienensis and C. oresbia, we speculate that these two species may be the same species. In conclusion, this study has enriched the chloroplast genome resources of Crataegus and provided valuable information for the phylogeny and species identification of this genus.
Collapse
Affiliation(s)
- Xien Wu
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Dengli Luo
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Yingmin Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Congwei Yang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
- *Correspondence: Ticao Zhang, ; Guodong Li,
| | - Guodong Li
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
- *Correspondence: Ticao Zhang, ; Guodong Li,
| |
Collapse
|
20
|
Xiong J, Xu Y, Liu X, Wang X, Shan S, Crabbe MJC, Zhao L, Fang H, Cheng G. Prospective association of dietary soy and fibre intake with puberty timing: a cohort study among Chinese children. BMC Med 2022; 20:145. [PMID: 35369873 PMCID: PMC8978387 DOI: 10.1186/s12916-022-02320-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/02/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Dietary phytoestrogens have been suggested to influence puberty timing, a critical stage for well-being in adulthood. We hypothesized that childhood soy intake might prospectively influence puberty timing and that dietary fibre and the key isoflavone metabolite equol might play roles. METHODS Cox proportional hazard regression models were performed in 4781 children (2152 girls and 2629 boys) aged 6-8 years old from the Chinese Adolescent Cohort Study for whom a food frequency questionnaire at baseline and information about potential confounders were available. Anthropometry and pubertal status including age at Tanner stage 2 for breast development (B2) or age at the initiation of gonadal growth (G2), and age at menarche (M) or voice break (VB) were assessed annually. Equol excretion was determined by urine samples from 1311 participants. RESULTS Among girls and boys, higher soy intake was associated with later puberty timing (hazard ratio (HR)-B2: 0.88 (95% CI, 0.80-0.96), p=0.02; HR-M, 0.87 (0.77-0.94), p=0.01; HR-G2, 0.91 (0.82-0.98), p=0.013; HR-VB, 0.90 (0.82-0.9), p=0.02), independent of prepubertal body fatness and fibre intake. These associations were more pronounced among children with a high urinary equol level (pfor-interaction ≤ 0.04) or with a high cereal fibre intake (pfor-interaction ≤ 0.06). Intake of dietary fibre or its subtype was not prospectively associated with puberty onset after adjusting for dietary soy intake (p≥0.06). CONCLUSION Higher childhood soy intake is prospectively associated with later puberty timing in both Chinese girls and boys, independent of prepubertal body fatness, and the association is particularly pronounced among individuals with a higher urinary equol level.
Collapse
Affiliation(s)
- Jingyuan Xiong
- West China School of Public Health and West China Fourth Hospital and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, People's Republic of China
| | - Yujie Xu
- West China School of Public Health and West China Fourth Hospital and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, People's Republic of China
| | - Xueting Liu
- West China School of Public Health and West China Fourth Hospital and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, People's Republic of China
| | - Xiaoyu Wang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Shufang Shan
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, OX2 6UD, UK.,Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton, LU1 3JU, UK
| | - Li Zhao
- West China School of Public Health and West China Fourth Hospital and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, People's Republic of China
| | - He Fang
- West China School of Public Health and West China Fourth Hospital and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, People's Republic of China
| | - Guo Cheng
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.
| |
Collapse
|
21
|
Yang L, Zhou Y, Chen L, Chen H, Liu W, Zheng W, Andersen ME, Zhang Y, Hu Y, Crabbe MJC, Qu W. Single enrichment systems possibly underestimate both exposures and biological effects of organic pollutants from drinking water. Chemosphere 2022; 292:133496. [PMID: 34990717 DOI: 10.1016/j.chemosphere.2021.133496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 10/08/2021] [Revised: 12/15/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Comprehensive enrichment of contaminants in drinking water is an essential step for accurately determining exposure levels of contaminants and testing their biological effects. Traditional methods using a single absorbent for enriching contaminants in water might not be adequate for complicated matrices with different physical-chemical profiles. To examine this hypothesis, we used an integrated enrichment system that had three sequential stages-XAD-2 resin, poly (styrene-divinylbenzene) and activated charcoal to capture organic pollutants and disinfection by-products (DBPs) from drinking water in Shanghai. Un-adsorbed Organic Compounds in Eluates (UOCEs) named UOCEs-A, -B, and-C following each adsorption stage were determined by gas chromatography-mass spectrometry to evaluate adsorption efficiency of the enrichment system. Meanwhile, biological effects such as cytotoxicity, effects on reactive oxygen species (ROS) generation and glutathione (GSH) depletion were determined in human LO2 cells to identify potential adverse effects on exposure to low dose contaminants. We found that poly-styrene-divinylbenzene (PS-DVB) and activated charcoal (AC) could still partly collect UOCEs-A and-B that the upper adsorption column incompletely captured, and that potential carcinogens like 2-naphthamine were present in all eluates. UOCEs-A at (1-4000), UOCEs-B at (1000-4000), and UOCEs-C at (2400-4000) folds of the actual concentrations had significant cytotoxicity to LO2 cells. Additionally, ROS and GSH change in cells treated with UOCEs indicated the potential for long-term effects of exposure to some mixtures of contaminants such as DBPs at low doses. These results suggested that an enriching system with a single adsorbent would underestimate the exposure level of pollutants and the biological effects of organic pollutants from drinking water. Effective methods for pollutants' enrichment and capture of drinking water should be given priority in future studies on accurate evaluation of biological effects exposed to mixed pollutants via drinking water.
