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Chen Z, Hong N, Yan C, Zheng Z, Xi J, Cao P. The potential of Paeonia lactiflora pall seeds oil as a pure natural cosmetics raw material: In Vitro findings. J Cosmet Dermatol 2024; 23:1875-1883. [PMID: 38450923 DOI: 10.1111/jocd.16204] [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: 11/21/2023] [Revised: 12/21/2023] [Accepted: 01/19/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND As a traditional Chinese herbal medicine, Paeonia lactiflora Pall is rich in various active ingredients such as polysaccharides and total flavonoids while having ornamental value. It has potential application value in the development of food and cosmetics. OBJECTIVE To study the in vitro efficacy of Paeonia lactiflora Pall seeds oil. METHODS Firstly, the levels of linolenic acid and linoleic acid in Paeonia lactiflora Pall seeds oil were quantified using gas chromatography. The impact of Paeonia lactiflora Pall seeds oil on the proliferation rate of B16F10 cells was assessed through the CCK-8 method, while the melanin content of B16F10 cells was determined using the sodium hydroxide lysis method. The inhibitory effects of Paeonia lactiflora Pall seeds oil on elastase, collagenase and hyaluronidase were evaluated by biochemical techniques in vitro. Lastly, the hen's egg chorioallantoic membrane test (HET-CAM) was conducted to confirm the absence of eye irritation caused by Paeonia lactiflora Pall seeds oil. RESULTS Paeonia lactiflora Pall seeds oil within a certain volume concentration range (0.5%-4%) had no effect on the proliferation of B16F10 cells. Paeonia lactiflora Pall seeds oil showed significant inhibition of elastase, collagenase and hyaluronidase. Notably, the highest concentration tested, 4% Paeonia lactiflora Pall seed oil, yielded the most pronounced outcomes without causing any irritation. CONCLUSION A certain concentration of Paeonia lactiflora Pall seeds oil has a significant effect on decreasing the melanin content in B16F10 cells and inhibiting the activities of elastase, collagenase, and hyaluronidase, which can provide a reference for the development of pure natural cosmetics raw materials.
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Affiliation(s)
| | - Ni Hong
- Huzhou Jiaheng Industrial Co., Ltd., Huzhou, China
| | - Cui Yan
- Huzhou Jiaheng Industrial Co., Ltd., Huzhou, China
| | | | - Jie Xi
- Huzhou Jiaheng Industrial Co., Ltd., Huzhou, China
| | - Ping Cao
- Huzhou Jiaheng Industrial Co., Ltd., Huzhou, China
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Xu Q, Zhang Y, Xu W, Liu D, Jin W, Chen X, Hong N. The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis. Nucleic Acids Res 2024; 52:3106-3120. [PMID: 38364856 PMCID: PMC11014328 DOI: 10.1093/nar/gkae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Chromatin accessibility plays a critical role in the regulation of cell fate decisions. Although gene expression changes have been extensively profiled at the single-cell level during early embryogenesis, the dynamics of chromatin accessibility at cis-regulatory elements remain poorly studied. Here, we used a plate-based single-cell ATAC-seq method to profile the chromatin accessibility dynamics of over 10 000 nuclei from zebrafish embryos. We investigated several important time points immediately after zygotic genome activation (ZGA), covering key developmental stages up to dome. The results revealed key chromatin signatures in the first cell fate specifications when cells start to differentiate into enveloping layer (EVL) and yolk syncytial layer (YSL) cells. Finally, we uncovered many potential cell-type specific enhancers and transcription factor motifs that are important for the cell fate specifications.
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Affiliation(s)
- Qiushi Xu
- Harbin Institute of Technology, Harbin, China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Yunlong Zhang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Wei Xu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangdong, China
| | - Dong Liu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
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3
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Cao W, Wang X, Luo K, Li Y, Sun J, Fu R, Zhang Q, Hong N, Cheung E, Jin W. Single cell analyses of cancer cells identified two regulatorily and functionally distinct categories in differentially expressed genes among tumor subclones. Heliyon 2024; 10:e28071. [PMID: 38524605 PMCID: PMC10958426 DOI: 10.1016/j.heliyon.2024.e28071] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024] Open
Abstract
To explore the feature of cancer cells and tumor subclones, we analyzed 101,065 single-cell transcriptomes from 12 colorectal cancer (CRC) patients and 92 single cell genomes from one of these patients. We found cancer cells, endothelial cells and stromal cells in tumor tissue expressed much more genes and had stronger cell-cell interactions than their counterparts in normal tissue. We identified copy number variations (CNVs) in each cancer cell and found correlation between gene copy number and expression level in cancer cells at single cell resolution. Analysis of tumor subclones inferred by CNVs showed accumulation of mutations in each tumor subclone along lineage trajectories. We found differentially expressed genes (DEGs) between tumor subclones had two populations: DEGCNV and DEGreg. DEGCNV, showing high CNV-expression correlation and whose expression differences depend on the differences of CNV level, enriched in housekeeping genes and cell adhesion associated genes. DEGreg, showing low CNV-expression correlation and mainly in low CNV variation regions and regions without CNVs, enriched in cytokine signaling genes. Furthermore, cell-cell communication analyses showed that DEGCNV tends to involve in cell-cell contact while DEGreg tends to involve in secreted signaling, which further support that DEGCNV and DEGreg are two regulatorily and functionally distinct categories.
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Affiliation(s)
- Wei Cao
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR
| | - Xuefei Wang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Kaiwen Luo
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yang Li
- Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Jiahong Sun
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ruqing Fu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Qi Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ni Hong
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Edwin Cheung
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR
| | - Wenfei Jin
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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Zhang Z, Liu Z, Hong N, Chen L. Effect of a second-generation motion correction algorithm on image quality and measurement reproducibility of coronary CT angiography in patients with a myocardial bridge and mural coronary artery. Clin Radiol 2024; 79:e462-e467. [PMID: 38135576 DOI: 10.1016/j.crad.2023.11.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023]
Abstract
AIM To determine the effect of second-generation motion correction (MC2) on image quality and measurement reproducibility of cardiac CT images in patients with a myocardial bridge and mural coronary artery (MB-MCA) compared to standard (STD) images without motion correction and with first-generation motion correction (MC1). MATERIALS AND METHODS A total of 66 patients with MB-MCA in the left anterior descending branch who underwent 256-detector CT with single-heartbeat acquisition were included. Images were reconstructed at 45% and 75% R-R intervals using STD, MC1, and MC2 algorithms. Image quality for MB-MCA was assessed by two observers on a four-point scale (1 = poor and 4 = excellent) and compared among STD, MC1, and MC2. Depth and length of MB, lumen area, and minimal diameter of MCA were measured and compared. RESULTS At 45% R-R interval, image quality scores were 1.59 ± 0.78, 2.21 ± 0.97, and 3.21 ± 0.62 for MCA, and 2.48 ± 0.79, 2.76 ± 0.75, and 3.58 ± 0.58 for MB with STD, MC1 and MC2, respectively. At 75% R-R interval, these values were 2.26 ± 0.60, 3.03 ± 0.89, and 3.59 ± 0.55 for MCA and 3.00 ± 0.93, 3.17 ± 0.83, and 3.80 ± 0.44 for MB. Although MC1 was superior to STD in displaying MCA, there was no statistical difference between the two algorithms for MB (p>0.05). Compared with STD and MC1, MC2 statistically improved image quality and interpretability for both MCA and MB and had narrower limits in interobserver agreement for measurements at both 45% and 75% R-R intervals. CONCLUSION MC2 improves CT image quality and measurement reproducibility in patients with MB-MCA compared to STD and MC1.
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Affiliation(s)
- Z Zhang
- Department of Radiology, Peking University People's Hospital, Beijing, 100044, China
| | - Z Liu
- Department of Radiology, Peking University People's Hospital, Beijing, 100044, China
| | - N Hong
- Department of Radiology, Peking University People's Hospital, Beijing, 100044, China
| | - L Chen
- Department of Radiology, Peking University People's Hospital, Beijing, 100044, China.
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Huang C, Wang X, Wang Y, Feng Y, Wang X, Chen S, Yan P, Liao J, Zhang Q, Mao C, Li Y, Wang L, Wang X, Yi W, Cai W, Chen S, Hong N, He W, Chen J, Jin W. Sirpα on tumor-associated myeloid cells restrains antitumor immunity in colorectal cancer independent of its interaction with CD47. Nat Cancer 2024; 5:500-516. [PMID: 38200243 DOI: 10.1038/s43018-023-00691-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 11/15/2023] [Indexed: 01/12/2024]
Abstract
Immunosuppressive myeloid cells hinder immunotherapeutic efficacy in tumors, but the precise mechanisms remain undefined. Here, by performing single-cell RNA sequencing in colorectal cancer tissues, we found tumor-associated macrophages and granulocytic myeloid-derived suppressor cells increased most compared to their counterparts in normal tissue and displayed the highest immune-inhibitory signatures among all immunocytes. These cells exhibited significantly increased expression of immunoreceptor tyrosine-based inhibitory motif-bearing receptors, including SIRPA. Notably, Sirpa-/- mice were more resistant to tumor progression than wild-type mice. Moreover, Sirpα deficiency reprogramed the tumor microenvironment through expansion of TAM_Ccl8hi and gMDSC_H2-Q10hi subsets showing strong antitumor activity. Sirpa-/- macrophages presented strong phagocytosis and antigen presentation to enhance T cell activation and proliferation. Furthermore, Sirpa-/- macrophages facilitated T cell recruitment via Syk/Btk-dependent Ccl8 secretion. Therefore, Sirpα deficiency enhances innate and adaptive immune activation independent of expression of CD47 and Sirpα blockade could be a promising strategy to improve cancer immunotherapy efficacy.
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Affiliation(s)
- Chunliu Huang
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xuefei Wang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yingzhao Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yongyi Feng
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiumei Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shan Chen
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Peidong Yan
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jing Liao
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Qi Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Chengzhou Mao
- Department of Anatomy and Histology, Shenzhen University Health Science Center, Shenzhen, China
| | - Yang Li
- Shenzhen People's Hospital, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Lixiang Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinyu Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wei Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Weibin Cai
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shoudeng Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China
| | - Ni Hong
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| | - Weiling He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Department of Gastrointestinal Surgery, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
| | - Jun Chen
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou, China.
- Jinfeng Laboratory, Chongqing, China.
| | - Wenfei Jin
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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Wang X, Wu X, Hong N, Jin W. Progress in single-cell multimodal sequencing and multi-omics data integration. Biophys Rev 2024; 16:13-28. [PMID: 38495443 PMCID: PMC10937857 DOI: 10.1007/s12551-023-01092-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 05/18/2023] [Accepted: 06/27/2023] [Indexed: 03/19/2024] Open
Abstract
With the rapid advance of single-cell sequencing technology, cell heterogeneity in various biological processes was dissected at different omics levels. However, single-cell mono-omics results in fragmentation of information and could not provide complete cell states. In the past several years, a variety of single-cell multimodal omics technologies have been developed to jointly profile multiple molecular modalities, including genome, transcriptome, epigenome, and proteome, from the same single cell. With the availability of single-cell multimodal omics data, we can simultaneously investigate the effects of genomic mutation or epigenetic modification on transcription and translation, and reveal the potential mechanisms underlying disease pathogenesis. Driven by the massive single-cell omics data, the integration method of single-cell multi-omics data has rapidly developed. Integration of the massive multi-omics single-cell data in public databases in the future will make it possible to construct a cell atlas of multi-omics, enabling us to comprehensively understand cell state and gene regulation at single-cell resolution. In this review, we summarized the experimental methods for single-cell multimodal omics data and computational methods for multi-omics data integration. We also discussed the future development of this field.
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Affiliation(s)
- Xuefei Wang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xinchao Wu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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Liu M, Kang B, Wu H, Peng B, Liu L, Hong N, Gu Q. Ethylene enhances resistance to cucumber green mottle mosaic virus via the ClWRKY70- ClACO5 module in watermelon plants. Front Plant Sci 2024; 14:1332037. [PMID: 38273961 PMCID: PMC10808359 DOI: 10.3389/fpls.2023.1332037] [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: 11/02/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024]
Abstract
Introduction Ethylene (ET) is involved in plant responses to viral infection. However, its molecular mechanisms and regulatory network remain largely unknown. Methods and results In the present study, we report that cucumber green mottle mosaic virus (CGMMV) in watermelon (Citrullus lanatus) triggers ET production by inducing the expression of ClACO5, a key gene of the ET biosynthesis pathway through transcriptome data analysis and gene function validation. The knock-down of ClACO5 expression through virus-induced gene silencing in watermelon and overexpressing ClACO5 in transgenic Nicotiana benthamiana indicated that ClACO5 positively regulates CGMMV resistance and ET biosynthesis. The salicylic acid-responsive transcription factor gene ClWRKY70 shares a similar expression pattern with ClACO5. We demonstrate that ClWRKY70 directly binds to the W-box cis-element in the ClACO5 promoter and enhances its transcription. In addition, ClWRKY70 enhances plant responses to CGMMV infection by regulating ClACO5 expression in watermelon. Discussion Our results demonstrate that the ClWRKY70-ClACO5 module positively regulates resistance to CGMMV infection in watermelon, shedding new light on the molecular basis of ET accumulation in watermelon in response to CGMMV infection.
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Affiliation(s)
- Mei Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Henan, China
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Baoshan Kang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Henan, China
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang, Henan, China
| | - Huijie Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Henan, China
| | - Bin Peng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Henan, China
| | - Liming Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Henan, China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qinsheng Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences,Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Henan, China
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Xinjiang, China
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Wang T, Yi X, Wu Y, He Y, Hong N, Wang G, Wang L. First Report of Lasiodiplodia pseudotheobromae Causing Necrosis and Canker Disease on Pear Tree in China. Plant Dis 2024. [PMID: 38173267 DOI: 10.1094/pdis-10-23-2217-pdn] [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] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Pear is popular among people, which is an important pillar industry in China. In March of 2023, dark brown necrotic lesions were discovered on the trunks of Pyrus pyrofolia cv. Osmanthus pear in orchard, Liuzhou City, Guangxi Zhuang Autonomous Region. In August, field investigation and sample collection were conducted in orchard. Forty pear trees were selected for symptomatic observation, which of 21 had lesions ranging from 10 to 24 per tree, and 19 with 1 to 8 lesions, respectively. To isolate the pathogen, small tissue pieces of 3 diseased pear trunk samples were disinfected with 75% ethanol for 1 minute, rinsed with sterile water, and dried with filter paper. The tissue pieces were placed on potato dextrose agar (PDA) plates and cultured in a dark incubator at 25℃. Six isolates with the similar morphology were obtained. One of the six isolates was randomly selected as the representative strain and named as GX-3. Mycelium grows with an average rate of 4.26 cm/d. The hypha is highly aerial, and is initially white and then turns black. Subsequently, pycnidia formed and secreted black mucus on the PDA medium after 28 days. The immature conidia were ellipsoid, colorless, hyaline, and unicellular, mostly becoming brown bicellular with longitudinal stripes at maturity. The conidial size was 22.5 to 32.6×12.1 to 19.7μm, and the average size was 28.4±2.3×16.7±2.0 μm (n=50), respectively. GX-3 colony morphology was consistent with that of Lasiodiplodia pseudotheobromae (Alves et al.2008). For molecular identification, the internal transcribed spacer of rDNA (ITS), translation elongation factor 1-α (TEF1-α), and β-tubulin regions were amplified using the primers ITS1/4, EF1-728F/986R, and Bt2a/Bt2b, respectively (White et al.1990; Carbone and Kohn 1999; Glass and Donaldson 1995). The obtained sequences of GX-3 were deposited in NCBI with Accession numbers OR655421, OR661231, and OR661230, respectively. The sequences of ITS, TEF1-α, and β-tubulin from GX-3 are 99.44%、99.67% and 99.78% identities with those of L. pseudotheobromae CBS 447.62, respectively. The phylogenetic analysis was performed by maximum likelihood method, revealing that GX-3 is closely clustered with the isolates of L. pseudotheobromae. Therefore, the GX-3 strain was identified as L. pseudotheobromae. GX-3 was further analyzed for its pathogenicity on pear. Firstly, the GX-3 mycelium plugs and spraying spore suspension with the concentration of 1×107 conidia/ml were applied on the stems of 4-month-old healthy birch-leaf pear (Pyrus betulifolia Bunge) potted seedlings by acupuncture needle method, meanwhile PDA and sterile water were used as controls. After 3 days of inoculation, stem surface of the birch-leaf pear exhibited dark brown lesions with slight surface depression, obvious dryness, and canker symptoms, while the control treatment showed no symptoms. The GX-3 was also inoculated on in vitro branches of 'Hosui', 'Hongxiangsu', 'Bodoqing' and 'Xuehua', showing dark brown canker lesions. The same pathogen can be successfully isolated from diseased stems and branches but not from the controls, which accomplishes Koch's postulates. L. pseudotheobromae has been widely reported that it can cause rot and canker on apple, walnut, hackberry, and so on (Xue et al. 2019; Wang et al. 2023; Liang et al. 2020). This is the first report of necrosis and canker disease caused by L. pseudotheobromae on pear in China, which is a potential threat to pear industry.
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Affiliation(s)
- Tianhao Wang
- Huazhong Agricultural University, 47895, College of Plant Science and Technology, Wuhan, Hubei , China;
| | - Xianrong Yi
- Department of Agriculture and Rural Affairs of Guangxi Zhuang Autonomous Region, 636602, Guangxi Characteristic Crop Research Institute, Guilin, Guangxi, China;
| | - Yuxiang Wu
- Huazhong Agricultural University, 47895, College of Plant Science and Technology, Wuhan, Hubei , China;
| | - Ying He
- Huazhong Agricultural University, 47895, College of Plant Science and Technology, Wuhan, Hubei , China;
| | - Ni Hong
- Huazhong Agricultural University, College of Plant Science and Technology , Wuhan, Hubei, China, Wuhan, HuBei, China, 430070;
| | - Guoping Wang
- Huazhong Agricultural University, 47895, College of Plant Science and Technology, Wuhan, Hubei , China;
| | - Liping Wang
- Huazhong Agricultural University, 47895, College of Plant Science and Technology, Wuhan, Hubei , China;
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Li L, Wang G, Zhang Y, Wang W, Zhu Y, Lyu Y, Wang Y, Zhang Y, Hong N. The functions of triple gene block proteins and coat protein of apple stem pitting virus in viral cell-to-cell movement. Mol Plant Pathol 2024; 25:e13392. [PMID: 37837244 PMCID: PMC10782654 DOI: 10.1111/mpp.13392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Apple stem pitting virus is a species in the genus Foveavirus in the family Betaflexiviridae. Apple stem pitting virus (ASPV) commonly infects apple and pear plants grown worldwide. In this study, by integrating bimolecular fluorescence complementation, split-ubiquitin-based membrane yeast two-hybrid, and Agrobacterium-mediated expression assays, the interaction relationships and the subcellular locations of ASPV proteins TGBp1-3 and CP in Nicotiana benthamiana leaf cells were determined. Proteins CP, TGBp1, TGBp2, and TGBp3 were self-interactable, and TGBp2 played a role in the formation of perinuclear viroplasm and enhanced the colocalization of TGBp3 with CP and TGBp1. We found that the plant microfilament and endoplasmic reticulum structures were involved in the production of TGBp3 and TGBp2 vesicles, and their disruption decreased the virus accumulation level in the systemic leaves. The TGBp3 motile vesicles functioned in delivering the viral ribonucleoprotein complexes to the plasma membrane. Two cysteine residues at sites 35 and 49 of the TGBp3 sorting signal were necessary for the diffusion of TGBp3-marked vesicles. Furthermore, our results revealed that TGBp1, TGBp2, and CP could increase plasmodesmal permeability and move to the adjacent cells. This study demonstrates an interaction network and a subcellular location map of four ASPV proteins and for the first time provides insight into the functions of these proteins in the movement of a foveavirus.
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Affiliation(s)
- Liu Li
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Guoping Wang
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Yue Zhang
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Wenjun Wang
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Yiting Zhu
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Yuzhuo Lyu
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Yanxiang Wang
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Yongle Zhang
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
| | - Ni Hong
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsHuazhong Agricultural UniversityWuhanChina
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10
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Li S, Zhu H, He Y, Hong N, Wang G, Wang L. BdCV1-Encoded P3 Silencing Suppressor Identification and Its Roles in Botryosphaeria dothidea, Causing Pear Ring Rot Disease. Cells 2023; 12:2386. [PMID: 37830600 PMCID: PMC10571871 DOI: 10.3390/cells12192386] [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: 08/29/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Pear ring rot disease is an important branch disease, caused by Botryosphaeria dothidea. With the discovery of fungal viruses, the use of their attenuated properties for biological control provides a new strategy for the biological control of fungal disease. RNA silencing is a major antiviral defense mechanism in plants, insects, and fungi. Viruses encode and utilize RNA silencing suppressors to suppress host defenses. Previous studies revealed that Botryosphaeria dothidea chrysovirus 1 (BdCV1) exhibited weak pathogenicity and could activate host gene silencing by infecting B. dothidea. The aim of our study was to investigate whether BdCV1 can encode a silencing suppressor and what effect it has on the host. In this study, the capability of silencing inhibitory activity of four BdCV1-encoded proteins was analyzed, and the P3 protein was identified as a BdCV1 RNA silencing suppressor in the exotic host Nicotiana benthamiana line 16c. In addition, we demonstrated that P3 could inhibit local silencing, block systemic RNA silencing, and induce the necrosis reaction of tobacco leaves. Furthermore, overexpression of P3 could slow down the growth rate and reduce the pathogenicity of B. dothidea, and to some extent affect the expression level of RNA silencing components and virus-derived siRNAs (vsiRNAs). Combined with transcriptomic analysis, P3 had an effect on the gene expression and biological process of B. dothidea. The obtained results provide new theoretical information for further study of interaction between BdCV1 P3 as a potential silencing suppressor and B. dothidea.
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Affiliation(s)
- Shanshan Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Haodong Zhu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying He
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Liping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
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11
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Li H, Liu H, Liu Y, Wang X, Yu S, Huang H, Shen X, Zhang Q, Hong N, Jin W. Exploring the dynamics and influencing factors of CD4 T cell activation using single-cell RNA-seq. iScience 2023; 26:107588. [PMID: 37646019 PMCID: PMC10460988 DOI: 10.1016/j.isci.2023.107588] [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: 12/14/2022] [Revised: 05/26/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023] Open
Abstract
T cell activation is a key event in adaptive immunity. However, the dynamics and influencing factors of T cell activation remain unclear. Here, we analyzed CD4 T cells that were stimulated with anti-CD3/CD28 under several conditions to explore the factors affecting T cell activation. We found a stimulated T subset (HSPhi T) highly expressing heat shock proteins, which was derived from stimulated naive T. We identified and characterized inert T, a stimulated T cell subset in transitional state from resting T to activated T. Interestingly, resting CXCR4low T responded to stimulation more efficiently than resting CXCR4hi T. Furthermore, stimulation of CD4 T in the presence of CD8 T resulted in more effector T and more homogeneous expressions of CD25, supporting that presence of CD8 T reduces the extreme response of T cells, which can be explained by regulation of CD4 T activation through CD8 T-initiated cytokine signaling and FAS/FASLG signaling.
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Affiliation(s)
- Hui Li
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongyi Liu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yifei Liu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xuefei Wang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shiya Yu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongwen Huang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiangru Shen
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qi Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ni Hong
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wenfei Jin
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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12
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Liu M, Kang B, Wu H, Aranda MA, Peng B, Liu L, Fei Z, Hong N, Gu Q. Transcriptomic and metabolic profiling of watermelon uncovers the role of salicylic acid and flavonoids in the resistance to cucumber green mottle mosaic virus. J Exp Bot 2023; 74:5218-5235. [PMID: 37235634 DOI: 10.1093/jxb/erad197] [Citation(s) in RCA: 2] [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: 09/21/2022] [Accepted: 05/24/2023] [Indexed: 05/28/2023]
Abstract
Understanding the mechanisms underlying plant resistance to virus infections is crucial for viral disease management in agriculture. However, the defense mechanism of watermelon (Citrullus lanatus) against cucumber green mottle mosaic virus (CGMMV) infection remains largely unknown. In this study, we performed transcriptomic, metabolomic, and phytohormone analyses of a CGMMV susceptible watermelon cultivar 'Zhengkang No.2' ('ZK') and a CGMMV resistant wild watermelon accession PI 220778 (PI) to identify the key regulatory genes, metabolites, and phytohormones responsible for CGMMV resistance. We then tested several phytohormones and metabolites for their roles in watermelon CGMMV resistance via foliar application, followed by CGMMV inoculation. Several phenylpropanoid metabolism-associated genes and metabolites, especially those involved in the flavonoid biosynthesis pathway, were found to be significantly enriched in the CGMMV-infected PI plants compared with the CGMMV-infected 'ZK' plants. We also identified a gene encoding UDP-glycosyltransferase (UGT) that is involved in kaempferol-3-O-sophoroside biosynthesis and controls disease resistance, as well as plant height. Additionally, salicylic acid (SA) biogenesis increased in the CGMMV-infected 'ZK' plants, resulting in the activation of a downstream signaling cascade. SA levels in the tested watermelon plants correlated with that of total flavonoids, and SA pre-treatment up-regulated the expression of flavonoid biosynthesis genes, thus increasing the total flavonoid content. Furthermore, application of exogenous SA or flavonoids extracted from watermelon leaves suppressed CGMMV infection. In summary, our study demonstrates the role of SA-induced flavonoid biosynthesis in plant development and CGMMV resistance, which could be used to breed for CGMMV resistance in watermelon.
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Affiliation(s)
- Mei Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Baoshan Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Huijie Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)- CSIC, Apdo. correos 164, 30100 Espinardo, Murcia, Spain
| | - Bin Peng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Liming Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Ni Hong
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinsheng Gu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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13
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Yang Y, He Y, Lv S, Zhu H, Wang T, Wang G, Hong N, Wang L. The PcMYB44-mediated miR397-PcLACs module regulates defence-induced lignification in pear resistance to fungal disease. Mol Plant Pathol 2023; 24:1107-1125. [PMID: 37312259 PMCID: PMC10423334 DOI: 10.1111/mpp.13357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 06/15/2023]
Abstract
Diseases caused by Alternaria alternata and Botryosphaeria dothidea diminish pear yield and quality, and restrict the pear agricultural industry. Lignification is a conserved mechanism for plant resistance against pathogen invasion. The regulatory mechanisms underlying defence-induced lignification in pear in response to fungal pathogen infection remain unknown. In this study, analysis of lignification level and lignin content in pear revealed that A. alternata and B. dothidea induced lignification, and transcriptomics showed that lignin biosynthesis was affected. To explore whether laccases (LACs) mediated by miR397 regulate lignification in pear, we investigated the role of PcmiR397 in repressing the expression of PcLACs using 5'-RNA ligase-mediated-RACE and co-transformation in tobacco. Opposite expression patterns for PcmiR397 and PcLAC target genes were observed in pear in response to pathogens. Transient transformation in pear demonstrated that silencing PcmiR397 and overexpressing a single PcLAC enhanced resistance to pathogens via lignin synthesis. To further reveal the mechanism underpinning the PcMIR397 response of pear to pathogens, the PcMIR397 promoter was analysed, and pMIR397-1039 was found to be inhibited by pathogen infection. The transcription factor PcMYB44 was up-regulated, and it bound to the PcMIR397 promoter and inhibited transcription following pathogen infection. The results demonstrate the role of PcmiR397-PcLACs in broad-spectrum resistance to fungal disease, and the potential role of PcMYB44 involved in the miR397-PcLAC module in regulating defence-induced lignification. The findings provide valuable candidate gene resources and guidance for molecular breeding to improve resistance to fungal disease in pear.