Collapse
Affiliation(s)
- Lan Yang
- Center for Water and Health, Key Lab of Health Technology Assessment, National Health Commission, Key Laboratory of Public Health and Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, P.O. Box 249, Yi Xue Yuan Road 138, Shanghai, 200032, China
| | - Ying Zhou
- Center for Water and Health, Key Lab of Health Technology Assessment, National Health Commission, Key Laboratory of Public Health and Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, P.O. Box 249, Yi Xue Yuan Road 138, Shanghai, 200032, China; Key Laboratory of Public Health and Safety, Ministry of Education, Department of Hygienic Chemistry, School of Public Health, Fudan University, P.O. Box 122, Yi Xue Yuan Road 138, Shanghai, 200032, China
| | - Li Chen
- Center for Water and Health, Key Lab of Health Technology Assessment, National Health Commission, Key Laboratory of Public Health and Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, P.O. Box 249, Yi Xue Yuan Road 138, Shanghai, 200032, China
| | - Hanyi Chen
- Center for Water and Health, Key Lab of Health Technology Assessment, National Health Commission, Key Laboratory of Public Health and Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, P.O. Box 249, Yi Xue Yuan Road 138, Shanghai, 200032, China
| | - Wenhao Liu
- Center for Water and Health, Key Lab of Health Technology Assessment, National Health Commission, Key Laboratory of Public Health and Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, P.O. Box 249, Yi Xue Yuan Road 138, Shanghai, 200032, China
| | - Weiwei Zheng
- Center for Water and Health, Key Lab of Health Technology Assessment, National Health Commission, Key Laboratory of Public Health and Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, P.O. Box 249, Yi Xue Yuan Road 138, Shanghai, 200032, China
| | - Melvin E Andersen
- Andersen ToxConsulting LLC, 4242 Granite Lake Court Denver, North Carolina, 28037, USA
| | - Yubing Zhang
- Department of Toxicology, School of Public Health, Fudan University, Yi Xue Yuan Road 138, Shanghai, 200032, China
| | - Yi Hu
- Center for Water and Health, Key Lab of Health Technology Assessment, National Health Commission, Key Laboratory of Public Health and Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, P.O. Box 249, Yi Xue Yuan Road 138, Shanghai, 200032, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, OX2 6UD, United Kingdom; Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton, LU1 3JU, UK
| | - Weidong Qu
- Center for Water and Health, Key Lab of Health Technology Assessment, National Health Commission, Key Laboratory of Public Health and Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, P.O. Box 249, Yi Xue Yuan Road 138, Shanghai, 200032, China.
| |
Collapse
|
22
|
Dong L, Jiang Z, Yang L, Hu F, Zheng W, Xue P, Jiang S, Andersen ME, He G, Crabbe MJC, Qu W. The genotoxic potential of mixed nitrosamines in drinking water involves oxidative stress and Nrf2 activation. J Hazard Mater 2022; 426:128010. [PMID: 34929594 DOI: 10.1016/j.jhazmat.2021.128010] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/26/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
Nitrosamine by-products in drinking water are designated as probable human carcinogens by the IARC, but the health effects of simultaneous exposure to multiple nitrosamines in drinking water remain unknown. Genotoxicity assays were used to assess the effects of both individual and mixed nitrosamines in finished drinking water produced by a large water treatment plant in Shanghai, China. Cytotoxicity and genotoxicity were measured at 1, 10-, 100- and 1000-fold actual concentrations by the Ames test, Comet assay, γ-H2AX assay, and the cytokinesis-block micronuclei assay; oxidative stress and the Nrf2 pathway were also assessed. Nitrosamines detected in drinking water included NDMA (36.45 ng/L), NDPA (44.68 ng/L), and NEMA (37.27 ng/L). Treatment with a mixture of the three nitrosamines at 1000-fold actual drinking-water concentration induced a doubling of revertants in Salmonella typhimurium strain TA100, DNA and chromosome damage in HepG2 cells, while 1-1000-fold concentrations of compounds applied singly lacked these effects. Treatment with 100- and 1000-fold concentrations increased ROS, GSH, and MDA and decreased SOD activity. Thus, nitrosamine mixtures showed greater genotoxic potential than that of the individual compounds. N-Acetylcysteine protected against the nitrosamine-induced chromosome damage, and Nrf2 pathway activation suggested that oxidative stress played pivotal roles in the genotoxic property of the nitrosamine mixtures.
Collapse
Affiliation(s)
- Lei Dong
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Zhiqiang Jiang
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Lili Yang
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Fen Hu
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Weiwei Zheng
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Health Technology Assessment, Ministry of Health, Fudan University, Shanghai 200032, China
| | - Peng Xue
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Songhui Jiang
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, China
| | | | - Gengsheng He
- Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of the Public Health Safety, Ministry of Education, Department of Nutrition and Food Hygiene, Fudan University, Shanghai 200032, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford OX2 6UD, United Kingdom; Institute of Biomedical and Environmental Science & Technology, University of Bedfordshire, Luton LU1 3JU, UK
| | - Weidong Qu
- Key Laboratory of the Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China; Center for Water and Health, School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Health Technology Assessment, Ministry of Health, Fudan University, Shanghai 200032, China.
| |
Collapse
|
23
|
Wang Y, Lin J, James C. Crabbe M, Yue XG. Association between Self-Rated Health and Depressive Symptoms in Rural Chinese Adults: A Cohort Study Based on Propensity Score Matching. International Journal of Mental Health Promotion 2022. [DOI: 10.32604/ijmhp.2022.020664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
24
|
Cao Q, Feng Y, Dai X, Huang L, Li J, Tao P, Crabbe MJC, Zhang T, Qiao Q. Dynamic Changes of DNA Methylation During Wild Strawberry ( Fragaria nilgerrensis) Tissue Culture. Front Plant Sci 2021; 12:765383. [PMID: 34917103 PMCID: PMC8669611 DOI: 10.3389/fpls.2021.765383] [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] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Tissue culture is an important tool for asexual propagation and genetic transformation of strawberry plants. In plant tissue culture, variation of DNA methylation is a potential source of phenotypic variation in regenerated plants. However, the genome wide dynamic methylation patterns of strawberry tissue culture remain unclear. In this study, we used whole-genome bisulfite sequencing (WGBS) to study genomic DNA methylation changes of a wild strawberry Fragaria nilgerrensis at six stages: from explants of shoot tips to outplanting and acclimation. Global methylation levels showed that CG sites exhibited the highest methylation level in all stages with an average of 49.5%, followed by CHG (33.2%) and CHH (12.4%). Although CHH accounted for the lowest proportion of total cytosine methylation, it showed the most obvious methylation change and the most of these changes occurred in the transposable element regions. The overall methylation levels alternately decreased and increased during the entire tissue culture process and the distribution of DNA methylation was non-uniform among different genetic regions. Furthermore, much more differentially methylated regions (DMRs) were detected in dedifferentiation and redifferentiation stages and most of them were transposable elements, suggesting these processes involved activating or silencing of amounts of transposons. The functional enrichment of the DMR-related genes indicated that genes involved in hormone metabolic processes, plant development and the stress response changed methylation throughout the tissue culture process. Finally, the quantitative real-time PCR (qRT-PCR) was conducted to examine the association of methylation and gene expression of a set of different methylated genes. Our findings give deeper insight into the epigenetic regulation of gene expression during the plant tissue cultures process, which will be useful in the efficient control of somaclonal variations and in crop improvement.