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Affiliation(s)
- Yuekun Yang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Ying He
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Shamei Lv
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Haodong Zhu
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Tingting Wang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Guoping Wang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Ni Hong
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Liping Wang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
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14
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Liu M, Wu H, Hong N, Kang B, Peng B, Liu L, Gu Q. Argonaute 1 and 5 proteins play crucial roles in the defence against cucumber green mottle mosaic virus in watermelon. Mol Plant Pathol 2023; 24:961-972. [PMID: 37118922 PMCID: PMC10346368 DOI: 10.1111/mpp.13344] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/04/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
RNA silencing, a core part of plants' antiviral defence, requires the ARGONAUTE, DICER-like, and RNA-dependent RNA polymerase proteins. However, how these proteins contribute to watermelon's RNA interference (RNAi) pathway response to cucumber green mottle mosaic virus (CGMMV) has not been characterized. Here, we identify seven ClAGO, four ClDCL, and 11 ClRDR genes in watermelon and analyse their expression profiles when infected with CGMMV. ClAGO1 and ClAGO5 expression levels were highly induced by CGMMV infection. The results of ClAGO1 and ClAGO5 overexpression and silencing experiments suggest that these genes play central roles in watermelon's antiviral defence. Furthermore, co-immunoprecipitation and bimolecular fluorescence complementation experiments showed that ClAGO1 interacts with ClAGO5 in vivo, suggesting that ClAGO1 and ClAGO5 co-regulate watermelon defence against CGMMV infection. We also identified the ethylene response factor (ERF) binding site in the promoters of the ClAGO1 and ClAGO5 genes, and ethylene (ETH) treatment significantly increased ClAGO5 expression. Two ERF genes (Cla97C08G147180 and Cla97C06G122830) closely related to ClAGO5 expression were identified using co-expression analysis. Subcellular localization revealed that two ERFs and ClAGO5 predominantly localize at the nucleus, suggesting that enhancement of resistance to CGMMV by ETH is probably achieved through ClAGO5 but not ClAGO1. Our findings reveal aspects of the mechanisms underlying RNA silencing in watermelon against CGMMV.
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Affiliation(s)
- Mei Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Huijie Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Ni Hong
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Baoshan Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Bin Peng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Liming Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
| | - Qinsheng Gu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina
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15
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Yuan Z, Li Z, Lu Y, Cao M, Hong N, Wang G, Cai L. Correction to: Molecular characterization of a novel amalgavirus infecting lilium spp. in China. Arch Virol 2023; 168:207. [PMID: 37462768 DOI: 10.1007/s00705-023-05826-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Affiliation(s)
- Zhihao Yuan
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhenfeng Li
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuexia Lu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Southwest University, Chongqing, 400712, China
| | - Ni Hong
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guoping Wang
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Cai
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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16
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Yuan Z, Li Z, Lu Y, Cao M, Hong N, Wang G, Cai L. Molecular characterization of a novel amalgavirus infecting lilium spp. in China. Arch Virol 2023; 168:181. [PMID: 37314504 DOI: 10.1007/s00705-023-05806-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/26/2023] [Indexed: 06/15/2023]
Abstract
A novel plant virus with a double-stranded (ds) RNA genome was detected in Lilium spp. in China by high-throughput sequencing and tentatively named "lily amalgavirus 2" (LAV2). The genomic RNA of LAV2 is 3432 nucleotides (nt) in length and contains two open reading frames (ORFs) that putatively encode a '1 + 2' fusion protein of 1053 amino acids (aa), generated by a '+1' programmed ribosomal frameshift (PRF). ORF1 encodes a putative 386-aa protein of unknown function, and ORF2 overlaps ORF1 by 350 nt and encodes a putative 783-aa protein with conserved RNA-dependent RNA polymerase (RdRp) motifs. The '+1' ribosomal frameshifting motif, UUU_CGN, which is highly conserved among amalgaviruses, is also found in LAV2. Sequence analysis showed that the complete genome shared 46.04%-51.59% nucleotide sequence identity with those of members of the genus Amalgavirus and had the most similarity (51.59% sequence identity) to lily amalgavirus 1 (accession no. OM782323). Phylogenetic analysis based on RdRp amino acid sequences showed that LAV2 clustered with members of the genus Amalgavirus. Overall, our data suggest that LAV2 is a new member of the genus Amalgavirus.
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Affiliation(s)
- Zhihao Yuan
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhenfeng Li
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yuexia Lu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Southwest University, 400712, Chongqing, China
| | - Ni Hong
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guoping Wang
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Li Cai
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China.
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17
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Zhou J, Chen G, Wang J, Zhou B, Sun X, Wang J, Tang S, Xing X, Hu X, Zhao Y, Peng Y, Shi W, Zhao T, Wu Y, Zhong H, Hong N, Ruan Z, Zhang Y, Jin W. Anti-PD-1 therapy achieves favorable outcomes in HBV-positive non-liver cancer. Oncogenesis 2023; 12:22. [PMID: 37080999 PMCID: PMC10119302 DOI: 10.1038/s41389-023-00468-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 03/31/2023] [Accepted: 04/14/2023] [Indexed: 04/22/2023] Open
Abstract
Anti-PD-1 therapy has shown promising outcomes in the treatment of different types of cancer. It is of fundamental interest to analyze the efficacy of anti-PD-1 therapy in cancer patients infected with hepatitis B virus (HBV) since the comorbidity of HBV and cancer is widely documented. We designed a multicenter retrospective study to evaluate the efficacy of anti-PD-1 therapy on non-liver cancer patients infected with HBV. We found anti-PD-1 therapy achieved much better outcomes in HBV+ non-liver cancer patients than their HBV- counterparts. We performed single-cell RNA sequencing (scRNA-seq) on peripheral blood mononuclear cells (PBMCs) from esophageal squamous cell carcinoma (ESCC) patients. We found both cytotoxicity score of T cells and MHC score of B cells significantly increased after anti-PD-1 therapy in HBV+ ESCC patients. We also identified CX3CR1high TEFF, a subset of CD8+ TEFF, associated with better clinical outcome in HBV+ ESCC patients. Lastly, we found CD8+ TEFF from HBV+ ESCC patients showing higher fraction of Exhaustionhi T than their HBV- counterpart. In summary, anti-PD-1 therapy on HBV+ non-liver cancer patients is safe and achieves better outcomes than that on HBV- non-liver cancer patients, potentially because HBV+ patients had higher fraction of Exhaustionhi T, which made them more efficiently respond to anti-PD-1 therapy.
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Affiliation(s)
- Jie Zhou
- Chongqing International Institute for Immunology, 400030, Chongqing, China
- Department of Oncology, Southwest Hospital, Army Medical University, 400038, Chongqing, China
| | - Guanming Chen
- School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Jiuling Wang
- Chongqing International Institute for Immunology, 400030, Chongqing, China
- Institute of Immunology, PLA, Army Medical University, 400038, Chongqing, China
| | - Bo Zhou
- School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xuemin Sun
- Chongqing International Institute for Immunology, 400030, Chongqing, China
- Institute of Immunology, PLA, Army Medical University, 400038, Chongqing, China
| | - Jinsong Wang
- Chongqing International Institute for Immunology, 400030, Chongqing, China
- Institute of Immunology, PLA, Army Medical University, 400038, Chongqing, China
| | - Shu Tang
- Institute of Cancer, Xinqiao Hospital, Army Medical University, 400038, Chongqing, China
| | - Xiangju Xing
- Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Chongqing Medical University, 400038, Chongqing, China
| | - Xiaofei Hu
- Department of Radiology, Southwest Hospital, Army Medical University, 400038, Chongqing, China
| | - Yang Zhao
- Department of Oncology, Southwest Hospital, Army Medical University, 400038, Chongqing, China
| | - Yu Peng
- Department of Oncology, Southwest Hospital, Army Medical University, 400038, Chongqing, China
| | - Wenjiong Shi
- Chongqing International Institute for Immunology, 400030, Chongqing, China
| | - Tingting Zhao
- Chongqing International Institute for Immunology, 400030, Chongqing, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 400054, Chongqing, China
| | - Yuzhang Wu
- Institute of Immunology, PLA, Army Medical University, 400038, Chongqing, China
| | - Hanbing Zhong
- School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Ni Hong
- School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Zhihua Ruan
- Department of Oncology, Southwest Hospital, Army Medical University, 400038, Chongqing, China.
| | - Yi Zhang
- Chongqing International Institute for Immunology, 400030, Chongqing, China.
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 400054, Chongqing, China.
| | - Wenfei Jin
- School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
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18
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Kim KJ, Hong N, Lee S, Shin S, Rhee Y. Exploratory use of romosozumab for osteoporosis in a patient with Hajdu-Cheney syndrome: a case report. Osteoporos Int 2023; 34:1005-1009. [PMID: 36622389 DOI: 10.1007/s00198-023-06668-z] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/30/2022] [Indexed: 01/10/2023]
Abstract
Hajdu-Cheney syndrome (HCS) is an inherited skeletal disorder caused by mutations in the Notch homolog protein 2 gene (NOTCH2). Treatment of this rare disease is challenging because there are no established guidelines worldwide. Previous case reports using bisphosphonates, denosumab, or teriparatide suggested that curative treatment for HCS did not exist yet in terms of preventing the disease progression. Therefore, the efficacy of romosozumab for osteoporosis in patients with HCS needs to be evaluated. Herein, we report the case of a 43-year-old woman who had progressive acro-osteolysis and repeated fractures since the age of 29 years. Next-generation sequencing confirmed HCS with a mutation at nucleotide 6758G>A, leading to Trp2253Ter replacement in NOTCH2. Romosozumab treatment was initiated because she had already received bisphosphonate for more than 10 years at other hospitals. After 1 year of romosozumab treatment, the bone mineral density (BMD) increased by 10.2%, 6.3%, and 1.3%, with Z scores of -2.9, -1.6, and -1.2 at the lumbar spine, femoral neck, and total hip, respectively. In addition, C-telopeptide was suppressed by 26.4% (0.121 to 0.089 ng/mL), and procollagen type I N-terminal propeptide increased by 18.7% (25.2 to 29.9 ng/mL). This was the first report of romosozumab treatment in patient with osteoporosis and HCS in Korea. One year of romosozumab treatment provided substantial gains in BMD with maintaining the last acro-osteolytic status without deteriorating, representing a possible treatment option for HCS.
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Affiliation(s)
- K J Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Korea University College of Medicine, 73 Inchon-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - N Hong
- Department of Internal Medicine, Severance Hospital, Endocrine Research Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - S Lee
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, 20, Ilsan-ro, Wonju-si, Gangwon-do, 26426, Republic of Korea
| | - S Shin
- Department of Internal Medicine, Severance Hospital, Endocrine Research Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Y Rhee
- Department of Internal Medicine, Severance Hospital, Endocrine Research Institute, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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Dong K, Xu C, Kotta‐Loizou I, Jiang J, Lv R, Kong L, Li S, Hong N, Wang G, Coutts RHA, Xu W. Novel Viroid-Like RNAs Naturally Infect a Filamentous Fungus. Adv Sci (Weinh) 2023; 10:e2204308. [PMID: 36515275 PMCID: PMC9875651 DOI: 10.1002/advs.202204308] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 07/27/2022] [Revised: 11/19/2022] [Indexed: 06/17/2023]
Abstract
To date, viroids have been found to naturally infect only plants, resulting in substantial losses for some crops. Whether viroids or viroid-like RNAs naturally infect non-plant hosts remains unknown. Here the existence of a set of exogenous, single-stranded circular RNAs, ranging in size from 157 to 450 nucleotides, isolated from the fungus Botryosphaeria dothidea and nominated B. dothidea RNAs (BdcRNAs) is reported. BdcRNAs replicate autonomously in the nucleus via a rolling-circle mechanism following a symmetric pathway. BdcRNA infection induces symptoms, because BdcRNAs can apparently modulate, to different degrees, specific biological traits (e.g., alter morphology, decrease growth rate, attenuate virulence, and increase or decrease tolerance to osmotic and oxidative stress) of the host fungus. Overall, BdcRNAs have genome characteristics similar to those of viroids and exhibit pathogenic effects on fungal hosts. It is proposed that these novel fungus infecting RNAs should be termed mycoviroids. BdcRNA(s) may be considered additional inhabitants at the frontier of life in terms of genomic complexity, and represent a new class of acellular entities endowed with regulatory functions, and novel epigenomic carriers of biological information.
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Affiliation(s)
- Kaili Dong
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Chuan Xu
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Ioly Kotta‐Loizou
- Department of Life SciencesFaculty of Natural SciencesImperial College LondonLondonSW7 2AZUK
- Department of ClinicalPharmaceutical and Biological ScienceSchool of Life and Medical SciencesUniversity of HertfordshireHatfieldAL10 9ABUK
| | - Jingjing Jiang
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Ruiying Lv
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Linghong Kong
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Shifang Li
- Environment and Plant Protection InstituteChinese Academy of Tropical Agricultural SciencesXueyuan Road, Longhua DistrictHaikouHainan571101P. R. China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100193P. R. China
| | - Ni Hong
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Guoping Wang
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
| | - Robert H. A. Coutts
- Department of ClinicalPharmaceutical and Biological ScienceSchool of Life and Medical SciencesUniversity of HertfordshireHatfieldAL10 9ABUK
| | - Wenxing Xu
- Hubei Hongshan LaboratoryWuhanHubei430070P. R. China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureWuhanHubei430070P. R. China
- Key Lab of Plant Pathology of Hubei ProvinceWuhanHubei430070P. R. China
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070P. R. China
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20
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Jon DI, Park E, Jung M, Hong N, Hong H, Sohn IK, Bahk WM. Latent profile analysis with MMPI-2 responses in military recruits referred for psychiatric symptoms in Korea. Sleep Med 2022. [DOI: 10.1016/j.sleep.2022.05.486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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21
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Xu W, Yang W, Zhang Y, Chen Y, Hong N, Zhang Q, Wang X, Hu Y, Song K, Jin W, Chen X. ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells. Nat Methods 2022; 19:1243-1249. [PMID: 36109677 DOI: 10.1038/s41592-022-01601-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/01/2022] [Indexed: 11/09/2022]
Abstract
Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. Here, we develop in situ sequencing hetero RNA-DNA-hybrid after assay for transposase-accessible chromatin-sequencing (ISSAAC-seq), a highly sensitive and flexible single-cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single nucleus. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from over 10,000 nuclei from the mouse cerebral cortex, we uncovered major and rare cell types and cell-type specific regulatory elements and identified heterogeneity at the chromatin level within established cell types defined by gene expression. Finally, we revealed distinct dynamics and relationships of gene expression and chromatin accessibility during an oligodendrocyte maturation trajectory.