Collapse
Affiliation(s)
- Qiang Cao
- School of Agriculture, Yunnan University, Kunming, China
| | - Yuxi Feng
- School of Agriculture, Yunnan University, Kunming, China
| | - Xiongwei Dai
- School of Agriculture, Yunnan University, Kunming, China
| | - Lin Huang
- School of Agriculture, Yunnan University, Kunming, China
| | - Jiamin Li
- School of Agriculture, Yunnan University, Kunming, China
| | - Pang Tao
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, China
| | - Qin Qiao
- School of Agriculture, Yunnan University, Kunming, China
| |
Collapse
|
25
|
Luo J, Zheng H, Wang S, Li D, Ma W, Wang L, Crabbe MJC. ABL1 and Cofilin1 promote T-cell acute lymphoblastic leukemia cell migration. Acta Biochim Biophys Sin (Shanghai) 2021; 53:1321-1332. [PMID: 34508625 DOI: 10.1093/abbs/gmab117] [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: 03/11/2021] [Revised: 06/15/2021] [Accepted: 08/07/2021] [Indexed: 11/13/2022] Open
Abstract
The fusion gene of ABL1 is closely related to tumor proliferation, invasion, and migration. It has been reported recently that ABL1 itself is required for T-cell acute lymphoblastic leukemia (T-ALL) cell migration induced by CXCL12. Further experiments revealed that ABL1 inhibitor Nilotinib inhibited leukemia cell migration induced by CXCL12, indicating the possible application of Nilotinib in T-ALL leukemia treatment. However, the interacting proteins of ABL1 and the specific mechanisms of their involvement in this process need further investigation. In the present study, ABL1 interacting proteins were characterized and their roles in the process of leukemia cell migration induced by CXCL12 were investigated. Co-immunoprecipitation in combination with mass spectrometry analysis identified 333 proteins that interact with ABL1, including Cofilin1. Gene ontology analysis revealed that many of them were enriched in the intracellular organelle or cytoplasm, including nucleic acid binding components, transfectors, or co-transfectors. Kyoto Encyclopedia of Genes and Genomes analysis showed that the top three enriched pathways were translation, glycan biosynthesis, and metabolism, together with human diseases. ABL1 and Cofilin1 were in the same complex. Cofilin1 binds the SH3 domain of ABL1 directly; however, ABL1 is not required for the phosphorylation of Cofilin1. Molecular docking analysis shows that ABL1 interacts with Cofilin1 mainly through hydrogen bonds and ionic interaction between amino acid residues. The mobility of leukemic cells was significantly decreased by Cofilin1 siRNA. These results demonstrate that Cofilin1 is a novel ABL1 binding partner. Furthermore, Cofilin1 participates in the migration of leukemia cells induced by CXCL12. These data indicate that ABL1 and Cofilin1 are possible targets for T-ALL treatment.
Collapse
Affiliation(s)
- Jixian Luo
- School of Life Sciences, Shanxi University, Taiyuan 030006, China
| | - Huiguang Zheng
- School of Life Sciences, Shanxi University, Taiyuan 030006, China
| | - Sen Wang
- School of Life Sciences, Shanxi University, Taiyuan 030006, China
| | - Dingyun Li
- School of Life Sciences, Shanxi University, Taiyuan 030006, China
| | - Wenli Ma
- School of Life Sciences, Shanxi University, Taiyuan 030006, China
| | - Lan Wang
- School of Life Sciences, Shanxi University, Taiyuan 030006, China
| | - M James C Crabbe
- School of Life Sciences, Shanxi University, Taiyuan 030006, China
- Wolfson College, University of Oxford, Oxford, Oxfordshire OX2 6UD, UK
- Institute of Biomedical and Environmental Science and Technology, University of Bedfordshire, University Square, Luton LU1 3JU, UK
| |
Collapse
|
26
|
Li X, Ren Z, Crabbe MJC, Wang L, Ma W. Genetic modifications of metallothionein enhance the tolerance and bioaccumulation of heavy metals in Escherichia coli. Ecotoxicol Environ Saf 2021; 222:112512. [PMID: 34271502 DOI: 10.1016/j.ecoenv.2021.112512] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 02/09/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Metallothioneins (MTs) are low molecular weight cysteine-rich proteins that bind to metals. Owing to their high cysteine (Cys) content, MTs are effective mediators of heavy metal detoxification. To enhance the heavy metal binding ability of MT from the freshwater crab Sinopotamon henanense (ShMT), sequence-based multiple sequence alignment (MSA) and structure-based molecular docking simulation (MDS) were conducted in order to identify amino acid residues that could be mutated to bolster such metal-binding activity. Site-directed mutagenesis was then used to modify the primary structure of ShMT, and the recombinant proteins were further enhanced using the SUMO fusion expression system to yield SUMO-ShMT1, SUMO-ShMT2, and SUMO-ShMT3 harboring one-, two-, and three- point mutations, respectively. The resultant modified proteins were primarily expressed in a soluble form and exhibited the ability to readily bind to heavy metals. Importantly, these modified proteins exhibited significantly enhanced heavy metal binding capacities, and they improved Cd2+, Cu2+ and Zn2+ tolerance and bioaccumulation in Escherichia coli (E. coli) in a manner dependent upon the number of introduced point mutations (SUMO-ShMT3 > SUMO-ShMT2 > SUMO-ShMT1 > SUMO-ShMT > control). Indeed, E. coli cells harboring the pET28a-SUMO-ShMT3 expression vector exhibited maximal Cd2+, Cu2+, and Zn2+ bioaccumulation that was increased by 1.86 ± 0.02-, 1.71 ± 0.03-, and 2.13 ± 0.02-fold relative to that in E. coli harboring the pET28a-SUMO-ShMT vector. The present study offers a basis for the preparation of genetically engineered bacteria that are better able to bioaccumulate and tolerate heavy metals, thus providing a foundation for biological heavy metal water pollution treatment.
Collapse
Affiliation(s)
- Xuefen Li
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - M James C Crabbe
- School of Life Science, Shanxi University, Taiyuan 030006, PR China; Wolfson College, University of Oxford, Oxford OX2 6UD, UK; Institute of Biomedical and Environmental Science & Technology, School of Life Sciences, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, University Square, Luton LU1 3JU, UK
| | - Lan Wang
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Wenli Ma
- School of Life Science, Shanxi University, Taiyuan 030006, PR China.
| |
Collapse
|
27
|
Geng Y, Guan Y, Qiong L, Lu S, An M, Crabbe MJC, Qi J, Zhao F, Qiao Q, Zhang T. Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation. BMC Biol 2021; 19:143. [PMID: 34294107 PMCID: PMC8296595 DOI: 10.1186/s12915-021-01079-0] [Citation(s) in RCA: 18] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments. Results We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two high- and two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations. Conclusions Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01079-0.