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Affiliation(s)
- Wei Xu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Weilong Yang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yunlong Zhang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yawen Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Brain Research Center and Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Qian Zhang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xuefei Wang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yukun Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Kun Song
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Brain Research Center and Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
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22
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He Y, Zou Q, Li S, Zhu H, Hong N, Wang G, Wang L. Molecular characterization of a new fusarivirus infecting Botryosphaeria dothidea, the causal agent of pear ring rot disease. Arch Virol 2022; 167:1893-1897. [PMID: 35668128 DOI: 10.1007/s00705-022-05492-w] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/19/2022] [Indexed: 11/25/2022]
Abstract
Here, a novel mycovirus, tentatively designated as "Botryosphaeria dothidea fusarivirus 2" (BdFV2), was discovered in Botryosphaeria dothidea strain JZ-3. The complete genome sequence is 6,271 nucleotides (nt) in length, excluding the poly(A) tail, and contains two putative open reading frames (ORFs). The larger ORF1 encodes a polypeptide of 1,552 amino acids (aa) with conserved RNA-dependent RNA polymerase (RdRp) domains and a viral helicase domain. The ORF1-encoded polypeptide shares 19.47-78.70% sequence identity with those of other fusariviruses and shares the highest sequence identity (78.70%) with the corresponding protein aa sequences of Neofusicoccum luteum fusarivirus 1 (NlFV1) isolate CBS110299. The small ORF2 encodes a hypothetical protein with 479 aa, which is predicted to contain a chromosome segregation protein SMC domain of unknown function. Sequence alignments and phylogenetic analysis indicated that BdFV2 is a distinct member of the recently established family Fusariviridae. BdFV2 appears to be a novel fusarivirus infecting a pathogenic B. dothidea strain that causes pear ring rot disease.
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Affiliation(s)
- Ying He
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Qi Zou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Shanshan Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Haodong Zhu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China
| | - Liping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, China.
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23
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Wu H, Liu M, Kang B, Liu L, Hong N, Peng B, Gu Q. AC5 protein encoded by squash leaf curl China virus is an RNA silencing suppressor and a virulence determinant. Front Microbiol 2022; 13:980147. [PMID: 36060769 PMCID: PMC9437540 DOI: 10.3389/fmicb.2022.980147] [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: 06/28/2022] [Accepted: 08/05/2022] [Indexed: 11/26/2022] Open
Abstract
Squash leaf curl China virus (SLCCNV) is a bipartite Begomovirus. The function of the protein AC5, which is encoded by SLCCNV, is unknown. Here, we confirmed that the 172-amino acids (aa) long AC5 protein of SLCCNV could suppress single-stranded RNA but not double-stranded RNA-induced post-transcriptional gene silencing (PTGS). Furthermore, we determined that the C-terminal domain (96–172 aa) of the AC5 protein was responsible for RNA silencing suppressor (RSS) activity via deletion mutant analysis. The AC5 protein can reverse GFP silencing and inhibit systemic silencing of GFP by interfering with the systemic spread of the GFP silencing signal. The SLCCNV AC5 protein was localized to both the nucleus and cytoplasm of Nicotiana benthamiana cells. Furthermore, deletion analysis showed that the putative nuclear localization signal (NLS, 102–155 aa) was crucial for the RNA silencing suppression activity of AC5. In addition, the AC5 protein elicited a hypersensitive response and enhanced potoao virus X (PVX) RNA accumulation in infected N. benthamiana plants. Using the infectious clones of the SLCCNV and SLCCNV-AC5 null mutants, mutational analysis confirmed that knockout of the AC5 gene abolished SLCCNV-induced leaf curl symptoms, showing SLCCNV AC5 is also a virulence determinant.
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Affiliation(s)
- Huijie Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Mei Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Baoshan Kang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Liming Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University/Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Bin Peng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Bin Peng,
| | - Qinsheng Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- *Correspondence: Qinsheng Gu,
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24
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Su C, Ding F, Wang W, Song Z, Ali Q, Ali M, Hong N, Wang G, Han H. Time-resolved fluorescent microsphere lateral flow biosensors for rapid detection of Candidatus Liberibacter asiaticus. Plant Biotechnol J 2022; 20:1235-1237. [PMID: 35445511 PMCID: PMC9241365 DOI: 10.1111/pbi.13828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/02/2022] [Accepted: 04/13/2022] [Indexed: 05/30/2023]
Affiliation(s)
- Cong Su
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan, China
| | - Fang Ding
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenjing Wang
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan, China
| | - Zhiyong Song
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan, China
| | - Qurban Ali
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mubassir Ali
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ni Hong
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Guoping Wang
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Heyou Han
- State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan, China
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25
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Xiao F, Xu W, Hong N, Wang L, Zhang Y, Wang G. A Secreted Lignin Peroxidase Required for Fungal Growth and Virulence and Related to Plant Immune Response. Int J Mol Sci 2022; 23:6066. [PMID: 35682745 PMCID: PMC9181491 DOI: 10.3390/ijms23116066] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 02/04/2023] Open
Abstract
Botryosphaeria spp. are important phytopathogenic fungi that infect a wide range of woody plants, resulting in big losses worldwide each year. However, their pathogenetic mechanisms and the related virulence factors are rarely addressed. In this study, seven lignin peroxidase (LiP) paralogs were detected in Botryosphaeria kuwatsukai, named BkLiP1 to BkLiP7, respectively, while only BkLiP1 was identified as responsible for the vegetative growth and virulence of B. kuwatsukai as assessed in combination with knock-out, complementation, and overexpression approaches. Moreover, BkLiP1, with the aid of a signal peptide (SP), is translocated onto the cell wall of B. kuwatsukai and secreted into the apoplast space of plant cells as expressed in the leaves of Nicotiana benthamiana, which can behave as a microbe-associated molecular pattern (MAMP) to trigger the defense response of plants, including cell death, reactive oxygen species (ROS) burst, callose deposition, and immunity-related genes up-regulated. It supports the conclusion that BkLiP1 plays an important role in the virulence and vegetative growth of B. kuwatsukai and alternatively behaves as an MAMP to induce plant cell death used for the fungal version, which contributes to a better understanding of the pathogenetic mechanism of Botryosphaeria fungi.
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Affiliation(s)
- Feng Xiao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.X.); (W.X.); (N.H.); (L.W.); (Y.Z.)
- Key Laboratory of Plant Pathology of Hubei Province, Wuhan 430070, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology, and Germplasm Creation of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenxing Xu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.X.); (W.X.); (N.H.); (L.W.); (Y.Z.)
- Key Laboratory of Plant Pathology of Hubei Province, Wuhan 430070, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology, and Germplasm Creation of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.X.); (W.X.); (N.H.); (L.W.); (Y.Z.)
- Key Laboratory of Plant Pathology of Hubei Province, Wuhan 430070, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology, and Germplasm Creation of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Liping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.X.); (W.X.); (N.H.); (L.W.); (Y.Z.)
- Key Laboratory of Plant Pathology of Hubei Province, Wuhan 430070, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology, and Germplasm Creation of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongle Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.X.); (W.X.); (N.H.); (L.W.); (Y.Z.)
- Key Laboratory of Plant Pathology of Hubei Province, Wuhan 430070, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology, and Germplasm Creation of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (F.X.); (W.X.); (N.H.); (L.W.); (Y.Z.)
- Key Laboratory of Plant Pathology of Hubei Province, Wuhan 430070, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology, and Germplasm Creation of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
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26
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Fu M, Bai Q, Zhang H, Guo Y, Peng Y, Zhang P, Shen L, Hong N, Xu W, Wang G. Transcriptome Analysis of the Molecular Patterns of Pear Plants Infected by Two Colletotrichum fructicola Pathogenic Strains Causing Contrasting Sets of Leaf Symptoms. Front Plant Sci 2022; 13:761133. [PMID: 35251071 PMCID: PMC8888856 DOI: 10.3389/fpls.2022.761133] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Colletotrichum fructicola infects pear leaves, resulting in two major symptoms: tiny black spots (TS) followed by severe early defoliation and big necrotic lesions (BnL) without apparent damage depending on the pathotypes. How the same fungal species causes different symptoms remains unclear. To understand the molecular mechanism underlying the resulting diseases and the diverse symptoms, two C. fructicola pathogenetic strains (PAFQ31 and PAFQ32 responsible for TS and BnL symptoms, respectively) were inoculated on Pyrus pyrifolia leaves and subjected to transcriptome sequencing at the quiescent stage (QS) and necrotrophic stage (NS), respectively. In planta, the genes involved in the salicylic acid (SA) signaling pathway were upregulated at the NS caused by the infection of each strain. In contrast, the ethylene (ET), abscisic acid (ABA), and jasmonic acid (JA) signaling pathways were specifically related to the TS symptoms caused by the infection of strain PAFQ31, corresponding to the yellowish and early defoliation symptoms triggered by the strain infection. Correspondingly, SA was accumulated in similar levels in the leaves infected by each strain at NS, but JA was significantly higher in the PAFQ31-infected as measured using high-performance liquid chromatography. Weighted gene co-expression network analysis also reveals specific genes, pathways, phytohormones, and transcription factors (TFs) associated with the PAFQ31-associated early defoliation. Taken together, these data suggest that specific metabolic pathways were regulated in P. pyrifolia in response to the infection of two C. fructicola pathotypes resulting in the diverse symptoms: JA, ET, and ABA accumulated in the PAFQ31-infected leaves, which negatively affected the chlorophyll metabolism and photosynthesis pathways while positively affecting the expression of senescence-associated TFs and genes, resulted in leaf yellowing and defoliation; whereas SA inhibited JA-induced gene expression in the PAFQ32-infected leaves, which led to hypersensitive response-like reaction and BnL symptoms.
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Affiliation(s)
- Min Fu
- Hubei Hongshan Laboratory, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Wuhan, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qing Bai
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hui Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yashuang Guo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuhong Peng
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Pengfei Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liang Shen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Wuhan, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenxing Xu
- Hubei Hongshan Laboratory, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Wuhan, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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27
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Wang Q, Xu Y, Yang X, Jia J, Zhou J, Zeng J, Yan X, Li J, Yue J, Guo J, Yang Y, Xia C, Hong N, Wang G, Peng S, Duan Y, Hartung JS, Ding F. Novel insight into the distribution and dissemination of Candidatus Liberibacter asiaticus, the causal agent of citrus Huanglongbing. Plant Biotechnol J 2022; 20:247-249. [PMID: 34800066 PMCID: PMC8753349 DOI: 10.1111/pbi.13753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Qinglian Wang
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Plant Biology (Huazhong Agricultural University)Ministry of EducationWuhanChina
| | - Yunlong Xu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Xiaofen Yang
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jin Jia
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jiale Zhou
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jiwu Zeng
- Fruit Tree Research InstituteGuangdong Academy of Agricultural ScienceGuangzhouChina
| | - Xiang Yan
- Ganzhou Citrus Research InstituteGanzhouChina
| | - Jinxue Li
- Institute of Tropical and Subtropical Cash CropsYunnan Academy of Agricultural ScienceBaoshanChina
| | - Jianqiang Yue
- Institute of Tropical and Subtropical Cash CropsYunnan Academy of Agricultural ScienceBaoshanChina
| | - Jun Guo
- Institute of Tropical and Subtropical Cash CropsYunnan Academy of Agricultural ScienceBaoshanChina
| | - Yi Yang
- Environment and Plant Protection InstituteChinese Academy of Tropical Agricultural ScienceHaikouChina
| | | | - Ni Hong
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Guoping Wang
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shu‐ang Peng
- Key Laboratory of Horticultural Plant Biology (Huazhong Agricultural University)Ministry of EducationWuhanChina
| | | | | | - Fang Ding
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Plant Biology (Huazhong Agricultural University)Ministry of EducationWuhanChina
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28
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Wang X, Shen X, Chen S, Liu H, Hong N, Zhong H, Chen X, Jin W. Reinvestigation of Classic T Cell Subsets and Identification of Novel Cell Subpopulations by Single-Cell RNA Sequencing. J Immunol 2022; 208:396-406. [PMID: 34911770 DOI: 10.4049/jimmunol.2100581] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022]
Abstract
Classic T cell subsets are defined by a small set of cell surface markers, while single-cell RNA sequencing (scRNA-seq) clusters cells using genome-wide gene expression profiles. The relationship between scRNA-seq clustered populations (scCPops) and cell surface marker-defined classic T cell subsets remains unclear. In this article, we integrated six bead-enriched T cell subsets with 62,235 single-cell transcriptomes from human PBMCs and clustered them into nine scCPops. Bead-enriched CD4+/CD45RA+/CD25- naive T and CD8+/CD45RA+ naive T cells were mainly clustered into their scCPop counterparts, while cells from the other T cell subsets were assigned to multiple scCPops, including mucosal-associated invariant T cells and NKT cells. The multiple T cell subsets forming one scCPop exhibit similar expression patterns, but not vice versa, indicating scCPop is a more homogeneous cell population with similar cell states. Interestingly, we discovered and named IFN signaling-associated gene (ISAG) high T (ISAGhi T) cells, a T cell subpopulation that highly expressed ISAGs. We further enriched ISAGhi T cells from human PBMCs by FACS of BST2 for scRNA-seq analyses. The ISAGhi T cell cluster disappeared on t-distributed stochastic neighbor embedding plot after removing ISAGs, whereas the ISAGhi T cell cluster showed up by analysis of ISAGs alone, indicating ISAGs are the major contributor of the ISAGhi T cell cluster. BST2+ and BST2- T cells showing different efficiencies of T cell activation indicate that a high level of ISAGs may contribute to quick immune responses.
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Affiliation(s)
- Xuefei Wang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xiangru Shen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Shan Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hongyi Liu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hanbing Zhong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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29
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Wang Q, Zou Q, Dai Z, Hong N, Wang G, Wang L. Four Novel Mycoviruses from the Hypovirulent Botrytis cinerea SZ-2-3y Isolate from Paris polyphylla: Molecular Characterisation and Mitoviral Sequence Transboundary Entry into Plants. Viruses 2022; 14:v14010151. [PMID: 35062353 PMCID: PMC8777694 DOI: 10.3390/v14010151] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
A hypovirulent SZ-2-3y strain isolated from diseased Paris polyphylla was identified as Botrytis cinerea. Interestingly, SZ-2-3y was coinfected with a mitovirus, two botouliviruses, and a 3074 nt fusarivirus, designated Botrytis cinerea fusarivirus 8 (BcFV8); it shares an 87.2% sequence identity with the previously identified Botrytis cinerea fusarivirus 6 (BcFV6). The full-length 2945 nt genome sequence of the mitovirus, termed Botrytis cinerea mitovirus 10 (BcMV10), shares a 54% sequence identity with Fusarium boothii mitovirus 1 (FbMV1), and clusters with fungus mitoviruses, plant mitoviruses and plant mitochondria; hence BcMV10 is a new Mitoviridae member. The full-length 2759 nt and 2812 nt genome sequences of the other two botouliviruses, named Botrytis cinerea botoulivirus 18 and 19 (BcBoV18 and 19), share a 40% amino acid sequence identity with RNA-dependent RNA polymerase protein (RdRp), and these are new members of the Botoulivirus genus of Botourmiaviridae. Horizontal transmission analysis showed that BcBoV18, BcBoV19 and BcFV8 are not related to hypovirulence, suggesting that BcMV10 may induce hypovirulence. Intriguingly, a partial BcMV10 sequence was detected in cucumber plants inoculated with SZ-2-3y mycelium or pXT1/BcMV10 agrobacterium. In conclusion, we identified a hypovirulent SZ-2-3y fungal strain from P. polyphylla, coinfected with four novel mycoviruses that could serve as potential biocontrol agents. Our findings provide evidence of cross-kingdom mycoviral sequence transmission.
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Affiliation(s)
- Qiong Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Zou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhaoji Dai
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, College of Plant Protection, Hainan University, Ministry of Education, Haikou 570100, China;
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Liping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: ; Tel.: +86-27-8728-2130; Fax: +86-27-8738-4670
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30
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Hou W, Duan L, Huang C, Li X, Xu X, Qin P, Hong N, Wang D, Jin W. Cross-Tissue Characterization of Heterogeneities of Mesenchymal Stem Cells and Their Differentiation Potentials. Front Cell Dev Biol 2021; 9:781021. [PMID: 34977025 PMCID: PMC8719164 DOI: 10.3389/fcell.2021.781021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 09/22/2021] [Accepted: 11/18/2021] [Indexed: 12/28/2022] Open
Abstract
Mesenchymal stem/stromal cells (MSCs) are promising cell sources for regenerative medicine and the treatment of autoimmune disorders. Comparing MSCs from different tissues at the single-cell level is fundamental for optimizing clinical applications. Here we analyzed single-cell RNA-seq data of MSCs from four tissues, namely umbilical cord, bone marrow, synovial tissue, and adipose tissue. We identified three major cell subpopulations, namely osteo-MSCs, chondro-MSCs, and adipo/myo-MSCs, across all MSC samples. MSCs from the umbilical cord exhibited the highest immunosuppression, potentially indicating it is the best immune modulator for autoimmune diseases. MSC subpopulations, with different subtypes and tissue sources, showed pronounced differences in differentiation potentials. After we compared the cell subpopulations and cell status pre-and-post chondrogenesis induction, osteogenesis induction, and adipogenesis induction, respectively, we found MSC subpopulations expanded and differentiated when their subtypes consist with induction directions, while the other subpopulations shrank. We identified the genes and transcription factors underlying each induction at the single-cell level and subpopulation level, providing better targets for improving induction efficiency.
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Affiliation(s)
- Wenhong Hou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Li Duan
- Department of Orthopedics, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
- Shenzhen Institute of Geriatircs, Shenzhen, China
| | - Changyuan Huang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Xingfu Li
- Department of Orthopedics, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Xiao Xu
- Department of Orthopedics, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Pengfei Qin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Daping Wang
- Department of Orthopedics, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
- *Correspondence: Daping Wang, ; Wenfei Jin,
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- *Correspondence: Daping Wang, ; Wenfei Jin,
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31
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Kuhn JH, Adkins S, Agwanda BR, Al Kubrusli R, Alkhovsky SV, Amarasinghe GK, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Basler CF, Bavari S, Beer M, Bejerman N, Bennett AJ, Bente DA, Bergeron É, Bird BH, Blair CD, Blasdell KR, Blystad DR, Bojko J, Borth WB, Bradfute S, Breyta R, Briese T, Brown PA, Brown JK, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Cheng Q, Chiaki Y, Chiapello M, Choi IR, Ciuffo M, Clegg JCS, Crozier I, Dal Bó E, de la Torre JC, de Lamballerie X, de Swart RL, Debat H, Dheilly NM, Di Cicco E, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolnik O, Drebot MA, Drexler JF, Dundon WG, Duprex WP, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Ferguson HW, Fooks AR, Forgia M, Formenty PBH, Fránová J, Freitas-Astúa J, Fu J, Fürl S, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gaskin T, Gonzalez JPJ, Griffiths A, Goldberg TL, Groschup MH, Günther S, Hall RA, Hammond J, Han T, Hepojoki J, Hewson R, Hong J, Hong N, Hongo S, Horie M, Hu JS, Hu T, Hughes HR, Hüttner F, Hyndman TH, Ilyas M, Jalkanen R, Jiāng D, Jonson GB, Junglen S, Kadono F, Kaukinen KH, Kawate M, Klempa B, Klingström J, Kobinger G, Koloniuk I, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Langevin SL, Lee B, Lefkowitz EJ, Leroy EM, Li S, Li L, Lǐ J, Liu H, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Marzano SYL, Massart S, McCauley JW, Melzer M, Mielke-Ehret N, Miller KM, Ming TJ, Mirazimi A, Mordecai GJ, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Olmedo-Velarde A, Palacios G, Pallás V, Pályi B, Papa A, Paraskevopoulou S, Park AC, Parrish CR, Patterson DA, Pauvolid-Corrêa A, Pawęska JT, Payne S, Peracchio C, Pérez DR, Postler TS, Qi L, Radoshitzky SR, Resende RO, Reyes CA, Rima BK, Luna GR, Romanowski V, Rota P, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sall AA, Salvato MS, Sang R, Sasaya T, Schulze AD, Schwemmle M, Shi M, Shí X, Shí Z, Shimomoto Y, Shirako Y, Siddell SG, Simmonds P, Sironi M, Smagghe G, Smither S, Song JW, Spann K, Spengler JR, Stenglein MD, Stone DM, Sugano J, Suttle CA, Tabata A, Takada A, Takeuchi S, Tchouassi DP, Teffer A, Tesh RB, Thornburg NJ, Tomitaka Y, Tomonaga K, Tordo N, Torto B, Towner JS, Tsuda S, Tu C, Turina M, Tzanetakis IE, Uchida J, Usugi T, Vaira AM, Vallino M, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Wang LF, Wang G, Wang Y, Wang Y, Waqas M, Wèi T, Wen S, Whitfield AE, Williams JV, Wolf YI, Wu J, Xu L, Yanagisawa H, Yang C, Yang Z, Zerbini FM, Zhai L, Zhang YZ, Zhang S, Zhang J, Zhang Z, Zhou X. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2021; 166:3567-3579. [PMID: 34786611 DOI: 10.1007/s00705-021-05266-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Bernard R Agwanda
- Zoology Department, National Museums of Kenya, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture & Technology, Nairobi, Kenya
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Andrew J Bennett
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | | | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Bird
- School of Veterinary Medicine, One Health Institute, University of California, Davis, Davis, CA, USA
| | - Carol D Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | | | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BX, UK
- National Horizons Centre, Teesside University, Darlington, DL1 1HG, UK
| | | | - Steven Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rachel Breyta
- University of Washington, Seattle, WA, USA
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Paul A Brown
- Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan, France
| | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service and Division of Virology, University of the Free State, Bloemfontein, Republic of South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Qi Cheng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yuya Chiaki
- Grape and Persimmon Research Station, Institute of Fruit tree and Tea Science, NARO, Higashihiroshima, Hiroshima, Japan
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Baños, Philippines
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elena Dal Bó
- CIDEFI, Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Rik L de Swart
- Department Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Humberto Debat
- Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas (UFYMA-CONICET), Córdoba, Argentina
| | - Nolwenn M Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, 94704, Maisons-Alfort, France
| | | | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - J Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität Berlin, Berlin, Germany
| | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Hugh W Ferguson
- School of Veterinary Medicine, St. George's University, True Blue, Grenada
| | | | - Marco Forgia
- Institute for sustainable plant protection, CNR, Turin, Italy
| | | | - Jana Fránová
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | | | - Jingjing Fu
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Stephanie Fürl
- Albrecht Daniel Thaer-Institute for Crop and Animal Sciences, Division Phytomedicine, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - María Laura García
- nstituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, I, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Thomas Gaskin
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
- Landwirtschaft und Flurneuordnung, Landesamt für ländliche Entwicklung, Frankfurt (Oder), Germany
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Hammond
- Floral and Nursery Plants Research Unit, United States Department of Agriculture, Agricultural Research Service, USNA, Beltsville, MD, USA
| | - Tong Han
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Hewson
- London School of Hygeine and Tropical Medicine, London, UK
| | - Jiang Hong
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Seiji Hongo
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
- Division of Veterinary Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | - John S Hu
- University of Hawaii, Honolulu, HI, USA
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Florian Hüttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - M Ilyas
- Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | | | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Gilda B Jonson
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Centre for Infection Research, Berlin, Germany
| | - Fujio Kadono
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | | | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Igor Koloniuk
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Kenji Kubota
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Eric M Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French National Research Institute for Sustainable Development (IRD), Montpellier, France
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Longhui Li
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Huazhen Liu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Marco Marklewitz
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Shin-Yi L Marzano
- United States Department of Agriculture, Agricultural Research Service , Washington, USA
| | - Sebastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology Laboratory, Liège University, Liege, Belgium
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | - Michael Melzer
- Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | | | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Tobi J Ming
- Molecular Genetics, Pacific Biological Station, Department of Fisheries and Oceans, Nanaimo, Canada
| | | | - Gideon J Mordecai
- Department of Medicine, Univeristy of British Columbia, Vancouver, Canada
| | | | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, Japan
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | | | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Adam C Park
- University of Hawaii, Honolulu, HI, USA
- Hawaii Department of Agriculture, Honolulu, HI, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - David A Patterson
- Fisheries and Oceans Canada, Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and Department of Entomology, Texas A&M University, College Station, USA
- Laboratory of Respiratory Viruses and Measles, Fiocruz, Rio de Janeiro, Brazil
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Carlotta Peracchio
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Liying Qi
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de Investigaciones Científico Tecnológico-Universidad Nacional de La Plata, La Plata, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA, 01536, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | | | - Maria S Salvato
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Angela D Schulze
- Molecular Genetics Lab, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xiǎohóng Shí
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Zhènglì Shí
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | | | - Yukio Shirako
- Asian Center for Bioresources and Environmental Sciences, University of Tokyo, Tokyo, Japan
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Guy Smagghe
- Faculty of Bioscience Engineering, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Sophie Smither
- CBR Division, DSTL, Porton Down, Salisbury, Wiltshire, UK
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | | | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany, and the Institute for Oceans and Fisheries, University of British Columbia, Vancouver, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shigeharu Takeuchi
- Japan Plant Protection Association Kochi Experiment Station, Konan, Kochi, Japan
| | - David P Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Amy Teffer
- Department of Forest Sciences, University of British Columbia, Vancouver, Canada
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Yasuhiro Tomitaka
- Kyushu Okinawa Agricultural Research Center, NARO, Koshi, Kumamoto, Japan
| | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), , Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV & CCHFV, Institut Pasteur, Paris, France
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Shinya Tsuda
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, People's Republic of China
| | - Massimo Turina
- National Institute of Optics, National Research Council of Italy (INO-CNR), Via Branze 45, 25123Brescia, Italy
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System,, Fayetteville, AR, 72701, USA
| | | | - Tomio Usugi
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Muhammad Waqas
- Key Laboratory of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Tàiyún Wèi
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, People's Republic of China
| | - Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jiangxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Lei Xu
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Caixia Yang
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Lifeng Zhai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, Hubei , People's Republic of China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, People's Republic of China
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Jinguo Zhang
- National Sand Pear Germplasm Repository in Wuchang, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, People's Republic of China
| | - Zhe Zhang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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Kuhn JH, Adkins S, Agwanda BR, Al Kubrusli R, Alkhovsky SV, Amarasinghe GK, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Basler CF, Bavari S, Beer M, Bejerman N, Bennett AJ, Bente DA, Bergeron É, Bird BH, Blair CD, Blasdell KR, Blystad DR, Bojko J, Borth WB, Bradfute S, Breyta R, Briese T, Brown PA, Brown JK, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Cheng Q, Chiaki Y, Chiapello M, Choi IR, Ciuffo M, Clegg JCS, Crozier I, Dal Bó E, de la Torre JC, de Lamballerie X, de Swart RL, Debat H, Dheilly NM, Di Cicco E, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolnik O, Drebot MA, Drexler JF, Dundon WG, Duprex WP, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Ferguson HW, Fooks AR, Forgia M, Formenty PBH, Fránová J, Freitas-Astúa J, Fu J, Fürl S, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gaskin T, Gonzalez JPJ, Griffiths A, Goldberg TL, Groschup MH, Günther S, Hall RA, Hammond J, Han T, Hepojoki J, Hewson R, Hong J, Hong N, Hongo S, Horie M, Hu JS, Hu T, Hughes HR, Hüttner F, Hyndman TH, Ilyas M, Jalkanen R, Jiāng D, Jonson GB, Junglen S, Kadono F, Kaukinen KH, Kawate M, Klempa B, Klingström J, Kobinger G, Koloniuk I, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Langevin SL, Lee B, Lefkowitz EJ, Leroy EM, Li S, Li L, Lǐ J, Liu H, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Marzano SYL, Massart S, McCauley JW, Melzer M, Mielke-Ehret N, Miller KM, Ming TJ, Mirazimi A, Mordecai GJ, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Olmedo-Velarde A, Palacios G, Pallás V, Pályi B, Papa A, Paraskevopoulou S, Park AC, Parrish CR, Patterson DA, Pauvolid-Corrêa A, Pawęska JT, Payne S, Peracchio C, Pérez DR, Postler TS, Qi L, Radoshitzky SR, Resende RO, Reyes CA, Rima BK, Luna GR, Romanowski V, Rota P, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sall AA, Salvato MS, Sang R, Sasaya T, Schulze AD, Schwemmle M, Shi M, Shí X, Shí Z, Shimomoto Y, Shirako Y, Siddell SG, Simmonds P, Sironi M, Smagghe G, Smither S, Song JW, Spann K, Spengler JR, Stenglein MD, Stone DM, Sugano J, Suttle CA, Tabata A, Takada A, Takeuchi S, Tchouassi DP, Teffer A, Tesh RB, Thornburg NJ, Tomitaka Y, Tomonaga K, Tordo N, Torto B, Towner JS, Tsuda S, Tu C, Turina M, Tzanetakis IE, Uchida J, Usugi T, Vaira AM, Vallino M, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Wang LF, Wang G, Wang Y, Wang Y, Waqas M, Wèi T, Wen S, Whitfield AE, Williams JV, Wolf YI, Wu J, Xu L, Yanagisawa H, Yang C, Yang Z, Zerbini FM, Zhai L, Zhang YZ, Zhang S, Zhang J, Zhang Z, Zhou X. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2021; 166:3513-3566. [PMID: 34463877 PMCID: PMC8627462 DOI: 10.1007/s00705-021-05143-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 02/06/2023]
Abstract
In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Bernard R Agwanda
- Zoology Department, National Museums of Kenya, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture & Technology, Nairobi, Kenya
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Andrew J Bennett
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | | | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Bird
- School of Veterinary Medicine, One Health Institute, University of California, Davis, Davis, CA, USA
| | - Carol D Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | | | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BX, UK
- National Horizons Centre, Teesside University, Darlington, DL1 1HG, UK
| | | | - Steven Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rachel Breyta
- University of Washington, Seattle, WA, USA
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Paul A Brown
- Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan, France
| | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service and Division of Virology, University of the Free State, Bloemfontein, Republic of South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Qi Cheng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yuya Chiaki