Collapse
Affiliation(s)
- Yupeng Geng
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China
| | - Yabin Guan
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China.,School of Life Sciences, Yunnan University, Kunming, 650504, China
| | - La Qiong
- Research Center for Ecology, College of Science, Tibet University, Lhasa, 850000, China
| | - Shugang Lu
- School of Life Sciences, Yunnan University, Kunming, 650504, China
| | - Miao An
- Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, OX2 6UD, UK.,Institute of Biomedical and Environmental Science & Technology, School of Life Sciences, University of Bedfordshire, Park Square, Luton, LU1 3JU, UK.,School of Life Sciences, Shanxi University, Taiyuan, 030006, China
| | - Ji Qi
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Fangqing Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650500, China. .,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Qin Qiao
- School of Agriculture, Yunnan University, Kunming, 650504, China.
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| |
Collapse
|
28
|
Affiliation(s)
- Rita Yi Man Li
- Department of Economics and Finance/Sustainable Real Estate Research Center, Hong Kong Shue Yan University, North Point, Hong Kong
| | - Xiao-Guang Yue
- School of Sciences, European University of Cyprus, Engomi, Cyprus
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford, United Kingdom
- Institute of Biomedical and Environmental Science and Technology, University of Bedfordshire, Luton, United Kingdom
- School of Life Sciences, Shanxi University, Taiyuan, China
| |
Collapse
|
29
|
Xiong W, Han Y, Crabbe MJC, Yue XG. Fiscal Expenditures on Science and Technology and Environmental Pollution: Evidence from China. Int J Environ Res Public Health 2020; 17:ijerph17238761. [PMID: 33255740 PMCID: PMC7728311 DOI: 10.3390/ijerph17238761] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/12/2020] [Accepted: 11/19/2020] [Indexed: 11/16/2022]
Abstract
Studying the driving factors of environmental pollution is of great importance for China. Previous literature mainly focused on the cause of national aggregate emission changes. However, research about the effect of fiscal expenditures on science and technology (FESTs) on environmental pollution is rare. Considering the large gap among cities in China, it is necessary to investigate whether and how FESTs affect environmental pollution among cities. We adopted three kinds of typical environmental pollutants including sulfur dioxide (SO2) emissions, wastewater emission, and atmospheric particulate matter less than 2.5 micrometers in diameter (PM2.5). Using the data of 260 prefecture-level cities over ten years in China, we found that FESTs play a significantly positive role in reducing sulfur dioxide (SO2) emissions and PM2.5 concentrations, but fail to alleviate wastewater emissions. Specifically, for every 1% increase in FESTs, SO2 emissions were reduced by 5.317% and PM2.5 concentrations were reduced by 5.329%. Furthermore, we found that FESTs reduced environmental pollution by impeding fixed asset investments and by promoting research and development activities (R&D). Moreover, the impacts of FESTs on environmental pollution varied across regions and sub-periods. Our results are robust to a series of additional checks, including alternative econometric specifications, generalized method of moments (GMM) analysis and overcoming potential endogeneity with an instrumental variable. Our findings confirm that government efforts can be effective on pollution control in China. Hence, all governments should pay more attention to FESTs for sustainable development and environmental quality improvements.
Collapse
Affiliation(s)
- Wanfang Xiong
- Department of Finance, School of Economics, Huazhong University of Science and Technology, Wuhan 430074, China;
| | - Yan Han
- School of Humanities and Social Science, Beijing Institute of Technology, Beijing 100081, China
- Correspondence: (Y.H.); (X.-G.Y.)
| | - M. James C. Crabbe
- Wolfson College, Oxford University, Oxford OX2 6UD, UK;
- School of Life Sciences, Shanxi University, Taiyuan 030006, China
- Institute of Biomedical and Environmental Science & Technology, School of Biological Sciences, University of Bedfordshire, Park Square, Luton LU1 3JU, UK
| | - Xiao-Guang Yue
- Department of Computer Science and Engineering, School of Sciences, European University Cyprus, Nicosia 1516, Cyprus
- CIICESI, ESTG, Politécnico do Porto, 4610-156 Felgueiras, Portugal
- Department of Business Sciences, University Giustino Fortunato, 82100 Benevento, Italy
- Correspondence: (Y.H.); (X.-G.Y.)
| |
Collapse
|
30
|
Guan Y, Qu P, Lu S, Crabbe MJC, Zhang T, Geng Y. Spatial genetic and epigenetic structure of Thlaspi arvense (field pennycress) in China. Genes Genet Syst 2020; 95:225-234. [PMID: 33177249 DOI: 10.1266/ggs.20-00025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 11/23/2022] Open
Abstract
Thlaspi arvense (field pennycress) is widespread in temperate regions of the northern hemisphere. We estimated the genetic and epigenetic structure of eight T. arvense populations (131 individuals) in China using amplified fragment length polymorphism and methylation-sensitive amplified polymorphism molecular-marker techniques. We detected low diversity at both genetic (mean = 0.03; total = 0.07) and epigenetic (mean = 0.04; total = 0.07) levels, while significant genetic (FST = 0.42, P < 0.001) and epigenetic (FST = 0.32, P < 0.001) divergence was found across the distribution range. Using Mantel testing, we found spatial genetic and epigenetic differentiation, consistent with isolation-by-distance models. We also identified a strong correlation between genetic and epigenetic differentiation (r = 0.7438, P < 0.001), suggesting genetic control of the epigenetic variation. Our results indicate that mating system, natural selection and gene flow events jointly structure spatial patterns of genetic and epigenetic variation. Moreover, epigenetic variation may serve as a basis of natural selection and ecological evolution to enable species to adapt to heterogeneous habitats. Our study provides novel clues for the adaptation of T. arvense.
Collapse
Affiliation(s)
- Yabin Guan
- School of Life Sciences, Yunnan University.,Institute of Ecology and Geobotany, School of Ecology and Environmental Sciences, Yunnan University
| | - Peng Qu
- Institute of Ecology and Geobotany, School of Ecology and Environmental Sciences, Yunnan University
| | - Shugang Lu
- Institute of Ecology and Geobotany, School of Ecology and Environmental Sciences, Yunnan University
| | - M James C Crabbe
- Wolfson College, Oxford University.,School of Life Sciences, Shanxi University.,Institute of Biomedical and Environmental Science and Technology, University of Bedfordshire
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine
| | - Yupeng Geng
- Institute of Ecology and Geobotany, School of Ecology and Environmental Sciences, Yunnan University
| |
Collapse
|
31
|
Geng Y, Chang N, Zhao Y, Qin X, Lu S, Crabbe MJC, Guan Y, Zhang T. Increased epigenetic diversity and transient epigenetic memory in response to salinity stress in Thlaspi arvense. Ecol Evol 2020; 10:11622-11630. [PMID: 33144988 PMCID: PMC7593180 DOI: 10.1002/ece3.6795] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/05/2020] [Accepted: 08/20/2020] [Indexed: 01/20/2023] Open
Abstract
Epigenetic diversity could play an important role in adaptive evolution of organisms, especially for plant species occurring in new and stressful environments. Thlaspi arvense (field pennycress), a valuable oilseed crop, is widespread in temperate regions of the northern hemisphere. In this study, we investigated the effect of salinity stress on the epigenetic variation of DNA methylation and epigenetic stress memory in pennycress using methylation-sensitive amplification polymorphism (MSAP) markers. We examined how the status of DNA methylation changes across individuals in response to salinity stress and whether such an effect of maternal stress could be transferred to offspring for one or two generations in nonstressed environments. Our results based on 306 epiloci indicated no consistent change of DNA methylation status in specific epiloci across individuals within the same conditions. In contrast, we found that the epigenetic diversity at population level increased significantly in response to the stimulation of salinity stress; and this "stimulation effect" could be transferred partially in the form of stress memory to at least two generations of offspring in nonstressed environments. In addition, we observed a parallel change in functionally important traits, that is, phenotypic variation was significantly higher in plants grown under salinity stress compared with those of control groups. Taken together, our results provide novel clues for the increased spontaneous epimutation rate in response to stress in plants, of potential adaptive significance.
Collapse
Affiliation(s)
- Yupeng Geng
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Na Chang
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Yuewan Zhao
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Xiaoying Qin
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
| | - Shugang Lu
- School of Life SciencesYunnan UniversityKunmingChina
| | - M. James C. Crabbe
- Wolfson CollegeOxford UniversityUK
- Institute of Biomedical and Environmental Science & TechnologyUniversity of BedfordshireLutonUK
- School of Life ScienceShanxi UniversityTaiyuanChina
| | - Yabin Guan
- Institute of Ecology and GeobotanySchool of Ecology and Environmental SciencesYunnan UniversityKunmingChina
- School of Life SciencesYunnan UniversityKunmingChina
| | - Ticao Zhang
- College of Chinese Material MedicaYunnan University of Chinese MedicineKunmingChina
| |
Collapse
|
32
|
Ma W, Li X, Wang Q, Ren Z, Crabbe MJC, Wang L. Tandem oligomeric expression of metallothionein enhance heavy metal tolerance and bioaccumulation in Escherichia coli. Ecotoxicol Environ Saf 2019; 181:301-307. [PMID: 31202929 DOI: 10.1016/j.ecoenv.2019.06.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 01/23/2019] [Revised: 04/25/2019] [Accepted: 06/07/2019] [Indexed: 06/09/2023]
Abstract
Metallothioneins (MTs) are a family of low molecular weight, cysteine-rich, metal-binding proteins, which play important roles in metal homeostasis and heavy metal detoxification. In our previous study, a novel full length MT cDNA was successfully cloned from the freshwater crab (Sinopotamon henanense). In the present study, tandem repeats of two and three copies of the crab MT gene were integrated by overlap extension PCR (SOE-PCR) and expressed in Escherichia coli. The SUMO fusion expression system was adopted to increase the stability and solubility of the recombinant MT proteins. The recombinant proteins were purified and their metal-binding abilities were further analyzed by the ultraviolet absorption spectral scan. Furthermore, the metal tolerance and bioaccumulation of E. coli cells expressing oligomeric MTs were determined. Results showed that the recombinant plasmids pET28a-SUMO-2MT and pET28a-SUMO-3MT were successfully constructed. SDS-PAGE analysis showed that the SUMO-2MT and SUMO-3MT were expressed mainly in the soluble forms. Oligomeric MTs expression significantly enhanced Cu, Cd or Zn tolerance and accumulation in E. coli in the order: SUMO-3MT˃SUMO-2MT˃SUMO-MT˃control. Cells harboring pET28a-SUMO -3MT exhibited the highest Cu, Cd or Zn bioaccumulation at 5.8-fold, 3.1-fold or 6.7-fold higher than that of the control cells. Our research could lay a foundation for large-scale preparation of MTs and provide a scientific basis for bioremediation of heavy metal pollution by oligomeric MTs.
Collapse
Affiliation(s)
- Wenli Ma
- School of Life Science, Shanxi University, Taiyuan, 030006, PR China.
| | - Xuefen Li
- School of Life Science, Shanxi University, Taiyuan, 030006, PR China
| | - Qi Wang
- School of Life Science, Shanxi University, Taiyuan, 030006, PR China
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan, 030006, PR China
| | - M James C Crabbe
- School of Life Science, Shanxi University, Taiyuan, 030006, PR China; Wolfson College, University of Oxford, Oxford, OX2 6UD, UK; Institute of Biomedical and Environmental Science & Technology, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | - Lan Wang
- School of Life Science, Shanxi University, Taiyuan, 030006, PR China
| |
Collapse
|
33
|
Chen Y, Liu A, Zhang Z, Hope C, Crabbe MJC. Economic losses of carbon emissions from circum-Arctic permafrost regions under RCP-SSP scenarios. Sci Total Environ 2019; 658:1064-1068. [PMID: 30677971 DOI: 10.1016/j.scitotenv.2018.12.299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Under rapid Arctic warming, the vast amount of labile organic carbon stored in Arctic permafrost soils poses a potentially huge threat. Thawing permafrost will release hundreds of billion tons of soil carbon into the atmosphere in the form of CO2 and CH4 that would further intensify global warming and bring more challenges to human society. In this study, we use the PInc-PanTher model to estimate carbon emissions from thawing permafrost in the circum-Arctic during 2010-2100 followed by the PAGE09 integrated assessment model to evaluate the net economic losses caused by these permafrost carbon emissions. Our results show that in terms of net present value (NPV), the release of CO2 and CH4 from circum-Arctic permafrost will generate estimated net economic losses of US$2.5 trillion (5-95% range: 0.3-11.2 US$ trillion) under the RCP4.5-SPP1 scenario and US$12.7 trillion (5-95% range: 1.6-41.8 US$ trillion) under the RCP8.5-SPP3 scenario between 2010 and 2100, which contribute ~4.9% and ~6.4% respectively of net economic losses of global carbon emissions.