- Grape and Persimmon Research Station, Institute of Fruit tree and Tea Science, NARO, Higashihiroshima, Hiroshima, Japan
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Baños, Philippines
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elena Dal Bó
- CIDEFI, Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Rik L de Swart
- Department Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Humberto Debat
- Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas (UFYMA-CONICET), Córdoba, Argentina
| | - Nolwenn M Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, 94704, Maisons-Alfort, France
| | | | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - J Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität Berlin, Berlin, Germany
| | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Hugh W Ferguson
- School of Veterinary Medicine, St. George's University, True Blue, Grenada
| | | | - Marco Forgia
- Institute for sustainable plant protection, CNR, Turin, Italy
| | | | - Jana Fránová
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | | | - Jingjing Fu
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Stephanie Fürl
- Albrecht Daniel Thaer-Institute for Crop and Animal Sciences, Division Phytomedicine, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - María Laura García
- nstituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, I, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Thomas Gaskin
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
- Landwirtschaft und Flurneuordnung, Landesamt für ländliche Entwicklung, Frankfurt (Oder), Germany
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Hammond
- Floral and Nursery Plants Research Unit, United States Department of Agriculture, Agricultural Research Service, USNA, Beltsville, MD, USA
| | - Tong Han
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Hewson
- London School of Hygeine and Tropical Medicine, London, UK
| | - Jiang Hong
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Seiji Hongo
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
- Division of Veterinary Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | - John S Hu
- University of Hawaii, Honolulu, HI, USA
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Florian Hüttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - M Ilyas
- Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | | | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Gilda B Jonson
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Centre for Infection Research, Berlin, Germany
| | - Fujio Kadono
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | | | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Igor Koloniuk
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Kenji Kubota
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Eric M Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French National Research Institute for Sustainable Development (IRD), Montpellier, France
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Longhui Li
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Huazhen Liu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Marco Marklewitz
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Shin-Yi L Marzano
- United States Department of Agriculture, Agricultural Research Service , Washington, USA
| | - Sebastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology Laboratory, Liège University, Liege, Belgium
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | - Michael Melzer
- Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | | | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Tobi J Ming
- Molecular Genetics, Pacific Biological Station, Department of Fisheries and Oceans, Nanaimo, Canada
| | | | - Gideon J Mordecai
- Department of Medicine, Univeristy of British Columbia, Vancouver, Canada
| | | | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, Japan
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | | | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Adam C Park
- University of Hawaii, Honolulu, HI, USA
- Hawaii Department of Agriculture, Honolulu, HI, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - David A Patterson
- Fisheries and Oceans Canada, Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and Department of Entomology, Texas A&M University, College Station, USA
- Laboratory of Respiratory Viruses and Measles, Fiocruz, Rio de Janeiro, Brazil
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Carlotta Peracchio
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Liying Qi
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de Investigaciones Científico Tecnológico-Universidad Nacional de La Plata, La Plata, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA, 01536, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | | | - Maria S Salvato
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Angela D Schulze
- Molecular Genetics Lab, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xiǎohóng Shí
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Zhènglì Shí
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | | | - Yukio Shirako
- Asian Center for Bioresources and Environmental Sciences, University of Tokyo, Tokyo, Japan
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Guy Smagghe
- Faculty of Bioscience Engineering, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Sophie Smither
- CBR Division, DSTL, Porton Down, Salisbury, Wiltshire, UK
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | | | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany, and the Institute for Oceans and Fisheries, University of British Columbia, Vancouver, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shigeharu Takeuchi
- Japan Plant Protection Association Kochi Experiment Station, Konan, Kochi, Japan
| | - David P Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Amy Teffer
- Department of Forest Sciences, University of British Columbia, Vancouver, Canada
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Yasuhiro Tomitaka
- Kyushu Okinawa Agricultural Research Center, NARO, Koshi, Kumamoto, Japan
| | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), , Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV & CCHFV, Institut Pasteur, Paris, France
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Shinya Tsuda
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, People's Republic of China
| | - Massimo Turina
- National Institute of Optics, National Research Council of Italy (INO-CNR), Via Branze 45, 25123Brescia, Italy
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System,, Fayetteville, AR, 72701, USA
| | | | - Tomio Usugi
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Muhammad Waqas
- Key Laboratory of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Tàiyún Wèi
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, People's Republic of China
| | - Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jiangxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Lei Xu
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Caixia Yang
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Lifeng Zhai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, Hubei , People's Republic of China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, People's Republic of China
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Jinguo Zhang
- National Sand Pear Germplasm Repository in Wuchang, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, People's Republic of China
| | - Zhe Zhang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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Fu R, Qin P, Zou X, Hu Z, Hong N, Wang Y, Jin W. A Comprehensive Characterization of Monoallelic Expression During Hematopoiesis and Leukemogenesis via Single-Cell RNA-Sequencing. Front Cell Dev Biol 2021; 9:702897. [PMID: 34722498 PMCID: PMC8548578 DOI: 10.3389/fcell.2021.702897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/13/2021] [Indexed: 12/30/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) is becoming a powerful tool to investigate monoallelic expression (MAE) in various developmental and pathological processes. However, our knowledge of MAE during hematopoiesis and leukemogenesis is limited. In this study, we conducted a systematic interrogation of MAEs in bone marrow mononuclear cells (BMMCs) at single-cell resolution to construct a MAE atlas of BMMCs. We identified 1,020 constitutive MAEs in BMMCs, which included imprinted genes such as MEG8, NAP1L5, and IRAIN. We classified the BMMCs into six cell types and identified 74 cell type specific MAEs including MTSS1, MOB1A, and TCF12. We further identified 114 random MAEs (rMAEs) at single-cell level, with 78.1% single-allele rMAE and 21.9% biallelic mosaic rMAE. Many MAEs identified in BMMCs have not been reported and are potentially hematopoietic specific, supporting MAEs are functional relevance. Comparison of BMMC samples from a leukemia patient with multiple clinical stages showed the fractions of constitutive MAE were correlated with fractions of leukemia cells in BMMCs. Further separation of the BMMCs into leukemia cells and normal cells showed that leukemia cells have much higher constitutive MAE and rMAEs than normal cells. We identified the leukemia cell-specific MAEs and relapsed leukemia cell-specific MAEs, which were enriched in immune-related functions. These results indicate MAE is prevalent and is an important gene regulation mechanism during hematopoiesis and leukemogenesis. As the first systematical interrogation of constitutive MAEs, cell type specific MAEs, and rMAEs during hematopoiesis and leukemogenesis, the study significantly increased our knowledge about the features and functions of MAEs.
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Affiliation(s)
- Ruiqing Fu
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China.,School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Pengfei Qin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xianghui Zou
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yun Wang
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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Wang Y, Wang G, Bai J, Zhang Y, Wang Y, Wen S, Li L, Yang Z, Hong N. A novel Actinidia cytorhabdovirus characterized using genomic and viral protein interaction features. Mol Plant Pathol 2021; 22:1271-1287. [PMID: 34288324 PMCID: PMC8435229 DOI: 10.1111/mpp.13110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
A novel cytorhabdovirus, tentatively named Actinidia virus D (AcVD), was identified from kiwifruit (Actinidia chinensis) in China using high-throughput sequencing technology. The genome of AcVD consists of 13,589 nucleotides and is organized into seven open reading frames (ORFs) in its antisense strand, coding for proteins in the order N-P-P3-M-G-P6-L. The ORFs were flanked by a 3' leader sequence and a 5' trailer sequence and are separated by conserved intergenic junctions. The genome sequence of AcVD was 44.6%-51.5% identical to those of reported cytorhabdoviruses. The proteins encoded by AcVD shared the highest sequence identities, ranging from 27.3% (P6) to 44.5% (L), with the respective proteins encoded by reported cytorhabdoviruses. Phylogenetic analysis revealed that AcVD clustered together with the cytorhabdovirus Wuhan insect virus 4. The subcellular locations of the viral proteins N, P, P3, M, G, and P6 in epidermal cells of Nicotiana benthamiana leaves were determined. The M protein of AcVD uniquely formed filament structures and was associated with microtubules. Bimolecular fluorescence complementation assays showed that three proteins, N, P, and M, self-interact, protein N plays a role in the formation of cytoplasm viroplasm, and protein M recruits N, P, P3, and G to microtubules. In addition, numerous paired proteins interact in the nucleus. This study presents the first evidence of a cytorhabdovirus infecting kiwifruit plants and full location and interaction maps to gain insight into viral protein functions.
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Affiliation(s)
- Yanxiang Wang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Guoping Wang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Jianyu Bai
- Laboratory of Fruit Trees DiseaseInstitute of Economic ForestryXinjiang Academy of Forestry SciencesUrumqiChina
| | - Yongle Zhang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ying Wang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shaohua Wen
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Liu Li
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zuokun Yang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ni Hong
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
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Zou Q, Gao Y, Wang Q, Yang Y, Wang F, Hong N, Wang G, Wang L. The full-length genome sequence of a novel mitovirus from Botryosphaeria dothidea, the causal agent of pear ring rot disease. Arch Virol 2021; 166:2881-2885. [PMID: 34338875 DOI: 10.1007/s00705-021-05189-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/08/2021] [Indexed: 10/20/2022]
Abstract
Here, we describe a novel mycovirus, tentatively designated as "Botryosphaeria dothidea mitovirus 3" (BdMV3), isolated from Botryosphaeria dothidea strain FJ, which causes pear ring rot disease in Fujian Province, China. The complete genome nucleotide sequence of BdMV3 is 2538 nt in length and contains a single 2070-nt open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) of 689 amino acids (aa) using the fungal mitochondrial genetic code. BLASTp analysis revealed that the RdRp of BdMV3 shares 28.91%-69.36% sequence identity (query sequence coverage more than 90%) with those of members of the genus Mitovirus, with the highest sequence identity of 69.36% and 68.79% to the corresponding RdRp aa sequences of Rhizoctonia solani mitovirus 10 and Macrophomina phaseolina mitovirus 4, respectively. Phylogenetic analysis based on RdRp aa sequences indicated that BdMV3 is a new member of the genus Mitovirus in the family Mitoviridae.
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Affiliation(s)
- Qi Zou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China
| | - Yunjing Gao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China
| | - Qiong Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China
| | - Yuekun Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China
| | - Fang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China
| | - Liping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China. .,Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, 430070, People's Republic of China.
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36
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Yang M, Xu W, Zhou X, Yang Z, Wang Y, Xiao F, Guo Y, Hong N, Wang G. Discovery and Characterization of a Novel Bipartite Botrexvirus From the Phytopathogenic Fungus Botryosphaeria dothidea. Front Microbiol 2021; 12:696125. [PMID: 34276630 PMCID: PMC8280476 DOI: 10.3389/fmicb.2021.696125] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/31/2021] [Indexed: 11/15/2022] Open
Abstract
In this study, we describe a novel positive, single-stranded (+ss) RNA mycovirus, named Botryosphaeria dothidea botrexvirus 1 (BdBV1), from a phytopathogenic fungus Botryosphaeria dothidea showing abnormal morphology and attenuated virulence. BdBV1 is phylogenetically related to Botrytis virus X (BotVX) and is the second potential member of the proposed genus Botrexvirus in the family Alphaflexiviridae. However, it differs from the monopartite BotVX in that BdBV1 possesses a bipartite genome comprised of two ssRNA segments (RNA1 and RNA2 with lengths of 5,035 and 1,063 nt, respectively). BdBV1 RNA1 and RNA2 encode putative RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes, which share significant identity with corresponding genes in both fungal and plant viruses. Moreover, open reading frames (ORFs) 2–4 of BdBV1 RNA1 shared no detectable identity with any known viral proteins. Immunosorbent electron microscopy (ISEM) analysis using an antibody against the virus CP generated in vitro revealed that BdBV1 is encapsidated in filamentous particles. A comparison of the biological effects of BdBV1 infection on symptoms and growth in isogenic lines of virus-free and virus-infected B. dothidea revealed that BdBV1 is probably involved in reduced growth and virulence of the host fungus. This study describes and characterizes a novel bipartite botrexvirus, which is closely related to uni- and multi-partite fungal and plant viruses and contributes useful information to a better understanding of virus evolution.
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Affiliation(s)
- Mengmeng Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Wenxing Xu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Xiaoqi Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zuokun Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanxiang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Feng Xiao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yashuang Guo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China.,Key Lab of Plant Pathology of Hubei Province, Wuhan, China
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Wang X, Guo Y, Du Y, Yang Z, Huang X, Hong N, Xu W, Wang G. Characterization of Diaporthe species associated with peach constriction canker, with two novel species from China. MycoKeys 2021; 80:77-90. [PMID: 34054325 PMCID: PMC8149378 DOI: 10.3897/mycokeys.80.63816] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/29/2021] [Indexed: 12/03/2022] Open
Abstract
Species of Diaporthe infect a wide range of plants and live in vivo as endophytes, saprobes or pathogens. However, those in peach plants are poorly characterized. In this study, 52 Diaporthe strains were isolated from peach branches with buds, showing constriction canker symptoms. Phylogenetic analyses were conducted using five gene regions: internal transcribed spacer of the ribosomal DNA (ITS), translation elongation factor 1-α (TEF), ß-tubulin (TUB), histone (HIS), and calmodulin (CAL). These results coupled with morphology revealed seven species of Diaporthe, including five known species (D. caryae, D. cercidis, D. eres, D. hongkongensis, and D. unshiuensis). In addition, two novel species D. jinxiu and D. zaofenghuang are introduced. Except for the previously reported D. eres, this study represents the first characterization of Diaporthe species associated with peach constriction canker in China, and contributes useful data for practicable disease management.