Collapse
Affiliation(s)
- Yating Chen
- College of Global Change and Earth System Science, Beijing Normal University, 100875 Beijing, China
| | - Aobo Liu
- College of Global Change and Earth System Science, Beijing Normal University, 100875 Beijing, China
| | - Zhihua Zhang
- Climate Modeling Laboratory, Department of Applied Mathematics, Shandong University, Jinan 250100, China; MOE Key Laboratory of Environmental Change and Natural Disaster, Beijing Normal University, 100875, China.
| | - Chris Hope
- Judge Business School, Cambridge University, Cambridge CB2 1AG, UK
| | - M James C Crabbe
- Wolfson College, University of Oxford, Oxford OX2 6UD, UK; Institute of Biomedical and Environmental Science & Technology, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, University Square, Luton LU1 3JU, UK
| |
Collapse
|
34
|
Li H, C. Crabbe MJ, Xu F, Wang W, Ma L, Niu R, Gao X, Li X, Zhang P, Ma X, Chen H. Seasonal variations in carbon, nitrogen and phosphorus concentrations and C:N:P stoichiometry in different organs of a Larix principis-rupprechtii Mayr. plantation in the Qinling Mountains, China. PLoS One 2017; 12:e0185163. [PMID: 28938020 PMCID: PMC5609765 DOI: 10.1371/journal.pone.0185163] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 09/07/2017] [Indexed: 11/18/2022] Open
Abstract
Understanding how concentrations of elements and their stoichiometry change with plant growth and age is critical for predicting plant community responses to environmental change. We used long-term field experiments to explore how the leaf, stem and root carbon (C), nitrogen (N) and phosphorous (P) concentrations and their stoichiometry changed with growth and stand age in a L. principis-rupprechtii Mayr. plantation from 2012-2015 in the Qinling Mountains, China. Our results showed that the C, N and P concentrations and stoichiometric ratios in different tissues of larch stands were affected by stand age, organ type and sampling month and displayed multiple correlations with increased stand age in different growing seasons. Generally, leaf C and N concentrations were greatest in the fast-growing season, but leaf P concentrations were greatest in the early growing season. However, no clear seasonal tendencies in the stem and root C, N and P concentrations were observed with growth. In contrast to N and P, few differences were found in organ-specific C concentrations. Leaf N:P was greatest in the fast-growing season, while C:N and C:P were greatest in the late-growing season. No clear variations were observed in stem and root C:N, C:P and N:P throughout the entire growing season, but leaf N:P was less than 14, suggesting that the growth of larch stands was limited by N in our study region. Compared to global plant element concentrations and stoichiometry, the leaves of larch stands had higher C, P, C:N and C:P but lower N and N:P, and the roots had greater P and C:N but lower N, C:P and N:P. Our study provides baseline information for describing the changes in nutritional elements with plant growth, which will facilitates plantation forest management and restoration, and makes a valuable contribution to the global data pool on leaf nutrition and stoichiometry.
Collapse
Affiliation(s)
- Hailiang Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | | | - Fuli Xu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Weiling Wang
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Lihui Ma
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Ruilong Niu
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xing Gao
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xingxing Li
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Pei Zhang
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xin Ma
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Haikui Chen
- College of Biological Science and Engineering, Beifang University of Nationalities, Yinchuan, Ningxia, P. R. China
| |
Collapse
|
35
|
Gu Z, Jin K, Crabbe MJC, Zhang Y, Liu X, Huang Y, Hua M, Nan P, Zhang Z, Zhong Y. Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome. Protein Cell 2016; 7:250-266. [PMID: 26861146 PMCID: PMC4818845 DOI: 10.1007/s13238-015-0240-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/24/2015] [Indexed: 02/03/2023] Open
Abstract
Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C (chromosome conformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r = 0.9, P < 2.2 × 1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation with some remote functional DNA elements like enhancers and promoters (Enhancer: hESC: r = 0.997, P = 2.3 × 10−4; IMR90: r = 0.934, P = 2 × 10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes.
Collapse
Affiliation(s)
- Zhuoya Gu
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Ke Jin
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - M James C Crabbe
- Department of Zoology, University of Oxford, Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK
- Institute of Biomedical and Environmental Science & Technology, Department of Life Sciences, University of Bedfordshire, Park Square, Luton, LU1 3JU, UK
| | - Yang Zhang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Xiaolin Liu
- School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yanyan Huang
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Mengyi Hua
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Peng Nan
- School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Zhaolei Zhang
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON, M5S 1A1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada.
| | - Yang Zhong
- School of Life Sciences, Fudan University, Shanghai, 200433, China.
- Institute of Biodiversity Science and Institute of High Altitude Medicine, Tibet University, Lhasa, 850012, China.
| |
Collapse
|
36
|
Chen H, Feng Y, Wang L, Yonezawa T, Crabbe MJC, Zhang X, Zhong Y. Transcriptome profiling of the UV-B stress response in the desert shrub Lycium ruthenicum. Mol Biol Rep 2014; 42:639-49. [DOI: 10.1007/s11033-014-3809-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/27/2014] [Indexed: 11/25/2022]
|
37
|
Crabbe MJC. Desarrollo de capacidades y desarrollo de políticas en áreas marinas protegidas de Belice, un ejemplo para la gestión integrada de la costa del Caribe. REV BIOL TROP 2014. [DOI: 10.15517/rbt.v62i0.15923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
38
|
|
39
|
Yang Z, Dong D, Zhang Z, Crabbe MJC, Wang L, Zhong Y. Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs. BMC Genomics 2012; 13 Suppl 7:S14. [PMID: 23281599 PMCID: PMC3521228 DOI: 10.1186/1471-2164-13-s7-s14] [Citation(s) in RCA: 12] [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] [Indexed: 11/11/2022] Open
Abstract
Background MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate the target gene expression at post-transcriptional level. They are widely involved in biological processes, such as embryonic development, cell division, differentiation, and apoptosis. Evidence suggests that miRNAs can constrain the variation of their target to buffer the fluctuation of expression. However, whether this effect can act on the genome-wide expression remains controversial. Results In this study, we comprehensively explored the stably expressed genes (SE genes) and fluctuant genes (FL genes) in the human genome by a meta-analysis of large scale microarray data. We found that these genes have distinct function distributions. miRNA targets are shown to be significantly enriched in SE genes by using propensity analysis of miRNA regulation, supporting the hypothesis that miRNAs can buffer whole genome expression fluctuation. The expression-buffering effect of miRNA is independent of the target site number within the 3'-untranslated region. In addition, we found that gene expression fluctuation is positively correlated with the number of transcription factor binding sites in the promoter region, which suggests that coordination between transcription factors and miRNAs leads to balanced responses to external perturbations. Conclusions Our study confirmed that the genetic buffering roles of miRNAs can act on genome expression fluctuation and provides insights into how miRNAs and transcription factors coordinate to cope with external perturbation.