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Affiliation(s)
- Xianhong Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, ChinaHuazhong Agricultural UniversityWuhanChina
| | - Yashuang Guo
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, ChinaHuazhong Agricultural UniversityWuhanChina
| | - Yamin Du
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, ChinaHuazhong Agricultural UniversityWuhanChina
| | - Ziling Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, ChinaHuazhong Agricultural UniversityWuhanChina
| | - Xinzhong Huang
- Research Institute of Pomology, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, ChinaKey Laboratory of Horticultural Crop Biology and Germplasm Creation of the Ministry of AgricultureWuhanChina
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, ChinaHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, Hubei, 430070, ChinaResearch Institute of Pomology, Fujian Academy of Agricultural SciencesFuzhouChina
| | - Wenxing Xu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, ChinaHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, Hubei, 430070, ChinaResearch Institute of Pomology, Fujian Academy of Agricultural SciencesFuzhouChina
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, ChinaHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, Hubei, 430070, ChinaResearch Institute of Pomology, Fujian Academy of Agricultural SciencesFuzhouChina
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Jung YW, Hong N, Kim CO, Kim HC, Youm Y, Choi JY, Rhee Y. The diagnostic value of phase angle, an integrative bioelectrical marker, for identifying individuals with dysmobility syndrome: the Korean Urban-Rural Elderly study. Osteoporos Int 2021; 32:939-949. [PMID: 33128075 DOI: 10.1007/s00198-020-05708-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/20/2020] [Indexed: 12/25/2022]
Abstract
UNLABELLED Low phase angle, a non-invasive bioimpedance marker, is associated with elevated odds of dysmobility syndrome and its components. Phase angle (estimated cutoffs: < 4.8° in men; < 4.5° in women) can be used to detect dysmobility syndrome in community-dwelling older adults as a simple, integrative screening tool. INTRODUCTION Dysmobility syndrome uses a score-based approach to predict fracture risk that incorporates the concepts of osteoporosis, sarcopenia, and obesity. Low phase angle (PhA), a simple, non-invasive bioelectrical impedance marker, was associated with low lean mass, high fat mass, and poor muscle function. We aimed to investigate the association between PhA and dysmobility syndrome, with the exploration of the diagnostic cutoffs. METHODS In a community-dwelling Korean older adult cohort, dysmobility syndrome was defined as the presence of ≥ 3 of the following components: osteoporosis, low lean mass, falls in the preceding year, low grip strength, high fat mass, and poor timed up and go performance. RESULTS Among the 1825 participants (mean age 71.6, women 66.7%), subjects were classified into sex-stratified PhA tertiles. The prevalence of dysmobility syndrome increased from the highest PhA tertile group to the lowest (15.50 to 2.45% in men; 33.41 to 12.25% in women, P for trend < 0.001). The mean PhA values decreased as the dysmobility score increased (5.33° to 4.65° in men; 4.76° to 4.39° in women, P for trend < 0.001). Low PhA (cutoff: < 4.8° in men; < 4.5° in women) was associated with twofold elevated odds of dysmobility syndrome after adjusting for age, sex, and conventional risk factors. Low PhA improved the identification of individuals with dysmobility syndrome when added to the conventional risk model (area under the curve, 0.73 to 0.75, P = 0.002). CONCLUSION Low PhA was associated with dysmobility syndrome and its components, independent of age, sex, body mass index, nutritional status, and inflammation.
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Affiliation(s)
- Y W Jung
- Division of Endocrinology, Endocrine Research Institute, Department of Internal Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - N Hong
- Division of Endocrinology, Endocrine Research Institute, Department of Internal Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - C O Kim
- Division of Geriatrics, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - H C Kim
- Department of Preventive Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Y Youm
- Department of Sociology, Yonsei University, Seoul, Korea
| | - J -Y Choi
- Department of Radiology, Yonsei University College of Medicine, Seoul, Korea
| | - Y Rhee
- Division of Endocrinology, Endocrine Research Institute, Department of Internal Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
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Lu Y, Di YP, Chang M, Huang X, Chen Q, Hong N, Kahkonen BA, Di ME, Yu C, Keller ET, Zhang J. Cigarette smoke-associated inflammation impairs bone remodeling through NFκB activation. J Transl Med 2021; 19:163. [PMID: 33882954 PMCID: PMC8061040 DOI: 10.1186/s12967-021-02836-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 01/07/2021] [Accepted: 04/16/2021] [Indexed: 01/23/2023] Open
Abstract
Background Cigarette smoking constitutes a major lifestyle risk factor for osteoporosis and hip fracture. It is reported to impair the outcome of many clinical procedures, such as wound infection treatment and fracture healing. Importantly, although several studies have already demonstrated the negative correlation between cigarette consume and impaired bone homeostasis, there is still a poor understanding of how does smoking affect bone health, due to the lack of an adequately designed animal model. Our goal was to determine that cigarette smoke exposure impairs the dynamic bone remodeling process through induction of bone resorption and inhibition of bone formation. Methods We developed cigarette smoke exposure protocols exposing mice to environmental smoking for 10 days or 3 months to determine acute and chronic smoke exposure effects. We used these models, to demonstrate the effect of smoking exposure on the cellular and molecular changes of bone remodeling and correlate these early alterations with subsequent bone structure changes measured by microCT and pQCT. We examined the bone phenotype alterations in vivo and ex vivo in the acute and chronic smoke exposure mice by measuring bone mineral density and bone histomorphometry. Further, we measured osteoclast and osteoblast differentiation gene expression levels in each group. The function changes of osteoclast or osteoblast were evaluated. Results Smoke exposure caused a significant imbalance between bone resorption and bone formation. A 10-day exposure to cigarette smoke sufficiently and effectively induced osteoclast activity, leading to the inhibition of osteoblast differentiation, although it did not immediately alter bone structure as demonstrated in mice exposed to smoke for 3 months. Cigarette smoke exposure also induced DNA-binding activity of nuclear factor kappaB (NFκB) in osteoclasts, which subsequently gave rise to changes in bone remodeling-related gene expression. Conclusions Our findings suggest that smoke exposure induces RANKL activation-mediated by NFκB, which could be a “smoke sensor” for bone remodeling. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02836-z.
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Affiliation(s)
- Yi Lu
- School of Medicine, Southern University of Science and Technology, No. 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, Guangdong, China.,Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, 518055, Guangdong, China
| | - Yuanpu Peter Di
- Department of Environmental and Occupational Health, University of Pittsburgh, 100 Technology Dr, Pittsburgh, PA, 15261, USA.
| | - Ming Chang
- School of Medicine, Southern University of Science and Technology, No. 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Xin Huang
- School of Medicine, Southern University of Science and Technology, No. 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Qiuyan Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Ni Hong
- School of Medicine, Southern University of Science and Technology, No. 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, Guangdong, China
| | - Beth A Kahkonen
- Department of Environmental and Occupational Health, University of Pittsburgh, 100 Technology Dr, Pittsburgh, PA, 15261, USA
| | - Marissa E Di
- Department of Environmental and Occupational Health, University of Pittsburgh, 100 Technology Dr, Pittsburgh, PA, 15261, USA
| | - Chunyan Yu
- Department of Urology & Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Evan T Keller
- Department of Urology & Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jian Zhang
- School of Medicine, Southern University of Science and Technology, No. 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, Guangdong, China. .,Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, 518055, Guangdong, China. .,Department of Urology, University of Pittsburgh, Pittsburgh, 15260, USA.
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40
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Yang Z, Zhang Y, Wang G, Wen S, Wang Y, Li L, Xiao F, Hong N. The p23 of Citrus Tristeza Virus Interacts with Host FKBP-Type Peptidyl-Prolylcis-Trans Isomerase 17-2 and Is Involved in the Intracellular Movement of the Viral Coat Protein. Cells 2021; 10:934. [PMID: 33920690 PMCID: PMC8073322 DOI: 10.3390/cells10040934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022] Open
Abstract
Citrus tristeza virus is a member of the genus Closterovirus in the family Closteroviridae. The p23 of citrus tristeza virus (CTV) is a multifunctional protein and RNA silencing suppressor. In this study, we identified a p23 interacting partner, FK506-binding protein (FKBP) 17-2, from Citrus aurantifolia (CaFKBP17-2), a susceptible host, and Nicotiana benthamiana (NbFKBP17-2), an experimental host for CTV. The interaction of p23 with CaFKBP17-2 and NbFKBP17-2 were individually confirmed by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Subcellular localization tests showed that the viral p23 translocated FKBP17-2 from chloroplasts to the plasmodesmata of epidermal cells of N. benthamiana leaves. The knocked-down expression level of NbFKBP17-2 mRNA resulted in a decreased CTV titer in N. benthamiana plants. Further, BiFC and Y2H assays showed that NbFKBP17-2 also interacted with the coat protein (CP) of CTV, and the complexes of CP/NbFKBP17-2 rapidly moved in the cytoplasm. Moreover, p23 guided the CP/NbFKBP17-2 complexes to move along the cell wall. To the best of our knowledge, this is the first report of viral proteins interacting with FKBP17-2 encoded by plants. Our results provide insights for further revealing the mechanism of the CTV CP protein movement.
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Affiliation(s)
- Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Yongle Zhang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- National Biopesticide Engineering Research Centre, Hubei Biopesticide Engineering Research Centre, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Liu Li
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Feng Xiao
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Z.Y.); (Y.Z.); (G.W.); (S.W.); (Y.W.); (L.L.); (F.X.)
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China
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Hong N, Siglinsky E, Krueger D, White R, Kim CO, Kim HC, Yeom Y, Binkley N, Rhee Y, Buehring B. Defining an international cut-off of two-legged countermovement jump power for sarcopenia and dysmobility syndrome. Osteoporos Int 2021; 32:483-493. [PMID: 32894301 PMCID: PMC7929946 DOI: 10.1007/s00198-020-05591-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/10/2020] [Indexed: 12/22/2022]
Abstract
UNLABELLED We aimed to establish jump power cut-offs for the composite outcome of either sarcopenia (EWGSOP2) or dysmobility syndrome using Asian and Caucasian cohorts. Estimated cut-offs were sex specific (women: < 19.0 W/kg; men: < 23.8 W/kg) but not ethnicity specific. Jump power has potential to be used in definitions of poor musculoskeletal health. PURPOSE Weight-corrected jump power measured during a countermovement jump may be a useful tool to identify individuals with poor musculoskeletal health, but no cut-off values exist. We aimed to establish jump power cut-offs for detecting individuals with either sarcopenia or dysmobility syndrome. METHODS Age- and sex-matched community-dwelling older adults from two cohorts (University of Wisconsin-Madison [UW], Korean Urban Rural Elderly cohort [KURE], 1:2) were analyzed. Jump power cut-offs for the composite outcome of either sarcopenia defined by EWGSOP2 or dysmobility syndrome were determined. RESULTS The UW (n = 95) and KURE (n = 190) cohorts were similar in age (mean 75 years) and sex distribution (68% women). Jump power was similar between KURE and UW women (19.7 vs. 18.6 W/kg, p = 0.096) and slightly higher in KURE than UW in men (26.9 vs. 24.8 W/kg, p = 0.050). In UW and KURE, the prevalence of sarcopenia (7.4% in both), dysmobility syndrome (31.6% and 27.9%), or composite of either sarcopenia or dysmobility syndrome (32.6% and 28.4%) were comparable. Low jump power cut-offs for the composite outcome differed by sex but not by ethnicity (< 19.0 W/kg in women; < 23.8 W/kg in men). Low jump power was associated with elevated odds of sarcopenia (adjusted odds ratio [aOR] 4.07), dysmobility syndrome (aOR 4.32), or the composite of sarcopenia or dysmobility syndrome (aOR 4.67, p < 0.01 for all) independent of age, sex, height, and ethnicity. CONCLUSION Sex-specific jump power cut-offs were found to detect the presence of either sarcopenia or dysmobility syndrome in older adults independent of Asian or Caucasian ethnicity.
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Affiliation(s)
- N Hong
- Department of Internal Medicine, Severance Hospital, Endocrine Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - E Siglinsky
- Osteoporosis Clinical Research Program, Department of Medicine, University of Wisconsin School of Medicine and Public Health, 2870 University Avenue, Suite 100, Madison, WI, 53705, USA
- UT Southwestern Medical Center, University of Texas Southwestern, Dallas, TX, USA
| | - D Krueger
- Osteoporosis Clinical Research Program, Department of Medicine, University of Wisconsin School of Medicine and Public Health, 2870 University Avenue, Suite 100, Madison, WI, 53705, USA
| | - R White
- Osteoporosis Clinical Research Program, Department of Medicine, University of Wisconsin School of Medicine and Public Health, 2870 University Avenue, Suite 100, Madison, WI, 53705, USA
| | - C O Kim
- Division of Geriatrics, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - H C Kim
- Department of Preventive Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Y Yeom
- Department of Sociology, Yonsei University College of Social Sciences, Seoul, Korea
| | - N Binkley
- Osteoporosis Clinical Research Program, Department of Medicine, University of Wisconsin School of Medicine and Public Health, 2870 University Avenue, Suite 100, Madison, WI, 53705, USA
| | - Y Rhee
- Department of Internal Medicine, Severance Hospital, Endocrine Research Institute, Yonsei University College of Medicine, Seoul, Korea.
| | - B Buehring
- Osteoporosis Clinical Research Program, Department of Medicine, University of Wisconsin School of Medicine and Public Health, 2870 University Avenue, Suite 100, Madison, WI, 53705, USA.
- Rheumazentrum Ruhrgebiet, Ruhr-Universität Bochum, Herne, Germany.
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Qin P, Pang Y, Hou W, Fu R, Zhang Y, Wang X, Meng G, Liu Q, Zhu X, Hong N, Cheng T, Jin W. Integrated decoding hematopoiesis and leukemogenesis using single-cell sequencing and its medical implication. Cell Discov 2021; 7:2. [PMID: 33408321 PMCID: PMC7788081 DOI: 10.1038/s41421-020-00223-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 05/25/2020] [Accepted: 10/01/2020] [Indexed: 12/30/2022] Open
Abstract
Single-cell RNA sequencing provides exciting opportunities to unbiasedly study hematopoiesis. However, our understanding of leukemogenesis was limited due to the high individual differences. Integrated analyses of hematopoiesis and leukemogenesis potentially provides new insights. Here we analyzed ~200,000 single-cell transcriptomes of bone marrow mononuclear cells (BMMCs) and its subsets from 23 clinical samples. We constructed a comprehensive cell atlas as hematopoietic reference. We developed counterpart composite index (CCI; available at GitHub: https://github.com/pengfeeei/cci) to search for the healthy counterpart of each leukemia cell subpopulation, by integrating multiple statistics to map leukemia cells onto reference hematopoietic cells. Interestingly, we found leukemia cell subpopulations from each patient had different healthy counterparts. Analysis showed the trajectories of leukemia cell subpopulations were similar to that of their healthy counterparts, indicating that developmental termination of leukemia initiating cells at different phases leads to different leukemia cell subpopulations thus explained the origin of leukemia heterogeneity. CCI further predicts leukemia subtypes, cellular heterogeneity, and cellular stemness of each leukemia patient. Analyses of leukemia patient at diagnosis, refractory, remission and relapse vividly presented dynamics of cell population during leukemia treatment. CCI analyses showed the healthy counterparts of relapsed leukemia cells were closer to the root of hematopoietic tree than that of other leukemia cells, although single-cell transcriptomic genetic variants and haplotype tracing analyses showed the relapsed leukemia cell were derived from an early minor leukemia cell population. In summary, this study developed a unified framework for understanding leukemogenesis with hematopoiesis reference, which provided novel biological and medical implication.
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Affiliation(s)
- Pengfei Qin
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yakun Pang
- State Key Laboratory of Experimental Hematology & National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine & Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Wenhong Hou
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Ruiqing Fu
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yingchi Zhang
- State Key Laboratory of Experimental Hematology & National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine & Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Department of Pediatric Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xuefei Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Guofeng Meng
- Institute of Interdisciplinary Integrative Biomedical Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology & National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine & Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Department of Pediatric Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Ni Hong
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology & National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China. .,Center for Stem Cell Medicine & Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
| | - Wenfei Jin
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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Wen S, Wang G, Yang Z, Wang Y, Rao M, Lu Q, Hong N. Next-Generation Sequencing Combined With Conventional Sanger Sequencing Reveals High Molecular Diversity in Actinidia Virus 1 Populations From Kiwifruit Grown in China. Front Microbiol 2020; 11:602039. [PMID: 33391218 PMCID: PMC7774462 DOI: 10.3389/fmicb.2020.602039] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/11/2020] [Indexed: 01/04/2023] Open
Abstract
Kiwifruit (Actinidia spp.) is native to China. Viral disease–like symptoms are common on kiwifruit plants. In this study, six libraries prepared from total RNA of leaf samples from 69 kiwifruit plants were subjected to next-generation sequencing (NGS). Actinidia virus 1 (AcV-1), a tentative species in the family Closteroviridae, was discovered in the six libraries. Two full-length and two near-full genome sequences of AcV-1 variants were determined by Sanger sequencing. The genome structure of these Chinese AcV-1 variants was identical to that of isolate K75 and consisted of 12 open reading frames (ORFs). Analyses of these sequences together with the NGS-derived contig sequences revealed high molecular diversity in AcV-1 populations, with the highest sequence variation occurring at ORF1a, ORF2, and ORF3, and the available variants clustered into three phylogenetic clades. For the first time, our study revealed different domain compositions in the viral ORF1a and molecular recombination events among AcV-1 variants. Specific reverse transcriptase–polymerase chain reaction assays disclosed the presence of AcV-1 in plants of four kiwifruit species and unknown Actinidia spp. in seven provinces and one city.
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Affiliation(s)
- Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Min Rao
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qian Lu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
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44
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Tanyi EK, Hong N, Sawyer T, Van Schenck JDB, Giesbers G, Ostroverkhova O, Cheng LJ. Strong exciton-plasmon coupling in dye-doped film on a planar hyperbolic metamaterial. Opt Lett 2020; 45:6736-6739. [PMID: 33325884 DOI: 10.1364/ol.402210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/22/2020] [Indexed: 06/12/2023]
Abstract
We experimentally demonstrate the direct strong coupling between the S0→S1 absorption transition of rhodamine 6G (R6G) dye molecules and the surface plasmon polaritons of a hyperbolic metamaterial (HMM) substrate. The surface plasmon mode was excited by a guided mode of the R6G-doped polymer thin film on the HMM. The coupling strengths of the interactions between the surface plasmon and two molecular exciton modes are greater than the average linewidths of the individual modes indicating a strong coupling regime. This is the first, to the best of our knowledge, experimental demonstration of the direct strong coupling between the resonance mode supported by the HMM and the dye molecules on the HMM surface, not embedded in the HMM structure. The study may provide the foundation for the development of novel planar photonic or electronic devices.
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45
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Liu H, Wang G, Yang Z, Wang Y, Zhang Z, Li L, Waqas M, Hong N, Liu H, Wang G, Hong N, Hong J, Zhang J, Xu L, Qi L. Identification and Characterization of a Pear Chlorotic Leaf Spot-Associated Virus, a Novel Emaravirus Associated with a Severe Disease of Pear Trees in China. Plant Dis 2020; 104:2786-2798. [PMID: 32997610 DOI: 10.1094/pdis-01-20-0040-re] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 06/11/2023]
Abstract
Pear chlorotic leaf spot (PCLS) is a recently emerged disease of commercially cultivated sandy pear (Pyrus pyrifolia) trees in central and southern China. By integrating high-throughput sequencing and conventional Sanger sequencing of reverse-transcription (RT)-PCR products, a novel emaravirus infecting pear trees was identified and molecularly characterized. The virus was provisionally named pear chlorotic leaf spot-associated virus (PCLSaV). PCLSaV shows the typical molecular features of members of the genus Emaravirus in the family Fimoviridae. It has a genome composed of at least five negative-sense RNA segments, with each containing a single open reading frame and two complementary 13-nucleotide stretches at the 5' and 3' termini. PCLSaV shows a close phylogenetic relationship with recognized emaraviruses but forms a separate clade. Moreover, double-membrane-bound bodies were observed in PCLSaV-infected tissues and in extracts of PCLSaV-infected leaves. For the first time, our study revealed the profile distribution of viral RNA reads from the RNA-seq libraries of three samples along the RNA1 to RNA5 of an emaravirus. Field surveys combined with specific RT-PCR assays revealed the presence of PCLSaV in almost all PCLS-diseased pear samples, strongly supporting the association of the virus with the PCLS disease. This study revealed the first emaravirus infecting pear trees and its association with a severe pear chlorotic leaf disease.
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Affiliation(s)
- Huazhen Liu
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guoping Wang
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zuokun Yang
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yanxiang Wang
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhe Zhang
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Longhui Li
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Muhammad Waqas
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ni Hong
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Huazhen Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guoping Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ni Hong
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jian Hong
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, Zhejiang 317502, China
| | - Jinguo Zhang
- National Sand Pear Germplasm Repository in Wuchang, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei 430064, China
| | - Lei Xu
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
| | - Liying Qi
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
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Han Z, Cui K, Placek K, Hong N, Lin C, Chen W, Zhao K, Jin W. Diploid genome architecture revealed by multi-omic data of hybrid mice. Genome Res 2020; 30:1097-1106. [PMID: 32759226 PMCID: PMC7462080 DOI: 10.1101/gr.257568.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 07/23/2020] [Indexed: 12/24/2022]
Abstract
Although mammalian genomes are diploid, previous studies extensively investigated the average chromatin architectures without considering the differences between homologous chromosomes. We generated Hi-C, ChIP-seq, and RNA-seq data sets from CD4 T cells of B6, Cast, and hybrid mice, to investigate the diploid chromatin organization and epigenetic regulation. Our data indicate that inter-chromosomal interaction patterns between homologous chromosomes are similar, and the similarity is highly correlated with their allelic coexpression levels. Reconstruction of the 3D nucleus revealed that distances of the homologous chromosomes to the center of nucleus are almost the same. The inter-chromosomal interactions at centromere ends are significantly weaker than those at telomere ends, suggesting that they are located in different regions within the chromosome territories. The majority of A|B compartments or topologically associated domains (TADs) are consistent between B6 and Cast. We found 58% of the haploids in hybrids maintain their parental compartment status at B6/Cast divergent compartments owing to cis effect. About 95% of the trans-effected B6/Cast divergent compartments converge to the same compartment status potentially because of a shared cellular environment. We showed the differentially expressed genes between the two haploids in hybrid were associated with either genetic or epigenetic effects. In summary, our multi-omics data from the hybrid mice provided haploid-specific information on the 3D nuclear architecture and a rich resource for further understanding the epigenetic regulation of haploid-specific gene expression.
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Affiliation(s)
- Zhijun Han
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.,Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Katarzyna Placek
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ni Hong
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Chengqi Lin
- Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Wenfei Jin
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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Yang M, Zhou X, Zhai L, Xiao F, Hong N, Wang G. Molecular characterization of a novel mycovirus infecting the phytopathogenic fungus Botryosphaeria dothidea. Arch Virol 2020; 165:1667-1670. [PMID: 32328855 DOI: 10.1007/s00705-020-04629-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/25/2020] [Indexed: 10/24/2022]
Abstract
In this study, we report the molecular characterization of a novel positive-sense single-stranded RNA (+ssRNA) mycovirus from Botryosphaeria dothidea strain G91, which we name "Botryosphaeria dothidea botourmiavirus 1" (BdBOV-1). The complete genome of BdBOV-1 is 2547 nucleotides (nt) long, contains one open reading frame (ORF) potentially encoding an RNA-dependent RNA polymerase (RdRp), and shows a close relationship to mycoviruses of the family Botourmiaviridae. Phylogenetic analysis based on the RdRp sequences confirmed that BdBOV-1 clustered together with the members of the family Botourmiaviridae. To the best of our knowledge, this is the first report of a +ssRNA mycovirus infecting B. dothidea.
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Affiliation(s)
- Mengmeng Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, People's Republic of China
| | - Xiaoqi Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Lifeng Zhai
- College of Life Science and Technology, Yangtze Normal University, Chongqing, 408000, People's Republic of China
| | - Feng Xiao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China.
- Key Lab of Plant Pathology of Hubei Province, Wuhan, 430070, Hubei, People's Republic of China.
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Liu M, Liang Z, Aranda MA, Hong N, Liu L, Kang B, Gu Q. A cucumber green mottle mosaic virus vector for virus-induced gene silencing in cucurbit plants. Plant Methods 2020; 16:9. [PMID: 32025236 PMCID: PMC6996188 DOI: 10.1186/s13007-020-0560-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/23/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND Cucurbits produce fruits or vegetables that have great dietary importance and economic significance worldwide. The published genomes of at least 11 cucurbit species are boosting gene mining and novel breeding strategies, however genetic transformation in cucurbits is impractical as a tool for gene function validation due to low transformation efficiency. Virus-induced gene silencing (VIGS) is a potential alternative tool. So far, very few ideal VIGS vectors are available for cucurbits. RESULTS Here, we describe a new VIGS vector derived from cucumber green mottle mosaic virus (CGMMV), a monopartite virus that infects cucurbits naturally. We show that the CGMMV vector is competent to induce efficient silencing of the phytoene desaturase (PDS) gene in the model plant Nicotiana benthamiana and in cucurbits, including watermelon, melon, cucumber and bottle gourd. Infection with the CGMMV vector harboring PDS sequences of 69-300 bp in length in the form of sense-oriented or hairpin cDNAs resulted in photobleaching phenotypes in N. benthamiana and cucurbits by PDS silencing. Additional results reflect that silencing of the PDS gene could persist for over two months and the silencing effect of CGMMV-based vectors could be passaged. CONCLUSIONS These results demonstrate that CGMMV vector could serve as a powerful and easy-to-use tool for characterizing gene function, controlling viral pathogens or even performing resistance breeding in cucurbits. Moreover, this study will possess considerable important reference value for developing different viral vectors.
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Affiliation(s)
- Mei Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
- Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Zhiling Liang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
| | - Miguel A. Aranda
- Centro de Edafologia y Biologia Aplicada del Segura (CEBAS)-CSIC, Apdo. Correos 164, Espinardo, 30100 Murcia, Spain
| | - Ni Hong
- Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Liming Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
| | - Baoshan Kang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
| | - Qinsheng Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 People’s Republic of China
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Wang W, Ren G, Hong N, Jin W. Exploring the changing landscape of cell-to-cell variation after CTCF knockdown via single cell RNA-seq. BMC Genomics 2019; 20:1015. [PMID: 31878887 PMCID: PMC6933653 DOI: 10.1186/s12864-019-6379-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 09/23/2019] [Accepted: 12/08/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND CCCTC-Binding Factor (CTCF), also known as 11-zinc finger protein, participates in many cellular processes, including insulator activity, transcriptional regulation and organization of chromatin architecture. Based on single cell flow cytometry and single cell RNA-FISH analyses, our previous study showed that deletion of CTCF binding site led to a significantly increase of cellular variation of its target gene. However, the effect of CTCF on genome-wide landscape of cell-to-cell variation remains unclear. RESULTS We knocked down CTCF in EL4 cells using shRNA, and conducted single cell RNA-seq on both wild type (WT) cells and CTCF-Knockdown (CTCF-KD) cells using Fluidigm C1 system. Principal component analysis of single cell RNA-seq data showed that WT and CTCF-KD cells concentrated in two different clusters on PC1, indicating that gene expression profiles of WT and CTCF-KD cells were systematically different. Interestingly, GO terms including regulation of transcription, DNA binding, zinc finger and transcription factor binding were significantly enriched in CTCF-KD-specific highly variable genes, implying tissue-specific genes such as transcription factors were highly sensitive to CTCF level. The dysregulation of transcription factors potentially explains why knockdown of CTCF leads to systematic change of gene expression. In contrast, housekeeping genes such as rRNA processing, DNA repair and tRNA processing were significantly enriched in WT-specific highly variable genes, potentially due to a higher cellular variation of cell activity in WT cells compared to CTCF-KD cells. We further found that cellular variation-increased genes were significantly enriched in down-regulated genes, indicating CTCF knockdown simultaneously reduced the expression levels and increased the expression noise of its regulated genes. CONCLUSIONS To our knowledge, this is the first attempt to explore genome-wide landscape of cellular variation after CTCF knockdown. Our study not only advances our understanding of CTCF function in maintaining gene expression and reducing expression noise, but also provides a framework for examining gene function.
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Affiliation(s)
- Wei Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Gang Ren
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ni Hong
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
| | - Wenfei Jin
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
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Hong N, Kim EJ, Kim H. The properties of mitochondria in glioma stem cells. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz413.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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