Collapse
Affiliation(s)
- Zhen Yang
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | | | | | | | | | | |
Collapse
|
40
|
Affiliation(s)
- M J C Crabbe
- University of Bedfordshire, Faculty of Creative Arts, Technologies & Science, Luton, UK.
| | | |
Collapse
|
41
|
Crabbe MJC. Computational biology approaches to plant metabolism and photosynthesis: applications for corals in times of climate change and environmental stress. J Integr Plant Biol 2010; 52:698-703. [PMID: 20666925 DOI: 10.1111/j.1744-7909.2010.00962.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Knowledge of factors that are important in reef resilience helps us to understand how reef ecosystems react following major anthropogenic and environmental disturbances. The symbiotic relationship between the photosynthetic zooxanthellae algal cells and corals is that the zooxanthellae provide the coral with carbon, while the coral provides protection and access to enough light for the zooxanthellae to photosynthesise. This article reviews some recent advances in computational biology relevant to photosynthetic organisms, including Beyesian approaches to kinetics, computational methods for flux balances in metabolic processes, and determination of clades of zooxanthallae. Application of these systems will be important in the conservation of coral reefs in times of climate change and environmental stress.
Collapse
Affiliation(s)
- M James C Crabbe
- LIRANS Institute for Research in the Applied Natural Sciences, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, Luton, UK.
| |
Collapse
|
42
|
Crabbe MJC. Topography and spatial arrangement of reef-building corals on the fringing reefs of North Jamaica may influence their response to disturbance from bleaching. Mar Environ Res 2010; 69:158-162. [PMID: 19819006 DOI: 10.1016/j.marenvres.2009.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 09/08/2009] [Accepted: 09/17/2009] [Indexed: 05/28/2023]
Abstract
Knowledge of factors that are important in reef resilience helps us understand how reefs react following major environmental disturbances such as hurricanes and bleaching. Here we test factors that might have influenced Jamaican reef resilience to, and subsequent recovery from, the 2005 bleaching event, and which might help inform management policy for reefs in the future: reef rugosity and contact of corals with macroalgae. In addition, we test in the field, on Dairy Bull reef, whether aggregated Porites astreoides colonies exhibit enhanced growth when exposed to superior competition from Acopora palmata, as has been found by experiment with the Indo-Pacific corals Porites lobata and the superior competitor Porites rus [Idjadi, J.A., Karlson, R.H., 2007. Spatial arrangement of competitors influences coexistence of reef-building corals. Ecology 88, 2449-2454]. There were significant linear relationships between rugosity and the increase in smallest size classes for Sidastrea siderea, Colpophyllia natans, P. astreoides and Agaricia species, and between rugosity and cover of the branching coral Acropora cervicornis. Linear extension rates of A. cervicornis and radial growth rates of P. astreoides were significantly lower (p<0.025; F>6) when in contact with macroalgae. Aggregated colonies of P. astreoides in contact with one another, one of which was in contact with the faster growing competitor A. palmata showed significantly greater growth rates than with just two aggregated P. astreoides colonies alone. These findings suggest that three dimensional topography and complexity is important for reef resilience and viability in the face of environmental stressors such as bleaching. Our findings also support the idea that aggregated spatial arrangements of corals can influence the outcome of interspecific competition and promote species coexistence, important in times of reef recovery after disturbance.
Collapse
Affiliation(s)
- M J C Crabbe
- LIRANS Institute for Research in the Applied Natural Sciences, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, Park Square, Luton LU1 3JU, UK.
| |
Collapse
|
43
|
Mallela J, Crabbe MJC. Hurricanes and coral bleaching linked to changes in coral recruitment in Tobago. Mar Environ Res 2009; 68:158-162. [PMID: 19570575 DOI: 10.1016/j.marenvres.2009.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Revised: 05/28/2009] [Accepted: 06/01/2009] [Indexed: 05/28/2023]
Abstract
Knowledge of coral recruitment patterns helps us understand how reefs react following major disturbances and provides us with an early warning system for predicting future reef health problems. We have reconstructed and interpreted historical and modern-day recruitment patterns, using a combination of growth modelling and in situ recruitment experiments, in order to understand how hurricanes, storms and bleaching events have influenced coral recruitment on the Caribbean coastline of Tobago. Whilst Tobago does not lie within the main hurricane belt results indicate that regional hurricane events negatively impact coral recruitment patterns in the Southern Caribbean. In years following hurricanes, tropical storms and bleaching events, coral recruitment was reduced when compared to normal years (p=0.016). Following Hurricane Ivan in 2004 and the 2005-2006 bleaching event, coral recruitment was markedly limited with only 2% (n=6) of colonies estimated to have recruited during 2006 and 2007. Our experimental results indicate that despite multiple large-scale disturbances corals are still recruiting on Tobago's marginal reef systems, albeit in low numbers.
Collapse
Affiliation(s)
- J Mallela
- Department of Life Sciences, The University of the West Indies, St. Augustine, The West Indies, Trinidad and Tobago.
| | | |
Collapse
|
44
|
Crabbe MJC, Konopka AK. Editors' note concerning a development of database analysis by Smith and Stein (2009). Comput Biol Chem 2009:S1476-9271(09)00070-X. [PMID: 19700369 DOI: 10.1016/j.compbiolchem.2009.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 07/22/2009] [Indexed: 10/20/2022]
Affiliation(s)
- M J C Crabbe
- University of Bedfordshire, Faculty of Creative Arts, Technologies & Science, Luton LU1 3JU, UK
| | | |
Collapse
|
45
|
Crabbe MJC. Scleractinian coral population size structures and growth rates indicate coral resilience on the fringing reefs of North Jamaica. Mar Environ Res 2009; 67:189-198. [PMID: 19269026 DOI: 10.1016/j.marenvres.2009.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 01/18/2009] [Accepted: 01/30/2009] [Indexed: 05/27/2023]
Abstract
Coral reefs throughout the world are under severe challenges from many environmental factors. This paper quantifies the size structure of populations and the growth rates of corals from 2000 to 2008 to test whether the Discovery Bay coral colonies showed resilience in the face of multiple acute stressors of hurricanes and bleaching. There was a reduction in numbers of colonies in the smallest size class for all the species at all the sites in 2006, after the mass bleaching of 2005, with subsequent increases for all species at all sites in 2007 and 2008. Radial growth rates (mm yr(-1)) of non-branching corals and linear extension rates (mm yr(-1)) of branching corals calculated on an annual basis from 2000-2008 showed few significant differences either spatially or temporally. At Dairy Bull reef, live coral cover increased from 13+/-5% in 2006 to 20+/-9% in 2007 and 31+/-7% in 2008, while live Acropora species increased from 2+/-2% in 2006 to 10+/-4% in 2007 and 22+/-7% in 2008. These studies indicate good levels of coral resilience on the fringing reefs around Discovery Bay in Jamaica.
Collapse
Affiliation(s)
- M J C Crabbe
- Institute for Research in the Applied Natural Sciences, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, Park Square, Luton, LU1 3JU, UK.
| |
Collapse
|
46
|
Abstract
The coral reef ecosystem forms part of a 'seascape' that includes land-based ecosystems such as mangroves and forests, and ideally should form a complete system for conservation and management. Aquaculture, including artisanal fishing for fish and invertebrates, shrimp farming, and seaweed farming, is a major part of the farming and gleaning practices of many tropical communities, particularly on small islands, and depends upon the integrity of the reefs. Climate change is making major impacts on these communities, not least through global warming and high CO(2) concentrations. Corals grow within very narrow limits of temperature, provide livelihoods for millions of people in tropical areas, and are under serious threat from a variety of environmental and climate extremes. Corals survive and grow through a symbiotic relationship with photosynthetic algae: zooxanthellae. Such systems apply highly co-operative regulation to minimize the fluctuation of metabolite concentration profiles in the face of transient perturbations. This review will discuss research on how climate influences reef ecosystems, and how science can lead to conservation actions, with benefits for the human populations reliant on the reefs for their survival.
Collapse
Affiliation(s)
- M James C Crabbe
- Faculty of Creative Arts, Technologies and Science, Institute for Research in the Applied Natural Sciences, University of Bedfordshire, Park Square, Luton LU1 3JU, UK.
| |
Collapse
|
47
|
Abstract
Climate change and global warming have severe consequences for the survival of scleractinian (reef-building) corals and their associated ecosystems. This review summarizes recent literature on the influence of temperature on coral growth, coral bleaching, and modelling the effects of high temperature on corals. Satellite-based sea surface temperature (SST) and coral bleaching information available on the internet is an important tool in monitoring and modelling coral responses to temperature. Within the narrow temperature range for coral growth, corals can respond to rate of temperature change as well as to temperature per se. We need to continue to develop models of how non-steady-state processes such as global warming and climate change will affect coral reefs.
Collapse
Affiliation(s)
- M James C Crabbe
- Luton Institute for Research in the Applied Natural Sciences, Faculty of Creative Arts, Technology and Science, University of Bedfordshire, Park Square, Luton, UK.
| |
Collapse
|
48
|
Crabbe MJC, Martinez E, Garcia C, Chub J, Castro L, Guy J. Growth modelling indicates hurricanes and severe storms are linked to low coral recruitment in the Caribbean. Mar Environ Res 2008; 65:364-368. [PMID: 18191447 DOI: 10.1016/j.marenvres.2007.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Revised: 11/21/2007] [Accepted: 11/22/2007] [Indexed: 05/25/2023]
Abstract
This study set out to test the hypothesis that hurricanes and tropical storms limit the recruitment and subsequent survival of massive non-branching corals on the barrier reef off the coast of Belize in the Gulf of Honduras. Overall, the surface areas of 523 individual coral specimens were measured, and recruitment dates were then modelled. There was no significant difference in coral cover or coral biodiversity between any of the sites studied (p > 0.1). There were significant differences in non-branching coral recruitment in years when hurricanes impacted the area (p < 0.05) compared with years when no hurricanes impacted the area. There were significantly more non-branching massive corals recruited in non-hurricane years (mean 7.7) than in hurricane years (mean 3.8; p = 0.011). When years with tropical storms are added to the years with hurricanes, there was significantly lower coral recruitment (mean 4.7) relative to non-storm or hurricane years (mean 7.4; p = 0.019). These results show that hurricanes and severe storms limited the recruitment and survival of massive non-branching corals of the Mesoamerican barrier reef and on patch reefs near the Belize coast in the Caribbean, and suggests that marine park managers may need to assist coral recruitment in years where there are hurricanes or severe storms.
Collapse
Affiliation(s)
- M James C Crabbe
- Luton Institute for Research in the Applied Natural Sciences, Faculty of Creative Arts, Technologies and Science, University of Bedfordshire, Park Square, Luton, UK.
| | | | | | | | | | | |
Collapse
|
49
|
Crabbe MJC. Global warming and coral reefs: Modelling the effect of temperature on Acropora palmata colony growth. Comput Biol Chem 2007; 31:294-7. [PMID: 17631417 DOI: 10.1016/j.compbiolchem.2007.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [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: 05/03/2007] [Accepted: 05/06/2007] [Indexed: 11/30/2022]
Abstract
Data on colony growth of the branching coral Acropora palmata from fringing reefs off Discovery Bay on the north coast of Jamaica have been obtained over the period 2002-2007 using underwater photography and image analysis by both SCUBA and remotely using an ROV incorporating twin lasers. Growth modelling shows that while logarithmic growth is an approximate model for growth, a 3:3 rational polynomial function provides a significantly better fit to growth data for this coral species. Over the period 2002-2007, involving several cycles of sea surface temperature (SST) change, the rate of growth of A. palmata was largely proportional to rate of change of SST, with R(2)=0.935. These results have implications for the influence of global warming and climate change on coral reef ecosystems.
Collapse
Affiliation(s)
- M James C Crabbe
- Luton Institute for Research in the Applied Natural Sciences, Faculty of Creative Arts, Technology and Science, University of Bedfordshire, Park Square, Luton LU1 3JU, UK.
| |
Collapse
|
50
|
Tuohy KM, Hinton DJS, Davies SJ, Crabbe MJC, Gibson GR, Ames JM. Metabolism of Maillard reaction products by the human gut microbiota--implications for health. Mol Nutr Food Res 2006; 50:847-57. [PMID: 16671057 DOI: 10.1002/mnfr.200500126] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [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] [Indexed: 11/10/2022]
Abstract
The human colonic microbiota imparts metabolic versatility on the colon, interacts at many levels in healthy intestinal and systemic metabolism, and plays protective roles in chronic disease and acute infection. Colonic bacterial metabolism is largely dependant on dietary residues from the upper gut. Carbohydrates, resistant to digestion, drive colonic bacterial fermentation and the resulting end products are considered beneficial. Many colonic species ferment proteins but the end products are not always beneficial and include toxic compounds, such as amines and phenols. Most components of a typical Western diet are heat processed. The Maillard reaction, involving food protein and sugar, is a complex network of reactions occurring during thermal processing. The resultant modified protein resists digestion in the small intestine but is available for colonic bacterial fermentation. Little is known about the fate of the modified protein but some Maillard reaction products (MRP) are biologically active by, e. g. altering bacterial population levels within the colon or, upon absorption, interacting with human disease mechanisms by induction of inflammatory responses. This review presents current understanding of the interactions between MRP and intestinal bacteria. Recent scientific advances offering the possibility of elucidating the consequences of microbe-MRP interactions within the gut are discussed.
Collapse
Affiliation(s)
- Kieran M Tuohy
- School of Food Biosciences, The University of Reading, Whiteknights, Reading, UK.
| | | | | | | | | | | |
Collapse
|